qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
9 | <p>I shipped 10 µL of my vector miniprep to a collaborator in a 1.5 mL eppendorf parafilmed shut and stuffed into a 50 mL conical with some paper-towel padding. However, something happened on the way and there was nothing (no liquid) in the tube when it arrived. They didn't make any comments about the microcentrifuge... | [
{
"answer_id": 36,
"pm_score": 5,
"text": "<p><strong>Summary</strong></p>\n\n<ul>\n<li>the 10 uL of plasmid miniprep may have been splattered in the cap of the tube (AnnaF)</li>\n<li>the eppendorf tube may have depressurized during air shipment and allowed the 10 uL to escape and evaporate</li>\n<li><s... | [
{
"answer_id": 17,
"pm_score": 4,
"text": "<p>Did they try to centrifuge the tube when it got there to push all the liquid to the bottom? I know that especially when working with such little amounts that even shaking it up a little can disperse the contents all over the tube.\nWe have received plasmids ... |
38 | <p>I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found:</p>
<ol>
<li><a href="http://openwetware.org/wiki/One_step_%27miniprep%27_method_for_the_isolation_of_plasmid_DNA" rel="nofollow">Using phenol/chloroform</a>
<ul>
<li>extract with phenol:chloroform:isoamylalcohol,</li>
<... | [
{
"answer_id": 55,
"pm_score": 3,
"text": "<p>In my experience, the P:C:I method will get you higher yields, and is a bit more simple (in steps and chems involved), but as @Mad Scientist has said, phenol use might be an issue. It depends on the age of your students.</p>\n"
}
] | [
{
"answer_id": 47,
"pm_score": 3,
"text": "<p>The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation <a href=\"http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1667\">similar to this one</a>. Nothing terribly toxic or requiring a fume hood (at le... |
58 | <p>We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic distance is probably less than 200 base pairs.</p>
<p>The two genes are expressed in opposite directions towards ea... | [
{
"answer_id": 55,
"pm_score": 3,
"text": "<p>In my experience, the P:C:I method will get you higher yields, and is a bit more simple (in steps and chems involved), but as @Mad Scientist has said, phenol use might be an issue. It depends on the age of your students.</p>\n"
}
] | [
{
"answer_id": 47,
"pm_score": 3,
"text": "<p>The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation <a href=\"http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1667\">similar to this one</a>. Nothing terribly toxic or requiring a fume hood (at le... |
90 | <p>I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional double-helix DNA as we know it? Have any serious alternatives been theorized?</p>
| [
{
"answer_id": 106,
"pm_score": 6,
"text": "<p>To follow up what mbq said, there have been a number of \"origin of life\" studies which suggest that RNA was a precursor to DNA, the so-called \"RNA world\" (1). Since RNA can carry out both roles which DNA and proteins perform today. Further speculations... | [
{
"answer_id": 95,
"pm_score": 5,
"text": "<p>There has been a recent report on Science, which had much return in the general press, in which a bacteria was identified that could live in an environment where arsenic was subsituted to phosphorus (one of the components of DNA, forming the backbone of the ... |
257 | <p>I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge is weak. </p>
<p>I'm finding it impossible to know where to look in a big book like Alberts, or to read Lodish with... | [
{
"answer_id": 266,
"pm_score": 4,
"text": "<p>MIT's OCW is weak when it comes to biology videos. </p>\n\n<p>UC Berkeley has some good video content for molecular and cell biology.</p>\n\n<ul>\n<li><p>See, for example, this playlist:\n<a href=\"http://www.youtube.com/playlist?list=59C08AE05E752758\">ht... | [
{
"answer_id": 258,
"pm_score": 3,
"text": "<p>This one is not precisely molecular and cell biology, but rather systems biology. It might help you as some kind of introduction, though:</p>\n\n<p><a href=\"http://www.youtube.com/watch?v=Z__BHVFP0Lk\">Systems biology lecture 1</a></p>\n\n<p>Also, if you a... |
328 | <p>In what ways has DNA been studied to see if there a "programmable" aspect to it? </p>
<p>Has nature produced anything resembling a Turing machine within the cell, perhaps using the "junk DNA" as its code? I expect nature's way would probably be very round-about and not compact.</p>
<p>NOTE: I am not asking about b... | [
{
"answer_id": 427,
"pm_score": 5,
"text": "<p>Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function. </p>\n\n<p>In the human genome, out of ~5 billion bases <a href=\"http://www.ornl.gov/sci/techresources/Human_Genome/faq/genenumber.shtml\">there are ... | [
{
"answer_id": 418,
"pm_score": 3,
"text": "<p>By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus. The answer is \"no\" for both. Well, sort of.</p>\n\n<p>Does noncoding DNA contain information? By definition, no. There are probab... |
344 | <p>There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of <a href="https://biology.stackexchange.com/questions/186/is-telomere-length-a-reliable-measure-of-health-lifespan">telomere length</a> during ce... | [
{
"answer_id": 362,
"pm_score": 6,
"text": "<p>The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.</p>\n\n<p>To set up the argument, we need two things:\nFirst, each individual has got a 'reproductive poten... | [
{
"answer_id": 404,
"pm_score": 3,
"text": "<p>Once could argue that we die because it is advantageous to get rid of mature individuals once they have reproduced. Because mature individuals have no more offspring to convey beneficial genes, those offspring which will benefit from knocking off their anc... |
378 | <p>I am very interested in the evolution of the evolution process itself. There are of course a lot of things that influence how evolution will work, but for this question, I am interested in things that are only related to the evolution process. Examples could be increase chance of mutations in newborns, change in rep... | [
{
"answer_id": 382,
"pm_score": 6,
"text": "<p>Bacteria such as E. coli are known to increase their mutation rate (by switching to a more error prone polymerase among other things) when under stress. This can mean being placed in a medium where it's not adapted to grow (<a href=\"http://www.ncbi.nlm.nih... | [
{
"answer_id": 379,
"pm_score": 4,
"text": "<p>I think this falls into your criteria but correct me if i'm wrong :).</p>\n\n<p>The <a href=\"http://en.wikipedia.org/wiki/HIV\">HIV</a> reverse transcriptase protein has evolved to have relatively low fidelity (leading to a high mutation rate in replicated... |
450 | <p>I know plants are green due to chlorophyll.</p>
<p>Surely it would be more beneficial for plants to be red than green as by being green they reflect green light and do not absorb it even though green light has more energy than red light.</p>
<p>Is there no alternative to chlorophyll? Or is it something else?</p>
| [
{
"answer_id": 462,
"pm_score": 8,
"text": "<p>Surely it would be even more beneficial for plants to be black instead of red or green, from an energy absorption point of view. And <a href=\"http://en.wikipedia.org/wiki/Solar_cell\" rel=\"noreferrer\">Solar cells</a> are indeed pretty dark.</p>\n\n<p>But... | [
{
"answer_id": 451,
"pm_score": 5,
"text": "<p>I believe it is because of a trade off between absorbing a wide range of photons and not absorbing too much heat. Certainly this is a reason why leaves are not black - the enzymes in photosynthesis as it stands would be denatured by the excess heat that wo... |
452 | <p>My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. Now in my AP Biology class we finally learned the specifics of how oxygen is used in the <a href="http://www.science... | [
{
"answer_id": 456,
"pm_score": 6,
"text": "<p>Oxygen is actually highly toxic to cells and organisms – <a href=\"http://en.wikipedia.org/wiki/Reactive_oxygen_species\" rel=\"noreferrer\">reactive oxygen species</a> cause <a href=\"http://en.wikipedia.org/wiki/Oxidative_stress\" rel=\"noreferrer\">oxida... | [
{
"answer_id": 455,
"pm_score": 5,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Superoxide\" rel=\"noreferrer\">Superoxide</a>, O<sub>2</sub><sup>−</sup> is created by the immune system in <a href=\"http://en.wikipedia.org/wiki/Phagocyte\" rel=\"noreferrer\">phagocytes</a> (including neutrophils, ... |
551 | <p>I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I g... | [
{
"answer_id": 556,
"pm_score": 4,
"text": "<p>It doesn't have very many reviews, but <a href=\"http://rads.stackoverflow.com/amzn/click/073820577X\">The Epic History of Biology</a> sounds like it's perfect.</p>\n\n<p>Flipping through the first chapter in the preview, it doesn't seem overly technical in... | [
{
"answer_id": 552,
"pm_score": 2,
"text": "<p>I don't know very many books that might be referred to as the Grand History of Biology or anything like that. That's...a big topic. Really big. How about some suggestions for good Biology/Medical History books accessible to lay people:</p>\n\n<ul>\n<li>And ... |
594 | <p>Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?</p>
| [
{
"answer_id": 615,
"pm_score": 6,
"text": "<p>I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very importan... | [
{
"answer_id": 597,
"pm_score": 4,
"text": "<p>As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A <a href=\"http://www.nature.com/news/frontier-experiments-tough-science-1.9723\">recent article</a> speculates that the <a href=\"http://en.wikipedia.org/wiki/We... |
623 | <p>From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to "accelerate" as we age.</p>
<p>Digging a little, most explanations I found basically reduced this to two reasons:</p>
<ul>
<li>As we age physically, a time frame of constant length becomes ever sm... | [
{
"answer_id": 1240,
"pm_score": 6,
"text": "<p>This is not really a biological answer, but a psychological one:</p>\n\n<p>One important fact to consider is that the perception of time is essentially a recollection of past experience, rather than perception of the present.</p>\n\n<p>Researchers who stud... | [
{
"answer_id": 713,
"pm_score": 3,
"text": "<p>There may be some clues in neurobiology.</p>\n\n<p>A possibility may be that a person's general emotional state may affect their perception of the passage of time, as argued in this <a href=\"http://www.robinson.cam.ac.uk/academic/robinson_rationality_luchi... |
757 | <p>As far as I understand, various abilities like flying, sight, hearing etc. were caused by slow evolution, where those with a greater ability to to these things had better chance of survival. (If this assumption is wrong, then I am happy to delete this question). </p>
<p>Are there, however, any documented examples o... | [
{
"answer_id": 7921,
"pm_score": 4,
"text": "<p>@kmm and @shigeta provided you with a nice observational account of sudden leaps in large organisms. However, if you want to look at where this is the norm and try to build a mathematical theory then you need to look at something much smaller; the prime ca... | [
{
"answer_id": 759,
"pm_score": 4,
"text": "<p><a href=\"http://rsbl.royalsocietypublishing.org/content/2/4/521.full?sid=36ce9d7f-9cc9-4c07-92f4-4808ec90f451\">Zuk et al. (2006)</a> document the rapid evolution of song-less crickets in a population of crickets that previously used song for courtship.</p... |
762 | <p>Humans have, in a relatively short amount of time, evolved from apes on the African plains to upright brainiacs with nukes, computers, and space travel. </p>
<p>Meanwhile, a lion is still a lion and a beetle is still a beetle.</p>
<p>Is there a specific reason for this? Do we have a particular part of brain that... | [
{
"answer_id": 766,
"pm_score": 6,
"text": "<p>We have the <a href=\"http://en.wikipedia.org/wiki/Human_accelerated_regions\">Human Accelerated Regions</a> (HARs) which are some of the most rapidly evolving RNA genes elements. While heavily conserved in vertebrates, they go haywire in humans and are lin... | [
{
"answer_id": 767,
"pm_score": 3,
"text": "<p>The ability to walk on two legs was hugely significant in human evolutionary development. This led to the hands being freed up to develop into precision tools rather than having to be durable for walking on rough terrain. Increased dexterity in the hands l... |
832 | <p>A student asked me this the other day and I thought that I would ask it again here. If one organism is said to be "more evolved" than another, what exactly does this mean?</p>
| [
{
"answer_id": 833,
"pm_score": 6,
"text": "<p>\"More evolved\" is actually meaningless in all contexts. See terdon's answer for a good explanation.</p>\n\n<p>In the strictest sense, an organism can be said to be more divergent than another when comparing both to an outgroup, such that there is an infer... | [
{
"answer_id": 834,
"pm_score": 4,
"text": "<p>I cannot improve on Thomas Ingalls' description of when \"more evolved\" is appropriately used, but the inappropriate/lazy use of the phrase is so prevalent that it deserves further comment. In my experience, the most common use of the phrase \"more evolved... |
884 | <p>This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.</p>
<p>Regarding Evolution, nothing, absolutely nothing, that a person does to herself in life can ... | [
{
"answer_id": 886,
"pm_score": 5,
"text": "<p>The assertion \"You cannot change in life what will be genetically inherited in any possible way\" is true, as you cannot (healthily) change the DNA in your germ cells.</p>\n\n<p>However, the assertion \"You cannot change in life what will be inherited in a... | [
{
"answer_id": 887,
"pm_score": 4,
"text": "<p>In general, Darwin's theory has been supported over and over again by experiments - our modern understanding of evolution is fundamentally what Darwin suggested. However, apart from appreciating many more details than Darwin ever could have, we also now kno... |
1,228 | <p>I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (<a href="http://www.sciencedirect.com/science/article/pii/S0092867400804031">Skowrya et al., 1997</a>). I have heard of phosphorylation sites, but I can't find out wh... | [
{
"answer_id": 1231,
"pm_score": 5,
"text": "<p>Phosphorylation can occur on specific amino acids only, what you have called phosporylation sites. These amino acids are Ser, Tyr, Asp, Thr and His. In theory any of these amino acids may be phosphorylated, but in reality it may not actually occur for a nu... | [
{
"answer_id": 1230,
"pm_score": 3,
"text": "<p>Phosphorylation requires exposed serine, threonine, tyrosine, or histidine residues (in eukaryotes). This is because the transfer of phosphate groups to proteins is mediated by a class of proteins called kinases. Kinases can have broad or specific activi... |
1,446 | <p>I don't know if this question applies to only humans but why can cones see much greater detail than rods? Is it possible to have a rod that can detect light intensity and color?</p>
| [
{
"answer_id": 1461,
"pm_score": 6,
"text": "<p>The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).\n<img src=\"https://i.stack.imgur.com/fF2eT.png\" alt=\"Spectral sen... | [
{
"answer_id": 1454,
"pm_score": 4,
"text": "<p>Cone cells are each connected to their own neurone. This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon. However in order to improve low light vision, multiple r... |
1,448 | <p><a href="http://www.uniprot.org/uniprot/P36659">CbpA</a> is DNA binding protein found in E. coli and binds non-specifically to curved DNA (<a href="http://dx.doi.org/10.1111/j.1365-2958.2010.07292.x">Cosgriff et al., 2010</a>), when the bacterium is in a static phase of growth. </p>
<p>The use of "curved DNA" confu... | [
{
"answer_id": 1461,
"pm_score": 6,
"text": "<p>The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).\n<img src=\"https://i.stack.imgur.com/fF2eT.png\" alt=\"Spectral sen... | [
{
"answer_id": 1454,
"pm_score": 4,
"text": "<p>Cone cells are each connected to their own neurone. This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon. However in order to improve low light vision, multiple r... |
1,495 | <p>I know death and cancer doesn't hurt humans' reproductive success. It's not helping either.</p>
<p>Why do we die? Why dying humans (all of us) are common? What's the point of dying?</p>
| [
{
"answer_id": 1496,
"pm_score": 6,
"text": "<p>Death is not only for humans. All 'complicated enough' organisms die (with a notable exception of <a href=\"http://en.wikipedia.org/wiki/Hydra_(genus)\" rel=\"nofollow noreferrer\">Hydra</a>, though you may argue when it comes to the complexity). It is is ... | [
{
"answer_id": 1497,
"pm_score": 3,
"text": "<p>Who is to say that having living Humans isn't hurting our reproductive success? Older non-reproducing humans cost the human network valuable resources and take up a sizeable portion of our living niche. Metabolically unstreamlined aged organisms are certai... |
1,515 | <p>This is my first post here, so please be gentle. I recently learned that I have Rh- blood (I'm A-), and was idly looking into blood types on Wikipedia. I was surprised to find that relatively few (~15% of all) humans have it, and most of those seem to be European. Looking just a little further, I found a bunch of cr... | [
{
"answer_id": 1539,
"pm_score": 4,
"text": "<p>Your question has many questions in it. </p>\n\n<p>As for the evolution of Rh factor, <a href=\"http://jhered.oxfordjournals.org/content/91/3/205.abstract\">Blancher and Apoil (2000)</a> attribute the high level of sequence similarity (92%) of the two <em>... | [
{
"answer_id": 9033,
"pm_score": -1,
"text": "<p>It's my opinion the rh antigen developed from toxoplasmosis infection. I only recently learned that this protozoan can actually insert its genes into a host's genome. Once it's in the genes, it can be passed in the germline. Toxoplasmosis can infect all p... |
1,838 | <p>On news, articles etc. experts talking about <strong>Genetically Modified Foods and Organisms</strong> often mentions about their disadvantages like, </p>
<ul>
<li>their potential to harm human health</li>
<li>allergies may become more intense, new allergy types may develop</li>
<li>possible damages to the environm... | [
{
"answer_id": 1844,
"pm_score": 5,
"text": "<p>GMO foods have a huge potential to make food cheaper to produce and more nutritious.</p>\n\n<p>The most common GMO foods have at least one gene added to them - an enzyme that makes the plant resistant to RoundUp - an herbicide made by the same company (Mon... | [
{
"answer_id": 1840,
"pm_score": 2,
"text": "<p>In terms of crops, plants that are grown for food, one advantage is the targeted modification of a single gene. Classical plant breeding is slow, imprecise and carries many traits of negative benefit. For example, if you cross plant variety A with variety ... |
2,075 | <p>A number of companies have started marketing LED lamps that can be switched to a red mode. The claim is that red light is less harmful to one's night vision. Given that our eyes are less sensitive to red light, though, I'm not convinced that that red light is any better than dim white light. So if "equivalent" lumin... | [
{
"answer_id": 3471,
"pm_score": 5,
"text": "<p>This is a very good question. Red light is routinely used by scientific laboratories to do low light dissections of retinas, and of course it is used in other low light contexts such as printing plate development.</p>\n\n<p>In both of the above contexts, ... | [
{
"answer_id": 2083,
"pm_score": 3,
"text": "<p>Another reason why red lights are now sponsorized for night illumination is because they are supposed to be safer in terms of interference on the circadian cycle. This is not related to better vision, but better health.</p>\n\n<p>The mammalian eye senses t... |
2,246 | <p>I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal sequence alignment to see how the sequences match.</p>
| [
{
"answer_id": 2258,
"pm_score": 4,
"text": "<p>There are various databases of homologs, for example:</p>\n\n<ul>\n<li><a href=\"http://eggnog.embl.de\">eggNOG</a></li>\n<li>Ensembl Compara (accessible via <a href=\"http://www.ensembl.org/biomart/martview\">BioMart</a>, I think)</li>\n<li><a href=\"http... | [
{
"answer_id": 2247,
"pm_score": 3,
"text": "<p>If I understand your question adequately, the <a href=\"http://genome.ucsc.edu\">Genome Browser</a> at UCSC is a great place to start. If you know the name of the gene, you can search for it. For example, <a href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?p... |
2,574 | <p>The main paper for the <em>Plasmodium palciparum</em> genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply that it prevented them using a clone-by-clone approach:</p>
<blockquote>
<p>Also, high-quality large ins... | [
{
"answer_id": 2612,
"pm_score": 4,
"text": "<p>The sequencing technologies that were developed in the last 20 years have a range of optimal use at an average A+T/G+C rate. Both highly AT-rich and GC-rich regions are complicated to process by the different sequencing technologies. Each technology has di... | [
{
"answer_id": 2575,
"pm_score": 3,
"text": "<p>I can't comment on how A+T richness complicates the sequencing process itself, but I can comment on complications that arise when annotating the sequence. <em>Ab initio</em> gene predictors are often based on hidden Markov models that are very sensitive to... |
2,602 | <p>I'm curious how much damage is potentially inflicted by shear stress by pipetting. I know that syringes used for stem cell injection can cause a lot of damage. However, to what extent does this happen with P20 and P200 pipette tips? Understandably the shear modulus of bacterial cells is significantly different from ... | [
{
"answer_id": 20890,
"pm_score": 5,
"text": "<p>This is an excellent question, I have been training people to culture cells for about 12 years and students have a hard time grasping this and appreciating the importance etc.</p>\n\n<p>What cells are usually experiencing during pipetting is analogous to ... | [
{
"answer_id": 2603,
"pm_score": 4,
"text": "<p>It's an easy experiment to do. Take your cells aliquot them into 10 microfuge tubes, and pipette each suspension increasing amount of times, stain with trypan blue and count.</p>\n\n<p>The most important factors will be which pipette-type you use; I would ... |
2,790 | <p>When people try to explain evolution, they tell me that evolution is a cumulative result of mutations & natural section of the more superior individuals of a particular species. I think I'm fairly convinced with this explanation.</p>
<p>But when I think about it, all of them assume that there was an organism, h... | [
{
"answer_id": 2806,
"pm_score": 5,
"text": "<p>Evolution or (as Darwin called it) \"descent with modification\" is a theory which explains the origin of the species NOT the origin of life. How the first life arose is <strong>completely irrelevant</strong> to the theory of evolution. What evolution do... | [
{
"answer_id": 2793,
"pm_score": 3,
"text": "<blockquote>\n <p>They teach us in Physics that the entropy of an isolated system is always increasing or at least constant. Then how can an organism be born under these conditions?</p>\n</blockquote>\n\n<p>The sun sends energy to the Earth, allowing for a d... |
3,177 | <p>We use electromagnetic communication everywhere these days. Cell phones, wifi, old-school radio transmissions, television, deep space communication, etc.</p>
<p>I'm curious about some of the possible reasons we have never seen biological systems having evolved to use electromagnetic, i.e. radio, for communication. ... | [
{
"answer_id": 3180,
"pm_score": 6,
"text": "<p>There is a very different mechanism for generation (and detection) of ultraviolet, visible and infrared light vs radio waves.</p>\n\n<p>For the first, it is possible to generate it using chemical reactions (that is, <a href=\"http://en.wikipedia.org/wiki/C... | [
{
"answer_id": 3178,
"pm_score": 2,
"text": "<p>A quick comparison between light and sound vs. Radio</p>\n\n<ul>\n<li><a href=\"http://en.wikipedia.org/wiki/Light\" rel=\"nofollow noreferrer\">Light</a>: Wavelength 380 nm -740 nm</li>\n<li><a href=\"http://en.wikipedia.org/wiki/Sound\" rel=\"nofollow no... |
3,304 | <p>Layman here. So I have never really quite understood this facet of human evolution, (or any other for that matter), in that, I understand the evolutionary process, but I get lost on the 'border' cases. </p>
<p>For example, we, as humans, evolved from monkeys, (to use the colloquial term, I am not a biologist by any... | [
{
"answer_id": 3305,
"pm_score": 6,
"text": "<p>Actually, your last paragraph is more the case than not.</p>\n\n<p><strong>There are currently three common definitions for delineating discrete species:</strong></p>\n\n<p>1) Phenotypically different from related species (looks or acts differently).</p>\n... | [
{
"answer_id": 3306,
"pm_score": 5,
"text": "<blockquote>\n <p>but I get lost on the 'border' cases.</p>\n</blockquote>\n\n<p>Not surprisingly, since there are no borders, and this is probably the greatest misunderstanding: Evolution is gradual. It’s not generally possible to say where a complex featur... |
3,315 | <p><a href="http://en.wikipedia.org/wiki/Hijra_%28South_Asia%29" rel="nofollow">Hijra</a> are people who have a penis (not sure if sexually active) but look much like a female (perhaps for some feminine biological property). Wikipedia says they are <em>"physiological males who have feminine gender identity"</em></p>
<... | [
{
"answer_id": 3317,
"pm_score": 5,
"text": "<p>When dealing with <em>humans</em>, there are only two <strong>Biological</strong> genders as defined by the presence or absence of the Y-Chromosome. If the Y-Chromosome is not present, or through some process gets totally deactivated, the human will appear... | [
{
"answer_id": 3318,
"pm_score": 0,
"text": "<p>As I read the Wikipedia article you reference, its useful to remember that conventional chromosomal definitions of gender, the genitals are soft tissue which has many recorded morphological abnormalities. <a href=\"http://en.wikipedia.org/wiki/Hermaphrodi... |
3,365 | <p>I have an AP Bio class where I have to name 3 properties of water and I chose adhesion and cohesion for one of them. I'm having trouble finding out how exactly trees use adhesion and cohesion to move water. There is a lot of different answers out there on the net. How do trees use adhesion and cohesion to move water... | [
{
"answer_id": 3378,
"pm_score": 4,
"text": "<p>In high school, we did an experiment that showed this.</p>\n\n<p>Basically, if you take a glass of water, and let it sit out, perhaps in front of an open window, it will eventually lose water due to evaporation. It may take a few days/weeks to really see a... | [
{
"answer_id": 3367,
"pm_score": 3,
"text": "<p>The mechanism is called \"capillary action\". It requires a tube of a small diameter and happens because of the adhesion of water to the walls and the cohesion within the water (=surface tension).</p>\n"
},
{
"answer_id": 60862,
"pm_score": 0,
... |
3,427 | <p>I've recently seen the term <em>synthetic biology</em> being used to describe research involving genetic modification of organisms. What is the difference between <em>synthetic biology</em> and <em>genetic engineering</em>?</p>
<p>Is it just a new term for the same thing, or is it something different? Does one of t... | [
{
"answer_id": 3434,
"pm_score": 4,
"text": "<p>My understanding is that synthetic biology is genetic engineering 2.0. The difference is in the approach. Whereas genetic engineering projects are usually ad hoc, synthetic biology aims to apply proper engineering principles such as standardisation, modula... | [
{
"answer_id": 3428,
"pm_score": 2,
"text": "<p>In genetics engineering we use and manipulate natural genetic elements but in synthetic biology we make new gene elements and network.</p>\n"
},
{
"answer_id": 3429,
"pm_score": 3,
"text": "<p>It seems to me that the difference is mainly se... |
5,007 | <p>I would like to know if evolution is continuing to happen in modern humans, assuming things like existence of the nuclear family structure, fidelity to one partner, etc. It seems to me the answer would be NO because evolution depends on differential reproductive rates, but in the modern world, all male humans have r... | [
{
"answer_id": 5008,
"pm_score": 6,
"text": "<p>It is certainly not true that \"all male humans have roughly 2.5 (or whatever the number) kids\". First of all, male and female humans have <em>exactly</em> the same reproductive rate. For obvious reasons, every time a male has offspring, a female must hav... | [
{
"answer_id": 5058,
"pm_score": 2,
"text": "<p>Darwin used the term “<em>descent with modification</em>” to describe evolution. That means <strong>a change between generations</strong> in the characteristics, or traits, of a population. It is a process which occurs by four processes - mutation, migrati... |
5,148 | <p>If a hermaphrodite animal (like slug, snail, etc) finds a partner they can mate immediately.</p>
<p>If another animal with "normal" reproduction (lets say a mouse) finds a partner they can only mate if they are opposite genders.</p>
<p>So it seems logical that the hermaphrodite way of reproduction is more successf... | [
{
"answer_id": 5150,
"pm_score": 6,
"text": "<p>Firstly I'll clarify that you are talking about <em>simultaneous</em> hermaphrodites rather than <em>sequential</em> hermaphrodites (1st one sex, then the other e.g. the limpet Patella vulgata).</p>\n\n<p>It is perhaps easiest to address the question by co... | [
{
"answer_id": 5347,
"pm_score": 1,
"text": "<p>I have been pondering this question for a while and I get what RG255 is saying. I'm just not sure I entirely buy it. Take earthworms, for example. They are simultaneous true hermaphrodites (as far as I understand). The anatomy doesn't have to be <em>that</... |
5,445 | <p>From the moment we learn to communicate, we always get told, whether by our parents, or our teachers, or by anyone else, to avoid the cold, or to put a jacket on to avoid catching a cold, to dry our hair before we go outside, because we'll get sick otherwise, so on and so forth. I also was diagnosed with a pneumonia... | [
{
"answer_id": 5511,
"pm_score": 5,
"text": "<p>it does not, really. unless we're talking about things like frostbite or severe hypothermia.</p>\n<p>it's a myth that it does.\nthe virus is more stable in colder air, however.</p>\n<p>see more here:</p>\n<p><a href=\"http://www.nytimes.com/2007/12/05/heal... | [
{
"answer_id": 5498,
"pm_score": -1,
"text": "<p>Most likely the energy to stay warm is not being used to fight infection. Also the virus is likely designed to operate with your respiratory system at a colder temperature more effective that the immune system is at that cooler temperature.</p>\n"
},
... |
5,524 | <p>Imagine humans were to colonize a distant planet and it was a single one-way trip. How many people would they need to bring?</p>
<p>Obviously 2 is the minimum, but that would result in a lot of inbreeding.</p>
<p>So what number is the minimum number of people you can have in an isolated community and still maintai... | [
{
"answer_id": 5526,
"pm_score": 6,
"text": "<p>Actually it is a very important question for laboratory animals (and, I imagine, endangered species) and was calculated to be 25 couples.</p>\n\n<p>With any number of animals (including humans), there is always some inbreeding happening, but you can reduce... | [
{
"answer_id": 15686,
"pm_score": -1,
"text": "<p>Inbreeding isn't negative at all, so one couple would suffice for colonization.</p>\n\n<p>Inbreeding fixes recessive traits and the ones displaying unwanted traits can be culled. Actually, inbreeding is one of the most potent weapons of evolution, it spe... |
5,588 | <p>Mammals, reptiles, arachnids, insects, etc are all as far as I am aware symmetrical in appearance.</p>
<p>Take a human for instance, make a line from the top of our head right down the middle. However, internally it is not the same. Our organs <em>excluding</em> the kidneys, lungs, reproductive organs, etc are not ... | [
{
"answer_id": 5601,
"pm_score": 6,
"text": "<p>First, I think it worthwhile considering 'Why would internal symmetry be beneficial?' Developmental simplicity jumps to mind immediately. You can also consider relationship to external organs; the stomach and esophagus are lined up with the mouth which is ... | [
{
"answer_id": 5760,
"pm_score": 3,
"text": "<p>Building on the answer given by Sean Connolly above, it would be very easy to imagine evolutionary scenarios where organs are more likely to develop asymmetrically than symmetrically.</p>\n\n<p>For instance, imagine an organism that has a simple digestive ... |
6,827 | <p>Why did humans/animals evolve to become self-aware of their own thoughts. That is, why don't humans act and compute like a machine, or walking zombie. In my mind, such creatures would still be as smart and equally capable of surviving, the only difference being they don't experience the phenomenon of self-awarenes... | [
{
"answer_id": 6831,
"pm_score": 4,
"text": "<p>There have been many proposals over the years as to why human consciousness has emerged and how, or even what it is. </p>\n\n<p>Most of us will not be surprised to know that there is no consensus about an answer here. Its hard to draw a trend from a sing... | [
{
"answer_id": 13624,
"pm_score": 2,
"text": "<p>I don't think you can ever ask or answer for that matter WHY questions in biology. The only answer there is: because it works. Asking why questions implies that there was a reason, and reason cannot exist alone by itself. Reason is held by someone or some... |
6,915 | <p>Obviously, the temperature of water does not affect its chemical composition. At least not in the ranges we are likely to drink it in. Yet it is clearly far more pleasant and refreshing to drink cool water than it is to drink tepid or warm water.</p>
<p>Is there actually any difference to the organism or is this ju... | [
{
"answer_id": 30657,
"pm_score": 5,
"text": "<p><strong>Short answer</strong>: Cold is pleasant only when your are not already freezing and cold might satiate thirst better because it acts as enhancer of the \"water intake flow meter\".</p>\n\n<hr>\n\n<p><strong>Is cold water more tasty than warm water... | [
{
"answer_id": 6922,
"pm_score": 3,
"text": "<p>I think it's because we are more often thirsty in a warm/hot/dry environment.<br>\nSince almost all of us have a house with a household furnace creating that warm/dry environment. </p>\n\n<p>Thus cold water would be more refreshing since it also cools us... |
7,492 | <p>I've been to local zoo the other day and one lizard caught my attention: its pupils are circular, which, I thought, is not usual for reptiles. Turns out it is, but now I can't find any explanation on why some animals have one kind of pupil and others have the other. Lizards can have both, and so can snakes. The only... | [
{
"answer_id": 7514,
"pm_score": 5,
"text": "<p>Circular pupils are <em>always</em> functionally superior to vertical pupils; a slit does not correctly focus light from all directions whereas a circular pupil does. If you observe cats when they're hunting at dawn and dusk*, they have big, circular pupil... | [
{
"answer_id": 7500,
"pm_score": 2,
"text": "<p>Your mention of cats hinted that vertical pupils have to do with night vision, and <a href=\"http://www.newscientist.com/article/mg16422167.600-the-last-word.html\" rel=\"nofollow\">indeed they do.</a></p>\n\n<p>The retinas of cats and other nocturnal anim... |
7,847 | <p>According to Wikipedia, muscle cramps are caused by the inability of myosin fibers to break free from the actin filaments during contraction, resulting in a prolonged contraction.</p>
<p>A lack of ATP would obviously produce cramping, as myosin requires ATP to become free from actin.</p>
<p>However, I have heard t... | [
{
"answer_id": 7859,
"pm_score": 4,
"text": "<p>The quick and simple answer:</p>\n\n<p>Cramps of a hypokalemic origin are much more common than those of a hyponatremic origin because the Na-K pump is more effective at moving potassium in comparison to sodium.\nAt the onset of a muscle contraction, the p... | [
{
"answer_id": 11302,
"pm_score": 2,
"text": "<p>Muscle contraction occurs when the brain tells the body to move. The brain then starts an action potential down the motor neurons, until it reaches the terminal bouton. At the terminal bouton, it releases the neurotransmitter, acetylcholine, which travels... |
7,854 | <p>A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell. </p>
<p>In general, in eukaryotes, episomes are closed circular DNA molecules that are replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses... | [
{
"answer_id": 7859,
"pm_score": 4,
"text": "<p>The quick and simple answer:</p>\n\n<p>Cramps of a hypokalemic origin are much more common than those of a hyponatremic origin because the Na-K pump is more effective at moving potassium in comparison to sodium.\nAt the onset of a muscle contraction, the p... | [
{
"answer_id": 11302,
"pm_score": 2,
"text": "<p>Muscle contraction occurs when the brain tells the body to move. The brain then starts an action potential down the motor neurons, until it reaches the terminal bouton. At the terminal bouton, it releases the neurotransmitter, acetylcholine, which travels... |
7,932 | <p>In physics, "almost everything is already discovered, and all that remains is to fill a few unimportant holes." (See <a href="http://en.wikipedia.org/wiki/Philipp_von_Jolly" rel="noreferrer">Jolly</a>.) Therefore, on Physics SE, people are veering off into different directions: <em>biology</em>, for example.</p>
<p... | [
{
"answer_id": 7937,
"pm_score": 7,
"text": "<p>Wheels are possible on the molecular level — bacterial flagella are rotating cores inside a molecular motor, but wheels larger than the flagellum have not really been found.</p>\n<p><img src=\"https://i.stack.imgur.com/1YlbP.jpg\" alt=\"enter image descrip... | [
{
"answer_id": 7938,
"pm_score": 4,
"text": "<p>Shigeta's molecular answer is spot on. However, at the large scale level I think the key problem with a biological wheel needs to be spelled out clearly: how does an organism with separate parts maintain these parts? Let's suppose that an organism evolves ... |
9,172 | <p>I made an answer on the Scifi.SE that can be read <a href="https://scifi.stackexchange.com/questions/37780/how-did-they-clone-other-breeds-of-dinosaur-other-than-the-one-in-the-blood-of-t/37806#37806">here</a>. It is about how the characters in the story Jurassic Park might have gotten DNA for all the species shown.... | [
{
"answer_id": 9174,
"pm_score": 6,
"text": "<p>So, a quick molecular biology lesson. </p>\n\n<ul>\n<li><strong>Proteins</strong> are the things that make up a good percentage of our cells (which make up a good percentage of <em>us</em>), and are the things that do the work of the cells - many are catal... | [
{
"answer_id": 9173,
"pm_score": 3,
"text": "<p>Just to clarify definitions, your <a href=\"http://en.wikipedia.org/wiki/Genome\" rel=\"noreferrer\">genome</a> is made up of sequences of DNA. DNA is constructed pairs of four nucleic acids, or nucleotides (A,G,T,C). That DNA has many <a href=\"http://en.... |
9,419 | <p>Reading this question, <a href="https://biology.stackexchange.com/questions/7932/why-are-there-no-wheeled-animals">Why are there no wheeled animals?</a>, I wondered why <strong>no organisms seem to make use of the tensile and other strengths of metal</strong>, as we do in metal tools and constructions. I am obviousl... | [
{
"answer_id": 9420,
"pm_score": 7,
"text": "<p>There are some cases, as hinted at by the comments. But these are relatively small amount of metal.</p>\n<p>It's not that there is no metal available. Iron in particular <a href=\"https://www.livescience.com/29263-iron.html\" rel=\"nofollow noreferrer\">is... | [
{
"answer_id": 9426,
"pm_score": 5,
"text": "<p>A few minor points to add to shigeta's excellent answer:</p>\n\n<p>Biological enzymes don't work well on metals. Some often incorporate metals (see <a href=\"https://en.wikipedia.org/wiki/Chelation\">chelation</a>) but elemental atoms aren't easy to proce... |
9,438 | <p>The recent <a href="http://www.the-scientist.com/?articles.view/articleNo/36624/title/New-Giant-Viruses-Break-Records/">news</a> about a new supermassive virus being discovered got me thinking about how we define viruses as non-living organisms whilst they are bigger than bacteria, and much more complex than we firs... | [
{
"answer_id": 9455,
"pm_score": 7,
"text": "<p>If this is a topic that really interests you, I'd suggest searching for papers/reviews/opinions written by <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=Didier+Raoult+mimivirus\">Didier Raoult.</a> Raoult is one of the original discoverers of the ma... | [
{
"answer_id": 9439,
"pm_score": 4,
"text": "<p>There are quite some different definitions of being \"alive\", but a common one includes the need to have responsiveness, growth, metabolism, energy transformation, and reproduction (found from the <a href=\"http://www.britannica.com/EBchecked/topic/340003... |
9,500 | <p>If we somehow remove pheromones, <strong>do animals experience a phenomenon similar to human "visual beauty" when looking at members of the opposite sex?</strong> For example, given a set of 20 female ducks observed through a glass panel, would male ducks attempt to court/mate with a small subset of female ducks fir... | [
{
"answer_id": 9503,
"pm_score": 4,
"text": "<p>There are numerous examples of visual attraction in animals. An absolute classic of an experiment, taught to most/all evolutionary biology students, is the <a href=\"http://www.treknature.com/gallery/photo139613.htm\" rel=\"nofollow\">widowbird</a> tail le... | [
{
"answer_id": 9502,
"pm_score": 3,
"text": "<p>Absolutely. Quality by appearance is sometimes a big part of mate selection and sometimes it is not. </p>\n\n<p>The size and cognitive capacity brain is probably important but not always. Primates are closest to us and have most similar tastes to us, <a ... |
10,376 | <p>I'm a maths major and I have an interest in learning biology. I know very, very little; I know how babies are made and that's about it. Could anyone recommend a stimulating text to read for its own sake and also to use to learn biology?</p>
| [
{
"answer_id": 10386,
"pm_score": 5,
"text": "<p>I found the Campbell Biology textbook to be quite comprehensive and approachable. I think many introductory biology courses use it.</p>\n\n<p><a href=\"http://rads.stackoverflow.com/amzn/click/0321558235\">http://www.amazon.com/Campbell-Biology-Edition-Ja... | [
{
"answer_id": 10378,
"pm_score": 3,
"text": "<p>There are tons of books and it is quite hard to find one that gives such a broad overview. <a href=\"https://www.amazon.ca/Campbell-Biology-9th-Jane-Reece/dp/0321558235/ref=sr_1_2?ie=UTF8&qid=1513808241&sr=8-2&keywords=campbell+biology\" rel=\... |
13,595 | <p>I read a story this week on Richard Lenski who has been 'evolving' <em>E. coli</em> for more than 50,000 generations now. One comment I read was from someone who doesn't accept Evolution who pointed out that we haven't seen a single celled organism 'evolve' into a multi-celled organism. Another person responded an... | [
{
"answer_id": 21525,
"pm_score": 5,
"text": "<blockquote>\n <p>How did multicellularity evolved?</p>\n</blockquote>\n\n<p><strong>It is an ongoing field of research - Some insights about the origin of multicellularity</strong></p>\n\n<p>This is a big ongoing field of research. To start with an example... | [
{
"answer_id": 13597,
"pm_score": 3,
"text": "<p>For one thing, larger organisms are much more energy efficient. This is what is known as <a href=\"http://en.wikipedia.org/wiki/Kleiber%27s_law\" rel=\"nofollow\">Kleiber's Law</a> where the caloric requirement scales as the 3/4 power to the body mass. <... |
14,414 | <p>After my online research on the subject, I learnt that, biologically speaking, many scientists believe that there is no such thing as a race. <em>Homo sapiens</em> as a species is only 200,000 years old, which has not allowed for any significant genetic diversification yet, and our DNA is 99.99% similar. I've read s... | [
{
"answer_id": 14419,
"pm_score": 7,
"text": "<p>Firstly, it's not true that you can't tell racial background from DNA. You most certainly can; it's quite possible to give fairly accurate phenotypic reconstruction of the features we choose as racial markers from DNA samples alone and also possible to id... | [
{
"answer_id": 14416,
"pm_score": 4,
"text": "<p><strong>Bias</strong></p>\n\n<p>When you say <code>phenotype</code> you mostly mean \"skin color\", \"size of the nose\", \"hair color\", \"shape of the eyes\", \"height\", and some others. All these traits that we manage to find to explain <a href=\"http... |
14,888 | <p>Approximately, how many <a href="https://en.wikipedia.org/wiki/Family_%28biology%29">families</a> have been identified?</p>
<p>I've often often come across figures for the total number of species on Earth. Recently, I found myself wondering about the encompassing ranks above them, specifically family, but I can't r... | [
{
"answer_id": 59068,
"pm_score": 4,
"text": "<p>The 2011 paper <a href=\"http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001127\" rel=\"noreferrer\">How Many Species Are There on Earth and in the Ocean?</a> indirectly answers this question as well as any other source you'll find I... | [
{
"answer_id": 14890,
"pm_score": 3,
"text": "<p>I don't know about other groups, but about plants, number of families depends on the system you follow. Recent version of The Plant List (1.1) estimates about 352 000 species of Angiosperms and lists over 400 families. See <a href=\"http://www.theplantlis... |
15,514 | <p>I've often heard that a population, human or otherwise, will continue to grow as long as there is food available (assuming nothing else is killing them off). It makes sense: if you have food you can live, and if nothing is hunting you you'll survive to reproduce.</p>
<p>I recently designed a piece of software to s... | [
{
"answer_id": 15516,
"pm_score": 6,
"text": "<p>No, I don't think auto-regulation explain much in the population sizes of predators. Group selection may explain such auto-regulation but I don't think it is of any considerable importance for this discussion.</p>\n\n<p>The short answer is, as @shigeta sa... | [
{
"answer_id": 15681,
"pm_score": 3,
"text": "<p>One of the possible adjustments of these mathematical models is to introduce a \"place to hide\", making some (small) percent of the prey population not accessible (or much more difficult to access) for predators. After the number of predators decreases f... |
15,555 | <p>So obviously, viruses are nonliving. But when my teacher was teaching viruses in the video (we're doing "flip" learning this semester), the way he described it, it seemed like the viruses responded to their environment in that they moved around until they found a cell of the right type, and then they latched on and ... | [
{
"answer_id": 15559,
"pm_score": 5,
"text": "<p>All of your reasoning is correct - viruses are <strong>not</strong> motile (i.e. not self-propelled). </p>\n\n<p>I don't understand why you think this would cause a difficulty in the case of bacteria.</p>\n\n<p><strong>Edit in response to comment @Remi.b<... | [
{
"answer_id": 15562,
"pm_score": 3,
"text": "<p>You are right, viruses are neither alive, nor are they moving by themselves. They are moved by passive movements (e.g. the bloodstream or movements of the air) until they meet their target cells. This can be either a cell in the human body (for flu viruse... |
15,736 | <p>I had laser eye surgery a decade ago, but in recent years my eyesight has become significantly myopic. I consulted an ophthalmologist to see if this was eye strain because I work at computers a lot, or part of a natural degradation of the eye over time, or both. My ophthalmologist seems to believe that in my case I'... | [
{
"answer_id": 15902,
"pm_score": 4,
"text": "<p>First of all, I should correct some points that were misunderstood. \nDon't change the question because this will lead to confusion.</p>\n\n<p>\"The way the lens becomes flat is by using spring-like connective tissue called choroids that pull it taught.\"... | [
{
"answer_id": 48445,
"pm_score": 2,
"text": "<p>I'm not a eye doctor but I do workout. I would like to say something about your metaphor or comparison from the ciliary muscle to the body muscles. </p>\n\n<p>Let's look at a workout. In a workout, you strain the muscle then relax the muscle repeatedly un... |
16,854 | <p>Why don't we breathe nitrogen while it makes most of the air?</p>
<p>Why do we always tend to breathe oxygen, not hydrogen and nitrogen?</p>
| [
{
"answer_id": 16864,
"pm_score": 5,
"text": "<p>I'd argue that we do \"breathe\" all those gases. Air that we inhale (at sea level) is about 78% N$_2$, 20.9% O$_2$, 1% argon, and smaller percentages of CO$_2$, neon, methane, etc. So all those gases are going into the lungs with every breath in.</p>\n\n... | [
{
"answer_id": 16856,
"pm_score": 0,
"text": "<p>Basically when air fills our alveoli, by the process of diffusion, only oxygen in the air is taken into the blood stream while the other gases along with the waste CO2 is exhaled. So you do breathe in nitrogen, but it is exhaled as it is by the body. The ... |
16,899 | <p>I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for software with which to do this, and I have tried using Dendroscope and TreeMap, but can't get to grips with them. </p>
<p>I want to produce something along the lines of this;</p>
<p><img src="https:... | [
{
"answer_id": 16923,
"pm_score": 5,
"text": "<h1>Dendroscope</h1>\n\n<p>Using <a href=\"http://ab.inf.uni-tuebingen.de/software/dendroscope/\" rel=\"noreferrer\">Dendroscope</a>, I opened the provided example file <code>trees.new</code>. This opens a new window with 16 trees in it.</p>\n\n<ol>\n<li>Shi... | [
{
"answer_id": 16900,
"pm_score": 2,
"text": "<p>I have to confess that I know nothing about phylogenetics and the associated software but according to the abstract of <a href=\"http://onlinelibrary.wiley.com/doi/10.1111/zoj.12027/abstract\" rel=\"nofollow noreferrer\">this article</a> it seems that the... |
17,077 | <p>Why does evolution not make life longer for humans or any other species?</p>
<p>Wouldn't evolution favour a long life?</p>
| [
{
"answer_id": 17091,
"pm_score": 7,
"text": "<p>Why do we age is a classical question in Evolutionary Biology. There are several things to consider when we think of how genes that cause disease, aging, and death to evolve.</p>\n\n<p>One explanation for the evolution of aging is the <a href=\"http://www... | [
{
"answer_id": 17078,
"pm_score": 5,
"text": "<p>This is a very good question.</p>\n\n<p>There is a big ongoing field of research called \"evolution of aging/senescence\" that tackles this question. I won't give you a complete overview of the different hypothesis the could explain why we age but here is... |
19,762 | <p>As I understand it, various animal traits have to evolve gradually, but what happens to the species that are "neither here nor there"?</p>
<p>To put it differently, if a species evolved from another, it did so because it's somehow better, right? So why are there examples of the original species not being extinct?</... | [
{
"answer_id": 19764,
"pm_score": 5,
"text": "<p><strong>Short answer</strong></p>\n\n<blockquote>\n <p>Why are there species rather than a long continuum?</p>\n</blockquote>\n\n<p>Three important reasons I could think of are sex, non-uniform adaptive landscape and ancestry.</p>\n\n<p><strong>Long answ... | [
{
"answer_id": 19763,
"pm_score": 3,
"text": "<p>Typically when both new and old species still exist it is because evolution pushed the new one into a different habitat or role. </p>\n\n<p>As a hypothetical example reef fish vs. deep water fish and their relative size. Let's say deep water fish evolve... |
19,873 | <p>Would I be able to genetically modify a plant at home? What equipment will be necessary? I think it might be a fun change from the 'norm' of regular hybridisation, to try some inter-family gene insertion, instead of staying within a genus. Are some plants easier to modify than others?</p>
| [
{
"answer_id": 19875,
"pm_score": 4,
"text": "<p>Well, that depends on your home. ;) I think it is not an easy process.</p>\n\n<p>There are <strong>two main methods</strong> that are used to genetically modify plants:</p>\n\n<p><strong>Using the bacterium</strong>, Agrobacterium tumifaciens, as a vector... | [
{
"answer_id": 19874,
"pm_score": 2,
"text": "<p>Yes, It is.</p>\n\n<p>An Indian Company IndieBB can help you get one.\n<a href=\"https://www.indiegogo.com/projects/indiebb-your-first-gmo\" rel=\"nofollow\">IndieBB: a DNA system designed to help you and your friends to explore genetic engineering and sy... |
20,437 | <p>recently i got into a debate with <a href="https://hinduism.stackexchange.com/posts/comments/4386?noredirect=1">this</a> question on hinduism.se ,</p>
<p>as the link given above shows, are sperms considered as living or non-living </p>
<p>as far as my knowledge is concerned, sperms undergo locomotion, senescence, ... | [
{
"answer_id": 20442,
"pm_score": 3,
"text": "<p>The question of what is living is nothing but a matter of definition. We can only tell you what are the standard definitions of what is a living thing but no absolute truth exist behind these definitions. Therefore, I am afraid that all discussions here w... | [
{
"answer_id": 20438,
"pm_score": -1,
"text": "<p>One requirement most biologists have to consider something living is the ability to reproduce. This is why viruses are generally not considered alive. They contain proteins and DNA or RNA, but require infecting a host cell and hijacking its replication m... |
20,657 | <p>Some people say that it's awful that humans eat animals. They feel that it's barbaric, because you're killing life and then on top of that, you're eating it, and that you should eat vegetation instead.</p>
<p>But isn't vegetation life too? Personally, I see no difference between animals and veg as all life has ce... | [
{
"answer_id": 20664,
"pm_score": 7,
"text": "<p>The answer to your question is <strong>yes</strong> it is certainly possible. </p>\n\n<p>At one time it was thought that there was something special about \"organic\" chemicals which meant that they could not be artificially synthesised out of fundamental... | [
{
"answer_id": 20659,
"pm_score": 5,
"text": "<p>Living organisms can be divided into hetrotrophs and autotrophs. Autotrophs like plants and algae are able to produce complex <em>organic</em> compounds from relatively simple <em>inorganic</em> components. They are satisfied with sunlight, water and othe... |
20,709 | <p>A vast majority of humans get at least some grey hair as they age. As far as I know this applies to both genders and all races. Presumably this means that at least some grey haired humans have noticeable reproductive advantage, or maybe they had it in the recent past.</p>
<p>Theoretically, because this feature is s... | [
{
"answer_id": 20715,
"pm_score": 4,
"text": "<blockquote>\n <p>Presumably this means that at least some grey haired humans have\n noticeable reproductive advantage, or maybe they had it in the recent\n past.</p>\n</blockquote>\n\n<p>No it doesn't. Natural selection is not that strong, it doesn't op... | [
{
"answer_id": 20721,
"pm_score": 2,
"text": "<p>I do not think there is a reproductive advantage in gray hair - it's the other way around: </p>\n\n<p>Normal colored hair has a reproductive advantage.\nBut it also has a cost in terms of substances needed to build it.</p>\n\n<p>I make the assumption here... |
20,912 | <p>Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.</p>
<ul>
<li>Survival of the fittest</li>
<li>Random mutation</li>
<li>Natural Selection</li>
</ul>
<p>All of these things seem to account for some ma... | [
{
"answer_id": 20913,
"pm_score": 6,
"text": "<p>This entire answer will be long, so read the short part first, then read the rest if you (or anyone else) is curious. Citations are included in the long section. I can include additional citations in the short section if needed.</p>\n\n<p><strong>Long Sto... | [
{
"answer_id": 20914,
"pm_score": 4,
"text": "<p><strong>About your question</strong></p>\n\n<p>This kind of very basic question has the drawback to need a very long answer. In consequence, your question might get some close vote. I'll do my best to help but you might want to look at some source of info... |
20,992 | <p>From what I understand, your body needs certain amounts of vitamins and minerals to maintain health. Why can't we just take enough pills to obtain these vitamins and minerals?</p>
| [
{
"answer_id": 20993,
"pm_score": -1,
"text": "<p>This is more of a biochemistry question and to be honest its a little bit out of my league because I have not had the necessary grad classes to explain nutrition but indeed I will try.</p>\n<p>Unknown metabolite cofactors and things like ionization, oxid... | [
{
"answer_id": 21338,
"pm_score": 3,
"text": "<p>I think the piece of missing information here is the distinction between <a href=\"http://fnic.nal.usda.gov/food-composition/macronutrients\" rel=\"nofollow noreferrer\"><i>macro</i>nutrients</a> and <a href=\"http://www.who.int/nutrition/topics/micronutr... |
23,873 | <p>This is a cross-cutting question but I think its core is about biology. Our society's need for energy is dramatically growing and we are messing up with our environment to answer them. Maybe another way to proceed would be to use the primary energy source that is the sun in the same way as it has been used throughou... | [
{
"answer_id": 23882,
"pm_score": 4,
"text": "<blockquote>\n <p>The most basic example of what I would like to talk about seems to be\n the algae powered lamp that has (apparently) been developped.</p>\n</blockquote>\n\n<p>I think you misunderstood the idea. That lamp uses <a href=\"http://en.wikipedi... | [
{
"answer_id": 23875,
"pm_score": 3,
"text": "<p>It is not possible to do this directly. Indirectly, it is possible, this is actually done by harvesting fruits - they contain the energy of the sunlight conserved in chemical compounds like sugars or starch and their cellular structures. The basic process... |
24,090 | <p>Corneas are donated and transplanted, but not the eyeball. </p>
<p>I don't understand. What is the purpose of donating a cornea without an eyeball to a blind person?</p>
| [
{
"answer_id": 24101,
"pm_score": 4,
"text": "<p>No-one can re-implant an entire eye, because the optic nerve has been severed in one who has lost an eye. A cornea can't be grafted to a glass eye. But blindness isn't only caused by loss of the entire orbit. It's also caused by cloudy corneas, which is t... | [
{
"answer_id": 24092,
"pm_score": 2,
"text": "<p>The eyeball is basically the sclera that surrounds the delicate inner structures of the eye (<a href=\"http://en.wikipedia.org/wiki/Eye\" rel=\"nofollow\">see wiki on the eye</a>). The cornea is the transparent window in front of the pupil that transmits ... |
24,126 | <p>Does each cell contain only a single copy of its genome? Or are there ever 'extra' copies present. </p>
<p><strong>Reason behind question</strong>: <em>Wondering whether gene mutations could be corrected by referencing a 'backup copy'.. If such a thing exists..</em></p>
| [
{
"answer_id": 24127,
"pm_score": 5,
"text": "<p>As a quick answer, yes, most human cells carry 2 copies of the genome and are known as <a href=\"http://en.wikipedia.org/wiki/Ploidy#Diploid\">diploid</a> cells. One copy comes from each of your parents, so they aren't identical, but usually pretty close.... | [
{
"answer_id": 24128,
"pm_score": 3,
"text": "<p>Diploid cells contain two copies of the genome. Additionally, each copy of the genome can have multiple copies of certain genes. Which can provide a level of protective redundancy.</p>\n\n<p>However, there are a number of potential problems with having mu... |
28,177 | <p>Lately I have seen a number of unrelated "scientific" debates over whether certain substances should be outlawed because they are toxic to humans. My initial, informal reaction is usually to respond that anything is toxic to humans if you give them a sufficiently large dose.</p>
<p>However, formally I don't know if... | [
{
"answer_id": 28179,
"pm_score": 6,
"text": "<p>I’ll answer this theoretically, since that’s how it has been posed. And if we’re ignoring practicalities, we may as well posit that the substance in question will be introduced directly into the bloodstream (This is, of course, simple to do in reality, bu... | [
{
"answer_id": 28178,
"pm_score": 3,
"text": "<p>There is a problem with definition of toxicity — things that are dangerous in large amounts aren't usually called toxic. In spite of this, you're right: everything can be dangerous to a human in large enough amounts, or if delivered improperly.</p>\... |
29,679 | <p>Does the brain really function like a computer as in, ultimately every response is related to a binary sequence based on whether particular neurons fire or not?</p>
| [
{
"answer_id": 29685,
"pm_score": 5,
"text": "<p>First of all, I would like to point out that making analogy between digital computers and the brain is often very misleading.</p>\n\n<p>That being said, my answer is, some scientists believe so, some don't.</p>\n\n<p>Several things to consider:</p>\n\n<ol... | [
{
"answer_id": 29734,
"pm_score": 3,
"text": "<p>While action potentials are usually binary, you should note that <a href=\"http://en.wikipedia.org/wiki/Synapse\">synaptic communication</a> between neurons is generally not binary. Most synapses work by <a href=\"http://en.wikipedia.org/wiki/Neurotransmi... |
29,795 | <p>How does a virus like HIV mutate into so many strains, and yet all of them are harmful to our immune system? What gives this virus the ability to mutate so efficiently?</p>
| [
{
"answer_id": 29960,
"pm_score": 3,
"text": "<p>Others have already touched the important points. Consider this as a summary.</p>\n\n<blockquote>\n <p>What gives HIV the ability to mutate?</p>\n</blockquote>\n\n<p>All organisms mutate by two mechanisms:</p>\n\n<ol>\n<li>Replication errors</li>\n<li>Mu... | [
{
"answer_id": 29796,
"pm_score": 2,
"text": "<p>Viral recombination produces genetic variation that contributes mostly to the evolution of the HIV-1 virus.</p>\n\n<p>HIV being an RNA Virus utilizes an enzyme called reverse transcriptase, which produces DNA from RNA. HIV also has <strong>two</strong> R... |
30,116 | <p>Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops?</p>
<p>In software development, these constructs have the following functions:</p>
<ul>
<li><strong>IF-statements:</strong> An IF statement executes the code in a subsequent code block if some specific condition is met.</li>
<li><strong>WHILE-l... | [
{
"answer_id": 30120,
"pm_score": 8,
"text": "<p>Biological examples similar to programming statements:</p>\n\n<ul>\n<li><code>IF</code> : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only wit... | [
{
"answer_id": 30117,
"pm_score": 4,
"text": "<p>There are certainly some comparisons that could be made between the way genes are expressed from DNA and logic functions, but they aren't great.</p>\n\n<p>But synthetic Biology is really a blossoming new field that is attempting to integrate logic functio... |
30,468 | <p>Why is the action of flexing the foot so that the toes move anteriorly/superiorly (i.e. in the direction opposite that which they move during plantar flexion) described as "dorsiflexion?" In the same vein, why is the top surface of the foot called the "dorsal surface?" </p>
<p>If anything, the action opposite to pl... | [
{
"answer_id": 30470,
"pm_score": 5,
"text": "<p>Anatomical terms must be able to fit a wide variety of organisms, from insects to fish, dogs, horses, chimpanzees to humans. That's why the terms are sometimes confusing to people who are thinking only of bipedal humans.</p>\n\n<p>In anatomy, the dorsum i... | [
{
"answer_id": 30469,
"pm_score": 2,
"text": "<p><em>Dors/dorsum</em> in Latin simply means \"back\", and it is rather normal and reasonable to use the equivalent term in English with regard to the extremities (hands and feet), see \"<a href=\"http://dictionary.cambridge.org/dictionary/british/know-sth-... |
31,546 | <p>Does anyone know of sources for learning bioinformatics, focused on genomics? I would like to learn a lot of skills I could apply potently in the workforce if I ever became adept at the fields. My computer science knowledge is weak, and my biology knowledge is mediocre, but I find the topics to be interesting.</p>
<... | [
{
"answer_id": 31558,
"pm_score": 4,
"text": "<p><a href=\"http://unixandperl.com/\" rel=\"nofollow\">Unix and Perl to the Rescue</a> by Keith Bradnam and Ian Korf is an excellent introductory book and guide for bioinformatics (Linux and Perl) in genomics. It includes exercises and starts with the very ... | [
{
"answer_id": 31552,
"pm_score": 3,
"text": "<p>Beginning Perl for Bioinformatics by Jim Tisdall <a href=\"http://shop.oreilly.com\">http://shop.oreilly.com</a> is quite good, in my opinion, and his sequel, Mastering Perl for Bioinformatics is also great. The focus is largely, but not exclusively genom... |
32,964 | <p>I'm an engineer by training and teaching myself the basics of cell and developmental biology. I'm using Scott F. Gilbert's Developmental Biology and Alberts' Essential Cell Biology right now, and they are both great resources.</p>
<p>Can you recommend good books on similar topics that are written in a non-textbook ... | [
{
"answer_id": 52730,
"pm_score": 2,
"text": "<p>For Biochemistry:</p>\n\n<p><a href=\"https://i.stack.imgur.com/uvPKf.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/uvPKf.jpg\" alt=\"enter image description here\"></a></p>\n\n<p>For Molecular Genetics:</p>\n\n<p><a href=\"https:... | [
{
"answer_id": 33010,
"pm_score": 0,
"text": "<p>Would you consider the New York Times a suitable level of detail (while admittedly not a book)? If so then you may want to peruse this collection:\n<a href=\"http://topics.nytimes.com/top/news/science/topics/biology_and_biochemistry/index.html\" rel=\"nof... |
35,337 | <p>Across the electromagnetic spectrum, 400-700 nm is a narrow spectrum of frequencies and focused in the region of short wavelengths. For example, radio waves cover a large range of frequencies unexploited by the visual system. So what biological reason is there that evolved us to use such a small frequency bandwidth ... | [
{
"answer_id": 35353,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nThe visible spectrum has the highest energy in sunlight at the earth's surface, explaining the gross location of the visible spectrum in life on earth. The specific frequency range varies across species and can be explai... | [
{
"answer_id": 35342,
"pm_score": -1,
"text": "<p>These wavelengths happen to satisfy two conditions.</p>\n\n<p>First, shorter wavelength photons (EM radiation) tend to be dangerous for biology. Even UV light (<350nm) is already can damage DNA. That is due to the fact that bond energies in biological... |
35,446 | <p>There are plenty of different hand soaps out there, as well as hand sanitizers. Is there an advantage to soaps that claim that they're antibacterial vs soaps that just say soap?</p>
<p>In particular I'm looking at Softsoap who offers normal soap and antibacterial soap. </p>
<p><strong><em>Examples:</em></strong></... | [
{
"answer_id": 35451,
"pm_score": 7,
"text": "<p>Short answer: There is no benefit for their use in households. </p>\n\n<p>Long answer: These soaps (see <a href=\"http://www.colgate.com/app/Softsoap/US/EN/Ingredients.cvsp\">here</a> for the complete list) contain the so called quaternary ammonium compou... | [
{
"answer_id": 35450,
"pm_score": 4,
"text": "<p>Chris has correctly identified the antibacterial agent in the hand soap depicted in the image in the question, and therefore his answer is superior as a direct answer. </p>\n\n<p>Nevertheless, other members of the Softsoap series of hand soap uses <a href... |
39,374 | <p>It's easy to find information about the biggest animals at land / at sea / in the air. But what was the biggest underground-living animal that ever existed?</p>
<ul>
<li>No animals that were forced to live underground (e.g. pit ponies)</li>
<li>The animal should live at least 95% of its life under the earth (e.g. f... | [
{
"answer_id": 57393,
"pm_score": 4,
"text": "<p><strong>Microchaetus rappi</strong>\nMicrochaetus rappi, the African giant earthworm, is a large earthworm in the Microchaetidae family, the largest of the segmented worms (commonly called earthworms). It averages about 1.36 m (4.5 ft) in length, but can ... | [
{
"answer_id": 39375,
"pm_score": 3,
"text": "<p>I don't know if there is a bigger animal, but the biggest <strong>mole</strong> is the <a href=\"https://en.wikipedia.org/wiki/Russian_desman\" rel=\"noreferrer\">Russian desman</a> with 400-520g and a length of \n18-21 cm (35-41cm including the tail)</p>... |
39,664 | <p>To be clear, I'm not doubting that <em>Homo sapiens</em> and <em>Homo neanderthalensis</em> did interbreed: of that much I'm convinced.</p>
<p>Within the past few years I've seen an upcropping of pop-sci articles discussing the interbreeding between pre-historic species of humans. In everything that I see in these a... | [
{
"answer_id": 39669,
"pm_score": 8,
"text": "<h1>Short answer</h1>\n<p>The concept of species is poorly defined and is often misleading. The concepts of <a href=\"https://en.wikipedia.org/wiki/Lineage_(evolution)\" rel=\"noreferrer\">lineage</a> and <a href=\"https://en.wikipedia.org/wiki/Monophyly\" r... | [
{
"answer_id": 39668,
"pm_score": 4,
"text": "<p>The definition of species is open for debate, and this is especially the case when you try to define it from a paleontology perspective. </p>\n\n<p><a href=\"https://en.wikipedia.org/wiki/Neanderthal\">Homo neanderthalensis</a> was first discovered and de... |
40,156 | <p>Let me explain... A friend and I read some articles, part of a Biology book, and watched a video on evolution. We then tried to explain what Evolution is to each other.</p>
<p>My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environmen... | [
{
"answer_id": 40165,
"pm_score": 5,
"text": "<p>I accidentally wrote a lot!</p>\n\n<p>I first discuss the term <em>Darwinian evolution</em>. I then describe the main evolutionary processes insisting on the two elements of interest in your question, that is <em>mutations</em> and <em>natural selection</... | [
{
"answer_id": 40158,
"pm_score": 1,
"text": "<p>Your description of Evolution seems more accurate than your friends. DNA cannot mutate with a particular goal in mind, mutations are random. Most mutations have no effect on an organism's survival, but some will be detrimental, and a few will helpful. Hel... |
40,964 | <p>I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, specifically during the process of mRNA translation.</p>
<p>I've tried to do some research online, but I could not find a r... | [
{
"answer_id": 65168,
"pm_score": 4,
"text": "<p>Although the question shows considerable effort to achieve clarity, the way it is phrased as:</p>\n\n<blockquote>\n <p>How many molecules of nucleoside triphosphate… [does] it take <em>to release enough energy</em></p>\n</blockquote>\n\n<p>still allows a... | [
{
"answer_id": 40973,
"pm_score": -1,
"text": "<p>First, during the initiation of translation, a small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An init... |
42,050 | <p>In my <a href="https://biology.stackexchange.com/questions/42033/what-are-we-missing-about-the-real-workings-of-the-evolutionary-process">last question</a> I asked why we don't see increased complexity in artificial life simulations of evolution. It seems I had fallen for a common misconception, that evolution was a... | [
{
"answer_id": 42053,
"pm_score": 7,
"text": "<p>I think possibly the problem here is the way you're approaching the issue.</p>\n\n<p>You're considering <em>improvement</em> as anything that increases the abilities or complexity of the organism—that isn't necessarily what an <em>improvement</em> is thou... | [
{
"answer_id": 42063,
"pm_score": 4,
"text": "<p><strong>Evolution is simply a process of change.</strong> It is a change in trait values of populations over time. It results from four mechanisms: mutation, migration, drift, and selection. The first three lead to random change from one generation to th... |
42,273 | <p>On <a href="http://ericturkheimer.blogspot.com/2015/05/the-heritability-of-everything.html">his blog</a>, Eric Turkheimer writes:</p>
<blockquote>
<p>[T]aken as a number, a unit of analysis, heritability coefficients are
funny things to aggregate on such a massive level. What exactly are
we supposed to make ... | [
{
"answer_id": 42280,
"pm_score": 6,
"text": "<p>Rather than discussing what heritability is not through wordy sentences, let's just talk about what heritability <strong>is</strong>. There are two \"types of heritability\":</p>\n\n<ul>\n<li><em>Heritability in the broad sense</em></li>\n<li><em>Heritabi... | [
{
"answer_id": 42445,
"pm_score": 3,
"text": "<p>Briefly, because remi.b gives a lot of good detail about this in his answer, (narrow sense) heritability is essentially a measure of how much of the phenotypic variance is explained by (additive) genetic variance. Phenotype (P) in an individual is the res... |
43,095 | <p>For me it seems reasonable that if I kept my gaze on a fixed point in a room with low light, a progressively brighter and better picture would appear before my eyes, just like a camera can see in the dark if the shutter speed is really slow, e.g. 4 seconds exposure. Why can't our brain do this trick as well (accumul... | [
{
"answer_id": 43100,
"pm_score": 7,
"text": "<p>For simplicity's sake, let's really reduce this to something like photography.</p>\n\n<p>A camera's aperture can stay open indefinitely, allowing the plate (or whatever is receiving and recording light) to \"collect and save the effect of photons\" over t... | [
{
"answer_id": 43097,
"pm_score": 2,
"text": "<p>What I believe you are referring to, is the phenomenon by which the camera adjusts light exposure by adjusting aperture. We can also do this, but it happens very fast. Go from a dark room to a brighter room and you will be blinded, but that effect soon su... |
45,942 | <p>A human encountering a tiger or a malaria plasmodium is likely to suffer, and the tiger/plasmodium is likely to gain from the transaction. Not necessarily a good example, and I am aware that a successful parasite avoids prematurely killing its host, but I can't see any fundamental difference.</p>
<p>Of course it's ... | [
{
"answer_id": 45964,
"pm_score": 4,
"text": "<p>Good question.</p>\n\n<p>There is no fundamental difference between parasites and predators.</p>\n\n<p><strong>Ecological Interaction</strong></p>\n\n<p>In terms of <a href=\"https://en.wikipedia.org/wiki/Ecological_relationship\" rel=\"nofollow noreferre... | [
{
"answer_id": 45946,
"pm_score": -1,
"text": "<p>A parasite may or may not kill the host. It's basic motive is to constantly derive nutrition from the host. More a sort of one time investment and as an interest you keep getting the nutrition.\nWhereas a predator's motive is to kill the host to satisfy ... |
46,016 | <p>I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell. Several papers report using a viral NLS, but is it absolutely necessary? Could Cas9 be trafficked to nucleus without addition of a NLS?</p>
| [
{
"answer_id": 45964,
"pm_score": 4,
"text": "<p>Good question.</p>\n\n<p>There is no fundamental difference between parasites and predators.</p>\n\n<p><strong>Ecological Interaction</strong></p>\n\n<p>In terms of <a href=\"https://en.wikipedia.org/wiki/Ecological_relationship\" rel=\"nofollow noreferre... | [
{
"answer_id": 45946,
"pm_score": -1,
"text": "<p>A parasite may or may not kill the host. It's basic motive is to constantly derive nutrition from the host. More a sort of one time investment and as an interest you keep getting the nutrition.\nWhereas a predator's motive is to kill the host to satisfy ... |
49,209 | <p>How has evolution created our blood, lungs and the heart?</p>
<p>We can't exist without blood, which transports the oxygen to all areas of our body. However, the blood needs a lung, which gives it the oxygen to transport. The blood also needs something which lets it flow through the whole body, which are our veins.... | [
{
"answer_id": 49218,
"pm_score": 6,
"text": "<p>While others have addressed the big picture aspects of your question, I think it would be useful to look at the specifics. </p>\n\n<p>Have a look at the heart (or more accurately, the <em>hearts</em>) of the earthworm: <a href=\"https://i.stack.imgur.com/... | [
{
"answer_id": 49211,
"pm_score": 3,
"text": "<p>This is a good question, but it has a vast scope, as you're talking about the progression of millions of different living animals over hundreds of millions of years, none of which are still alive, so we have to make inferences based on what we observe in ... |
49,214 | <p>In the Krebs cycle, where do the hydrogens and electrons that NAD+ and FAD accept come from? It seems that citric acid only loses two hydrogens because it starts out with eight hydrogens and then becomes oxaloacetic acid, which has four hydrogens. </p>
| [
{
"answer_id": 49218,
"pm_score": 6,
"text": "<p>While others have addressed the big picture aspects of your question, I think it would be useful to look at the specifics. </p>\n\n<p>Have a look at the heart (or more accurately, the <em>hearts</em>) of the earthworm: <a href=\"https://i.stack.imgur.com/... | [
{
"answer_id": 49211,
"pm_score": 3,
"text": "<p>This is a good question, but it has a vast scope, as you're talking about the progression of millions of different living animals over hundreds of millions of years, none of which are still alive, so we have to make inferences based on what we observe in ... |
50,420 | <p>What was the first piece of work in computational biology? I'm ideally looking for a paper.</p>
<p>I am not interested in works that involve data management or data analysis but work that model biological processes through numerical simulations or numerical approximations of analytical results.</p>
| [
{
"answer_id": 50445,
"pm_score": 4,
"text": "<p>Another nomination, if you include infectious disease epidemiology as part of biology and hence computational simulations of epidemics as part of computational biology:</p>\n\n<p><a href=\"http://www.jstor.org/stable/2342553\" rel=\"noreferrer\">Measles p... | [
{
"answer_id": 50423,
"pm_score": 3,
"text": "<p>I don't believe you'll ever find the <em>first</em> work in bioinformatics (or computational biology, as you put it), however the field really <strong>began</strong> in the times of accumulating data about protein biochemistry. Computational biologists (b... |
50,599 | <p>I have a modest collection of insect specimens that I caught, prepared, mounted, and dried myself. I'm entirely an amateur collector, so my procedure may be causing me this trouble now, but here's how I preserved them.</p>
<ol>
<li>Killed in the freezer</li>
<li>Placed in a sealed container on a dry platform, with ... | [
{
"answer_id": 50619,
"pm_score": 5,
"text": "<p>I ran into the same issue when collecting bees in a hot, humid environment. As <code>arboviral</code>stated, freezing is a great way to help with the infection but keep in mind:</p>\n\n<ul>\n<li>It may not kill all of your pests</li>\n<li>It will not kee... | [
{
"answer_id": 50613,
"pm_score": 3,
"text": "<p>As @picapica says, these look like beetles of the genus <em>Anthrena</em>: museum beetles, furniture carpet beetles or something similar. I'd lean towards furniture carpet beetle (<em>Anthrena flavipes</em>) myself, but this isn't a species ID question.</... |
51,556 | <p>We heard this animal outside in Western Washington (Port Townsend area) during the late evening. I think it is a bird, but it honestly sounds sort of like some creepy woman singing or something. The audio is linked below. The sound (in the audio) was repeated for a long time at random intervals averaging probably ev... | [
{
"answer_id": 51572,
"pm_score": 3,
"text": "<p>I asked the same question on another forum here: <a href=\"http://www.birdforum.net/showthread.php?p=3454684\" rel=\"nofollow\">http://www.birdforum.net/showthread.php?p=3454684</a>. </p>\n\n<p>It looks like another possibility is a <strong>barred owl</st... | [
{
"answer_id": 51563,
"pm_score": 2,
"text": "<p>My guess is an owl, possibly a great horned owl, which are found in the <a href=\"https://www.google.com.sg/search?q=owls+in+western+washington&gws_rd=cr&ei=IQnZV8GdMMLO0gT6gqCQAg\" rel=\"nofollow\">area</a> and can <a href=\"http://www.learner.or... |
52,046 | <p>I hope this is a good place to ask such question. I have to do some data analysis on RNA-seq data from human cells. I am currently searching for tools to help me with that. Specifically, I would need some tools to analyze the gene expression from the data. Something to help me plot the expression of selected genes i... | [
{
"answer_id": 52112,
"pm_score": 4,
"text": "<p>You will likely need a tool to \"map\" the reads on the reference genome.\nYou may find such a reference genome, together with annotations, here:\n<a href=\"ftp://ussd-ftp.illumina.com/\" rel=\"nofollow noreferrer\">ftp://ussd-ftp.illumina.com/</a>.</p>\n... | [
{
"answer_id": 52261,
"pm_score": 2,
"text": "<p>While I also agree @bli that R and Python (in particular <code>Bioconductor</code>) have more than enough packages for you to compare gene expression. You <em>shouldn't</em> align your reads with bwa or bowtie because they don't take introns into consider... |
53,313 | <p>Is there a lower limit to the difference in wavelength (colour) our eyes can detect? If so, is this consistent between individuals? Are there any other traits correlated with precise colour vision?</p>
| [
{
"answer_id": 54449,
"pm_score": 3,
"text": "<p>The eye really on can sense 3 colors, or to be more precise it only has three types color sensitive each of which detects a large range of wavelengths with no way to distinguish between them within the same cone. We only determine color by the different l... | [
{
"answer_id": 53472,
"pm_score": 0,
"text": "<p>First, it depends a lot of the brightness. And also, of the part of the spectrum: we have high accuracy between red-green (since 2 of the cone have close sensitiveness), and very few in deep red and violet (were mostly a single cone reacts).</p>\n\n<p>As ... |
53,328 | <p>Imagine you hit your foot at a table leg and it hurts a while or you got a tiny graze. Those injuries aren't an infection but could these things still be called an inflammation?</p>
<p>Is it necessary that in both cases cells are damaged to induce a cascade of hormones? Or with other words, is there always an infla... | [
{
"answer_id": 54449,
"pm_score": 3,
"text": "<p>The eye really on can sense 3 colors, or to be more precise it only has three types color sensitive each of which detects a large range of wavelengths with no way to distinguish between them within the same cone. We only determine color by the different l... | [
{
"answer_id": 53472,
"pm_score": 0,
"text": "<p>First, it depends a lot of the brightness. And also, of the part of the spectrum: we have high accuracy between red-green (since 2 of the cone have close sensitiveness), and very few in deep red and violet (were mostly a single cone reacts).</p>\n\n<p>As ... |
57,128 | <p>How forgetting things is helpful for the brain or the human body biologically? This <a href="https://www.google.co.in/url?sa=t&source=web&rct=j&url=https://www.psychologytoday.com/blog/mind-blender/201403/why-forgetting-the-past-can-be-good-thing&ved=0ahUKEwj41aGi1MjSAhWMtY8KHaoJBbwQFghaMAg&usg... | [
{
"answer_id": 57136,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nIt has been shown that loss of long-term memories may enhance the retrieval of others. Short-term working memory is explicitly designed to be volatile and non-lasting. However, there are many other types of memories wher... | [
{
"answer_id": 57133,
"pm_score": 3,
"text": "<p>Memory is formed by building connections between nerve cells (i.e. neurons). These connections are called synapses. The synapses form a network between several (or tens or hundreds) of neurons, therefore giving us the ability to retrieve something we had ... |
57,145 | <blockquote>
<p>A recent study has provided evidence that two types of equine (horse) herpes viruses have an unusually broad host range. This fact supports which of the following statements?</p>
<p>a. The lytic cylce occurs in horses while the lysogenic cycle occurs only in other species.</p>
<p>b. The virus is transmi... | [
{
"answer_id": 57136,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nIt has been shown that loss of long-term memories may enhance the retrieval of others. Short-term working memory is explicitly designed to be volatile and non-lasting. However, there are many other types of memories wher... | [
{
"answer_id": 57133,
"pm_score": 3,
"text": "<p>Memory is formed by building connections between nerve cells (i.e. neurons). These connections are called synapses. The synapses form a network between several (or tens or hundreds) of neurons, therefore giving us the ability to retrieve something we had ... |
57,356 | <p>My science textbook says this:</p>
<blockquote>
<p>Evolution should not be equated with progress. In fact, there is no real 'progress' in the idea of evolution. Evolution is simply the generation of diversity and the shaping of the diversity by environmental factors. The only progressive trend in evolution seems ... | [
{
"answer_id": 57454,
"pm_score": 5,
"text": "<p>I'm glad you've asked the question as it is a common layman misunderstanding.</p>\n\n<h1>Dog vs Human</h1>\n\n<p>Your example comparing humans and dogs is actually very central to the logical flaw that yields many to equate evolution with progress.</p>\n\... | [
{
"answer_id": 57360,
"pm_score": 2,
"text": "<p>When you say, humans are more advanced than dogs, from what perspective are you saying that from? Is it in the capacity to use intelligence, to build and create, to do the math, to climb trees? If it is any of these, you are right: humans are better at us... |
57,479 | <p>As far as I know, humans have 23 pairs of chromosomes, each one which contains a particular amount of genes. But in the "last" pair, men have a XY pair chromosome, and women have a XX pair chromosome. Does the missing "leg" of the XY pair make men to have fewer genes than women, and if so, how many genes do each sex... | [
{
"answer_id": 57480,
"pm_score": 6,
"text": "<p>It is true that the Y chromosome is shorter than the X chromosome and that there are more genes on the X chromosome.</p>\n\n<blockquote>\n <p>Do men have fewer genes?</p>\n</blockquote>\n\n<p>One could (mis)understand three things in the expression \"num... | [
{
"answer_id": 57501,
"pm_score": 0,
"text": "<p>Note - this is a very simple way to present things, and don't have the ambition to be a biology thesis. </p>\n\n<p>Men do not have fewer genes than women, but fewer allels (variations of a gene); the allels on the x-y chromosome pair are not necessarily t... |
58,769 | <p>Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I sometimes read and hear that inbreeding among humans also causes decreased intelligence, especially emotional and social ... | [
{
"answer_id": 59018,
"pm_score": 4,
"text": "<p>There is indeed evidence that inbreeding in humans lowers intelligence of offspring. </p>\n\n<blockquote>\n <p>In summary, our comprehensive assessment revealed that parental consanguinity and degree of inbreeding was significantly associated with depres... | [
{
"answer_id": 59022,
"pm_score": 2,
"text": "<p>Inbreeding, in nature at large, has one primary effect, as you said. It increases the chances of two copies of harmful, recessive alleles. Consequently, offspring are much more likely to suffer from genetic and/or degenerative diseases.</p>\n\n<p>As for i... |
59,062 | <p>Some sources say that gametes are haploid, some say that they are diploid.</p>
<p>I'm confused.</p>
| [
{
"answer_id": 59111,
"pm_score": 3,
"text": "<p>Actually there is some confusion here, and that's quite excusable, because it's extremely common reading that <strong>monoploid</strong> and <strong>haploid</strong> are synonyms and have the same meaning. However, they are different terms. According to H... | [
{
"answer_id": 59063,
"pm_score": 1,
"text": "<p>Don't get confused by the number of chromosomes. Haploid refers to 1 set of chromosome, diploid refers to 2 set of chromosomes, triploid means 3 set of chromosomes. They don't represent the numbers of chromosome present on a set. </p>\n\n<p>We human being... |
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