qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
20,298 | <p>My <em>very</em> basic understanding is DNA gets transcribed into RNA by effectively replacing thymine with uracil, then RNA is translated to make proteins. Looking at it from an engineering perspective, it would appear that, while the RNA to protein translation is non-trivial, the DNA to RNA transcription process is rather redundant: As it's just a simple replacement, why not start with RNA in the first place? My assumption therefore is that there is something about the RNA molecule (e.g., too reactive, too unstable, etc.) that requires it to be put in "cold storage" as DNA.</p>
<p>I don't have a background in genetics or biology, so could someone ELI5 why DNA is needed?</p>
| [
{
"answer_id": 20302,
"pm_score": 3,
"text": "<p>Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets.</p>\... | [
{
"answer_id": 20299,
"pm_score": 0,
"text": "<p>OK, I found this on <a href=\"http://en.wikipedia.org/wiki/DNA,_RNA_and_proteins:_The_three_essential_macromolecules_of_life#Why_DNA_is_best_for_encoding_genetic_information\" rel=\"nofollow\">Wikipedia</a>. I probably should have checked there first!</p>... |
20,444 | <p>We have a long protocol that we are optimizing that includes DpnI digestion of a PCR product (to remove any of the template DNA if it's methylated, and while we're not certain in the blind tests, likely relevant DNA will be methylated).</p>
<p>I'm wondering if we can extend the DpnI incubation/reaction time to 4-5 hours. This will make concurrent steps in the screen easier to manage. Has anyone extended DpnI digestions? How "leaky" or nonspecific of a process can it be?</p>
<p>Thanks.</p>
| [
{
"answer_id": 20469,
"pm_score": 3,
"text": "<p>According to <a href=\"http://stanxterm.aecom.yu.edu/wiki/data/Product_manuals_attach/quikchange2xl.pdf\" rel=\"nofollow\">this instruction</a> it can be done for 1 hour but this is for large plasmids. I agree with Chris that it should not be of a problem... | [
{
"answer_id": 55045,
"pm_score": 0,
"text": "<p>My mentor taught me that we can do DpnI digestion for minimum 4 hours and maximum 12 hours. I have ever left the reaction until around 16 hours (?) but the result was okay. My mentor recommended to put at 4oC after 12 hours, if we cannot continue the work... |
20,449 | <p>If a healthy human is at a certain muscle state and then experiences muscular atrophy solely due to disuse/lack of exercise, is it easier to gain that muscle back than if the human had never reached that certain muscle state. If so, is there a name for this effect. The reason I'm wondering is because it seems like muscle mass was definitely periodic in ancient times when food would become scarce during the winter, and that an increased ability to put back on muscle might have developed evolutionary-wise. I thought that this would fit best in biology, let me know if this isn't the case.</p>
| [
{
"answer_id": 20469,
"pm_score": 3,
"text": "<p>According to <a href=\"http://stanxterm.aecom.yu.edu/wiki/data/Product_manuals_attach/quikchange2xl.pdf\" rel=\"nofollow\">this instruction</a> it can be done for 1 hour but this is for large plasmids. I agree with Chris that it should not be of a problem... | [
{
"answer_id": 55045,
"pm_score": 0,
"text": "<p>My mentor taught me that we can do DpnI digestion for minimum 4 hours and maximum 12 hours. I have ever left the reaction until around 16 hours (?) but the result was okay. My mentor recommended to put at 4oC after 12 hours, if we cannot continue the work... |
20,464 | <p>A girl pretended having a piece of food in her hand and pointed it to a Barbary Macaque in Gibraltar. As a response he made this facial expression to her. What does this mean?</p>
<p><img src="https://i.stack.imgur.com/VLdkB.jpg" alt="GibraltarBarbaryMacaqueExpressions"></p>
| [
{
"answer_id": 20469,
"pm_score": 3,
"text": "<p>According to <a href=\"http://stanxterm.aecom.yu.edu/wiki/data/Product_manuals_attach/quikchange2xl.pdf\" rel=\"nofollow\">this instruction</a> it can be done for 1 hour but this is for large plasmids. I agree with Chris that it should not be of a problem... | [
{
"answer_id": 55045,
"pm_score": 0,
"text": "<p>My mentor taught me that we can do DpnI digestion for minimum 4 hours and maximum 12 hours. I have ever left the reaction until around 16 hours (?) but the result was okay. My mentor recommended to put at 4oC after 12 hours, if we cannot continue the work... |
20,486 | <p>Vomit comes from gastric acid, right? And in gastric acid there is HCl and HCl is corrosive (strong), how come when I vomit, it doesn't destroy things that it (as the vomit) hits (such as floor, table)?</p>
| [
{
"answer_id": 20487,
"pm_score": 6,
"text": "<p>First of all, it is corrosive. People which are bulimic often get problems with their teeth getting damaged by the permanent exposure to the acidic stomach fluids. See the paper for more information:</p>\n\n<ul>\n<li><a href=\"http://informahealthcare.com... | [
{
"answer_id": 20517,
"pm_score": 4,
"text": "<p>As Chris said it's a matter of a low concentration for a small amount of time. Most people clean up their vomit rather than leave it to sit. Most people who vomit also have recently eaten something which triggers the reflex but also dilutes the acid or ma... |
20,589 | <p>Super simple question, but I can't find the answer on the Internet (and I'm in a foreign country so the library is not English.) As the title says, what is the smallest scale at which blood vessels, nerves, lymphatic vessels, bronchi, renal structures, etc.. are deterministic (same for most of the population)? For example, I'd imagine capillaries are pretty much random, while (most?) people have an aorta, so where does the pattern break? Is there a scale at which an animal's body is probably similar to their siblings but dissimilar to a complete stranger? Or is it just a statistical distribution thing (the smaller you go the more standard deviation you get)?</p>
| [
{
"answer_id": 20591,
"pm_score": 3,
"text": "<p>Indeed a very good question. I'm afraid it might remain without a proper anatomy-based answer, but my intuition would tend towards agreeing with \"the smaller you get, the more deviation you'll find\".</p>\n\n<p>Or rather, I would expect the same principl... | [
{
"answer_id": 20599,
"pm_score": 2,
"text": "<p>The answer is... basically none. The variability is high, and can also happen in the macroscopic range. If you want a quick-and-dirty idea of the fraction of the population presenting a certain variability in humans, I would suggest a good anatomy atlas o... |
20,653 | <p>In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex. </p>
<p>Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?</p>
| [
{
"answer_id": 20655,
"pm_score": 3,
"text": "<p>In birds and reptiles females are the heterogametic sex with allosome configuration <code>ZW</code>. However it has been <a href=\"http://www.newscientist.com/blogs/shortsharpscience/2010/11/boa-constrictors-born-by-virgi.html\" rel=\"nofollow\">reported<... | [
{
"answer_id": 20662,
"pm_score": 2,
"text": "<blockquote>\n <p>Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?</p>\n</blockquote>\n\n<p>Here are a bunch of cases and specific examples that may interest you</p>\n\n<ul>\n<li><p>Th... |
20,731 | <p>It is well known that the European colonists brought many infectious diseases to the Americas, and that these had a deadly effect on the native populations, because they had no immunity to them. Were there any local infectious diseases to which the colonists were not immune? I’ve never heard of such. I’m not aware that the colonists suffered any epidemics, or that they brought any new and unusual diseases back to Europe.</p>
<p>Why not? Is this merely an accident of history, that there were no infectious diseases in the Americas which did not already exist in Eurasia? Or is there some explanation?</p>
| [
{
"answer_id": 20732,
"pm_score": 6,
"text": "<p>In \"Guns, Germs, and Steel\" Jared Diamond includes quite a bit on this topic. His conclusion is that Europeans, and old world humans in general were much more exposed to their farm animals, often living in the same buildings. This allowed a much greater... | [
{
"answer_id": 20733,
"pm_score": 4,
"text": "<p>There is at least one important exception - it is generally thought that <a href=\"http://en.m.wikipedia.org/wiki/History_of_syphilis\">syphilis</a> came to Europe from the Americas.</p>\n"
},
{
"answer_id": 52281,
"pm_score": 0,
"text": "... |
20,754 | <p>In relation to microbiology and the naming of the various areas of the plant as it relates to microbial inhabitance, I am confused as to the difference between the terms <strong>endorhiza</strong> and <strong>rhizosphere</strong>.</p>
<p>In <a href="http://books.google.com.au/books?id=pQyRyIdm7O0C&pg=PA131&lpg=PA131&dq=Phyllosphere%20%22stems%22&source=bl&ots=VAvyV0LpP1&sig=GKHLjD6vRhMmZ-Wkt7hi9t17C8M&hl=en&sa=X&ei=Mbj6U_CyCI2LuATo3oKIBw&ved=0CDkQ6AEwBQ#v=onepage&q=rhizosphere%20%22roots%22&f=false" rel="nofollow noreferrer">this</a> case I see rhizosphere referred simply to as the 'roots', but in <a href="http://www.ncbi.nlm.nih.gov/pubmed/21947430" rel="nofollow noreferrer">this</a> case I also see endorhiza explained simply as 'roots' also.</p>
<p>However in <a href="http://www.ncbi.nlm.nih.gov/pubmed/9115091" rel="nofollow noreferrer"><em>this</em></a> case, I see a further explanation for endorhiza (which does make sense etymologically): 'internal root tissues'.</p>
<p>Does this mean <em>endorhiza</em> is be a sub-term for the area inside the roots, and the larger area of the rhizome in general represented by <em>rhizosphere</em>, and that is the difference?</p>
| [
{
"answer_id": 21587,
"pm_score": 3,
"text": "<p>Healthy plant growth depends on a microbial community that lives around and inside the roots of plants <a href=\"http://link.springer.com/article/10.1007/s11627-001-0122-y\" rel=\"nofollow noreferrer\">(Bais et al. 2001)</a>. Roots secrete from the roots ... | [
{
"answer_id": 20758,
"pm_score": 0,
"text": "<p>The rhizosphere is the <em>narrow region of soil that is directly influenced by root secretions and associated soil microorganisms</em> <a href=\"http://en.wikipedia.org/wiki/Rhizosphere#cite_note-2\" rel=\"nofollow\">(wiki)</a></p>\n\n<p>And endorrhiza (... |
20,915 | <p>For most animals, the whole bottom of their face sticks out and they have a snout with a mouth and nose at the end. But humans have a flat face and just a nose that sticks out. We used to have the whole face sticking out, but our jaws got smaller and smaller. Because our noses still needed space to do their job, they had to stay sticking out. People who come from very cold areas have bigger noses than people from where it is hot, so they can warm the air up more.</p>
<p><strong>Why has our nose evolved with the nostrils facing down? Is it because we were water animals, and that would help with water coming in?</strong></p>
| [
{
"answer_id": 20926,
"pm_score": 4,
"text": "<p>I have not been able to find any studies that look specifically at the genetic mechanism for nose development. I certainly do not know but I'll offer up two hypotheses. </p>\n\n<p>My first hypothesis is that the elongated nose is a remnant of the elongate... | [
{
"answer_id": 34341,
"pm_score": -1,
"text": "<p>Ive found that the study of this feature, the nose is far from complete.Although we see the evolution of other mammals and their faces has a great deal to do with there ability to survive different enviornments I believe it , our snozz is a genetic mutat... |
20,937 | <p>How many Type II restrictions enzymes are currently available (commercially) for purchase as of the date of this posting (September 1, 2014)</p>
| [
{
"answer_id": 21047,
"pm_score": 3,
"text": "<p>A quick look in <a href=\"http://rebase.neb.com/\" rel=\"nofollow\">REBASE</a> finds 15999 type II restriction enzymes of which 616 are listed as having suppliers. Obviously some of these will share recognition and cut sites.</p>\n"
}
] | [
{
"answer_id": 20940,
"pm_score": 2,
"text": "<p>The <a href=\"http://www.biocompare.com/Cloning-and-Expression/6525-Restriction-Enzymes/\" rel=\"nofollow\">Restriction Enzymes</a> section at <a href=\"http://www.biocompare.com\" rel=\"nofollow\">Biocompare</a> is likely not comprehensive, but short of ... |
21,216 | <p>I was just sitting with my hand next to my nose and I realized that air was only coming out of the right nostril. Why is that? I would think I would use both, it seems much more efficient. Have I always only been breathing out of my right nostril?</p>
| [
{
"answer_id": 21220,
"pm_score": 9,
"text": "<p>Apparently you're not the first person to notice this; in 1895, a German nose specialist called Richard Kayser found that we have tissue called erectile tissue in our noses (yes, it is very similar to the tissue found in a penis). This tissue swells in on... | [
{
"answer_id": 21219,
"pm_score": 7,
"text": "<p>This is a natural phenomenon called the nasal cycle. It is discussed in this paper by <a href=\"http://www.ijpp.com/IJPP%20archives/1994_38_2/133-137.pdf\" rel=\"noreferrer\">Telles et al. (1994)</a>, among many others. The nostrils are used on an alterna... |
21,268 | <p>I spotted this dove in a park. It was foraging among Rock Doves, Seagulls, Ibises and a few others.</p>
<p>It appears similar to Pied Rock Doves, but I am not certain if this is correct.</p>
<p><img src="https://i.stack.imgur.com/KVf6l.jpg" alt="enter image description here"></p>
<p>Any idea what the name of this dove is?</p>
| [
{
"answer_id": 21270,
"pm_score": 4,
"text": "<p>It's a pied version of the Rock Pigeon (<em>Columbia livia</em>), aka Rock Dove. According to the <a href=\"http://www.allaboutbirds.org/guide/rock_pigeon/lifehistory\" rel=\"nofollow\">Cornell Lab of Ornithology</a>, the pied variety of Rock Pigeon is on... | [
{
"answer_id": 21283,
"pm_score": 2,
"text": "<p>Also called Piebald (Pied for short as mentioned above.) It's a pretty common mutation among different animals. Dogs, deer, and snakes such as the ball python exhibit this trait. So yeah, your bird is still a rock dove.</p>\n"
},
{
"answer_id": 10... |
21,272 | <p>In <a href="https://aviation.stackexchange.com/a/8554/1467">this answer</a> on aviation.SE a comparison is made between the shapes of airplanes wings and the shapes of birds wings. It concludes with the following remark:</p>
<blockquote>
<p>After all, no bird has winglets. Not a single one.</p>
</blockquote>
<p>In addition to be a disputable assertion (the wing tips such as the eagle's could be considered akin to a "winglet" of the fanned type) this has stricken me as based on a quite wrong assumption of how evolution works.</p>
<p>I tried to make my point in the comments only to reach this point:</p>
<blockquote>
<p>So you consider evolved wings as not mature. The winglet modification is just waiting to happen? Nature never tried it, in >100 million years of biological flight? Could be, yes. But is extremely unlikely. That settles it for me.</p>
</blockquote>
<p>Am I correct in identifying this in a wrong interpretation of the evolutionary process?</p>
<p>As I understand the evolutionary process, the current bird wings are not necessarily perfect, are simply the version that so far has given the best advantage. The lack of "winglets" in birds cannot then be explained simply by assuming that they do not improve the wing, but it could also be that there has never been an evolutionary pressure to evolve them or that since birds flap their wings they would be detrimental instead of beneficial or whatever other reason.</p>
<p>Is my understanding of the evolutionary process correct? if not, where am I at fault?</p>
<hr>
<p>As a small addendum, another user cited the "Spandrels" in comparison to the above debate, could someone explain what could have been the meaning of the comparison?</p>
| [
{
"answer_id": 21275,
"pm_score": 5,
"text": "<p>I looked up winglets so I had context for this answer. I'm interpreting winglets as the <a href=\"http://www.airspacemag.com/flight-today/how-things-work-winglets-2468375/?no-ist\" rel=\"noreferrer\">vertical tips at the end of airplane wings</a>. If so, ... | [
{
"answer_id": 21273,
"pm_score": 3,
"text": "<p>There are two possibilites with evolutionary processes: The development either never went into this direction or it brought no advantages. Besides this two possibilities the claims from the other forum are wrong. Birds (not all of them though) do have win... |
21,527 | <p>In most biomes on earth, and certainly in the most densely-populated, the best camouflage color or pattern for an animal would be a variant of green, so as to blend in with the leaves and grasses of the surrounding environment. Whether predator or prey, the art of not being seen is hugely important in the natural world, and yet to the best of my knowledge there isn't a single mammal on the planet with fur that is even partially green.</p>
<p>Is there a reason for that? It seems like animals have evolved some pretty crazy color patterns to break up their silhouette or blend into the background, but why haven't any mammals taken the obvious route of "look like leaves"?</p>
<p>Is it really THAT not-easy being green?</p>
| [
{
"answer_id": 21534,
"pm_score": 5,
"text": "<p>The technical answer is: Because the coloration of skin and hair is done by the two forms of melanin: Eumelanin, which is dark brown to black and Pheomelanin which is yellow to red. This enables colors from white (not pigmentation) to black (dense eumelan... | [
{
"answer_id": 21548,
"pm_score": 3,
"text": "<p>Just to add a different dimension to the answer from @Chris. Not all animal colouration is produced by melanin. A whole range of bright colours in insects, birds and reptiles comes under the heading of <a href=\"http://en.wikipedia.org/wiki/Structural_col... |
21,535 | <p>I've been facing this lately, where I will wake up in the middle of the night after sleeping for perhaps 2-3 hours and be wide awake, but when I go back to sleep, I wake up more tired than before.</p>
<p>Can anyone shed some light on this?</p>
| [
{
"answer_id": 21601,
"pm_score": 2,
"text": "<p>Sleep duration certainly affects the quality of sleep, but it is nowhere near a simple correlation. It is just one of many factors, and these factors don't work in isolation. Statistically speaking, it's a multivariate model - and one which includes a dif... | [
{
"answer_id": 21582,
"pm_score": 0,
"text": "<p>From experience I cannot say quality is dependent on duration. For example, you can take a 30 minute power nap and feel much more refreshed than sleeping 8 hours. It may have something to do with dehydration and hunger during the long periods of sleep tha... |
21,541 | <p>Million of years ago there lived dinosaurs up to 36 m high. About 10,000 years ago lived <em>Machairodontinae</em> -compared to cats today they were huge. About 400,000 years ago lived <em>Mammuthus trogontherii</em>: it reached over 4 m at the shoulder. And these are just some examples.</p>
<p>Todays biggest living creatures look small compared to previous. So my question is, why are all creatures getting smaller? Why doesn't evolution generate any big creatures with size comparable to the dinosaurs?</p>
| [
{
"answer_id": 21601,
"pm_score": 2,
"text": "<p>Sleep duration certainly affects the quality of sleep, but it is nowhere near a simple correlation. It is just one of many factors, and these factors don't work in isolation. Statistically speaking, it's a multivariate model - and one which includes a dif... | [
{
"answer_id": 21582,
"pm_score": 0,
"text": "<p>From experience I cannot say quality is dependent on duration. For example, you can take a 30 minute power nap and feel much more refreshed than sleeping 8 hours. It may have something to do with dehydration and hunger during the long periods of sleep tha... |
21,597 | <p>Does anybody recognize this picture and can tell me what organ it came from?
<img src="https://i.stack.imgur.com/SRCvi.png" alt="enter image description here"></p>
| [
{
"answer_id": 21608,
"pm_score": 3,
"text": "<p><strong>Update 3:</strong> Credit should go to @Cornelius and @DMSever for initially identifying the tissue correctly. I incorporated D M Sever's answer into mine (Update 2,below) because his answer is being down voted for brevity, but he is a recognized ... | [
{
"answer_id": 21606,
"pm_score": 3,
"text": "<p>I'm not really sure, but it seems like a cross section of intestinal villi / intestinal glands from the large intestine.</p>\n\n<p>Here are some images:</p>\n\n<ul>\n<li>Jubal Harshaw. <a href=\"http://www.shutterstock.com/pic-20628100/stock-photo-large-i... |
21,636 | <p>This image appears on the cover of Peter Gabriel's album New Blood. It appears to be a photograph of some microscopic biological cell. But it doesn't look like a blood cell to me. What kind of cell is it? </p>
<p><img src="https://i.stack.imgur.com/4iDWB.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 21655,
"pm_score": 5,
"text": "<p>This is an embryonic stem cell on the tip of a needle photographed on a scanning electron microscope (SEM). The image was taken by Steve Gschmeissner, see here for the <a href=\"http://www.sciencephoto.com/media/214491/view\">original</a>.</p>\n"
}
] | [
{
"answer_id": 21648,
"pm_score": 3,
"text": "<p>This looks like a macrophage to me, which is a white blood cell. Try Googling \"macrophage sem\" to see similar images (SEM = scanning electron microscopy/micrograph).</p>\n\n<p>The clue is the nature of the cell surface - those ruffles reflect the macro... |
21,825 | <p>Many cells in the human body can divide and reproduce, making healing possible. Neurons, however, cannot reproduce, which makes diseases affecting the brain particularly crippling. Why can't neurons divide - that is, what makes them different from "normal" cells? Are there any ways to artificially stimulate neuron cell division?</p>
| [
{
"answer_id": 21840,
"pm_score": 5,
"text": "<p>Neurons do not divide due to the reasons mentioned in Cornelius's answer. However, some new neurons can be generated in adults (Ref: <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK10920/\">Neuroscience, 2nd edition</a>).</p>\n\n<p>Generation of new neuron... | [
{
"answer_id": 21826,
"pm_score": 4,
"text": "<p><strong>Morphological point of view</strong></p>\n\n<p>Neurons cannot divide because they lack <a href=\"http://en.wikipedia.org/wiki/Centriole\">centrioles</a>.</p>\n\n<blockquote>\n <p>Because centrioles function in cell division, the fact that neurons... |
21,868 | <p>I am trying to get standard ECG by using PhysioNet's <a href="http://physionet.org/cgi-bin/atm/ATM" rel="nofollow noreferrer">ATM</a> with parameters</p>
<p><img src="https://i.stack.imgur.com/Wjozi.png" alt="enter image description here"></p>
<p>but I get</p>
<p><img src="https://i.stack.imgur.com/AB9yx.png" alt="enter image description here"></p>
<p>It should be something like</p>
<p><img src="https://i.stack.imgur.com/4aFMc.png" alt="enter image description here"></p>
<p><strong>How can you get complete standard 12-lead ECG out of Physionet database?</strong></p>
| [
{
"answer_id": 34347,
"pm_score": 1,
"text": "<p>PTB Diagnostic ECG database <a href=\"http://www.physionet.org/physiobank/database/ptbdb/\" rel=\"nofollow\">here</a>. \nReview <a href=\"http://www.beecardia.com/physiobank/database/ptbdb/\" rel=\"nofollow\">here</a>.</p>\n"
}
] | [
{
"answer_id": 21869,
"pm_score": 2,
"text": "<p>I don't think that all leads are available.</p>\n\n<p>I looked at the <strong>Signals</strong> combobox for different databases. This combobox seems to be the list of all available leads.</p>\n\n<p>For example, take a look at <strong>iafdb</strong> (Intra... |
23,110 | <p>I have heard that offspring can't grow taller than either of their parents but I've also heard that sometimes some gene activation can skip generations. Is it possible for a child to grow taller than their tallest parent?</p>
| [
{
"answer_id": 23142,
"pm_score": 5,
"text": "<p><strong>People can grow taller than their parents.</strong> Anecdotally: I'm 185 cm, my parents are 155 cm and 178 cm. <a href=\"http://en.wikipedia.org/wiki/Joakim_Noah\">Joakim Noah</a>, an NBA basketball player is 211 cm, his <a href=\"http://en.wikipe... | [
{
"answer_id": 23111,
"pm_score": 1,
"text": "<p>Yes it is quite possible, recall nature vs nurture. I myself am slightly taller than both of my parents by about a head. As long as you have sufficient nutrition it should be quite possible.</p>\n\n<p>And what you said about gene activation skipping gener... |
23,243 | <p>Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here?</p>
<p>Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue increases the error rate by 40 fold.</p>
<p>I don't quite understand the above two statements. Can anyone explain in detail to me? Thanks!</p>
| [
{
"answer_id": 23255,
"pm_score": 3,
"text": "<p>DNA polymerase must catalyse the addition of 4 different nucleotides to the growing strand. This means that it cannot directly determine which base to incorporate at a specific point (how would it 'know' which base to incorporate and how it would it chang... | [
{
"answer_id": 23249,
"pm_score": 2,
"text": "<p>High-fidelity DNA polymerases have several safeguards to protect against both making and propagating mistakes while copying DNA. </p>\n\n<p>Such enzymes have a significant binding preference for the correct versus the incorrect nucleoside triphosphate dur... |
23,246 | <p>I was wondering how protein denaturation works.</p>
<ol>
<li>Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation irreversible in most cases if only non-covalent bonds are involved?</li>
<li>Is it possible to denature protein by rapid changes in electromagnetic field or pressure? (The articles I have read so far mention only stress factors like sudden pH, osmolarity, temperature changes...)</li>
<li>How can I protect a protein against denaturation? e.g. in PCR we use a heat resistant DNA polymerase, so certain amino acid sequences might protect against heat denaturation, but I need reassurance about this.</li>
</ol>
| [
{
"answer_id": 23795,
"pm_score": 3,
"text": "<p>I investigated the topic too, so here is my answer.</p>\n\n<p>To understand thermodinamic stability of water solved globulins or membrane proteins (all of them proteins hereafter) we have to understand protein folding. Proteins have a 3d structure (compos... | [
{
"answer_id": 23247,
"pm_score": 3,
"text": "<p>Really the question how does protein folding work? But let me answer your questions...</p>\n\n<p>1) Very few proteins have disulfide bonds <a href=\"https://en.wikipedia.org/wiki/Disulfide_bond#Occurrence_in_proteins\" rel=\"nofollow\">(usually secreted ... |
23,264 | <p>Are there organisms that have incorporated (manmade) plastic into their lives in any way? Either in their diet, or as a part of their body?</p>
| [
{
"answer_id": 23265,
"pm_score": 4,
"text": "<blockquote>\n <p>Biodegradable waste is a type of waste which can be broken down, in a\n reasonable amount of time, into its base compounds by micro-organisms\n and other living things, regardless of what those compounds may be.</p>\n</blockquote>\n\n<ul... | [
{
"answer_id": 23376,
"pm_score": 2,
"text": "<p>I don't know if this qualifies as \"<em>incorporated ... into their lives</em>\", but <a href=\"http://en.wikipedia.org/wiki/Hermit_crab\" rel=\"nofollow noreferrer\">Hermit crabs</a> use all sorts of man-made materials as housing/protection. If you do a ... |
23,360 | <p>So with the working definition of Eugenics: "the aim to improve the human gene pool". What are key features that distinguish Eugenics from evolution by natural selection? I mean, besides that natural selection occurs naturally.</p>
| [
{
"answer_id": 23363,
"pm_score": 4,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Selection\" rel=\"nofollow\">Selection</a> is a mechanism of evolution which favours specific forms of traits over others, this can cause the spread of beneficial mutations through a population.</p>\n\n<p><a href=\"h... | [
{
"answer_id": 23361,
"pm_score": 0,
"text": "<p>In principle, eugenics is just like selective breeding of animals and plants. For example, dogs have been bred for a variety of traits to fit into several niches, and corn has been bred to produce large yields in several climates. Eugenics would attempt t... |
23,774 | <p>Each year, large volumes of crop are harvested from fields. </p>
<ul>
<li>Where does this biomass get replenished from?</li>
</ul>
| [
{
"answer_id": 23782,
"pm_score": 3,
"text": "<p>There are <a href=\"http://en.wikipedia.org/wiki/Biogeochemical_cycle\" rel=\"nofollow\">biogeochemical cycles</a> for the building stones of the biomass (e.g. hydrogen, carbon, nitrogen, oxygen, etc...), so all of these atoms are recycled. To recycle the... | [
{
"answer_id": 23781,
"pm_score": 2,
"text": "<p>The matter in plants is mostly carbon, hydrogen, oxygen, and nitrogen, with various metal ions and some sulfur and phosphorus. The carbon, hydrogen, and oxygen are taken from carbon dioxide in the air and water from the soil through <a href=\"http://en.wi... |
23,791 | <p>I'm trying to think of places where a biofilm could develop other than on medical equipment or food processing equipment such as stainless steel mechanized blades or knives. I'm thinking more along the lines of biofilms on typical house hold things such as the bottoms of shower curtains</p>
| [
{
"answer_id": 24136,
"pm_score": 1,
"text": "<p>Try thinking about places that are not very often cleaned and disinfected such as the toilet. Not only that, but the bottoms of shower curtains and in drains. Plaque on teeth is a biofilm, catheters, in/on wounds.</p>\n"
}
] | [
{
"answer_id": 23796,
"pm_score": 2,
"text": "<p>They can certainly <a href=\"http://www.biofilm.montana.edu/resources/pubs/98-025.html\" rel=\"nofollow\">develop in the toilet</a>. Just try not to disinfect for a week...</p>\n\n<p>Another place is the surface of living organisms, e.g. <a href=\"http://... |
23,842 | <p>Why does a cockroach not die after its head is cut off?</p>
| [
{
"answer_id": 23847,
"pm_score": 4,
"text": "<p>Based on an article <a href=\"http://www.scientificamerican.com/article/fact-or-fiction-cockroach-can-live-without-head/\">here</a>, unlike humans, cockroaches have an open circulatory system. They don't have a huge network of blood vessels like that of h... | [
{
"answer_id": 24150,
"pm_score": 2,
"text": "<p>Cockroaches are insects which means their brain is distributed.</p>\n\n<blockquote>\n <p>The predominant characteristics of the cockroach central nervous\n system (CNS) are its segmented nature and decentralization of control\n processes (<strong>Ganih... |
23,850 | <p>Fish are often plagued by external parasites, which are presumably difficult for them to remove.</p>
<p>There are well known cases where large fish come to coral reefs and allow smaller fish to pick off their parasites. See below a moray eel being "cleaned" by a shrimp.</p>
<p><img src="https://i.stack.imgur.com/Tq935.jpg" alt="enter image description here"></p>
<p>Some fish, like sunfish, even get cleaned up by birds: <a href="https://www.youtube.com/watch?v=U60obmWODLQ" rel="nofollow noreferrer">https://www.youtube.com/watch?v=U60obmWODLQ</a></p>
<p>But on land, we have many social animals that solve this problem more directly by grooming each other. How come the fish never seem to do this? Many of them are already social, and I imagine they wouldn't have much trouble digesting the external parasites. Why don't they groom each other?</p>
| [
{
"answer_id": 23870,
"pm_score": 3,
"text": "<p>All cases of same species grooming I know of involve animals with a certain amount of dexterity. For example (images from <a href=\"https://en.wikipedia.org/wiki/Social_grooming#In_non-human_animals\" rel=\"nofollow noreferrer\">wikipedia</a>):</p>\n\n<ul... | [
{
"answer_id": 23853,
"pm_score": 1,
"text": "<p>Something from my imagination: Probably the first fishes were of small size with some of them evolving to be big. The variation in the sizes of the fishes is larger compared to the variation in the sizes of mammals(picture elephants and rats with whales a... |
23,977 | <p>I was always curious, why do chameleons have this strange gait?</p>
| [
{
"answer_id": 64188,
"pm_score": 4,
"text": "<p>The movement you observed serves two functions:</p>\n<ol>\n<li><strong>Imitation of leaves</strong> to protect against predators</li>\n<li><strong>Improved stereoscopic vision</strong> while scanning for their own prey</li>\n</ol>\n<h1>Imitation of leaves... | [
{
"answer_id": 24187,
"pm_score": -1,
"text": "<p>Predators are very good at spotting moving targets, as movements will easily stand out from inanimate objects and vegetation.\nMost prey will prefer to hide or just run if they are spotted by predators.\nBut the chameleons prefer to blend in with the veg... |
23,981 | <p>I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. <strong>What online resources exist for finding out what a given protein binds or otherwise interacts with?</strong></p>
<p>I am aware of <a href="http://www.uniprot.org/" rel="nofollow">Uniprot</a> and <a href="http://www.phosphosite.org/homeAction.do" rel="nofollow">Phosphosite</a> which have proved useful but I am wondering if there are others that I am not aware of. </p>
<p>Again: the question I am trying to answer is "which proteins from list A interact with proteins from list B and vice-versa?" </p>
| [
{
"answer_id": 64188,
"pm_score": 4,
"text": "<p>The movement you observed serves two functions:</p>\n<ol>\n<li><strong>Imitation of leaves</strong> to protect against predators</li>\n<li><strong>Improved stereoscopic vision</strong> while scanning for their own prey</li>\n</ol>\n<h1>Imitation of leaves... | [
{
"answer_id": 24187,
"pm_score": -1,
"text": "<p>Predators are very good at spotting moving targets, as movements will easily stand out from inanimate objects and vegetation.\nMost prey will prefer to hide or just run if they are spotted by predators.\nBut the chameleons prefer to blend in with the veg... |
24,056 | <p>We are all familiar with the examples of symbiotic relationships in nature consisting of two agents, like lichen or the co-evolvement between certain birds and flowering plants.</p>
<p>Do we know of any mutually symbiotic relationships that has three of a even higher number of agents?</p>
<p>Edit: To make a implicit distinction clear, let's specify that the agents in question have distinctive and fully interdependent roles in the symbiosis. In contrast to a scenario where a range of bird species might co-evolve for a single specific flower and have the same role as pollinators in the symbiosis.</p>
<p>This image represents my current models in thinking about this:</p>
<p><img src="https://i.stack.imgur.com/s7jBI.png" alt="conceptual network types"></p>
<p>The type I'm searching for here is mainly the "3-agent symbiosis", but the bidirectional one is of interest as well.</p>
| [
{
"answer_id": 24073,
"pm_score": 4,
"text": "<p>I think what you are asking for is "<em>Multiple Mutualism</em>". Normally,</p>\n<blockquote>\n<p>Most of the known cases of multiple mutualism involve relationships in\nwhich two of the partners are at the same organizational level—usually\ntwo... | [
{
"answer_id": 24059,
"pm_score": 2,
"text": "<p>The human body contains a few billion microbes (more than human cells), so we live in symbiosis with many different species. Some of them protect us from infections, some of them help in the digestion, and so on... So I think the human body fulfills your ... |
24,074 | <p>I watched this movie, where they rented hearts to people for a year. I wonder if it is possible to transplant a heart indefinitely from person to person, or does the heart have a lifetime? So, do human organs age and eventually die, or is it possible to transplant organs indefinitely? What is the limiting factor for life of human organs?</p>
| [
{
"answer_id": 24077,
"pm_score": 4,
"text": "<p>First of all, it will be practically impossible to make an estimation of how long a transplanted organ will live and how many times it could be transplanted. However, it is relatively safe to say that it will not live forever. </p>\n\n<p>To be able to rec... | [
{
"answer_id": 24075,
"pm_score": 3,
"text": "<p>The median lifetime of an organ transplant is <a href=\"http://en.wikipedia.org/wiki/Transplant_rejection\" rel=\"nofollow\">some 5 to 10 years</a> mainly due to chronic rejection mediated by host-versus-graft immune responses. Hence long-term transplant... |
24,387 | <p>Is there any stem cell or biogel method that exist for muscle and tendon lengthening?</p>
<p>It is known that height surgery is limit to six inches with two surgeries and three inches each, it is also true that there is limit because the muscle and tendons could stretch no more. Is there some research about this? </p>
| [
{
"answer_id": 24522,
"pm_score": 3,
"text": "<p>In doing search into muscle stem cells, I found some articles which discuss roles of <a href=\"https://en.wikipedia.org/wiki/Myosatellite_cell\" rel=\"nofollow\">satellite stem cells</a> and non satellite cells involved in muscle regeneration: (<a href=\... | [
{
"answer_id": 24445,
"pm_score": 2,
"text": "<p>Limb lengthening surgery is usually used to treat sequelae caused by bone disease, trauma, pygmyism or inflammation. I personally do not recommend to use surgical methods to increase height. Typically Limb Lengthening requires Achilles pre-lengthening sur... |
24,555 | <p><a href="https://biology.stackexchange.com/a/2280/3885">This answer</a> explains the sensation of extremities "falling asleep" as a result of sustained pressure on a nerve. The answer links to an external web page that says that the feeling "quickly goes away once the pressure is relieved." </p>
<p>In my experience, however, it doesn't usually go exactly like this. For me at least, usually what happens is I will start feeling a tingling sensation in my feet after sitting in an awkward position for an extended period of time. If I ignore the sensation for long enough, it continues to get worse until I finally do stand up. But after I stand up, rather than the sensation quickly disappearing, I find that usually it suddenly gets much worse for a period of time. What started as an annoying tingling when I was sitting quickly turns into something quite uncomfortable upon standing up, even to the point where I am not able to walk around properly until the sensation passes a few minutes later.</p>
<p>But once I am standing up, the nerve shouldn't be pinched anymore, so why does the sensation of my foot being "asleep" remain for a few minutes after standing up, and why does it actually seem to briefly get worse <em>after</em> I have already stood up and "unpinched" the nerve?</p>
| [
{
"answer_id": 25856,
"pm_score": 3,
"text": "<p><a href=\"http://www.orthochirurg.com/resources/journals/Current%20Concepts%20Review/Pathophysiology%20of%20nerve%20compression%20syndromes%20response%20of%20peripheral%20nerves%20to%20loading.pdf\" rel=\"nofollow\">This paper</a>, while mainly dealing wi... | [
{
"answer_id": 25807,
"pm_score": 1,
"text": "<p>Paresthesia is defined as the abnormal sensation of the skin, such as numbness, tingling, pricking or burning. Paresthesia is a diverse medical condition and the definitions seems too vague. Most of the books define Paresthesia as a symptom of some other ... |
24,561 | <p>I can't remember which question it was, but in the past here, it was explained to me that memory is actively stored in the brain, rather than "physically". Meaning, memories are made up of the brain's activity, not its physical cell structure.</p>
<p>I'm not sure I have that right though. I mean, that, for one thing seem inefficient and overly complex. It seems like a vast amount of energy would be required to store so much information in the form of activity patterns. Maybe I misunderstood. So I'm asking. If my brain lost all of its energy (activity) for a moment (for example, one second), would my memory be gone too? </p>
| [
{
"answer_id": 24570,
"pm_score": 3,
"text": "<p><strong>Summary</strong>\nWorking memory on a current task could be distorted, but I cannot find a reason to suggest sudden loss of electrical information would permanently alter short or long term memory.</p>\n\n<p>Hopefully a neuroscientist can answer w... | [
{
"answer_id": 24567,
"pm_score": 1,
"text": "<p>I found the answer to my question <a href=\"https://biology.stackexchange.com/questions/5405/do-memories-have-mass/5408#5408\">here</a>, however not linked to a duplicate question, so I'll quote:</p>\n\n<blockquote>\n <p>Memories are represented in the b... |
24,668 | <p>I've learned that plants transform glucose into sucrose before sending it into phloem. But the process seems to be complex and energy comsuming. Why should plants do it? Is it really necessary?</p>
| [
{
"answer_id": 24672,
"pm_score": 5,
"text": "<p>Glucose, fructose and galactose are the three dietary monosaccharides. Glucose and Fructose are simple monosaccharides found in plants. A monosaccharide is the basic unit of carbohydrate and the simplest form of sugar, glucose are aldose and Fructose are... | [
{
"answer_id": 43534,
"pm_score": -1,
"text": "<p>there is no free glucose in the photosynthesis. Stop to spread that myth. The net product is G3P. The end products of photosynthesis are sucrose and starch, but never glucose. Do you test glucose in the leaves? No... it is always for starch. ;) The G3P i... |
24,708 | <p>I have come up with what I thought was a clever idea: Store the agarose gels I pour, and only cut as many lanes as I need to run later, minimizing wasted agarose (and wasted effort/time) when I need to make many electrophereses using a small number of lanes.</p>
<p>I realized that over time, the EtBr would diffuse out of my gel into the buffer that the gels are kept in. Since I add 2 µl of EtBr to 50 ml gel, and the gels were kept in 400 ml TAE buffer, I added 16 µl EtBr to the buffer, reasoning that now concentrations are equal and no net diffusion will take place.</p>
<p>However, after several weeks, I noticed that the EtBr signal from the gel is severely weakened. What can I do to fix this? I can see the following options:</p>
<ul>
<li>Use higher concentration of EtBr in the buffer (how much?)</li>
<li>Change buffer weekly, adding fresh EtBr every time</li>
<li>Cover the transparent container with aluminum foil to prevent hypothetical photobleaching</li>
</ul>
<p>Which one is most likely to solve my problem? Should I just give up, and throw away gels that are older than a day or two (I want to avoid this option, because of the record keeping needed to track when the gel was last made)?</p>
| [
{
"answer_id": 26063,
"pm_score": 3,
"text": "<p>To increase storage life: after gel solidifies, dampen it with running buffer. Wrap the gel in polyvinyl chloride. Place in plastic container with a lid. Store in fridge in dark. It will last for a year as long as you re-dampen it with buffer each time yo... | [
{
"answer_id": 24724,
"pm_score": 0,
"text": "<p>I'm not quite sure what you are doing. Are you running the whole gel each time and cutting off the lanes you've used, or only putting the lanes you desire into the tank and leaving the rest outside?</p>\n\n<p>If the former then the ethidium bromide will b... |
24,775 | <p>So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk.</p>
<p>I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into another program, for example Trinity, to run an assembly on the FASTQ file without ever having to write all that data to disk. For large datasets, this could actually save quite a bit of time in aggregate.</p>
<p>Has anyone done something similar? I am going to try and experiment with the technique soon, but I a) don't know much about the mkfifo process to begin with and b) am unsure of how this procedure would work for paired-end data where fastq-dump is splitting the SRA file as it goes. How would one specify which output would go to which pipe?</p>
<p>EDIT: A (hypothetical) example:</p>
<blockquote>
<p>mkfifo fileStream</p>
<p>fastq-dump SRR123456 > fileStream</p>
<p>Trinity --single fileStream misc_args</p>
</blockquote>
<p>That should take the fastq-dump data and stream it into the named pipe "fileStream", which can then be used to stream data into Trinity. I don't know enough about all of the commands, however, to know if this makes any sense.</p>
<p>I would welcome any thoughts from more experienced users!</p>
<p>EDIT: Added update as an answer below.</p>
| [
{
"answer_id": 25806,
"pm_score": 4,
"text": "<p>fastq-dump can write to stdout ; the <code>-Z</code> option allows you to do that. This, you can pipe to any downstream process. [<a href=\"http://codextechnicanum.blogspot.in/2014/06/sra-to-gzipped-fastq.html\" rel=\"nofollow\">An example</a>]. Also see ... | [
{
"answer_id": 25811,
"pm_score": 2,
"text": "<p>As WYSIWYG pointed out, fastq-dump can output to STDOUT, so if you want to combine it with named pipes, you'd do:</p>\n\n<pre><code>mkfifo mydata.fifo\nfastq-dump -Z mydata.sra > mydata.fifo &\ncat mydata.fifo # or whatever\nrm mydata.fifo\n</code>... |
24,786 | <p>Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is better dealt with outside the nucleus...but why?</p>
| [
{
"answer_id": 25789,
"pm_score": 5,
"text": "<p>Nice question which leads to the fundamentals of DNA and RNA.</p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/DNA\" rel=\"noreferrer\">DNA</a> (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic... | [
{
"answer_id": 25792,
"pm_score": 3,
"text": "<p>Addition to Jvrek's answer based on the comments. Most RNA degradation mechanisms catalysed by different RNAses (RNAse-A and RNAse-S, for example), involve the 2'-OH. Therefore the repertoire of RNAses is selective towards RNA and not DNA because of the 2... |
25,922 | <p>I've seen snakes get captured in sacks and I've wondered if the snake would get dizzy if the sack were twirled around. I have not done any tests (and don't plan to) because snakes scare me. </p>
| [
{
"answer_id": 25927,
"pm_score": 5,
"text": "<p>Probably don't do any experiments that involve shoving reptiles in a sack and swinging them around your head, as someone will surely call the ASPCA on you.</p>\n\n<p>The type of dizziness that is associated with spinning around is called \"vertigo\". From... | [
{
"answer_id": 25937,
"pm_score": 4,
"text": "<p>Dizziness is caused by a continuing rotation of the fluids in the semi-circular canals of the vestibular system that transmit rotation information to the brain. After prolonged rotation of the body, the circular canal fluids are engaged in a rotating moti... |
25,941 | <p>I know that it is common to say, "use hot water when washing your hands" or when you've got a cut, "wash your hands with warm water," etc. I was wondering, why is this the case? Since bacteria grow in warm environments, you would think that it might be beneficial for bacteria. Is this just another myth or is this actually true?</p>
| [
{
"answer_id": 25942,
"pm_score": 6,
"text": "<p>The bacteria wouldn't see any benefit from the warm water in the ~30-60 seconds you're washing your hands, neither would hot water \"sterilize\" your hands at temperatures you could tolerate. The reason you wash your hands with hot water is because the ho... | [
{
"answer_id": 25943,
"pm_score": 3,
"text": "<p>The goal of hand washing is to remove surface debris, including foreign pathogens. Most things that most people encounter on a daily basis dissolve more easily in hot water than in cold water. Thus, hot water around 100° F is used to facilitate this debri... |
26,012 | <p>After listening to a scientific talk, I had this question that why in the natural selection process, are the L-amino acids selected over the D- form. However, we still we produce D-amino acids; specifically in the brain there is a higher concentration of D- amino acids. One possible reason is that they act as neurotransmitters.</p>
| [
{
"answer_id": 26013,
"pm_score": 4,
"text": "<p>As you say yourself, biological molecules are usually available in both chiralic possibilities, yet nature uses only one of the two possibilities. At some point in our molecular evolution (and at a very early one) L-amino acids were stochastically \"chose... | [
{
"answer_id": 26029,
"pm_score": 3,
"text": "<p>The current thinking amongst biophysicists is that if we all woke up tomorrow to find that someone had edited the book of life so as to exchange all of the L-'s and D-'s (and made similar mirroring changes to all of the molecules that any protein interact... |
26,014 | <p>If I go into a green room (all walls are semitransparent and green) and spend some time - around 10+ min - in there, when I come out all my eyes see is white as pink. I see no (or very few other) colors due to this for a while - around 2 minutes. What is the science behind this? Why do eyes lose color perception in this case?</p>
| [
{
"answer_id": 26027,
"pm_score": 4,
"text": "<p>To explain the neurophysiological background to the existing answers I would like to add the following:</p>\n\n<p>The effect you are describing (pinkish appearance of white) is generally referred to as a <strong>negative after image</strong> and it is a d... | [
{
"answer_id": 26015,
"pm_score": 4,
"text": "<p>First recall that <strong>pink is white minus green</strong>, more or less.\nNow, your perception can be explained by adaptation: Neurons try to control their gain (amplification factor) to have roughly the same range of output. So if there's a lot of sti... |
26,119 | <p>Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is, is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?</p>
<p>If these things are not known, how do we know it's actually a code then?</p>
<p>Thanks!</p>
| [
{
"answer_id": 26122,
"pm_score": 4,
"text": "<p>As already mentioned by Stefan, the \"histone\" code is not really a universal code; it is restricted to eukaryotic systems and even then, not unambiguous. It is, at present related to two kinds of histone modifications and their correlation with the tran... | [
{
"answer_id": 26121,
"pm_score": 0,
"text": "<p>It's not a code in the strict sense of the word. With proteins and nucleic acids you have a strictly defined set of letters and strict rules for them to match one another (note that in some cases atypical base pairing occurs in nucleic acids). The \"code\... |
26,216 | <p>Opponent process is a color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner (<a href="https://en.wikipedia.org/wiki/Opponent_process" rel="noreferrer">source</a>).</p>
<p>What is the advantage of opponent color against RGB color? For example, in object recognition or edge detection?</p>
<p>Can we say that it provides some level of invariance to changes in brightness?</p>
| [
{
"answer_id": 26228,
"pm_score": 3,
"text": "<p>RGB color is a more direct representation of the \"raw input\" received by the (human) eye, since the three types of cone cell have responsivity spectra that roughly correspond to red, green, and blue light:</p>\n\n<p><img src=\"https://upload.wikimedia.o... | [
{
"answer_id": 27486,
"pm_score": 2,
"text": "<p>The first question, namely what is the <em>advantage of color opponency 'against' RGB</em>, is technically incorrect. The opponent system (Red/Green; Blue/Yellow and brightness channels) is physiologically situated in the neuronal retinal layer and higher... |
26,233 | <p>I have trouble identifying a tree that I saw on a vacation. This is the image:
<img src="https://i.stack.imgur.com/ISdqx.jpg" alt=""></p>
<p>I would like to know the name of the tree, I only know that its not European.</p>
| [
{
"answer_id": 26247,
"pm_score": 3,
"text": "<p>I think you should look into trees in the <a href=\"http://en.wikipedia.org/wiki/Rubiaceae\" rel=\"nofollow noreferrer\">Rubiaceae</a> family (which is very large with ~6500 species in total). Many species there have spherical inflorescences, and some are... | [
{
"answer_id": 26234,
"pm_score": 2,
"text": "<p>The fruit strongly resembles immature <a href=\"http://en.wikipedia.org/wiki/Lychee\" rel=\"nofollow noreferrer\">lychee</a> (<em>Litchi chinensis</em>). Since I have only seen the fruit, I cannot comment on whether the flower looks correct. The flowers a... |
26,261 | <p>The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't there be a similar chemical molecule like tRNA which can directly read from DNA and exclude the mRNA intermediate. Also is the current translation process optimal in the sense that can there be a system which does not need mRNA or a similar intermediate altogether. Or is the presence of an intermediate a necessary requirement.</p>
| [
{
"answer_id": 26262,
"pm_score": 4,
"text": "<p>One reason is that an intermediate like mRNA allows for higher amounts of protein expression. You can have multiple mRNA molecules that are translated simultaneously. If you read directly from DNA you can have at most two translations in parallel.</p>\n\n... | [
{
"answer_id": 26263,
"pm_score": 2,
"text": "<p>I don't have a lot of references for this, but it's too long for a comment.</p>\n\n<p>Separating the roles of RNA and DNA helps to better control protein production and gene replication. If ribosomes worked directly on DNA, it would probably be very hard ... |
26,383 | <p><strong>Note: question rewritten to prevent misunderstanding and make it more answerable</strong></p>
<p>I know that some small animals like C. elegans display surprising sophistication with a very small number of cells. But I wonder, among the animals with known/estimated cell count, which has the fewest cells? </p>
<p>To make the question answerable, please note these constraints: </p>
<ul>
<li>I'm only asking about members of the kingdom <em>Animalia</em>, so single cell organisms and colonials like Vovox are excluded. If there are single cell organisms which are classified under Animalia (I think there aren't, but not 100% sure), I still want to know about the smallest multicellular animal. </li>
<li>I'm only asking about species where we can distinguish <em>individuals</em>. If some kind of polyp or sponge is just a bunch of cells which can merge with or separate from other cells and remain a viable organism, it's not interesting. </li>
<li>Please only consider species where the adult form reaches some size and <em>stops growing</em>. (Macroscopic) examples like the tapeworm, which continues building more proglottides throughout life, or fish which continue getting larger as they age, are excluded.</li>
<li>If the species consists of distinctive, stable "subgroups" of different sizes, <em>the smallest size subgroup</em> counts. For dogs, the size of the average chihuahua counts. For C. elegans, the size of the hermaphrodite (959 cells vs 1031 in the male) counts. </li>
<li>What counts is the number of cells in a <em>healthy adult</em> of the species or the relevant subgroup. For non-eutelic animals, make that the average healthy adult. Not the smallest ever observed exemplar, and also not amputated or stunted exemplars.</li>
<li>I am aware that we haven't discovered all microscopic animals yet, and haven't counted the cells of all discovered ones. Still, I'd like info on the <em>current level of knowledge</em>, including current known cell count, evidence that something has less than the current lowest known-for-sure count, and other relevant information. </li>
</ul>
| [
{
"answer_id": 26419,
"pm_score": 5,
"text": "<p><a href=\"https://en.wikipedia.org/wiki/Rotifer\">Rotifers</a> are microscopic protostomes with around 1000 cells apiece. <a href=\"http://www.elasmo-research.org/education/topics/r_matter_of_scale.htm\">This website</a> claims the smallest rotifers have... | [
{
"answer_id": 26385,
"pm_score": 3,
"text": "<p>I don't know about all known animals, or actual cell count. However, males of the wasp <a href=\"http://en.wikipedia.org/wiki/Dicopomorpha_echmepterygis\"><em>Dicopomorpha echmepterygis</em></a> are considered the smallest known insects with a body size o... |
26,444 | <p>Originally, life evolved from non-living matter. Why is life only generated from other life nowadays, and why doesn't it evolve from inanimate matter, like it did originally billions of years ago, when life evolved on Earth?</p>
<p>Maybe I should reword this further. Living organisms reproduce other living organisms but the first living organism came from non living material or chemicals. So could life be created in a laboratory as it originally was ? Originally the process leading to a life form took one billion years, so would this be the answer to my question that it takes too long and that is why it is not being repeated again ?</p>
| [
{
"answer_id": 27456,
"pm_score": 4,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Abiogenesis\">Abiogenesis</a>, the development of living things from non living matter, is not something we know much about, since it happened about 4 billion of years before we were around and haven't reproduced it ... | [
{
"answer_id": 27442,
"pm_score": 2,
"text": "<p>There are two questions here:</p>\n\n<ul>\n<li>Why does life only generate life?</li>\n<li>Why doesn't life continue to be generated on Earth?</li>\n</ul>\n\n<p>The first one is easy. We don't only generate life. If that were true, it might be illegal to ... |
27,444 | <p>In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE. </p>
| [
{
"answer_id": 27456,
"pm_score": 4,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Abiogenesis\">Abiogenesis</a>, the development of living things from non living matter, is not something we know much about, since it happened about 4 billion of years before we were around and haven't reproduced it ... | [
{
"answer_id": 27442,
"pm_score": 2,
"text": "<p>There are two questions here:</p>\n\n<ul>\n<li>Why does life only generate life?</li>\n<li>Why doesn't life continue to be generated on Earth?</li>\n</ul>\n\n<p>The first one is easy. We don't only generate life. If that were true, it might be illegal to ... |
27,475 | <p>Somewhere in evolutionary history <em>homo</em> started walking upright and became bipedal. You hear these hypotheses that, by walking upright, they could see better across the grassy savannas to escape predators, find food, find fellow humans etc. However, the most parsimonious way to accomplish looking farther across the grassy plains is by growing taller - much less adaptations necessary and hence more favorable from an evolutionary perspective. Other hypotheses say <em>homo</em> freed his hands to carry things. Quite fine, but some apes are known to carry around stuff. Moreover, walking on all fours increases running speed (you don't have to see far if you can escape faster) and apes climb trees better (what's a better place to hide from predators?). Hence my question: <strong>Why has bipedalism been favored in evolution?</strong> </p>
| [
{
"answer_id": 28245,
"pm_score": 4,
"text": "<p>As already pointed it out, there is no scientific consensus on the answer to this question. This is because it is hard to test proposed explanations and it's likely that several factors interacted.</p>\n\n<p>All of these have been claimed to be the explan... | [
{
"answer_id": 28244,
"pm_score": 2,
"text": "<p>I doubt you are going to be satisfied with any answer since the authorities on the matter can't test the many hypothesis and don't all agree. Around the time of homo erectus (1.89 million years ago), hominids began walking upright on a more permanent basi... |
27,478 | <p>The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton expresses the genotype of the actor $j$ in terms of the genotype of the recipient of
the behavior, $i$. The genotype of $j$ is decomposed in two parts,
``genes which are copies by direct replication of genes in $i$; the
other part consists of non-replica genes'' (Hamilton 1970, p. 1219).
Hamilton (1970) further defines $q_{i}$ as the gene frequency of the
replica part, $b_{ij}$ represents the replica fraction, and $q$ is the average gene frequency in the population. From these definitions Hamilton (1970) jumps to the equality:
\begin{equation}
E (q_{j}) = \frac{1}{1-b_{i}}\left\{ (b_{ij} - b_{i})q_{i} + (1-b_{ij})q\right\}
\end{equation}
where
\begin{align*}
b_{i} = \frac{1}{n}\sum_{j}b_{ij}
\end{align*}</p>
<p><strong>How did Hamilton derive the above equation?</strong> </p>
<hr>
<p>Here is what <em>I think</em> Hamilton is doing. My impression is that the above equation expresses $E(q_j | q_i)$ as a linear regression on $q_i$. In other words, I think the above equation is equivalent to:</p>
<p>$E(q_j | q_i) = E(q_j) + \beta (q_i - E(q_i))$</p>
<p>$E(q_j | q_i) = q + \beta (q_i - q)$</p>
<p>In fact, this equation is equivalent to Hamilton's equation if the regression coefficient is:</p>
<p>$\beta = (b_{ij} - b_i) / (1 - b_i)$</p>
<p>However, I haven't been able to derive this regression coefficient. Given that $\beta = Cov (q_j, q_i)/Var (q_i)$, I suspect that the way to go is to rewrite $q_j$ and $q_i$ in terms of $b_{ij}$ and $b_i$ and calculate the regression coefficient.</p>
<hr>
<p><strong>Reference:</strong></p>
<p>Hamilton 1970 "Selfish and Spiteful Behaviour in an Evolutionary Model"
<a href="http://www.nature.com/nature/journal/v228/n5277/abs/2281218a0.html" rel="nofollow noreferrer">http://www.nature.com/nature/journal/v228/n5277/abs/2281218a0.html</a></p>
<hr>
<p><img src="https://i.stack.imgur.com/qOtTC.png" alt="Excerpt from Hamilton's paper"></p>
| [
{
"answer_id": 28245,
"pm_score": 4,
"text": "<p>As already pointed it out, there is no scientific consensus on the answer to this question. This is because it is hard to test proposed explanations and it's likely that several factors interacted.</p>\n\n<p>All of these have been claimed to be the explan... | [
{
"answer_id": 28244,
"pm_score": 2,
"text": "<p>I doubt you are going to be satisfied with any answer since the authorities on the matter can't test the many hypothesis and don't all agree. Around the time of homo erectus (1.89 million years ago), hominids began walking upright on a more permanent basi... |
27,648 | <p>I was looking into the following problem:<br>
<img src="https://i.stack.imgur.com/R5KaR.png" alt="Who would win? 1 trillion lions or the sun?">
Obviously, the solution lies in how much energy either can output per unit of time.<br>
The total energy output of the sun is $3.8×10^{26} \frac{J}{s}$.<br>
The number of lions alone pales in comparison ($10^{12}$). </p>
<p>However, I'm now trying to figure out how many lions it would take to have an output equal to the sun, but I seem to be having a hard time finding good data. </p>
<p>What's the peak energy output of a lion per second (or where/how can I find such information)?</p>
| [
{
"answer_id": 27652,
"pm_score": 6,
"text": "<p>Wow, as an astrophysicist who has just logged into biology SE for the first time, I didn't think I'd have a question I could immediately answer.</p>\n\n<p>You are correct about the Sun's output, so what about the lion.</p>\n\n<p>If the lion is in its usua... | [
{
"answer_id": 27649,
"pm_score": 3,
"text": "<p>The sun will win until you have enough lions to form a star sized mass.</p>\n\n<p>Assuming that your lions have an average mass of <strong>200kg</strong>, which is <a href=\"http://www.scribd.com/doc/15574755/Relative-Body-Mass-of-the-Lion-and-Tiger\" rel... |
27,736 | <p>This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so forth in the landing. With the artificial "wombs" intact, he populates the planet with clones of himself.</p>
<p>If he wanted to introduce enough variation (without making up new genes, only rearranging) in the population to allow them to be able to reproduce naturally without inbreeding problems, would he be able to? In particular, could he make a woman?
Alternately, could a woman (without a Y chromosome) do the the inverse?</p>
<p>At the risk of introducing bias into the answers, the plot as it stands assumes he is a male and he CAN'T do any of the above and he is restricted to clones.</p>
| [
{
"answer_id": 27750,
"pm_score": 4,
"text": "<p><em>This answer also involves some speculations as the question is about a good theoretical framework for a science fiction.</em></p>\n\n<p>You can find in <a href=\"https://biology.stackexchange.com/questions/17410/could-a-sperm-be-altered-to-contain-a-f... | [
{
"answer_id": 27742,
"pm_score": 3,
"text": "<p>A woman (assuming no mosaicism) has two X chromosomes in the nuclei of her cells (except for oocytes). A man, in every cell with a nucleus (except for spermatocytes), has only one, pluripotent or not. </p>\n\n<p>The only way he could make a female would b... |
27,792 | <p>How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?</p>
<p>The book's answer is $20^{12}$.</p>
<p>However, I disagree. This result distinguishes the following two polypeptides even though they are exactly the same polypeptide:</p>
<p>(Met)x11-Glu</p>
<p>and</p>
<p>Glu-(Met)x11</p>
<p>Am I right? How would I otherwise answer this question? My background in probabilities is very weak.</p>
| [
{
"answer_id": 27803,
"pm_score": 4,
"text": "<p>Judging from what you have said, I assume that combinatorics is not a problem to you.</p>\n\n<p>I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids ar... | [
{
"answer_id": 27794,
"pm_score": 3,
"text": "<p>Think of the amino acid choices as 12 seats. In the first seat, we have 20 choices. In the next seat, we have 20 choices, and this continues. Therefore, we have that \n$$\n\\underbrace{20\\cdots 20}_{12\\text{ times}} = 20^{12}\n$$\nFor your question abou... |
27,799 | <p>Why draw blood from veins rather than arteries? Is it more convenient or safer?</p>
| [
{
"answer_id": 27800,
"pm_score": 7,
"text": "<p>Veins have several advantages over arteries. From a purely practical standpoint, veins are easier to access due to their superficial location compared to the arteries which are located deeper under the skin. They have thinner walls (much less smooth muscl... | [
{
"answer_id": 27801,
"pm_score": 4,
"text": "<p>Right of the bat, veins are superficial so it is much easier to hit a vein than an artery. Arterial sticks are very difficult if you are not practiced at them while veins are much much easier. Also arterial sticks have a very specific purpose usually for ... |
27,839 | <p>My biology textbook mentions that DNA is antiparallel and it got me wondering - can DNA be parallel? What would happen if it was parallel? Could DNA still replicate correctly?</p>
| [
{
"answer_id": 27840,
"pm_score": 5,
"text": "<p>Interestingly the answer is yes. The problem with parallel strands is that the DNA is not pairing in the known way it does when it is combined anti-parallel (or Watson-Crick-pairs). \nI have found different images illustrating the problems:</p>\n\n<p><img... | [
{
"answer_id": 55436,
"pm_score": 1,
"text": "<p>There is another issue here which is more biological. In general, the enzymes that replicate and \"read\" DNA run in one direction along the single strand of DNA that they are operating on. The fact that the other strand of DNA is running in the opposit... |
27,887 | <p>My sister is in 9th grade biology and her teacher avoided answering the question of how we actually study the inside of a cell. I haven't taken biology in a while but I'd like to give her an answer. </p>
<p>Can someone roughly summarize how we actually learn about what goes on inside a cell? Just mentioning a few of the most common or used techniques would be fine. </p>
<p>Note: I hope this isn't a bad question. It's a bit vague. But I didn't want to leave her without a decent answer.</p>
| [
{
"answer_id": 27888,
"pm_score": 4,
"text": "<p>Techniques to look at whole cells are: <strong>Light microscopy</strong> (cells, large organelles), <strong>electron microscopy</strong> (detailed analysis of subcellular structures and even proteins) and <strong>confocal fluorescence miscroscopy</strong>... | [
{
"answer_id": 27889,
"pm_score": 2,
"text": "<p>Beyond the conventional methods listed by Chris Stronks, Berkley Labs have far advanced the state of the art in probing the internal structures of cells using x-ray tomography. See:\n<a href=\"http://ncxt.lbl.gov/\" rel=\"nofollow\">http://ncxt.lbl.gov/</... |
27,980 | <p>There are many programmed cell death pathways, but some cells show a greater preference for some over the other. I'm wondering as to why if necrosis is an inflammatory response that causes damage to neighboring cells, why some cells would prefer this as opposed to a more controlled mechanism such as apoptosis or even autophagy. </p>
| [
{
"answer_id": 27986,
"pm_score": 4,
"text": "<p>There is actually no preference for apoptosis or necrosis in cells of the human body - both types can occur in all cells and they have different triggers. The main differences can be seen in this figure (from <a href=\"https://en.wikipedia.org/wiki/Necros... | [
{
"answer_id": 27983,
"pm_score": 2,
"text": "<p>Necrosis can be described as accidental cell death or damage, triggered possibly from external environmental factors such as exposure to radiation, toxins, excessive heat and etc...whereas, Apoptosis is a programmed form of a cell death mechanism. This pr... |
28,047 | <p>This <a href="http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CancerCellsInCulture.html" rel="nofollow">website on cultured cancer cells</a> () says cancer cells <em>may be immortal</em>. </p>
<p>I am wondering if there has been any research done to find if cancer cells are really immortal. </p>
<ol>
<li>How old is the still maintained living oldest culture of cancer cells?</li>
<li>Has there been any research done on replicative senescence of Cancer Cells invitro?</li>
</ol>
<p>Edit 1:</p>
<p>If there is some data relating to the number of replications the cells have undergone, it will be very useful</p>
| [
{
"answer_id": 28051,
"pm_score": 5,
"text": "<p>The HeLa cell line is undoubtedly the most used and investigated <strong>human</strong> immortal tumor cell line. Extracted from a cervical tumor from Henrietta Lacks in 1951 at Johns Hopkins hospital, Baltimore, MD these cells proved immortal and are st... | [
{
"answer_id": 36152,
"pm_score": -1,
"text": "<p>Terminology involved makes everything lie a bit.</p>\n\n<p>All the \"immortality\" and so complicate things a bit. We perceive life as life of our individual bodies. Thus if our body is immortal, that means that it is persistent, without us bothering abo... |
28,066 | <p>Many organisms have their common names identical to their scientific names. For example, there exist apes of the genus <em>Gorilla</em> known commonly as gorillas, and plants of the genus <em>Delphinium</em> known as delphiniums. </p>
<p>However, are there any examples of the common name of an organism overlapping with the scientific name of another organism, therefore causing ambiguity when the organism's name is spoken aloud? If written with correct formatting, this should not cause a problem in any case, due to the formatting specifically describing a genus/species. </p>
| [
{
"answer_id": 28067,
"pm_score": 5,
"text": "<p>One great example I know of is the <a href=\"http://en.wikipedia.org/wiki/Platypus\">duck-billed platypus</a> (<em>Ornithorhynchus anatinus</em>), often simply called a platypus, which shares its name with the <a href=\"http://en.wikipedia.org/wiki/Platy... | [
{
"answer_id": 28081,
"pm_score": 3,
"text": "<p>Plants known commonly as geraniums belong to the genus <em>Pelargonium</em>. </p>\n\n<p>Similarly, plants known commonly as cranesbills belong to the genus <em>Geranium</em>.</p>\n"
},
{
"answer_id": 85507,
"pm_score": 2,
"text": "<p><a hr... |
28,088 | <p>I'm simplifying things here:</p>
<blockquote>
<p><strong>A.</strong> Does a woman bleed <strong>constantly</strong>, like a drop every 10 minutes? Two hours without pad or tampon and your underwear is dirty?</p>
</blockquote>
<p>or</p>
<blockquote>
<p><strong>B.</strong> Does a woman bleed <strong>suddenly</strong> a bigger amount of menstruation fluid? Then hours might pass before it happens again?</p>
</blockquote>
<p>or</p>
<blockquote>
<p><strong>C.</strong> Both.</p>
</blockquote>
<p>Might be a stupid question. I'm sorry. I read all the other information on the internet but no one answers this one for some reason. I read girls should change the pads and tampons a few times a day (like every 6 hours). Does that mean A is correct?</p>
<p>Thanks for any helpful information!</p>
<p><em>(Well, I guess I'm male.)</em></p>
<p><strong>Edit:</strong><br>
What I want to know: If I was a woman, how would I experience the days of period bleedings? From what I read in the comments and answer(s), one should expect A (constant bleeding) and should wear pads/tampons all the time (for 2 to 7 days) and sometimes one could also experience an exceptional heavier bleeding (B)? Are there (healthy) women who would experience B most of the time? I visited Wikipedia and other random sites but they all have the other important information without answering my question. <em>(Also I will be glad to accept an answer, which satisfies my need for knowledge.)</em></p>
| [
{
"answer_id": 28184,
"pm_score": 1,
"text": "<p>This isn't much of an answer but here goes... Two things; it depends on which day of the period it is. There can be rather brief, heavy bleeding on the later part of the first day or sometime during the second. On most others days, the bleeding will be li... | [
{
"answer_id": 28094,
"pm_score": 3,
"text": "<p>The answer is both. Different women experience menstruation differently depending on the levels of different hormones in their body, personal medical conditions, medications, on their age, and the activities they do in their lives. Bleeding is due to the ... |
28,468 | <p>Iodine and related biological iodine-carrying hormones are phylogenetically very old, at least according to Wikipedia. Humans use iodine as a metabolic indicator, as do axolotls and apparently most multicellular life.</p>
<p>So why? Growth hormones, sex hormones, et cetera don't require strange heavy elements not used for anything else. It's not a requirement of transcription factors that they contain iodine.</p>
<p>All I've got for hints is that selenium forms an essential part of deiodinases, as well as forming an essential part of thioredoxin reductase. Thioredoxin is a component used to reduce things around the cell, like thiols and RNA bits and so on and so forth, which I could see being worth the evolutionary cost of running down some selenium.</p>
<p>What's the point of iodine? People have iodine deficiency 'all the time' (it's common enough to be named). Is that a product of agriculture somehow? Are there any advantages to using iodine for metabolic hormones? If there are, what are they? </p>
| [
{
"answer_id": 40082,
"pm_score": 3,
"text": "<p><strong>Iodine in us</strong></p>\n\n<p>Iodine is found in two main hormones, T3 and T4. They affect every part of the body, and are important for cell-cell signaling. Wikipedia says:</p>\n\n<blockquote>\n <p>The thyronines act on nearly every cell in th... | [
{
"answer_id": 28487,
"pm_score": 2,
"text": "<p>Classical thyroid hormones implement a very flexible signaling mechanism. Basically, they comprise two aromatic rings that are connected via an oxygen atom. Optionally, they may contain organic side chains and inorganic iodine atoms.</p>\n\n<p>In the case... |
28,520 | <p>The general understanding is that when I touch an object, I perceive its (relative) temperature.</p>
<p>A metal object at room temperature, however, will often feel cool to the touch.</p>
<p>This leads me to believe that the skin senses heat flux in addition to, or instead of temperature.
(The metal conducts heat well, and therefore creates a greater flux when touched than a more insulative material.)</p>
<p>I am unfamiliar with the chemical process by which temperature or flux is converted into meaningful signals.</p>
<p>Do humans perceive temperature or heat-flux? (or both?)</p>
| [
{
"answer_id": 28530,
"pm_score": 4,
"text": "<p><strong>Short answer</strong></p>\n\n<p>Humans sense <em>temperature differences</em>.</p>\n\n<p><strong>Background</strong><br>\n<sup>(Including edits based upon comments)</sup> </p>\n\n<p>Because the question is \"Do humans <strong><em>perceive</em></st... | [
{
"answer_id": 28522,
"pm_score": 3,
"text": "<p>This is the modified answer in response to the discussion:</p>\n\n<h2>Facts:</h2>\n\n<ol>\n<li><p>There are warmth and cold receptors in the body at two places: The Peripheral receptors and the Central Receptors</p></li>\n<li><p>The peripheral receptors a... |
29,655 | <p>I was under the impression that both ends of a muscle contract. For instance, the fibers of the biceps run parallel to the humerus so I thought they pulled toward the middle. </p>
<p>But now I'm confused because it sounds like the contraction of the fibers doesn't necessarily have to parallel the motion of the muscle itself. In other words, just because the fibers contract doesn't mean that the muscle lengthens or shortens in a particular direction. </p>
<p>Can someone clarify if muscles contract in both directions? </p>
<p>Or perhaps a better question is do muscle contract in a particular direction and is this the same direction that the fibers contract or does the muscle as a whole move in a different direction in comparison to the direction the fibers are contracting? </p>
| [
{
"answer_id": 29660,
"pm_score": 4,
"text": "<p>The muscular fibers (or more exactly the actin and myosin filaments) are contracted towards each other. This makes them \"move to the middle\" and you build up a force on both sides of the muscle. See this image (from the Wikipedia), which illustrates thi... | [
{
"answer_id": 29666,
"pm_score": 2,
"text": "<p>Muscles do contract in both directions. To understand this better you need to know few things:</p>\n\n<ol>\n<li><p>The smallest unit of a muscle is called myofiber or a muscle fiber. It is basically a multinucleated elongated cell. Each muscle fiber is co... |
29,662 | <p>My ten year old son was reading car number plates that were too fast, too far away and at the wrong angle for any of us to read or even believe that it was possible for him to read. We thought he was lying as he reeled off the whole number plate and not just some. My husband went across the road to prove him wrong and get him to admit he was making it up but he wasn't. We even asked people in the restaurant and waiting staff for their opinion and everyone was blown away. I'm totally astonished and slightly freaked out by his sight and I'm hoping someone can explain for me.</p>
<p><strong>Specifics</strong></p>
<ul>
<li>I believe it was approx 20-25 metres away and I am under guessing.</li>
<li>He had only 1 or 2 seconds as the cars drove left to right. </li>
<li>Cars would be travelling 30/40 kmph along that road. </li>
<li>We were sitting in the restaurant at night time so not in a car
ourselves</li>
</ul>
| [
{
"answer_id": 29681,
"pm_score": 5,
"text": "<p>The \"normal\" visual acuity in the Anglosphere is the 20/20 vision which means that on a <a href=\"http://en.wikipedia.org/wiki/Snellen_chart\">Snellen chart</a> characters with 8,86 mm height can be read conveniently from a distance of approximately 6 m... | [
{
"answer_id": 29664,
"pm_score": 4,
"text": "<p><strong>Short answer</strong></p>\n\n<p>Visual acuity decreases with age. Your son's age is within the age range that visual acuities are best. Acuity starts to decrease from about age 45. \n<br>\n<br></p>\n\n<p><strong>Background</strong></p>\n\n<p><stro... |
29,702 | <p>I have come across some species of living organisms who are able to emit light at whim. Can that ability be incorporated into a portion of human skin (a specialized tissue)?</p>
| [
{
"answer_id": 29715,
"pm_score": 3,
"text": "<p>Genetic modification of any cell to overexpress a <em>fluorescent</em> protein will <strong>not</strong> 'generate' light, per-say: fluorophores absorb particular wavelengths and re-emit in less energetic wavelengths, dispersing some energy as heat. <em>(... | [
{
"answer_id": 29705,
"pm_score": 2,
"text": "<p>Yes, the fibroblasts of skin cells can quite easily be Transfected with a fluorescent gene such as GFP. Fluorescence doesn't actually produce light, the fluorescent molecule just changes the wavelength of light shining on it. </p>\n\n<p>Fibroblasts can al... |
29,730 | <p>What is called the "area size that an animal usually lives in" or "needs for a normal life"? Is there any specific term?</p>
| [
{
"answer_id": 29744,
"pm_score": 4,
"text": "<p>To avoid confusion I just want to add to fileunderwater's answer the equivalent words we use to describe the \"area size a population/species lives in\".</p>\n\n<p>The spatial range a single individual occupies is generally called <code>home range</code> ... | [
{
"answer_id": 29732,
"pm_score": 3,
"text": "<p>Are you looking for '<a href=\"http://en.wikipedia.org/wiki/Home_range\">Home range</a>' (see also the definition in <a href=\"http://global.britannica.com/EBchecked/topic/270112/home-range\">Encyclopaedia Britannica</a>)? Generally, 'home range' is defin... |
29,812 | <p>I am trying to find out how these networks can be linked together. I know that Protein-protein interaction networks and metabolic networks both fall under the Intra-cellular type of biological networks that describe the cellular functioning. But what is the relationship between them?</p>
<p>Thank you very much.</p>
| [
{
"answer_id": 29824,
"pm_score": 2,
"text": "<p>Proteins interact with each other often for regulation purposes and for localization of several enzymatic reactions for increased efficiency. For example, some proteins inhibit their binding partners. Or DNA replication complex is made of bunch of protein... | [
{
"answer_id": 29816,
"pm_score": 1,
"text": "<p>In short, proteins in Protein-protein interaction networks perform a function by directly interacting with one another. They may for instance bind to one another forming permanent or momentary complexes (e.g. insulin binding to insulin receptor or the pi... |
29,857 | <p>Since as long as I have been doing cell culture, the word confluency has been used to describe the percentage growth of cells or area covered by them. However, no dictionary that I have found uses this word. I was wondering if anyone could reliably state where the meaning comes from or how the association began, and truly what it means. I don't believe I can post this on another Stack Exchange because the word doesn't have even a resembling meaning in the dictionary. Cell culture is such an integral part of cell biology, medical research and biological manufacturing. And this term is an integral part of cell culture. I was surprised to be unable to reliably verify its meaning.</p>
| [
{
"answer_id": 29864,
"pm_score": 4,
"text": "<p>Besides the etymologic explanation that @aandreev gave, in cell culture this term is commonly used to describe the density of adherent cells and it is used as a measure of their proliferation. It is usually combined with an estimated (or counted) percenta... | [
{
"answer_id": 29863,
"pm_score": 2,
"text": "<p>con- (com-) is prefix that usually means \"togetherness\", joining. Root fluency/fluent comes from latin <em>fluere</em>, to flow.</p>\n\n<p>Source: Google's definitions for <a href=\"https://www.google.com/search?q=con-%20definition&oq=con-%20definit... |
29,943 | <p>We currently have a problem of increasing $\ce{CO2}$ in the atmosphere. But assuming we find a way to carbon sink it, what is the minimum $\ce{CO2}$ we need to leave in the atmosphere to provide a source for plants to photosynthesize? I'm assuming this may vary per plant, and that we could choke plants so they're less productive - but at some point they will starve to death if we remove too much $\ce{CO2}$.</p>
<p><strong>Where does this point lie?</strong></p>
<p>Approximations, or a specific data point (say for one plant, or one type of plant) would be an adequate place to start.</p>
<p>Current atmosphere composition is $\pu{0.035\%}$ carbon dioxide. In the past it has been higher (has it ever been lower?), which <em>in theory</em> has resulted in higher plant growth - but I've seen some contradictory statements about higher Carbon Dioxide.</p>
<p>(related: <a href="https://biology.stackexchange.com/questions/3043/what-is-the-effect-of-a-pure-oxygen-environment-on-a-plant?rq=1">What is the effect of a pure-oxygen environment on a plant?</a>)</p>
| [
{
"answer_id": 59784,
"pm_score": 4,
"text": "<p>The values provided in the <a href=\"https://biology.stackexchange.com/a/44685/24284\">other answer</a> are actually related to the minimum values experienced by land plants in the past, not the theoretical minimum possible concentration of CO<sub>2</sub>... | [
{
"answer_id": 44685,
"pm_score": -1,
"text": "<p>Minimum concentration in PPM to support plant life varies from 185 ppm to 225 ppm. We are at 433 ppm at the moment. Prior to this Ice Age cycle that started about 3 1/2 million years ago the PPM Norm was between 900 and 1120 ppm. For reference if anybod... |
30,005 | <p>Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice. </p>
<p>I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?</p>
| [
{
"answer_id": 30018,
"pm_score": 6,
"text": "<p>Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.</p>\n\n<p><img src=\"https://i.stack.imgur.com/3bT7ym.jpg\" alt=\"enter image description here\"></p>\n\n<p>Als... | [
{
"answer_id": 30008,
"pm_score": 3,
"text": "<p><a href=\"http://pets.thenest.com/skin-pigmentation-cats-11322.html\" rel=\"noreferrer\">This source</a> seems to suggest that cats' skin colour is determined by their fur colour, as the same genes expressed in the fur which produce the colours (melanins)... |
30,370 | <p>Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) and $O^{c}$(mutation in the operator, the site where the repressor binds).</p>
<p>$I^{c}$ mutants are usually recessive: the Lac Repressor cannot bind to the operator, however, if a wild-copy of the gene is present in a merodiploid, the inducible pattern of expression is restored, because the Lac Repressor acts in trans (that is, it will inhibit expression of both operons when lactose is not present).</p>
<p>However, I've <a href="http://ocw.mit.edu/courses/biology/7-03-genetics-fall-2004/lecture-notes/lecture16.pdf">read</a> that there's a strain ($lacI^{d}$) which is dominant, so the expression is constitutive even in the presence of the normal repressor. According to the article linked, abnormal subunits may mix with normal subunits, resulting in a disfunctional tetramer, even if a wild type lacI is also present.
In terms of protein structure, why some mutations may have this effect and be dominant while other mutations do not interfere with normal copies of the protein and are recessive?</p>
| [
{
"answer_id": 30373,
"pm_score": 3,
"text": "<p>The lac repressor act as a tetramere molecule and requires <strong>all 4</strong> of the subunit to be able to bind DNA to act on the operon and repress β-galactosidase expression.</p>\n\n<p>The \"all 4\" is the key here, if <strong>any of the 4 subunits ... | [
{
"answer_id": 30462,
"pm_score": 2,
"text": "<p>Concerning the difference between dominant vs. recessive mutations, in general, recessive, or loss-of-function mutations, are much more frequent than dominant, or gain-of-function, mutations, because there are many different ways to \"break\" or inactivat... |
30,437 | <p>When does the second polar body gets expelled from the egg nucleus during oogenesis ? I know that it occurs after the entry of the sperm into the secondary oocyte but does it occur before the fertilization or in the period between the entry of the sperm and fertilization ? </p>
| [
{
"answer_id": 30574,
"pm_score": 2,
"text": "<p>As stated in the <a href=\"https://biology.stackexchange.com/a/30440/3340\">answer by @CDB</a>, these polar bodies don't last too long, and the second polar body which forms as the result of meiosis II, extrude only <strong>after</strong> fertilisation. T... | [
{
"answer_id": 30440,
"pm_score": 0,
"text": "<p>Polar bodies will usually undergo apoptosis in about 17 to 24 hours after the egg forms (the final stages of telophase II (cytokinesis)) because they have relatively little cytoplasm and shunted organelle development (<a href=\"https://www.ncbi.nlm.nih.go... |
30,560 | <p>As long as we only look at humans the differences are clear: males have chromosomes XY, produce sperm and don't get pregnant. Females have chromosomes XX, produce egg cells and bear babies. But when you consider other species, things are more complicated: in birds, it's females who carry the Y chromosomes. In pipefish and sea horses, it's the males who get pregnant. So maybe the only reliable criterion to tell if an animal is a male or a female is looking at its reproductive cells, and decide if they look like spermatozoa or egg cells. But then there are male and female plants, where none of the methods above applies.</p>
<p>So how do you tell, in general, who's male and who's female in a species? Or is the distinction arbitrary?</p>
| [
{
"answer_id": 30562,
"pm_score": 6,
"text": "<p>Sexes (male and female) are generally defined in terms of <a href=\"http://en.wikipedia.org/wiki/Anisogamy\" rel=\"noreferrer\"><strong><em>Anisogamy</em></strong></a>, which means that there are size differences between the <a href=\"http://en.wikipedia.... | [
{
"answer_id": 30572,
"pm_score": 2,
"text": "<p>In general, It's pretty much the reproductive cells with plants and animals. The male's unique cells (sperm, pollen) fertilizes the female's unique cells (egg, ovule). The resulting offspring develops and hatches from within the female's egg/ovule. Now... |
30,628 | <p>Why do many plants produce such large fruits(apples and strawberries,for example) if those contain only relatively small seeds? </p>
| [
{
"answer_id": 30633,
"pm_score": 5,
"text": "<p>The short answer: Fruits are large compared to seeds because humans have made them large. </p>\n\n<p>In the natural environment, there is a different set of evolutionary pressures. A fruit has to be able to successfully propagate itself using its seeds, w... | [
{
"answer_id": 30632,
"pm_score": 2,
"text": "<p>Because seeds are not appealing to animals and they can only be carried by animals if they are made appealing - there are exceptions of course such as <a href=\"http://antranik.org/wp-content/uploads/2011/06/cockleburs-fruits-1024x957.jpg?9873a6\" rel=\"n... |
30,630 | <p>The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH<sub>2</sub>) that can potentially form a peptide bond. </p>
<p><img src="https://i.stack.imgur.com/O2Vp5.jpg" alt="enter image description here"> <br><br>
<sup>Source: <a href="http://cultureofchemistry.fieldofscience.com/2010/12/calm-amino-acids.html" rel="nofollow noreferrer">The Culture of Chemistry</a></sup></p>
<p>Does this property of amino acids means that each amino acid can form a peptide bond in any combination? In other words, are there certain amino acid doublets in existence that never pair up? </p>
| [
{
"answer_id": 34205,
"pm_score": 3,
"text": "<p>Short answer: there are no restrictions <em>in principle</em> on which amino acids can follow which. That means that <em>in principle</em> you can have polypeptide in any configuration: AAAA, WQWQWQ <em>etc</em>.</p>\n\n<p>Problem is that polypeptides mus... | [
{
"answer_id": 30643,
"pm_score": 3,
"text": "<p>It seems like you may be thinking along the lines of DNA, where adenine pairs only with thymine and guanine with cytosine.</p>\n\n<p>Unlike DNA, amino acid chains are single-stranded...<img src=\"https://i.stack.imgur.com/awhY7.jpg\" alt=\"example chain o... |
30,746 | <p>What diagnostic applications, if any, are there in using bioluminescence to detect cancer or tumors (in vivo)?</p>
| [
{
"answer_id": 30750,
"pm_score": 3,
"text": "<p>Not in human but you can use this technique with genetically modified model organisms as described <a href=\"http://www.ingentaconnect.com/content/aalas/cm/2004/00000054/00000006/art00005?token=004a10c8405847447b49762f7b7342425e2079475833757e6f4f2858592f3... | [
{
"answer_id": 30748,
"pm_score": 0,
"text": "<p><em>In vivo</em>, none.</p>\n\n<p>Bioluminescence is cool, but it's not a powerful light source. Even if you could tag a cancer cell (all of them), unless it were on your skin or in your eye, you wouldn't be able to see it, even with some kind of scope. <... |
30,839 | <p>I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.</p>
<p>CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amount of gRNA and/or of the protein.</p>
<p>I need to insert the gene, without the need of targeting some specific place. </p>
<p>Is this possible in some way with CRISPR?</p>
<p>I know that there may be better technique to do this, but I can only use CRISPR.</p>
| [
{
"answer_id": 30983,
"pm_score": 4,
"text": "<p>A paper was published about a week ago in Nature Biotechnology and adresses your question, <a href=\"http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3190.html\" rel=\"nofollow\">Maruyama T et al., 2015</a>. I must say I found the authors' strateg... | [
{
"answer_id": 30919,
"pm_score": 0,
"text": "<p>I'm going to preface this answer with the disclaimer that I have never used CRISPR/Cas, and there is a fair amount of speculation here.</p>\n\n<p>But I think that efficient CRISPR mediated knock-in probably has three parts, targeting, integration, and sel... |
31,055 | <p>I have heard that a reference genome such as humans is generated by randomly choosing samples from a group of donors. But why do we call the DNA sequence generated as a reference? Why should we believe those few samples can represent all humans, from which we need to align with?</p>
| [
{
"answer_id": 31056,
"pm_score": 5,
"text": "<p>The main reason is because the genetic differences between individuals of the same species are <em>tiny</em>. For the vast majority of studies, they can simply be ignored. </p>\n\n<p>Differences between individuals are usually (not always, but mostly) dif... | [
{
"answer_id": 31164,
"pm_score": 0,
"text": "<p>Reference genomes do not accurately represent the set of genes of any single person.it is created by fragments of various donors, which when built,is used as a template for creating the real genome. Though we will find All humans are 99.9 per cent identic... |
31,135 | <p>The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?</p>
<p>Can someone explain why we have gluconeogenesis and when it is used?</p>
| [
{
"answer_id": 31136,
"pm_score": 5,
"text": "<p>Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as... | [
{
"answer_id": 44243,
"pm_score": 0,
"text": "<p>Gluconeogenesis occurs during prolonged starvation or overnight fasting, mostly in liver and kidney to provide glucose to brain and RBCs. As brain and red blood cells require continuous glucose for their activity, this process comes in handy. The steps in... |
31,334 | <p>In my textbook it is stated that the T3 hormone produced at the thyroid gland is 3-5 times more biologically active than T4.</p>
<p>How is being active defined and how can this effect be measured?</p>
| [
{
"answer_id": 31436,
"pm_score": 2,
"text": "<p>Activity of a hormone represents the efficacy of the hormone in causing the intended effect.</p>\n\n<p>In case of T3 vs T4, though T4 is the majority fraction, T3 is more active, meaning it is much more efficacious in effecting the results. </p>\n\n<p>The... | [
{
"answer_id": 31346,
"pm_score": 1,
"text": "<p>Biological activity has a range of definitions, but in this case I believe it to mean that the T3 hormone is produced at a rate 3-5x that of T4. This can be measured with fluorescent tags. Typically, fluorescent tagging uses a reactive derivative of a flu... |
31,660 | <p>This bug is crawling all around the house it stays within the shadows and moves very very slow, i have never seen it jump or run, it just moves very slowly</p>
<p><img src="https://i.stack.imgur.com/NYA4x.jpg" alt="DSC_108"></p>
<p>P.S. those bugs as u can see are smaller than 1mm so it's hard to take better pictures but i will get better ones tomorrow</p>
<p>P.S. the hairs are not hairs they are wool from the carpets, i just got married in october 2014 and everything in the house is new, including the flat, it was built in january 2014.</p>
<p><a href="https://www.dropbox.com/sh/knxjw6psd793anb/AADuYjPZAmTRHmZjgKy4_Wdza?dl=0" rel="nofollow noreferrer">Bug pictures with a 1 mm thick pencil refill</a></p>
<p>it is very similar to what's in this picture, but i couldn't take a picture of it because it's tooo tiny</p>
<p>I really need to know what it is so I can deal with it :(</p>
<p>Edit: once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles and I don't think it is a termite because I don't find any piles of eaten wood</p>
<p>EDIT 2:
More pictures:</p>
<p><strong>-- Stage 1 --</strong></p>
<p><img src="https://i.stack.imgur.com/fV4tb.jpg" alt="Insect 1 of 2 Stage 1 of 2 Pic 1 of 4">
<img src="https://i.stack.imgur.com/a7Qdj.jpg" alt="Insect 1 of 2 Stage 1 of 2 Pic 2 of 4">
<img src="https://i.stack.imgur.com/aCxLf.jpg" alt="Insect 1 of 2 Stage 1 of 2 Pic 3 of 4">
<img src="https://i.stack.imgur.com/dvXlc.jpg" alt="Insect 1 of 2 Stage 1 of 2 Pic 4 of 4"></p>
<p><strong>-- Stage 2 --</strong></p>
<p><img src="https://i.stack.imgur.com/cQlzd.jpg" alt="Insect 1 of 2 Stage 2 of 2 Pic 1 of 2">
<img src="https://i.stack.imgur.com/L8ZmH.jpg" alt="Insect 1 of 2 Stage 2 of 2 Pic 2 of 2"></p>
<p><strong><a href="http://youtu.be/qR7s6LbbdOM" rel="nofollow noreferrer">-- Video for stage 2 --</a></strong></p>
<p>I don't know what it is but I know that there is ones young in age i call them stage 1 they are unable to move</p>
<p>and there are ones I call stage 2 older in age and bigger in size and they can move and I think they can bite too</p>
<p><strong>-- Insect 2 --</strong> 5mm by 5mm</p>
<p><img src="https://i.stack.imgur.com/FyS8k.jpg" alt="Insect 2 of 2 Pic 1 of 2"> <img src="https://i.stack.imgur.com/5U7mk.jpg" alt="Insect 2 of 2 Pic 2 of 2"></p>
<p>I found this one across the hall from the others and I do't know if it's related, i found it dead but I haven't sprayed that side with insecticides i sprayed the other side so it's possible that it was with the others but ran and died far from them.</p>
<p>EDIT: More photos</p>
<p>P.S. I found those moving in daylight (now)</p>
<p><img src="https://i.stack.imgur.com/Zm85H.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/pzxSz.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/VKDCc.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/8C2r1.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/azAPx.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/3zIsy.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/mdhrd.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/j6UFL.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/2XgAm.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/cp397.jpg" alt="enter image description here"><img src="https://i.stack.imgur.com/BbydD.jpg" alt="enter image description here"></p>
<p>when i blew a little air i think i turned it</p>
<p><img src="https://i.stack.imgur.com/jTDFq.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 31790,
"pm_score": 4,
"text": "<p>Insect 1 is a:</p>\n<blockquote>\n<p><strong>Booklice</strong></p>\n<p><strong>Introduction</strong></p>\n<p>Booklice, also called psocids, are not true lice. While they resemble lice in size and shape, booklice feed only on fungi or mold. If you find the... | [
{
"answer_id": 31676,
"pm_score": 2,
"text": "<p><strong>Update:</strong> This is an <em>incorrect</em> answer. From the poster's <a href=\"https://biology.stackexchange.com/questions/31660/i-have-a-black-tiny-bug-crawling-all-over-the-house#comment53444_31790\">comment</a> above: \"<code>Clearer pictur... |
34,044 | <p>I'm a bit curious as to how frame-shift mutation works. If you shift one amino acid towards another. How does this not affect the entire chromosome? Wouldn't this mean that the organism would be absolutely "scrambled" as it would essentially be "missing" a whole chromosome...Or having a chromosome that did all kinds of wrong things at least?</p>
<p>Thanks.</p>
| [
{
"answer_id": 34050,
"pm_score": 4,
"text": "<p>For transcription, the cell uses different signals from start- or stop- codons to determine the start and end of a transcript (see this <a href=\"http://en.wikipedia.org/wiki/Transcription_%28genetics%29#Major_steps\" rel=\"noreferrer\">wiki page</a>). Co... | [
{
"answer_id": 34049,
"pm_score": 2,
"text": "<p>First of all, for a frame shift mutation to occur nucleotides (not amino acids) are either deleted or inserted into the sequence. Read about <a href=\"http://en.wikipedia.org/wiki/Frameshift_mutation\" rel=\"nofollow noreferrer\">details</a> on this wiki... |
34,306 | <p>Is there any actual difference between inoculation and vaccination or are these terms interchangeable? </p>
<p>In case the difference exists, would it be correct to say that inoculation is purposefully infecting a person with a pathogen in a controlled way, even when the person is already infected, to induce immunity while vaccination is administering dead or weakened pathogens to a healthy person as a preventive measure to check future infections?</p>
<p>Also, would it be correct to say that vaccination is an advanced form of inoculation? </p>
| [
{
"answer_id": 34310,
"pm_score": 4,
"text": "<p>Both are forms of immunisation. </p>\n\n<p>Inoculation is exactly that. A live organism is introduced in a controlled way, so as to minimise the risk of infection, and is essentially the same process followed by many people in history. It is inherently r... | [
{
"answer_id": 44560,
"pm_score": 3,
"text": "<p>In a general sense and as per the current scientific parlance, inoculation is used to mean introduction of a microbe to a system. This can refer to immunization procedures as well as for addition of a microbe to a culture medium in microbiological procedu... |
34,397 | <p>Are blood vessels classified as organs? Organs compose of 2 or more tissues and perform a certain function. Blood vessels have 3 different tissues and perform a function (transport blood), yet I do not see them being identified as an organ. Why is this? Are they organs? Or do they hold their own classification?</p>
| [
{
"answer_id": 34398,
"pm_score": 5,
"text": "<p>The cardiovascular system is usually lumped together as an organ. So blood vessels would be included here but you are right in that this is a bit strange being that it includes the heart and the vasculature.</p>\n"
}
] | [
{
"answer_id": 34402,
"pm_score": 4,
"text": "<p>I don't know if they are classified as organs, but basically, blood vessels match the criteria for being organs.</p>\n\n<p>Quoting <a href=\"http://www.siumed.edu/~dking2/crr/cvguide.htm#vessels\">SIU School of Medicine</a>:</p>\n\n<blockquote>\n <p>Bloo... |
34,409 | <p>I've read a lot about cockroaches but was unable to find how they contribute to the ecological environment. Does anyone know?</p>
| [
{
"answer_id": 34412,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nCockroaches are an integral part of the food chain. </p>\n\n<p><strong>Background</strong><br>\nCockroaches are an important <strong>source of food</strong> for a number of organisms, such as arthropods, birds, and mamma... | [
{
"answer_id": 34410,
"pm_score": 4,
"text": "<p>They don't have to \"contribute\" as such. All they have to do is survive and pass on their genes to their offspring. Any benefits that they have (in terms of detritus cleaned up, etc.) or harms that they cause is purely coincidental.</p>\n\n<p>There's no... |
34,650 | <p><img src="https://i.stack.imgur.com/PkdTf.jpg" alt="enter image description here" /></p>
<p>I came across a black cicada in northwest Missouri last week (May 2015). I am only familiar with brown cicadas. What makes this black one different? Is it a different species, or do the brown cicadas change color at some point in adulthood?</p>
| [
{
"answer_id": 34651,
"pm_score": 4,
"text": "<p>A little digging on wikipedia seems to have answered my question. This picture of a 17 year cicada, <a href=\"http://en.wikipedia.org/wiki/Magicicada_septendecim\" rel=\"noreferrer\">Magicicada septendecim</a> is pretty close to what I saw.\n<img src=\"ht... | [
{
"answer_id": 74325,
"pm_score": 1,
"text": "<p>It's difficult to be sure without seeing the specimen more from the side (or ventrally), but the lack of visible orange color between the eye and the wing articulation suggests that it could be one of two other 17-year cicada species, <em>Magicicada cassi... |
34,683 | <p><a href="https://i.stack.imgur.com/0RwtN.png" rel="noreferrer"><img src="https://i.stack.imgur.com/0RwtN.png" alt="enter image description here"></a></p>
<p>I was watching a nice <a href="https://www.youtube.com/watch?v=iES23rXuMr4" rel="noreferrer">little video</a> on youtube but couldn't help but notice how snappy smaller animals such as rats and chipmunks move. By snappy I mean how the animal moves in almost discrete states pausing between each movement. </p>
<p>Is this a trivial observation or something inherent in the neuro-synapse or muscular make-up of these animals?</p>
<p><a href="https://i.stack.imgur.com/p9aPR.png" rel="noreferrer"><img src="https://i.stack.imgur.com/p9aPR.png" alt="Bikke the Chipmunk Yawning and Stretching"></a></p>
| [
{
"answer_id": 34688,
"pm_score": 7,
"text": "<p><strong>Short answer</strong><br>\nIntermittent locomotion can <em>increase the detection of prey</em> by predators (e.g. rats), while it may lead to <em>reduced attack rates</em> in prey animals (e.g., rats and chipmunks). It may also <em>increase physi... | [
{
"answer_id": 34717,
"pm_score": 4,
"text": "<p>In addition to @AliceD's excellent answer, I would like to add that a simple mechanistic relationship between body size and \"snappiness\" may explain the observed pattern.</p>\n\n<p><strong>Basics of biophysics</strong></p>\n\n<p>Difference in snappiness... |
34,722 | <p>My understanding:</p>
<p>In Hardy-Weinberg problems the frequency of a homozygous recessive genetic occurrence in a population is $q^2$. So if 1 in 100 people in a population have albinism (homozygous recessive disorder) then we say the frequency is $q^2=1/100$.</p>
<p>We then say, to find the frequency of the allele count $q$ that $q=\sqrt{1/100}= 1/10$.</p>
<p>I don't understand why we say this. Why would the allele count be the square root of the population frequency? There's 2 alleles per person. Why isn't it x2 or /2 instead?
I suppose my problem is understand <strong>what exactly is p and q</strong>.</p>
| [
{
"answer_id": 34728,
"pm_score": 3,
"text": "<p>First of, let me correct your equation: $q = \\sqrt{\\frac{1}{100}} = \\frac{1}{10} = 0.1 ≠ 10 $.</p>\n\n<p><strong>From allele frequency to genotype frequency</strong></p>\n\n<p>Imagine you were to randomly sample an allele from a population of allele wh... | [
{
"answer_id": 34727,
"pm_score": 1,
"text": "<p>To understand population genetics and the Hardy-Weinberg equilibrium you first need to clearly separate <strong>genotype frequencies</strong> (the frequency of individuals in a population having a genotype) and <strong>allele frequencies</strong> (the fre... |
34,827 | <p><a href="http://en.wikipedia.org/wiki/Triclosan">Triclosan</a> is a chemical often referred to as a "biocide" instead of an "antibiotic". However, its <a href="http://en.wikipedia.org/wiki/Triclosan#Mechanism_of_action">mode of action</a> seems to suggest that it is an antibiotic. </p>
<blockquote>
<p>Triclosan binds to bacterial enoyl-acyl carrier protein reductase
(ENR) enzyme, which is encoded by the gene FabI. This binding
increases the enzyme's affinity for nicotinamide adenine dinucleotide
(NAD+). This results in the formation of a stable, ternary complex of
ENR-NAD+-triclosan, which is unable to participate in fatty acid
synthesis.</p>
</blockquote>
<p>This is nearly identical to the action of many other antibiotics, such as penicillins (inhibits cell wall synthesis enzymes), quinolones (inhibit DNA gyrase) or sulfonamides (inhibit folate synthesis). </p>
<p>In fact, <a href="http://www.ncbi.nlm.nih.gov/pubmed/11506900">this paper</a> describes the mechanism of resistance to triclosan and notes that it is identical to many antibiotics. Why then, is triclosan not classified as an antibiotic and is still prophylatically used in so many places (such as hospitals)?</p>
| [
{
"answer_id": 34829,
"pm_score": 4,
"text": "<p>I agree with @Chris that this is mostly a matter of definitions - </p>\n\n<p>Greenfacts defines <a href=\"http://www.greenfacts.org/glossary/abc/biocide.htm\" rel=\"nofollow\"><strong>biocides</strong></a> as: </p>\n\n<blockquote>\n <p>According to the B... | [
{
"answer_id": 34828,
"pm_score": 2,
"text": "<p>I think this is mostly a semantic differentiation, when you look up definitions for antibiotics you can find very narrow which only include the classic and modern antibiotics, while others include almost everything which has an bacteriocidal (or also anti... |
34,877 | <p>In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and what defines a genetic marker?</p>
<p>There are many different KINDS of genetic markers as defined by wikipedia, RFLP, SNP and many more. But when you click these, you get a <strong>technique</strong> not a sequence. So I'm confused as to whether markers are techniques to find DNA sequences or if they are literally DNA sequences?
If they are literally DNA sequences, are they sequences that <strong>everyone</strong> has?
Example of RFLP: </p>
<blockquote>
<p>In molecular biology, restriction fragment length polymorphism, or
RFLP (commonly pronounced “rif-lip”), is a technique that exploits
variations in homologous DNA sequences.</p>
</blockquote>
| [
{
"answer_id": 34879,
"pm_score": 1,
"text": "<p>Genetic markers are sequences of DNA that tend to co-occur with some biological property, in a population.</p>\n<h3>Examples</h3>\n<p>E.g. Imagine you have 200 individuals in a population. 100 individuals have some sequence GGGCCCGGGCCC at some locus (pos... | [
{
"answer_id": 34899,
"pm_score": 2,
"text": "<p>As hello_there_andy (and also the Wikipedia page) has indicated, genetic markers are DNA sequences that can be used to distinguish individuals (can also be tissues, cells, etc.).</p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/Linkage_analysis\" rel=\"no... |
34,931 | <blockquote>
<p>One of the problems that occur during (artificial) neural network training is called overfitting. The error on the training set is driven to a very small value, but when new data is presented to the network the error is large. The network has memorized the training examples, but it has not learned to generalize to new situations.</p>
</blockquote>
<p>The human brain does not overfit when training at some task, but becomes better and better instead. Why? Or conversely, why do artificial neural networks overfit when are trained too much, in contrast with the human brain?</p>
| [
{
"answer_id": 34960,
"pm_score": 5,
"text": "<p>I would say the human brain overfits all the time! Gambling addiction, superstition and anxiety disorders are all examples of overfitting. We are optimized for seeking patterns and avoiding threats. Our brains mess this up all the time! But having said t... | [
{
"answer_id": 37033,
"pm_score": 2,
"text": "<p>Like any statistical learner, the human brain surely experiences overfitting. You can convince people of lots of things that aren't true by showing them biased examples.</p>\n\n<p>That said, don't forget that the tasks by which we judge artificial intelli... |
34,973 | <p><strong>My Background:</strong></p>
<p>I'm a mathematics graduate student with a physics background. I have a very little biology knowledge and a little knowledge of machine learning and statistics.</p>
<p><strong>Topic:</strong></p>
<p>I recently found out about the following computational biology breakthrough: A computer managed to independently develop an explanatory theory for a 120 year old problem in biology. It is detailed in the popular media <a href="http://www.wired.co.uk/news/archive/2015-06/05/computer-develops-scientific-theory-independently"><strong>here</strong></a> and <a href="http://www.popularmechanics.com/science/a15886/computer-scientific-theory/"><strong>here</strong></a> and in great detail in this <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004295"><strong>paper</strong></a>.</p>
<p><strong>Questions:</strong></p>
<p>I lack domain expertise but I'm very curious as to how this was possible and why it happened now. For example:</p>
<ul>
<li>Were these methods novel (from a machine learning perspective), or does the novelty lie in using old tools/techniques and adapting them to a
workable problem?</li>
<li>Mathematically speaking, what kind of models were produced by the computer? Are these standard in this field of genetics/biology? Is this area particularly mathematically tractable?</li>
<li>What about this particular biological problem made it amenable to this machine learning approach?</li>
<li>What other kinds of low hanging fruit (in biology or science in general) could we expect to see tackled with these techniques?</li>
</ul>
| [
{
"answer_id": 34975,
"pm_score": 5,
"text": "<p>The fruit, sadly, does not hang so low.</p>\n<h1>Short version</h1>\n<p>Lobo et al (the work you refer to) is a nice and not especially novel application of basic Systems Biology modeling approaches to the wound healing system in flat worms. The main barr... | [
{
"answer_id": 34982,
"pm_score": 4,
"text": "<p>The paper by Lobo and Levin is an attempt to learn a model that represents the inner workings of a biological system by fitting parameters to data. This is a common topic in \"systems biology\", a model-based approach to studying biology that is popular i... |
34,981 | <p>I am thinking the role of doxorubicin's pathways in cancers such as leukemia and lymphoma:</p>
<ul>
<li>topoisomerase inhibitor and inhibit DNA activity</li>
<li>intercalant - intercalant DNA bases and inhibit DNA activity</li>
</ul>
<p>I am interested in which of these mechanisms are most relevant in leukemia and lymphoma. </p>
<p>How does doxorubicin work in leukemia and lymphoma?</p>
| [
{
"answer_id": 34975,
"pm_score": 5,
"text": "<p>The fruit, sadly, does not hang so low.</p>\n<h1>Short version</h1>\n<p>Lobo et al (the work you refer to) is a nice and not especially novel application of basic Systems Biology modeling approaches to the wound healing system in flat worms. The main barr... | [
{
"answer_id": 34982,
"pm_score": 4,
"text": "<p>The paper by Lobo and Levin is an attempt to learn a model that represents the inner workings of a biological system by fitting parameters to data. This is a common topic in \"systems biology\", a model-based approach to studying biology that is popular i... |
35,007 | <p>I took an undergrad class in genetics. I felt it was not too intensive and I do not feel prepared for grad school (if I can manage to get in.) </p>
<p>Does anyone know of a preferably free resource for learning genetics? </p>
<p>I know the field is very large, but I would like to be competent in the field, considering I also want to learn more about genomics as well. And I figure one must first have a fundamental understanding of either computer science or biology to be successful in genomics, both of which I lack. </p>
| [
{
"answer_id": 35009,
"pm_score": 4,
"text": "<p>As you said, the question is pretty broad. Genetics is a big gigantic field and it is quite hard to know what you are exactly looking for. If you could refine into one of the subfields (molecular genetics, population genetics, phylogenetics, etc..) it wou... | [
{
"answer_id": 35017,
"pm_score": 3,
"text": "<p>I work at the Wellcome Trust Sanger Institute, one of the world's largest genomics centres. We do maintain a website for the public wanting to learn about genomics, but it might be a bit basic for you: <a href=\"http://www.yourgenome.org\" rel=\"noreferre... |
35,191 | <p>Trees use carbon dioxide and produce oxygen in the presence of sunlight. </p>
<p>But is there any other source? </p>
<p>If yes, are trees the most important source of oxygen, or is there any other source which produce more than trees do?</p>
| [
{
"answer_id": 35192,
"pm_score": 6,
"text": "<p><a href=\"https://www.usgs.gov/special-topics/water-science-school/science/how-much-water-there-earth\" rel=\"nofollow noreferrer\">71% of the earth's surface is taken up by water</a>. Not surprisingly therefore, the seas are an important source of oxygen... | [
{
"answer_id": 35193,
"pm_score": 3,
"text": "<p>I am not sure which class of organisms have the <strong>highest</strong> contribution in oxygen production but <a href=\"https://en.wikipedia.org/wiki/Diatom\">diatoms</a> do have a significant contribution. The introduction in <a href=\"http://www.pnas.o... |
35,242 | <p>My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am reading a review of EGF signaling (<a href="http://www.ncbi.nlm.nih.gov/pubmed/23953842" rel="nofollow">Epidermal growth factor receptor targeting in cancer: A review of trends and strategies</a> by Chetan Yewale, et. al.), and it states that "Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins." This statement makes absolutely no sense to me, and makes me question my understanding of signal transduction. I think of ligands as freely floating molecules that may eventually come into contact with the cell membrane and attach to some receptor. But a ligand expressed as an integral membrane protein? This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells). Integral membrane protein ligands would only be useful for autocrine signaling, which I don't think is true of EGF.</p>
| [
{
"answer_id": 35244,
"pm_score": 4,
"text": "<p>In biology ligand is a very broad term. Everything is called a ligand that has a receptor for it, regardless whether it is free or membrane-bound. There is very much sense in membrane bound ligands, because many cells in our body are capable of actively m... | [
{
"answer_id": 35246,
"pm_score": 3,
"text": "<p>A perfectly reasonable definition of a ligand from <a href=\"https://en.wikipedia.org/wiki/Ligand_(biochemistry)\" rel=\"nofollow noreferrer\">Wikipedia</a>:</p>\n<blockquote>\n<p>In biochemistry and pharmacology, a ligand is a substance that forms a comp... |
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