qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
60,018 | <p>I've been reading my textbook and it refers to prions as a normal protein with a helpful function but it can turn into a disease causing form. However, I look in my other textbook and it refers to the word prion as solely being a disease causing protein.</p>
<p>I'd like to know which is the correct definition. Ie. Would I be correct in saying "The prion protein is normally involved in synaptic transmission but can turn into a disease causing form"?</p>
<p>Thanks in advance!</p>
| [
{
"answer_id": 60020,
"pm_score": 6,
"text": "<p>The normal isoform of the protein is called PrP<sup>C</sup>, which stands for <em>cellular prion protein</em>, while the infectious isoform is called PrP<sup>SC</sup>, which stands for <em>scrapie prion protein</em>.</p>\n\n<p>According to Riesner (2003):... | [
{
"answer_id": 60021,
"pm_score": 2,
"text": "<p>The Wikipedia definition of prions is quite clear I think:</p>\n\n<blockquote>\n <p>Prions are infectious agents composed entirely of a protein material\n that can fold in multiple, structurally abstract ways, at least one of\n which is transmissible t... |
60,042 | <p>I teach A&P for bio non majors. I have a special needs student whose accommodation requires a word bank for any anatomy identification questions I have on the exam. I would like to present the student with a 'master wordbank' (presumably hundreds of words in length) that would act as a word bank for all the exams in the course. I'm surprised to be unable to find much of anything online. Has anyone seen something like this?</p>
| [
{
"answer_id": 60020,
"pm_score": 6,
"text": "<p>The normal isoform of the protein is called PrP<sup>C</sup>, which stands for <em>cellular prion protein</em>, while the infectious isoform is called PrP<sup>SC</sup>, which stands for <em>scrapie prion protein</em>.</p>\n\n<p>According to Riesner (2003):... | [
{
"answer_id": 60021,
"pm_score": 2,
"text": "<p>The Wikipedia definition of prions is quite clear I think:</p>\n\n<blockquote>\n <p>Prions are infectious agents composed entirely of a protein material\n that can fold in multiple, structurally abstract ways, at least one of\n which is transmissible t... |
60,626 | <p>What causes tooth decay bacteria or acids?</p>
<p>I've been told that it is a combination of both but why would bacteria eat enamel? There are much easier supplies of protein for bacteria to munch through (such as gums) and many of the elements within enamel are not needed for bacteria to respire. Is bacteria eating enamel a myth and if not why do they do it?</p>
| [
{
"answer_id": 60644,
"pm_score": 4,
"text": "<p>While I can't find any specific sources regarding <em>bacteria</em> eating enamel, I highly doubt this is what's happening in our mouths. I doubt this because your point is likely true - minerals in enamel provide no added benefit to the bacteria. I would... | [
{
"answer_id": 60630,
"pm_score": 2,
"text": "<p>Bacteria feed upon food particle left between n around the teeth and feed upon them. They also produce metabolic acid which corrodes tooth enamel.</p>\n"
},
{
"answer_id": 60756,
"pm_score": 1,
"text": "<p>The bacteria actually aren't eati... |
60,841 | <p>I know this is a very basic question, but it is not too clear to me what is the unit of measure of branch length in phylogenetic trees.
I have come to understand that it is usually expressed in number of substitutions/site/some unit of time.
What is that "some unit of time"? Generations?
Does it depend on what method of tree construction I am using (NJT, MP, ML)?</p>
<p>Thank you for your time.</p>
| [
{
"answer_id": 60872,
"pm_score": 4,
"text": "<p>When you estimate a phylogenetic tree, be it by likelihood, parsimony, or distance (like NJ), the lengths will be given in units of substitutions per site, with no time information. For example from <a href=\"http://epidemic.bio.ed.ac.uk/how_to_read_a_phy... | [
{
"answer_id": 60843,
"pm_score": 0,
"text": "<p>The length of branch indicate time in years (or whatever standard objective unit of time). It would make little sense (although one could argue that it'd be interesting to look at) to build a tree of life where time is in generation as the generation time... |
60,949 | <p>I was reading an <a href="http://www.diffen.com/difference/Crab_vs_Lobster" rel="noreferrer">article</a>, which it mentions that lobsters do not have a nervous system:</p>
<blockquote>
<p>Lobsters have very poor eyesight and no nervous system. They walk slowly
on the sea floor but are capable of swimming backwards by the curling
and uncurling movement of their abdomen.</p>
</blockquote>
<p>But in <a href="https://en.wikipedia.org/wiki/Nervous_system" rel="noreferrer">Wikipedia</a>, I read that only 3 types of multi cellular animals do not posses a nervous system:</p>
<blockquote>
<p>The only multicellular animals that have no nervous system at all are
sponges, placozoans, and mesozoans, which have very simple body plans.</p>
</blockquote>
<p>Which none of them seemed like a lobster to me. In <a href="https://biology.stackexchange.com/a/23889/31503">this</a> answer, it is claimed that every living organism feels pain somehow.</p>
<p>Now I would like to know the answers of these questions:</p>
<ol>
<li>Is the article about the lobsters true? They have no nervous system which means they feel no pain even if killed?</li>
<li>Is the claim in the answer true? Literally one of the claims must be wrong, since they conflict with each other somehow.</li>
</ol>
| [
{
"answer_id": 60977,
"pm_score": 3,
"text": "<p>Before answer, What intuitively seems: </p>\n\n<ul>\n<li><p>Lobsters structurally contains sense-organs like eye and antennae, and output organs like muscles through which they move. So plausibly these organs should be plausibly connected to its contro... | [
{
"answer_id": 60956,
"pm_score": 3,
"text": "<p>Yes they feel pain, at least in certain areas of their body without a doubt. Research has been done to test whether they feel pain consciously (a signal to the brain that is perceived allows for learned response) or if it is just a reflex response (Nocice... |
61,191 | <p>I have two questions concerning self-exciting neurons in the brain.</p>
<ol>
<li><p>Have directly self-exciting neurons been oberved, i.e. neurons with an axon terminal building a synapse with one of its own dendrites.</p></li>
<li><p>Does self-excitation work?</p></li>
</ol>
<p>I guess that self-excitation can only work when the following time constants fit to each other:</p>
<ul>
<li>refactory period of the neuron's membrane voltage (approx 1 milliseconds)</li>
<li>run time of the signal along the axon </li>
<li><a href="http://snl.salk.edu/~zador/PDF/1309.pdf" rel="nofollow noreferrer">refactory period of the synapse (approx 5-6 milliseconds)</a></li>
</ul>
<p>I tried to estimate a typical run time by taking a not untypical axon length of 1cm = 0.01m and dividing it by a typical <a href="https://en.wikipedia.org/wiki/Nerve_conduction_velocity" rel="nofollow noreferrer">nerve propagation speed</a> of 10 m/sec, getting 0.001 sec = 1 millisecond. Direct self-excitation would not work because the synapse would not be ready when the self-exciting signal arrives.</p>
<p>The other way around: Only when the run time is longer than the two refactory periods direct self-excitation might work.</p>
<p>Once again: Are there known examples of direct self-excitation in the human brain or nervous system?</p>
| [
{
"answer_id": 61202,
"pm_score": 5,
"text": "<p><strong>Short Answer</strong></p>\n\n<p>Yes, <a href=\"https://en.wikipedia.org/wiki/Autapse\" rel=\"noreferrer\">autapses</a> exist, though the role of <em>excitatory</em> autapses in particular is unclear.</p>\n\n<p><strong>Long Answer</strong></p>\n\n<... | [
{
"answer_id": 62510,
"pm_score": 2,
"text": "<p>Self excitation can also be realized via leaky ion channels causing a constant rate of depolarization. This is for example the case for the generation of the heart beat by <a href=\"https://en.wikipedia.org/wiki/Cardiac_pacemaker\" rel=\"nofollow noreferr... |
61,228 | <p>I am writing a fictional novel about an extensively genetically engineered man, unbeknownst to him, who gets into trouble on a regular basis. The man is physically large and strong, very fast (tiger-like hand speed), and he has exceptional sensibilities such as night vision, hearing and smell. The FBI gets some of his saliva from a crime scene and creates a DNA fingerprint from it. </p>
<p>My question/s is: could the technicians/scientists who perform the DNA fingerprinting procedure for the FBI be able to tell that this man is different from other humans? Would it be possible for someone to be human and have a different number of chromosomes? Does all DNA fingerprinting appear as bar codes and mean nothing until compared to a sample? </p>
<p>Please forgive my ignorance on the subject. Thank you for any input. </p>
<p>Chris </p>
| [
{
"answer_id": 61229,
"pm_score": 3,
"text": "<p><strong>Could the technicians/scientists who perform the DNA fingerprinting procedure for the FBI be able to tell that this man is different from other humans?</strong></p>\n\n<p>If by different you mean genetically engineered, it depends on whether the <... | [
{
"answer_id": 61230,
"pm_score": 2,
"text": "<p>To answer the questions separately:</p>\n\n<h3>1 - \"Could the scientists tell that this man is different from other humans?\"</h3>\n\n<p>The functional basis of DNA fingerprinting, is to use regions of DNA that are known to be highly variable between ind... |
61,329 | <p>Turns out that you can do indoor farming these days via hydroponics and specialised LED lights. My mother, who has a large garden, warns me from exploring this as a hobby. She mentions that 'plants need to sleep too' and that having a LED light on them 100% of the time might be bad for them. </p>
<p>Is there any sense in this? Is it true that plants would grow suboptimally if the sun was on them 100% of the time or would they in fact grow quicker? Is there any research on this? </p>
| [
{
"answer_id": 61331,
"pm_score": 4,
"text": "<p>The quote as phrased is a bit non-sensical really because it mostly hinges on what you define as 'sleep' or 'rest'. Plants, like most living things, including us, are far from dormant at night.</p>\n\n<p>It's true that <a href=\"https://link.springer.com/... | [
{
"answer_id": 61330,
"pm_score": 1,
"text": "<p>Yes, as long as there is light there is photosynthesis going on. The light/dark cycle allows your plants to process what they created and rest a bit. It is good for them and encourages adequate growth.</p>\n\n<p><a href=\"http://www.popsci.com/blog-networ... |
62,502 | <p><a href="http://www.bbc.co.uk/programmes/p0577kbz" rel="nofollow noreferrer">This week's podcast</a> of the BBC's Science in Action includes a section by <a href="https://twitter.com/RoryJGalloway" rel="nofollow noreferrer">Rory Galloway</a> (<code>12:20</code> to <code>18:30</code>) covering the <a href="http://www.dinosaursofchina.co.uk/" rel="nofollow noreferrer">Dinosaurs of China</a> exhibit currently hosted by <a href="http://www.wollatonhall.org.uk/" rel="nofollow noreferrer">Wollaton Hal</a> at the University of Nottingham, and includes an interview with curator <a href="https://plesiosauria.com/dr_adam_stuart_smith.php" rel="nofollow noreferrer">Dr. Adam Smith</a>.</p>
<p>The exhibit is of highly detailed dinosaur fossils from <a href="https://en.wikipedia.org/wiki/Liaoning" rel="nofollow noreferrer">Liaoning, China</a> where detailed feather structures were well preserved and have been analyzed in great detail.</p>
<p>One section caught my attention:</p>
<blockquote>
<p><strong>Rory Galloway:</strong> "The similarity between dinosaurs and birds was far more than superficial though. Eventually a branch of small, theropod dynosaurs evolved into the birds that fly around today. But curator Adam Smith says, if we concentrate on flight alone, it gets quite difficult to know exactly which branch of the dinosaurs actually became our birds."</p>
<p><strong>Adam Smith:</strong> "Flight is really important and that’s why it evolves many times. Some of the earliest flying dinosaurs, such as the microraptor actually had four wings, not two."</p>
</blockquote>
<p>The Wikipedia article on the <a href="https://en.wikipedia.org/wiki/Microraptor" rel="nofollow noreferrer">Microraptor</a> is quite long and includes a lengthy, technical discussion on just how these four wings might have been used. It seems that it is (currently) generally believed that these dinosaurs had the capability of powered flight, and that they could actually take off from the ground, rather than climb trees, jump, and simply glide.</p>
<p>This is with <em>four wings</em>.</p>
<p>There are many variety of insects with four wings and the two pair are used in a variety of different ways. But these dinosaurs are much larger, of the order of a kilogram.</p>
<p><strong>Question:</strong> Have there been any complete simulations of the mechanics of four-winged dinosaur flight, showing how the wings would have been used to take off from the ground and gain altitude? A movie or animation of the coordinated flapping of the front versus rear pair of wings would be great. These days the numerical models and computing power are within reach, but it would still be a substantial effort, so I'm not sure if this has been done yet or not.</p>
<p>I'm assuming that this is not currently believed to be the branch of dinosaur that eventually evolved into modern birds, but it's a fascinating branch nonetheless.</p>
<p><strong>below:</strong> from <a href="https://en.wikipedia.org/wiki/File:Microraptor_scale.png" rel="nofollow noreferrer">here</a>.</p>
<p><a href="https://i.stack.imgur.com/Edz3y.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Edz3y.png" alt="enter image description here" /></a></p>
| [
{
"answer_id": 62505,
"pm_score": 4,
"text": "<p>Note nowhere in the article does it mention the rear wings flapping. The rear wings do not provide lift, they are acting as control surfaces to improve stability and maneuverability. (think of the tail of a plane).earlier/proto flies have far more demand ... | [
{
"answer_id": 77725,
"pm_score": 3,
"text": "<p>There is a good attempt at a simulation of 4 winged flight of <em>Microraptor</em> on <a href=\"https://www.youtube.com/watch?v=-fyxUxGdrns\" rel=\"nofollow noreferrer\">BBC's Planet Dinosaur</a>.</p>\n\n<p>There's <a href=\"https://www.youtube.com/watch?... |
62,518 | <p>My background is in math and I know very little about biology. The few biology books that I've looked at seem to explain what is known (or what is believed), but don't really explain how we know what is known. For a specific example, when I hear that "DNA makes RNA and RNA makes protein", I would like to know things like:</p>
<ul>
<li>How do we know that DNA makes RNA?</li>
<li>How do we know that RNA makes protein?</li>
<li>How do we know that there is such a thing as "protein" in the first place and how do we know what it is?</li>
<li>How do we know that there is such a thing as RNA and how do we know what RNA is?</li>
</ul>
<p>Can you recommend any books that do a good job of explaining how we know what we know in molecular biology and genetics? </p>
| [
{
"answer_id": 62540,
"pm_score": 5,
"text": "<p>This is not my favourite book on molecular biology (Alberts is my favourite, and Lodish is the runner up), but I'd recommend <strong>The Cell, A Molecular Approach</strong>, by Geoffrey Cooper</p>\n\n<p>This book has, for every chapter, one or more boxes ... | [
{
"answer_id": 62519,
"pm_score": 3,
"text": "<p>You may want to try <strong>A History of Molecular Biology</strong> by Michel Morange, it is currently in its third edition, It will not cover everything (proteins are discovered much earlier), you are asking for a wide swath of biology, but it should get... |
62,641 | <p><a href="http://www.bbc.com/news/science-environment-40585299" rel="noreferrer">BBC News recently published an article</a> saying that:</p>
<blockquote>
<p>An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ...
The team sequenced the bacterial DNA to retrieve the gif and the image, verifying that the microbes had indeed incorporated the data as intended. </p>
</blockquote>
<p><a href="https://i.stack.imgur.com/uG4SB.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/uG4SB.jpg" alt="This is the image:"></a></p>
<p>The news article shows an image of a hand (shown above) and a short film (not shown here) of a horse rider that was encoded into the DNA <em>"using a genome editing tool known as Crispr [sic]"</em>. </p>
<p>My question is, what does this mean? Did the scientists break down an image into 0's and 1's and (install?) it into bacteria? How does a scientist (download?) an image into bacteria and then (redownload?) the image later? How does DNA hold information of a picture that can be (downloaded)?</p>
| [
{
"answer_id": 62658,
"pm_score": 5,
"text": "<p>Just to add what might have been missing in the beautiful answer by @iayork. I just want to give a more simple picture of the encoding done in the <em>E. coli</em> DNA.</p>\n\n<ul>\n<li><p>First for the <strong>rigid strategy</strong> in which 4 pixel col... | [
{
"answer_id": 62645,
"pm_score": 5,
"text": "<p>The image was not in the DNA as such, only as an abstract representation that could be converted into an image from knowledge of the code. Briefly, they encoded the image into DNA, using a couple of different strategies in which DNA represented pixels --... |
62,840 | <p>I understand that in many isolated islands, such as the Galapagos, there are no large predators. I find this observation interesting because it has been suggested that the lack of predators unleashes the evolution of new and bizarre species.</p>
<p>However, as new species evolved there (and increase their size, with respect their ancestors), why no small predator species evolved into a large predator species? Or can new predators evolve from herbivorous animals?</p>
<p>This may be a difficult question, because we may not know the natural history in such great details. More specifically, I wonder if, in general, there is some pressure against the selection of predators or if there are counter examples which show that small isolated islands evolved their own apex predator.</p>
| [
{
"answer_id": 62841,
"pm_score": 4,
"text": "<p>Larger predators need a large range on which to find potential prey. An island might be bigger than the normal range of a predator, but too small to support a large enough breeding population (because of inbreeding, and because a brief lack of food, disea... | [
{
"answer_id": 62842,
"pm_score": 2,
"text": "<p><strong>Not such a simple and clear pattern</strong></p>\n\n<p>What you are talking about is called <a href=\"https://en.wikipedia.org/wiki/Insular_dwarfism#Dwarfism_versus_gigantism\" rel=\"nofollow noreferrer\">insular dwarfism</a>. The process is not a... |
63,912 | <p>While having a dental surgery, I've got this question that why I can still talk, open/close my mouth, move my lips and so on while I can't feel anything at all in my mouth?</p>
<p>If the local anesthesia interrupts the alert that goes through brain, how is the muscle still functional? Is it some sort of one-way interruption which only disables the alert that go <em>"from"</em> the nerve <em>"to"</em> the brain? Or are there different nerves for this task?</p>
| [
{
"answer_id": 63924,
"pm_score": 4,
"text": "<p>@Nicolai's answer is not entirely correct.</p>\n\n<p><strong>Background</strong></p>\n\n<p>The most common <a href=\"https://en.wikipedia.org/wiki/Local_anesthetic\" rel=\"noreferrer\">local anesthetics</a> are all the \"-caine\" drugs - like novocaine, l... | [
{
"answer_id": 63917,
"pm_score": 1,
"text": "<p>The answer to this question boils down to 'because local anesthesia does not interrupt the nerves themselves'.</p>\n\n<p>From the <a href=\"https://en.wikipedia.org/wiki/Local_anesthetic\" rel=\"nofollow noreferrer\">wiki article</a> on local anesthetics ... |
64,057 | <p>I sneeze a lot, at various times and various "volumes", and often wonder about the speed of the sneeze itself, i.e. the speed of the air coming out of the nose while sneezing.</p>
<p>What is the average speed of that, in humans? Are there any records for such a thing?</p>
| [
{
"answer_id": 64062,
"pm_score": 5,
"text": "<p>Mainstream understanding is that a sneeze is 100 mph, or ~45 m/s. However, this isn't even close to being true..</p>\n\n<p>A study in 2013 (see link below) was conducted where they investigated the airflow dynamics of sneezing and breathing, and discovere... | [
{
"answer_id": 64060,
"pm_score": 3,
"text": "<h2>About 35-40mph</h2>\n\n<p>According to the <a href=\"http://www.discovery.com/tv-shows/mythbusters/mythbusters-database/sneeze-travel-100-mph/\" rel=\"noreferrer\">Mythbursters</a> who subjected this to their tests showed that their own sneezes went arou... |
64,059 | <p>Humans have the tendency to get <a href="https://en.wikipedia.org/wiki/Kuru_(disease)" rel="nofollow noreferrer">certain prion diseases</a> when eating human flesh. It's known animals can get <a href="https://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy" rel="nofollow noreferrer">prion diseases</a> as well.</p>
<p>Does cannibalism among other animal species also make them more susceptible to get a prion disease, and are there distinctions between mammals doing so and other orders like reptiles, birds, fish etc.?</p>
| [
{
"answer_id": 64258,
"pm_score": 3,
"text": "<p>It is perhaps worth looking into more historically established prion diseases in noncarnivorous animals, like sheep. If prion diseases were <em>only</em> transmitted by consuming prion-rich brain tissue, then they should be extremely rare (produced via un... | [
{
"answer_id": 64065,
"pm_score": 2,
"text": "<p>An individual (animal or human) acquires a prion disease when they consume meat that contains prions (proteins that are mishapen enough to drastically change their functionality), which subsequently causes proteins within the individual to misfold into th... |
64,087 | <p>Here is my confusion: we can see colored light of different wavelengths: form red to violet. To my understanding, these stimuli cause a confirmational change in the photoreceptors in our eyes and results in a STP that eventually leads to an "all or nothing" action potential that sends another signal, again an all or nothing action potential through the optic chiasm to the occipital lobe and we perceive the colors as we see them. </p>
<p>My question is <strong>*how does this signaling work? *</strong>; How can a minor stimulus, resulting in an "all or nothing" chain of action potentials be converted into something as specific as the vision of color? </p>
<p><strong><em>Asked another way, how does variation in a confirmational change at a receptor that results in "all or nothing" signaling lead to specific signals being sent such as colored vision ?</em></strong></p>
<p>PS: I dont know jack about sensory physiology </p>
| [
{
"answer_id": 64088,
"pm_score": 4,
"text": "<p><strong>Short answer</strong><br>\nAction potentials generated to different colors are indeed similar throughout the nervous system and do not encode color as such. Instead, the different color- sensitive cells in the retina are connected to different neu... | [
{
"answer_id": 64097,
"pm_score": -1,
"text": "<blockquote>\n <p>How can a minor stimulus, resulting in an \"all or nothing\" chain of action potentials be converted into something as specific as the vision of color?</p>\n</blockquote>\n\n<p>Visual phototransduction is the one of answers to your questi... |
64,203 | <p>If I understand this correctly during interphase most of the DNA strand is tightly wound around histones in the form of nucleosomes, to conserve space in the nucleus. Yet RNA polymerase in order to work needs a part of DNA to be temporarily unwound. How does the polymerase find the particular part of the DNA (and especially the promoter for a gene coding the protein needed to be synthesised) in this mass of tightly wound DNA?</p>
| [
{
"answer_id": 64398,
"pm_score": 3,
"text": "<p>This answer will be a very broad overview and is based largely on information from the textbook <em>\"Molecular Biology of the Gene\"</em> by Watson et al. (which I highly recommend). </p>\n\n<p><strong>Nucleosomes are dynamic structures.</strong></p>\n\n... | [
{
"answer_id": 64362,
"pm_score": 0,
"text": "<p>Nucleosome is a structure formed when negatively charged DNA is wrapped around positively charged histone octamer. \nNow, for transcription only one strand of DNA is copied to RNA having polarity 3'-->5' known as Template strand, the other strand known a... |
64,207 | <p>Weismann conducted the experiment — <a href="https://en.wikipedia.org/wiki/August_Weismann" rel="noreferrer">described in Wikipedia</a> — of removing the tails of 68 white mice, repeatedly over 5 generations, and reporting that no mice were born in consequence without a tail or even with a shorter tail. This was intended to refute the <a href="https://en.wikipedia.org/wiki/Lamarckism" rel="noreferrer">Lamarckian</a> idea of of acquired characteristics.</p>
<p>However, surely <em>five generations is too short a time to observe a change in an organ</em> when the fossil record indicates that such changes in animals took millions of years. Was this not known at the time and does it invalidate the experiments?</p>
| [
{
"answer_id": 64210,
"pm_score": 5,
"text": "<p><em>If you are reading this after 31st July 2017 it will seem somewhat disconnected from the question. This is because the question has been extensively edited since I wrote this answer.</em></p>\n<hr>\n<p>Anyone who is interested in the work of <a href=\... | [
{
"answer_id": 64209,
"pm_score": 2,
"text": "<blockquote>\n <p>[D]oesn't it take around millions of years for an organ to disappear or appear</p>\n</blockquote>\n\n<p>No, not necessarily. But whether this claim is true or not is not so much the point of your question.</p>\n\n<p><strong>False Negative ... |
64,220 | <p>When one's stomach contents enter one's esophagus, a burning sensation usually ensues. Is this from the enzyme pepsin breaking apart your cells or just from the acid?</p>
| [
{
"answer_id": 64210,
"pm_score": 5,
"text": "<p><em>If you are reading this after 31st July 2017 it will seem somewhat disconnected from the question. This is because the question has been extensively edited since I wrote this answer.</em></p>\n<hr>\n<p>Anyone who is interested in the work of <a href=\... | [
{
"answer_id": 64209,
"pm_score": 2,
"text": "<blockquote>\n <p>[D]oesn't it take around millions of years for an organ to disappear or appear</p>\n</blockquote>\n\n<p>No, not necessarily. But whether this claim is true or not is not so much the point of your question.</p>\n\n<p><strong>False Negative ... |
64,373 | <p>I was always told that when the human ear goes deaf to a specific sound (auditory frequency), then that sound is heard one last time, and upon fading away, will never be able to be heard again. </p>
<p>Is this in fact true? If so, why do we hear that sound (which seems to happen randomly and is somewhat loud for a split second) just before the ear becomes deaf to it? </p>
<p>Ultimately speaking, what exactly happens as the human ear <em>naturally</em> goes deaf?</p>
| [
{
"answer_id": 64720,
"pm_score": 3,
"text": "<p>I don't think you will hear the frequency \"one last time\", before it fades away. More likely you will slowly lose your range of hearing from high to low frequency.</p>\n\n<p><a href=\"https://www.youtube.com/watch?v=1JE8WduJKV4\" rel=\"nofollow noreferr... | [
{
"answer_id": 64577,
"pm_score": 2,
"text": "<p>Hearing loss is caused by different things, but your probably thinking of age-related hearing loss.</p>\n\n<p>When people go deaf, it is be because \"hair cells\" in the ear break.</p>\n\n<p>This breakage results from overly loud frequencies, or just rand... |
64,443 | <p>I have unfortunately just skimmed through the recent open access paper <a href="https://www.nature.com/articles/s41598-017-06055-9" rel="nofollow noreferrer">Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species</a> (M. Cardinale et al. Scientific Reports 7, Article number: 5791 (2017) doi:10.1038/s41598-017-06055-9)</p>
<p>It reports an extensive analysis of a group of kitchen sponge specimines. From the abstract:</p>
<blockquote>
<p>Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH–CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm–like structures occurred. Image analysis showed local densities of up to 5.4 * 1010 cells per cm3, and confirmed the dominance of Gammaproteobacteria. <strong>Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.</strong> (emphasis added)</p>
</blockquote>
<p>A quick take-home message from the paper is that typical efforts to try to re-sanitize used sponges may only shift the sponges bacterial population toward a more potentially pathogenic population, and that it is probably a better idea to simply dispose of the sponge perhaps weekly and get a fresh one instead of microwaving it.</p>
<p>There's a nice write-up in the NYTimes science section, <a href="https://www.nytimes.com/2017/08/04/science/sponges-bacteria-microwaving-cleaning.html" rel="nofollow noreferrer">Cleaning a Dirty Sponge Only Helps Its Worst Bacteria, Study Says</a>:</p>
<blockquote>
<p>Stop. Drop the sponge and step away from the microwave.</p>
<p>That squishy cleaning apparatus is a microscopic universe, teeming with countless bacteria. Some people may think that microwaving a sponge kills its tiny residents, but they are only partly right. It may nuke the weak ones, but the strongest, smelliest and potentially pathogenic bacteria will survive.</p>
<p>Then, they will reproduce and occupy the vacant real estate of the dead. And your sponge will just be stinkier and nastier and you may come to regret having not just tossed it, suggests a study published last month in <a href="https://www.nature.com/articles/s41598-017-06055-9" rel="nofollow noreferrer">Scientific Reports</a>.</p>
</blockquote>
<p>Personally I've always hated the whole concept of kitchen sponges and now feel vindicated. Isn't something that can trap biomatter (bacteria, food particles) and keep it moist for extended periods of time the antithesis of what you would want to clean your dishes with?</p>
<p><strong>Question:</strong> Aren't sponges simply a bad idea for washing dishes in the first place?</p>
<p>I'm not looking for opinion, rather I'm asking about <em>policy and practice</em>. Since what we do in the privacy of our own kitchen sink is our own, I'd like to ask if kitchen sponges are generally approved for use in restaurants or institutional food preparation settings? Do they have sterilization protocols? Does this paper speak to those?</p>
<hr />
<p><strong>Background:</strong></p>
<p><a href="https://i.stack.imgur.com/APVic.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/APVic.jpg" alt="enter image description here" /></a></p>
<p><strong>above:</strong> "(A) Kitchen sponges, due to their porous nature (evident under the binocular; (B)) and water-soaking capacity, represent ideal incubators for microorganisms. Scale bar (B): 1 mm. (C) Pie charts showing the taxonomic composition of the bacterial kitchen sponge microbiome, as delivered by pyrosequencing of 16S rRNA gene libraries of 28 sponge samples (top and bottom samples of 14 sponges, respectively). For better readability, only the 20 most abundant orders and families are listed." From <a href="https://www.nature.com/articles/s41598-017-06055-9" rel="nofollow noreferrer">here</a>.</p>
<p><a href="https://i.stack.imgur.com/YnJh3.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/YnJh3.jpg" alt="enter image description here" /></a></p>
<p><strong>above:</strong> "Neighbor-joining phylogenetic tree of the ten most abundant OTUs in the analyzed kitchen sponges, as retrieved by pyrosequencing of 16S rRNA gene amplicon libraries. The relative abundance (percentage of the total sequence dataset) and the detection frequency (number of sponges where they were detected) are given in parenthesis after the OTU number. The most similar reference sequences retrieved by BLAST and EzTaxon alignment (type strains only) were included in the tree, followed by the corresponding accession numbers. Red circles indicate risk group 2 organisms, according to the German Technical Rule for Biological Agents No. 466 (TRBA 46631). Numbers at the nodes indicate percentage values of 1000 bootstrap re–samplings (only percentages ≥ 50 are shown). Scale bar represents substitution rate per nucleotide position." From <a href="https://www.nature.com/articles/s41598-017-06055-9" rel="nofollow noreferrer">here</a>.</p>
| [
{
"answer_id": 64461,
"pm_score": 3,
"text": "<p>If your question is, indeed,</p>\n\n<blockquote>\n <p>I'm asking about the nature of sponges, and if it's a good idea to use them to wash dishes and I'd like to stay focused on that.</p>\n</blockquote>\n\n<p>I can answer that.</p>\n\n<p>I like the sponge... | [
{
"answer_id": 64447,
"pm_score": -1,
"text": "<p>The best solution is to keep the bacteria in an incredibly hostile environment to prevent bacterial growth in the first place rather than letting the sponges rot and re-sanitizing them after the fact. Additionally, keep unused sponges in a container of a... |
64,484 | <p>Do foods like spicy peppers have less bacteria on their interior due to their capsaicin content? Probably not, but it seems like they could. Or I guess in other words: does capcaicin provide any benefit from anti-bacterial properties? </p>
| [
{
"answer_id": 64521,
"pm_score": 4,
"text": "<p>In 2014, a <a href=\"https://www.omicsonline.org/open-access/antimicrobial-properties-of-chili-peppers-2332-0877.1000145.pdf\" rel=\"noreferrer\">review article</a> was pushlished by the Department of Food Science and Nutrition at the University of Minnes... | [
{
"answer_id": 64508,
"pm_score": 0,
"text": "<p>Yes it has some bacteriostasis and antibacterial properties, The only way for you to find it is to do some Agar and similar tests on chillis to find out about their microbes. You will probably find that some chillis have zero bacteria inside them, and tha... |
64,537 | <p>What could be the cause of these white strings on the leaves of our sour cherry tree? Is it some kind of fungus or an insect?
<a href="https://i.stack.imgur.com/WGZVI.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/WGZVI.jpg" alt="Strings1"></a>
<a href="https://i.stack.imgur.com/pHqvu.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/pHqvu.jpg" alt="Strings2"></a></p>
<p>Also, i don't know if it's related or not, but on the other side of the tree brown spots started to appear also on the leaves:
<a href="https://i.stack.imgur.com/2zCc5.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/2zCc5.jpg" alt="Spots"></a></p>
<p>I live in Hungary, if the climate is relevant.</p>
| [
{
"answer_id": 64544,
"pm_score": 3,
"text": "<p>The picture is too blurry for an exact determination.\nFrom what I see it might be <em><a href=\"https://en.wikipedia.org/wiki/Metcalfa_pruinosa\" rel=\"nofollow noreferrer\">Metcalfa pruinosa</a></em> or a related species, which is an insect of the order... | [
{
"answer_id": 64540,
"pm_score": 2,
"text": "<p>This sort of thing happened to one of my plants. When I took a closer look at the plant, it was a group of white aphids. The brown coloration of the leaves of your cherry tree was relevant because aphids can sometimes kill the entire plant that they fee... |
64,719 | <p>Is there any API where I can input chromosome location and it will provide us gene names, for example input chr: 1 location 154714693:154754070 and it will return a list of gene names or ID within this region? </p>
| [
{
"answer_id": 64725,
"pm_score": 3,
"text": "<p>With R biomaRt you can retrieve them.</p>\n\n<blockquote>\n <p>library(biomaRt)</p>\n \n <p>ensembl = useMart(\"ensembl\",dataset=\"hsapiens_gene_ensembl\")</p>\n \n <p>filterlist <- list(\"1:154714693:154754070\",\"protein_coding\")</p>\n \n <p... | [
{
"answer_id": 64726,
"pm_score": 0,
"text": "<p>The NCBI as an API called 'E-utilities' (see <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK25499\" rel=\"nofollow noreferrer\">short intro</a>) that allows access to almost all their databases. It's a bit tricky to get used to it (and sometimes it wants... |
64,735 | <p>DNA is known to have a double-helical structure. Do any other molecules have this structure?</p>
| [
{
"answer_id": 64738,
"pm_score": 7,
"text": "<p>A few examples:</p>\n<hr />\n<h2><a href=\"https://en.wikipedia.org/wiki/Starch\" rel=\"noreferrer\">Starch</a></h2>\n<p>A polymer of glucose that can form a double helix and functions primarily as energy storage in plants.</p>\n<p><a href=\"https://i.sta... | [
{
"answer_id": 64736,
"pm_score": 4,
"text": "<p>Yes, <a href=\"https://en.wikipedia.org/wiki/RNA#Double-stranded_RNA\" rel=\"noreferrer\">double-stranded RNA</a> as found in <a href=\"https://en.wikipedia.org/wiki/Double-stranded_RNA_viruses\" rel=\"noreferrer\">some viruses</a>.</p>\n"
},
{
"a... |
64,743 | <p>It has always been said that sexual reproduction produces offsprings which are superior to their parents, due to the variations which they acquire causing them to survive better in their environment. That's because we can think of meiosis occurring at some level of their life cycle resulting in the variations in the final offspring.
But what when we talk about bisexual organisms, might they be plants, animals or any other life form? Can't there be variations in their offsprings if they produce them asexually? It's like when they undergo gamete formation in different male and female structure present in that single parent, they'll surely undergo meiosis(if the parent is not haploid undoubtedly) forming the gametes which are dissimilar in their genetic makeup. When these fertilize, shouldn't they show variations?</p>
| [
{
"answer_id": 64738,
"pm_score": 7,
"text": "<p>A few examples:</p>\n<hr />\n<h2><a href=\"https://en.wikipedia.org/wiki/Starch\" rel=\"noreferrer\">Starch</a></h2>\n<p>A polymer of glucose that can form a double helix and functions primarily as energy storage in plants.</p>\n<p><a href=\"https://i.sta... | [
{
"answer_id": 64736,
"pm_score": 4,
"text": "<p>Yes, <a href=\"https://en.wikipedia.org/wiki/RNA#Double-stranded_RNA\" rel=\"noreferrer\">double-stranded RNA</a> as found in <a href=\"https://en.wikipedia.org/wiki/Double-stranded_RNA_viruses\" rel=\"noreferrer\">some viruses</a>.</p>\n"
},
{
"a... |
65,015 | <p>At school, we've been taught that human infants produce rennin/chymosin (which aids in the digestion of milk). More specifically, it is the peptic cells in the stomach which secrete <em>prorennin</em>, the inactive form of rennin (in addition to <em>pepsinogen</em>, the pepsin proenzyme).</p>
<p>User @another'homosapien's answer <a href="https://biology.stackexchange.com/questions/57531/what-inactivates-pepsin-in-infants">here</a> also seems to concur with this (excellent answer by the way, I enjoyed reading it).</p>
<p><strong>However</strong></p>
<p>According to Mod. @AliceD's answer <a href="https://biology.stackexchange.com/questions/57472/digestion-of-milk-in-humans/57862#57862">here</a> (yet another excellent answer):</p>
<blockquote>
<p>...in humans there is only a chymosin pseudogene present...</p>
</blockquote>
<p>Which (probably?) implies that humans (infant or otherwise) do <strong>not</strong> produce rennin.</p>
<p>I managed to get my hands on the <em>Textbook of Medical Physiology</em> (Guyton and Hall, South-Asian edition), and according to the book (Chapter <em>Gastric secretions</em>, page 406) peptic cells produce a large quantity of pepsinogen. There is, however, <strong>no mention</strong> of prorennin. I even flipped over to the <em>Appendix</em> at the back to look up "Rennin", but it turns out there is absolutely no mention of rennin in the book.</p>
<hr>
<p>My questions,</p>
<ul>
<li><p>Some sources claim that rennin <strong>is</strong> produced in human (infants). Is this true?</p></li>
<li><p>Other sources claim that rennin is <strong>not</strong> produced in humans ( we have a pseudogene for it though). Is this correct (I mean the "rennin-is-not-produced" bit, not the "pseudogene" bit)?</p></li>
<li><p><em>If</em> rennin <strong>is</strong> produced in humans only during infancy, what stops it from being produced as we mature? (I'm asking this because every source I've seen that claims that rennin is produced in humans, explicitly states that is done so during infancy...which would suggest that rennin is not produced in adults)</p></li>
</ul>
| [
{
"answer_id": 65017,
"pm_score": 4,
"text": "<p>Scanning various reviews it seems that everyone who mentions the possibility of a human chymosin refers to a single paper. So for example <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988022/pdf/nihms547796.pdf\" rel=\"noreferrer\">this 2014 rev... | [
{
"answer_id": 65016,
"pm_score": 3,
"text": "<p>I think the answer is really that is isn't clear, though I only searched a bit and found mostly old papers.</p>\n\n<p>It seems like people have found immunoreactivity to anti-rennin antibodies in human infants, but that doesn't necessarly mean rennin is p... |
65,174 | <p>To clarify at first, I have very little knowledge in biology and paleontology so there might be very obvious things I overlook.</p>
<p>According to the evolution theory, there must be a graduate evolution process over millions of years such that the skull and the horns of the Triceratops gradually appear over time. However why there is no fossil record of such "intermediate" form between Triceratops and earlier dinosaurs? I mean there must be some intermediate dinosaurs that has a short skull that almost looks like a small mountain on the neck and very short horns. However based on my internet search I can't find any information that confirms existence of such intermediate dinosaurs. </p>
<p>I just want to know is there any such evidence of graduate evolution among paleontologists or the evolution of dinosaurs is still much based on speculation (without firm evidence)?</p>
| [
{
"answer_id": 65184,
"pm_score": 5,
"text": "<p>Yes, there are many early examples of ceratopsians before Triceratops. The oldest clear member of the lineage is <a href=\"https://www.nature.com/news/2002/020321/full/news020318-5.html\" rel=\"noreferrer\">Liaoceratops</a>: \"the oldest ceratopsian ever ... | [
{
"answer_id": 74568,
"pm_score": 0,
"text": "<p>If you are looking to a more recent evolution of Triceratops you can follow the cladogram to the subfamily Chasmosaurinae and then to the tribe Triceratopsini. You'll find there Eotriceratops, which looks very much like a bigger Triceratops and might has ... |
65,275 | <p>I have come across many articles stating that female mosquitoes suck blood from vertebrate hosts to develop their eggs. Some also state that they need proteins, carbohydrates, iron etc., from human blood. But none of them (as far as I know) have stated what components exactly are needed from blood for their egg development. If proteins, what kind of proteins? </p>
| [
{
"answer_id": 65276,
"pm_score": 4,
"text": "<p>According to the Introduction to <a href=\"http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122716\" rel=\"nofollow noreferrer\">this paper</a>:</p>\n\n<blockquote>\n <p>Attractiveness to biting insects is important in medical contexts, ... | [
{
"answer_id": 65309,
"pm_score": 1,
"text": "<p>Mosquitoes generally feed on plant nectar and fruit juice. Male mosquitoes do not take blood, so when you feel a mosquito plunge into your skin and start siphoning your blood, you can bet it is a female, every time.\nfemale mosquitoes need nectar for nour... |
65,342 | <p>Pages I've read about worms' respiratory systems says that the skin needs to be wet (covered in mucus) or oxygen won't diffuse across the skin. Why? If there is more oxygen outside the worm's skin than inside, what prevents it from diffusing across the skin, even if the skin is dried out?</p>
| [
{
"answer_id": 71799,
"pm_score": 3,
"text": "<p><strong>The quick answer</strong>: When the skin dries, the lipids in the cell membranes of the skin tissue undergo a phase transition which makes the membranes less permeable for oxygen.</p>\n\n<p><strong>Explanation</strong>: The lipids of the cell memb... | [
{
"answer_id": 65459,
"pm_score": -1,
"text": "<p>Respiration in aquatic organisms involves diffusion of dissolved gases present in the aquatic medium across their permeable cell membrane . In worms which lives in moist environment the skin functions as a respiratory surface and requires the surface to ... |
65,409 | <p>Generally, viruses are infectious in nature and there are several cancer-causing viruses that are known (i.e. <a href="https://en.wikipedia.org/wiki/Oncovirus" rel="nofollow noreferrer">oncovirus</a>)</p>
<p>My question is:
<em>Are these oncoviruses infectious in nature? If so, what is the way in which they can be transmitted?</em></p>
<p>(<strong>edit</strong>:<em>just a background to connect the title and the question</em> (as mentioned by user iayork):While reading my text(which led me to the doubt) I was considering the virus as a causal organism and the disease as cancer(malignant tumour cells).The cancer cells are non-contagious however I wanted to understand if the disease was.Thus I was interested on the routes of the transmission of the viruses.Also note (which I had already asked user Chris in the comment) <em>"most cancer disease are non contagious but if cancer disease was due to virus if it was contagious or not"</em></p>
| [
{
"answer_id": 65414,
"pm_score": 5,
"text": "<p>The question title and the question itself ask two slightly (but critically) different questions. </p>\n\n<ul>\n<li>Can cancers caused due to viruses be contagious? <strong>NO</strong></li>\n<li>Are these oncoviruses infectious in nature? <strong>YES</str... | [
{
"answer_id": 65410,
"pm_score": 4,
"text": "<p>Yes, Oncoviruses are infectious in nature. A good example is the <a href=\"https://en.wikipedia.org/wiki/Human_papillomavirus_infection\" rel=\"noreferrer\">Human Papilloma Virus</a>, which does not immediately cause cancer, but can cause precancerous les... |
65,417 | <p>In glycolysis, glucose is converted to glucose 6-phosphate so it can not diffuse out of the membrane. Then it is converted to fructose 6-phosphate. </p>
<p>Why is this? Perhaps it makes it less stable so it is easier to break down into pyruvate? </p>
<p>That is just a guess, is anyone able to provide more information about this?</p>
| [
{
"answer_id": 65611,
"pm_score": 1,
"text": "<p><strong>Clarifying the question</strong></p>\n\n<p>The pathway of glycolysis starts a hexose (glucose), but at a certain point — the aldolase reaction — two molecules of a triose are generated, then interconverted to the same triose, after which the pathw... | [
{
"answer_id": 65421,
"pm_score": 3,
"text": "<p>Avoiding diffusion is one reason to phosphorylate glucose, the other is that it is removed from the osmotic balance between inside and outside of the membrane, so it can be transported at a high rate.</p>\n\n<p>The <a href=\"https://en.wikipedia.org/wiki/... |
65,423 | <p>In our school textbook, it is written that sometime forest fires can occur due to rubbing of two horsetails. In the image that I searched online, the plant itself looks thin and rod like with leaflike structures arising from nodes. But many other plants have similar structure. So it might not be its morphology. </p>
<p>What special thing about horsetail starts the fire? Why don't other plants show same thing?</p>
| [
{
"answer_id": 65426,
"pm_score": 3,
"text": "<p>I didn't believe this was a real thing, and I'm still very skeptical, but it is something that's claimed to happen!</p>\n\n<blockquote>\n <p>Their stems & leaves have a siliceous epidermis, so if rubbing b/n 2 horsetails occurs, a forest fire may be ... | [
{
"answer_id": 69870,
"pm_score": 0,
"text": "<p>Could be that horsetails, as primitive plants, in certain soils, accumulate and concentrate atoms (hyperaccumulators) and just like certain minerals that spark or certain compounds that flare when dry, are source of ignition ie <a href=\"https://en.wikipe... |
65,671 | <p>Why do retroviruses (e.g.HIV) convert their RNA genome to DNA (using reverse transcriptase) and then transcribe it back into viral RNA (and translate that into viral proteins). Surely to replicate their genome it would be simpler to use RNA-dependent RNA polymerases as RNA viruses like Measles Virus do.</p>
| [
{
"answer_id": 65702,
"pm_score": 3,
"text": "<p>I am going to focus the answer on mainly \"why HIV virus has evolved such mechanisms to go from RNA to DNA and back to RNA when it could simply use the first RNA to make its copies\". While others have already discussed the broad point, I will discuss mor... | [
{
"answer_id": 65699,
"pm_score": 1,
"text": "<p>Viruses are one of the particles whose evolutionary origin is still a mystery to scientists. Various hypotheses have been presented but none of them have been proven so far.</p>\n\n<p>However, as one of our commenters has said, \"What works, works and wha... |
65,691 | <p>It is common when analyzing paired-end whole-genome shotgun sequencing data to check for and eliminate PCR duplicates. The reasoning is that the probability of sampling a fragment of the genome of the same exact length from the same exact position in the genome multiple times is <em>extremely</em> low. Therefore, if you see multiple read pairs with the same exact sequence in both pairs, these don't represent independent events but are multiple copies of the same event.</p>
<p>My question is whether PCR duplicates can be reverse complements of each other. All the PCR duplicates I've observed myself have been exactly the same sequence on exactly the same strand. Is there a technical reason why this is the case, or is it possible that PCR duplicates could not be on the same strand as each other?</p>
| [
{
"answer_id": 65702,
"pm_score": 3,
"text": "<p>I am going to focus the answer on mainly \"why HIV virus has evolved such mechanisms to go from RNA to DNA and back to RNA when it could simply use the first RNA to make its copies\". While others have already discussed the broad point, I will discuss mor... | [
{
"answer_id": 65699,
"pm_score": 1,
"text": "<p>Viruses are one of the particles whose evolutionary origin is still a mystery to scientists. Various hypotheses have been presented but none of them have been proven so far.</p>\n\n<p>However, as one of our commenters has said, \"What works, works and wha... |
65,743 | <p>In this <a href="https://www.youtube.com/watch?v=DP53WAkQ5Yc" rel="nofollow noreferrer">video</a> Richard Dawkins talk about intermediate fossils. He describes how the whales were evolved from a common ancestor who lived on land.</p>
<p>But his theory sounds more like a devolution. I thought evolution was coming from the sea to the land and then to the skies. Are there more examples where species evolve back and forth between the ocean and land or skies?</p>
<p><a href="https://i.stack.imgur.com/bo08R.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/bo08R.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 65747,
"pm_score": 3,
"text": "<blockquote>\n <p>Does evolution go only in one direction?</p>\n</blockquote>\n\n<p>No, it does not. There is no such thing as a goal of evolution at making things fly or at making things intelligent or whatever. There is no intrinsic directionality.</p>\n\... | [
{
"answer_id": 65750,
"pm_score": -1,
"text": "<p>Evolution helps an organism to be successful in the environment in which it lives. In this case, the organism evolved to suit it's aquatic environment. So there's nothing called devolution. For example, the cave proteus is blind while it's ancestors wer... |
65,759 | <p>I know, this question is opinion-based, but where else should I ask it (or how could I ask it <em>here</em> without being flagged "opinon-based!")?</p>
<p>Which neuronal simulators - in the line of <a href="https://www.neuron.yale.edu/neuron/" rel="nofollow noreferrer">NEURON</a> and <a href="http://www.genesis-sim.org/" rel="nofollow noreferrer">GENESIS</a> - are the "best", "mostly used", "mostly influential" today, not only in supercomputing, but also for small scale (personal) use?</p>
<p>The one I found best - even though designed for large scale applications - for my small scale (personal) requirements was <a href="http://www.nest-simulator.org/" rel="nofollow noreferrer">nest</a>, an explicit successor of NEURON. I have the impression, that <strong>nest</strong> is "better" for me than NEURON, in terms of usability, visualization, <a href="https://en.wikipedia.org/wiki/Data_exploration" rel="nofollow noreferrer">data exploration</a>, ... but I don't know if there aren't even better neuro-simulation tools.</p>
<p>Would anyone mind giving his/her opinion?</p>
| [
{
"answer_id": 65747,
"pm_score": 3,
"text": "<blockquote>\n <p>Does evolution go only in one direction?</p>\n</blockquote>\n\n<p>No, it does not. There is no such thing as a goal of evolution at making things fly or at making things intelligent or whatever. There is no intrinsic directionality.</p>\n\... | [
{
"answer_id": 65750,
"pm_score": -1,
"text": "<p>Evolution helps an organism to be successful in the environment in which it lives. In this case, the organism evolved to suit it's aquatic environment. So there's nothing called devolution. For example, the cave proteus is blind while it's ancestors wer... |
66,129 | <p>I recently watched this video which showed the evolution of facial features of the modern man
<a href="https://youtu.be/-69K7E0UlBI" rel="noreferrer">https://youtu.be/-69K7E0UlBI</a></p>
<p>I'm wondering what evolutionary advantage did we get by having our face from this-
<a href="https://i.stack.imgur.com/0h26c.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/0h26c.jpg" alt="Australopithecus"></a>
(reconstruction of the face of <em>Australopithecus</em>)</p>
<p>To this-
<a href="https://i.stack.imgur.com/PZwUQ.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/PZwUQ.jpg" alt="modern man"></a>
(<em>Homo sapien sapien</em>)</p>
<p>"<strong>In other words for what advantage did nature selected our present face?</strong>"</p>
| [
{
"answer_id": 66134,
"pm_score": 3,
"text": "<p>There are many things going into the evolution of our face. It is not as simple as discussing a single trait. Your question is therefore quite broad. So I will just pick up three different traits and talk a little bit about them. Those traits are</p>\n<ul... | [
{
"answer_id": 66164,
"pm_score": 1,
"text": "<p>The most unusual features of the human face on a purely visual basis is our nose and our chin.</p>\n\n<p>OUr chin has been hotly debated I know of no less than five separate hypothesis about its development. The <a href=\"http://journals.plos.org/plosone/... |
66,144 | <p><strong>Background</strong></p>
<p>The claim ...</p>
<blockquote>
<p>Most of the genetic diversity in humans is in Africa</p>
</blockquote>
<p>... is quite common. On Biology.SE, it is easy to find posts that make this claim. Consider for example:</p>
<ul>
<li><a href="https://biology.stackexchange.com/questions/14414/do-humans-have-enough-biological-differences-to-be-grouped-into-races-or-subspec/14419#14419">Do humans have enough biological differences to be grouped into races or subspecies?</a></li>
<li><a href="https://biology.stackexchange.com/questions/36241/how-do-we-know-the-human-species-arose-in-africa/36248#36248">How do we know the human species arose in Africa?</a></li>
<li><a href="https://biology.stackexchange.com/questions/65484/what-is-the-correct-classification-of-population-groups-of-homo-sapiens/65486#65486">What is the correct classification of population groups of homo sapiens?</a></li>
</ul>
<p><strong>Question</strong></p>
<ul>
<li>Is the claim true?</li>
<li>What fraction of the total genetic diversity is present in Africa?</li>
</ul>
<p>I understand that the term genetic diversity is often used in a vague sense. Please make sure to explain what statistics has been considered in the study you would refer to when giving estimates of what fraction of the genetic diversity is found in Africa. Note that I am not asking "why is it true?" but only "is it true"?</p>
| [
{
"answer_id": 66240,
"pm_score": 4,
"text": "<p>Here is a tree based on mitochondrial DNA variations in human populations.</p>\n\n<p><a href=\"http://onlinelibrary.wiley.com/doi/10.1002/humu.20921/epdf\" rel=\"noreferrer\">van Oven M, Kayser M. Hum Mutat. 2009 Feb;30(2):E386-94. \nUpdated comprehensiv... | [
{
"answer_id": 66234,
"pm_score": 3,
"text": "<p>I've found two papers that provide some information on this, but no definitive answer. </p>\n\n<p><a href=\"https://www.nature.com/nature/journal/v526/n7571/full/nature15393.html\" rel=\"noreferrer\">The 1000 Genomes Project Consortium (2015)</a> analysed... |
66,343 | <p>Our molecular biology teacher told us that a double helix of DNA was composed of <strong>two</strong> DNA molecules linked together by hydrogen bonds. The thing is, until now, I always thought a DNA molecule was composed of two strands, those being polynucleotides, both of them being linked together. I can't find a link which is saying the same as my teacher, even if it seems technically correct to call a double helix a dimer of two DNA molecules.</p>
<p>I was curious to know what was the exact terminology.</p>
| [
{
"answer_id": 66348,
"pm_score": 3,
"text": "<p><em>As you pointed out, though this may be basic biology, seeking clarification when receiving conflicting information is a good thing. Don't feel embarrassed for asking. :)</em></p>\n\n<hr>\n\n<blockquote>\n <p>.. our molecular biology teacher told us t... | [
{
"answer_id": 66351,
"pm_score": 4,
"text": "<p>Hmm, I think that the teacher is actually correct and that the previous explanation, although very nicely referring to text book diagrams, is a little misleading. </p>\n\n<p>The issue here is the nature of a hydrogen bond within the DNA structure. Within ... |
66,829 | <p>From <a href="https://en.wikipedia.org/wiki/Vitamin" rel="noreferrer">wikipedia</a></p>
<blockquote>
<p>A vitamin is an organic compound and an essential nutrient that an organism requires in limited amounts.</p>
</blockquote>
<p>There are many essential nutrients to an organism. Glucose for example. However, not all of them are classified as vitamins. Is there a clear, non-arbitrary definition of vitamin? If not, who decide what ought to be called a vitamin?</p>
| [
{
"answer_id": 66831,
"pm_score": 4,
"text": "<p>1) Vitamin D is a bit of an umbrella term that actually refers to a whole group of related molecules. One of these, vitamin D$_3$ (<a href=\"https://en.wikipedia.org/wiki/Cholecalciferol\" rel=\"noreferrer\">cholecalciferol</a>) is formed spontaneously fr... | [
{
"answer_id": 66832,
"pm_score": 2,
"text": "<p>Please keep reading the Wikipedia article, it clarifies substantially in the next several lines, for example (emphasis mine):</p>\n\n<blockquote>\n <p>An organic chemical compound (or related set of compounds) is called a vitamin when the organism <stron... |
66,858 | <p>I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the <a href="https://www.ebi.ac.uk/thornton-srv/databases/CSA/" rel="nofollow noreferrer">Catalitic Site Atlas</a> to get the information on the catalytic site, but since they don't offer an easy way for me to download the structure data programmatically I downloaded it from the <a href="https://www.rcsb.org/pdb/home/home.do" rel="nofollow noreferrer">RSCB PDB</a> by downloading the fasta sequence. When checking for the catalytic sites it wasn't matching what the CSA was telling me and that's when I realized that they are different files. Take for example the 3nos, the CSA presents the following <a href="https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=3nos&SUBMIT_PDB=SEARCH%20CSA" rel="nofollow noreferrer">sequence</a>:</p>
<p><strong>MGNLKS...</strong></p>
<p>While the PDB presents the following <a href="https://www.rcsb.org/pdb/download/viewFastaFiles.do?structureIdList=3NOS&compressionType=uncompressed" rel="nofollow noreferrer">sequence</a>:</p>
<p><strong>PKFPRV...</strong></p>
<p>Why aren't they the same sequence if it's the same protein?</p>
<p>Sorry if it's a noob question, I'm not a biologist, just a computer scientist who happens to like bioinformatics.</p>
<p><strong>Important info:</strong></p>
<p>The CSA data comes from <a href="https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=3nos&SUBMIT_PDB=SEARCH%20CSA" rel="nofollow noreferrer">here</a> while the PDB data comes from <a href="https://www.rcsb.org/pdb/explore/explore.do?structureId=3nos" rel="nofollow noreferrer">here</a></p>
| [
{
"answer_id": 66884,
"pm_score": 3,
"text": "<p>Crystallography results (pdb files) almost always contain a truncated sequence. </p>\n\n<p>Both ends of a protein are often flexible (even in a crystal) and don't result in enough data for a good fit. The corresponding residues are removed from the model ... | [
{
"answer_id": 66882,
"pm_score": 1,
"text": "<p>One sequence is partly contained in the other (highlighted).</p>\n\n<p>So the CSA sequence is (FASTA format, truncated):</p>\n\n<p>>sp|P29474|NOS3_HUMAN Nitric oxide synthase, endothelial OS=Homo sapiens GN=NOS3 PE=1 SV=3<br>\n MGNLKSVAQEPGPPCGLGLGLGLGLCG... |
66,878 | <p>Recently while visiting a shop with electronics I saw a fridge with a huge advertisment sticker going more or less like this:</p>
<blockquote>
<p>There's blue light source in this fridge so there will be less bacteria inside and your fruits will have larger quantities of vitamins.</p>
</blockquote>
<p>Can it be true? How can dead (picked, transported and refrigerated) fruit produce more vitamins? How does blue light affect this? </p>
<p>Furthermore I thought that only UV light kills bacteria. </p>
<p>Therefore my question is: how much truth was on that sticker?</p>
| [
{
"answer_id": 68860,
"pm_score": 2,
"text": "<h2>Maybe a little bit?</h2>\n\n<p>There are two claims here, so let's talk about them individually. I'm not sure how this light is being produced (probably LED), but it'll have a wavelength somewhere between 400 and 500 nanometers.</p>\n\n<h3>Reduced bacter... | [
{
"answer_id": 66879,
"pm_score": -1,
"text": "<p>Good question. Asian fridge moguls want to shine blue light on your chopped fruit, mostly, rather than save your life from a hazardous food.</p>\n\n<p>Some <a href=\"https://www.google.fr/search?q=National%20University%20of%20Singapore%20(NUS)%20have%20s... |
67,033 | <p>I've read on Wikipedia that only people who work with <em>Y. pestis</em> and people in 3<sup>rd</sup> world countries get vaccinated against it:</p>
<blockquote>
<p>Since human plague is rare in most parts of the world, routine vaccination is not needed other than for those at particularly high risk of exposure</p>
</blockquote>
<p>But I know that it is easy for plague to conquer Europe. All your need is just some fleas and half of the continent dies, as proved in history.</p>
<p>So why does no one in Europe get vaccinated against plague?</p>
| [
{
"answer_id": 67039,
"pm_score": 4,
"text": "<p>Ask yourself when was the last time that you went to a friend's home and had to worry about getting flea bites? Modern cities still have lots of rats, but modern construction, pesticides, and hygiene have greatly reduced the number of encounters between f... | [
{
"answer_id": 67036,
"pm_score": 2,
"text": "<p>Because antibiotics are relatively cheap and effective against Y. pestis. Also our easy access to high quality healthcare ensure that diseased individuals are rapidly isolated and threated. Therefore the benefits of the vaccine does not outweigh the riscs... |
67,735 | <p>We've been learning about fruits (and the various categories thereof) in class; among them we have the <strong>nut</strong> and the <strong>drupe</strong>.</p>
<p>My textbook differentiates between those terms as:</p>
<blockquote>
<ul>
<li><p>Nut: It is a single-seeded indehiscent, dry fruit.</p>
</li>
<li><p>Drupe: A fleshy fruit with a stony endocarp.</p>
</li>
</ul>
</blockquote>
<hr />
<p>How here's the problem.</p>
<p>My textbook lists the walnut (fruit) as a <strong>nut</strong>. But <a href="https://en.wikipedia.org/wiki/Walnut" rel="noreferrer">Wikipedia disagrees on this point</a>, calling it a <strong>drupe</strong> instead.</p>
<hr />
<p>I'd like a second opinion, since both my book and Wikipedia have had reliability "issues" in the past.</p>
<p><strong>Q- Is a walnut (fruit) a (botanical) nut or a drupe?</strong></p>
| [
{
"answer_id": 67752,
"pm_score": 5,
"text": "<p>Walnut (genus <a href=\"https://en.wikipedia.org/wiki/Walnut\" rel=\"noreferrer\"><em>Juglans</em></a>) fruits are <strong>nuts</strong>, not drupes.</p>\n\n<p>It is indeed a difficult fruit to classify regarding the traditional classification (\"dry\" vs... | [
{
"answer_id": 67736,
"pm_score": 4,
"text": "<blockquote>\n <p>A true nut, botanically speaking, is a hard-shelled pod that contains\n both the fruit and seed of the plant, where the fruit does not open to\n release the seed to the world. Some examples of botanical nuts are\n chestnuts, hazelnuts, ... |
67,870 | <p>I always thought that a molecule of DNA was made of two polynucleotides each making up one strand of the molecule... Is that right?</p>
| [
{
"answer_id": 67892,
"pm_score": 3,
"text": "<p>The term molecule was coined by chemists to describe small entities in which the atoms are joined by covalent bonds. When one is talking about large biological entities involving non-covalent bonds (proteins, nucleic acids) the strict definition often con... | [
{
"answer_id": 67876,
"pm_score": 2,
"text": "<p>In general, it is right since with the term <em>DNA</em> you commonly refer to the double-stranded DNA. However, you need to be aware that DNA may exist in different forms.</p>\n\n<p><strong><a href=\"https://en.wikipedia.org/wiki/DNA#ssDNA\" rel=\"nofoll... |
67,961 | <p>All cells have the same genome and differ only by the expression pattern. Is it possible to determine the tissue origin of a cell based on its DNA sequence using short tandem repeat (STR) analysis or copy number variation (CNV) analysis?</p>
| [
{
"answer_id": 67962,
"pm_score": 3,
"text": "<p>The answer is in the question but I suppose you wanted to ensure you were not missing some info.</p>\n\n<p><strong>Answer</strong></p>\n\n<p>The DNA sequence is the same in all cells of a multicellular organism. Only the expression pattern varies among ti... | [
{
"answer_id": 67992,
"pm_score": 0,
"text": "<p>i would rather start with an assumption that <em>no</em> two cells in the human body have the same genome. Mutations occur frequently; most of them are repaired, but some remain unrepaired. Human body is a genetic mosaic.</p>\n\n<p>Abyzov et al. (Genome R... |
68,091 | <p>Often, in science, when we have evidence that doesn't fit our paradigm, we bend it until the paradigm collapses.</p>
<p>Although there is plenty of decent evidence for evolution, is there anything that does not fit the evolutionary paradigm? Is there any biological evidence that is not suggestive of or seems to disprove evolution? Or is everything merely hunky-dorey?</p>
| [
{
"answer_id": 68096,
"pm_score": 4,
"text": "<p>Evolution is a broad field of knowledge. There are definitely a few elements of our current theory of evolution that does not perfectly match observations. However, those concern small details and might not of much interest to you. Here are a few examples... | [
{
"answer_id": 68135,
"pm_score": 2,
"text": "<p>I agree with Remi.b that there are some things we don't yet fully understand. However, Darwin got it right. A theory is an explanation of observations. It is laid out to be disproven. Evolution, as a theory, has stood 158 years of attack without being dis... |
68,124 | <p>Are there any cases when the name of a genus equal to the name of a higher taxon: family, order, class, etc. in botany and zoology?</p>
| [
{
"answer_id": 68181,
"pm_score": 3,
"text": "<p>I answer for botany: no.</p>\n\n<p>The <a href=\"http://www.iapt-taxon.org/nomen/main.php\" rel=\"nofollow noreferrer\">International Code of Nomenclature for algae, fungi, and plants</a> has strict requirements on names: </p>\n\n<p>Article 16.1 has:</p>\... | [
{
"answer_id": 68127,
"pm_score": 1,
"text": "<p>If you take all the taxons into consideration, yes, it can sort of happen - particularly on the genus/species level. The confusion is generally avoided since species are usually referred to by genus and species, using the name twice, whereas the genus is ... |
68,151 | <p>It is known that some species are more likely to born male than female (and some maybe vice versa). I understand that it is due to evolutionary perspective (average number of adult males is close to that of females), I want to know about how it is regulated.</p>
<p>What I thought is that spermatozoa are made by half as Y and half as X chromosome. Then mitosis and meiosis and the probability that one of them will die is equal for both types. So, somewhere I feel lost.</p>
<p>Also, can it be regulated by female body or not? According to <a href="https://www.ncbi.nlm.nih.gov/pubmed/9198313" rel="nofollow noreferrer">this paper</a> claiming that hormone levels in women affect the likelyhood to born son. Possibly it is just because they choose males that are more likely to have more Y spermatozoa than X, but if it is some chemical mechanism to regulate that I'd like to know.</p>
<p>I'm not asking only about humans, mechanisms can be similar in almost all mammals. I'm not asking about other species: I know some are regulated by temperature, etc. This question is only about mammals.</p>
| [
{
"answer_id": 72711,
"pm_score": 1,
"text": "<blockquote>\n<p>What processes regulate the sex of offspring?</p>\n</blockquote>\n<p>The processes rulating the sex of offspring may occur in both males and females and be direct or indirect.</p>\n<blockquote>\n<p>What I thought is that spermatozoa are made... | [
{
"answer_id": 68154,
"pm_score": 0,
"text": "<p>In theory spermatozoa are indeed produced in a 50:50 X:Y ratio. However, there are factors which can change the ratio, such as <a href=\"https://www.newscientist.com/article/dn19048-bumpology-choosing-the-sex-of-your-child/\" rel=\"nofollow noreferrer\">h... |
68,161 | <p>What is the difference — if any — between <em>"higher plants"</em> and <em>"vascular plants"</em>?</p>
<p>On <a href="https://en.wikipedia.org/wiki/Vascular_plant" rel="nofollow noreferrer" title="Wikipedia">Wikipedia</a>, <em>"higher plants"</em> redirects to <em>"vascular plants"</em>, which seems like an indication that both terms are essentially the same.</p>
<p>Is one of the terms preferred over the other?</p>
| [
{
"answer_id": 68196,
"pm_score": 4,
"text": "<blockquote>\n <p>Is one of the terms preferred over the other?</p>\n</blockquote>\n\n<p>Absolutely: <em>\"vascular plants\"</em> is the preferred one. <em>\"Higher plants\"</em> should be avoided. Here is a long explanation:</p>\n\n<h3>The Great Chain of B... | [
{
"answer_id": 68164,
"pm_score": 3,
"text": "<h3>The difference is specificity.</h3>\n<p>Higher plant is kind of a general term which refers to their complexity, but is not a very precise term. As per <a href=\"https://en.oxforddictionaries.com/definition/higher_plants\" rel=\"noreferrer\">Oxford Dict... |
68,194 | <p>After reading <a href="https://www.lrb.co.uk/v29/n20/jerry-fodor/why-pigs-dont-have-wings" rel="nofollow noreferrer">this rant</a> by Fodor, as a layperson, I was idly wondering whether it would be possible to artifically select for flight in pigs. Of course by that time the porcine lineage will probably comprise an entirely new species, but what would be the first step in our breeding experiment? And how would it develop thence, hypothetically speaking?</p>
| [
{
"answer_id": 68217,
"pm_score": 3,
"text": "<p><strong>Intro course to evolutionary biology</strong></p>\n<p>I doubt you can get much from the below answer. At the end of the day, the only thing that would really allow you to increase your knowledge is probably an intro course to evolutionary biology ... | [
{
"answer_id": 68207,
"pm_score": 1,
"text": "<p>Evolution really is all about random rolls of the dice, with natural selection deciding the outcome. The question of pigs flying has a precedence. Birds evolved from therapod dinosaurs (one of which is T-rex). But birds have an awful lot of adaptations fo... |
68,327 | <p>Male and female brains are wired differently according to <a href="https://www.theguardian.com/science/2013/dec/02/men-women-brains-wired-differently" rel="noreferrer">this article</a>:</p>
<blockquote>
<p>Maps of neural circuitry showed that on average women's brains were highly connected across the left and right hemispheres, in contrast to men's brains, where the connections were typically stronger between the front and back regions.</p>
</blockquote>
<p>But since learning in the brain is associated with changes of connection
strengths between neurons, this could be or not the result of learning.
What about physical differences from birth? Are there differences in size, regions, chemical composition, etc. from birth? </p>
| [
{
"answer_id": 68329,
"pm_score": 8,
"text": "<p><strong>Short answer</strong><br>\nYes, men and women's brains are different before birth. </p>\n\n<p><strong>Background</strong><br>\nFirst off, learning effects versus genetic differences is the familiar nature versus nurture issue. Several <strong>gen... | [
{
"answer_id": 68333,
"pm_score": 5,
"text": "<blockquote>\n <p>What about physical differences from birth? Are there differences in size, regions, chemical composition, etc. from birth?</p>\n</blockquote>\n\n<p>One significant, inherent difference between male and female human brains [from birth &... |
68,443 | <p>Domestic breeding of animals (and plants) by humans seems to match some of the definitions of evolution I have been able to find:</p>
<ul>
<li>"a process that results in heritable changes in a population spread over many generations." (the TalkOrigins website)</li>
<li>"cumulative inherited change in a population of organisms through time leading to the appearance of new forms" (Merriam-Webster)</li>
<li>"Changes in the heritable attributes of populations of organisms over time" (this SE's 'evolution' tag info)</li>
</ul>
<p>But other definitions seem to be less of a fit:</p>
<ul>
<li>"the way in which living things change and develop over millions of years" (Cambridge)<br>
<em>(domestic breeding does not take millions of years)</em></li>
<li>"The process by which different kinds of living organism are believed to have developed from earlier forms during the history of the earth" (Oxford)<br>
<em>(Does breeding lead to different 'kinds' or organisms?)</em></li>
<li>"The gradual development of more complex organisms from simpler ones" (Chambers)<br>
<em>(Breeding may not result in more complex organisms)</em></li>
</ul>
<p>I've seen people argue that domestic breeding can not be considered evolution, because domestic breeding:</p>
<ol>
<li>does not involve natural selection</li>
<li>doesn't direct towards 'fitness'</li>
<li>does not lead to new species</li>
<li>decreases, rather than increases, the size of the gene pool (is this actually true?)</li>
<li>does not (or may not) lead to more complex organisms</li>
</ol>
<p>I was not able to find whether or not there is a general consensus among experts from relevant fields on whether domestic breeding can be considered evolution. Is there?</p>
<p><em><strong>EDIT</strong>: I've made the list of arguments I've heard against calling it evolution a bit clearer, and also added an extra one.</em><br>
<em><strong>EDIT 2</strong>: Added why the second set of definitions seem to exclude domestic breeding as evolution</em></p>
| [
{
"answer_id": 68446,
"pm_score": 4,
"text": "<p>Yes, selective breeding results in evolution.</p>\n\n<p><strong>Definitions of evolution</strong></p>\n\n<p>I don't understand why you say that for 3 of the definitions you found, selective breeding would not be considered as evolution. To me, all of thes... | [
{
"answer_id": 68445,
"pm_score": 2,
"text": "<p>The answer is \"yes\". Evolution is defined as a change in heritable characteristics of a population over generations, and to me, there is no reason not to define domestic animals as populations. </p>\n\n<p>The statements you list can all be refuted:</p>\... |
68,528 | <p>I read several different articles about virology, including the Wikipedia article on viruses and none of them explain how a virus is isolated. Some talk of injecting a virus into a chicken egg, but this does not isolate the virus, it just reproduces it.</p>
<p>If a researcher filters the particles in a serum to get those of a particular size, it proves nothing, because every creature has many thousands of different viruses in their blood, so any sample filtered by size will potentially have hundreds of different viruses in it, all the same size range. How can they possibly be separated?</p>
| [
{
"answer_id": 92560,
"pm_score": 1,
"text": "<p>I eventually figured out the answer to this question after reading some introductory textbooks on virology.</p>\n\n<p>Though, as another answer states, there are many different possible techniques to isolate a virus, there is one basic approach that can b... | [
{
"answer_id": 68544,
"pm_score": 1,
"text": "<p>There are many ways. In many cases especially traditionally viruses of interest were either the only virus present, or overwhelmingly more abundant than other types, so simple dilution will end up with a single virus type. Differential growth can help; ma... |
68,736 | <p>At what point in the cell cycle do cells start to become tumorous? Do they have abnormal characteristics to begin with; if so what are they? </p>
| [
{
"answer_id": 69037,
"pm_score": 2,
"text": "<p>Cancer cells don't start to become cancerous at a specific stage of the cell cycle; you will find that while uncontrolled proliferation is a hallmark of cancer, different cancers acquire alterations in different phases of the cell cycle. BRCA-deficient ca... | [
{
"answer_id": 68761,
"pm_score": 0,
"text": "<p>The question assumes that tumorigenesis is a cellular problem. My answer is a counter-question: <em>Is tumorigenesis a cellular problem?</em></p>\n\n<p>Sonnenschein & Soto (2018) Methods Mol Biol 1702: 15-26; emphasis mine:</p>\n\n<blockquote>\n <p>[... |
68,742 | <p>I have a black mulberry (<em>Morus sp.</em>) in my garden (or 2 actually). <a href="https://en.m.wikipedia.org/wiki/Morus_(plant)" rel="nofollow noreferrer">According to the information I could find it is a deciduous tree</a>. The trees in my garden do indeed lose their leaves. However, as most native trees start to color yellow/brown/red in september and have lost all leaves by now, the mulberry doesn't. It remains green until the frost kicks in and only then drops its (still green) leaves. It almost looks like it doesn't want to drop its leaves, but is forced to so so. This can be seen at the picture below. Hence my question:
Is mulberry also deciduous in warm winters such as the mediterranean? And is it normal that leaves are still green when dropped?</p>
<p><a href="https://i.stack.imgur.com/TzBDU.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/TzBDU.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 69037,
"pm_score": 2,
"text": "<p>Cancer cells don't start to become cancerous at a specific stage of the cell cycle; you will find that while uncontrolled proliferation is a hallmark of cancer, different cancers acquire alterations in different phases of the cell cycle. BRCA-deficient ca... | [
{
"answer_id": 68761,
"pm_score": 0,
"text": "<p>The question assumes that tumorigenesis is a cellular problem. My answer is a counter-question: <em>Is tumorigenesis a cellular problem?</em></p>\n\n<p>Sonnenschein & Soto (2018) Methods Mol Biol 1702: 15-26; emphasis mine:</p>\n\n<blockquote>\n <p>[... |
68,765 | <p>I am a computer science student and I'm interested in algorithmic aspects of cancer! Once I heard that there exist more bacteria in human body than our own cells, I wondered that why bacteria, which divide faster than cell bodies, do not cause something like cancer in body? Isn't it evolutionary more probable for bacteria to gain aggressive properties and invade human tissues? Or maybe is it the case that bacteria really produce some lethal colonies like cancers in the body?</p>
<p>One difficulty with cancers is that cancer is a very complex disease because of it's intra-tumor and inter-tumor heterogeneity. Isn't it more probable for bacteria to cause extremely heterogenous infections with regard to existing simple evolutionary models which are used to describe cancer?</p>
| [
{
"answer_id": 68781,
"pm_score": 4,
"text": "<p>Cancer is not inherently more lethal than bacterial infections. That's simply an artifact of the time we live in. Broad spectrum <a href=\"https://en.wikipedia.org/wiki/Antibiotics\" rel=\"noreferrer\">anti-bacterial drugs</a> we invented in the 1st half ... | [
{
"answer_id": 68825,
"pm_score": 1,
"text": "<p>Charle's E. Grant's answer, that bacteria are typically different from us and hence easier to kill, is most of the answer. Remember that this applies not only to drugs but to our immune system, which can have difficulty detecting cancers (while catching m... |
69,392 | <p>I am investigating the early uses of <em>E. coli</em> as a model organism. Sadly, many early 20th century papers are not in English. In those that are, I have been unable to find explicit statements as to why a researcher chose to use <em>E. coli</em> as a <strong>model organism</strong>. </p>
<p>Does anyone know of early literature in which this reasoning is stated? I imagine that prior to the widespread use of <em>E. coli</em>, scientists would have had to argue why they chose to use it to investigate biological phenomena not limited to this bacterium alone. </p>
| [
{
"answer_id": 69418,
"pm_score": 4,
"text": "<p><strong>Historical Fallacies implicit in the Question</strong></p>\n\n<blockquote>\n <ol>\n <li>“…why a researcher chose to use <em>E. coli</em> as a model organism.”</li>\n </ol>\n</blockquote>\n\n<p>Researchers did <strong>not</strong> work with <em>... | [
{
"answer_id": 69393,
"pm_score": 2,
"text": "<p>When I read your question the first thing that came to my mind was that <em>Escherichia coli</em> is one of the most common bacteria in human faeces. Of course, the ease of finding and collecting the bacterium (I'm not claiming that the modern source of <... |
70,093 | <p>It seems some very specific alloys like implant surgical steel and titanium don't cause inflammation in the human body, but when I asked my doctor about it, they simply said "it just has some chemical property that doesn't cause it." </p>
<p>So...what exactly is special about these metals compositions as to not cause inflammation like most other things would? </p>
| [
{
"answer_id": 70106,
"pm_score": 3,
"text": "<p><strong>Some can</strong></p>\n<p>First the terms you are looking for is biocompatibility and bioactivity. The study of them is called biomaterial science. Both fields are relatively new so complete answers do not exist, there has been a certain amount of... | [
{
"answer_id": 70095,
"pm_score": 0,
"text": "<p>Surgical steel doesn't cause inflammation because (i) it has very little solubility, and (ii) what little iron ions do get dissolved into bodily fluids are chemically too simple to be recognized by the immune system and trigger an immune response. Moreove... |
70,172 | <p>I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find the 13-kb non-spacer sequence. Are the spacer regions not yet sequenced due to difficulty in sequencing a repetitive region? Thanks for your help.</p>
| [
{
"answer_id": 70173,
"pm_score": 2,
"text": "<p>Managed to find the complete sequence of the repeating unit:</p>\n\n<p><a href=\"https://www.ncbi.nlm.nih.gov/nuccore/U13369\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/nuccore/U13369</a></p>\n"
}
] | [
{
"answer_id": 73972,
"pm_score": 0,
"text": "<p>To the best of my knowledge, of the estimated 500 copies of rDNA repeats in the human genome only 1 and half repeats has been sequenced and published. Mammalian rDNA repeats are hard to clone and appear unstable in yeast and e coli.</p>\n"
},
{
"... |
70,233 | <p>I have <em>Prunus persica</em> peach pits that have two seeds.</p>
<p>My question is simple: </p>
<p>Do the seeds have the same DNA? (are they identical twins?)</p>
<p><a href="https://i.stack.imgur.com/YEk2R.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/YEk2R.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 70535,
"pm_score": 3,
"text": "<p><strong>Polyembryony</strong> occurs when a single fertilized egg produces more than 1 embryo. This is the process that produces genetically identical twins.</p>\n\n<p>Although polyembryony is common in some plants, I found limited information about polye... | [
{
"answer_id": 70532,
"pm_score": -1,
"text": "<h2>Of course they are.</h2>\n\n<p>They're both from the same peach, so they both have identical DNA. It's like when a mother has twins or triplets, all of the babies will have the same genetic code, since they all came from the same egg. So if there are tw... |
70,348 | <p>I am a 3rd timer postdoctoral fellow with some experience in molecular biology and biochemistry, but major skills in Zoology and Natural History. I am studying some natural extracts, and isolating compounds.</p>
<p>Some biological samples come in limited amounts (e.g. invertebrate haemolymph), hampering analytical methods that rely on larger amounts. For instance, establishing UV-Vis spectra of extracts is a usual non-destructive method for approaching unknown samples and estimating general parameters, done with a spectrophotometer. </p>
<p>The microvolume-scaled spectrophotometer system popularly known as 'Nanodrop' has been around labs since almost two decades now. Its use has been usually limited to fast purity & concentration estimations for DNA & RNA in molecular biology labs.</p>
<p>I am considering using the nanodrop to estimate parameter of other biological and chemical samples. The manual says most commonly used solvents are compatible with the system. I have however yet found no-one else who has tried using Nanodrop for different applications.</p>
<p>Please, anyone here who has experimented using a Nanodrop system with other biological samples and extracts could comment on the experience? </p>
| [
{
"answer_id": 70370,
"pm_score": 3,
"text": "<p>The Nanodrop is a generic UV-visible spectrophotometer. According to the manufacturer, <a href=\"https://www.thermofisher.com/order/catalog/product/ND-ONE-W\" rel=\"nofollow noreferrer\">the latest model can measure absorbance <strong>from 190 to 850 nm</... | [
{
"answer_id": 70371,
"pm_score": 1,
"text": "<p>I used the Nanodrop for the measurement of the absorbance at 600 nm of bacterial cultures, as well as nucleic acid preparations. However, I switched to using another spectrophotometer (Spetrophotometer, Ultrospec 2100 pro, UV/Visible Spectrophotometer, Am... |
70,604 | <p>If I were to harvest an agave plant for its nectar, would it kill the plant? I have watched videos of the process and it seems quite invasive.</p>
| [
{
"answer_id": 70606,
"pm_score": 3,
"text": "<p>When harvesting agave nectar, generally the whole plant is harvested at once to get to the core, where most of the sap is. There isn't exactly an easy way to continually get nectar from the agave plant since it is herbaceous, whereas something like maple ... | [
{
"answer_id": 70610,
"pm_score": 2,
"text": "<p>Agave is more closely related to asparagus and hyacinths than to cactus. They are perrenial, you can harvest the lowest half of the leaves to make it look like a little palm tree, it will die after flowering, it takes 10-15 years to flower.</p>\n"
},
... |
70,755 | <p>If a DNA from an ancient human, for example the cheddar man, is still intact, can you make an offspring today using that intact DNA?</p>
<p><a href="https://www.theguardian.com/science/2018/feb/07/first-modern-britons-dark-black-skin-cheddar-man-dna-analysis-reveals" rel="nofollow noreferrer">https://www.theguardian.com/science/2018/feb/07/first-modern-britons-dark-black-skin-cheddar-man-dna-analysis-reveals</a></p>
| [
{
"answer_id": 70786,
"pm_score": 3,
"text": "<p>You could, however the DNA is not that intact, there is a steady rate of loss of the genes... </p>\n\n<p>mtDNA is degraded to an average length of 1 base pair after 6,830,000 years at −5 °C (see wiki: ancient dna). that's a speed of 1 base pair every 412 ... | [
{
"answer_id": 70756,
"pm_score": 1,
"text": "<p>scientifically yes, legally probably not as it would fall under human cloning/experimentation laws in most countries.</p>\n\n<p>Artificial insemination with sperm with inserted genomes or artificial sperm already exists in mammals. Reconstructing genomes ... |
70,923 | <p>I've been learning about life on coral reefs. Recently I've become aware of the damage to coral reefs caused by tourism and inexperienced divers:
1) Corals have a thin membrane which keeps them healthy. Touching them could break this membrane, causing infection which can lead to death.
2) Stepping on, leaning on, and sitting on coral could smash their polyps.</p>
<p>I am not against being responsible as a diver, respecting nature, arriving and leaving without a trace. I'm just curious what the difference is between human and animal contact. Parrot fish eat coral, taking bites out of it, leaving exposed areas and this damages the coral. I've seen footage of sharks having feeding frenzies on reefs, where they smash into the reef during the commotion and while trying to catch their prey. Fish rub up against coral and peck at them to get algae, and crustaceans walk on the coral with legs that seems like it would break the thin protective membrane on the coral.</p>
<p>Obviously, as humans we technically do not belong in their world, so I'm sure there are reasons for damage with that alone; but why does marine life causing damage not cause actual damage? Or does it, and it just repairs differently or faster somehow?</p>
| [
{
"answer_id": 70927,
"pm_score": 5,
"text": "<p>You are absolutely correct in regards that marine life does cause damage to corals. In particular, parrotfish have been found to play an important role in regulating the biodiversity of coral reefs through their feeding behavior. Certain species of parrot... | [
{
"answer_id": 70933,
"pm_score": 3,
"text": "<p>OTOH, it is indeed true that a coral reef can be overgrazed by animals. An example that readily comes to mind is the infestation of the Great Barrier Reef by the <a href=\"https://en.wikipedia.org/wiki/Crown-of-thorns_starfish\" rel=\"noreferrer\">crown-o... |
71,060 | <p>If an organism on Earth has got DNA, would it always have C,T,G,A?</p>
| [
{
"answer_id": 71076,
"pm_score": 2,
"text": "<blockquote>\n <p>If an organism on Earth has got DNA, would it always have C,T,G,A?</p>\n</blockquote>\n\n<p>Yes! All three domains of life (Archaea, Bacteria and Eukaryota) as well as all DNA viruses use these four same <a href=\"https://en.wikipedia.org/... | [
{
"answer_id": 71065,
"pm_score": 2,
"text": "<p>Yes, there are no variations on this. There are 3 domains of life; Archaea, Bacteria and Eukaryota. All use these identical nucleotides. All use all four of them, and this is one of many lines of evidence for the single origin of life on Earth.</p>\n"
}... |
71,312 | <p>Is there a point where too much CO<sub>2</sub> is bad for a plant? Basically when there is too much CO<sub>2</sub> in the air can a plant get sick?</p>
<p>Since plants <a href="https://en.wikipedia.org/wiki/Photosynthesis" rel="noreferrer">photosynthesize</a> and <em>need</em> CO<sub>2</sub> to generate glucose and store starch, and since chemical reactions are pushed toward their end product when the reagent concentrations are increased, one would expect that more CO<sub>2</sub> would be better, at least lead to increased growth and survival rates.</p>
<p><strong>Is there a ceiling where CO<sub>2</sub> gets toxic?</strong></p>
| [
{
"answer_id": 71313,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nIt has been shown that plants may already suffer from doubling the atmospheric CO<sub>2</sub> concentration from 340 to 610 ppm, something that might happen during the next hundred years or so based on current emissions.... | [
{
"answer_id": 71332,
"pm_score": 4,
"text": "<p>It depends upon the plant species. </p>\n\n<p>As explained in <a href=\"http://www.nature.com/articles/227744a0\" rel=\"nofollow noreferrer\">Algae thrive under Pure CO2</a> <em>Nature</em> 227, pages 744–745 (15 August 1970): </p>\n\n<p><em>Cyanidium ... |
71,412 | <p>To my understanding, Pasteur’s experiment demonstrates that life is only made from life. If this is true, then how could <a href="https://en.wikipedia.org/wiki/Abiogenesis" rel="nofollow noreferrer">origin of life (aka. abiogenesis)</a> ever have happened?</p>
<p>It seems to me that Pasteur’s experiment and the theory according to which there is abiogenesis contradict each other. Do they?</p>
| [
{
"answer_id": 71414,
"pm_score": 3,
"text": "<p>Pasteur’s experiments demonstrated that the appearance of living matter in spoiled food (soured wine and the like) was not due to so-called <em>spontaneous generation</em> of living organisms, but due to the multiplication of pre-existing but invisible mi... | [
{
"answer_id": 71413,
"pm_score": 2,
"text": "<p>Pasteur proved that <strong>modern lifeforms</strong> can't form from non-living things. That doesn't prove that there is some hard and bright line that prevents a micell containing enzymatic RNA from changing a bit into something we would recognize as \... |
71,784 | <p>I found some popular articles (e.g. <a href="https://www.nbcnews.com/science/science-news/bacteria-have-ability-see-eye-opening-study-finds-n515141" rel="nofollow noreferrer">nbcnews</a> and <a href="http://www.iflscience.com/environment/bacteria-can-actually-see-acting-tiny-eyeballs/" rel="nofollow noreferrer">iflscience</a>) that bacteria can "see," but I highly doubt it's in the same way as people do just from looking at the limitations in the vision of small animals like insects. So what exactly are bacteria capable of "seeing" or what are the limitations of their vision?</p>
| [
{
"answer_id": 71785,
"pm_score": 3,
"text": "<p>Simple answer is that many simple organisms, including bacteria, carry light-sensitive molecules. One example is <a href=\"https://en.wikipedia.org/wiki/Halorhodopsin\" rel=\"nofollow noreferrer\">halorhodopsin</a> (not bacterial but archaeic). This is a ... | [
{
"answer_id": 71788,
"pm_score": 2,
"text": "<p>Because bacteria are extremely small, the principles of optics prevent them from having lenses or other organs capable of determining the direction from which light is incident. On the other hand, an entire spherical bacterium can potentially act as a le... |
72,016 | <blockquote>
<p><a href="https://www.learner.org/courses/biology/textbook/proteo/proteo_3.html" rel="nofollow noreferrer">https://www.learner.org/courses/biology/textbook/proteo/proteo_3.html</a></p>
<p>Despite advances in techniques for determining protein structure, the structures of many proteins are still unknown...</p>
</blockquote>
<p>My question is why? We have many researchers all over the world. We know what our 3 billion DNA is. The governments invest billions of money into medical research. We should have sufficient human resources and technology.</p>
<p>What's stopping us determining structure for all proteins? We need more money? We need more people? We need better technology?</p>
| [
{
"answer_id": 72058,
"pm_score": 3,
"text": "<blockquote>\n <p>What's stopping us determining structure for all proteins? We need\n more money? We need more people? We need better technology?</p>\n</blockquote>\n\n<p>Each unknown structure has a different story. Importantly, not all of the proteins h... | [
{
"answer_id": 72045,
"pm_score": 0,
"text": "<p>The answer is most likely priorities. Yes, the process is easier, but it still requires at least some effort and time, which is better spent on other things. As such, grants are unlikely to be given for such trivial work - and this is researchers' job, so... |
72,103 | <p>"the location of a certain gene on a chromosome " is the definition I know for locus. ı just read that a gene is not necessarily present on a locus. how would that be possible?</p>
| [
{
"answer_id": 72104,
"pm_score": 3,
"text": "<p>A locus is not necessarily the position of a gene. It is a position in the genome, whether or not, there is a gene at this position. A locus often refers to the position of a SNP (which may well be outside a coding region) or any other type of genetic mar... | [
{
"answer_id": 72106,
"pm_score": 2,
"text": "<p>Like you said in your question - \"locus\" means location. A locus may be anywhere on a chromosome - an entire \"gene\" coding locus, a non-coding locus (junk DNA), a regulatory sequence locus (example - the promoter region of a gene), or just a single n... |
72,176 | <p>In his explanation of the Evolutionary Stable Strategy, in the Selfish Gene, Richard Dawkins repeats a couple of times, that a population of hawk-type males would make the ground for a dove-type individual to spreat his genes, because the dove always retreats against a hawk and if an average hawk loses every second match, than he'll be worse off than the dove that always retreats and stays unhurt.</p>
<p>My question is - how dose a male, that does not win a single contest for a mate and therefore doesn't get to mate at all, spreat his genes?
Does the ESS imply that there are ways to breed bypassing the contest?</p>
| [
{
"answer_id": 72177,
"pm_score": 3,
"text": "<p><strong>Game theory</strong></p>\n\n<p>Your question is not as specific to biology as you may think. The hawk-dove game is a type of game in game theory, a field of mathematics. Game theory is used in biology, in economics, in psychology and many other di... | [
{
"answer_id": 72187,
"pm_score": 0,
"text": "<p>A male that does not mate will not spread his genes. Females might, if they have the option to reproduce asexually. However, this is probably not the answer you are after though. What you need to do is to look at the <strong>assumptions behind the game th... |
72,178 | <p>Different breeds of common domesticated animals such as horses and dogs clearly show different behaviour, instincts, social relationships and similar, due to their biological inheritance. Still they can easily mate with other breeds of the same species. This also applies to wild animals, for example the wolfs living in the rainforest on the Canadian west coast prey on fish (and are maybe expected, with time, to go through a similar transformation as the predecessor to dolphins, that where actually wolf like animals, did when they resettled to the oceans) while inland wolfs prey on moose and elk etc, which requires completely different hunting technique, tactics, pack size and so on.</p>
<p>Are there any similar examples for humans? I reckon that living in the jungle or in the desert or on Greenland should reward different behaviours/traits that influence behaviour. Also going from a hunter-gatherer society to an agricultural society should reward different behaviours, social skills and similar aspect of human life.</p>
<p>Are humans like other animals in this respect (any examples?) or are we unique (?) in the animal kingdom when it comes to the influence of genetics on our behaviour?</p>
<p>One reason I ask is that I got second hand (without sources) information claiming that the natives of Mexico has the highest prevalence, of any population measured, of genes that are known to be connected with/causing ADHD. Mexico was also one the last places on the planet where humankind settled.</p>
<p>The argument went something like this: "during prehistoric time individuals with ADHD tendencies tended to be more adventurous than their peers and therefore traveled further". If this is true, people in Mexico's behaviour should be slightly different from people in current Kenya and Tanzania (by many scientists claimed to the birthplace of humankind), at least if you measure ADHD related traits.</p>
| [
{
"answer_id": 72177,
"pm_score": 3,
"text": "<p><strong>Game theory</strong></p>\n\n<p>Your question is not as specific to biology as you may think. The hawk-dove game is a type of game in game theory, a field of mathematics. Game theory is used in biology, in economics, in psychology and many other di... | [
{
"answer_id": 72187,
"pm_score": 0,
"text": "<p>A male that does not mate will not spread his genes. Females might, if they have the option to reproduce asexually. However, this is probably not the answer you are after though. What you need to do is to look at the <strong>assumptions behind the game th... |
72,236 | <p>I just heard the following complaint from a comedienne.</p>
<blockquote>
<p>Humans are the only animal that is completely useless for the first twenty five years of life.</p>
</blockquote>
<p>Obviously this is just a joke but it is true that primates and especially humans do have profoundly long juvenile periods compared with most animals. It's got me wondering whether humans really do spend the most time in sexual immaturity.</p>
<p>Unfortunately I have found this question hard to search because Google thinks I'm asking about the longest gestation period (which seems to be a much more popular question). To be clear, <strong>I am not asking about the longest gestation period.</strong></p>
| [
{
"answer_id": 72244,
"pm_score": 4,
"text": "<p>As you indicate in your question, the average age of sexual maturity is probably the best way to approach this, since immaturity is usually how juveniles are defined. Age of puberty is also different in boys and girls (the same goes for many animals), and... | [
{
"answer_id": 98327,
"pm_score": 1,
"text": "<p><a href=\"https://www.wired.com/2013/12/the-creature-feature-10-fun-facts-about-the-tuatara-or-just-the-tuatara-of-us/\" rel=\"nofollow noreferrer\">This article</a> provides general facts about Tuataras, one of which is:</p>\n<blockquote>\n<p><strong>Tua... |
72,707 | <p>Several sources all caution that silent mutations and synonymous substitutions are not the same thing and should not be confused. But they seem to draw different actual distinctions between the terms:</p>
<ol>
<li><a href="https://en.wikipedia.org/wiki/Mutation#Small-scale_mutations" rel="noreferrer">This Wikipedia page</a> and <a href="https://www.biology-online.org/dictionary/Silent_mutation" rel="noreferrer">this biology dictionary entry</a> define a silent mutation as a point substitution that replaces a single codon by another codon that codes for the same amino acid, and therefore does not directly change the amino acid sequence that is coded for. It defines a synonymous substitution as a silent mutation that occurs in an exon. Under these definitions, a synonymous substitution is a special case of a silent mutation.</li>
<li><a href="https://en.wikipedia.org/wiki/Silent_mutation" rel="noreferrer">This Wikipedia page</a> and <a href="http://judgestarling.tumblr.com/post/57494092909/mutations-synonymous-nonsynonymous-silent" rel="noreferrer">this blog post</a> define a silent mutation as any mutation that does not have any phenotypic effects, and defines a synonymous substitution as a point substitution to a degenerate codon (anywhere in the genome, as far as I can tell). It points out that such synonymous substitutions can still have indirect phenotypic ("nonsilent") effects by affecting translation and transcription. Under these definitions, a silent mutation is a special case of a synonymous substitution (namely, one that doesn't have any indirect phenotypic effects).</li>
<li><a href="https://en.wikipedia.org/wiki/Synonymous_substitution" rel="noreferrer">This Wikipedia page</a> uses similar definitions to the one in #2, except it explicitly requires that a synonymous substitution occurs in an exon.</li>
</ol>
<p>Clearly these definitions are not all compatible. (#2 and #3 are very similar and could perhaps be excused as minor variants on the same definition, but they clearly conflict strongly with #1 - they disagree on which of "silent mutation" and "synonymous substitution" is a special case of the other!) Is there a standardized distinction in the biology community between these terms, or is it just the case that everyone uses conflicting definitions and we should ask people to clarify the senses in which they're using these terms?</p>
| [
{
"answer_id": 72723,
"pm_score": 3,
"text": "<p>Silent mutations are those which have no phenotypic effect and it seems important to note that these could occur in coding regions and non-coding regions alike. Synonymous mutations, on the other and, are confined to coding regions. Because these mutation... | [
{
"answer_id": 72721,
"pm_score": 3,
"text": "<p>I would say that silent mutations, as they have <a href=\"https://www.nature.com/scitable/definition/silent-mutation-10\" rel=\"nofollow noreferrer\">been defined</a>, are a subset (or perhaps even same as) of synonymous mutations. However, the term, \"si... |
73,597 | <p>After one year in college, I am quite surprised with the number of different abbreviations used in biology for the same thing. </p>
<p>I wonder if there are any rules for naming something new in biology, for example new genes, or if it is just up to the researchers without restriction? If there are rules, how did the confusion arise?</p>
| [
{
"answer_id": 73634,
"pm_score": 4,
"text": "<p>Elsewhere on SE Biology I have answered a related question regarding <a href=\"https://biology.stackexchange.com/questions/50936/origin-of-enzyme-names/50947#50947t\"><em>enzyme</em> names</a>. Here I will restrict myself to <em>genes</em>, as it seems th... | [
{
"answer_id": 73609,
"pm_score": 3,
"text": "<p>There are rules. Both genes and proteins are regulated in their formats, and standardized in terms of capitalization and italics. Different species have different rules. So for example <em>SHH</em> is a human gene, and <em>Shh</em> is the homologue in mou... |
73,642 | <p>A friend of mine has recently told me that dinosaurs were "killed by flowers". I was a bit surprised and so I googled. And I did find a lot of recent articles in popular media on this topic, probably based on <a href="https://ojs.library.queensu.ca/index.php/IEE/article/view/6802" rel="noreferrer">this</a>. To me it doesn't sound convincing at all, but I'm an outsider. Does anyone think that there's more to that than just a usual journalistic overhype?</p>
| [
{
"answer_id": 73646,
"pm_score": 5,
"text": "<h1>Things in the paper that strike me as suspicious</h1>\n<h3>Associating toxic plant defenses with the Cretaceous</h3>\n<blockquote>\n<p>Although there continues to be uncertainty about precisely when plants\nfirst evolved toxic defenses, this period of an... | [
{
"answer_id": 73643,
"pm_score": 4,
"text": "<p>No, it's not convincing; angiosperms evolved in the middle part of the dinosaurs' reign, not the end, and toxins evolve slowly which gives herbivores a chance to compensate, also conifers can be riddled with toxins just as easily. </p>\n\n<p>Lastly, the i... |
73,664 | <p>EDIT: please feel free to suggest books that are the closest you can come up with to what I'm looking for, even if it doesn't exactly overlap! </p>
<p>I am very well acquainted with the theory of evolution as informally taught. E.g. I don’t need a book that explains the theory, or refutes popular misconceptions.</p>
<p>Instead, I am looking for a formal theory of evolution as a process, and I am not specifically interested in the biological aspect of evolution, but in evolution as a more generally occuring process. </p>
<ul>
<li>How do we formally state the different assumptions of Darwinian evolution? (Random change, heritability, natural selection).</li>
<li>What happens if we change these different assumptions? (Non-random mutation? Maybe, selection criteria that are influenced by the mutations, rather than independent of it)</li>
<li>Are there quantitatively different results of evolution based on these assumptions?</li>
<li>Something I find very interesting: What kind of non-biological evolutionary processes can we describe formally? E.g. evolution based on some form of non-random mutation, or based on different types of heritability. What are the different implications of different formal assumptions. How do these differences apply to different evolutionary systems? (E.g. evolution of ideas, cultures, computer viruses, evolutionary algorithms).</li>
</ul>
<p><strong>In summary, I am looking for a book that introduces in a very abstract way the properties of evolutionary systems (does not have to be focused on biological evolution. I’m interested in the formal properties of such systems).</strong></p>
<p>NOTE: I am NOT asking about a book on modelling highly specific processes that apply to specific biological systems, such as population dynamics of preditor-prey relations. <strong>I’m interested in general, abstract theoretical analysis of the notion of an evolutionary process in general.</strong> </p>
| [
{
"answer_id": 73815,
"pm_score": 2,
"text": "<p>The theoretical framework that best fits the kinds of questions you have in mind is <a href=\"https://en.wikipedia.org/wiki/Evolutionary_game_theory\" rel=\"nofollow noreferrer\">evolutionary game theory</a>.</p>\n\n<p>The foundational text is perhaps May... | [
{
"answer_id": 73668,
"pm_score": 2,
"text": "<p>As a body of literature, that covers quite a broad range of topics that have been discussed at length in many, many papers. Of course, you might find something out of a broad-level textbook (I suggest Futuyma's <a href=\"https://rads.stackoverflow.com/amz... |
73,735 | <p>As it's established that life's design is a product of evolution, what advantage does emotions like sadness play in the life of an individual/species ?</p>
| [
{
"answer_id": 73773,
"pm_score": 3,
"text": "<p>I‘ll answer from a perspective I‘ve been studying in Psychology, but can‘t provide sources. If this is not within the scope of this SE, I‘d kindly ask to either add appropriate sources to my answer or close it.</p>\n\n<p>Sorrow is an emotion that has spec... | [
{
"answer_id": 73762,
"pm_score": 0,
"text": "<p>This is just a thought......... overtime the animal brain has developed and became more sophisticated. Included in this process has been the development of emotions, such as love, need to perpetuate the genetic line, ability to feel a sense of loss and he... |
73,747 | <blockquote>
<p>In a hypothetical species of butterfly, wing spots are controlled by a single locus where BB individuals have blue spots, YY individuals have yellow spots, and BY individuals have green spots. Ten years ago, a previous collector randomly collected 1000 butterflies and reported finding 90 blues, 420 greens, and 490 yellows. You collect 40 blues, 320 greens, and 640 yellows. Has there been evolution in this population? If yes, is natural selection involved?</p>
</blockquote>
<p>I have had many attempts at this question I calculated the p and q frequency for each using HW model.</p>
<p>For 10 years ago: 90+90+420/2000=0.3 BB
490+490+420/2000=0.7 YY</p>
<p>For now : 40+40+320/2000=0.2 BB
640+640+320/2000= 0.8YY</p>
<p>But I dont think I can know if evolution happened and natural selection from this (because Y allele in yellow for instance includes heterozygotes as well).</p>
<p>What do I do? Do I calculate the expected number of each and put it in Chi square test but how would I get natural selection from that? Please help</p>
| [
{
"answer_id": 73773,
"pm_score": 3,
"text": "<p>I‘ll answer from a perspective I‘ve been studying in Psychology, but can‘t provide sources. If this is not within the scope of this SE, I‘d kindly ask to either add appropriate sources to my answer or close it.</p>\n\n<p>Sorrow is an emotion that has spec... | [
{
"answer_id": 73762,
"pm_score": 0,
"text": "<p>This is just a thought......... overtime the animal brain has developed and became more sophisticated. Included in this process has been the development of emotions, such as love, need to perpetuate the genetic line, ability to feel a sense of loss and he... |
73,893 | <p>During a whole day breathing, how many kcal or watts do we get from the oxygen we breathe?</p>
| [
{
"answer_id": 73898,
"pm_score": 4,
"text": "<p>I know that you already picked an answer, but I found an alternative answer for you. On average a person consumes <a href=\"https://health.howstuffworks.com/human-body/systems/respiratory/question98.htm\" rel=\"nofollow noreferrer\">550 litres of oxygen i... | [
{
"answer_id": 73894,
"pm_score": 2,
"text": "<p>Oxygen does not provide any calories (energy) or watts (power), just the same as a water bottle states it contains zero calories. Energy is held within glucose, or other macromolecules than can be broken down to supply electrons that generate ATP, or oth... |
74,004 | <p><a href="https://i.stack.imgur.com/uozSh.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/uozSh.jpg" alt="This plant looks more like a shrub - not a tree"></a></p>
<p>It stays the same color when ripe. It's about the same size as a pear. Grows in sub tropical climate of Meghalaya, India.</p>
<p><a href="https://i.stack.imgur.com/FFzuK.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/FFzuK.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 74018,
"pm_score": 4,
"text": "<p>I think this looks a lot like a pale variety of <a href=\"https://en.m.wikipedia.org/wiki/Solanum_muricatum\" rel=\"noreferrer\">Solanum Muricatum</a> or Pepino dulce/melon/pear.</p>\n\n<p><a href=\"https://i.stack.imgur.com/wNDfb.jpg\" rel=\"noreferrer\"... | [
{
"answer_id": 74005,
"pm_score": 3,
"text": "<p>It looks like Tinda (<em>Praecitrullus fistulosus</em>), also known as round melon, Indian round gourd, Indian baby pumpkin, apple gourd, or Indian squash.</p>\n\n<p><a href=\"https://i.stack.imgur.com/QGz0B.jpg\" rel=\"noreferrer\"><img src=\"https://i.s... |
74,027 | <p>The environment is the ultimate cause of population stabilization. Considering the environment to turn harsh for the survival of a species.How to adapt better to this change-by evolution or by mutation?</p>
| [
{
"answer_id": 74018,
"pm_score": 4,
"text": "<p>I think this looks a lot like a pale variety of <a href=\"https://en.m.wikipedia.org/wiki/Solanum_muricatum\" rel=\"noreferrer\">Solanum Muricatum</a> or Pepino dulce/melon/pear.</p>\n\n<p><a href=\"https://i.stack.imgur.com/wNDfb.jpg\" rel=\"noreferrer\"... | [
{
"answer_id": 74005,
"pm_score": 3,
"text": "<p>It looks like Tinda (<em>Praecitrullus fistulosus</em>), also known as round melon, Indian round gourd, Indian baby pumpkin, apple gourd, or Indian squash.</p>\n\n<p><a href=\"https://i.stack.imgur.com/QGz0B.jpg\" rel=\"noreferrer\"><img src=\"https://i.s... |
74,214 | <p>I know that antibiotics usually have properties affecting specifically bacterial cells, like by inhibiting peptidoglycan synthesis. but do any antibiotics exist affecting eukaryotic cells, like yeast or other fungi? I read in a text that "most" eukaryotic cells are resistant against antibiotics and that confused me.</p>
<p>Regardless of whether it can be used against bacteria or not, is there any kind of antibiotic effective against fungi, or any kind of eukaryotic cell? </p>
| [
{
"answer_id": 74222,
"pm_score": 3,
"text": "<p>The term <a href=\"https://en.m.wikipedia.org/wiki/Antibiotic\" rel=\"nofollow noreferrer\">antibiotic</a> typically refers to chemicals effective against bacteria. There are <a href=\"https://en.m.wikipedia.org/wiki/Antimicrobial\" rel=\"nofollow norefer... | [
{
"answer_id": 74257,
"pm_score": 1,
"text": "<p>Yes, there is. The Azole class of drugs, for example, are used to treat (eukaryotic) fungal infections. One such drug is clotrimazole which targets cytochrome p450 which is responsible for the synthesis of ergosterol (a mimetic of cholesterol; not found i... |
76,255 | <p>DNA is how a species stores genetic information. Somehow the body needs to know what to do with this information. somehow the "machinery" that translates the DNA into proteins needs to be passed along with it.</p>
<p>Could this machinery also be encoded within the DNA? Or does it come automatically from some physical/chemical properties of dna? Or is it already present within the sperm/egg?</p>
<p>I am thinking if the dna somehow contains information on how to build the machinery to interpret it, we might be able to get a whole new understanding of how it works.</p>
| [
{
"answer_id": 76260,
"pm_score": 3,
"text": "<p>Your question is very general, but it has a simple answer.</p>\n\n<p><strong>Yes.</strong> The protein machinery which interacts, reads, structures and manipulates the DNA strands is coded for in the DNA.</p>\n\n<p>By way of example: one enzyme which open... | [
{
"answer_id": 76261,
"pm_score": 2,
"text": "<p>The machinery that manipulates and read the DNA (e.g. <a href=\"https://en.wikipedia.org/wiki/Helicase\" rel=\"nofollow noreferrer\">helicase</a>, <a href=\"https://en.wikipedia.org/wiki/Ribosomal_RNA\" rel=\"nofollow noreferrer\">rRNA</a> and <a href=\"h... |
76,308 | <p>I read on Wikipedia that 2,3 BPG binds with the deoxygenated state of hemoglobin and helps in stabilizing it. It was also written that it helps release remaining oxygen from the hemoglobin. How? </p>
<p><a href="https://en.m.wikipedia.org/wiki/2,3-Bisphosphoglyceric_acid" rel="nofollow noreferrer">https://en.m.wikipedia.org/wiki/2,3-Bisphosphoglyceric_acid</a></p>
| [
{
"answer_id": 76315,
"pm_score": 3,
"text": "<p>You've answered your own question. The association/dissociation of oxygen is an equilibrium reaction. If you stabilize one state, you move the equilibrium to that state. 2,3-BPG helps release oxygen from Hb exactly by binding and stabilizing deoxy-Hb.</p>... | [
{
"answer_id": 76541,
"pm_score": 0,
"text": "<p>From more mechanistic point of view, 2,3-biphosphoglycerate contains 2 negatively charged phosphate groups, which interacts with positively charged groups of each beta-chain within deoxyhaemoglobin decreasing the oxygen affinity (see good old <a href=\"ht... |
76,327 | <p>in this <a href="https://www.youtube.com/watch?v=rD5uNAMbDaQ" rel="nofollow noreferrer">video</a> at 5:28, the narrator talks about a "vat-grown all-purpose sieve organ" called <strong>Kliver</strong> that would do away with both liver and kidney transplant. But i don't seem to find online resources about the same. Is that terminology popular in scientific literature, and if so, how would synthetic biology accomplish that? articles about the same will also be appreciated. </p>
| [
{
"answer_id": 76315,
"pm_score": 3,
"text": "<p>You've answered your own question. The association/dissociation of oxygen is an equilibrium reaction. If you stabilize one state, you move the equilibrium to that state. 2,3-BPG helps release oxygen from Hb exactly by binding and stabilizing deoxy-Hb.</p>... | [
{
"answer_id": 76541,
"pm_score": 0,
"text": "<p>From more mechanistic point of view, 2,3-biphosphoglycerate contains 2 negatively charged phosphate groups, which interacts with positively charged groups of each beta-chain within deoxyhaemoglobin decreasing the oxygen affinity (see good old <a href=\"ht... |
76,329 | <p><strong>This is a question about education.</strong> <strong>I am trying to come up with a very visual and clear example, to explain a particular concept in evolution.</strong></p>
<p>The concept I am trying to explain is, </p>
<blockquote>
<p><em>the fact that an animal does not need to understand <strong>why</strong> it's doing something in order for that behaviour to be selected</em> </p>
</blockquote>
<p>(by "why" I mean, the evolutionary/functional role of that behaviour, the reason why it increases the animal's fitness).</p>
<p>Students who don't yet intuitively understand evolution, sometimes mistakenly think that in the theory of evolution, animals need to <strong>understand</strong> why their behaviour is leading to offspring in order to do that behaviour. (they might say: "the bee looks for flowers because it wants to feed his children", although bees (probably) don't actually make this computation, but simply act on stimuli). </p>
<p>(Note by the way that this is not simply about anthropomorphization: e.g. humans also don't need to understand what sex is for, in order to produce offspring).</p>
<hr>
<p><strong>What I'm looking for is an example of an animal, and a behaviour that is characteristic for that animal, that very clearly shows this principle:</strong></p>
<ul>
<li><p>It should be clear and intuitive, that the animal doesn't understand "why" it's doing what it's doing, because to reason about this would <strong>clearly</strong> be too complicated for the animal (I don't think the bee example really satisfies this).</p></li>
<li><p>It should be visual, and memorable.</p></li>
</ul>
| [
{
"answer_id": 76315,
"pm_score": 3,
"text": "<p>You've answered your own question. The association/dissociation of oxygen is an equilibrium reaction. If you stabilize one state, you move the equilibrium to that state. 2,3-BPG helps release oxygen from Hb exactly by binding and stabilizing deoxy-Hb.</p>... | [
{
"answer_id": 76541,
"pm_score": 0,
"text": "<p>From more mechanistic point of view, 2,3-biphosphoglycerate contains 2 negatively charged phosphate groups, which interacts with positively charged groups of each beta-chain within deoxyhaemoglobin decreasing the oxygen affinity (see good old <a href=\"ht... |
76,532 | <p><img src="https://i.stack.imgur.com/doUlg.jpg" alt="enter image description here">
This bugs are everywhere in my house and we've tried so many home remedies, but they won't leave. Can anyone help us!?</p>
| [
{
"answer_id": 76534,
"pm_score": 3,
"text": "<p>That is an Indian meal moth <em>Plodia interpunctella</em>. Family Pyralidae. They are very common household pests. <a href=\"https://www.doyourownpestcontrol.com/indian_meal_moth.htm\" rel=\"nofollow noreferrer\">https://www.doyourownpestcontrol.com/indi... | [
{
"answer_id": 76535,
"pm_score": 2,
"text": "<p>This is probably a common <a href=\"https://en.m.wikipedia.org/wiki/Indianmeal_moth\" rel=\"nofollow noreferrer\">flour moth</a> or a similar pyralid species. It has probably laid eggs in some cereal-derived products (pasta, cous cous, but also rice, oatm... |
76,809 | <p>I know the answer is no. But what then explains the name of these receptors being specific to Cannabinoid found in cannabis? Aren't Cannabinoid receptors exclusive to Cannabinoid? Why are they named like that, if not? </p>
| [
{
"answer_id": 76818,
"pm_score": 4,
"text": "<h3>Receptors</h3>\n<p>Any drug or compound with specific effects has a receptor. You can read about this general concept in Goodman and Gillman's The Pharmacological Basis of Therapeutics. Chapter 1 introduces the concept, chapters 3 and 5 expand further. A... | [
{
"answer_id": 76828,
"pm_score": 3,
"text": "<p>In addition to De Novo's excellent answer, I would like to add that <strong>sometimes, the fact that we have receptors for something is precisely a sign that we should <em>not</em> consume that thing</strong>. </p>\n\n<p>When it comes to taste and smell i... |
76,852 | <p>Yesterday I had a BBQ with some friends. The sun had already set and the only light source left (besides some ambient light from the world around) was a low energy light bulb.</p>
<p>After a while I started to see lighting changes in the faces of my friends and the number plates of their cars. It felt like someone toggled the light very fast. When looking at the wall or the light directly I didn't notice any flickering.</p>
<p>In my country the power grid is running at 50 Hz. Is it possible that I actually saw the flickering caused by the alterations in the power grid or am I just going insane?</p>
| [
{
"answer_id": 76853,
"pm_score": 6,
"text": "<p><strong>Short answer</strong><br>\nYes, the flickering of a light bulb <em>may</em> be noticeable, and yes, that's directly related to the mains frequency. However, since the flickering of a bulb is about two times higher than the temporal limits of our v... | [
{
"answer_id": 76867,
"pm_score": 3,
"text": "<p>A lamp flickers at 2x the mains frequency, i.e. 100 or 120 Hz, and that is typically not noticeable to human eyes. It is visible to chicken and insects. </p>\n\n<p>That being said, a low quality lamp or a lamp at end-of-life may also flicker at 50 or 60 H... |
77,017 | <p>Could someone explain to me the role played by the Fc region of an antibody as well as the purpose of isotype switching? According to <a href="https://en.wikipedia.org/wiki/Antibody" rel="nofollow noreferrer">Wikipedia</a>, it's to allow the antibody to be usable by different Fc receptors, but I don't get what Fc receptors are for.</p>
<p>For context, </p>
<ol>
<li>I'm reading about affinity maturation and learning about how ecological and evolutionary processes --- division, selection, and mutation --- drive the maturation of B cells leading to high-affinity plasmocytes that can better target a foreign antigen. Because all this happens on the Fab fragment, it makes sense to me why the Fab region is important in the antibody.</li>
<li>I'm not trained in cell biology. </li>
<li>My goal is to understand the general purpose of the Fc region and how isotype switching may be a major determinant for specific immunological or physiological outcomes, although I'd love to hear anything interesting! </li>
</ol>
<p>Thanks in advance! </p>
| [
{
"answer_id": 77030,
"pm_score": 3,
"text": "<p><strong>Preamble</strong></p>\n\n<p>From the point of view of understanding I think it is better to talk about the constant and variable regions of antibodies, rather than Fab and Fc, as these are historical designations for <em>fragments</em> of the mole... | [
{
"answer_id": 77127,
"pm_score": 0,
"text": "<p>The Fc region is composed of the two heavy chain constant regions, and its amino acid composition differs between the different classes of immunoglobulin (antibody). The Fc region of the five immunoglobulin (Ig) classes (IgA, D, E, G, and M)confers upon e... |
77,246 | <p>Do oysters feel pain when you bite into the inside, or when you crack open the shell? I tried google searching it to no avail. When you bite inside the oyster or when you break the shell to open the oyster, does it feel pain?</p>
<p>EDIT: (Since some people think that mine is a duplicate) I'm asking if the oysters feel pain when we eat the inside, or when we crack open their shell. To the least of my knowledge, ants and oysters have a different body so I don't know if they do feel pain.</p>
| [
{
"answer_id": 77254,
"pm_score": 7,
"text": "<p>There are fundamental problems with defining what it means for an animal to feel pain, especially when the animal is a life form as different from us as an oyster.</p>\n\n<p>I wasn't able to find any specific info online about oysters, but there is quite ... | [
{
"answer_id": 77250,
"pm_score": 2,
"text": "<p>Referring to this <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896133/\" rel=\"nofollow noreferrer\">research article</a> on PubMed, oysters have their sensory system and organisation like humans. So any change or invasion in the system of Oyst... |
77,537 | <p>I'm reading this paper <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562283/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562283/</a> , but I cannot make sense of what MPS nor how should I read the pictures that make use of this method.</p>
<p>The authors say</p>
<blockquote>
<p>The MPS, beyond classical representations such as the waveform and spectrogram (Figure 1A and B, upper and middle panels), displays the time-frequency power in modulation across both spectral and temporal dimensions (Figure 1A and B, lower panels). The MPS has become a particularly useful tool in auditory neuroscience because it provides a neurally and ecologically relevant parameterization of sounds</p>
</blockquote>
<p>I'm clueless about what the meaning of <strong>time-frequency power in modulation across both spectral and temporal dimensions</strong>. Can someone provide a brief explanation about this and MPS?</p>
| [
{
"answer_id": 77546,
"pm_score": 3,
"text": "<p>A time-frequency graph also know as a TF distribution, is a spectrogram, a spectrograph, a sonogram, a waterfall display of sound. They are all different names for the same thing. They look like this: </p>\n\n<p><a href=\"https://www.google.fr/search?q=do... | [
{
"answer_id": 77554,
"pm_score": 2,
"text": "<p>MPS is the two-dimensional Fourier transform of the spectrogram. Assuming that you know what a Fourier transform and a spectrogram is, the MPS method consists in treating the spectrogram as an image on which to apply the Fourier transform. Thus, one can e... |
77,803 | <p>In a handout the following is stated:</p>
<blockquote>
<p>Amylose is insoluble in water, therefore a good storage compound e.g. in stroma of chloroplasts</p>
</blockquote>
<p>This is with regard to the chemical structure of the molecule.</p>
<p>However it has left me wondering, what is it intrinsically about the structure of a molecule that makes it soluble/insoluble in water?</p>
<p>My thoughts at this stage are perhaps to do with whether the molecule is hydrophobic, and if that is the case - how is amylose hydrophobic?</p>
| [
{
"answer_id": 88487,
"pm_score": 3,
"text": "<p>The availibity of -OH groups for hydrogen bonding with polar water molecules is reduced in amylose due to its coiled nature (resulting in part by H-bonds between the glucose monomers). Amylopectin is even less soluble due to the additional 1-6 glycosidic... | [
{
"answer_id": 77837,
"pm_score": 1,
"text": "<p>There are a couple of other questions that address this point indirectly:\n<a href=\"https://biology.stackexchange.com/questions/38830/solubility-of-amylopectin-and-glycogen-in-water\">here</a> and <a href=\"https://biology.stackexchange.com/questions/663... |
77,805 | <p>I think most biologists here on this site will not consider my question below to be unfit for posting on Biology SE. </p>
<p>I came across <a href="http://understand-islam.net/Articles/TheHadeethontheFly.pdf" rel="nofollow noreferrer">this</a> article about the hadeeth (a hadeeth is a saying of the Prophet Muhammad (peace be upon him)) on a fly:</p>
<blockquote>
<p>"If a housefly falls in the drink of anyone of you, he should dip it (in the
drink), for the one of its wings has a disease and the other has the cure of
the disease." [Bukhari, vol. 4: 537].</p>
</blockquote>
<p>where an attempt is made to show the truthfulness of the hadeeth with an experiment: they dip a fly into water in a petri dish wholly and partially in another petri dish and different kinds of bacteria appear in each petri dish. This experiment is carried out 3 times and results are different in each round. (Please, read that article thoroughly before answering) I want to know biologists' point of view on that experiment, i.e. </p>
<p>Do you believe this hadeeth based on the experiment? (i. e. do you consider it to be pseudoscience or not? If yes, please provide your proofs.)</p>
<p>Can pathogenic bacteria arise in such an impressive quantity in water just by dipping fly into water? If yes, could you explain how?</p>
<p>Do you agree with the notion in the hadeeth 'he should dip it (in the drink)? </p>
<p>Thanks very much for your answers in advance!</p>
| [
{
"answer_id": 77806,
"pm_score": 4,
"text": "<p><strong>Rephrasing your question</strong></p>\n<p>Allow me to start by saying that I barely know the term Hadeeth / Hadith mean. Of course I have checked on <a href=\"https://en.wikipedia.org/wiki/Hadith\" rel=\"nofollow noreferrer\">wikipedia</a> but its... | [
{
"answer_id": 77867,
"pm_score": 0,
"text": "<p>\"If a housefly falls in the drink of anyone of you, he should dip it (in the drink), for the one of its wings has a disease and the other has the cure of the disease.\"</p>\n\n<p><strong>The quoted text above is not meant literally(!), it is a metaphor</... |
77,847 | <p>I have a forward primer with Tm 85 degree Celcius. I cannot change this primer. But I have two options for the reverse primer. One with Tm 65 degree Celcius (Annealing at 65 degree Celcius) and another with 72 degree Celcius (Annealing at 72 degree Celcius).
First of all, will either of the primers work for me?
If so, which pair would be better?</p>
| [
{
"answer_id": 77806,
"pm_score": 4,
"text": "<p><strong>Rephrasing your question</strong></p>\n<p>Allow me to start by saying that I barely know the term Hadeeth / Hadith mean. Of course I have checked on <a href=\"https://en.wikipedia.org/wiki/Hadith\" rel=\"nofollow noreferrer\">wikipedia</a> but its... | [
{
"answer_id": 77867,
"pm_score": 0,
"text": "<p>\"If a housefly falls in the drink of anyone of you, he should dip it (in the drink), for the one of its wings has a disease and the other has the cure of the disease.\"</p>\n\n<p><strong>The quoted text above is not meant literally(!), it is a metaphor</... |
77,928 | <p>Here is <a href="https://www.practo.com/healthfeed/hot-bath-tubs-can-kill-male-fertility-14002/post" rel="noreferrer">the link</a> where urologists are warning men not to take hot water baths.</p>
<p>Why does it affect only males' fertility? Why not females also? </p>
| [
{
"answer_id": 77930,
"pm_score": 4,
"text": "<p>A mature human sperm has some mitochondria, a nucleus, an acrosome, and a flagellar apparatus. That's it. Because of the lack of other organelles in the sperm, they have to be kept in a kind of 'cold storage' so that they are viable for at least some time... | [
{
"answer_id": 77931,
"pm_score": 2,
"text": "<p>To keep sperm viable in natural body conditions, they are kept at a relative lower temperature than the body temperature, and this can achieved by the scrotum. As sperm is produced in testis, and testis are situated in the scrotum outside the main part of... |
77,956 | <p>In an <a href="https://newatlas.com/child-abuse-dna-genetic-biomarker/56588/" rel="nofollow noreferrer">article on biomarkers of child abuse</a>, the author referred to an "epigenetic mark on a person's DNA". It's a popular science article, so the language may reflect a combination of the journalist's scientific competency and his or her desire to communicate complex topics efficiently to a lay audience. Is that an example of such language?</p>
<p>My understanding was that anything in the realm of "epigenetics" is happening to something other than DNA. Is it technically correct to refer to an "epigenetic mark on a person's DNA"? Correct enough? Only potentially misleading? I'm trying to wrap my head around the whole epigenetics concept.</p>
| [
{
"answer_id": 77930,
"pm_score": 4,
"text": "<p>A mature human sperm has some mitochondria, a nucleus, an acrosome, and a flagellar apparatus. That's it. Because of the lack of other organelles in the sperm, they have to be kept in a kind of 'cold storage' so that they are viable for at least some time... | [
{
"answer_id": 77931,
"pm_score": 2,
"text": "<p>To keep sperm viable in natural body conditions, they are kept at a relative lower temperature than the body temperature, and this can achieved by the scrotum. As sperm is produced in testis, and testis are situated in the scrotum outside the main part of... |
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