qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
10,803 | <p>What kind of objects can be qualified as artifacts? How do we distinguish such objects?</p>
| [
{
"answer_id": 10815,
"pm_score": 3,
"text": "<p>An artifact in biology usually refers to experimental error or other spurious results. In the context of microbiology, you will get artifacts if, for example, you sneeze on the plate you are growing a colony on. </p>\n\n<p>The term is generally used for ... | [
{
"answer_id": 14884,
"pm_score": 0,
"text": "<p>This is a very good question! There are many factors there so the list would be very long. There are many kinds of artifacts too, some related to processes and the other on technical devices. Some of the processes we do not know or we have not defined tho... |
10,806 | <p>Why do different bacteria have different shapes? Is it only related to their function?</p>
| [
{
"answer_id": 10812,
"pm_score": 5,
"text": "<p>Reasons for Bacteria with different shapes as given in <a href=\"http://en.wikipedia.org/wiki/Bacteria\">Wikipedia/Bacteria</a>:</p>\n\n<blockquote>\n <p><em>The wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is imp... | [
{
"answer_id": 20167,
"pm_score": 1,
"text": "<p>As for how certain bacteria achieve their shapes, the cell wall plays an important role. Almost all bacteria have a cell wall made of a substance called peptidoglycan, a mesh of peptides and saccharides that provides rigidity and strength to the bacteria.... |
10,816 | <p>I thought about this statement a while ago:</p>
<blockquote>
<p>Natural selection sucks, it says those who love too much (or too many) will die the easiest and fastest. Sad but true.</p>
</blockquote>
<p>Only family (biologically of course) should be loved. This isn't rather an ethics question but whether those who love too many or too much die easiest. true?</p>
<p><strong><em>NEW QUESTION</strong></em>: What about if you love your subject, mathematics, to death? You'll give up meditating, personality, gym, friends, goldfish, everything just to find out new theorems. What is the take on this? </p>
<p>Surely you'll take a bird's eye view right after the accomplishment (or perhaps failure sometimes) and see what you've accumulated in losses (or in earnings). But Is it in the right path of the true purpose?</p>
<p>Given the person is highly into itself, such that it operates on an ideology instead of what the current trends are (in this case, stay healthy^^), it would be great to love. Nothing else would matter. </p>
<p>Biologically, it wouldn't make sense. <strong>If I loved something like mathematics, how in the world could I produce babies?</strong> Geniuses like Erdos never had children but, my god take a look at his work.</p>
<p>^^I'm not sure if my claim is correct, which is the matter of this question: </p>
<p><strong>Should we stay healthy or go beyond our health (as the Curie's did) to discover science?</strong></p>
| [
{
"answer_id": 10817,
"pm_score": 4,
"text": "<p>The idea that we only love our family according to biology is not true, but its also not clear what people mean by the word 'love'. There are many ways to interpret that word!</p>\n\n<p>Hope this doesn't totally suck any romantic ideas out of you, but me... | [
{
"answer_id": 10826,
"pm_score": 2,
"text": "<p>Shigeta brings up the question of altruism which Richard Dawkins famously explains in the context of evolution in The Selfish Gene. This is probably the easiest way to translate feelings of love into biology.</p>\n\n<p>EO Wilson has also addressed the ide... |
10,819 | <p>If the reason <em>Why Men Don't Listen and Women Can't Read Maps</em> is genetic, then one of the genes in the Y chromosome is to blame and in theory could be identified.</p>
<p>Correct or incorrect?</p>
| [
{
"answer_id": 10825,
"pm_score": 5,
"text": "<p>\"<em>Blame</em>\" is a strong word. The human Y chromosome has <a href=\"http://uswest.ensembl.org/Homo_sapiens/Location/Chromosome?chr=Y;r=Y:1-59373566\">only a few dozen protein-coding genes</a>. One of the most important, for males anyway, is <a hre... | [
{
"answer_id": 13968,
"pm_score": 2,
"text": "<p>Imagine a culture where girls are chastised for taking risks, and heavily punished when they take risks and fail, but where boys are encouraged to take risks, and praised highly when things work out their way. </p>\n\n<p>Wouldn't you expect that when put... |
10,829 | <p>Everytime I see a ladybug I ask myself this question.
Why does every ladybug have a different amount of points on its back? Is it because of its age? Or because of its genes? Is it inheritable?</p>
| [
{
"answer_id": 10833,
"pm_score": 5,
"text": "<p>The spots on the back of Ladybugs over the surface is defense mechanism to avoid predators. The spots come in different shapes and different numbers. Some say that those dots tell us their age. Since some ladybugs have 24 spots which means its age would b... | [
{
"answer_id": 10832,
"pm_score": 2,
"text": "<p>It is because of genes, and is completely inheritable! First I want point out that there spots, or points, do not change over time. Rather the spot number and location is fixed when Coccinellidae are pupa (tween aged insects). </p>\n\n<p>You will noti... |
10,841 | <p>This article about <a href="http://news.ufl.edu/2013/10/08/alzheimers-test/" rel="nofollow">testing for Alzheimer's</a>, via changes in the ability to smell, said:</p>
<blockquote>
<p>She thought of peanut butter because, she said, it is a “pure odorant”
that is only detected by the olfactory nerve and is easy to access.</p>
</blockquote>
<p>I'm not clear on what that means. Assuming a person had their mouth closed, then wouldn't <em>any</em> odor be detected only by the olfactory nerve? Wouldn't a lemon, say, work exactly the same?</p>
| [
{
"answer_id": 13762,
"pm_score": 3,
"text": "<p>To answer this question, you need some background info first.</p>\n\n<p>There are three \"systems\" used for the sense of smell. The first is the olfactory system. This system allows us to recognize what a smell is. You can tell the difference between gar... | [
{
"answer_id": 10844,
"pm_score": 2,
"text": "<p>I could not find a concrete definition after searching several sources, but after reading a few papers I think the term <strong>Pure Odorant</strong> refers to its Olfactory Bulb profile. Peanut Butter will stimulate specific Olfactory nerves, and <em>onl... |
10,885 | <p>What dissociates first - the last tRNA, mRNA and release factors or the subunits of ribosomes?</p>
<p>I tried searching this from Lehninger but couldn't get a clean answer.</p>
| [
{
"answer_id": 10890,
"pm_score": 3,
"text": "<p>Shigeta's got a point: the ribosome is latched onto the mRNA so those two are intrinsically linked. You're really asking whether the ribosome comes off first or whether the tRNA does, but it's actually the new polypeptide, which makes sense:</p>\n\n<bloc... | [
{
"answer_id": 10888,
"pm_score": 1,
"text": "<p>just off the top of my head... since the ribosome is made of 2 large complexes which assemble and clamp onto the mRNA, <a href=\"http://en.wikipedia.org/wiki/File%3aProtein_translation.gif\" rel=\"nofollow\">I'd say it was the tRNA first, then the ribosom... |
10,906 | <p>Can parasite, microbes be passed from mother to fetus through the placenta ?</p>
<p>I know some like HIV can be.</p>
| [
{
"answer_id": 10913,
"pm_score": 4,
"text": "<p>Pregnant mothers can indeed pass on various microbes to their fetuses but it is not always directly through the placenta, as the placenta can be protective. Although the blood of the mother and fetus do not mix directly, the two can interact. Maternal p... | [
{
"answer_id": 10908,
"pm_score": 2,
"text": "<p>Parasite are organisms, and they can pass through mother to her child while its in hers womb. Toxoplasma gondii is an example, it passed from mother to child as it moves through her body, and since child is present inside her, of course it will get into t... |
10,917 | <p>I'm used to working with bacteria - some of the more common laboratory strains sometimes come with an order from some vendors. What's the most convenient source to order <a href="http://wiki.yeastgenome.org/index.php/Commonly_used_strains" rel="nofollow">common straings of Saccharomyces</a> for lab work? </p>
| [
{
"answer_id": 10913,
"pm_score": 4,
"text": "<p>Pregnant mothers can indeed pass on various microbes to their fetuses but it is not always directly through the placenta, as the placenta can be protective. Although the blood of the mother and fetus do not mix directly, the two can interact. Maternal p... | [
{
"answer_id": 10908,
"pm_score": 2,
"text": "<p>Parasite are organisms, and they can pass through mother to her child while its in hers womb. Toxoplasma gondii is an example, it passed from mother to child as it moves through her body, and since child is present inside her, of course it will get into t... |
10,946 | <p>Most of the time, our genes have common interests with our "self".</p>
<p>We reproduce well if and only if our genes reproduce well.</p>
<p>In some cases, like in bees, the haploid bees can survive better if they help their queen reproduce.</p>
<p>In humans and other species, are there samples that give individuals "incentive" to help non family member to reproduce for the sake of their genes.</p>
<p>So </p>
<ol>
<li>No filial altruism</li>
<li>No reciprocal altruism</li>
</ol>
<p>So I need a sample between individual based evolution and gene base evolution.</p>
<p>For example, many genocide are done against the best and brightest. I wonder what sort of genes encode "kill the best and brightest" and how does that kind of gene survive well in the gene pool?</p>
| [
{
"answer_id": 10947,
"pm_score": 3,
"text": "<p>The prototypical example of this is <em>t</em>, whose existence was predicted by <a href=\"http://en.wikipedia.org/wiki/Robert_Trivers\" rel=\"nofollow\">Robert Trivers</a> and featured prominently in <a href=\"http://en.wikipedia.org/wiki/Selfish_gene\" ... | [
{
"answer_id": 10949,
"pm_score": 1,
"text": "<p>Complex behaviours like altruism rarely boil down to a single gene, so it's hard to find a concrete example.</p>\n\n<p>This is one lead:\n<a href=\"http://scan.oxfordjournals.org/content/early/2010/10/28/scan.nsq083.full\" rel=\"nofollow\">http://scan.oxf... |
10,988 | <p>If I am not mistaken, during exposure to electricity sources it is the magnitude of the current and not the voltage that kills the human body. If so, what is the order of magnitude of current that human body can sustain, and for what duration? How do defibrillators exploit this?</p>
| [
{
"answer_id": 10990,
"pm_score": 3,
"text": "<p>According to Wikipedia <a href=\"http://en.wikipedia.org/wiki/Electric_shock\" rel=\"nofollow noreferrer\">Electric shock</a>, the Magnitude of electric shock to a body is mainly due to current as well as voltage. Various factor of the environment will al... | [
{
"answer_id": 11069,
"pm_score": 1,
"text": "<p><a href=\"http://www.allaboutcircuits.com/vol_1/chpt_3/4.html\" rel=\"nofollow\">This article</a> deals with the issue in detail.</p>\n"
}
] |
11,009 | <p>Going back to my high school days we were taught about dominant and recessive genes. We were taught how to calculate the geneotype and pheneotype of potential offspring using a small table (forgotten the actual table name). But it never occurred to me then what determines if a gene is dominant or recessive and how this is carried out biologically.</p>
<p>Take my example below, there is a 50% change that an offspring will carry both the tall (T) and short (t) genes. What determines that the tall gene T has a dominant effect over the short gene t. </p>
<p>Now, I know that there is going to be differences between the different genes (i.e. eye colour), but is there a general description any one and provide which states how a gene becomes dominant and how the dominant effect is carried out biologically.</p>
<p><img src="https://i.stack.imgur.com/X3IFx.gif" alt="enter image description here"></p>
| [
{
"answer_id": 11010,
"pm_score": 4,
"text": "<p>Dominance is seldom complete. Owing to effects like co-dominance, incomplete dominance, collaborative (additive) effects of polygenes, our classical concept of dominance doesn't work. Having said that, there are certain ways in which a gene, if showing co... | [
{
"answer_id": 11040,
"pm_score": 2,
"text": "<p>Fisher and Wright provided two different models in order to explain why newly arisen mutations tend to be recessive. I am not sure though if this answer your question!</p>\n\n<p><strong>Fisher's model</strong></p>\n\n<blockquote>\n <p>\"...there is a ten... |
11,059 | <p>I am novice to biochemistry and biology in general. I am reading Lehninger Principles of Biochemistry, and I found the following sentence at the beginning of the chapter on glycolysis:</p>
<blockquote>
<p>A bacterium such as Escherichia coli can obtain from glucose the carbon
skeletons for every amino acid, nucleotide, coenzyme, fatty acid, or
other metabolic intermediate it needs for growth.</p>
</blockquote>
<p>Does this mean that <em>E.coli</em> can survive in a medium containing H₂O and glucose alone? <em>E.coli</em> can synthesize any other nutrient it needs?</p>
| [
{
"answer_id": 11062,
"pm_score": 4,
"text": "<p>The minimum requirement for <em>E. coli</em> and other bacteria to grow and survive is called <strong>minimal medium</strong>. It's even defined at <a href=\"http://www.merriam-webster.com/medical/minimal%20medium\" rel=\"nofollow\">Merriam-Webster</a>:<... | [
{
"answer_id": 11060,
"pm_score": 2,
"text": "<p>Yes, but no. In other words, this quote is not probably not true in the ways you'd think. Bacteria <em>can</em> survive on practically nothing for long periods of time, but whether you call that life is subjective. </p>\n\n<p>Nitrogen is necessary for al... |
11,074 | <p>I'm a newbie in biology and medicine. I understand that Henrietta Lacks provided the cells that formed the HeLa cell line with which much research has been done. Henrietta Lacks died of cancer. If we assume that she did not have cancer, every cell in her body could divide for an infinite period of time, and she never sustained any trauma ever, would Henrietta Lacks have been immortal?</p>
<p>Thanks,
mj</p>
| [
{
"answer_id": 11079,
"pm_score": 4,
"text": "<p>No, there was nothing special about Henrietta Lacks, apart from the fact that her cells have been used for so many years (without her knowledge or consent, by the way). She was not immortal, her tumor cells were. The HeLa cell line comes from her <a href=... | [
{
"answer_id": 11076,
"pm_score": 2,
"text": "<p>I believe your question is unclear, but if am I am understanding the question as:</p>\n\n<blockquote>\n <p>If H.L., or anyone, did not develop cancer, was never introduced to any physical insult, would they be immortal?</p>\n</blockquote>\n\n<p>The answe... |
11,102 | <p>Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1? By “marginal” I mean predictive power beyond other known effects, e.g., the race of the parents, the mother’s weight, season of birth (list from <a href="http://www.stat.columbia.edu/~gelman/presentations/ziff.pdf" rel="nofollow">this presentation</a> by Andrew Gelman).</p>
<p>I know that many claims that some variable can predict a child have been accused of resting on shaky statistics (see the presentation linked to above). But the sex of preceding children seems like it could be a strong predictor.</p>
<p>UPDATE: answering fileunderwater's question</p>
<blockquote>
<p>Can you expand on why (by what mechanisms) you think that it could be a strong predictor? Male sex-chromosome bias in sperm?</p>
</blockquote>
<p>Yes, sex-chromosome bias was my first thought. I almost focused my question specifically on that but the fact that I saw maternal weight listed as a predictor in the Gelman presentation made me think there might be other relevant factors that I wouldn't think of. So I broadened the scope of the question.</p>
| [
{
"answer_id": 11124,
"pm_score": 4,
"text": "<p>For those who are interested in sex ratio bias itself, the <a href=\"https://en.wikipedia.org/wiki/Human_sex_ratio\" rel=\"nofollow noreferrer\">enWikipedia article</a> is pretty good.</p>\n\n<p>As for predictive power, a Bayesian might tell you that by k... | [
{
"answer_id": 40742,
"pm_score": 2,
"text": "<p>Probably YES.</p>\n\n<p>An analysis of data from about 8 million births shows that there is positive correlation. Please see <a href=\"http://biorxiv.org/content/early/2015/11/16/031344\" rel=\"nofollow\">http://biorxiv.org/content/early/2015/11/16/031344... |
11,133 | <p>Here is the Wright-Fisher model of genetic drift:</p>
<p>$$\frac{(2N)!}{k!(2N-k)!}p^kq^{2N-k} \Leftrightarrow \binom{2N}{k}p^kq^{2N-k}$$</p>
<p>where $\binom{2N}{k}$ is the binomial coefficient.</p>
<p>This formula gives the probability of obtaining $k$ copies of an allele at generation $t+1$ given that there are $p$ copies of this allele at generation $t$. $N$ is the population size and $2N$ is the number of copies of each gene (this model applies to diploid population only).</p>
<p><strong>From this formula, how can we calculate the probability of extinction of an allele in say 120 generations starting at a given frequency, let's say 0.2?</strong></p>
<p>and</p>
<p><strong>How can we calculate the probability of extinction rather than fixation of an allele present at frequency $p$ if we wait an infinite amount of time?</strong></p>
| [
{
"answer_id": 11143,
"pm_score": 3,
"text": "<p><strong>update</strong></p>\n\n<p><strong>The answer is <a href=\"https://math.stackexchange.com/questions/585578/biology-wright-fisher-model-of-genetic-drift\">here</a>!</strong></p>\n\n<hr>\n\n<p><strong>Original comment/answer</strong></p>\n\n<p><a hre... | [
{
"answer_id": 20466,
"pm_score": 1,
"text": "<p>Here is a simple proof that the probability of fixation given an infinite time is indeed p (in a finite population, otherwise there will be no fixation):\nLet's look at all 2N gametes in the population. Eventualy, according to the Wright-Fisher model, onl... |
11,152 | <p>I ran an enrichment analysis with custom annotations using TopGO and surprisingly I obtained new GO terms inside the significant GO terms. </p>
<p>Is that possible? The only reason I can imagine this is possible is because TopGO adds new GO terms based on the input GO terms, since GO ontology is structured hierarchically.</p>
<p>Please let me know if you need more details about the experiment.</p>
<p>Code:</p>
<p><a href="https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing" rel="nofollow">https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing</a></p>
<p>TopGO output:</p>
<p><a href="https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing" rel="nofollow">https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing</a></p>
<p>Thanks, Bernardo</p>
| [
{
"answer_id": 11143,
"pm_score": 3,
"text": "<p><strong>update</strong></p>\n\n<p><strong>The answer is <a href=\"https://math.stackexchange.com/questions/585578/biology-wright-fisher-model-of-genetic-drift\">here</a>!</strong></p>\n\n<hr>\n\n<p><strong>Original comment/answer</strong></p>\n\n<p><a hre... | [
{
"answer_id": 20466,
"pm_score": 1,
"text": "<p>Here is a simple proof that the probability of fixation given an infinite time is indeed p (in a finite population, otherwise there will be no fixation):\nLet's look at all 2N gametes in the population. Eventualy, according to the Wright-Fisher model, onl... |
11,156 | <p>I always wondered what ophthalmologists see inside someone's eye and what they're looking for. The whole thing is a mystery to me. Are there any photos of what the eye of a patient looks like from the doctor's point of view?</p>
| [
{
"answer_id": 11251,
"pm_score": 3,
"text": "<p>The name of the instrument is <a href=\"http://en.wikipedia.org/wiki/Ophthalmoscope\" rel=\"nofollow\">ophthalmoscope</a>. It is used to determine the health status of your retina. Retina is the one of the few places in the body where you can observe the ... | [
{
"answer_id": 11163,
"pm_score": 0,
"text": "<p>They look at retina. Google for it. The look of retina can evident of some diseases. This is the subject of medical education.</p>\n"
}
] |
11,166 | <p><strong>Background</strong></p>
<p>To improve sleep by reducing blue-light melatonin disruption, I wear night-glasses that filter short wavelengths (e.g. something like <a href="https://www.google.com.au/search?q=blue%20light%20blocking%20glasses&site=imghp&tbm=isch&tbo=u&source=univ" rel="nofollow noreferrer">these</a>). With these glasses on, both the top and bottom bars of this test image will appear visually identical:</p>
<p><img src="https://i.imgur.com/H8I3fFz.png" alt="RGB wavelength image. Bottom bar with zero blue value">
<sub>(Source: Personally derived from this public domain <a href="http://commons.wikimedia.org/wiki/File:Linear_visible_spectrum.svg" rel="nofollow noreferrer">image</a> and released to public domain)</sub></p>
<p>But the colour spectrum you "see" while filtering the blue light will not appear to be either of these bars; instead some partially de-saturated hybrid of the two. I think this is probably due to a pervasive blue wavelength of the LCD back-light regardless of defined colour contrast.</p>
<p>However, there is something else odd going on. If I wear these glasses for several hours and then remove them for some reason - all the blue colours I should see will be muted, partially de-saturated or even interpreted as a shade of green for at least several minutes afterwards (I haven't stop-watched the effect). Freaky.</p>
<p><strong>Question</strong></p>
<p>Why is this selective shift of colour perception occurring for a while after removing wavelength filtered glasses?</p>
| [
{
"answer_id": 76132,
"pm_score": 3,
"text": "<p>The short answer is you don't see light you see a reconstruction of your environment made by a learning organ, <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/17344377?dopt=Abstract&holding=npg\" rel=\"nofollow noreferrer\">your brain adapts to changes ... | [
{
"answer_id": 74267,
"pm_score": 0,
"text": "<p>Wearing colored glasses forces the eyes to work harder to see the normal colors the way they are supposed to be seen. In other words, when you wear, say, green glasses, the sort that overwhelmingly turn everything green, the eyes are trying harder to det... |
11,223 | <p>I have read that IQ is highly heritable.</p>
<p>How could this be tested?</p>
<p>For honest testing, it seems to me that only children who were abandoned should have been tested, to exclude education effect. Was it really done?</p>
<p><strong>UPDATE</strong></p>
<p>Intelligence is one of the traits, that can be inherited both by genes and by education. You can't educate your children to have blue eyes, but you can educate them to count or to read.</p>
<p>So, to study heritability of intelligence, educational inheritance should be excluded.</p>
<p>I know that usual way to study heritability is to compare variability for monozygotic and dizigotic twins. Being sufficient for other traits, this method is highly insufficient for intelligence (which is obvious). Having identical perception system, monozygotic twins will respond identically to an education, so they will be more closely educated, even if IQ is completely independent of genes.</p>
<p>So, to study IQ heritability, subjects should be studied under different education conditions. I.e. they should be abandoned by parents and/or adopted separately. </p>
<p>My question is: was this done or not?</p>
<p>If not, then the question is, how education effects were eliminated? </p>
<p>Also I would like to know, if my reasoning about why just studying twins is insufficient is wrong.</p>
| [
{
"answer_id": 11226,
"pm_score": 4,
"text": "<p>I don't really know what you mean by \"abandoned children\". Adopted children? Children in the wild? Have you read the <a href=\"https://en.wikipedia.org/wiki/Heritability_of_IQ\">Wikipedia article</a> on the subject? If you want to know how it was st... | [
{
"answer_id": 11275,
"pm_score": 2,
"text": "<p>A classic study of IQ heritability is Skodak & Skeels (1949). They studied heritability of IQ in children who were adopted at a very young age, with IQ data of the children, of their biological mothers, and of their adoptive mothers. It is important t... |
11,240 | <p>There are many <a href="http://en.wikipedia.org/wiki/Species#Definitions_of_species" rel="noreferrer">definitions of "species"</a> which usually take the form</p>
<blockquote>
<p>Two individuals are of the same species if ...</p>
</blockquote>
<p>An implied (rarely made explicit) property of any sensible species definition is that the relation <strong>"is the same species as"</strong> should be an <strong><a href="http://en.wikipedia.org/wiki/Equivalence_relation" rel="noreferrer">equivalence relation</a></strong> (the reason why this is sensible is that only such a relation partitions the set of all individuals into <em>equivalence classes</em>, that is, separate species). In particular, it should be <strong>transitive</strong>, that is</p>
<blockquote>
<p>If A and B are of the same species, and B and C are of the same
species, then it follows that A and C are also of the same species.</p>
</blockquote>
<br>
<h3>It appears to me that all species definitions in use violate that property.</h3>
<br>
<h1>Example</h1>
<p>Are the <strong>Chihuahua</strong> <img src="https://i.stack.imgur.com/rRIrN.jpg" alt="enter image description here" /> and the <strong>Great Dane</strong> <img src="https://i.stack.imgur.com/3R0zY.jpg" alt="enter image description here" /> of the same species?</p>
<p>Not according to the "biological" species definition, which states:</p>
<blockquote>
<p>Two individuals are of the same species if and only if they can <strong>produce fertile offspring.</strong></p>
</blockquote>
<p>Since that is (presumably) not true of Chihuahua and Great Dane, according to that definition, the two dog breeds are not of the same species.</p>
<h2>However...</h2>
<p>Let us say that the Chihuahua can produce fertile offspring with the <strong>Dachshund</strong>...</p>
<p><img src="https://i.stack.imgur.com/lHzsW.jpg" alt="enter image description here" /></p>
<p>... and the Dachshund with the <strong>Golden Retriever</strong>...</p>
<p><img src="https://i.stack.imgur.com/TpUqC.jpg" alt="enter image description here" /></p>
<p>... and that at last with the <strong>Great Dane</strong> as desired.</p>
<p>Then, if we assume transitivity, Chihuahua and Great Dane <em>are</em> of the same species <strong>- contradiction!</strong></p>
<br>
<h1>Another Example</h1>
<p>Are the <strong>Chimpanzee</strong> <img src="https://i.stack.imgur.com/KnHwQ.jpg" alt="enter image description here" /> and the <strong>White Oak</strong> <img src="https://i.stack.imgur.com/RDoOH.jpg" alt="enter image description here" /> of the same species?</p>
<p>Intuitively, they are of course not, the very idea seems ridiculous. Sure enough, with the definition (a variation of the "genetic" species definition)</p>
<blockquote>
<p>Two individuals are of the same species if and only if <strong>their genome differs in less than 0.5% of base pairs.</strong></p>
</blockquote>
<p>the two are indeed <em>not</em> of the same species.</p>
<p><strong>However, we can again construct a "chain" of intermediate individuals, each of which is similar enough to its predecessor to satisfy the definition, eventually connecting Ape and Tree and violating transitivity again.</strong></p>
<br>
<h1>My question to biologists: How is this problem resolved in practice? Are there any species definitions that preserve transitivity?</h1>
| [
{
"answer_id": 11243,
"pm_score": 5,
"text": "<p>I am pretty sure you cannot jump from an oak tree to an ape with whatever common definition of species you're using. But this is some kind of practical implication of your question.</p>\n\n<p>The concept of species was already being used by Aristotle and ... | [
{
"answer_id": 104731,
"pm_score": 0,
"text": "<p>Membership of nominal species is certainly an equivalence relation. For instance, membership of Canis familiaris, or domestic dog. Dogs are not wolves, and wolves are not dogs. But all domestic dogs are the same species. But of course, some taxonomists r... |
11,250 | <p>Martin Nowak in his book "Evolutionary Dynamics" talks about a given correlation between genome size and mutation rate.</p>
<p>What correlation does exactly exist between these two concepts?</p>
<ul>
<li><p>Is it a linear correlation?</p></li>
<li><p>What is the coefficient of correlation?</p></li>
<li><p>Does this correlation exist in many different taxa?</p></li>
</ul>
<p>One will need to make whether we talk about mutation rate per base per generation or for the whole genome.</p>
<p>Some references to accompany claims are welcome!</p>
| [
{
"answer_id": 17174,
"pm_score": 3,
"text": "<p>Bradwell et al. report RNA viruses with the smallest genome may have particularly high mutation rates. A particular bug was shown to have about 1.4 x $10^{-4}$ substitutions per nucleotide per round of copying (high for viruses generally) and the authors ... | [
{
"answer_id": 17178,
"pm_score": 2,
"text": "<p>I'd clarify the above that the mutation rate is probably linear with the number of bases in the cell, since they are caused by random collision with ionizing radiation most of the time. </p>\n\n<p>The number of mutations retained will vary though by orga... |
11,255 | <p>Do you know some examples of virus or a viroid (or a prion) that originated from a known living organism? How does the virus/viroid/prion lives? Does it paratize the organism from which the virus originated?</p>
<p>UPDATE</p>
<p>Thanks to the first answers I have examples of newly originated prions. Does someone know such an example about viruses?</p>
| [
{
"answer_id": 11257,
"pm_score": 2,
"text": "<p>Prion diseases are still very poorly understood, but one of the dominant theories is that they are misfolded proteins that cause disease by catalyzing the misfolding of more proteins of the same type. If that is the case, then they arise from the organis... | [
{
"answer_id": 11284,
"pm_score": 0,
"text": "<p>Prion diseases arise spontaneously fairly often. There are only ~170 total cases of human infection by mad cow disease, but there are ~50 cases/year of Creutzfeldt-Jakob disease, which is a spontaneous strain of prion diseases in humans. There is a stron... |
11,276 | <p>I'm not sure if this question belongs more in physics or biology (or maybe even computer science)... but biology seemed to fit more.</p>
<p>What changes in the state of our brains when we learn things? Because I looked on the internet and I learned about artificial neural networks, and every resource I've found teaches of neural networks that have weights that are trained/evolved and then are static at runtime; you simply train the weights and then once you use them in simulations, they never change.</p>
<p>Purely feedforward neural networks that rely on this can't react to new situations differently if they've experienced it before. They react exactly the same each time.</p>
<p>I suppose that theoretically, a recurrent neural network that was big enough could really learn, but in practice, these have been used as purely memory slots for an existing method defined by the weights, not as storage of new methods of doing things.</p>
<p>So my question is, physically, chemically, biologically, what changes in the neurons and the connections between them when we learn things? I don't think we really understand how it comes together on a grand scale yet, but I'm pretty sure we've figured out that much. I want to learn how to model a simplified version of it mathematically/programmatically.</p>
| [
{
"answer_id": 11293,
"pm_score": 3,
"text": "<p>What changes in the process of learning:</p>\n\n<ol>\n<li><p>The connections (the way one neuron is connected to another). New synapses can form or dissolve in the process of learning. The glial cells such as astrocytes and microglia can facilitate this p... | [
{
"answer_id": 64282,
"pm_score": 0,
"text": "<p>During learning, LTP (long term potentiation) or LTD (long term depression) can result in post synaptic neurons altering their responses to neurotransmitter release by the pre synaptic neurons. This is achieved at the post synaptic cell by increasing or d... |
11,351 | <p>I am planning a fitness assay of <em>Drosophila melanogaster</em>. I'd like to get a good measure of lifetime reproductive success (lrs) but I don't want to count all the offspring produced over a lifetime by 100's of focal flies. The solution I am toying with is to count offspring production over the first few days or weeks. But before I commit to this I need to know if there is existing research material on the following: </p>
<p><strong>Does early reproductive output correlate well with lrs?</strong> (this could be a low correlation if a fly trades early-life offspring production for late-life offspring production)</p>
<p><strong>How much of a fly's reproductive output does one need to count before they have a good estimator of lrs?</strong> (does counting the offspring produced in the first day of life correlate well to overall lrs or do I need to count more - 5 days, 10 days, 50 days...)</p>
| [
{
"answer_id": 19456,
"pm_score": 1,
"text": "<p>Just finished an experiment (yesterday) where I measured lifetime reproductive success (LRS) of a few hundred flies, with measures taken from 24 hours of production every 7 days over the entire life of the fly. From this I can now answer the question.</p>... | [
{
"answer_id": 17318,
"pm_score": 1,
"text": "<p>I haven't done LRS but I don't see a reason why you couldn't make that measurement over only a few days, if you keep this method consistent through out all your populations. Just as a control you might have to do a complete LRS to see if you get any patte... |
11,377 | <p>What is the difference between Coding Sequences (CDS) and cDNA?</p>
<p>Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured mRNA?</p>
| [
{
"answer_id": 11386,
"pm_score": 5,
"text": "<p>The difference boils down to <a href=\"http://en.wikipedia.org/wiki/Untranslated_region\" rel=\"noreferrer\">UnTranslated Regions</a>. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (alm... | [
{
"answer_id": 11380,
"pm_score": 2,
"text": "<p>The definition of coding sequence is, to my mind, a little confusing. It is actually the sequence of DNA in the gene which has the <strong>same</strong> sequence as the corresponding mRNA (except it has T instead of U). Now, you will often see definitions... |
11,397 | <p>How many Botulinum toxin molecules or grams are contained in one medical unit of Botox?</p>
| [
{
"answer_id": 12404,
"pm_score": 3,
"text": "<p>1 unit is approximately 10 pg</p>\n\n<p><a href=\"http://www.rxlist.com/myobloc-drug.htm\" rel=\"nofollow\">Source</a></p>\n\n<blockquote>\n <p>One unit of MYOBLOC (botulinum toxin type b) corresponds to the calculated median lethal intraperitoneal dose ... | [
{
"answer_id": 106727,
"pm_score": 2,
"text": "<p>A Botox unit is essentially a measure of a defined amount of biological activity and corresponds to a fixed number of botulinum toxin molecules.\nThe <a href=\"https://pubmed.ncbi.nlm.nih.gov/19945003/\" rel=\"nofollow noreferrer\">biological potency</a>... |
11,400 | <p>The standard answer found in intro course to evolutionary biology to the question:</p>
<blockquote>
<p>what is evolution?</p>
</blockquote>
<p>is:</p>
<blockquote>
<p>It is a change in allele frequency over time!</p>
</blockquote>
<p>I believe a complete definition should encompass the following concepts:</p>
<ul>
<li>mutations </li>
<li>copy number variation (<a href="http://en.wikipedia.org/wiki/Copy-number_variation" rel="nofollow noreferrer">CNV</a>)</li>
<li>codon usage</li>
<li>chromosome numbers</li>
<li>phenotypic change (whether heritable or not)</li>
<li>Complex phenotypic trait such as plasticity and developmental noise</li>
<li>maybe some other things...</li>
</ul>
<p>My questions are:</p>
<ol>
<li>Would it be worth it to talk about phenotype in a definition of evolution?</li>
<li>What are the alternative definitions that have been proposed?</li>
<li>What is your definition?</li>
</ol>
<hr>
<p>Note: I would rather talk about genetic evolution, but if you think it is worth making one definition for genetic and cultural (and some other stuff maybe) evolution, you're free to suggest it!</p>
| [
{
"answer_id": 44309,
"pm_score": 3,
"text": "<p><strong>What is evolution?</strong></p>\n\n<p>In a non-biological sense, <em>evolution</em> means change:</p>\n\n<blockquote>\n <p><a href=\"http://www.dictionary.com/browse/evolution\" rel=\"nofollow\">\"a process of [...] change\"</a></p>\n</blockquote... | [
{
"answer_id": 13403,
"pm_score": 2,
"text": "<p>Theoretical biology spans multiple disciplines and the unaccompanied term <em>evolution</em> is defined differently in each:</p>\n\n<p>As such chemical evolution is different from time evolution in physics and many other systems in theoretical biology tha... |
13,414 | <p>I found this photo in a <a href="https://www.facebook.com/photo.php?fbid=628341997202095&set=a.370464582989839.74242.113791238657176&type=1&theater" rel="noreferrer">local news page</a>. The page claims that this fish is a new species that was found by a Malaysian fisherman. Is this true or is it a known fish and already has a name?</p>
<p><img src="https://i.stack.imgur.com/LvGHD.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 13443,
"pm_score": 5,
"text": "<p>The front part of the fish looks like part of the cranium of a fish. I'd bet that the tusks have been \"made\" by removing some bones in the middle.</p>\n\n<p>Well, after having looked at the links given by Remi.b, it seems that it's not even necessary to... | [
{
"answer_id": 59406,
"pm_score": 5,
"text": "<p>This is a species in the <a href=\"https://en.wikipedia.org/wiki/Armored_searobin\" rel=\"nofollow noreferrer\"><strong>Peristediidae</strong></a> family, commonly called <strong>armored searobins</strong> or <strong>armored gurnards</strong>.</p>\n<block... |
13,433 | <p>Why does sodium-potassium pump consume about 2/3 energy of a cell ?</p>
<p>A.maintains appropriate membrane potential</p>
<p>B.helps in co-transport</p>
<p>I think it should be A. </p>
| [
{
"answer_id": 13452,
"pm_score": 3,
"text": "<p>I can't yet comment, so here's a (sort of) answer:</p>\n\n<p>I've only ever heard the \"2/3 of cellular expenditure\" rule applied to neurons, and frankly, it wouldn't make much sense in any cell other than a neuron. The Guyton and Hall Textbook of Medic... | [
{
"answer_id": 13453,
"pm_score": 1,
"text": "<blockquote>\n <p>Why does sodium-potassium pump consume about 2/3 energy of a cell ?</p>\n</blockquote>\n\n<p>It's A, assuming we're talking about a cell-type that heavily utilizes the potential.</p>\n\n<p>On to some of the comments...</p>\n\n<blockquote>\... |
13,454 | <p>The <a href="http://en.wikipedia.org/wiki/Semen#Composition_of_human_semen">seminal fluid</a> contains fructose as the main energy source for the sperm and not glucose. </p>
<blockquote>
<p>Why is fructose and not glucose the primary energy source for these
sperm, since glucose is the preferred energy source for most other
tissues?</p>
</blockquote>
| [
{
"answer_id": 13505,
"pm_score": 4,
"text": "<p>I have been searching this for a while and I got something of an answer, which I am posting below. </p>\n\n<p>There are primarily two advantages of using the <a href=\"http://en.wikipedia.org/wiki/Polyol_pathway\">polyol pathway</a> and <a href=\"http://... | [
{
"answer_id": 71217,
"pm_score": -1,
"text": "<p>If glucose was used in place of fructose it would get used up very quickly as it has a high glycemic index but fructose has low glycemic index and gets used up slowly by the spermatozoa so that they can survive for many days (upto 3) in the females body ... |
13,470 | <p>If a brain is exposed to an intermittent light source, are specific areas going to fire? If yes, which of them? Is there a experimental data about this effect? </p>
| [
{
"answer_id": 13493,
"pm_score": 4,
"text": "<p>It is thought that there are no active optical receptors in the brain normally, its possible some effect might show up in the future, it would be minor at best. </p>\n\n<p>Shining light into the brain is standard procedure in <a href=\"http://en.wikipedia... | [
{
"answer_id": 43482,
"pm_score": 0,
"text": "<p><strong>Short answer</strong><br>\nIllumination of neurons with light of varying wavelengths can activate them, causing them to fire action potentials. It may, however, not be the photons that activate the neurons <em>per se</em>, but the resulting temper... |
13,488 | <p>Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?</p>
| [
{
"answer_id": 16429,
"pm_score": 3,
"text": "<p>It does make a difference on polyacrylamide. A and C are faster while G and T are slower.</p>\n\n<p>Image from <a href=\"http://www.ncbi.nlm.nih.gov/pmc/?cmd=Search&term=461182%5Bpmid%5D\" rel=\"nofollow noreferrer\">publication</a>:</p>\n\n<p><img sr... | [
{
"answer_id": 16426,
"pm_score": 1,
"text": "<p>Practically speaking I have never seen a difference, but the agarose gels usually used in the lab do not have the highest resolution. There is one paper showing that the form (A- or B- form) and the GC-content play a role since DNA molecules of higher GC ... |
13,501 | <blockquote>
<p>In a small tribal population, the frequencies of two alleles A and a
at a particular locus were 0.3 and 0.7, respectively. However, not all
the individuals with genotype aa could live up to the reproductive age
and the relative fitness of this genotype was found to be 0.5. The
remaining genotypes had a relative fitness of 1. What is the expected
percentage of heterozygotes among newborns in the next generation?</p>
</blockquote>
<p>My answer is : 37 % but the answer given 43.52 %</p>
<p>I did the following : First I assumed the population to be of 100 individuals and then I counted the no of individuals with respective genotypes. Then I assumed that each person leaves 1 offspring except the aa ones which leave 0.5 offsprings and then I calculated the new genotype frequency from this.</p>
| [
{
"answer_id": 13508,
"pm_score": 4,
"text": "<p>Your reasoning is incorrect, because once you have the number of individuals surviving after the 50% mortality you can't just give them all one identical offspring, you have to mate them with one another.</p>\n<p>However, I can't get the answer given, ins... | [
{
"answer_id": 13516,
"pm_score": 3,
"text": "<p>This is basically the same solution as @AlanBoyd's answer, but since he asked me to, I will post my solution as well (also a reason to try out $\\mathcal{MathJax}$ a bit more).</p>\n\n<p>Assuming:</p>\n\n<p>$f(A)=p=0.3, \\\\f(a)=q=0.7$ </p>\n\n<p>and the ... |
13,504 | <p>This image was included in something I was browsing through.
It reminds me of my lion head rabbit, but the head shape doesn't match.</p>
<p>Is this some kind of Siberian wild rabbit?</p>
<p><img src="https://i.stack.imgur.com/DP670.jpg" alt="Its sooooo fluuuuuufy!!!" /></p>
| [
{
"answer_id": 100731,
"pm_score": 3,
"text": "<p>This does indeed seem to be a <strong>viscacha</strong>, which are actually found in South America (not Siberia). Their morphological similarity to rabbits is simply a case of <a href=\"https://en.wikipedia.org/wiki/Convergent_evolution\" rel=\"nofollow ... | [
{
"answer_id": 13532,
"pm_score": 3,
"text": "<p>Thanks to @Satwik's tip about google image search, I was able to figure out that the animal in question is a <a href=\"http://en.wikipedia.org/wiki/Viscacha\" rel=\"noreferrer\">Viscacha</a>. Though the source answer is thanks to <a href=\"http://www.redd... |
13,518 | <p>I am hoping to measure growth rates of a bacterial culture in several growth conditions. I am concerned that these growth conditions may cause cell death, which would lead to a decreased correspondence between optical density and number of live cells, so I want to independently measure the number of live cells. I understand that plating serial dilutions of a culture and counting the number of colonies to calculate the Colony Forming Units (CFU) per mL is the gold standard for measuring the number of viable cells. However, I have seven different conditions I want to test in parallel, and making 3+ plates for each condition (to do serial dilutions) and taking measurements at several points in the growth curve leads to a <em>lot</em> of plates. In general this method seems more labor intensive than what I need. I am mostly doing this as a sanity check, so it seems like a lot of work just for a sanity check. </p>
<p>My question is: are there any alternative methods to CFU plating for measuring cell viability, given that I am doing a lot of experiments in parallel? I don't have access to a FACS machine, so cell sorting won't work. I have read <a href="https://biology.stackexchange.com/questions/11368/measuring-algae-growth-or-death">this question</a> on measuring live cells in algae. I'm not sure that a hemocytometer is the right alternative for my particular high-throughput application (though you could convince me otherwise). The best answer to this question would compare from experience the precision, accuracy, sensitivity, and ease of use of this alternative method with CFU plating.</p>
<p>Thanks!</p>
| [
{
"answer_id": 13522,
"pm_score": 4,
"text": "<p>I've only used it for mammalian work, but the <a href=\"http://www.roche-applied-science.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=10001&partNumber=3.8.9.5.1.3#tab-0\">Cedex HiRes Analyzer</a> from Roche is pretty sweet. From their <a hre... | [
{
"answer_id": 59241,
"pm_score": 0,
"text": "<p>A company called HemoGenix offers a CFU alternative/replacement assay. It's called HALO PCA (progenitor cell alternative). We have used it with great success. It does, however, require an instrument. We use a bioluminescence plate reader, but it looks lik... |
13,625 | <p>Do people often blow out the air from their lungs when living in cold climatic conditions to keep their lungs warm?</p>
<p>I ask this question because it could connect to how people in different areas construct linguistic sounds. </p>
<p>For example, the Germanic families of Language (German, English,...) use a lot of air from the lungs to construct the sound? </p>
<p>Is that because the Europeans living in cold climate often blow out a lot of air from the lung to keep warm and as a result gradually they construct air-driven linguistic sounds?</p>
<p>For people living in warm climates (ex: Sino-Tibetan language like Chinese, Thai), we mostly use the tongue to construct sounds, and we use very little air from our lungs to make sound.</p>
<p>I posted this question to some forums & some people said it’s baloney. However, there's one thing for sure, the environment shapes how local people construct sound. People construct the sound like that because it is constrained by something. One thing can not stand alone, it must be the karma or outcome of something else.</p>
| [
{
"answer_id": 13629,
"pm_score": 2,
"text": "<p>Heat loss hypothesis:</p>\n\n<p>I would rather think that blowing while speaking means that one has to inspire often and therefore he would lose much heat by convection. According this hypothesis, I would rather expect to see southern people blowing lots ... | [
{
"answer_id": 13642,
"pm_score": 2,
"text": "<blockquote>\n <p>In a cold climate, do people often blow out the air from their lungs a lot when living in the cold condition to keep their lungs warm?</p>\n</blockquote>\n\n<p>No, and it wouldn't make any sense: breathing more means inhaling more cold air... |
13,655 | <p>While reading an article on mitochondrial inheritance I came across <a href="http://dx.doi.org/10.1093/humupd/dmq002" rel="nofollow">this link</a>.</p>
<p>The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. How is this regulated?</p>
| [
{
"answer_id": 14149,
"pm_score": 1,
"text": "<p>This is a topic which seems to be not very clear yet. References say that this is obviously dependent on the tissue and the \"gene dosage\" seems to play a role, and that this is probably regulated by a yet unknown factor (see \"<a href=\"http://www.ncbi.... | [
{
"answer_id": 13656,
"pm_score": 1,
"text": "<p>Mitochondria divide by binary fission. The regulation of this division differs between eukaryotes. In many single-celled eukaryotes, their growth and division is linked to the cell cycle.</p>\n"
}
] |
13,669 | <p>I am an Indian with a small thin stature with some deposition of fat around my belly.I was wondering if genes play a role in fat deposition in the body for Indian, Chinese, European or African people. Fat deposition may differ among all these people around the belly, thighs etc.
These people also differ in their stamina and speed naturally.</p>
<blockquote>
<p>For example here in India in the game of cricket there has been no
fast bowler out of 1.2 billion people who can do fast bowling
because it requires a lot of strength and stamina.Also on field
athleticism is also very bad compared to Australian or South African
players.I assume that may be its because of some cultural or genetic
problem.</p>
</blockquote>
| [
{
"answer_id": 13670,
"pm_score": 4,
"text": "<p>All these characteristics you observe (speed, ability to play cricket, belly size, height, etc…) are what what we call in biology a list of phenotypic traits. Basically, the phenotype is a characteristic of an organism that we can eventually measure or de... | [
{
"answer_id": 80649,
"pm_score": 1,
"text": "<p>DNA testing is a growing trend in athletics since 2016 to design training regimens by analyzing a range of 40 genes that encode for different physical traits <a href=\"https://www.dnafit.com/science/\" rel=\"nofollow noreferrer\">(scroll down for a list o... |
13,678 | <p>Flatus frequency is affected by diet, so I was wondering if flatus production solely depends on the food eaten, meaning that some people never ever release flatus because they don't eat any flatus-producing food. I guess if they say they don't, they're probably in denial...</p>
| [
{
"answer_id": 13670,
"pm_score": 4,
"text": "<p>All these characteristics you observe (speed, ability to play cricket, belly size, height, etc…) are what what we call in biology a list of phenotypic traits. Basically, the phenotype is a characteristic of an organism that we can eventually measure or de... | [
{
"answer_id": 80649,
"pm_score": 1,
"text": "<p>DNA testing is a growing trend in athletics since 2016 to design training regimens by analyzing a range of 40 genes that encode for different physical traits <a href=\"https://www.dnafit.com/science/\" rel=\"nofollow noreferrer\">(scroll down for a list o... |
13,680 | <p>In every non-life example I can envision, a copy of a copy is always a degraded or less pure version of the original unless some outside influence acts to correct the copy back toward the ideal represented by the original. Photocopies get blurrier with each generation. Casts from a mold are distorted from the original from which the mold was made. In fact, each cast degrades the mold itself. When data is copied on computers or across networks, parity checks verify that no mistakes were made, but even then, every long once in a while, combinations of errors can cause a false positive in a parity check. So given enough time, the copies would degrade.</p>
<p>In eukaryotes, new individual organisms always begin as a zygote, so in all kingdoms, reproduction boils down to the genesis of a single cell. This involves correctly building the DNA as well as all of the other complex architecture of the cell. Why doesn't this cell degrade like every other example I can think of? In fact, cells are capable of such perfect reproduction that the system generally supports the introduction of additional randomness in order to promote the possibility of productive change. I can think of some probable contributing factors that make this work, but I must be missing something. I can't imagine that this model would actually work the way it does - so well in fact that the design actually improves over time. What am I missing or underestimating?</p>
<p><strong>Contributing Factors (I guess):</strong></p>
<p><em>Perfect Building Blocks:</em> Cellular development follows a pattern at every level, and ultimately operates all the way down to the molecular level. At that level, nearly all building blocks are identical. Life is built of stable atoms, not something like plutonium, and in the rare event that an atom does change, the result is simply a different kind of atom, which still tends toward a stable form in the long term. Because the structures of life are ultimately made of stable components that are plentiful everywhere in the environment, the essential structures being copied are precise and can be copied precisely. Photocopies and casts are not precise to the molecular level, so copying them is more approximate by nature. Digital data propagation, however, is a very similar process. Bits are also theoretically perfect building blocks.</p>
<p><em>Fitness Correction:</em> When mistakes do degrade the reproduction process, rather than maintaining or randomly improving upon it, there is a correction mechanism that removes the defects from the process. Those defects do not survive to reproduce. This evolutionary process acts to keep the reproductive pattern focused back upon a theoretical ideal which is independent of a specific physical form to be copied. <code>This seems like the most essential element of the explanation, because it is ultimately only through progression that digression can be avoided, but it is also the part that seems the most dubious. Astronomical quantities of defects would have to be produced before developing just one advantageous feature. I would expect living creatures to be 99% defective with only 1% surviving to breed. I would expect 99.9% of zygotes to expire without being born or sprouting from seed. I would expect all sexual organs (ovaries, testes, stamen, etc.), if not the majority of the whole body, to be mostly dead cells, with just a few successes surviving to fertilization. I would expect 99.9% of the genome to be experimental, almost completely unusable liability to the species. Essentially, I would expect premature death to far outweigh successful life everywhere and at all times. And even so, I would still expect evolution to be even slower than it has been.</code></p>
<p><em>Mutation Management Mechanisms:</em> I understand that there are mechanisms in reproduction that decrease the likelihood of mutation in more established and stable parts of the genome compared with sections that are more open for discussion - epigenetic structures, HOX genes, etc. Portions of all genomes have been established and functional for hundreds of millions of years, so I gather that there are mechanisms for protecting them (I suspect probably far more than we have yet discovered).</p>
<p><strong>Note:</strong> The numbers I present are fuzzy and are based not on calculations but on general impressions I get of the magnitude of the numbers involved and the relative rareness of useful mutations. Is there any place where this kind of calculation has been performed with more realistic approximations of probabilities?</p>
| [
{
"answer_id": 13683,
"pm_score": 6,
"text": "<p>You have clearly given this a lot of thought. Unfortunately, as @adam.r said, you are laboring under certain misapprehensions. The quick answer is that each generation does not \"improve\" on the last. That is a common misconception. In a bit more detail:... | [
{
"answer_id": 13763,
"pm_score": 3,
"text": "<p>I’ll add a slightly different perspective, although terdon’s answer already contains the relevant facts.</p>\n\n<p>The thing that makes DNA endure in the face of imperfect copying is that, like computer storage, it’s <em>digital</em>. The <a href=\"https:... |
13,691 | <p>What happens if one looks directly at infrared LEDs? Sometimes I see this kind of LED at night as red dots and I'm also courious about it.</p>
<p>I was wondering what would happen if one looks directly to these LEDs, because we see them everywhere like in remote controls, CCTV cameras, sensors, etc.</p>
<p>What is the difference between infrared and visible light to our eyes?
(I mean why is it impossible to look directly to visible light while we can look to infrared?)</p>
<ul>
<li>LED: Light-emitting diode</li>
</ul>
<p><img src="https://i.stack.imgur.com/emyzJ.jpg" alt="Infrared LEDs"></p>
| [
{
"answer_id": 13694,
"pm_score": 5,
"text": "<p>Infrared wavelengths are EM waves of longer wavelengths than visible light. Also, visible waves are more energetic than IR waves.</p>\n\n<p>Because of this, Visible light has the ability to excite organic receptor molecules in our eyes called Rods and Con... | [
{
"answer_id": 65968,
"pm_score": 1,
"text": "<p>here's a similar question. some studies say that it may cause cataracts if you see enough of them, also the eye may receive a lot of a wavelength while dilated. that's a technical thing about sunglasses, if a sunglass dilates your pupil but IR flashes thr... |
13,695 | <p>I am not a biologist but I just wonder if all species are interdependent. I mean if the tiger becomes extinct does it affect the ecosystem? If the mosquito or mouse become extinct does it affect the environment and us?</p>
<p>I am asking because this question was raised by one of my friends when I was in favor of protecting tigers, lions but I had no answer to "<strong>tiger extinction will not affect humans</strong>".</p>
<p>So, is it true that the extinction of any species will affect all other species?</p>
| [
{
"answer_id": 13697,
"pm_score": 3,
"text": "<p>The problem is not really that we don't understand some stuff (lthough this is certainly true) but that an ecosystem, or the biosphere is a highly complex network of interactions. This network is continuously displaying some <a href=\"http://en.wikipedia.... | [
{
"answer_id": 13765,
"pm_score": 2,
"text": "<p>Remi.b's answer is spot on - predicting the effects of losing a given species is nigh on impossible. However, I do think that there are some general trends that can give us some intuition, and make the campaign to protect certain species more than just an... |
13,791 | <p>Only mammals have mammaries and mammary glands.</p>
<p>What evolutionary factors determines the number of mammaries (nipples/teats/breasts) a species has? </p>
<p>Is it always an even number? </p>
| [
{
"answer_id": 13829,
"pm_score": 4,
"text": "<p>The number of mammary glands a species has is related to litter size. The relationship generally follows the \"one-half rule,\" which states that the average litter size is equal to half the number of mammaries. The number of mammaries also tends to put a... | [
{
"answer_id": 13866,
"pm_score": 2,
"text": "<p>As an addition to the excellent post by Erin.</p>\n\n<p>As a name-giving key feature,mammals have mammary glands.<br>\n\"<em>Animals that are bilaterally symmetric have mirror symmetry in the sagittal plane</em>\", which includes Chordates such as mammals... |
13,810 | <p>I am sure many of us know the feeling of that tingling chill down our spines when listening to certain music. </p>
<p>I experienced this most when my younger brother played an emotional piano piece for a talent show (brought me to tears). </p>
<ul>
<li>What causes that? </li>
<li>Is music the only stimulus to elicit that spine-tingling? </li>
<li>And in terms of evolution, why?</li>
</ul>
| [
{
"answer_id": 13815,
"pm_score": 3,
"text": "<p>It is called a frisson, and actually, there has been a study about it, available <a href=\"http://www.cogsci.msu.edu/DSS/2008-2009/Huron/HuronFrisson.pdf\" rel=\"nofollow\">here</a>.\nThe frisson is kind of the same you get from cold weather, fear, or... ... | [
{
"answer_id": 15148,
"pm_score": 2,
"text": "<h1>Music and Emotions</h1>\n<p>The most difficult problem in answering the question of how music creates emotions is likely to be the fact that assignments of musical elements and emotions can never be defined clearly. The solution of this problem is the T... |
13,832 | <p>Both names are widely used, with what appears to me as a slight prevalence of “epinephrine” in scientific literature and an overwhelming prevalence of “adrenaline” in popular media.</p>
<p>Are there any well-documented and/or well-motivated guidelines for the usage of these terms?</p>
| [
{
"answer_id": 13833,
"pm_score": 4,
"text": "<p>Apparently I asked too soon. Summarizing my recent findings, I conclude that <strong>adrenaline</strong> is the better term.</p>\n\n<p>To be more explicit, here is why:</p>\n\n<ul>\n<li>The US National Library of Medicine <a href=\"http://www.nlm.nih.gov/... | [
{
"answer_id": 13874,
"pm_score": 2,
"text": "<p>Epinephrine and norepinephrine is used in the US mainly. This is where the term epi-pen comes from. Everywhere else we tend to use Adrenaline and noradrenaline. Epinephrine is typically only used in literature arising from the US or US English speaking co... |
13,864 | <p>Down's syndrome occurs when either the egg or the sperm cell contain on extra chromosome 21. To my understanding, women are born with all the egg cells in place already, so there's no further cell divisions, and thus no further chance of having one cell with an extra chromosome. </p>
<p>Now, the chance of having a baby with Down's syndrome <a href="https://en.wikipedia.org/wiki/Down_syndrome#Epidemiology">increase with age</a>:</p>
<blockquote>
<p>At maternal age 20 to 24, the probability is one in 1562; at age 35 to 39 the probability is one in 214, and above age 45 the probability is one in 19</p>
</blockquote>
<p>Why is this so, when the egg cells are complete at birth?</p>
| [
{
"answer_id": 13868,
"pm_score": 4,
"text": "<blockquote>\n <p>The frequency rises with maternal age due to a peculiarity of meoisis\n in female mammals. Meiosis is originated in the fetal ovary,\n arresting at metaphase I with the homologous chromosomes aligned for\n segregation. Cells remain in... | [
{
"answer_id": 17061,
"pm_score": 2,
"text": "<p>The chance of having a child with Down's Syndrome does not only have to do with cell division, but the mechanism that allows spontaneous abortion to occur <a href=\"http://www.sciencedaily.com/releases/2006/10/061012184355.htm\" rel=\"nofollow noreferrer\... |
13,926 | <p>The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular).
How do you account for the presence of more variation among of proteins than there are in genes? </p>
<p>The simple answer would be "there are more proteins than genes", but I'm more interested in why. Is it sufficient to say that during gene expression a single gene codes for multiple proteins (Alternative Splicing) and ribosomes translating mRNA to polypeptide chains (Posttranslational modification)? Could someone expand more on this? </p>
| [
{
"answer_id": 13927,
"pm_score": 5,
"text": "<p>There are several concepts to understand:</p>\n\n<ol>\n<li>Alternative splicing\n\n<ul>\n<li>From one gene, several proteins can be constructed depending on which introns are spliced.</li>\n</ul></li>\n<li>Tissue-specific genetic expression\n\n<ul>\n<li>G... | [
{
"answer_id": 13935,
"pm_score": 3,
"text": "<p>To comment on the \"why\" question: I would say that its a relatively simple way to get a high number of proteins with more or less slight differentiations. This can include exons which are only present in special environments or cell types and so on. It ... |
13,956 | <p>For example,</p>
<p>say species A is common ancestor of B, and C. Species B is a common ancestor of D and E.</p>
<p>We would expect that there will be more genetic similarity between D and E than D and C. And those genetic similarity must exist in B.</p>
<p>In other word, we won't expect genetic similarity that don't "cross" the common ancestor or the evolutionary tree.</p>
<p>The exception is probably genetically engineered bacteria.</p>
<p>That being said, am I correct?</p>
<p>Some people say that we have similarity with pigs and chimps even though our common ancestors may be to far off. That won't happen right?</p>
<p>To summarize</p>
<p>I expect that evolutionary tree will form a well, tree. Genetic similarity would infect "nearby" trees and can't jump between trees without connectors, such as common ancestors.</p>
<p>Is that what we observe for ALL species?</p>
| [
{
"answer_id": 13983,
"pm_score": 3,
"text": "<p><em>You have an excellent answer from Remi.b already but I just wanted to add/emphasise this (because there is always more than one way of explaining something and IMO the site benefits from having many answers to the questions)...</em></p>\n\n<p><strong>... | [
{
"answer_id": 13957,
"pm_score": 3,
"text": "<p>Your question seems rather confused to me, I don't quite understand it. Below I try to explain some stuff, I am not quite sure it would help you finding the answer to your question. Let me know if it helps you and how I can improve this answer.</p>\n\n<p>... |
13,959 | <p>Chimps are our closer relative.</p>
<p>Any genetic similarity between humans and chimps must exist on the common ancestor.</p>
<p>Pig branch out sooner. So, any genetic similarity between humans and pigs must be on common ancestor between humans and pigs. That must be on common ancestor between humans and chimps.</p>
<p>But chimps may evolve differently.</p>
<p>Hmmm... I am confused.</p>
<p>Actually is there any?</p>
| [
{
"answer_id": 13961,
"pm_score": 4,
"text": "<p>Yes there are! </p>\n\n<p>I think it would make more intuitive sense to you if you would have switched the words chimps and humans in your question: </p>\n\n<blockquote>\n <p>Are there genetic similarity between chimps and pigs that don't exist in humans... | [
{
"answer_id": 13966,
"pm_score": 2,
"text": "<p>This question doesn't make a lot of sense. Humans, chimps and pigs are all eukaryotes, share a lot of sequence similarity due to common ancestry. We are all vertebrates, we are all placental mammals. So there is a lot of similar sequence between us, mo... |
13,986 | <p><a href="https://biology.stackexchange.com/questions/8282/why-is-saltatory-conduction-faster-than-continuous-conduction">Here</a> is the original question which inspired my question. As explained by the answers there, the reason saltatory conduction in myelinated neurons is faster than non-myelinated conduction is because the capacitance of the membrane is lowered by reducing the number of channels (Channel density) or equivalently, increasing the spacing between channels. I also did a preliminary study of membrane electrodynamic modelling <a href="http://www.scholarpedia.org/article/Cable_theory" rel="nofollow noreferrer">here</a> and <a href="http://www.scholarpedia.org/article/Electrical_properties_of_cell_membranes" rel="nofollow noreferrer">here</a>. </p>
<p>From what I gathered from the linked question, the decreased capacitance overcompensates the effect of absence of channels reinforcing the sodium current, and on the whole, increases the speed of conduction by allowing the depolarizing potential to travel to the adjacent node faster than in case of an unmyelinated fibre. In view of this, I have a question:- </p>
<blockquote>
<p><strong>Why does lower capacitance increase "the effectiveness of nearby
nodes" or allow the depolarizing voltage to "travel not by ion
diffusion, but as an electric field"? I am comfortable with capacitors
and related physics, but why would lower capacitance allow propagation
of the changing voltage as an electric field, is still unclear to me?
(The links I have placed also help quantify the problem
mathematically. This allows us to say that $\lambda$, or the rate of spatial
decay of potential, increases, decreasing the effective
length of the neuron. Why should its decrease help faster conduction?)</strong></p>
<p>And another question is, <strong>how would reduced density of sodium voltage
gated channels cause a decreased capacitance?</strong></p>
</blockquote>
| [
{
"answer_id": 24260,
"pm_score": 3,
"text": "<p>Very nice question! I'll go through your three questions sequentially.</p>\n\n<p><strong>Q1: Why does lower capacitance increase \"the effectiveness of nearby nodes\" or allow the depolarizing voltage to \"travel not by ion diffusion, but as an electric f... | [
{
"answer_id": 24231,
"pm_score": 2,
"text": "<p>The Hodgkin-Huxley model:</p>\n\n<p>$$I=C_m\\frac{dV}{dt} + g_k(V_m - V_k) + g_{Na}(V_m - V_{Na}) + g_l(V_m- V_l)$$</p>\n\n<p>Where $C_m$ is membrane capacitance per unit area and $g_i$ are membrane conductances.</p>\n\n<p>Reducing the number of channels ... |
13,989 | <p>Plasmid pBr322 includes two genes that confer antibiotic resistance: a gene for ampicillin and a gene for tetracycline. The cutting site for the restriction enzyme BamH1 is in the middle pf the tetracycline resistance gene. The cutting site for the restriction enzyme Pvu1 is in the middle of the ampicillin resistance gene.</p>
<p>If you were using a cell culture plate that contained ampicillin, which restriction enzyme (BamH1 or Pvu1) would you use to cut the plasmid and excise the gene you wanted to insert?</p>
<p><strong>Attempt</strong>:</p>
<p>I would assume you need to use Pvu1 since the cutting site is in the ampicillin resistance gene, but the correct answer is BamH1. Why?</p>
<p>Any help would be awesome! Thanks!</p>
| [
{
"answer_id": 13990,
"pm_score": 4,
"text": "<p>Remember than Pvu1 <strong>cuts</strong> in the middle of <em>Amp<sup>R</sup></em>, and when you insert your gene you'll be disrupting its function, meaning that any transformed colonies will no longer be able to grow on Amp-containing media. This is why ... | [
{
"answer_id": 13992,
"pm_score": 1,
"text": "<p>I would go with BamH1 enzyme as the cut site in pBr322 is BamHI 375 and ss you are plating it in a ampicillin plate you need the ampicillin resistant gene to be intact for screening so by using BamHI you will not disrupt the Amp resistant gene</p>\n"
}... |
13,994 | <p>People can dream, dogs can dream, cats probably too when they are sleeping.</p>
<p>What about other creatures? </p>
<p>Can a bird dream?</p>
<p>Do rats have dreams?</p>
<p>Are there any studies about that kind of thing? What is the most simple organism that have brain structures that allow them dreaming during the sleep?</p>
| [
{
"answer_id": 13990,
"pm_score": 4,
"text": "<p>Remember than Pvu1 <strong>cuts</strong> in the middle of <em>Amp<sup>R</sup></em>, and when you insert your gene you'll be disrupting its function, meaning that any transformed colonies will no longer be able to grow on Amp-containing media. This is why ... | [
{
"answer_id": 13992,
"pm_score": 1,
"text": "<p>I would go with BamH1 enzyme as the cut site in pBr322 is BamHI 375 and ss you are plating it in a ampicillin plate you need the ampicillin resistant gene to be intact for screening so by using BamHI you will not disrupt the Amp resistant gene</p>\n"
}... |
13,997 | <p>T cells are formed in bone marrow and mature in Thymus. How are they transported from bone marrow to thymus ? Through the lymph vessels ?</p>
| [
{
"answer_id": 15924,
"pm_score": 3,
"text": "<p>The progenitor cells of T-cells (they do not develop into T-cells and show their characteristics before reaching the thymus) are mobilized into the bloodstream and enter the thymus from it by crossing the endothelial barrier. The figure shows schematicall... | [
{
"answer_id": 14030,
"pm_score": -1,
"text": "<p>prothymocytes are attracted to the thymus from the Bone Marrow by a chemotaxis , thymotaxin, a factor from thymic epithelial cells.\nthen it enters into the thymic cortex where Thy-1 and terminal deoxynucleotidyl transferase (TdT) is expressed. During T... |
14,022 | <p>what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other
and how does one go on to prove this
many thanks</p>
| [
{
"answer_id": 14028,
"pm_score": 3,
"text": "<p>Expanding on the comment by @Chris:</p>\n\n<p><strong>Short Answer</strong></p>\n\n<p>Overlapping sequences imply <strong><em>evolutionarily conserved regions</em></strong>, i.e. preserved by evolution through time due to theirs having some important func... | [
{
"answer_id": 14029,
"pm_score": 0,
"text": "<p>it means those region are conserved if you compare two sequence and find similarity one example is the hox coding region which is conserved and it shows similarity</p>\n"
}
] |
14,045 | <p>And especially three points : </p>
<ul>
<li><p>in which chromosomes is it located (especially for the human case) ?</p></li>
<li><p>how do we know about it ?</p></li>
<li><p>does the proportion and composition vary a lot from one eukaryot to another ?</p></li>
</ul>
| [
{
"answer_id": 14028,
"pm_score": 3,
"text": "<p>Expanding on the comment by @Chris:</p>\n\n<p><strong>Short Answer</strong></p>\n\n<p>Overlapping sequences imply <strong><em>evolutionarily conserved regions</em></strong>, i.e. preserved by evolution through time due to theirs having some important func... | [
{
"answer_id": 14029,
"pm_score": 0,
"text": "<p>it means those region are conserved if you compare two sequence and find similarity one example is the hox coding region which is conserved and it shows similarity</p>\n"
}
] |
14,047 | <p>When performing a DNA cloning, sometimes PCR amplicon is run in agarose and it is detected by ethidium bromide marking under UV light. After that, gel is sliced, DNA extracted from gel....... until eventually you have your transgenic organism. The thing is that when doing so, you use the very same DNA sample that was "contaminated" by ethidium bromide, so does this DNA you are using for transformation contain ethidium bromide? if so, how can it affect in numbers to mutation risk? </p>
| [
{
"answer_id": 14049,
"pm_score": 4,
"text": "<p>Purified DNA contains negligible amounts of ethidium bromide. PCR and gel clean-up kits remove it quite well. There is, though, a risk of mutation from the fact that you're visualizing the gel in UV light with ethidium bromide. The risk of mutation from U... | [
{
"answer_id": 14145,
"pm_score": 2,
"text": "<p>While it is possible to get mutations from the ethidium bromide, this is hardly the only source of mutations in the process. Taq itself will introduce mutations fairly frequently, so sequence sensitive procedures typically use a higher accuracy (but slow... |
14,054 | <p>I know that the probability of life existing on a habitable planet is pretty slim. But, how likely is it that it hapenned millions of times in the same planet? Or was it only a few species that evolved into millions of other different species over time?</p>
| [
{
"answer_id": 14056,
"pm_score": 3,
"text": "<p>We can be reasonably certain that ALL species that exist today share a common ancestor, a common origin. Every single species we have even encountered, for example, uses a long chain of nucleotides (DNA or RNA<sup>1</sup>) to store its genetic information... | [
{
"answer_id": 14055,
"pm_score": 2,
"text": "<p>The fantastic number of species that one can observe today is not a fixed value. This number changes over time. These changes are not caused by De Novo origin of life but by two processes which are:</p>\n\n<ul>\n<li><a href=\"http://en.wikipedia.org/wiki/... |
14,065 | <p>Latent toxoplasmosis affects up to 1/3 of the human population and up to 40% of the population in Australia. I have heard that latent toxoplasmosis has many significant undesirable effects on personality, such as decreased novelty-seeking behaviour, and decreased intelligence quotient.</p>
<p>While these changes are statistically significant, I'm wondering if anyone knows the magnitude of these personality and cognitive changes, since a statistically significant result doesn't necessarily imply that there is a large difference in personality between those who are infected and those who aren't infected. Also, can one succeed in an academic career path if one becomes infected with toxoplasmosis?</p>
| [
{
"answer_id": 14087,
"pm_score": 3,
"text": "<p>I believe its the other way around - humans may engage in riskier and more novel behavior when infected... which is the most interesting part of the story. Its not cut and dried, but I think its quite possible that risky behavior increases. </p>\n\n<p><e... | [
{
"answer_id": 98622,
"pm_score": 1,
"text": "<p>It is my understanding that toxoplasmosis can increase productivity and the brain's ability to understand things. It is when there is a toxo flare that behaviors can become irrational and angry. Knowing this can help as well as being in touch with when yo... |
14,067 | <p>Where in the body are self antigens important? In terms of central tolerance and autoimmunity, but also in terms of T cell activation?</p>
| [
{
"answer_id": 14087,
"pm_score": 3,
"text": "<p>I believe its the other way around - humans may engage in riskier and more novel behavior when infected... which is the most interesting part of the story. Its not cut and dried, but I think its quite possible that risky behavior increases. </p>\n\n<p><e... | [
{
"answer_id": 98622,
"pm_score": 1,
"text": "<p>It is my understanding that toxoplasmosis can increase productivity and the brain's ability to understand things. It is when there is a toxo flare that behaviors can become irrational and angry. Knowing this can help as well as being in touch with when yo... |
14,088 | <p>I am working on a project for health center. It involves the creation of a database of all diseases. Currently I want to classify disease on the base of their category based on international standard.<br>
Did anyone know where i can find one, I did a lot of research but was only able to come across this which seem not very useful to me: <a href="http://www.cdc.gov/nchs/icd.htm" rel="nofollow">ICD</a> </p>
| [
{
"answer_id": 14089,
"pm_score": 4,
"text": "<p>The two I know of off the top of my head are</p>\n<ul>\n<li><p><a href=\"http://www.omim.org/\" rel=\"noreferrer\">OMIM</a> : Online Mendelian Inheritance in Man. This is very good and very well organized but only deals with inheritable diseases, no infec... | [
{
"answer_id": 14092,
"pm_score": 2,
"text": "<p>I don't know if you're also interested in mental health issues, but the DSM (<a href=\"http://www.dsm5.org/about/Pages/Default.aspx\" rel=\"nofollow\">Diagnostic and Statistical Manual of Mental Disorders</a>) is the standard typology for that subject are... |
14,106 | <p>I'm not very well informed about all the things related to biology and the current achievements of science in this field so if I'm wrong in anything I say, please let me know. </p>
<p>Many times I've come across a theory that the meaning of life itself is procreation - we simply live in order to make our species exist as long as possible. In the light of this theory, units like homosexuals or infertile people are totally useless and there's no really reason for them to exist from biological point of view. Though it's pretty obvious that in order to make us want to reproduce, something like joy of having sexual intercourse and life in general has been created. That's why units who only lack in ability to reproduce do live and most of the time they're fine.</p>
<p>Evolution doing adjustments in us in order to make us feel happy during our life seems to be understandable, but what about death? I've read that during death, a larger amount of DMT substance is being released in the brain - compound which is known from it's psychedelic effects, which in most cases are euphoric. It looks like we're not meant to feel 'bad' while dying, which is nice, but my question is - is it known why? What could be the evolutionary reason to create this mechanism? The unit which is about to die is not going to be useful anymore, so why bother? I'd like to somehow understand logic behind this. </p>
| [
{
"answer_id": 14146,
"pm_score": 4,
"text": "<p>The issue I suspect you are struggling with is the anthropomorphization of the evolutionary process. Evolution is an optimization process driven by random mechanisms...i.e. there is often not a \"reason\" for why certain things are the way they are. Evo... | [
{
"answer_id": 14144,
"pm_score": 2,
"text": "<p>Dimethyltryptamine have been identified as normal constituents of human blood, urine,cerebrospinal fluid.Dimethyltryptamine is an N-methylated indoleamine derivative, a serotonergic hallucinogen.It apparently acts as an agonist at some types of serotonin... |
14,115 | <p>I have heard that "air in the GI tract" results in flatulence and burping etc, however I initially assumed that the "empty" GI tract was a hollow tube filled with air anyway.</p>
<p>So on an empty stomach (or "empty" GI tract rather), does the GI tract collapse due to the pressure in the surrounding cavities, or is the GI tract normally a hollow tube filled with air, and flatulence merely a result of "excess" air?</p>
| [
{
"answer_id": 14116,
"pm_score": 4,
"text": "<p>Under normal circumstances the stomach and GI tract have very little \"gas\" in them - whether it be flatus, air, CO<sub>2</sub>, or anything else - and so are essentially collapsed with the walls against each other. However, gas is continually being prod... | [
{
"answer_id": 14129,
"pm_score": 2,
"text": "<p>If you look below you can see two X rays. One with bowel obstruction on the right and a normal on the left. On an X ray air bubbles are black as indicated. Under normal circumstances as you can see there is very little air in the stomach and GI tract, alt... |
14,120 | <p>Is it possible for cells from the same tumor to have different genetic material, and if so, to what degree is it possible (how fast do they mutate) ?</p>
| [
{
"answer_id": 14122,
"pm_score": 4,
"text": "<p>Cancer cells and normal cells differ on the genetic basis but they share the same genetic background, so they have not different DNA in the sense of two different people. They have to be different, since cancer cells have to accumulate mutations on a numb... | [
{
"answer_id": 65519,
"pm_score": 1,
"text": "<p>A) It absolutely is very common for extensive genetic heterogeneity to exist in tumours, including between individual cells. Talha already posted links to some very good reviews from Charlie Swanton and colleagues so I will just add in a citation for sing... |
14,130 | <p>The section of retina shows a layered arrangement of the various retinal cells. Starting from the inside (where the light strikes first) is the nerve fibre layer, ganglionic layer, amacrine cell layer, bipolar cell layer, horizontal cell layer and finally rods and cones (and that too in inverted position, i.e. the actual receptor portions are farther inwards). </p>
<blockquote>
<p><strong>Why is this stratification inverted?</strong> If the receptors would have been the innermost cells, they could have received the maximum
quantity of unaltered light. Does this "inverted" arrangement, i.e.
arrangement with the receptor cell behind a screen of several other
layers not hinder the process of photoreception by blocking a lot of
incident light and hence the formed image? <strong>What is, if any,
advantage of this reverse arrangement?</strong> </p>
</blockquote>
<p><img src="https://i.stack.imgur.com/KE7y5.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 14142,
"pm_score": 4,
"text": "<p>I don't have an other explanation than pointing to evolution. It was obviously not a problem to evolve the way it did. One article I found (see \"<a href=\"http://www.arn.org/docs/odesign/od192/invertedretina192.htm\" rel=\"nofollow\">The Inverted Retina:... | [
{
"answer_id": 108282,
"pm_score": 0,
"text": "<p>There is most likely no advantage to this arrangement and it probably is the result of the evolutionary history of the eye. Evolution always work by means of small adjustments from something that works into something that works better. During the course ... |
14,168 | <p>Do you have recommendations for a book that presents the different algorithm used in theoretical evolutionary biology?</p>
<p>I don't mean evolutionary or genetic algorithms (otherwise this question would not be a good fit for Biology.SE) but algorithms applied to evolutionary biology. I am not interested in statistical procedures and algorithms to reconstruct phylogenetic trees, to annotate DNA sequences or to find out synonymous changes by comparing sequences of closely related species. I am not interested in introductory book on programming.</p>
<p>I am interested to computational modeling applied population genetics, kin selection, game theory, population range expansion, simulating sexual reproduction, selection for different sex determination system, evolution for robustness/evolvability, evolution of codon usage, evolution of genetic code, evolution of cognition, evolution of multicellularity, …</p>
<p>I don't quite know if one book that encompass all these subjects exist. If not, I wold welcome suggestions of book that present the algorithmic used in some but not all of these subjects.</p>
<p>Searching a bit in amazon, I easily found tons of book but don't quite know if they fit my expectations. Below are some examples</p>
<p><a href="http://www.amazon.fr/The-Engine-Complexity-Evolution-Computation-ebook/dp/B00APDGG9G/ref=sr_1_1?ie=UTF8&qid=1388169820&sr=8-1&keywords=computation+biology+evolution" rel="noreferrer">Evolution as computation</a></p>
<p><a href="http://rads.stackoverflow.com/amzn/click/069109666X" rel="noreferrer">Individual based modeling and ecology</a></p>
<p><a href="http://www.amazon.fr/Models-Algorithms-Genome-Evolution-Cedric-ebook/dp/B00FA1PTHI/ref=sr_1_2?ie=UTF8&qid=1388169832&sr=8-2&keywords=computation+biology+evolution" rel="noreferrer">Models and algorithm for genome evolution</a></p>
<p><a href="http://rads.stackoverflow.com/amzn/click/0521538564" rel="noreferrer">modelling for field biologists</a></p>
<p><a href="http://rads.stackoverflow.com/amzn/click/0878933913" rel="noreferrer">Practical computing for biologist</a></p>
<p><a href="http://www.amazon.fr/Evolution-As-Computation-Workshop-Princeton/dp/3642630812/ref=sr_1_4?ie=UTF8&qid=1388169832&sr=8-4&keywords=computation+biology+evolution" rel="noreferrer">Evolution as computation</a></p>
<p><a href="http://www.amazon.fr/Genetic-Evolutionary-Computation-Medical-Applications/dp/0470748133/ref=sr_1_6?ie=UTF8&qid=1388169832&sr=8-6&keywords=computation+biology+evolution" rel="noreferrer">Genetic and evolutionary computation</a></p>
<p><a href="http://www.amazon.fr/Genetic-Algorithms-Structures-Evolution-Programs/dp/3642082335/ref=sr_1_69?ie=UTF8&qid=1388166676&sr=8-69&keywords=evolution+algorithm" rel="noreferrer">Genetic algorithms+ data structures = evolution programs</a></p>
<p><a href="http://www.amazon.fr/The-Missing-Algorithm-Cooperation-Prediction/dp/1581125992/ref=sr_1_119?ie=UTF8&qid=1388169248&sr=8-119&keywords=evolution+algorithm" rel="noreferrer">The missing algorith</a></p>
<p><a href="http://www.amazon.fr/Cellular-Model-Mathematical-Bioinformatics-Computational/dp/613381960X/ref=sr_1_1?ie=UTF8&qid=1388169453&sr=8-1&keywords=algorithm+theoretical+biology" rel="noreferrer">Cellular Model: Mathematical and theoretical biology, Algorithm, Data structure, Bioinformatics, Computational biology, Artificial life, Computer simulation</a></p>
<p><a href="http://www.amazon.fr/Natural-Artificial-Models-Computation-Biology/dp/3642386369/ref=sr_1_3?ie=UTF8&qid=1388169453&sr=8-3&keywords=algorithm+theoretical+biology" rel="noreferrer">Natural-Artificial-Models-Computation-Biology</a></p>
<p><a href="http://www.amazon.fr/An-Introduction-Genetic-Algorithms-Paper/dp/0262631857/ref=sr_1_61?ie=UTF8&qid=1388166452&sr=8-61&keywords=evolution+algorithm" rel="noreferrer">An-Introduction-Genetic-Algorithms-Paper</a></p>
| [
{
"answer_id": 14191,
"pm_score": 4,
"text": "<p>What you are describing usually falls under the category of computational biology or just mathematical biology. Unfortunately, the biggest part of this field is bioinformatics, or the application of statistical and/or dynamical programming techniques to s... | [
{
"answer_id": 14183,
"pm_score": 2,
"text": "<p>Have you looked into \"Fundamental of Molecular Evolution\" by Dan Graur & Li.</p>\n\n<p>Another suggestion in line of population genetics and different evo. theories would be -\nEvolutionary Genetics: Concepts and Case studies\n(Multi-author book. Ed... |
14,172 | <p>I'd like to clear something up about antibodies that I'm not sure I've understood in the articles I've read. Looking at concepts such as "affinity maturation", "monovalent antigens" and "polyvalent antigens" it seems as if there are multiple antibodies which can bind to the same antigen. (Although I think I'm right in saying that individual antibodies can only bind to one antigen?) However, when I read sentences like "It has been estimated that humans generate about 10 billion different antibodies, each capable of binding a distinct epitope of an antigen" on the Wikipedia page (for antibody) it does make it sound like it's one antibody per antigen? Is this the case? Or is it one antibody per epitope. Either way, to put this question in a nutshell:</p>
<p>Is it true to say that the same substance could bind with (and, therefore, be recognised by) more than one antibody, or not?</p>
<p>Also, if the answer is no, does that mean that antibodies with different binding affinities are classed as the same antibody or not?</p>
| [
{
"answer_id": 14174,
"pm_score": 3,
"text": "<p>Let's clarify the terms. An <em>antigen</em> is a molecule that can be associated with a particular substance (virus, pollen, dander.) When an immunoglobulin or <em>antibody</em> recognizes an antigen it binds to a specific <em>epitope</em>. An antibody r... | [
{
"answer_id": 14400,
"pm_score": 0,
"text": "<p>Yes -</p>\n\n<p>Its all binding kinetics - even a monoclonal antibody will bind many different antigens. The affinity/avidity will be different depending on the interactions. The target antigen may have the lowest known K_d, but antibodies will still bind... |
14,289 | <p>I have seen <strong>haploid</strong> cancer cells (I think it was leukemia cells) in a lab. </p>
<p>Sperms and eggs are haploid but are not destroyed by the body because they are protected by other cells surrounding them. </p>
<p>My questions : </p>
<ul>
<li><p>How are haploid and diploid cells differentiated by our immune system ?</p></li>
<li><p>Why are the haploid cancer cells not killed ? I know I could as well ask why any cancer cells are not killed but I want to know if there is anything specific about these cells ?</p></li>
<li><p>How are these cells generated ? (By meiosis ?!)</p></li>
</ul>
| [
{
"answer_id": 14300,
"pm_score": 3,
"text": "<p>Now that I did some research on this, it seems to be a very rare condition of acute lymphoblastic leukemia (ALL), see this article:\"<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/6953994\" rel=\"nofollow\">Chromosomes and causation of human cancer and leuk... | [
{
"answer_id": 80029,
"pm_score": 0,
"text": "<p>The recent publication in pancreatic neuroendocrine cancer <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054670/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054670/</a> revealed about one third of patients have a ... |
14,299 | <p>My book keeps giving different indicators as to whether the promoters are on the coding or template strand.</p>
<ul>
<li><p>It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that the -10 and -35 regions are binding sites for RNA polymerase.</p></li>
<li><p>It also says that CAAT and GC, unlike -35 in prokaryotes, can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand, with the transcription complex attached.</p></li>
</ul>
<p>All the sequences are written 5'-TATAAA-3' (for example). This also implies they are on the coding strand, since the template strand will then be 3'->5' which is the direction that transcription happens in.</p>
<p>Obviously I'm confused, and hope someone can clarify this. In which strand can I find the promoters? Does stuff act on the promoter sequence itself, or its complementary sequence? If the promoter can also be on the other strand, should it be reversed?</p>
| [
{
"answer_id": 14302,
"pm_score": 4,
"text": "<p>The answer to this question depends upon the definition of the word 'promoter'.</p>\n\n<p>In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this p... | [
{
"answer_id": 14308,
"pm_score": 3,
"text": "<p>Promoter doesn't <em>sit</em> anywhere.. it is just <em>present</em> .. the <strong>transcription factor</strong> <em>sits</em> on it :P</p>\n\n<p>Jokes apart.. Adding a little more information to Alan Boyd's answer: </p>\n\n<p>As Alan Boyd points out, th... |
14,309 | <p>What is the smallest oligocelluar organism?</p>
<p>How many cells does it have?</p>
<p><strong>EDIT</strong></p>
<p>The question is motivated by this <a href="https://philosophy.stackexchange.com/questions/9072/if-there-is-life-then-there-is-more-complex-life-as-well#comment22856_9095" title="and it is not 100% clear that even if given relatively benign environmental conditions the development of multicelluar organisms with differentiated tissues (my definition of complex life) will occur with (near) ceartainty.">comment@Philosophy.SE</a></p>
<p><strong>EDIT as recommended in comments</strong></p>
<p>I'm looking for an example of an organism made of very few (the fewer, the better) sister cells (obtained by mitosis or aggregation) that are morphologically and functionally different. I would accept examples of species that exist in different "conformation" (unicellular and multicellular).</p>
| [
{
"answer_id": 14317,
"pm_score": 3,
"text": "<p>The classic example, though I am sure there are others that are smaller, is the slime mold <a href=\"http://en.wikipedia.org/wiki/Dictyostelium_discoideum\" rel=\"nofollow noreferrer\"><em>Dictyostelium discoideum</em></a>:</p>\n\n<p><img src=\"https://i.... | [
{
"answer_id": 14420,
"pm_score": 2,
"text": "<p>Not sure, whether it fits in your requirement (since it was not clear for me with the terdon's answer), but I'd also mention plasmodia and other cases of species with syncytial organization: they have multiple nuclei, sometimes have even macroscopic sizes... |
14,315 | <p>Can you think of collective and swarm behaviors as "intelligence"? Would such a concept apply to a) ant colonies and b) fish swarms?</p>
| [
{
"answer_id": 14316,
"pm_score": 4,
"text": "<p>Intelligence is something which has to have a definition, and there are many, but I would cautiously say no. </p>\n\n<p>The reason that I say this is because swarming behavior can be largely reproduced by a <a href=\"http://en.wikipedia.org/wiki/Swarm_beh... | [
{
"answer_id": 14380,
"pm_score": 1,
"text": "<p>When we talk about \"artificial intelligence\" we are talking about the ability to solve problems not directly specified in the code. It doesn't need to have \"intention\" or \"conscience\", as @shigeta suggests. So, I'd say swarms are intelligent, it's j... |
14,341 | <p>I was wondering how the body "remembers" viruses after having once overcome them, and while reading <a href="http://science.howstuffworks.com/life/human-biology/immune-system13.htm" rel="nofollow">this article</a> on the immune system (page 14, Vaccinations), I read:</p>
<blockquote>
<p>There are many diseases that, if you catch them once, you will never catch again. Measles is a good example, as is chicken pox. What happens with these diseases is that they make it into your body and start reproducing. The immune system gears up to eliminate them. In your body you already have B cells that can recognize the virus and produce antibodies for it. However, there are only a few of these cells for each antibody. Once a particular disease is recognized by these few specific B cells, the B cells turn into plasma cells, clone themselves and start pumping out antibodies. This process takes time, but the disease runs it course and is eventually eliminated. However, while it is being eliminated, other B cells for the disease clone themselves but do not generate antibodies. This second set of B cells remains in your body for years, so if the disease reappears your body is able to eliminate it immediately before it can do anything to you.</p>
</blockquote>
<p>Which made me wonder, instead of vaccinating people with weakened forms of the disease, getting their B cells to activate as described, what would be wrong with growing large colonies of B cells for a given virus and injecting them into someone who has never had the disease so that one can go straight to the last sentence of that paragraph, having many of those B cells in place before the virus is ever experienced?</p>
| [
{
"answer_id": 14346,
"pm_score": 3,
"text": "<p>Remember first that the human body nearly always, although there are exceptions, rejects any non-genetically identical graft placed into it, and therefore one cannot prepare a general colony of B-cells to confer immunity to the population at large. Howeve... | [
{
"answer_id": 14366,
"pm_score": 1,
"text": "<p>There is also some work with programming a patients own stem cells to become long lived plasma blasts for broadly neutralizing antibodies against HIV (and other diseases I assume). Although you are essentially asking what is harder...eliciting these broad... |
14,370 | <p>Does anyone routinely do RNA isolation from zebrafish embryos?</p>
<p>I have embryos from different stages but all below 24hpf. This is the protocol I follow:</p>
<ol>
<li>Take 10-20 embryos</li>
<li>Wash once with milliQ water</li>
<li>Treat with 1mg/ml Proteinase-K (5min with gentle shaking) to dechorionate</li>
<li>Wash again with milliQ water</li>
<li>Remove water and add 250 µl Trizol</li>
<li>Homogenize by pippeting</li>
<li>add 750µl more of trizol</li>
<li>Do the standard trizol extraction step (with chlorofom)</li>
<li>Take the aqueous phase and wash again with 200µl chloroform</li>
<li>Precipitate RNA with isopropanol</li>
<li>Wash thrice with 70% ethanol</li>
<li>dissolve in nuclease free water</li>
</ol>
<p>Despite all this I get a poor A260/A230 : ~0.4</p>
<p>Moreover, this happens consistently in all samples. The RNA bands look fine on the gel.</p>
<p>I have done RNA isolation many times from cell lines and tissues and never faced this problem. Is this common with zebrafish embryos? Is there a way to fix this other than by using kits?</p>
| [
{
"answer_id": 23293,
"pm_score": 3,
"text": "<p>This addition to the protocol worked out and good RNA quality was obtained:</p>\n\n<p><strong>Homogenization</strong></p>\n\n<ul>\n<li>Homogenized the embryos, suspended (and frozen) in trizol by passing through 2ml insulin syringes. (About 10 times).</li... | [
{
"answer_id": 14373,
"pm_score": 3,
"text": "<p>Usually I had no problems with RNA extractions - from various cultured cells as well as a number of different tissues from mouse. If I look at your protocol this is pretty much the same as the one we used or the one recommended <a href=\"http://www.ncbi.n... |
14,377 | <p>I've read about safe doses of radiation, briefly. Why is there such a thing a safe dose? Can't any radiation give you cancer? Why is it more and more dangerous to take in larger and larger doses? Just because the body can't recover as easily? Is there something fundamentally more damaging about larger doses of radiation, as opposed to smaller more frequent doses? I suppose this could go to a health forum, but I don't know of one, and I came about this question via thinking about Physics.</p>
| [
{
"answer_id": 14379,
"pm_score": 3,
"text": "<p>Great question. It is unfortunate that more people don't understand what "radiation" is and how it affects biology.</p>\n<p>Firstly, you must distinguish between ionizing radiation and non-ionizing radiation.\nWikipedia <a href=\"https://en.wiki... | [
{
"answer_id": 14378,
"pm_score": 1,
"text": "<p>First of all: Technically speaking there is no such thing as a safe dose in radiation like you can say for drugs or toxins. This is because every single event of radiation can cause damage that can cause cancer. </p>\n\n<p>Besides that, there is no need t... |
14,392 | <p>I have a list of mouse genes, but all our analysis happens for human genes. Is that possible to translate these mouse genes to human genes? and is there any tool that can help me on this? </p>
<p>I am mostly a computer science guy, I am not sure this is even possible. However, according to someone, this could happen, I don't expect a full conversion though. </p>
<p>Thanks. </p>
| [
{
"answer_id": 14397,
"pm_score": 3,
"text": "<p>I would recommend using <a href=\"http://www.ensembl.org/biomart\" rel=\"nofollow\">Biomart</a> from Ensembl. This is basically a Swiss Army Knife for converting gene names into various IDs, getting corresponding locations on the chromosomes and so on. Yo... | [
{
"answer_id": 14403,
"pm_score": 0,
"text": "<p>Sounds like you are searching for homologs of mouse genes in human genome. <a href=\"http://blast.ncbi.nlm.nih.gov/Blast.cgi\" rel=\"nofollow\">BLAST</a> should be able to help you finding that. You might want to find the sequences for the mouse genes on ... |
14,424 | <p>I'm having difficulty finding an explanation of how single primer amplification of DNA works in the literature available to me, can anyone explain the methodology and what it accomplishes?</p>
| [
{
"answer_id": 14432,
"pm_score": 2,
"text": "<p>This process is called sequence-independent single primer amplification (or in short SISPA). Its used to amplify unknown sequences for amplification, for example in unknown viruses.\nThe primers used for this process contain random sequences which should ... | [
{
"answer_id": 14430,
"pm_score": 0,
"text": "<p>single primer amplification is used to find unknown regions of DNA if you have no idea what to use as a primer further upstream. It works on the idea that any primer given a certain temperature will misprime. That it, it will anneal to a non specific loca... |
14,426 | <p>I guess, we could infer that the structure of an amino acid has the same functional units as RNA is used to synthesise it. Therefore, from a logical point of view it would make sense that genes are expressed as proteins.
However, why is this the case; why are genes expressed as proteins rather than any other type of bio molecules? Also, from what are other bio molecules expressed if not for genes? </p>
| [
{
"answer_id": 14432,
"pm_score": 2,
"text": "<p>This process is called sequence-independent single primer amplification (or in short SISPA). Its used to amplify unknown sequences for amplification, for example in unknown viruses.\nThe primers used for this process contain random sequences which should ... | [
{
"answer_id": 14430,
"pm_score": 0,
"text": "<p>single primer amplification is used to find unknown regions of DNA if you have no idea what to use as a primer further upstream. It works on the idea that any primer given a certain temperature will misprime. That it, it will anneal to a non specific loca... |
14,540 | <p>As far as I know, the DNA sequence becomes shorter every time a cell divides.<br>
A shorter sequence results in information loss and aging characteristics.<br>
<br>
As a countermeasure, shouldn't one stay young and healthy at least longer, if the DNA in a cell is changed with a "better" DNA (from years ago... let's say your DNA was extracted with the age of 20 and you reinsert it every 10 years or so)?
<br><br></p>
<p>If this is true, then (as for today's technology)<br>
- is it already possible to perfectly reproduce the DNA? (I only found articles about XNA)<br>
- is it possible to easily replace the DNA in all human cells? (I found articles about bacteria inserting pieces of DNA into human cells)</p>
| [
{
"answer_id": 14541,
"pm_score": 3,
"text": "<p>Lots of questions here. I recommend taking college level courses in Biochemistry, Molecular Biology, and Medical Physiology, and Geriatrics. </p>\n\n<p>There are other issues than just DNA. Systemic failure is system-wide, and probably most of the issues ... | [
{
"answer_id": 14548,
"pm_score": 1,
"text": "<blockquote>\n <p>As far as I know, the DNA sequence becomes shorter every time a cell\n divides. A shorter sequence results in information loss and aging\n characteristics.</p>\n</blockquote>\n\n<p>Neither telomeres nor aging are nearly that simple.</p>\... |
14,543 | <p>I saw a concept on the Internet that says "the strength of genetic drift is inversely proportional to the population size". I don't know why they are <strong>inversely proportional</strong>? Can somebody explain? Thank you all! </p>
| [
{
"answer_id": 14545,
"pm_score": 5,
"text": "<p><strong>Plane Crash Analogy</strong></p>\n\n<p><em>4 people in a plane crash</em></p>\n\n<p>In a small aeroplane, there are 2 people that wear a blue shirt and 2 people that wear a green shirt. The plane crashes, half of the people died. The 2 survivors a... | [
{
"answer_id": 14544,
"pm_score": 3,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Genetic_drift\" rel=\"nofollow noreferrer\"><strong>Genetic drift</strong></a> refers to changes in allele frequencies that are due to random sampling effects, and not selection. If you sample alleles from a finite p... |
14,577 | <p><img src="https://i.stack.imgur.com/GCdm7.png" alt="enter image description here"></p>
<p>I do not understand how to solve this question. I know that RNAse will cut smaller pieces of RNA.</p>
<p>The answer given is A</p>
| [
{
"answer_id": 14580,
"pm_score": 4,
"text": "<p>The question is a bit vague in some important parts, so I'll have to make a few assumptions about what the authors likely meant.</p>\n\n<p>RNAses are enzymes that degrade RNA. There are a few different ones that lead to different kinds of degradation. The... | [
{
"answer_id": 14578,
"pm_score": 2,
"text": "<p>RNA can fold and will therefore migrate faster than DNA. So it shows up as the band which is towards the positive front. After RNAse treatment you'll lose that band. So the answer is A</p>\n"
}
] |
14,582 | <p>We know that a glass gets cracked when it undergoes sudden change in temperature. But what will happen in the case of a human body if it changes from the maximum(>35℃) to the minimum temperature(<35℃) suddenly?</p>
| [
{
"answer_id": 14589,
"pm_score": 3,
"text": "<p><em>Disclaimer: the answer is very broad and covers both the situations I am confident about, as well as those I understand only superficially.</em> </p>\n\n<p>The outcome depends on particular temperatures.</p>\n\n<p>Example - <a href=\"http://en.wikiped... | [
{
"answer_id": 80246,
"pm_score": 1,
"text": "<p>Blood vessels tighten as the diferencial between the body temperature and the external temperature start to even out and the excess heat/energy disperses from the body to the environment. There should be a slowdown of heartbeat rate as less effort is app... |
14,595 | <p>This is an excerpt from a <a href="http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html" rel="nofollow">paper</a>:</p>
<blockquote>
<p>T>C mutations at NpTpN trinucleotides, also found in hepatocellular carcinomas, shows strong transcriptional strand bias with more T>C mutations on the transcribed than untranscribed strands</p>
</blockquote>
<p>What exactly is meant by "transcribed" strand: the sense strand or the template strand ?</p>
<p>I tried looking up for it but couldn't find any definition. </p>
| [
{
"answer_id": 14599,
"pm_score": 4,
"text": "<p>In my opinion they <strong>should</strong> mean the template strand, and they probably do. Perhaps if we had a link to the paper we could have examined the language more closely.</p>\n\n<p><a href=\"http://mbe.oxfordjournals.org/content/26/1/131.abstract\... | [
{
"answer_id": 14596,
"pm_score": 2,
"text": "<p>Remember that DNA is double stranded and each strand has a chemical direction. Genes are read by the ribosome in the 3' to 5' direction so that the DNA 'forward' direction is defined in this direction. This is the direction of transcription.</p>\n\n<p>E... |
14,657 | <p>According to the article <a href="http://www.google.com/hostednews/afp/article/ALeqM5hFUbEO1ciJQxU6WfzSBwyIHAxfzw?docId=c6a93e4c-3f4c-481e-ba52-eaa180e359d0">Dark skin and blue eyes: How Europeans once looked</a>:</p>
<blockquote>
<p>It is widely accepted that Man's oldest common forefather was dark
skinned, and that people became more pale as they moved further north
out of Africa into colder climates with less sunlight.</p>
</blockquote>
<p>I thought that humans' oldest common ancestor was light-skinned, because</p>
<ol>
<li>Dark-skinned people have white palms and soles, but light-skinned people have more consistent skin tones. This suggests that light skin is more ancestral and dark skin evolved to protect skin from the sun.</li>
<li>Bonobo chimpanzees, our closest primate cousins, look like they have light skin under black hair.</li>
</ol>
<p>I understand we all originate in Africa, but I thought that the environmental conditions in Africa were different from today. How do we know that the first humans were dark-skinned?</p>
| [
{
"answer_id": 14660,
"pm_score": 5,
"text": "<p>According to <a href=\"https://en.wikipedia.org/wiki/Human_skin_color\">wikipedia</a>, \"comparisons between known skin pigmentation genes in chimpanzees and modern Africans show that dark skin evolved along with the loss of body hair about 1.2 million ye... | [
{
"answer_id": 14664,
"pm_score": 5,
"text": "<p>The first modern humans evolved about 200.000 years ago in Africa. When they lost their body hair (or at least most of it), they needed some other protection of their skin from the sun - otherwise they are prone to develop melanoma. Melanin is such a prot... |
14,693 | <p>Some time last year, I found an article on Wikipedia about the smallest something to be able to reproduce. </p>
<p>I don't remember exactly what it was, but I am fairly certain that after the initial discovery another of the previous organism (this one slightly smaller) was discovered.</p>
<p>I think that the smallest something might have been the smallest self-replicating protein, or smallest self-replicating molecule, or something like that.</p>
<p>It was not mentioned in this thread: <a href="https://biology.stackexchange.com/questions/1382/which-organism-has-the-smallest-genome-length">Which organism has the smallest genome length?</a></p>
<p>It had a strange, stand-out name and I believe it was discovered in the 90s.</p>
| [
{
"answer_id": 14694,
"pm_score": 3,
"text": "<p>You're probably thinking of the Spiegelman Monster. It was actually discovered in 1965, but it was discovered that it became shorter over time in 1997.</p>\n\n<p>It also wasn't included in that thread, and it has a strange name. </p>\n\n<p><a href=\"http:... | [
{
"answer_id": 85197,
"pm_score": -1,
"text": "<p>A research team (Lee et al.) has discovered what maybe the smallest known self replicating RNA molecule - actually a 32-unit-long \"a-helical peptide\" whatever that is. It is based on the yeast transcription factor GCN4. The 32 peptide sequence is so sm... |
14,734 | <p>It seems that <a href="http://en.wikipedia.org/wiki/Encephalization_quotient" rel="nofollow">dolphins have (among?) the highest encephalization quotients found outside of humans</a>, higher even than chimpanzees. By the "use it or lose it" principle this indicates that intelligence must be particularly valuable in their niche. Why is that? They are predatory and social, and both of those are associated with intelligence, but why are dolphins smarter than other predatory pack animals? For example, is there something about being an air-breathing organism living in water that makes having a high <a href="http://en.wikipedia.org/wiki/Encephalization_quotient" rel="nofollow">EQ</a> particularly adaptive?</p>
| [
{
"answer_id": 14741,
"pm_score": 3,
"text": "<p>It's less about the brain size, I think, more about the metabolic cost of brains. Brains are among the most costly organs to keep what it comes to oxygen demand. Air-breathing increases available oxygen for the body, hence mammals have larger brains that ... | [
{
"answer_id": 14735,
"pm_score": 3,
"text": "<p>It might not fully answer your question…</p>\n\n<p><strong>Cost of having a heavy brain</strong></p>\n\n<p>Generally speaking, having a heavy organ is an important cost for flying animals, a medium cost for terrestrial animals and a low cost for marine an... |
14,736 | <p>I had a homework question that I could not figure out.</p>
<p>It states:</p>
<blockquote>
<p>A woman has cystic fibrosis in her family and did not want to have a
child that suffered from the disease. She and her spouse went for
genetic testing and counselling. She tested positive as a carrier and
her spouse tested negative, and their first child was born with cystic
fibrosis. Explain how this could happen.</p>
</blockquote>
<p>This doesn't make sense because the punnet square would be:</p>
<p>$$
\begin{array}{c|c|c}
& A & A \\
\hline
A & AA & AA \\
\hline
a & Aa & Aa
\end{array}
$$</p>
<p>This says there are no two recessive alleles which can cause cystic fibrosis.</p>
| [
{
"answer_id": 14792,
"pm_score": -1,
"text": "<p>I asked my Biology teacher and she said that the if the father is not a carrier, he must have the disease. So the father is aa.</p>\n"
}
] | [
{
"answer_id": 14737,
"pm_score": 3,
"text": "<p>If really cystic fibrose is expressed only in homozygotes, then here are some possible explanations:</p>\n\n<ul>\n<li>Mutation\n<ul>\n<li>very improbable</li>\n</ul></li>\n<li>Autofecundation\n<ul>\n<li>very improbable</li>\n</ul></li>\n<li>False Negative... |
14,745 | <p>And would a very accurate sensitive system for detecting circulating tumor cells (which detects 1 cell per 50 billion) be useful as a screening tool ?</p>
| [
{
"answer_id": 14869,
"pm_score": 3,
"text": "<p>Tumour cells can also metastasise using the lymphatic system. They first need to detach (produce enzymes that break down the extracellular matrix or any adherent molecules etc). Then they need to survive in the blood which is really hard with all the mech... | [
{
"answer_id": 42964,
"pm_score": 1,
"text": "<p>Screening programs are ruled out following sharp guidelines, like the so-called <a href=\"http://apps.who.int/iris/bitstream/10665/37650/1/WHO_PHP_34.pdf\" rel=\"nofollow\"> Wilson' criteria</a> and subsequent <a href=\"http://www.who.int/bulletin/volumes... |
14,747 | <p>I am not by any means a biologist - so go easy.</p>
<p>What would be a method for determining whether or not a patient has cancer based only on a genomic sequence?</p>
<p><strong>Update</strong> Thanks for the help in revising the questions.</p>
<ol>
<li><p>What information is extractable once a genome has been sequenced?</p></li>
<li><p>Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.</p></li>
</ol>
| [
{
"answer_id": 14772,
"pm_score": 3,
"text": "<p>Answering your question 2: </p>\n\n<blockquote>\n <p>Is it possible to derive whether or not a person has cancer based only\n on the genome which was sequenced? i.e. Are there anomalies to look\n out for to detect the cancer.</p>\n</blockquote>\n\n<p>I... | [
{
"answer_id": 14748,
"pm_score": 2,
"text": "<blockquote>\n <p>When sequencing a human's (i hope im stating this correctly) genome is\n there a difference between the genome before and after the patient is\n found to have developed some sort of cancer.</p>\n</blockquote>\n\n<p>If you are asking if c... |
14,749 | <p>I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to <a href="http://en.wikipedia.org/wiki/HER2/neu" rel="nofollow">ERBB2</a> as a gene and a pathway. I don't have solid biology background. What exactly means when we refer to ERBB2 as a pathway? Does it refer to activity of a protein encoded by ERBB2?</p>
| [
{
"answer_id": 14761,
"pm_score": 2,
"text": "<p>ErbB2 is a receptor tyrosine kinase. This is a class of receptors, which are located in the membrane ob the cell and which pass signals from the outside of the cell into it, so it can for example react to changing conditions. </p>\n\n<p>ErbB2 (which is al... | [
{
"answer_id": 14750,
"pm_score": 2,
"text": "<p>ERBB2 appears to be a (tyrosine kinase) receptor; that is, it lives in the cell membrane; with a part that sticks outside of the cell, and part that sits inside. When the right molecule attaches to the outside part, the inside part changes shape, which a... |
14,808 | <p>It seems so simple that if my brain can tell my right hand to do something, then it should be able to tell equally well to the left ? This seems like a pretty major evolutionary advantage. Why haven't we evolved so during millions of years ?</p>
| [
{
"answer_id": 14866,
"pm_score": 3,
"text": "<p>Having a dominant side is advantageous. Instead of seeing it as the brain influences our fine motor skill, think of it the other way round. The way we use our hands or any other part of our body sends feedback to the brain to increase the portion of the b... | [
{
"answer_id": 14823,
"pm_score": -1,
"text": "<p>A simple answer to this is that at some point our brain's architecture was wired to have a dominant side, at which point it became too expensive evolutionarily to have drastic brain re-organisation or size changes.</p>\n\n<p>Another answer to this is tha... |
14,831 | <p><strong>Theoretical question</strong></p>
<ul>
<li>Can diploidy (or polyploidy) evolve from a haploid lineage in the absence of sexual reproduction ?</li>
<li>For what theoretical reason? How can such evolution take place?</li>
</ul>
<p><strong>Empirical evidence</strong></p>
<p>Beside theoretical answers I'd like to also ask for empirical examples:</p>
<ul>
<li>Are there any examples of diploid (or polyploid) species that reproduce exclusively asexually, and for which sexual reproduction never occurred in the evolutionary lineage of this species?</li>
</ul>
<p>Or in other words,</p>
<ul>
<li>Does diploidy (or polyploidy) exist in lineages that has never underwent sexual reproduction?</li>
</ul>
<p><strong>Is my assumption correct?</strong></p>
<p>I am assuming that in eukaryotes haploidy appeared before diploidy. Is this assumption correct?</p>
<hr>
<p>By sexual reproduction I mean that the genome of the offspring is a combination (with or without recombination/crossover) of two parent individuals. I don't mean reproduction with sexes (or with mating types). I welcome the discussion of self-fertilization if needed.</p>
| [
{
"answer_id": 14886,
"pm_score": 4,
"text": "<p>I can only offer a partial answer on the <strong>theoretical aspects</strong>. I don't know if you are familiar with the mid-90s papers by Otto et al. (<a href=\"http://www.genetics.org/content/131/3/745\" rel=\"nofollow noreferrer\" title=\"Otto & Go... | [
{
"answer_id": 14894,
"pm_score": 2,
"text": "<p>This is not on theoretical grounds, but here is an existence proof: a number of bacteria, which reproduce asexually, are polyploid. <a href=\"http://schaechter.asmblog.org/schaechter/2010/11/of-terms-in-biology-bacterial-ploidy.html\" rel=\"nofollow\">Her... |
14,856 | <p>Is there a linear connection between muscle size and the power it can produce?
If not, why? And what is the true correlation if any, can it be described with an appropriate function? What other factors modify it? (Red/white fiber for instance?)</p>
| [
{
"answer_id": 14865,
"pm_score": 3,
"text": "<p>The short answer to your question is that the work output from a muscle is a combination of physiological cross-sectional area, length, fiber type, and recruitment (how many motor units are activated).</p>\n<p>Read on for more details.</p>\n<p>Force outpu... | [
{
"answer_id": 14862,
"pm_score": 0,
"text": "<p>The muscular fiber cross section and length would be proportional to its strength, but there are also many <a href=\"https://en.wikipedia.org/wiki/Skeletal_striated_muscle\" rel=\"nofollow\">different kinds of cellular types and structures</a> which can r... |
14,859 | <p>I found this picture in my study materials.
I think it is too schematic and ignores the big pictures.</p>
<p><img src="https://i.stack.imgur.com/V6cgi.png" alt="enter image description here"></p>
<p>I think the thing connected to the hormone is receptor.
The second messanger is then connected to the receptor which stimulates the effector cell in the cytosol.
The cell then response both to cytosol and to extracellular space.
<strong>How do you understand this picture?</strong></p>
<p><strong>Do you know any similar pictures which present the same thing but clearer and more exactly?</strong></p>
| [
{
"answer_id": 14863,
"pm_score": 3,
"text": "<p>I think the schematic you have there and the one that @Masi posted are pretty good. A better way of getting a grasp of intercellular signaling would be to study a specific hormone and understand how each of the elements in the block diagrams here could v... | [
{
"answer_id": 14860,
"pm_score": 0,
"text": "<p>I found this picture from my old study materials which I edited little to show the I/e and E/c spaces.</p>\n\n<p><img src=\"https://i.stack.imgur.com/hx5zY.png\" alt=\"enter image description here\"></p>\n"
}
] |
14,899 | <p>I've recently heard a podcast, in which <a href="http://en.wikipedia.org/wiki/Helen_Fisher_%28anthropologist%29#Four_broad_personality_styles" rel="nofollow noreferrer">Dr. Helen Fisher suggests that there are "4 broad personality types"</a>, and each one is associated with a particular neurotransmitter:</p>
<blockquote>
<p>The corresponding Platonic thinking style, Keirsey temperament type (according to some readers, not Fisher herself), and color can be seen in parenthesis.</p>
<ul>
<li>Explorer (creative; Artisan temperament, yellow) = <strong>dopamine</strong></li>
<li>Builder (sensible; Guardian temperament, blue) = <strong>serotonin</strong></li>
<li>Director (reasoning; Rational temperament; red) = <strong>testosterone</strong></li>
<li>Negotiator (intuitive; Idealist temperament; green) = <strong>estrogen/oxytocin</strong></li>
</ul>
</blockquote>
<p>I'm interested <strong>if there's indeed scientific evidence</strong> to support that for different people their <strong>affinity for a certain neurotransmitter</strong> is increased to such degree that it manifests in a noticeable difference in personality?</p>
| [
{
"answer_id": 14971,
"pm_score": 3,
"text": "<p>Dr. Helen Fisher's conclusions are plain bunkum. What does it even mean when she says associated with a particular neurotransmitter? The sheer work required to even get at this question is vast and difficult so it is unsurprising that she is venturing as ... | [
{
"answer_id": 14912,
"pm_score": 0,
"text": "<p>I know that the Keirsey model itself is rather unsubstantiated. It's a sort of simplified version of MBTI. So I am not sure if relating the neurotransmitters to Keirsey temperament would work due to the fallibility of temperaments.\nHowever, different neu... |
14,951 | <p>I thought there were only two centrioles per cell, that convert to the basal body at some point during the cell cycle. I also thought there's one basal body per cilium, so I'm not clear on where the other basal bodies are coming from. I'd like to know the distribution of basal bodies and centrioles throughout the cell cycle in multi-ciliated organisms/cells.</p>
| [
{
"answer_id": 24534,
"pm_score": 1,
"text": "<p>There is a single basal body per cilium. During cell division the centrosome has two centrioles, however, during the differentiation of citiated cells, there is an amplification of basal bodies that nucleate from the centrioles. </p>\n\n<p>In multiciliate... | [
{
"answer_id": 17471,
"pm_score": 1,
"text": "<p>It seems that there is one basal body per cilium in multiciliated cells. Centriole duplication (as far as I understand, a basal body is just a different name for a centriole that is attached to a cilium) is tightly coupled to the cell-cycle. There is alwa... |
14,979 | <p>Assume you have an exam which has 5 extensive questions and 60 minutes.
You do not have time to cover most if you write everything in essay format.
If you start to write essays, you do not really have time to cover all mechanisms and so on.</p>
<p>I just heard that one student did the exam with by list format, for instance</p>
<blockquote>
<p>sitting -> venous return down & skeletal muscles not working correctly -> trombus. </p>
</blockquote>
<p>and then describing relevant mechanisms similarly and combining the their roles shortly.</p>
<p>Another morphology of H. pylori</p>
<blockquote>
<p>Curved (spiral shape), Gram-negative, 2-4 micrometer long, coccoid forms in older cultures, </p>
</blockquote>
<p><strong>Is there any official standard or unofficial accepted way how to answer questions in Physiology/Medicine?</strong></p>
| [
{
"answer_id": 14984,
"pm_score": 3,
"text": "<p>Given the highly variable nature of such processes and systems, it's unlikely that a common standard is feasible or sensible. In medical questions, a bottom-up order like in your example usually makes sense, starting with the most specific known cause and... | [
{
"answer_id": 14982,
"pm_score": 1,
"text": "<p>I usually answer in a extensive and descriptive way, and I try to put as much information as possible. If it's a process I usually add a little diagram. If there are lot of attributes to add sometimes I do lists, but usually teachers don't like them an it... |
15,006 | <p>Research projects with artificial life generally use creatures that are haploid. The offspring randomly inherit some genes from one parent, and some genes from the other parent.</p>
<p>Q1: Are there any biological species which reproduce similarly? I.e., they're haploid, but the offspring aren't clones. Perhaps hermaphroditic species like slugs or some plants?</p>
<p>Q2: Is there a name for this type of reproduction? If not, I guess I'll call it "pseudosexual" since it's a simplified form of true sexual reproduction.</p>
| [
{
"answer_id": 15018,
"pm_score": 3,
"text": "<p>Generally, all diploid species pass through a haploid phase in their life. This is called the <a href=\"http://en.wikipedia.org/wiki/Alternation_of_generations\" rel=\"nofollow noreferrer\">alternation of generations</a> and the cycle may be presented lik... | [
{
"answer_id": 78972,
"pm_score": 2,
"text": "<ol>\n<li>I don't know any example of haploid, but (pseudo)sexually reproducing artificial life (and hardly any at all existed 4 years ago when the question was posted!). So I assume you meant in-silico life. Then, yes, usually as you described. </li>\n<li>... |
15,015 | <p>I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that manually.</p>
<p>Is there any existing tool or script that can fetch all those entries from a database and extract the correct subset of the sequence? </p>
| [
{
"answer_id": 15065,
"pm_score": 3,
"text": "<p>I will edit this if you update your question with more information, but for the moment I am assuming you have access to a Linux/Unix system and that your file of accessions looks like this:</p>\n\n<pre><code>A00145.1 123 456\n</code></pre>\n\n<p>Where th... | [
{
"answer_id": 15030,
"pm_score": 3,
"text": "<p>From ENA</p>\n\n<blockquote>\n <p>To retrieve results by a single identifier for all records other than\n Taxon and Project please, use the following URL syntax:</p>\n \n <p><a href=\"http://www.ebi.ac.uk/ena/data/view/\" rel=\"nofollow\">http://www.e... |
15,017 | <p>What is the mechanism?
In other words, how does the tRNA know whether the codon is in 5' to 3' direction? I also heard that anything that is translated from 3' to 5' direction is degraded. Is it true? </p>
| [
{
"answer_id": 15020,
"pm_score": 4,
"text": "<p>The tRNA is not acting alone, it has the help of the <a href=\"http://en.wikipedia.org/wiki/Ribosome\" rel=\"noreferrer\">Ribosome</a>. </p>\n\n<p><img src=\"https://i.stack.imgur.com/vArV7.png\" alt=\"enter image description here\"></p>\n\n<p>The Ribosom... | [
{
"answer_id": 15036,
"pm_score": 2,
"text": "<p>I think that there is no reason in principle why early evolution couldn't have landed on a translation mechanism going 3'>5'. There are, however, clear biochemical reasons why the transcript itself has to be made in a 5'>3' direction. So in this alternati... |
15,082 | <p>What are 5' and 3' in DNA and RNA strands? Please clarify with some images and please use simple English.</p>
| [
{
"answer_id": 15085,
"pm_score": 6,
"text": "<p>The 5' and 3' mean \"five prime\" and \"three prime\", which indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA strand a \"direct... | [
{
"answer_id": 15086,
"pm_score": 3,
"text": "<p>The no 5 and 3 are the carbon no of the carbon skeleton ring of deoxyribose as similar as any other organic compound. In any nucleic acid, RNA or DNA 3' refers to the 3rd carbon of sugar ribose or deoxyribose which is linked to OH group and 5' linked t... |
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