qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
782 | <p>Today I wondered what the first organism to evolve vision would have been. I assume that it would have been kind of primitive and basic, but of course extremely innovative and eventually useful to a wide variety of beings. </p>
<p>It also makes sense that the evolution of vision would have accompanied the evolution of advanced brain functions in almost every case. So, do biologists have any idea as to what the first species to use vision would have been? </p>
<p>(By vision, I mean having some organ on your body that receives photons and has some signaling pathway that converts photons into a biochemical set of signals)</p>
| [
{
"answer_id": 818,
"pm_score": 5,
"text": "<p>I'll address the question in the title \"At which time did sight evolve for the first time?\" by assuming that by the evolution of vision, we mean the evolution of the eye.</p>\n\n<p>Molluscs are an excellent phylum to investigate this question because they... | [
{
"answer_id": 803,
"pm_score": 4,
"text": "<blockquote>\n <p>\"To me, it also makes sense that the evolution of sight would have accompanied the evolution of advanced brain functions in almost every case.\" </p>\n</blockquote>\n\n<p>Not necessarily! For instance, think of <a href=\"http://en.wikipedia... |
894 | <p>[Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe. I'm not interested in debating creationism.]</p>
<p>According to Wikipedia<sup>[<a href="http://en.wikipedia.org/wiki/Michael_Behe">1</a>]</sup>:</p>
<blockquote>
<p>In Darwin’s Black Box (Behe 1996) I claimed that the bacterial
flagellum was irreducibly complex and so required deliberate
intelligent design. The flip side of this claim is that the flagellum
can’t be produced by natural selection acting on random mutation, or
any other unintelligent process. To falsify such a claim, <strong>a scientist
could go into the laboratory, place a bacterial species lacking a
flagellum under some selective pressure (for mobility, say), grow it
for ten thousand generations, and see if a flagellum--or any equally
complex system--was produced.</strong> If that happened, my claims would be
neatly disproven.</p>
</blockquote>
<p>[emphasis mine.]</p>
<p>As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications). [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity<sup>[<a href="http://dx.doi.org/10.1073/pnas.0535335100">2</a>]</sup>.] This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).</p>
<blockquote>
<p><strong>Question</strong>: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?</p>
</blockquote>
<p>Experiments reproducing steps in evolution seem to turn out much easier than I would have expected <em>a priori</em>, e.g. reproductive isolation of fruit flies<sup>[<a href="http://dx.doi.org/10.2307/2409365">3</a>]</sup>, experimental evolution of multicellularity<sup>[<a href="http://dx.doi.org/10.1073/pnas.1115323109">4</a>]</sup>, so perhaps Behe's experiment would also be surprisingly easy to implement.</p>
<p>References:</p>
<ol>
<li><p><a href="http://en.wikipedia.org/wiki/Michael_Behe">Wikipedia: Michael Behe</a></p></li>
<li><p><a href="http://dx.doi.org/10.1073/pnas.0535335100"> <strong>Blocker A, Komoriya K, Aizawa S-I</strong>. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.</a></p></li>
<li><p><a href="http://dx.doi.org/10.2307/2409365"> <strong>Dodd DMB</strong>. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.</a></p></li>
<li><p><a href="http://dx.doi.org/10.1073/pnas.1115323109"> <strong>Ratcliff WC, Denison RF, Borrello M, Travisano M</strong>. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.</a></p></li>
</ol>
| [
{
"answer_id": 895,
"pm_score": 5,
"text": "<p>The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and ... | [
{
"answer_id": 1729,
"pm_score": 3,
"text": "<p>You may be interested in <a href=\"http://www.talkdesign.org/faqs/flagellum.html\" rel=\"noreferrer\">this</a> paper and a <a href=\"http://www.youtube.com/watch?v=SdwTwNPyR9w\" rel=\"noreferrer\">video</a> that summarizes it. It seems to be made quite cle... |
954 | <p>I am reading <a href="http://wiki.answers.com/Q/What_is_the_difference_between_male_meiosis_and_female_meiosis_for_humans#ixzz1lpTjjXvT">the answer</a> and I am getting confused by the sentence: </p>
<blockquote>
<p>At the end of meiosis I females have two daughter cells and meiosis II
only occurs if and when fertilization occurs by a sperm cell.</p>
</blockquote>
<p>The clause suggests me that meiosis II starts after the sperm has ignited the fertilization process in female: I do not know how that exactly works.</p>
<p><a href="http://en.wikipedia.org/wiki/Human_fertilization">Wikipedia</a> says:</p>
<blockquote>
<p>The process of fertilization involves a sperm fusing with an ovum.</p>
</blockquote>
<p>So female meiosis II must happen before the sperm fuses with the ovum.
Sperm must ignite some process in female that puts female meiosis II going on before sperm can fuse with egg. <strong>Is that right?</strong> How is that going to happen?</p>
| [
{
"answer_id": 955,
"pm_score": 5,
"text": "<p>Primary oocytes are formed prenatally and reain suspended in prophase of meiosis I for years until the onset of puberty. An oocyte completes meiosis I as its follicle matures (during ovulation) resulting in a secondary oocyte and the FIRST polar body. After... | [
{
"answer_id": 2624,
"pm_score": 2,
"text": "<p>Untill puberty the follicles grown from primordial to antral stage (secondary folliccle) and oocytes are arrested in diplotene of profase I of meiosis I, without polar body, with a nucleous called germinative vesicle. After puberty, with gonadotrophis, the... |
963 | <p>I know that <a href="http://en.wikipedia.org/wiki/Statistical_power">power analysis</a> is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power analysis. Mostly, researchers seems to use a rule of thumb (three technical, three biological replicates is a common one).</p>
<p>Should I be doing a power analysis each time I design an experiment, or can I just use one of the common biology rules of thumb? If not, what are the consequences for the validity of my results? And is there a situation where I will be <em>required</em> to use power analysis, which makes it advantageous to get used to doing it now?</p>
| [
{
"answer_id": 1015,
"pm_score": 5,
"text": "<p>You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.</p>\n\n<p><strong>Yes</strong></p>\n\n<p>It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you s... | [
{
"answer_id": 965,
"pm_score": 4,
"text": "<p>In order to calculate power, you need to know the <em>variance</em> of the data being collected. You can only estimate this prior to actually gathering the data itself, so any <em>a priori</em> power calculation is itself just an estimate.</p>\n\n<p>This is... |
967 | <p>When carrying out some germination tests on species in the <a href="http://en.wikipedia.org/wiki/Cucurbitaceae">Cucurbitaceae</a>, I notice that young plants of this family produce a lot of clear fluid when they are dissected. Most plants I dissect do not produce any fluid, even ones which appear to be turgid and have large cells. Why do cucurbits do this, and what's the fluid?</p>
| [
{
"answer_id": 1015,
"pm_score": 5,
"text": "<p>You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.</p>\n\n<p><strong>Yes</strong></p>\n\n<p>It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you s... | [
{
"answer_id": 965,
"pm_score": 4,
"text": "<p>In order to calculate power, you need to know the <em>variance</em> of the data being collected. You can only estimate this prior to actually gathering the data itself, so any <em>a priori</em> power calculation is itself just an estimate.</p>\n\n<p>This is... |
973 | <p>If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before they will become degraded?</p>
| [
{
"answer_id": 1237,
"pm_score": 4,
"text": "<p>I've found that extracted RNA using commercial kits has stayed stable for many years at -80 C. I would certainly aliquot it before freezing however as RNA is particularly sensitive to freeze-thaw cleavage.</p>\n"
}
] | [
{
"answer_id": 5147,
"pm_score": 2,
"text": "<p>We can keep extracted RNA in -80°C for a few weeks, but before the start of any experiments, it needs to be validated by gel electrophoresis.</p>\n"
},
{
"answer_id": 11128,
"pm_score": 1,
"text": "<p>I keep my RNA in 1mM sodium citrate pH ... |
1,008 | <p>There are numerous examples of sessile animals (sponges, barnacles etc.) but are there any examples of motile plants? If not, why not? Surely mobility would have conferred an evolutionary advantage to some plant species. I am specifically thinking of locomotion here.</p>
| [
{
"answer_id": 1021,
"pm_score": 5,
"text": "<p>It depends how you define <strong>locomotion</strong>.</p>\n\n<p>If you take it to mean <strong>moving from one place to another</strong>, then yes, almost all plants do this at some stage during their life cycle. Primarily seeds and pollen move around, an... | [
{
"answer_id": 1023,
"pm_score": 3,
"text": "<p>Many plants crawl by sending out ground vines and replant themselves in neighboring positions. But that's not what you are asking I think. </p>\n\n<p>I don't know if there are any land dwelling leaf bearing plant forms that move. </p>\n\n<p>In the water... |
1,035 | <p>Which organism has the sharpest vision in terms of distance and spectrum. Please propose any other useful measure.</p>
| [
{
"answer_id": 108494,
"pm_score": 4,
"text": "<p>A good measure for "sharpest vision" is known as acuity of vision. Visual acuity denotes the ability to perceive detail and resolve temporal motion. This metric informs how sharp or blurred an organism perceives its surroundings. There is softw... | [
{
"answer_id": 1548,
"pm_score": 3,
"text": "<p><a href=\"http://deepblue.lib.umich.edu/bitstream/2027.42/23426/1/0000374.pdf\" rel=\"noreferrer\">This paper</a> suggests that bats have a comparatively high depth of focus.</p>\n\n<p>It's believed that <a href=\"http://landsat.gsfc.nasa.gov/education/com... |
1,037 | <p>How did the red blood cell in humans get to lose its nucleus (and other organelles)? Does the bone marrow just not put the nucleus in, or is it stripped out at some stage in the construction of the cell?</p>
| [
{
"answer_id": 1039,
"pm_score": 6,
"text": "<p>Red blood cells are initially produced in the bone marrow with a nucleus. They then undergo a process known as enucleation in which their nucleus is removed. Enucleation occurs roughly when the cell has reached maturity. According to one research (<a href=... | [
{
"answer_id": 14491,
"pm_score": 3,
"text": "<p>Shown to be in mice & rats (and sick humans), the cell-cell interaction between a macrophage (this is a big engulfing cell required for immunity) and young red blood cells (RBC), is known as the erythroblastic island (commonly known as EBI). If you go... |
1,038 | <p>In the antibody-mediated immune response, when the helper T cell gets activated by the costimulus (IL-2 and TNF-α secreted by the APC) which in turn produces IL-2, IL-2 acts in an autocrine manner. I'm just wondering why does IL-2 have to be secreted? Why doesn't it just exert an affect while it's already inside the helper T cell? What's the point of autocrine signalling? </p>
<p>I hope the answer isn't going to be, "Well, that's just the way it is..." because paracrine and endocrine make sense and have advantages, but autocrine just seems a bit extra. </p>
| [
{
"answer_id": 1039,
"pm_score": 6,
"text": "<p>Red blood cells are initially produced in the bone marrow with a nucleus. They then undergo a process known as enucleation in which their nucleus is removed. Enucleation occurs roughly when the cell has reached maturity. According to one research (<a href=... | [
{
"answer_id": 14491,
"pm_score": 3,
"text": "<p>Shown to be in mice & rats (and sick humans), the cell-cell interaction between a macrophage (this is a big engulfing cell required for immunity) and young red blood cells (RBC), is known as the erythroblastic island (commonly known as EBI). If you go... |
1,045 | <p>As my textbook <em>An Introduction to Genetic Analysis</em> points out, yeast mitochondrial DNA has approximately 78 kb of genetic data, while the human mitochondrial DNA contains 17 kb. Is there any evolution reason for this drastic change in size? Also, are there any particularities about mitochondrial function that have been compromised with this reduction in size?</p>
<hr>
<h2>References</h2>
<ul>
<li><strong>Griffiths, Anthony J. F.</strong> <em>An Introduction to Genetic Analysis.</em> New York: W.H. Freeman, 2000.</li>
</ul>
| [
{
"answer_id": 1414,
"pm_score": 4,
"text": "<p>One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed <a href=\"http://en.wikipedia.org/wiki/Homing_endonuclease\">homing endonucleases genes</a> (HEGs). These genes are typically found in ... | [
{
"answer_id": 1046,
"pm_score": 2,
"text": "<p>Shorter DNA would allows easier synthesis, but more introns could allow for more different transcription factors to influence gene expression. </p>\n\n<p>Human mitochondria probably does not need to be as adaptable as mitochondria in yeast, since the a hu... |
1,056 | <p>I found such a clause:</p>
<blockquote>
<p>The general principle is that mitosis creates somatic cells and
meiosis creates germ cells.</p>
</blockquote>
<p>However, I cannot agree. Each gametogonium needs to go through mitosis before it can enter meiosis I. So in that case mitosis is happening with germ cells so the clause is false.</p>
<p>I would rephrase the sentence to be</p>
<blockquote>
<p>The general principle is that meiosis creates only germ cells with the possibility of a decrease in chromosome number, while mitosis can create both somatic and germ cells while the ploidy stays constant.</p>
</blockquote>
<p>Ok, not perfect.</p>
<p><strong>How would you say the main general difference between mitosis and meiosis?</strong></p>
| [
{
"answer_id": 2097,
"pm_score": 4,
"text": "<p>If the question is about the one and only most important difference between mitosis and meiosis, then the answer \"meiosis reduces ploidy\" is probably correct. But if the list of important differences is open, it would be critical to add that mitosis gene... | [
{
"answer_id": 2096,
"pm_score": 2,
"text": "<p>According to all I've learned and heard, the only thing consistent about meiosis is that it reduces ploidy because homologous chromosomes are separated. (Not necessarily diploid to haploid - it can be polyploid as well, although odd ploidies usually seem ... |
1,093 | <p>Do cows produce more milk than it is required for their calves? It seems like cows are able to provide milk all the time (all year around). Is it so? Or do they, like other mammals, produce milk only in ammounts requeired by their offspring? </p>
| [
{
"answer_id": 1402,
"pm_score": 4,
"text": "<p>Dairy cows are bred, or selected to give milk. So they do produce excessively. The normal bovine wild type, like other mammals, not only produce less milk, but also will tend to stop lactating when the calf is not nursing. </p>\n\n<p>I would be intereste... | [
{
"answer_id": 1413,
"pm_score": 5,
"text": "<p>The average domesticated dairy cow produces far more milk than would be required to feed their calf. All cows, wild and domesticated, will only lactate in the period between their calf's birth and weaning. Milk is calf-food, and when there's no calf, there... |
1,103 | <p>What is the most heat-tolerant (or heat loving - hyperthermophile) organism so far identified? What adaptations does this organism have in order to endure such high temperatures?</p>
| [
{
"answer_id": 1108,
"pm_score": 5,
"text": "<p><em>Methanopyrus kandleri</em> has been able to grow and proliferate at temperatures of up to 122°C when under around 20atm (<a href=\"http://dx.doi.org/10.1073/pnas.0712334105\" rel=\"nofollow\">Takai et. al. 2008</a>). This was achieved in the lab but t... | [
{
"answer_id": 1140,
"pm_score": 3,
"text": "<p>I'd add that biochemically speaking, animals and microorganisms from thermal vents tend to have a higher GC content in their genomes, which makes it more thermostable.</p>\n\n<p>All of the proteins are adapted to work at higher temperature. There are a hi... |
1,157 | <p>The Guardian ran an article a while back talking about GM gene's <a href="http://www.guardian.co.uk/science/2000/may/28/gm.food" rel="noreferrer">jumping to bacteria</a> in an eater's intestine. Has other research confirmed this phenomenon?</p>
| [
{
"answer_id": 1162,
"pm_score": 5,
"text": "<p>No.</p>\n\n<p>There is nothing special about a piece of GM DNA when compared to any other random piece of DNA. If this phenomenon happened at any detectable level, we'd have found eukaryotic DNA in bacterial genomes/plasmids long before the introduction of... | [
{
"answer_id": 1163,
"pm_score": 3,
"text": "<p>Of far greater concern is the transfer of genetic material between bacteria in which antibiotic resistance is conferred. The <em>firmicutes</em> in your poop is not at all the same genetically speaking as the <em>firmicutes</em> in my poop. Polymorphisms a... |
1,198 | <p>I was reading the answers to the question: <a href="https://biology.stackexchange.com/questions/775/how-and-where-in-the-human-brain-are-memories-stored">How and where, in the human brain, are memories stored?</a> and, as expected, LTP and LTD came out.</p>
<p>Every time I read about LTP/LTD there is always something that bugs me a lot.</p>
<p>When I read papers about LTP/LTD (OK, I should really say "when I browse", as I'm not exactly in that area of neurosciences, and that is probably the reason why I am confused by this) I always see these very neat experiments where stimulating a neuron in a certain way increases/decreases its further responses. Then, I look at the time axes on the graphs, or read the Methods, and I see that the LTP was induced and analysed few minutes after the stimulus.</p>
<p>So my questions are:</p>
<ol>
<li>Is there <strong>clear</strong> evidence that LTP is involved in <strong>long-term</strong> memory (not counting 1 hour as long-term...)?</li>
<li>Has LTP/LTD been shown <em>in vivo</em> after <strong>long</strong> period of time (e.g. months).</li>
<li>For those who work in the field, is there a strong belief that LTP/LTD are the <strong>only</strong> phenomena underlying memory?</li>
</ol>
| [
{
"answer_id": 1313,
"pm_score": 3,
"text": "<blockquote>\n <p>Is there clear evidence that LTP is involved in long-term memory (not\n counting 1 hour as long-term...)? Has LTP/LTD been shown in vivo\n after long period of time (e.g. months).</p>\n</blockquote>\n\n<p>This <em>Journal of Neuroscience... | [
{
"answer_id": 1236,
"pm_score": 2,
"text": "<p>Good questions. I don't think that LTP has been (or will be) shown to be THE mechanism for long term memory. It is one of many mechanisms, all with different time courses, that contribute to the modification of synaptic efficiencies.</p>\n\n<p>One mechanis... |
1,208 | <p>I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.</p>
<p>The sequence files would be used for teaching and for testing automation methods.</p>
<p>Students would be assigned one unique sequence file and asked to look at it (eg. using gORF) and to identify it (using BLASTn).</p>
<p>The sequence file would thus need to contain only the sequence data (no meta data about species or gene).</p>
<p>I would need an associated answer sheet.</p>
| [
{
"answer_id": 1431,
"pm_score": 4,
"text": "<p>Here is the approach I ended up using, in part thanks to all the contributions here.</p>\n\n<p>The associated R script is below or can be downloaded from:</p>\n\n<p><a href=\"https://github.com/edielivon/Useful-R-functions/tree/master/Education\" rel=\"nof... | [
{
"answer_id": 1210,
"pm_score": 2,
"text": "<p>This is probably not the most elegant way but you could go to <a href=\"http://www.ncbi.nlm.nih.gov/nuccore\" rel=\"nofollow\">NCBI</a> and search for nucleotide sequences from a given organism (eg., txid9606[Organism:exp] gives all sequences from Homo sap... |
1,220 | <p>I'm volunteering for a biohacker lab - <a href="http://www.biocurious.org">biocurious</a> in Sunnyvale. The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet. </p>
<p>I'd like to set up some glycerol stab stocks of some E. coli strains, but i'm told even untransformed (i.e. no plasmid) bacteria will get funny after a while at -20°C. It would also be good to hear how long you can keep a plasmid transformed strain at -20°C. </p>
<p>Can anyone be specific about what happens and how long it takes when you store them at -20°C for long periods of time? </p>
<p>I have done a little reading for competent cells and I guess they stay active for about 4 days without a -80°C freezer.</p>
| [
{
"answer_id": 1233,
"pm_score": 4,
"text": "<p>Gergana covered the \"why\" part of your question. +1</p>\n\n<p>If all you have at the moment is a -20°C and mostly what you want to store is <em>E. coli</em> harboring plasmids, I'd recommend preparing plasmid DNA and storing that at -20°C. The DNA will s... | [
{
"answer_id": 1225,
"pm_score": 4,
"text": "<p>I think that cells get damaged at -20°C not because they are stored for a long period of time, but because they undergo cycles of thawing and freezing (the ice crystals that form damage them).</p>\n\n<p>I never keep cells at -20°C. I store them at -80°C in... |
1,352 | <p>According to the BBC documentary "Wild About Pandas", about half of panda birth result in twins. Why do they have such a high probability compared to other mammals? What factor(s) control that fraction in general for mammals?</p>
<h2>Additional question about the allometry formula:</h2>
<p>I am a little surprised that it is not the ratio between the neonatal mass and the adult body mass that enters the formula, but just the neonatal mass. Any ideas on that?</p>
| [
{
"answer_id": 1361,
"pm_score": 4,
"text": "<p>Charnov and Ernest (2006) present data on offspring number per year and neonatal mass for 532 species of mammals. The two are related by the linear regression equation:</p>\n\n<p><code>ln(offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )</code></p>\n\n<p>... | [
{
"answer_id": 1412,
"pm_score": 2,
"text": "<p>Basically a summary and details-filled version of the above.</p>\n\n<p>Based on </p>\n\n<ul>\n<li>ln(number of offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )<br>\n(c.f. Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size \nTrade‐Off in Mamm... |
1,372 | <p>From my understanding free radicals play a slight role in ageing.</p>
<p>In what ways are they so damaging, and can a restricted diet reduce production of free radicals?</p>
| [
{
"answer_id": 1373,
"pm_score": 4,
"text": "<p>Free radicals are damaging because their unpaired electrons (or not fully filled valence shell) makes them highly reactive species. They are often considered together with highly oxidizing \"reactive oxygen species\" (ROS) such as peroxides. They are espec... | [
{
"answer_id": 1396,
"pm_score": 3,
"text": "<p>Nice answer by Poshpaws +1. Free radicals can damage membranes (especially important for mitochondrial and endoplasmic reticulum membrane function), DNA (genes, telomeres, and mitochondrial DNA, eg), and microsomes. These are the things we consider with r... |
1,375 | <p>This morning I saw a bird that I have never seen before. Since it was quite big, I'm very interested in knowing its name.</p>
<p>The bird was quite big, at least 2-3 times of a common blackbird. The wings were completely black but the whole back strip was quite yellow. Also the tail was yellow. The tail widens towards the end.</p>
<p>The bird flew very strange... it trundled towards the ground and then flew back up some meters before trundling down again. I observed the bird in Zurich, Switzerland at the outer border of the city. A big forest is quite near and there are some huge trees very close to the bird.</p>
<p>Then one last thing to add: I'm not really sure about that, but it could be that the bird had a nest on top of a big tree.</p>
<p>Any ideas which bird that could be?</p>
| [
{
"answer_id": 31179,
"pm_score": 4,
"text": "<p>Following your answer to my comment, I deduced the “yellow” color to be more brownish as there is not big bird with really bright yellow color (like the golden oriole). \n With these parameters I search as well in the ornitho.ch database (all observations... | [
{
"answer_id": 1380,
"pm_score": 3,
"text": "<p>Hmmmm... the only one I can think of fitting at least in part your description would be the golden oriole (<em>Oriolus oriolus</em>). </p>\n\n<p>I say partly because it definitely is not 2-3 times a blackbird, could be slightly bigger, but on average it is... |
1,419 | <p>There are many cases when people commit altruism. One is relationship. I am willing to die for 2 of my children or 8 nieces, say an evolutionary psychologist. Another is reciprocal altruism, which is just a selfish cooperation rather than true altruism.</p>
<blockquote>
<p>In the 1930s J.B.S. Haldane had full grasp of the basic quantities and
considerations that play a role in kin selection. He famously said
that, "I would lay down my life for two brothers or eight cousins".[8]
Kin altruism is the term for altruistic behaviour whose evolution is
supposed to have been driven by kin selection.</p>
</blockquote>
<p>Is it possible that humans may be altruists not for their 2 children or 8 nieces but to say, 1000 people that are similar to them.</p>
<p>If so, how does "Be altruist to 1000 of people similar to you" evolve?</p>
<p>Note: If the answer is negative, then we will have a hard time understanding voting. Why sacrifice your time. However, if the answer is positive that humans do love other humans "a little bit" then voting, or even suicide bombing make sense. Those humans sacrifice their little time to improve reproductive success of those who are similar to them.</p>
<p>Answer DOES NOT have to be about humans. If you can show me why strong/weak chimps tend to help each other or whether alpha males like one another, that'll do. Of course, naturally we would expect that leaders need followers and followers need leaders. But sometimes there are behavior that defy even this complementary nature.</p>
<p>Similarity does not have to be genetic. For example, fellow programmers and fellow engineers tend to be gang up.... Or does it have to be genetic?</p>
| [
{
"answer_id": 2115,
"pm_score": 4,
"text": "<p>The above answers are good, but have unfortunately confused some of the concepts in the theory, I will do my best to explain.</p>\n\n<p>What we are assessing is how does one behaviour evolve, links with cooperation and altruism are applications of this. Th... | [
{
"answer_id": 1421,
"pm_score": 3,
"text": "<p>The question's a little broad, but I'll answer the question in the title: how does \"be altruist[ic] to those who are similar to you\" evolve. It turns out one way is discussed by a simple theoretical model called the \"green-beard\" model. In essence, ... |
1,439 | <p>A Chinese man has been <a href="http://www.chinadaily.com.cn/photo/2011-07/12/content_12892492.htm">drinking gasoline</a> to relieve his pain for 25 years. How does the human body metabolize gasoline? Also, what are the side-affects to gasoline? </p>
| [
{
"answer_id": 1533,
"pm_score": 4,
"text": "<p>Just to add an answer to the 'how does the body process gasoline?' portion of the question, the liver and kidney would be doing most of the work of removing the stuff from the system once it was absorbed in the digestive tract. </p>\n\n<p>The liver does m... | [
{
"answer_id": 1440,
"pm_score": 3,
"text": "<p>Prolonged exposure to high concentrations of n-hexane (>1,000 ppm) has resulted in decreased sperm count and degenerative changes in the testes of rats but not those of mice.\nAcute Data: Gasoline: Dermal LD50>5 ml/kg (Rabbit) LC50> 4500 ppm (Rat) Oral LD5... |
1,502 | <p>In humans the Appendix is a vestigial organ. Does it serve no apparent purpose in all the vertebrates that have one?</p>
| [
{
"answer_id": 1504,
"pm_score": 5,
"text": "<p><a href=\"http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01809.x/full\" rel=\"noreferrer\">Smith et al. (2009)</a> provide a survey of the morphology of the cecal appendix. One current hypothesis is that the appendix provides \"safe harbor\" f... | [
{
"answer_id": 1503,
"pm_score": 3,
"text": "<p>Aside from humans, it is largely rodents and most notably rabbits that have an appendix. Therefore, using rabbits as my example:</p>\n\n<p>In rabbits, the appendix is thought to have a key role in the development of the immune system. Specifically it has... |
1,573 | <p>When humans get the common cold, a common symptom is a stuffy or runny nose. Is that the body's immune response or is that the virus's doing?</p>
| [
{
"answer_id": 16984,
"pm_score": 4,
"text": "<p>There are different causes and mechanisms behind runny and stuffy nose.\nI cover them separately below.</p>\n\n<h2>Runny nose</h2>\n\n<p>My professor of pathoanatomy and pathophysiology says that the correct answer here is <strong>serous inflammation</str... | [
{
"answer_id": 1597,
"pm_score": 4,
"text": "<p>It's mainly caused by swelling of large veins and by an increase in vascular permeability that leads to an accumulation of fluids in the nasal mucosa. These effects are mediated, at least in part, by bradykinin and histamine, and can be counteracted by epi... |
1,581 | <p>I've been thinking about this one, but I can't seem to find what causes this difference.</p>
<p>All fishes that I've seen have their tail fin positioned vertical:</p>
<p><img src="https://i.stack.imgur.com/MCLkv.jpg" alt="Fish"></p>
<p>But all the marine mammals I know have their tail positioned horizontal:</p>
<p><img src="https://i.stack.imgur.com/ZwQZj.jpg" alt="Dolphin"></p>
<p>Why is there this difference? Is it because it's mammals compared to fish? Or could fish as well have horizontal tail fins?</p>
| [
{
"answer_id": 9980,
"pm_score": 5,
"text": "<p>While fish tend to move from side to side (lateral undulation) for which a vertical tail makes sense, the land ancestors of marine mammals had their limbs under them and so their spines were already adapted to up and down movement (dorsoventral undulation)... | [
{
"answer_id": 1584,
"pm_score": 4,
"text": "<p>Cetaceans (i.e., marine mammals) evolved from certain ancient land based mammals, thus the tail is essentially convergent evolution of the tail function.</p>\n"
},
{
"answer_id": 21136,
"pm_score": 2,
"text": "<p>I've thought about this man... |
1,605 | <p>To start with, I do not have a sound knowledge in biology or any formal education in the area.</p>
<p>I was told that one of the definition of a species is a reproductive barrier, which means that if two animals can't reproduce, they are of different species. The barrier can be either the inability of the sperm to fertilize an egg, or a physical trait that inhibits reproduction, e.g. a cricket species that has a different mating song than another species or two species of flies, one that mates on yellow flowers, and the other on red flowers.</p>
<p>But what happens when, while two species can't reproduce, but there is a "chain" of "intermediate" sexual partners that can produce reproductive connection step by step. Like 6 degrees to Kavin Bacon, but with animal sex.</p>
<p>I'll try to explain with an example:</p>
<p>A Great Dane and a Miniature Pinscher dogs can't mate due to obvious size differences. But The Pincher can mate with a German Pincher (a slightly bigger breed of Pincher), which can mate with a Doberman Pincher. And the Doberman can mate with a German Shepard which can mate with a Great Dane.</p>
<p>I've also heard that such things happen with birds and crickets, where there is an original species, from which evolved several other, and while the original species (which still exists) can mate with all the new species. Some new species can't mate with some, or all of the other new species.</p>
<p>How are such species are defined, and at what point dogs stop being dogs anymore?</p>
| [
{
"answer_id": 1623,
"pm_score": 4,
"text": "<blockquote>\n <p>How are such species are defined, and at what point dogs stop being\n dogs anymore?</p>\n</blockquote>\n\n<p>This is a bit like the is-Pluto-a-planet-discussion. A group of scientists have to come together and hold a big conference.\nYou h... | [
{
"answer_id": 1828,
"pm_score": 3,
"text": "<p>There are many definitions of a species, which may or may not include the concept of reproductive barrier. The <a href=\"http://www.encyclopedia.com/topic/biological_species_concept.aspx#1-1O6%3abiologicalspeciesconcept-full\" rel=\"noreferrer\">Biological... |
1,611 | <p>"<a href="http://www.boots.com/en/Boots-Pharmaceuticals-Cold-Defence-Nasal-Spray-20ml_1224268/" rel="nofollow noreferrer">Cold Defence</a>" nasal sprays are recommended to be taken either preventatively or in the early stages of a cold. The active ingredient in these sprays is <em>Carrageenan</em>. After some research, the active compound is <em>Iota-Carrageenan</em> (<em>ι-Carrageenan</em>). </p>
<p>This study by <a href="http://dx.doi.org/10.1186/1465-9921-11-108" rel="nofollow noreferrer">Eccles et al<sup>[1]</sup></a> shows that this drug is clinically effective. The study was only designed to test efficacy rather than to explain the mechanism, however. A fleeting mention is provided in the discussion section:</p>
<blockquote>
<p>The above results suggest that the treatment with Iota-Carrageenan reduces the viral replication. Consequently fewer cells are infected, the immune reaction against the viruses is less pronounced and fewer symptoms occur.</p>
</blockquote>
<p><img src="https://i.stack.imgur.com/8hUS3.jpg" alt="ι-Carrageenan"></p>
<p><strong>How does <em>ι-Carrageenan</em> produce an anti-viral effect?</strong></p>
<ol>
<li><a href="http://dx.doi.org/10.1186/1465-9921-11-108" rel="nofollow noreferrer"><strong>Eccles R, Meier C, Jawad M, Weinmüllner R, Grassauer A, Prieschl-Grassauer E</strong>. 2010. Efficacy and safety of an antiviral Iota-Carrageenan nasal spray: a randomized, double-blind, placebo-controlled exploratory study in volunteers with early symptoms of the common cold. Respiratory Research, 11:108, doi:10.1186/1465-9921-11-108.</a></li>
</ol>
| [
{
"answer_id": 1623,
"pm_score": 4,
"text": "<blockquote>\n <p>How are such species are defined, and at what point dogs stop being\n dogs anymore?</p>\n</blockquote>\n\n<p>This is a bit like the is-Pluto-a-planet-discussion. A group of scientists have to come together and hold a big conference.\nYou h... | [
{
"answer_id": 1828,
"pm_score": 3,
"text": "<p>There are many definitions of a species, which may or may not include the concept of reproductive barrier. The <a href=\"http://www.encyclopedia.com/topic/biological_species_concept.aspx#1-1O6%3abiologicalspeciesconcept-full\" rel=\"noreferrer\">Biological... |
1,614 | <p>Why do we turn images upside down again rather than dealing with them directly, still vertically rotated after passing through our lens? </p>
<p>I don't see how that would cause any problems, and how we'd ever be able to figure out if we are presented with flipped images after getting used to interacting based on visual input, whether flipped or not. </p>
<p>What am I missing?</p>
| [
{
"answer_id": 2664,
"pm_score": 5,
"text": "<p>The basis of this question is a <a href=\"https://cogsci.stackexchange.com/q/337/29\">common misconception</a>, and unfortunately the accepted answer by @CHM is also based on this common misconception. The misconception is based on the <a href=\"http://en.... | [
{
"answer_id": 1642,
"pm_score": 2,
"text": "<p>I think you're oversimplifying the problem. Think about gravitation.</p>\n\n<p>Take this informal example: at any point on a massive sphere, you can define \"bottom\" such that any massive object with weight less than that of the sphere is subject to an at... |
1,622 | <p>I have read that different optical imaging techniques such as such as wide-field microscopy, confocal microscopy or STED microscopy can theoretically achieve a different spatial resolution. </p>
<p>However, I was only able to find information about the STED microscopy's spatial resolution (5.8 nm) on Wikipedia.</p>
<p>Does anybody know of any references or recommended reading (preferably free) where I can learn more about different optical microscopy methods and how the cope with the diffraction limit?</p>
| [
{
"answer_id": 1624,
"pm_score": 4,
"text": "<p>The theoretical resolution for an optical microscope depends on the wavelength used, but is close to 0.22 um (220 nm). Confocal microscopy does not greatly improve axial resolution; it dramatically improves the in-plane resolution (x and y directions, by e... | [
{
"answer_id": 1625,
"pm_score": 2,
"text": "<p>A <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/21929850\" rel=\"nofollow\">couple</a> of <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/19489737\" rel=\"nofollow\">review</a> articles you could read up on.</p>\n\n<p>1) Leung BO, Chou KC. Review of super-reso... |
1,640 | <p>Some fruits such as pumpkins can grow to be 100 lbs. Under different conditions, the same variety of pumpkin can produce a 15 lb. fruit. Both plants are healthy, and look the same except for their size difference. If I took two red apple trees and planted them in extreme opposite conditions, the fruit size would be nearly the same. The fruit quantity would be lowered in the tree grown under poor conditions. Why do fruits have such a variable range of acceptable sizes?</p>
| [
{
"answer_id": 1647,
"pm_score": 4,
"text": "<p>Pumpkins, squashes in general, grow on vines, while apples grow on trees. Vines are fast growing and trees are not. Zucchini can be quite large; cucumbers, too. Pears, plums, peaches and other tree fruits do have a reduced variation in fruit size. While I ... | [
{
"answer_id": 8881,
"pm_score": 2,
"text": "<p>Bigger pumpkins have more seeds than smaller pumpkins. When they get ideal nutrition the plant tries to make as many seeds as it can to take advantage of the windfall. Many of these vines with big fruit potential grow in compost and rotting material. So th... |
1,648 | <p>Regarding the bacteria found in Mono Lake, CA that scientists believe uses or can use arsenic in its DNA backbone where life as we know it uses phosphorus (according to their experiments depriving the microbes of phosphorus and providing much arsenic), have researchers conjectured and tested whether the energy currency molecule used is also arsenic-based instead of ATP?</p>
| [
{
"answer_id": 2290,
"pm_score": 4,
"text": "<p>I'd have to agree that it's highly improbably that the GFAJ-1 strain used nucleoside triarsenates as an energy source. There are three main lines of evidence pointed out in the <em>Science</em> reviews that were published after the initial publication of t... | [
{
"answer_id": 2282,
"pm_score": 3,
"text": "<p>This is a cool topic/question. </p>\n\n<p>To answer your question. The hypothesis was based on the conjecture that there was so little phosphorus in the culture medium that phosphorous would have been replaced by arsenic in all its roles in the cell. IF ... |
1,773 | <p>I recently had a conversation with a rather <em>unusual</em> gentleman who was, let's say, more than a little partial to conspiracy theories. He has this idea that governments are lowering "nanowires" from drones, to inject people with chemicals that modify their genetics in order to reduce their lifespan dramatically, or change their opinions and thoughts.</p>
<p>Clearly this man was a fruitcake, and the complexities of his psychology probably warrant a whole separate debate, but he did get me thinking about the theoretical side of how such a thing might be done.</p>
<p>So, as such, I have a few questions on the matter:</p>
<ol>
<li>Is it even <em>theoretically possible</em> to alter human genetics using only an injected substance? I'd imagine trying to get a single DNA change to propogate through the entire body without being killed off by the immune system would be near impossible.</li>
<li>Since we are aware of genetic markers that are related to predispositions to certain medical conditions (e.g. heart problems, cancers, high blood pressure, strokes, etc), is it possible to modify human DNA to create these issues in a living person?</li>
<li>Has much research gone into how genetics affects thought and opinion, or the way we perceive and react to situations at an emotional level? If so, is it <em>theoretically</em> possible to alter this at a biological level?</li>
</ol>
<p>I'm certainly not advocating any of this, and I apologise for the unusual nature of the question, but it's something I certainly find interesting to think about!</p>
| [
{
"answer_id": 1776,
"pm_score": 4,
"text": "<p>First of all it is important to note that, within certain limits, human DNA is not much different than, say, a mouse DNA: it has the same structure, it is constituted by the same bases etc etc. Therefore it is teorethically possible (leaving aside ethical ... | [
{
"answer_id": 1775,
"pm_score": 3,
"text": "<p>Concerning the first question, it is very well possible to alter human genetics by injecting a highly radio-active substance that will eventually cause mutations almost all cells. The lifespan will be dramatically reduced, however and the condition is know... |
1,805 | <p>Pretty much this. I've been wondering if any of the yogourt and other "health" foods containing living probiotic cultures survive digestion to populate our intestines? If so, is there peer-reviewed evidence you could point me to?</p>
| [
{
"answer_id": 1823,
"pm_score": 4,
"text": "<p>Apparently, some do and some don't.</p>\n\n<p>I just tried searching for <a href=\"http://www.google.com/search?q=yogurt+lactobacillus+survival\"><em>yogurt lactobacillus survival</em></a> on Google, and the first hit I got was an article titled <a href=\"... | [
{
"answer_id": 1806,
"pm_score": 3,
"text": "<p>When I took Microbio we had a entire lecture on this. My professor's view was that they do not survive due to the pH of the stomach. He told us that there are microbiologist on both sides as to whether they do make it to the intestine (or enough of them t... |
1,808 | <p>I am curious what animal is this. It is/lives inside some kind of cocoon, about 1 cm in length. They are attached to walls and to the ceiling, but sometimes they fall off. Inside the structure there is a small worm that can come out at both ends alternatingly. It can then hold on to the ground to move the cocoon around. They are said to feed on paper.</p>
<p><img src="https://i.stack.imgur.com/Yd5Lh.jpg" alt="slightly better picture of animal"></p>
| [
{
"answer_id": 6833,
"pm_score": 4,
"text": "<p>This little dude is not a Caddisfly, but a true moth, <em>Tinea pellionella</em>, a case making clothing moth. Confusing because they do resemble caddisfly larvae cocoons more so than those of their own family (Tineidae). Sort blurb <a href=\"http://way... | [
{
"answer_id": 1949,
"pm_score": -1,
"text": "<p>This is a wild stab in the dark, so downvote me as you see fit: Caddis fly larvae (Insect Order Trichoptera). I thought caddis larvae were aquatic though.</p>\n"
},
{
"answer_id": 2356,
"pm_score": 0,
"text": "<p>This is probably caterpill... |
1,814 | <p>I had this thought while bathing:</p>
<p>Assume a <em>perfectly</em> developed physical human body and anatomy in terms of size, dimensions and proportions. In theory, if I cut the body vertically into two <em>exact halves</em> from the center of the head downwards, <strong>would the two halves weigh the same?</strong></p>
<p>I tend to think that the 2 halves would weigh differently, and if so, I find this quite interesting because it is strange to me that our body would - <em>perhaps unecessarily</em> - evolve in such a manner that requires it to balance itself on a symmetrical skeleton.</p>
<p>Are there any topics that touches on this... phenomenon?</p>
| [
{
"answer_id": 1816,
"pm_score": 4,
"text": "<p>The two halves likely do weigh approximately the same. Since the density of most tissues that are not filled with air is basically equal, it doesn't matter that, e.g., heart, spleen, and stomach are on the left and liver is (mostly) on the right. In the le... | [
{
"answer_id": 1815,
"pm_score": 3,
"text": "<p>Humans, like all vertebrates, belong in subregnum <a href=\"http://en.wikipedia.org/wiki/Bilateria\">bilateria</a>, a broad class of animals whose characteristic trait is having a <a href=\"http://en.wikipedia.org/wiki/Bilateral_symmetry\">bilaterally symm... |
1,836 | <p>Do we <strong>clearly</strong> know what the <em>living closest relative of the dinosaurs</em> are? And connected to the first question, in scientific manner how do we know these relationship between extinct species and living ones? </p>
| [
{
"answer_id": 1888,
"pm_score": 5,
"text": "<p>In general the answer is always the same: you construct a <a href=\"http://en.wikipedia.org/wiki/Phylogeny\"><strong>phylogenetic tree</strong></a>. In order to locate different species on this tree in relation to each other, you use various features to co... | [
{
"answer_id": 2034,
"pm_score": 3,
"text": "<p>Extending Konrad Rudolph's answer, research has been conducted into reconstructing the phylogenetic tree via protein sequence data of the <a href=\"http://en.wikipedia.org/wiki/Tyrannosaurus\" rel=\"noreferrer\"><em>T. rex</em></a> (one of the latest livin... |
1,870 | <p>In the case of mammals like giraffes and koalas, is that bacteria common on the plants they eat so when a baby starts to try to stick something besides its mother's milk in its mouth, it can't digest the cellulose at all the first time, but along with the cellulose, into its mouth went some cellulose-digesting flora that then begins a lifelong colony in the animal's gut? Is that about how it happens?</p>
| [
{
"answer_id": 1876,
"pm_score": 4,
"text": "<p>I would not expect this to be any different than other animals - they get the flora from the environment. Key components of the environment for newborns are:</p>\n\n<ol>\n<li>Birth canal</li>\n<li>Den / living quarters</li>\n<li>Skin / fur of mother, espec... | [
{
"answer_id": 1878,
"pm_score": 3,
"text": "<p>I don't know about ruminants, but baby rabbits (and presumably other lagomorphs) apparently acquire the necessary intestinal flora by consuming their mother's <a href=\"http://en.wikipedia.org/wiki/Cecotropes\">cecotropes</a>.<sup>[1]</sup></p>\n\n<p><sup>... |
1,896 | <p>I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case study and a lot of my initial research showed that anything larger than a protein is too much to work with for now.</p>
<p>So my question. Where can I find protein DNA sequences in some standard format. I've looked at NCBI but I have no idea what I'm looking at or if I'm downloading the right stuff. Is there a link that I can go to that will have a listing of a bunch of difference protein sequences that I can download? </p>
| [
{
"answer_id": 1898,
"pm_score": 4,
"text": "<p><a href=\"http://www.ncbi.nlm.nih.gov/genbank/\">GenBank</a> and <a href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">RefSeq</a> have a huge collection of DNA sequences that can be downloaded in Fasta format. GenBank makes it very easy to search for sequences (... | [
{
"answer_id": 1897,
"pm_score": 3,
"text": "<p>A standard format would be the <a href=\"http://en.wikipedia.org/wiki/FASTA_format\">FASTA format</a>.</p>\n\n<p>If you have a few proteins of interest that you would like to look at you can simply select 'Nucleotide' at the top of the <a href=\"http://www... |
1,899 | <p>Has there been any definitive research about handedness being genetic? Also, why is right-handedness clearly dominant in humans? I'm interested in evolutionary theories, as well as any molecular explanation (if known).</p>
| [
{
"answer_id": 1898,
"pm_score": 4,
"text": "<p><a href=\"http://www.ncbi.nlm.nih.gov/genbank/\">GenBank</a> and <a href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">RefSeq</a> have a huge collection of DNA sequences that can be downloaded in Fasta format. GenBank makes it very easy to search for sequences (... | [
{
"answer_id": 1897,
"pm_score": 3,
"text": "<p>A standard format would be the <a href=\"http://en.wikipedia.org/wiki/FASTA_format\">FASTA format</a>.</p>\n\n<p>If you have a few proteins of interest that you would like to look at you can simply select 'Nucleotide' at the top of the <a href=\"http://www... |
1,943 | <p>Do any animals other than humans undergo menopause?</p>
<p>Also, is there any difference between animals in captivity and animals in the wild as regards menopause? For example, even if menopause has been observed in a captive member of a particular ape species, do individuals of that species typically live long enough in the wild to also undergo menopause?</p>
<p>I guess here's what I'm really getting at: is menopause a common thing in the animal kingdom, or is it only a common thing in humans?</p>
| [
{
"answer_id": 1946,
"pm_score": 6,
"text": "<p><strong>Yes. Menopause is common for long-lived mammals.</strong> For instance, in the wild, killer whales go in a sort of menopause as reported in 2009 by Ward et al. <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/19192288\">Front Zool. 2009 Feb 3;6:4</a>. ... | [
{
"answer_id": 50602,
"pm_score": -1,
"text": "<p>Only three — humans, killer whales, and pilot whales. (<a href=\"http://www.sciencemag.org/news/2010/06/mathematics-menopause\" rel=\"nofollow\">Reference</a>)</p>\n\n<blockquote>\n <p>Among long-lived animals, scientists have found only three sp... |
1,989 | <p>It is said that genes are <em>partly</em> responsible for the choices we make in our life; our genes help to create our environment, and then that environment can influence our personality. So, beside genes, what else is responsible for the other choices? Is there something else at work?</p>
| [
{
"answer_id": 1990,
"pm_score": 4,
"text": "<p>Many genetic studies in this area have found that variation in serotonin receptors associates with differences in a number of personality traits. That one gene, or a very small number, turns up time and time again for something so complex as human personal... | [
{
"answer_id": 1998,
"pm_score": 2,
"text": "<p>Furthermore the genotype of the individual does not represent the phenotype, it is about the expression profile of the genes rather than just their presence.</p>\n"
},
{
"answer_id": 2085,
"pm_score": 3,
"text": "<p>The problem you are look... |
2,039 | <p>I am aware that circular DNA can be both relaxed and super coiled. However when running an agarose gel of the circular plasmid along with singly digested plasmid with BamHI and HindIII, I see 1 band for the linearized plasmid (lanes 2-5) (as expected) but 5 bands for the circular plasmid (lanes 6 and 7).</p>
<p>What are these various conformations?</p>
<p><img src="https://i.stack.imgur.com/FTKGw.jpg" alt="1% agarose gel, 1 and 2 indicate plasmid from prep'd from 2 colonies and are essentially replicates. Both plasmid from 1 and 2 was digested singly with BamHI and HindIII (apologies for incorrect label "BamH""></p>
| [
{
"answer_id": 2040,
"pm_score": 4,
"text": "<p>I don't have hands on it, but I will not be surprised if supercoiled DNA migrates at different distances according to some <strong>inner topological conformation</strong> (i.e., more or less coiled AND/OR more or less nicked). Similarly, this picture highl... | [
{
"answer_id": 2042,
"pm_score": 2,
"text": "<p>Gianpaolo is correct that you are seeing the different conformations of circular DNA.</p>\n\n<p>Growing plasmids up in bacteria produces 3 main forms: relaxed, coiled and super-coiled.</p>\n\n<ul>\n<li>Relaxed tends to run a little higher than the expected... |
2,050 | <p>I have heard that there is no limit on the growth of trees, but then why do some trees, such as boxelders and poplars, tend to live shorter than redwoods, for example? Some advertisements for improved lombardy poplars state that their trees have an extended life span, up to 75 years? The trees with shorter life spans seem to weaken at a certain age, and then contract diseases more easily. </p>
| [
{
"answer_id": 19623,
"pm_score": 3,
"text": "<p>The answer to this could be that there are <strong>many factors</strong> contributing to the length of the life of tree species.</p>\n\n<p><strong>Climate</strong>: You can see that trees that have a reputation of becoming really old live in environments ... | [
{
"answer_id": 2613,
"pm_score": -1,
"text": "<p>Although most plants can potentially reproduce sexually, there are some plants that effectively always reproduce by shedding off branches which, when they fall in the right conditions, grow into new 'clones' of the same tree, which the exact genetic mater... |
2,068 | <p>As indicated by <a href="https://biology.stackexchange.com/questions/594/why-are-amino-acids-in-biology-homochiral">this</a> question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are they simply excreted? Are there enzymes (perhaps not in humans) that convert a D-amino acid to a L- one?</p>
| [
{
"answer_id": 2070,
"pm_score": 5,
"text": "<p>For the most part they are not used. there are amino acid racemases, which interconvert L- and D- forms of some specific amino acids, which may be used in some particular biosynthetic or metabolic pathways. </p>\n\n<p>In particular I'm thinking of firefl... | [
{
"answer_id": 2098,
"pm_score": 0,
"text": "<p>many D-amino acids are not used at all, although some have rather elaborate metabolism, both synthesis and utilization: D-alanine for example.</p>\n"
},
{
"answer_id": 3353,
"pm_score": 3,
"text": "<p>You may also be interested in <strong>D... |
2,180 | <p>I'm aware that hair can be curly because of the disulfide bond interactions in between cysteine amino acids in alpha-keratin filaments. However, I'm curious as to the biochemistry involved in straightening hair with a straightening iron, as well as with "perming" hair. </p>
<p>What happens at the molecular level? I suspect that a straightening iron simply disrupts the present disulfide bonds, but I'm only speculating.</p>
| [
{
"answer_id": 2243,
"pm_score": 4,
"text": "<p><strong>For straightening hair with a flat iron</strong>:</p>\n\n<p><a href=\"http://www.ccmr.cornell.edu/education/ask/index.html?quid=708\">This source</a> provided by bobthejoe states that temporarily straightening hair involves the breaking of hydrogen... | [
{
"answer_id": 43330,
"pm_score": 2,
"text": "<p>When disulfide bonds break it leads to hydrogen bonds, which then changes the shape of the alpha keratin protein. Therefore, that is why the hair changes from straight to curly or vice versa. It's the ability of the hydrogen hydrogen weak force that allow... |
2,239 | <p>I can see from Wikipedia that there are possibly thousands of harmful mutations that have been cataloged and linked to disease. There are also unnumbered neutral mutations. But, does anyone know how many "beneficial" mutations have been cataloged in scientific literature?</p>
| [
{
"answer_id": 2242,
"pm_score": 4,
"text": "<p>That would be hard to say because really beneficial mutations become well distributed through the genome. Basically the differences between us and chimpanzees are a catalog of all the beneficial (or completely neutral) mutations since the ~4.7 M years sin... | [
{
"answer_id": 2245,
"pm_score": 3,
"text": "<p>Just continue scrolling down wikipedia: there are also listed two examples of <a href=\"http://en.wikipedia.org/wiki/Mutation#Beneficial_mutations\">beneficial mutations</a>: the one conferring HIV resistance, and the one conferring malaria resistance.</p>... |
2,398 | <p>I remember hearing that trees and other plants actually obtain a large amount of their mass from the carbon floating in the air, not the ground beneath them. Does the makeup of air actually contain enough carbon to support this theory, and is a tree's surface area actually large enough to obtain the amount of carbon it needs directly from the air?</p>
| [
{
"answer_id": 2400,
"pm_score": 6,
"text": "<p>The vast majority of a tree's <em>carbon</em> comes from the air, which <a href=\"http://en.wikipedia.org/wiki/Carbon_dioxide_in_Earth%27s_atmosphere\">averages 0.03-0.04% by volume (300-400 ppmv) CO<sub>2</sub></a>. This is fixed through photosynthesis a... | [
{
"answer_id": 2401,
"pm_score": 4,
"text": "<p>Yes. In fact the organic compounds' mass comes <em>mostly</em> from the air, since Photosynthesis essentially builds up glucose by only adding hydrogen to CO₂. The 2 H₂O → 2H₂ + O₂ reaction can be treated seperately, as was determined by Sam Ruben and Mich... |
2,414 | <p>I once remember reading (15 years ago) that dinosaurs had two brains. One for their head and another one for their digestive functions. What is the current opinion on this theory? Has more evidence become available? </p>
| [
{
"answer_id": 2416,
"pm_score": 4,
"text": "<p>It would appear that at one time it was thought that a "gap" in the skeleton of a <em>Stegosaurus</em> was a space for another brain. This is now thought to be a storage space for extra food.</p>\n<p>Googling your question brings up a number of a... | [
{
"answer_id": 8234,
"pm_score": 0,
"text": "<p>I saw that some big dinosaurs got a second neuron group near their back legs to overcome some nerves signal delay problems. Not sure about that.</p>\n"
},
{
"answer_id": 81940,
"pm_score": 2,
"text": "<p>This is a myth based on comments abo... |
2,440 | <p>Recently, I heard on <a href="http://www.bbc.co.uk/programmes/b01fhysj" rel="nofollow">this</a> health-related radio programme that it was better to take a half dose of paracetamol and a half dose of ibuprofen together, rather than the full dose of either one, for acute pain. Could anyone explain the reasons for this ? Could it be something along the lines of there being diminishing returns to higher doses, so you get more bang for the buck, as it were, for the first half of a dose than the second, but due to possible toxicity or drug interactions, two full doses are not recommended ?</p>
<p>In the same radio programme it was stated that caffeine also helps. Can anyone explain that ?</p>
| [
{
"answer_id": 2794,
"pm_score": 4,
"text": "<p>There are many different reasons for an acute pain and inflammation (both directly via pain receptors, and indirectly via swelling etc.) plays not the least role in this phenomenon. Therefore the combination of a classic analgesic without anti-inflammatory... | [
{
"answer_id": 2802,
"pm_score": 0,
"text": "<p>Whilst Alexander Galkin gives some great information, I think there's a fundamental reason why that particular pain relief strategy is best, and it hasn't been mentioned yet.</p>\n\n<p>The reason is simply that when you take Ibuprofen or Paracetamol (a ful... |
2,463 | <p>Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?</p>
<p>I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.
<img src="https://i.stack.imgur.com/NUXRK.jpg" alt="enter image description here"></p>
<p>Another cat was thumping her head against a door to "knock" and indicate that the cat is outside. </p>
<p>To me, these gestures appeared as clear expressions of intent or emotional state.</p>
<p>Other experiment involved "trained" geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human). </p>
<p>Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.</p>
<p>For example I repeatedly see geese assume this gesture to intimidate other geese.
<img src="https://i.stack.imgur.com/NXohS.jpg" alt="enter image description here"></p>
<p>As a human, I'm very conditioned to vocal and eye related coordination, and this "non-verbal" language is fascinating to me.</p>
<p><strong>Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?</strong> </p>
<p><strong>Is it true that this communication uses their entire body and not just the vocal cords?</strong> </p>
<p>Is there some "foundation" language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?</p>
<p>Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with? </p>
| [
{
"answer_id": 2464,
"pm_score": 4,
"text": "<p>The closest reason that I know of for such behaviour is simple conditioning!</p>\n\n<p>B. F. Skinner conducted some fairly famous experiments with pigeons, where he put hungry pigeons in cages, and randomly administered the food. The pigeons associated the... | [
{
"answer_id": 57213,
"pm_score": 2,
"text": "<p>Darwin wrote a classical book on the subject, <a href=\"https://en.wikipedia.org/wiki/The_Expression_of_the_Emotions_in_Man_and_Animals\" rel=\"nofollow noreferrer\">The Expression of the Emotions in Man and [other] Animals</a>. Among other things, he sho... |
2,527 | <p>Hydroxyapatite is the main component of tooth enamel. It contains phosphorus in the form of phosphates, pyrophosphates etc. that are found to exhibit the the property of phosphorescence. But why don't the teeth glow in the dark ?</p>
| [
{
"answer_id": 2538,
"pm_score": 6,
"text": "<p>Just to add a little more on the interface between optics and dentistry:</p>\n\n<p>Whilst teeth do not phosphoresce, they do in fact autofluoresce.</p>\n\n<p>The differential auto fluorescence of healthy tooth and carious tooth has been used for the early ... | [
{
"answer_id": 2530,
"pm_score": 4,
"text": "<p>Firstly, phosphorus does not exhibit phosphorescence on its own (don't let words mislead you, they often don't mean what they seem like): See <a href=\"http://en.wikipedia.org/wiki/Phosphorescence#Materials\">http://en.wikipedia.org/wiki/Phosphorescence#Ma... |
2,549 | <p>Roughly, what I know is, when we eat food it goes into our: Stomach > Small Intestine > Large Intestine > Rectum. So, it just moves through a digestive pipe.</p>
<p>What I don't understand is, <strong>what part of the food is responsible for blood's color and how does the food that we eat mixes with blood?</strong></p>
| [
{
"answer_id": 2550,
"pm_score": 5,
"text": "<p>The red colour of blood isn't actually to do with food at all. The primary purpose of the blood is to carry oxygen to all the cells that require it to release energy. Red Blood Cells are filled with an iron containing pigment called <a href=\"http://en.w... | [
{
"answer_id": 2551,
"pm_score": 3,
"text": "<p>In essence, some of your food contains iron (especially red meat). This is taken up by your body and integrated into the haemoglobin protein which red blood cells contain in high amounts.</p>\n\n<p>The iron in haemoglobin can bind oxygen (it does this when... |
2,650 | <p>The most recent <a href="http://en.wikipedia.org/wiki/Race_%28human_classification%29#CITEREFLiebermanHamptonLittlefieldHallead1992">survey</a> I could find was from 1985 which said that 16% of biologist disagreed that "[t]here are biological races in the species Homo sapiens."</p>
<p>I was wondering if there's been a change in this position.</p>
| [
{
"answer_id": 2652,
"pm_score": 4,
"text": "<p>This has been <a href=\"https://skeptics.stackexchange.com/q/399/82\">investigated extensively</a> on <a href=\"https://skeptics.stackexchange.com/\">skeptics.stackexchange.com</a>.</p>\n\n<p>Unfortunately, it’s not easy to determine a scientific consensus... | [
{
"answer_id": 2655,
"pm_score": 4,
"text": "<p>Anatomically modern humans are less than 200K years old, left Africa (or possibly Africa and Arabia) only 60K years ago, and migrate quite a lot (think of the Mongol invasion). So you would not expect to have clear divisions into subspecies. And indeed a... |
2,688 | <p>The adrenal medulla is less of a 'real' endocrine organ like the others in the endocrine system and much more an extension of the sympathetic nervous system. In fact, its chromaffin cells are modified neurons by descent and secrete adrenalin and some noradrenalin upon stimulation by sympathetic preganglionic fibres, effectively turning the medulla into a sort of 'endocrine ganglion' with the whole cardiovascular system as its 'postganglionic fibres'.</p>
<p>Adrenalin in the circulation seems to have pretty much the same effect as all the adrenergic neurons of the sympathetic nervous system (which innervates all blood vessels, organs etc.): arteriole constriction, cardiac output increase, breath rate increase, pupil dilation, glucagon secretion and insulin inhibition, stimulation of glycolysis and glycogenolysis etc.</p>
<p>So what is the purpose of the adrenal medulla, if all of the effects which the endocrine adrenalin produces are essentially the same as those produced by the sympathetic mass response?</p>
| [
{
"answer_id": 5686,
"pm_score": 2,
"text": "<p>I have found the answer to the purpose of the adrenal medulla to be <em>flexibility</em>. Just like regulation for example of gene expression or metabolism occurs on many levels with different speeds and permanences of their effects, signalling needs to be... | [
{
"answer_id": 5687,
"pm_score": 1,
"text": "<p>I would argue that the adrenal medulla is a real endocrine tissue for the following reasons. First and foremost, it fits the definition of an endocrine tissue, which is to produce and secrete hormones in a regulated manner. You've already highlighted the p... |
2,698 | <p>When is it best to use Hoechst vs. DAPI for nuclear staining? They seem to be very similar on paper. Are there situations where one is clearly preferable?</p>
| [
{
"answer_id": 5338,
"pm_score": 4,
"text": "<p>The Hoechst 33342 dye is similar to DAPI in that both are UV-excited, minor groove-binding, and emit signals proportional to total DNA content. Both are maximally excited around 355 nm and emit around 460 nm. A UV light source is required, which may harm ... | [
{
"answer_id": 5343,
"pm_score": 3,
"text": "<p>DAPI and Hoechst 33342 (there are different Hoechst dyes, 33342 is one of the most commonly used) have very similar spectral characteristics. The only point is that DAPI is much better excited at 405 nm than Hoechst. Some microscopes and flow cytometers no... |
2,701 | <p>Why does the butterfly have a cocoon stage in its life cycle? It could have simply grown up within the egg/cocoon, and emerged as a butterfly. Instead it is first an egg, then a worm, then a chrysalis, and finally after some time a butterfly. </p>
| [
{
"answer_id": 2779,
"pm_score": 5,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Holometabolism\" rel=\"noreferrer\">Holometaboly</a> is believed to have evolved only once (<a href=\"http://www.bioone.org/doi/abs/10.1664/10-RA-011.1\" rel=\"noreferrer\">Labandeira, 2011</a>), but is arguably the m... | [
{
"answer_id": 2714,
"pm_score": 2,
"text": "<p>The butterfly is the reproductive stage while the larvae all it does is eat an accumulates energy to be succesfull during the reproductive phase. \nIn terms of adaptation this life cycle would be much more efficent.</p>\n"
},
{
"answer_id": 2734,
... |
2,705 | <p>Imagine that we take a population of horses, split them in half and place them in completely different environments. The two species will evolve separate from each other and because the environment is different, the outcome of evolution will be different.</p>
<p>But at what point can you say that these horses have evolved into two different species?</p>
<p>(I do know that they would probably go extinct if we conducted this exact experiment, but this experiment is just to give an example)</p>
| [
{
"answer_id": 2708,
"pm_score": 6,
"text": "<p>I think LuketheDuke's answer is an oversimplification of the biological species concept (possibly resulting from the dictionary having a poor definition). The definition he gives is one of many which are in current use, and is made redundant by many types ... | [
{
"answer_id": 2706,
"pm_score": 1,
"text": "<p>The biological definition of a <em>species</em> on <a href=\"http://dictionary.reference.com/browse/species\" rel=\"nofollow\">Dictionary.com</a> is as follows;</p>\n\n<blockquote>\n <p>The major subdivision of a genus or subgenus, regarded as the basic c... |
2,756 | <p>The question is pretty simple: what is happening molecularly when hair turns grey or white? I would imagine that it is due to the lack of a particular compound. I'm also interested in why some people's onset of grey hair happens much later than others.</p>
| [
{
"answer_id": 2765,
"pm_score": 5,
"text": "<p>Each individuals <a href=\"http://en.wikipedia.org/wiki/Hair_color\">hair colour</a> is determined by the particular pigment they produce (called melanin - the same stuff in your skin that makes you tan).</p>\n\n<p>As the body ages this pigment (produced b... | [
{
"answer_id": 77859,
"pm_score": 1,
"text": "<p>The reason for this is that catalase, the enzyme responsible for catalyzing the breakdown of hydrogen peroxide on the surface of the skin, diminishes as we age.The \"greying\" is the the effects of bleaching of the hair fiber as result of the increased pe... |
2,817 | <p>The selected answer to <a href="https://biology.stackexchange.com/questions/1041/how-does-a-plant-grow-before-photosynthesis-is-possible">How does a plant grow before photosynthesis is possible?</a> indicates that a sprout grows beneath the soil using the food stored within the seed. </p>
<p>Does this limited ready food place a restriction upon the depth to which a seed may be placed and still develop into a plant? What depth will be best applicable for a given plant/tree seed? Is there a mathematical relationship known?</p>
| [
{
"answer_id": 2830,
"pm_score": 4,
"text": "<p>The general mathematical relationship requires an allometric equation. There are not as many for seedlings as there are for mature trees (but see the answer by @Richard-smith for a specific example). But lets start with a basic assumption that the emerging... | [
{
"answer_id": 2829,
"pm_score": 3,
"text": "<p>To answer your specific questions...</p>\n\n<p><strong>Does nutrient availability limit emergence depth?</strong><br>\nYes, the size of the nutrient store in the seed does impose a theoretical limit on the maximum depth at which seed germination and emerge... |
2,875 | <p>A friend of mine told me once about a documentary movie he saw some years ago. On this movie he saw scientists talking about particular experiment. This experiment involved rats and probably electrical traps. The rat had to get to the cheese, there were traps on the shortest route to it, and obviously it got shocked few times. What is interesting is that my friend says that when they took its offspring (probably born later) they avoided those traps.</p>
<p>I'm aware that its not how "genetic memory" works. Its not memory of individual, but of species (so it requires evolution). This is what I'm trying to explain to him, but he says "he knows what he saw". </p>
<p>Anyway <strong>maybe someone</strong> here <strong>is aware of such an experiment</strong>. I believe that he is wrong about something (or conclusions drawn where changed later), so I would like to find out more about it. </p>
<p>To sum up:</p>
<ul>
<li>Its not Tryon's Rat Experiment</li>
<li>It involved: rats, traps (probably electrical), more then one path to cheese, rat's offspring and some sort of memory/learning amongst rats.</li>
</ul>
| [
{
"answer_id": 2876,
"pm_score": 7,
"text": "<p>The phenomenon you're talking about was a fad in the 60's, called 'interanimal memory transfer'. It started out when <a href=\"http://en.wikipedia.org/wiki/James_V._McConnell\">James McConnell</a> performed a later-discredited experiment in which he found ... | [
{
"answer_id": 3359,
"pm_score": 3,
"text": "<p>This is somewhat unrelated, and for that, I apologize, but I find it truly fascinating, and I believe you will too.</p>\n\n<p>Zebra finches are a song bird that have become a popular model organism for behavioral research. They have a very stereotypical pa... |
2,934 | <p>Is there any evolutionary reason for glucose being the "main" molecule used as a source of energy, beginning with glycolysis and subsequently cellular respiration (after being converted to two pyruvate molecules)? Or did this particular biochemical pathway arise "by fluke" early on in the history of life?</p>
<p>A colleague of mine told me that it was because as shown below, all of beta-D-glucose's hydroxyl substituents are all equatorially positioned (when in the correct chair conformation), which lends to its general stability.</p>
<p><img src="https://i.stack.imgur.com/4I3b7.png" alt="Beta-D-Glucose">
Image taken from <a href="http://upload.wikimedia.org/wikipedia/commons/thumb/b/bb/Beta-D-Glucose.svg/620px-Beta-D-Glucose.svg.png" rel="noreferrer">the Wikimedia Commons</a>.</p>
<p>Could this have played a factor in the beginnings of energy metabolism, and if so, why? </p>
| [
{
"answer_id": 2964,
"pm_score": 5,
"text": "<p>I thought this was a great question. In particular because it hints at two questions. The first is 'why carbohydrates are used to store energy' in general. The second being 'why glucose rather than other carbohydrates?' in particular. </p>\n\n<p>Glucose ... | [
{
"answer_id": 2963,
"pm_score": 3,
"text": "<p>This is only a guess but I hope somewhat educated, so refute me. The establishment of glucose as nutritional molecule is mainly linked with the availability of carbohydrates in the environment, i.e. plants as nutrition. Before plants evolved however, there... |
2,944 | <p>I am somewhat new to evolutionary biology, having studied it on my free time as a computer science student. There is one particular thing that has always bothered me for which I have not seen a good treatment, relating to adaptations to the environment with respect to genetic diversity. If it is possible for a population to adapt to rapid environmental changes, and they don't have an adaptation for dealing with change directly (such as a complex brain), it seems to me that every generation must have present within them almost every possible environmental adaptation that the population is capable of expressing (including many irrelevant ones and a few relevant to the particular environmental challenge). Otherwise, it may take too many generations to deal with a change, which may be disastrous for the population.</p>
<p>So my question would be: how does an evolutionary biologist explain the mechanics behind the ability for a population to adapt quickly? Are most environmental changes slow or gradual enough that the population has a few generations to happen upon the mutations that will allow it to survive, and have generally been successful in this regard for 3.5 billion years? Or, are a large majority of possible adaptations present in almost every generation, and just serve no purpose or advantage for most of the population if the provided "benefit" is unneeded (i.e., are effectively neutral)? Or something in between?</p>
| [
{
"answer_id": 44228,
"pm_score": 3,
"text": "<p>It is a good question. The question is hard to answer though because </p>\n\n<ul>\n<li>The answer is not completely resolved</li>\n<li>There are many influential parameters hidden behind this question.</li>\n</ul>\n\n<p>Your question, as I understand it, ... | [
{
"answer_id": 3077,
"pm_score": 2,
"text": "<p>Great question! A lot of things affect how quickly a population or species can adapt to a new environment, including population size, mutation rate, generation time, standing genetic diversity, and selective pressure.</p>\n\n<p>The diversity of life encomp... |
3,043 | <p>Just read <a href="https://biology.stackexchange.com/questions/1466/whats-the-effect-of-oxygen-deficit-on-plants">What's the effect of oxygen deficit on plants?</a> ; and wondered whether the opposite would have any effect on a plant.</p>
<p>That is to say, if a potted plant were placed under a bell-jar and the air within replaced by pure oxygen would the plant starve? If the environment/soil were loosely radioactive, would it make a difference?</p>
| [
{
"answer_id": 3047,
"pm_score": 4,
"text": "<p>Ask yourself, where would the plant take the carbon for construction of all kind of molecules, most important the cell membrane and cell wall of newly divided cells. Plants do not eat! So they have to get their carbon from somewhere else.</p>\n"
}
] | [
{
"answer_id": 3062,
"pm_score": 3,
"text": "<p>As hinted in other answers, the key problem with a pure oxygen environment would be the inability to photosynthesise caused by the absence of carbon dioxide.</p>\n<p>The overall equation for photosynthesis (the process in which energy from the sun is harne... |
3,050 | <p>Since the new queens-to-be have wings, it means that ants either evolved from insects that can fly, or insects that can fly evolved from ants, or that we have a case of parallel evolution (which is unlikely).</p>
<p>Now, what evolutionary benefit is there to <em>not</em> have wings?</p>
| [
{
"answer_id": 3054,
"pm_score": 5,
"text": "<p>Certainly ants evolved from insects that could fly. All the earliest wasps (ants are specialized wasps) could fly.</p>\n\n<p>Building and maintaining wings is expensive in terms of energy. That's an obvious evolutionary advantage to not having wings. So... | [
{
"answer_id": 3091,
"pm_score": 3,
"text": "<p>Building on Noah Snyder's answer…</p>\n\n<p>Having wings could also be <em>expensive</em> in other ways. For example, energy aside, maybe the growth of wings relies on some special nutrients, which were scarce in the environment of the first ancestors of m... |
3,064 | <p>What length are the shortest strings of DNA not present in any known person's genome, and what are they?</p>
<p>And is there a database online by which I could find this out?</p>
| [
{
"answer_id": 23355,
"pm_score": 3,
"text": "<p>Sequences that don't appear in a genome are called <a href=\"http://en.wikipedia.org/wiki/Nullomers\" rel=\"nofollow\">\"nullomers\"</a>.</p>\n\n<p>That article claims that there are <strong>no 10bp sequences</strong> that don't appear in the human genome... | [
{
"answer_id": 3075,
"pm_score": 3,
"text": "<p>The human genome contains less than 4<sup>16</sup> base pairs, so, even after including a factor of 2 for the two strands and another to allow for some genetic variation, there must certainly exist some 17-base string not found in either strand of the geno... |
3,097 | <p>For some species the Darwin's theory evolution makes perfect sense. I can easily imagine how, for example, the giraffe has evolved to its current appearance: the natural selection was favoring individuals that could consume more vegetable food from trees using longer necks, and some individuals were getting at birth necks longer than average by pure genetic randomness and the long neck trait was being propagated to descendant individuals by means of genetic inheritance. I have no problem with understanding this kind of evolution.</p>
<p>Now let's have a look at the bat and its relatives. The bat is one of the few mammals that have something to do with flying and the only one that took flying to the bird level. Paleontologically, first mammals date to the dinosaur era and initially looked similar to the present-day shrew (which looks much like a mouse). The question is: how in the world prehistoric mouse-like creatures could grow wings over time? It impossible to believe that some mouse-like individuals were getting wing-like limbs by mutation and the "wings" were growing out accompanied with the knowledge of how the "wings" can actually be used. Ok, then maybe first wings were tiny moth-size wings and then grew larger? But where natural selection would come into play in this case? Such mouse-like individuals would have no advantage over their wingless relatives and thus would not be able to transfer those wing-growing genes to their descendants, quite the contrary, such individuals with useless mutations that interfere with their ability to walk would be suppressed by natural selection and therefore "weeded out".</p>
<p>So what is the story behind the bat's wings and is the Darwin's theory really able to support it?</p>
| [
{
"answer_id": 3099,
"pm_score": 7,
"text": "<p>Take a look at this little fellow:</p>\n\n<p><a href=\"http://commons.wikimedia.org/wiki/File:Polatouche-estonien.jpg\" rel=\"noreferrer\"><img src=\"https://upload.wikimedia.org/wikipedia/commons/2/2e/Polatouche-estonien.jpg\" alt=\"Flying squirrel\"></a>... | [
{
"answer_id": 3098,
"pm_score": 4,
"text": "<p>Perhaps you didn't realise that bats' wings are equivalent to the front limbs of other mammals? They aren't extra limbs, just adapted ones, and the wings are formed from flaps of skin between the 'fingers'.</p>\n\n<p>Taking that into account, I don't even ... |
3,165 | <p>Having watched a lot of olympians the last few weeks, I was struck by how many of them have actually spent their wholes lives/careers training for their one event (be in running a marathon, or throwing a javelin). This is of course unsurprising - a lot of people take their sport very seriously - but I wondered to what degree these athletes are predisposed to becoming atheletes, and to what degree they just 'happened' to end up doing it.</p>
<p>I've had a bit of a search around, but have been unable to find any studies (although there is an awful lot of media attention to the topic) that actually study the interaction between nature (genetics) and nurture (environment/training etc) in the context of top-end athletes.</p>
<p>It is quite clear to me that the answer is of course 'both', but to what degree? Have any common genetic variants/loci been identified, or is 'athleticism' a far too complex trait for this? Thanks.</p>
| [
{
"answer_id": 5165,
"pm_score": 4,
"text": "<p>For all types of athlete, their ability is determined by both genetic and environmental factors (nature and nurture). The degree to which each contributes ultimately depends on the demands of the sport.</p>\n\n<p>As an example let's compare basketball and ... | [
{
"answer_id": 5045,
"pm_score": -1,
"text": "<p>I don't think this will ever be answered, mostly because studying the long-term effects of athletic training is very difficult. People constantly change their training methods, habits, and schedule, so controls are nearly impossible to construct.</p>\n\n<... |
3,211 | <p>Flies have a short lifespan, therefore evolution should technically happen over a shorter period of time (years).</p>
<p>Flies die all the time from getting hit by cars on the motorway.</p>
<p>Those flies that don't go near the motorways have a greater chance of reproducing.</p>
<p>If this was an advantage (motorway avoidance = not dying), shouldn't more and more flies be avoiding the motorway?</p>
<p>Cars have been around since, roughly ~1950. That's 60 years.</p>
<p>Why don't flies avoid the motorway?</p>
| [
{
"answer_id": 3221,
"pm_score": 4,
"text": "<p>\"in the long run we're all dead men\" - John Keynes</p>\n\n<p>First is the fact that flies have adapted their way around cars long long ago by giving up longevity for faster breeding; flies are cheap and they just don't care if they get hit by a car. The... | [
{
"answer_id": 3217,
"pm_score": 3,
"text": "<p>Flies can and do evolve quickly thanks to a short generational time. However, your question seems to stem from a misunderstanding of what evolution entails.</p>\n\n<p>Evolution occurs when the genome mutates. Why it mutates isn't particularly relevant, but... |
3,266 | <p>Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment. What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA (or its Martian equivalent)?</p>
| [
{
"answer_id": 3268,
"pm_score": 4,
"text": "<blockquote>\n <p>Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment.</p>\n</blockquote>\n\n<p><a href=\"http://www.news-press.com/videonetwork/1769239255001/Curiosity-not-looking-to-detect-life-on-Mars\">But not, inciden... | [
{
"answer_id": 3267,
"pm_score": 3,
"text": "<h3>Answer to your title:</h3>\n\n<p><a href=\"http://dictionary.reference.com/browse/extraterrestrial?s=t\">ex•tra•ter•res•tri•al</a> [ek-struh-<em>tuh</em>-<strong>res</strong>-tree-<em>uhl</em>]</p>\n\n<p><em>adjective</em></p>\n\n<ol>\n<li>outside, or ori... |
3,275 | <p>I was wondering this as I considered how effective panting would be for humans as a means of cooling.</p>
| [
{
"answer_id": 3288,
"pm_score": 3,
"text": "<p><a href=\"http://host.madison.com/wsj/news/local/ask/article_2c020ce8-f82a-11e0-b065-001cc4c03286.html\" rel=\"noreferrer\">This article</a> quotes a professor of respiratory physiology that says \"dogs are built to pant just right. The mechanics of their ... | [
{
"answer_id": 3277,
"pm_score": 1,
"text": "<p>Not knowing the physiology or the literature, I can say based on personal observations that dogs, even when extremely hot or exhausted, mix in a routine of deep inhales and exhales to their panting. Perhaps this prevents unwanted side effects of their coo... |
3,296 | <p>I know that parasitic wasp larvae can live for a long time inside their live host (eg. caterpillar), but I always thought that they kill the host when they eventually get out of it. But I've seen a <a href="http://www.youtube.com/watch?v=vMG-LWyNcAs" rel="nofollow noreferrer">film</a>, where it's shown that not only can a caterpillar survive the emergence of a wasp larva, but also the parasites infect the host with some kind of virus that changes the behaviour of the caterpillar to protect the wasp’s pupa. Is it possible and common among parasitic wasps? What species of wasps and viruses cause such effect?</p>
| [
{
"answer_id": 89250,
"pm_score": 3,
"text": "<p>Another example is the wasp species <em>Dinocampus coccinellae</em>, which lays its eggs inside certain species of ladybug/ladybird - most notably the \"twelve-spotted lady beetle\" (<em>Coleomegilla maculata</em>). It also infects the \"seven spot\" lady... | [
{
"answer_id": 3301,
"pm_score": 3,
"text": "<p>The species of wasp in the video you link to is <em>Cotesia glomerata</em>. Furthermore, there is at least one other species, <em>Glyptapanteles</em>, which parasitizes other caterpillar species in the same way and induces the same behaviour in its host.</... |
3,299 | <p>Some butterflies, such as the UK native Peacock butterfly (<a href="https://www.google.co.uk/search?q=butterfly&sugexp=chrome,mod=5&um=1&ie=UTF-8&hl=en&tbm=isch&source=og&sa=N&tab=wi&ei=0B02UP7HLYWa0QXLpoCgCQ&biw=1600&bih=775&sei=0h02UJPQB6KI0AXNwYA4#um=1&hl=en&safe=off&tbm=isch&sa=1&q=peacock%20butterfly&oq=peacock%20butterfly&gs_l=img.3..0l9j0i5.7042.10989.0.11060.24.19.3.2.2.1.277.2983.1j10j6.17.0...0.0...1c.yTA7IQEyKSw&pbx=1&bav=on.2,or.r_gc.r_pw.r_qf.&fp=2434384cfc018328&biw=1600&bih=775">Google Image Search</a>) have markings on their wings that look just like eyes, complete with a white fleck to imitate a convex, transparency effect, as though the "eye" is reflecting sunlight.</p>
<p>Presumably, this pattern is designed to deter prospective predators, because the predator will see a creature with massive eyes looking at them and think twice before attacking.</p>
<p>But how did the pattern evolve? Was the first one a fluke / a genetic mutation that happened to work, or is there another explanation?</p>
<p>For possible bonus points, is there any way of telling when this occurred, and therefore making a guess as to which creature's eye is being imitated?</p>
| [
{
"answer_id": 3357,
"pm_score": 4,
"text": "<p>There has been quite a bit of study on the development of <em>eyespots</em>. How did they evolve is still unclear, but several experiments have elucidated the molecular mechanisms underlying their formation.</p>\n\n<p>The <a href=\"http://en.wikipedia.org/... | [
{
"answer_id": 3300,
"pm_score": 3,
"text": "<p>You're correct with the genetic mutation bit. A basic explanation would be:</p>\n\n<p>Some gene or genes became mutated that lead to the coloration you see, and the end result was that the butterfly or butterflies with the mutated gene were able to produce... |
3,346 | <p>I've read a lot on both sides of the debate of low carb vs low fat diets trying to make some sense of what is being proposed. The lipid hypothesis runs roughly along the lines that we have lots of observational epidemiological evidence that eating a high fat diet correlates heart disease/obesity/enter disease of choice.</p>
<p>An alternative hypothesis is that high carbohydrate diets cause these things. Since the studies haven't been done, there is not the correlation to point to. This hypothesis is believable (to some people) due to the well-understood biological pathway: Carbohydrates turn to glucose, which causes an insulin release, and insulin regulates fat storage, so high carbohydrate diets lead to weight gain (see a biochemsitry textbook for a more detailed explanation).</p>
<p>My question is: Does the lipid hypothesis have any biological pathway for which there could be proposed a causal relation rather than just a correlation? Of all the speakers/writers on this topic, the low carb advocates always clearly describe the causal relation, whereas the low fat advocates never say <em>why</em> eating fat should cause weight gain.</p>
<p>Note: I'm not interested in discussing the merits of the studies, but rather the proposed causal mechanism.</p>
| [
{
"answer_id": 3397,
"pm_score": 3,
"text": "<p>I think you're confounding two separate things.</p>\n\n<p>The Lipid Hypothesis is about the creation of atherosclerosis (<em>only</em> atherosclerosis) and was proposed as an explanation for why plaques of cholesterol, fatty acids, and somatic cells form i... | [
{
"answer_id": 3373,
"pm_score": 2,
"text": "<p>You are mistaken in that the \"lipid hypothesis\" has no physiological basis like the carbohydrate biological pathways. Lipids and carbohydrates are produced and catabolized mutually from each other in the body. It's all the calories that matter (okay, pro... |
3,374 | <p>With many foods today containing chemicals, agents and preservatives etc... What biological criteria must a new food and its constituent components satisfy biologically, to be defined as edible? </p>
<p>For example do they look at the chronic/acute affects of chemicals in the body? </p>
<p>This question is just limited to chemicals, if a new fruit was discovered, how would it be decided if it was edible or not?</p>
| [
{
"answer_id": 3375,
"pm_score": 3,
"text": "<p>As far as I know, edibility (wow, I'm surprised that passes the spell checker!) is not a strictly defined term, biologically or otherwise. Humans have been around eating and drinking stuff long before the scientific method was around to study this question... | [
{
"answer_id": 3376,
"pm_score": 0,
"text": "<p>This is more a legal question, so I'll quote from what is lex in the EU:</p>\n\n<p>Regulation (EC) No 178/2002 of the European Parliament and of the Council of 28 January 2002 laying down the general principles and requirements of food law, establishing th... |
3,408 | <p>From <a href="http://newswatch.nationalgeographic.com/2012/08/29/university-of-cape-town-researchers-believe-they-have-found-a-single-dose-cure-for-malaria/" rel="nofollow">National Geographic</a>, there has been a lot of hype on Kelly Chibale's work from University of Cape Town on the aminopyridine MMV390048. Unfortunately, this was from an announcement from an internal meeting so there is very little literature on the compound.</p>
<p>So I ask, does anyone have good literature on the compound?</p>
| [
{
"answer_id": 3438,
"pm_score": 1,
"text": "<p>It turns out that TomD is the winner. That particular paper is an amino-pyridine class and exhibits single-dose efficacy. Amazingly, the other two papers mentioned by Satz and Alan Boyd are leads for other classes of compounds with Satz's paper focused on ... | [
{
"answer_id": 3412,
"pm_score": 3,
"text": "<p>This may be the paper you are looking for:</p>\n\n<p><a href=\"http://dx.doi.org/10.1016/j.bmcl.2012.06.010\" rel=\"nofollow\"><strong>Ongaroraa DSB, Gutb J, Rosenthalb PJ, Masimirembwac CM, Chibale K</strong>. 2012. Benzoheterocyclic amodiaquine analogues... |
3,460 | <p>I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA".</p>
<p>I'm just an interested layperson but I thought all combinations of three base pairs encoded one amino acid, with some amino acids being encoded by more than one combination of base pairs.</p>
<p>But if that were true then all of our DNA would encode something.</p>
<p>Or if only a tiny percentage of our DNA is "coding" that would mean that the vast majority of possible combinations of three base pairs don't represent any amino acid.</p>
<p>Or it could mean that there are a small number of "meaningless" combinations of three base pairs, but that those combinations are vastly overrepresented in our genome.</p>
<p>Which is correct? What am I missing?</p>
| [
{
"answer_id": 3461,
"pm_score": 4,
"text": "<p>You are correct in thinking that any sequence of bases corresponds, via the genetic code, to a sequence of amino acids. However not all stretches of DNA are actually transcribed into mRNA for translation into proteins. For this to happen the stretch of DNA... | [
{
"answer_id": 3462,
"pm_score": 3,
"text": "<p>You bring up a good point. \"Coding\" is a term that obviously carries some historical baggage that is gradually becoming less and less relevant. \"Coding DNA\" has typically been used to refer to DNA that encodes one or more functional protein products, w... |
3,479 | <p>I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done along these lines for the DNA. </p>
| [
{
"answer_id": 3492,
"pm_score": 3,
"text": "<blockquote>\n <p>a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system</p>\n</blockquote>\n\n<p>Why do you think that? Because it’s an endothermic reaction?</p>\n\n<p>Consider that mutations don’t happen “just like... | [
{
"answer_id": 3489,
"pm_score": 1,
"text": "<p>I'm going to attempt an answer to this at the level of undergraduate biochemistry: apologies in advance if this is not sufficiently sophisticated.</p>\n\n<p>The most frequent spontaneous mutation is deamination of cytosine to uracil (hydrolysis with loss o... |
3,487 | <p>When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The Selfish Gene" -- for example, the reasoning why "discriminate in favor of one's own eggs" strategy is employed by Guillemots, in "Genesmanship" chapter, page 103. I won't quote it in full since it's a page worth of text).</p>
<p>Another example of such a wall of English is (Dawkins-inspired) Bio.SE question: " <a href="https://biology.stackexchange.com/questions/2022/why-is-grudger-an-evolutionary-stable-strategy">Why is 'Grudger' an evolutionary stable strategy?</a> "</p>
<p>When a biologist tries to actually model evolutionary development to see which traits would win, they would need to somehow teach the computer to implement that model: what the environmental factors are, what the genotype involved is, how exactly it's expressed in different phenotypal and extended phenotypal traits, and how environment would affect an individual with that phenotype.</p>
<p>My question is: <strong>is there some sort of standard way to build such a model? A domain specific language</strong> (in computer science terminology) that is used by many different biologists or some standard modeling packages/software? E.g. some sort of special XML format, etc...</p>
<p>Or is it always just hand-built custom implementation by individual researchers for their current model?</p>
<hr>
<p>Just to clarify:</p>
<ul>
<li><p>I'm NOT asking what the models look like theoretically. <strong>I'm asking what language/format (if any standard one exists) is used to encode them to run simulations</strong>.</p></li>
<li><p>If there are discrepancies between the type/purposes of models, the ones I'm most interested in are game theoretical ones.</p></li>
</ul>
| [
{
"answer_id": 3500,
"pm_score": 4,
"text": "<p>The field most closely associated with game theoretic models in biology is evolutionary game theory. If modeling is required, then the typical paradigm is agent-based modeling, and a good introductory book is:</p>\n\n<blockquote>\n <p>Yoav Shoham and Kevi... | [
{
"answer_id": 3488,
"pm_score": -1,
"text": "<p>There is no single way to build such a model. They can vary from a simple mathematical statement like <a href=\"http://en.wikipedia.org/wiki/Kin_selection#Hamilton.27s_rule\" rel=\"nofollow\">Hamilton's rule</a> (rB>C) to the chemical diffusion models us... |
3,491 | <p>I find that people generally distinguish between love and infatuation. Is there a physiological difference between the two? Or are they biologically identical, and the difference is circumstantial?</p>
| [
{
"answer_id": 3626,
"pm_score": 4,
"text": "<p>Assuming that our emotions are the psychological manifestations of chemical changes in our bodies (an assumption I have no trouble with but one that others may take umbrage at), any emotion will be different.</p>\n\n<p>If your brain can distinguish between... | [
{
"answer_id": 3656,
"pm_score": 2,
"text": "<p>Using the <a href=\"http://en.wikipedia.org/wiki/Triangular_theory_of_love\" rel=\"nofollow\">Triarchic Theory of Love</a> proposed by Robert Sternberg, love is divided into three components:</p>\n\n<ol>\n<li>Intimacy</li>\n<li>Passion</li>\n<li>Commitment... |
3,545 | <p>I am reading through the ENCODE papers, which is taking me well out of my comfort zone in terms of modern laboratory techniques. At the risk of asking a question which may well be thoroughly answered somewhere else on the internet, I was hoping for a brief explanation of nuclear transfection.</p>
<p>In <a href="http://genomebiology.com/2012/13/9/R50">Whiteld et all</a>, they describe the direct assay of transcription factor binding site efficacy in human cells. To do this, they transfect a luciferase plasmid, presumably into the nucleus of the cell (because they subsequently observe that the luciferase plasmid is transcribed).</p>
<p>Reading through Materials and Methods and getting to the supplementary file, they disclosed their transfection protocol. The relevant reagants appear to be:</p>
<p>FuGene 6 </p>
<blockquote>
<p>a nonliposomal formulation designed to transfect plasmid DNA into a wide variety of cell lines with high efficiency and low toxicity. </p>
</blockquote>
<p>(From Promega's website.)</p>
<p>Lipofectamine LTX</p>
<blockquote>
<p>efficient reagent for plasmid delivery and protein expression</p>
</blockquote>
<p>(From Invitrogen's website.)</p>
<p>PLUS reagent</p>
<blockquote>
<p>PLUS™ Reagent is used in conjunction with transfection reagents, such as Lipofectamine™, to enhance transfection in adherent cell lines. </p>
</blockquote>
<p>(From Invitrogen's website.)</p>
<p>Apparently, the protocol is to combine the DNA plasmid with transfection reagent, wait a few minutes, and then add in the cells, and incubate at 37ºC for 24 hours. That's all that is required to get the plasmid into the nucleus.</p>
<p>I have consulted Wikipedia and Strachan and Read's Human Molecular Genetics 4th edition, but been unable to answer my question about this technique.</p>
<p>I think I have a pretty clear understanding of how these reagents are able to get through the cell's lipid membrane, but I don't have a similar understanding of <strong>how the DNA then passes to the nucleus</strong>.</p>
<p>In Human Molecular Genetics 4th edition, I can find only one paragraph about plasmid transfer across a nuclear membrane, page 704: "Transport of plasmid DNA to the nucleus of non-dividing cells is very inefficient because the plasmid DNA often cannot enter nuclear membrane pores. Various methods can be used to faciliate nuclear entry such as conjugating specific DNA sequences or protein sequences (nuclear localization seuqences) that are known to facilitate nuclear entry, or compacting the DNA to a small enough size to pass through the nuclear pores."</p>
<p>But nothing in the materials and methods section of Whiteld et. all mentions any of these techniques. I'm sure they would have mentioned if their plasmid included a DNA conjugation sequence, so that can't be it. Perhaps these reagents implicitly include some sort of DNA compaction polycation, such as PEG-CK30?</p>
<p>Isn't the cytoplasm an extremely hostile place for DNA plasmids? Shouldn't they just flail around in the cytoplasm until they are digested?</p>
<p>Or perhaps these vectors sneak into the nucleus during mitosis? (This is a theory that just occurred to me when contemplating the "non-dividing" qualification in the Strachan quote.)</p>
<p>Since the question isn't addressed in the paper, I can only assume the answer is elementary and something that a professional cell biologist would be expected to know. I've run out of obvious next steps for finding the answer, so I beg pardon in advance for asking it.</p>
| [
{
"answer_id": 3546,
"pm_score": 4,
"text": "<p>My attempt to find an answer has suggested that no-one knows how the DNA gets into the nucleus.</p>\n\n<p>This fairly recent paper reports attempts to track the pathway of DNA entry and transfer to the nucleus.</p>\n\n<blockquote>\n <p>Le Bihan <em>et al<... | [
{
"answer_id": 10788,
"pm_score": 0,
"text": "<p>This is a question that keeps coming up now and then when PhDs or post-docs discuss transfection. A probable answer for which I do not have supporting literature is this: If you have the transfection complex in the medium while the cells are dividing, it ... |
3,566 | <p>It is a <a href="http://en.wikipedia.org/wiki/List_of_countries_by_life_expectancy#List_by_the_United_Nations_.282005.E2.80.932010.29">well-known fact</a> that women tend to outlive men. </p>
<p>I often hear people unscientifically stating that men generally generally die younger because of the higher stress encountered in their work lives. I would personally immediately rule this out, as who's to say that that women's (past) home lives just weren't as stressful? Also, shouldn't we see a narrowing of difference in age with the recent gender equality issues? Since the trend in question still occurs in virtually all countries of the world, I think it's safe to assume that the phenomenon is purely physiological. </p>
<p>I am curious as to <em>the most sound scientific theories or known reasons</em> for why women typically outlive men. Finally, I understand that aging in itself is not a process that's completely understood, and thus am not expecting a "complete list" of factors.</p>
| [
{
"answer_id": 3716,
"pm_score": 4,
"text": "<p>In a study on longevity in 121 countries, women tended to outlive men by about 5 years [<a href=\"http://dx.doi.org/10.1002/ajhb.20879\" rel=\"nofollow\">1</a>]. The suggested causes for this are numerous, some of which are temporally, geographically, or c... | [
{
"answer_id": 3709,
"pm_score": 3,
"text": "<blockquote>\n <p>Although many studies have shown that there are trade-offs between\n longevity and reproduction, whether such trade-offs exist in humans\n has been a matter of debate [1,2]. In many species, including humans,\n males live shorter than fe... |
3,590 | <p>Biological systems are pretty good at measuring fairly long times, for example, menstrual cycles (month), or puberty (years). Counting days or years seems to be implausible, and chemical concentration also seems implausible. What are the physiological processes that are involved in keeping track of such long periods? Is it just a long sequence of finite state changes?</p>
<p>I understand there are environmental correlates such as seasonal changes and relative position of celestial objects to measure the relative time, but regardless of these external cues, I suspect that a pretty good internal clock for longer time scale could exist. For example, the time to menopause can actually be thought of as a counting mechanism of a shorter clock which is the menstrual cycle. But, how does the body know when to stop growing? I cannot think of biological processes with such long time constants that is stable.</p>
| [
{
"answer_id": 3609,
"pm_score": 4,
"text": "<p>The short answer is: we do not know exactly, although we do have some insights.</p>\n\n<p>I will take the example of puberty.</p>\n\n<p>Although a clear definition of puberty is lacking, it is quite clear that it corresponds to a period where gonadal funct... | [
{
"answer_id": 3603,
"pm_score": 2,
"text": "<p>Though chemical concentration seems implausible, at the deepest level it is the cause.</p>\n\n<p>On a smaller scale - how does a eukaryotic cell know when it is ready to divide? By the concentration of different cyclins and CDKs. They are produced all the ... |
3,662 | <p>Concerning medicine, what are the differences between antibiotics and antibacterials?</p>
| [
{
"answer_id": 3663,
"pm_score": 5,
"text": "<p>An antibacterial is any compound that will kill or at least slow down the growth of <em>strictly</em> bacteria, a domain of prokaryotes.</p>\n\n<p>An antibiotic is often used synonymously, but denotes a compound that kills or slows down the growth of any <... | [
{
"answer_id": 3671,
"pm_score": 2,
"text": "<p>Antibiotics are a broader range of antimicrobial compounds which can act on fungi, bacteria, and other compounds. Although antibacterials come under antibiotics, antibacterials can kill only bacteria.</p>\n\n<p>Penicillin was the first discovered by Alexan... |
3,664 | <p>From wikipedia:
Biomagnetism is the phenomenon of magnetic fields produced by living organisms. </p>
<p>The present scientific definition took form in the 1970s, when an increasing number of researchers began to measure the magnetic fields produced by the human body. The first valid measurement was actually made in 1963,[1] but the field began to expand only after a low-noise technique was developed in 1970.[2] Today the community of biomagnetic researchers does not have a formal organization, but international conferences are held every two years, with about 600 attendees. Most conference activity centers around the MEG (magnetoencephalogram), the measurement of the magnetic field of the brain.</p>
<p>Do viruses produce such a field?</p>
| [
{
"answer_id": 3670,
"pm_score": 1,
"text": "<p><em>Please excuse the phrasing, which is not scientifically rigorous</em>. The post only serves as a starting point.</p>\n\n<p>Any <em>electric current</em> (the net movement of electrons) induces an magnetic field, and any magnetic field in turn induces a... | [
{
"answer_id": 3669,
"pm_score": 1,
"text": "<p>Every atom produces a magnetic field, so the formally correct answer would be \"yes\" (assuming that viruses belong to the tree of life, which is disputed -- otherwise, one would not use the prefix 'bio').</p>\n\n<p>However, biomagnetism as a science (and ... |
3,713 | <p>Just what the title states.
It stems from observation & personal experience that a person/dog/cat/monkey is more likely to relieve oneself immediately after it wakes up from the peak-sleep cycle of it's body-clock. Is this observation true? What causes this behaviour ?</p>
| [
{
"answer_id": 3719,
"pm_score": 3,
"text": "<p>I think we can actually go farther than mere behavioral argumentation. The separation of the autonomous nervous system into parasympathetic and sympathetic is, one the one hand, associated with the sleep/wake cycle, on the other with parasympathetic/sympat... | [
{
"answer_id": 3714,
"pm_score": 1,
"text": "<p>I'm prefixing this one by saying that I don't actually agree with you (also, I think the old nut that the plural of \"anecdote\" is not \"data\").</p>\n\n<p>That having been said: wouldn't the simplest explanation just be \"because it was likely a long tim... |
3,720 | <p>In the process of mitosis that starts from zygote, how do different cells appear? What happens that some cells become one type and some another? </p>
<p>For example, is there a cell that divides into a blood cell and a skin cell?</p>
| [
{
"answer_id": 3719,
"pm_score": 3,
"text": "<p>I think we can actually go farther than mere behavioral argumentation. The separation of the autonomous nervous system into parasympathetic and sympathetic is, one the one hand, associated with the sleep/wake cycle, on the other with parasympathetic/sympat... | [
{
"answer_id": 3714,
"pm_score": 1,
"text": "<p>I'm prefixing this one by saying that I don't actually agree with you (also, I think the old nut that the plural of \"anecdote\" is not \"data\").</p>\n\n<p>That having been said: wouldn't the simplest explanation just be \"because it was likely a long tim... |
3,737 | <p>I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.</p>
<p>Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.</p>
<p>So it lead me to the question: How come people can get headaches if the brain has no nerves?</p>
| [
{
"answer_id": 3740,
"pm_score": 6,
"text": "<p>Brain, indeed, cannot feel pain, as it lacks pain receptors (nociceptors). However, what you feel when you have a headache is not your brain hurting -- there are plenty of other areas in your head and neck that do have nociceptors which can perceive pain, ... | [
{
"answer_id": 3745,
"pm_score": 2,
"text": "<p>That the brain doesn't have pain receptors has somewhat drifted into the corpus of general knowledge, perpetuated by pamphlets, books and documentaries.<br>\nYour question caused me to look up wikipedia. <a href=\"http://en.wikipedia.org/wiki/Headache\" re... |
3,739 | <p>People who are overweight and wish to lose weight, often do so because they are concerned about looking too big. Their increased size is attributed to an increased volume of fat.</p>
<p>When people try to lose weight however, they often quantify their goals in terms of weight, not volume.</p>
<p>So my question is, is the <strong>volume</strong> of an adipocyte cell always directly proportional to the <strong>weight</strong> of the fat stored within the cell? </p>
<p>If not, what factors would increase/decrease the size of the adipocyte cell for a given mass of stored fat?</p>
| [
{
"answer_id": 3779,
"pm_score": 2,
"text": "<p>Chris asked, \"what factors would increase/decrease the size of the adipocyte cell for a given mass of stored fat?\"</p>\n\n<p>For an obese person, subcutaneous and visceral fat is composed of 40% immune cells, while that number is ~10% in lean individuals... | [
{
"answer_id": 3748,
"pm_score": 2,
"text": "<p>Adipocytes (fat cells) change in size quite a bit with nutrient and particularly fat uptake. </p>\n\n<p>Take a look at this <a href=\"http://www.jlr.org/content/43/6/986.full\" rel=\"nofollow noreferrer\">paper</a> which is about identifying adipocyte size... |
4,932 | <p>What we know about our mammal ancestors that were alive (and survived) at the extinction event 65 million years ago?</p>
| [
{
"answer_id": 4933,
"pm_score": 5,
"text": "<p>Many of them looked like little rodents. However, several distinct mammalian lineages were already present, including <a href=\"https://en.wikipedia.org/wiki/Monotreme\" rel=\"nofollow noreferrer\">Monotremes</a>, marsupials and placental mammals. Througho... | [
{
"answer_id": 4958,
"pm_score": 2,
"text": "<p>A recent genetic analysis suggests that they were probably bigger that we thought before :</p>\n\n<p><a href=\"http://www.newscientist.com/article/dn22343-mammals-ancestor-was-not-as-puny-as-we-thought.html\" rel=\"nofollow\">http://www.newscientist.com/ar... |
4,962 | <p>These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?</p>
| [
{
"answer_id": 4964,
"pm_score": 7,
"text": "<p>First, a note on spelling. Both \"ortholog\" and \"orthologue\" are correct, one is the American and the other the British spelling. The same is true for homolog and paralog.</p>\n\n<p>On to the biology. Homology is the blanket term, both ortho- and paralo... | [
{
"answer_id": 4963,
"pm_score": 3,
"text": "<p>Both orthologs and paralogs are types of homologs, that is, they denote genes that derive from the same ancestral sequence.</p>\n\n<p>Orthologs are corresponding genes in different lineages and are a result of speciation, whereas paralogs result from a gen... |
4,965 | <p>Earlier this week I was looking at some bivalve shells that had ornate patterns which ranged in color from a light orange-pink to a deep orange-red. Here is an image I found online that seems to be of the same type of shell:</p>
<p><img src="https://i.stack.imgur.com/y7knN.jpg" alt="example clamshell"></p>
<p>The friend who was with me said, "I wonder where the color comes from." We were trying to look for two shells with similar colors, patterns, and approximately equal sizes, and it was hard, even though we were looking through a large collection of similar shells.</p>
<p>What determines this ornate pigmentation? Is it influenced by environmental factors such as the minerals in the water? Does it have anything to do with the age or health of the organism? Or is it purely genetic? Is this determined by the same basic biological principle that determines the color of human hair, or is there something different at work in shells?</p>
| [
{
"answer_id": 5017,
"pm_score": 3,
"text": "<p>This post is pretty well written and seems to say that <a href=\"http://www.conchologistsofamerica.org/articles/y1997/9703_Rosenberg.asp\" rel=\"nofollow\">the evolutionary forces that produce shell color like this is not known</a>. There are suggestions ... | [
{
"answer_id": 73130,
"pm_score": 0,
"text": "<p>I would think that the minerals that are in the immediate environment have quite a bit to do with the color that is manifested in each shell. </p>\n"
},
{
"answer_id": 79879,
"pm_score": 2,
"text": "<p>We were wondering the same thing afte... |
4,990 | <p>In the biogas process you often measure Volatile solid and Total solids. Can any one explain these concepts more accurately and why it is interesting to look at these properties. </p>
<p>The biogas process I refer to is a process of fermenting waste food materials and slaugther house waste in to bio fuels, consisting largely of methane. The fermentation is conducted in anaerobic milieu in large plants. </p>
<p>Total solids and Volatile solid are measurements on the sludge the currently fermented waste,(the gooey stuff that is in the bio-reactor).</p>
| [
{
"answer_id": 5002,
"pm_score": 3,
"text": "<p>Total solids (TS): The part of the sludge that remain after drying at 105$^{\\circ}$C for 20 hours:</p>\n\n<p>$$ TS(\\%) = \\frac{\\textrm{weight dried at } 105^{\\circ}C}{\\textrm{wet weight} }\\times 100 $$</p>\n\n<p>Volatile solids (VS): The part of the... | [
{
"answer_id": 7097,
"pm_score": 2,
"text": "<p>For the definition, see Pelle's answer.\nFor the reasons, both are easy and cheap to measure and can tell you a lot about your material if you have similiar mterial to compare. TS is often used to asses howa material can be handled (pumpable, stackable)\nI... |
5,124 | <p>A follow-up to <a href="https://biology.stackexchange.com/questions/5117/how-does-hemoglobin-free-blood-transport-oxygen">How does hemoglobin-free blood transport oxygen?</a> </p>
<p>I'm unsure about the use of physiology/metabolism in the title there. The question in mind is whether this reversible binding makes an organism slower, or faster; perhaps more capable of surviving in rarefied atmosphere.</p>
<p>EDIT:
I apologize that my comment made it appear this question is only about the Icefish; it is not. There are still other species (for instance, molluscs, and arachnids) which acquire oxygen by means other than haemoglobin.</p>
| [
{
"answer_id": 5135,
"pm_score": 2,
"text": "<p>The classic example of a hemoglobin adaptation to high altitude is found in the case of the <a href=\"http://en.wikipedia.org/wiki/Bar-headed_goose\" rel=\"nofollow\">bar-headed goose</a>, <em>Anser indicus</em>.</p>\n\n<p>This bird undertakes very high al... | [
{
"answer_id": 5132,
"pm_score": 2,
"text": "<p>I don't understand your question either, but my response is to the question in the title. Oxygen has low saturation in blood plasma, so humans require <a href=\"http://en.wikipedia.org/wiki/Hemoglobin\" rel=\"nofollow noreferrer\">hemoglobin</a> to serve a... |
5,144 | <p>I'm thinking about neurons in the brain that are used for "thinking". As I read about <strong>action potentials</strong>, I see that an Axon is connected to a Dendrite of a neighboring cell and that there are <a href="http://en.wikipedia.org/wiki/Nerve_impulse#Initiation" rel="nofollow">neurotransmitters involved in the signal propagation</a> from cell to cell. </p>
<p>I'm interested in learning how action potential propagation gets terminated. Let's say a message from the brain region A to brain region B has been delivered through action potentials.</p>
<ul>
<li>How does the region B know <strong>not to "route"</strong> the action potential further down the chain of neurons?</li>
<li>How does the region A know that the message has been sent, to <strong>stop sending more</strong> messages?</li>
</ul>
| [
{
"answer_id": 5146,
"pm_score": 2,
"text": "<p>I'm not a Neurologist or Neuroscientist, so I can only share what I know about the subject!</p>\n\n<p><strong>TL:DR</strong></p>\n\n<ul>\n<li>Cease sensation</li>\n<li>Neuronal recovery period prevents further signaling</li>\n<li>Neurotransmitter inhibitio... | [
{
"answer_id": 5173,
"pm_score": 1,
"text": "<p>The neuron doesn't need to know \"not to \"route\"\" an AP because this is not necessarily it's default response.</p>\n\n<p>Upon receiving an AP from another neuron (via either an a chemical synapse or a gap junction) the next neuron receives a signal. The... |
5,255 | <p>If a dopamine is released at T=0 and binds to receptor D2, what determines the time when the concentration of this neurotransmitter bound to the receptor reaches half of the original concentration? In other words, when will the effect of neurotransmitter on the intercell signalling fall in half?</p>
<p><strong>Is there any time estimate of how quickly the brain thinks that neurotransmitter has "fulfilled its purpose" and is to be re-uptaken?</strong> Or is this process completely random?</p>
<p>Thank you for your input!</p>
| [
{
"answer_id": 5257,
"pm_score": 3,
"text": "<p><strong>The half life of dopamine in the extracellular space is of the order of 200 milliseconds.</strong></p>\n\n<p><a href=\"http://www.jneurosci.org/content/27/38/10196.full.pdf\" rel=\"nofollow\">Yavich,L. (2007) Site-Specific Role of Catechol-O-Methyl... | [
{
"answer_id": 5256,
"pm_score": 3,
"text": "<p>Dopamine (DA) secreted by neurons is selectively reuptaken by the dopamine transporter (DAT), present on nerve terminals.</p>\n\n<p><a href=\"https://i.stack.imgur.com/oKVAL.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/oKVAL.png\"... |
5,278 | <p>Occasionally, after someone's been, there is an awful acrid smell lying about long after them. What causes this? The food that they've eaten? Urea less dilute due to dehydration?</p>
<p>If it helps I've noticed it only with older males.</p>
| [
{
"answer_id": 5281,
"pm_score": 3,
"text": "<p>The odor comes from <a href=\"http://en.wikipedia.org/wiki/Urea\" rel=\"nofollow\">urea</a>. Urea will slowly undergo displacement to become ammonia, but when it's fresh, it has a strong odor. Other odors do come from food, notably coffee and (in some of t... | [
{
"answer_id": 5285,
"pm_score": 1,
"text": "<p>Urea could be one. Also, be aware that there are other sources of urine. Asparagus is a famous one. I am still amused because I once thought something was really off with me ( a male, not older yet) when my urine smelled. I panicked and then found out that... |
5,322 | <p>Is territoriality (recognizing a geographic location, and challenging another member of the same species and gender) only in the domain of the male of a species? Are there any species out there where the female of the species identifies, defines, and protects her territory? What about any species where territoriality is gender neutral (<em>tic</em> humans excluded!)?</p>
<p>I thought of bees, but that is a community affair - even if it is a matriarchial society.</p>
| [
{
"answer_id": 5327,
"pm_score": 4,
"text": "<p>Absolutely not. In many spiders and insects, the female holds the territory. Many spiders for instance have much larger females than males - in these species the female can be > 10x bigger than the male and the male may not even eat during its lifetime. ... | [
{
"answer_id": 5378,
"pm_score": 2,
"text": "<p>Both sexes of red squirrels defend exclusive year round territories.\nSee <a href=\"http://www.jstor.org/stable/10.2307/1948536\" rel=\"nofollow\">Smith 1968</a> or <a href=\"http://www.jstor.org/stable/3504443\" rel=\"nofollow\">Steele 1998</a>.</p>\n"
... |
5,352 | <p>This is a biology+physics question. Since there is no biology section, I am asking here.</p>
<p>In brain, when a neuron reaches to threshold value, it fires an action potential. In most graphics, that is shown as 40 mV. An example is
<img src="https://i.stack.imgur.com/m7alk.png" alt="here"></p>
<p>Neuron's this potential reaches to all synapses where this neuron is connected to, and chemically transferred to other neuron and transformed into electric charge again.</p>
<p>My question is, because in artificial models not shown, if that whole 40 mV is distributed to those synapses according to synapse strengths, or do all synapses take a total 40 mV which is like creating a potential while it is not there?</p>
<p>Another small question is if the collected potential is stored in neuron if it cannot reach to threshold value like a capacitor in circuit?</p>
<p><img src="https://i.stack.imgur.com/jVOVg.png" alt="enter image description here"></p>
| [
{
"answer_id": 5370,
"pm_score": 4,
"text": "<p>I think you are really wondering how axonal morphology affects the voltage along the axon. The short answer to your question is that <em>each synaptic terminal sees the same voltage</em> because that voltage is generated \"fresh\" at each site. This has <e... | [
{
"answer_id": 5353,
"pm_score": 1,
"text": "<p>Here is a pretty good animation of neurotransmission:\n<a href=\"http://www.mind.ilstu.edu/curriculum/neurons_intro/neurons_intro.php\" rel=\"nofollow\">google:Neurotransmitter action potential</a></p>\n\n<p>What they don't show there very well is that the... |
5,359 | <p>I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein.</p>
<p>Things that I've been able to think of are low producing transcription factors and novel fusion proteins.</p>
| [
{
"answer_id": 5388,
"pm_score": 3,
"text": "<p>There are some funded projects and analyses available just for this purpose. </p>\n\n<p>Structural genomics or high throughput structure projects take all available peptide sequences group them into families and make sure sequence families pointing to mos... | [
{
"answer_id": 5364,
"pm_score": 2,
"text": "<p>This is how I would do it:</p>\n\n<ol>\n<li><p>Download the UniProt/SWISSPROT flat file for bacteria from <a href=\"ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_bacteria.dat.gz\" rel=\"nofollow... |
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