qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
50,788 | <p>Is post-transcriptional regulation of gene expression (for example regulation by microRNAs) a type of epigenetic gene expression regulation? </p>
<p>I think we can categorize it as epigenetic since the DNA sequence is not changed, but I have never come across that terming in any papers. Does someone have any idea, or know of any papers that categorize post-transcriptional regulation as epigenetic?</p>
| [
{
"answer_id": 50798,
"pm_score": 3,
"text": "<p>miRNAs and other post-transcriptional regulators are very well \"genetic\". They are encoded by genetic elements, are expressed and are affected by mutations. Just because this mode of regulation was not well known previously, it should not be classified ... | [
{
"answer_id": 50791,
"pm_score": 1,
"text": "<p><strong>On epigenetic and genetic effects:</strong></p>\n<p>Changes to the genome can be of two key types: genetic and epigenetic. Genetic changes are those which cause changes in the nucleotide sequence. Epigenetic are changes to the genome that do not i... |
50,867 | <p>I am currently trying to see if 2 bacteria contains plasmids or not. I had used promega plasmid extraction kit on the bacteria. I ran a gel electrophoresis (.8% gel) with the extract product, however its not showing the presents of any DNA. I also ran the product through Nanodrop (2000) and these where the concentrations I got:</p>
<p>1 : 6.5 ng/ul & 260/280 = 1.56<br>
2 : 49.4 ng/ul & 260/280: 1.96</p>
<p>Based on experience, I want to say #1 contains no plasmids, however #2 may have a small concentration of plasmids. Please give me your opinion on what to conclude. Also, if there is another test I can try to do to confirm plasmid presents or not, please let me know. </p>
| [
{
"answer_id": 51683,
"pm_score": 3,
"text": "<p>I don't know how much culture volume you used, but the amounts you have look more like a medium/high copy plasmid. I don't know if that's what you'd expect for a natural plasmid. </p>\n\n<p>In addition to the other answer, it could also be sheared genomic... | [
{
"answer_id": 50871,
"pm_score": 2,
"text": "<p>Having a positive reading on the Nanodrop but no band on the gel can be due to a number of different issues (not exhaustive):</p>\n\n<ol>\n<li>An incorrectly zeroed sample</li>\n<li>Incomplete staining of the gel</li>\n<li>Contamination of the sample</li>... |
50,934 | <p>A lot of sources tell me that RBCs contain a number of enzymes, and that these serve multiple functions from maintaining the structure and elasticity of the corpuscle wall, to preventing the oxidation of iron (ferrous) in Haemoglobin to the +3 Ferric state.</p>
<p>But what none of them say, is what problems (if any) arise when the iron is oxidised. Hence the question, why avoid the Ferric state?</p>
<p>I'm still a high-schooler and from what I've learnt, is that the higher the oxidation state of the cation, the higher its polarising power (Fajan's Rules) hence stronger the bond. So wouldn't iron in the Ferric state be able to bind with oxygen better, and isn't that desirable? ( Or is oxygen <em>release</em> to tissues going to be problematic? )</p>
<p>If the Ferric state is desirable, then why do RBCs have mechanisms (the enzymes mentioned earlier) in place to <em>prevent</em> the oxidation of the Ferrous to the Ferric state?</p>
<p>Thanks!</p>
| [
{
"answer_id": 51042,
"pm_score": 4,
"text": "<blockquote>\n <p>Q. “What problems (if any) arise when the iron is oxidised?”</p>\n \n <p>A. Haemoglobin will be converted to methaemoglobin which cannot bind oxygen.</p>\n</blockquote>\n\n<p>To quote from the article on <a href=\"https://en.wikipedia.or... | [
{
"answer_id": 51036,
"pm_score": 2,
"text": "<blockquote>\n <p>what problems (if any) arise when the iron is oxidised:\n Nothing. </p>\n</blockquote>\n\n<p>It's part of the transfer job :)\nHemoglobin from RBCs is responsible for oxygen transfer through your blood vessels all around your body and oxy... |
51,236 | <p>If you watched the last Olympics like me you probably also observed that most medallists in running events were black. Why is that? I discussed this with university grad friends and researchers and we only came up with hypotheses but nobody had an actual explanation. Is it cultural, genetic, other reasons or nobody really know?</p>
<p><strong>Update:</strong></p>
<p>Sprint and distance running requiring different attributes for being the best, let separate this question in two parts: <strong>1) Sprint (i.e. 100m)</strong> and <strong>2) Distance running (@Forest already provided a great answer for this)</strong>.</p>
<p><em>Note: I know this question can potentially bring disrespectful answers/comments, but I'm hopeful that this site and its members can answer this interesting question. Otherwise, I'll simply erase my question.</em></p>
| [
{
"answer_id": 51250,
"pm_score": 6,
"text": "<p>It's an interesting question and one that has been asked before. NPR did a <a href=\"http://www.npr.org/sections/parallels/2013/11/01/241895965/how-one-kenyan-tribe-produces-the-worlds-best-runners\">story</a> in 2013 on this topic, but their question was... | [
{
"answer_id": 51239,
"pm_score": 4,
"text": "<p>Take a look at Will Grover's answer <a href=\"https://www.quora.com/Why-are-the-fastest-black-sprinters-faster-than-the-fastest-white-sprinters\" rel=\"nofollow noreferrer\">here</a>, I will cite the genetic diveristy explantion here, I think that sounds ... |
51,414 | <p>I have read the phrase 'T3 is three to four times more potent than T4' several times both in books and <a href="https://en.wikipedia.org/wiki/Thyroid_hormones" rel="nofollow">websites</a>. But isn't T4 a prohormone of T3? Why do then these sources talk about its potency as a hormone(I suppose)?</p>
| [
{
"answer_id": 51518,
"pm_score": 3,
"text": "<p>It is necessary to distinguish between <em>classical</em> and <em>non-classical</em> actions of thyroid hormones.</p>\n\n<p><em>Classical action</em> involves nuclear THR (or TR) receptors (TR alpha1, TR beta1, TR beta2). They are activated by T3, 3,5-T2,... | [
{
"answer_id": 51421,
"pm_score": -1,
"text": "<p>I don’t know, but I suspect that T4 was characterized first and fulfils the classic definition of a hormone being secreted by a gland and carried in the blood to its target. </p>\n\n<p>Potency is the measure of some biological or biochemical assay of the... |
51,560 | <p>Humans seem to be the only animal whose females have breasts that permanently have a "full" appearance, ie a prominent amount of tissue even when not lactating, whereas other species' breasts seem to almost totally "deflate" when not longer lactating.</p>
<p>Why is that? </p>
<p>This feature has costs to the organism; significant biomass is dedicated and perhaps mobility is impacted. Given there are costs, for the feature to have come into existence, evolution/adaptation principles suggest there must have been some advantage.</p>
<p>Is there some biological advantage?<br>
Are they vestiges of an adaptation that gave a significant advantage to some prior species or in some specific (presumably cold) prior environmental conditions?
Is there any credible research to support certain reasons?</p>
<hr>
<p>My suspicion is that although genders can be distinguished easily enough, even from a distance, using other secondary characteristics, the answer may have an anthropological/social answer, rather than a biological one.</p>
| [
{
"answer_id": 54454,
"pm_score": 4,
"text": "<p>You may be interested in <a href=\"http://www.sciencedirect.com/science/article/pii/0162309595000023\" rel=\"noreferrer\">Breast asymmetry, sexual selection, and human reproductive success</a>.</p>\n\n<p>Abstract:</p>\n\n<blockquote>\n <p>Breasts of huma... | [
{
"answer_id": 51731,
"pm_score": 0,
"text": "<p>Even though human females' breasts appear full, they're only filled with milk after giving birth or parturition. Other times they're mostly made up of fat. \nAnd they're full mostime probably only to signal the males that they're capable of raising a baby... |
52,289 | <p>In Hofstadter's <a href="https://en.wikipedia.org/wiki/G%C3%B6del,_Escher,_Bach" rel="noreferrer"><em>Gödel, Escher, Bach: An Eternal Golden Braid</em></a> (GEB), the following claim appears:</p>
<blockquote>
<p>...in the species <em>Felis catus</em>, deep probing has revealed that it is indeed possible to read the phenotype directly off the genotype. The reader will perhaps better appreciate this remarkable fact after directly examining the following typical section of the DNA of <em>Felis catus</em>:</p>
<p>...CATCATCATCATCATCATCAT...(<strong>OP note:</strong> truncated because, you get it)</p>
</blockquote>
<p>Is this true? A cursory search for the DNA of <em>Felis catus</em> gives me <a href="http://cnso.nova.edu/forms/jose_lopez_felismitochondrialgenome_genomics_1996.pdf" rel="noreferrer">this 1996 paper</a> by Lopez, Cevario, and O'Brien and the given sequence does not appear – there are some instances of "CAT" but not repeated enough to make it as remarkable as claimed in GEB.</p>
<p>I don't know enough Biology to judge the veracity of this claim. Some points I am considering are:</p>
<ul>
<li>GEB is full of wordplays. However, the tone of this part of the text does not sound like one to me.</li>
<li>GEB was written/published around 1978. The paper I linked to – which was cited by some 236 others according to Google – was published in 1996, way after GEB's time. If my impression that Lopez et al.'s work is significant because it is the first time <em>Felis catus</em> has been sequenced, then there is no way Hofstadter could've known of it when he wrote GEB. Then again, I don't know enough Biology that there might be some nuance to Lopez et al.'s paper that I'm missing (i.e., the results of the paper might not be mutually exclusive to the claim made in GEB).</li>
<li>GEB has reference notes and bibliography and there is no reference cited to back this claim. However, GEB does not attempt to be a rigorous academic thesis and the references is only called upon more when Hofstadter quotes other works directly while the bibliography is a list of readings which the reader may want to check out, regarding the main thesis of the book.</li>
</ul>
<p>So are cats recursions with no base cases?</p>
| [
{
"answer_id": 52291,
"pm_score": 8,
"text": "<p>The <a href=\"https://www.ncbi.nlm.nih.gov/assembly/?term=Felis%20catus\" rel=\"nofollow noreferrer\"><em>Felis catus</em> genome</a> has been published, annotated, and updated quite a bit since 1996, including spans of so-called intergenic regions, which... | [
{
"answer_id": 52301,
"pm_score": 6,
"text": "<p>While <a href=\"https://biology.stackexchange.com/a/52291/10456\">Matt's answer</a> is perfectly correct, it is important to note that the sequence $(CAT)_n$ in DNA is not restricted to cats, and you would expect to find it anywhere. </p>\n\n<p>For exampl... |
52,977 | <p>If life formed on earth by natural laws, why can't we observe the formation of life from matter today? Is it because this is a rare phenomenon? It seems just after formation of earth life formed on earth and around 2-3 billion years has passed. It must be enough time for life to form several times from scratch.</p>
| [
{
"answer_id": 52982,
"pm_score": 5,
"text": "<p>The first life was probably so fragile and simple we would likely not even recognise it if it did appear. We don't know exactly how, or where, life first appeared but nearly all theories suggest simple collections of enzymes in protected environments that... | [
{
"answer_id": 52986,
"pm_score": -1,
"text": "<p>The answer may be that life did not form on Earth. There is not even the slightest hint of evidence that life formed on Earth. The known facts about early lifeforms on Earth from fossils and everything we know about geology of the early Earth and the Ear... |
52,990 | <p>I am searching for an un-encoded data file with common and scientific names for example of a few hundred species or tens of thousands, where I can search the common and scientific labels of organisms. </p>
| [
{
"answer_id": 52994,
"pm_score": 5,
"text": "<p>Uniprot has a list of the controlled vocabulary for common and scientific names of species listed <a href=\"http://www.uniprot.org/docs/speclist\" rel=\"nofollow noreferrer\">here</a>.</p>\n\n<p>An example entry:</p>\n\n<pre><code>ACAER E 111511: N=Acant... | [
{
"answer_id": 52993,
"pm_score": 4,
"text": "<p>Maybe not a direct answer to your question, depending on what you mean with \"unencoded data file\", but the <a href=\"http://www.gbif.org\">Global Biodiversity Information Facility (GBIF)</a> has an <a href=\"http://www.gbif.org/developer/species\">API</... |
54,131 | <p>Can I imagine the difference between the model of the grandma neuron and the model of interconnected neuron network so that the information isn't primarily stored in the neurons (respectively in their states) but in the connections between them.</p>
| [
{
"answer_id": 54142,
"pm_score": 4,
"text": "<blockquote>\n <p>Is the information in the Brain stored in the connections rather than\n in the neurons ?</p>\n</blockquote>\n\n<p>It depends on what information you are referring to.</p>\n\n<p>The brain does not just store one type of information,the mod... | [
{
"answer_id": 54135,
"pm_score": 1,
"text": "<p>The physiology of memory is still poorly understood, but there are some generalizations we can work with:</p>\n\n<p>There are four \"types\" of memory which the human brain works with.</p>\n\n<p><strong>Sensory memory</strong> is very short-term (millisec... |
54,966 | <p>I am a newbie studying campbell biology. just a quick question about virus.
When viral genome(RNA) expose itself in the host cell, why does the host cell not eliminate the genome since it apparently not belong to the cell ? Is there any mechanism that the host cell can detect and eliminate the viral genome as in the step 2,3 in the figure below ?</p>
<p>Thanks in advance !
<a href="https://i.stack.imgur.com/wKKhT.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/wKKhT.png" alt="enter image description here"></a></p>
| [
{
"answer_id": 55003,
"pm_score": 3,
"text": "<p>Your image illustrates the replication cycle of a <a href=\"https://en.wikipedia.org/wiki/Negative-sense_single-stranded_RNA_virus\" rel=\"nofollow noreferrer\">negative-sense single-stranded RNA virus</a>, where the viral genome needs to be \"inverted\" ... | [
{
"answer_id": 54968,
"pm_score": 0,
"text": "<p>If you are trying to ask if the RNA can be destroyed, it is not likely unless you don't utilize <a href=\"https://en.wikipedia.org/wiki/Small_interfering_RNA\" rel=\"nofollow noreferrer\">siRNA</a>. </p>\n\n<p>SiRNA, a mechanism involved in the regula... |
55,282 | <p>I know that the bradford assay is a very standard way of measuring protein concentration after e.g. a purification. However, in the lab that I work in now they normally only use nano drop at the 280nm wavelength. </p>
<p>How trustworthy is this concentration? Say that I e.g. get 2.5 mg/mL, could I really trust this?</p>
| [
{
"answer_id": 55285,
"pm_score": 4,
"text": "<p>That depends strongly on your protein and how exact you need this concentration. Both tests (Bradford and the measurement at 280nm) only do an approximation. </p>\n\n<p>The measurement at 280nm relies on the interaction of aromatic aminoacids with the UV ... | [
{
"answer_id": 55288,
"pm_score": 3,
"text": "<p>The nanodrop should have an option that allows you to input an \"extinction coefficient\". This is a measurement of how much one mole of your protein will absorb at 280nm. The nanodrop will use this value to give you an accurate concentration reading.</p>... |
55,632 | <p>In my introductory biology class, we are learning about biomolecules. The textbook says fats are a more efficient energy store than carbohydrates.</p>
<p>So my question is - why would plants store their energy as carbohydrates and not as fats, if fats are a more efficient energy store?</p>
| [
{
"answer_id": 55636,
"pm_score": 4,
"text": "<p>There are quite some reasons for why plants prefer carbohydrates for energy storage rather than fats. I will reach some of them one at a time.</p>\n\n<ul>\n<li><p><strong>Fat hates water:</strong> By just applying some common sense, one would get to know ... | [
{
"answer_id": 57191,
"pm_score": 4,
"text": "<p>The question was:</p>\n\n<blockquote>\n <p>Why would plants store their energy as carbohydrates and not as fats, <strong>if fats are a more efficient energy store</strong>?</p>\n</blockquote>\n\n<p>But before trying to answer it you have to be quite clea... |
56,723 | <p>I am trying to find a case/study where scientists documented a mutation in an animal or human that was to the benefit of the host.</p>
<p>The closest thing I have been able to find is sickle cell anemia (SCA) helping to fight malaria. However, the life expectancy for people with SCA is 40 – 60 years, and in 1973 it was only 14 years (<a href="https://www.nhlbi.nih.gov/health/health-topics/topics/sca" rel="nofollow noreferrer">source</a>). I am looking for another case, preferably one that is not life-threatening.</p>
<p><strong>Are there any other cases where a beneficial mutation — one where the good outweighs the bad — was documented?</strong></p>
<p>By beneficial I simply mean that it helps or protects the host in some way, while not causing substantial harm. As in my example of SCA it can benefit the host if the host lives in an area with malaria. However, it is also life threatening and reduces the life expectancy of the host. </p>
<p>If — for example — SCA would only cause pain and not be life-threatening, then it would (in my opinion) be a beneficial mutation. While not <em>purely</em> beneficial, it would still increase the life expectancy of people living in an area with a high occurrence of malaria.</p>
| [
{
"answer_id": 56936,
"pm_score": 4,
"text": "<p><strong>Lactase persistence</strong></p>\n\n<p>This is a somewhat unusual example but has been well studied, and would seem to satisfy the criteria of the question. Let me start by quoting the <a href=\"https://en.wikipedia.org/wiki/Lactase_persistence\" ... | [
{
"answer_id": 56732,
"pm_score": 4,
"text": "<p>The answer depends on what you mean by \"observed\".</p>\n\n<p>Bacteria acquire antibiotic resistance genes all the time, for example. This happens 'in the wild', but you can see in the lab that bacteria can become resistant overnight - I'd call that 'obs... |
57,486 | <p>Suppose a poisonous snake bites you; this will likely cause hypertension, and it will result in your heart rate increasing dramatically.</p>
<p>Because of the high rate of heart beats, your body will make the snake poison circulate throughout the whole body even faster. This will likely bring about death even faster. (definitely <strong>100%</strong> disadvantage)</p>
<p>Why do heart beats increase when we are in a state of tension even though it is to our disadvantage? </p>
| [
{
"answer_id": 59847,
"pm_score": 2,
"text": "<p>The heart rate increases due to any acute stress, it is part of the <a href=\"https://en.wikipedia.org/wiki/Fight-or-flight_response\" rel=\"nofollow noreferrer\">flight or fight response</a>. This is part of the responses that readies the body for rapid ... | [
{
"answer_id": 58248,
"pm_score": 0,
"text": "<p>Because it's a poison so it has to do it's work which is making as much harm as it's possible.</p>\n\n<p>Also, I'm not sure if heart beats faster because of poison or because of how you react for being in danger.\nIf it's because of the danger then it wor... |
59,243 | <p>I have always been taught that enzymes can catalyze both the forward and reverse reaction, and will increase the reaction rate in both directions. I understand that the thermodynamics of the reaction are not altered by the enzyme, but I have yet to find a good answer / example for an enzyme that actually does this. (E.g. can a nuclease join DNA together if the products are in excess? Can a protease form a peptide bond?) I am having difficulty finding a resource online that actually justifies this claim without just saying "Yes enzymes work both ways."</p>
| [
{
"answer_id": 59246,
"pm_score": 5,
"text": "<p>Enzymes alter the rate of a reaction by lowering activation energy; they have no effect on the reaction equilibrium ($\\ce{K_{eq}}$). Since $\\ce{K_{eq}=\\frac{k_f}{k_r}}$ and $\\ce{K_{eq}}$ is constant, an increase in forward rate ($\\ce{k_f}$) requires ... | [
{
"answer_id": 59245,
"pm_score": 3,
"text": "<blockquote>\n <p>Examples of enzymes working in reverse?</p>\n</blockquote>\n\n<p>Except three enzymes of <a href=\"https://en.wikipedia.org/wiki/Glycolysis#Sequence_of_reactions\" rel=\"noreferrer\">Glycolysis</a> (Hexokinase, PFK-I and Pyruvate kinase) a... |
60,846 | <p>Given the following:</p>
<ul>
<li>bruises are caused by minor trauma which breaks blood vessels beneath the skin, causing bleeding</li>
<li>the mechanism by which bleeding stops is clotting</li>
<li>blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks</li>
</ul>
<p>why is it that people don't die from bruises? What mechanism does the human body have to keep this from happening?</p>
| [
{
"answer_id": 60849,
"pm_score": 7,
"text": "<blockquote>\n <p>blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks</p>\n</blockquote>\n\n<p>This statement is primarily true only for blood ... | [
{
"answer_id": 60850,
"pm_score": -1,
"text": "<p>Bruises usually damage capillaries (think of them as being side roads well away from the expressway and major routes). Just as closing down a few side roads in a lightly populated suburban or rural area a mile away from a major interstate is unlikely to ... |
61,059 | <p>I've seen innumerable antiseptic, mouthwash, handwash advertisements that claim to be able to eliminate as much as 99.9% of <strong>all</strong> germs over a surface...but why not the remaining 0.1% (i.e- why can't they eliminate <em>all</em> germs)?</p>
<hr>
<p>Clarifications:</p>
<p><strong>What they mean by "germs":</strong></p>
<p>Being a student of Biology, I can tell that the term "germs" is crudely defined. I would prefer to use "pathogens" (less ambiguous), and I suppose the guys that market these products have (roughly) the same idea in mind. Pathogens normally include bacteria (monerans), protozoans, fungi and viruses... so I guess these are the "germs" they're talking about.</p>
<p><strong>What I'm looking for in an answer:</strong></p>
<p>Why is it that these (commercial) products can't eliminate 100% of all pathogens? Is this due to the inability of antiseptics to act on a particular (class of) organisms? If so, what's the problem there? Or is it because, the guys who market stuff like this assume an arbitrary amount (0.1%) of the pathogens present on a surface (say, the human hand) is located in microscopic niches that are inaccessible to the antiseptic solution? (<strong>If</strong> it isn't possible to provide a blanket statement in this regard, use of <em>Listerine</em> as an example will suffice)</p>
<p><strong>In other words:</strong></p>
<p>Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?</p>
<p><strong>Also,</strong></p>
<p>Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?</p>
| [
{
"answer_id": 61060,
"pm_score": 5,
"text": "<p>This is actually an interesting question! Let me answer both the parts separately, taking the example of Listerine<sup>®</sup> mouthwash.</p>\n\n<blockquote>\n <p>Is an antiseptic's inability to eliminate 100% of all germs due to its \"chemistry\", or is... | [
{
"answer_id": 61071,
"pm_score": 2,
"text": "<p>I agree with answer of @another 'Homo sapien' - to 99.9% :-) but there is another angle on it:</p>\n\n<p>From millions of bacteria present, few might be genetically different enough to be able to deal with whatever chemical mechanism it supposed to kill t... |
61,161 | <p>Whilst our experiences shape the specifics of our brains throughout life, we know that there are a lot of shared properties between us. We all share the same basic layout as, for example, the V1 cortex is always in the same place. Thus it is evident that whilst some of the neural development is experience-dependent, some of it is hereditary/genetic or "hard wired". </p>
<p>It would seem to me that the extent to which the brain is "hard wired" depends on the species. Humans seem to have a lot more room for specialisation in life, whereas some animals don't exhibit much individuality, tending to follow very regular behavioural patterns that have no doubt evolved over time, subject to natural selection.</p>
<p>I have read up to some degree on how experience-dependent development works, but have been largely unable to find any detailed research into how experience-independent development works. That is, how does DNA encode these "hard wired" neural circuits?</p>
<p>Furthermore, the human brain contains some 100 billion neurons. If I assume that maybe 1% of them are "hard wired" into circuits from birth, that's still a billion neurons, each with several connections to other neurons that need to be somehow coded into a DNA sequence which only amounts to a couple of gigabytes worth of data. So how is the complex structure of these "hard wired" (experience-independent) neural circuits encoded in such a limited amount of DNA? How much of the brain is actually hard wired in this way and how much is open to experience-based development? Am I right in associating this process with the phenomenon of "instinct", that is, "hard coded" behavioural patterns in animals which appear to be hereditary?</p>
<p>Is there a name for this field of study? Specifically the study of how neural circuits are generated in the earliest stages, to lay down the high level structure of the brain before experience-based development can take over?</p>
| [
{
"answer_id": 68551,
"pm_score": 3,
"text": "<p>This is one of the most important question in neurosciences and we are far from understanding it. This is also the topic of the entire subfield of neurodevelopment (to answer your last question).</p>\n\n<p>First, you are right that the exquisite degree an... | [
{
"answer_id": 61162,
"pm_score": 0,
"text": "<p>This is a cool question and while I'm not a neuro(bio)logist, I've tried to quickly look into this.</p>\n\n<p>Basically what you are asking for is the part of the (human) <a href=\"https://en.wikipedia.org/wiki/Connectome\" rel=\"nofollow noreferrer\">con... |
62,532 | <p>As the question states, got curious and I was wondering if monogamy is an innate human behaviour or is it because of how we built society (religion, traditions, etc.)?</p>
<p>Let's say we go back in time, would we see humans settling down with a single partner at a time and caring for their children as a couple for life or would they reproduce with several leaving the mothers with their children?</p>
<p>Thanks!</p>
| [
{
"answer_id": 62535,
"pm_score": 6,
"text": "<p>Humans are believed to be mostly <a href=\"http://www.sciencedirect.com/science/article/pii/S0376635700001182\" rel=\"nofollow noreferrer\">serial monogamists</a> with a noticeable components of secret <a href=\"https://books.google.com/books?hl=en&lr... | [
{
"answer_id": 62534,
"pm_score": 2,
"text": "<p>I just read a book on the Evolution of Sex and one of the questions was why primates have lost the estrous cycle. The thought was that the sexual desire of the female anytime rather then periodically tends to keep the male \"at Home\" ensuring survival o... |
62,557 | <p>Say pathogenic bacteriaA makes toxinA, which had D-amino acids instead of L-amino aids, does this difference in chirality <strong>cause</strong> a different conformational change in the receptor or enzyme, thus leading to either deactivation of the enzyme or signal transduction pathway or activation of a different pathway?</p>
<p>I understand what chirality is in the concept of organic chemistry — rotating plane polarized light, ingold-prelog system etc; however I never leaned what structural feature of chiral molecules changes the way they react inside a cell.</p>
<p>I do NOT understand HOW changes in chirality can be associated with cellular toxicity.</p>
<p>links:
<a href="https://www.ncbi.nlm.nih.gov/pubmed/24752840" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/24752840</a></p>
<p><a href="http://www.jomb.org/uploadfile/2014/0113/20140113053743849.pdf" rel="nofollow noreferrer">http://www.jomb.org/uploadfile/2014/0113/20140113053743849.pdf</a></p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960212/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960212/</a></p>
| [
{
"answer_id": 62535,
"pm_score": 6,
"text": "<p>Humans are believed to be mostly <a href=\"http://www.sciencedirect.com/science/article/pii/S0376635700001182\" rel=\"nofollow noreferrer\">serial monogamists</a> with a noticeable components of secret <a href=\"https://books.google.com/books?hl=en&lr... | [
{
"answer_id": 62534,
"pm_score": 2,
"text": "<p>I just read a book on the Evolution of Sex and one of the questions was why primates have lost the estrous cycle. The thought was that the sexual desire of the female anytime rather then periodically tends to keep the male \"at Home\" ensuring survival o... |
62,624 | <p>It seems like a useful ability to be able to detect many different things about, say, another organism. A lot of mammals have this ability. Why not humans? Did we evolve it out or never develop it?</p>
| [
{
"answer_id": 62633,
"pm_score": 4,
"text": "<p>Humans' poor sense of smell is a myth, borne of 19th century speculation rather than actual data. This is described in an excellent recent <a href=\"http://science.sciencemag.org/content/356/6338/eaam7263/\" rel=\"noreferrer\">paper in Science</a> , \"Poo... | [
{
"answer_id": 62629,
"pm_score": -1,
"text": "<p>This is a question relegated to evolutionary biology. Our sense of smell is as it is because that is part of our evolution and it is what works best for us. Also consider that you used the word \"powerful\" The word is arbitrary when comparing the sense... |
65,225 | <p>Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences. </p>
<p>However, during the last American government shutdown in 2013, BLAST was <a href="https://tuckerinfo.wordpress.com/2013/10/01/federal-resources-affected-by-govt-shutdown/" rel="noreferrer">rendered unusable</a> due to lack of funding. </p>
<p>The incumbent president is also <a href="http://www.bbc.com/news/world-us-canada-41020779?ocid=socialflow_facebook&ns_mchannel=social&ns_campaign=bbcnews&ns_source=facebook" rel="noreferrer">threatening to shutdown the government</a> if funding for the Mexican border wall is not approved by the Democrats. </p>
<p>What are some alternatives for NCBI BLAST that are reasonably fast, easy to use, and would not be rendered unusable in the event of American government shutdowns? Ideally, the tools should encompass all of the standard BLAST sub-functions (pblast, PSI-blast, etc). </p>
| [
{
"answer_id": 65228,
"pm_score": 5,
"text": "<p>b.nota is correct - Just further adding to his answer. The <a href=\"http://www.insdc.org/\" rel=\"nofollow noreferrer\"><strong>International Nucleotide Sequence Database Collaboration (INSDC)</strong></a> is a consortium between <a href=\"http://www.ddb... | [
{
"answer_id": 65226,
"pm_score": 2,
"text": "<p>I think via Europe (<a href=\"http://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html\" rel=\"nofollow noreferrer\">EBI</a>) will be an option, but I am not sure if it uses the American server or if its run on European servers.</p>\n"
},
{
"answe... |
66,664 | <p><strong>Edit:</strong>
This question is very similar to <a href="https://biology.stackexchange.com/questions/23901/comparative-leg-sizes">this</a> and related to <a href="https://biology.stackexchange.com/questions/51243/what-is-the-anatomical-term-for-a-two-jointed-leg">this one</a> (though the latter focuses on homology instead of scaling laws). However, <em>the answer to this question is far more comprehensive</em>, in particular it offers a plausible explanation <em>why</em> horse legs evolved as they did (vs human or even rhino legs).</p>
<p>Large grazing mammals such as horses, moose, and cows tend to have relatively thin legs despite being up to ~1000kg. For example, this rider's and her horse's legs appear to have about the same cross-sectional area both for below and above the "knee":
<a href="https://i.stack.imgur.com/2h5FB.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/2h5FB.jpg" alt="tight fitting pants"></a></p>
<p>If this horse is 500 kg (a mid-range mass for horses), each leg would have to support 125 kg, compared to only 37.5 kg for a 75 kg adult. Why don't we see a corresponding difference in cross-section?</p>
| [
{
"answer_id": 66668,
"pm_score": 7,
"text": "<p>Elephant, rhinoceros, &c all have much thicker legs in proportion. The answer, I think, lies in the fact that the animals you mention all evolved as cursorial animals (that is, they run to escape predators). Less mass in the lower leg means it swing... | [
{
"answer_id": 66675,
"pm_score": -1,
"text": "<p>You're assuming that horses and cows are still subject to Darwinian evolution. In fact breeding of domestic animals has mostly been controlled rather carefully by humans, to breed for characteristics which <em>we</em> feel are favourable, even if those ... |
67,198 | <p>Obviously, humans can survive underwater for a short while. I've assumed this is because at some point it benefited us to stop breathing momentarily, and so we evolved a respiratory system that was able to take short breaks. </p>
<p>Similarly, fish can survive outside of water for a short while. However, I can't think of a single instance for most fish where they may have needed to evolve that ability. Even their ancestors originated from aquatic environments, so I don't think it's a residual ability they no longer need. </p>
<p>Why did fish evolve a respiratory system that could take breaks like ours can? </p>
| [
{
"answer_id": 67199,
"pm_score": 3,
"text": "<p><strong>Do not have too a \"panselectionist\" view of evolution!</strong></p>\n\n<p>You can survive in a bath of mercury for a little while. You can survive naked in the outer space for a while (see <a href=\"https://physics.stackexchange.com/questions/30... | [
{
"answer_id": 67693,
"pm_score": 0,
"text": "<p>The answer is simple. A fishes gills are exposed to air that is oxygen rich. Gills can take oxygen from the air. We do not inhale water, so humans under water must hold their breath. I am assuming the question is not referring to lungfish, who have modifi... |
67,227 | <p>I've been checking life expectancy figures for men versus women in many countries of the world and the figures for men sometimes are terrifying. Countries like Russia have a 12 years gap in disfavor of men. Developed countries have usually a 4-5 years gap in disfavor of men. My country Argentina has a 7 years gap. African countries and middle east countries where supposedly women have a harder life because of religion have usually a 3 years gap in disfavor of men. So far I haven't found a single country where men lives more than women. </p>
<p>Now I know there are more men than women who dies in homicides, suicides, work accidents, wars, etc. men are more likely to get addictions because of depression, etc. but aside of all that, is there any biological reason why men lives less than women everywhere? </p>
| [
{
"answer_id": 67231,
"pm_score": 6,
"text": "<p>There are both biological and social factor for that:</p>\n<h1>Biological</h1>\n<ul>\n<li>Females have two X chromosomes. When mutations in genes of the X chromosome occur, females have a second X to compensate. Males, on the other hand gave just one chr... | [
{
"answer_id": 67228,
"pm_score": 3,
"text": "<p>There are a lot of factors playing in here. You've pointed out the surface reasons that can sometimes contribute: work accidents, style of life, etc. However, there are biological causes as you suspected.</p>\n<p>Probably the most obvious has to do with... |
68,400 | <p>Centimorgan's aren't physical distances. The analogy that I could come up with is if you had an array with 10 items,</p>
<pre><code>A = [a, b, c, d, e, f ,g ,h ,i ,j, k]
</code></pre>
<p>The distance of <code>a</code> in the array is closer to <code>b</code> than <code>k</code>, ie A[0] is closer to A[1] than A[10] so that the centimorgan of A[0] and A[1] is less than A[0] and A[10]?</p>
| [
{
"answer_id": 68405,
"pm_score": 3,
"text": "<p>I personally like to talk in Morgan (M), instead of centiMorgan (cM), because the Morgan has a more intuitive meaning than one-hundredth of its value.</p>\n\n<p><strong>Morgan</strong></p>\n\n<p>If two loci are at distance 1M, it means the expected number... | [
{
"answer_id": 68404,
"pm_score": 0,
"text": "<p>1 centimorgan is equivalent to the percent recombination frequency for 2 genes during the crossing over step of meiosis. You can calculate it with</p>\n\n<p>(number of recombinant offspring)/(total number of offspring) * 100%</p>\n\n<p>and the result will... |
68,426 | <p>Actually, I am unfamiliar to biology, so when I read a thesis, the term "binding capacity" and "binding affinity" are really confusing.
Since my major is unrelated to biology, I don't know correct definition. Is there anyone who can explain differences between them clearly? Any references would be helpful, thanks!</p>
| [
{
"answer_id": 68405,
"pm_score": 3,
"text": "<p>I personally like to talk in Morgan (M), instead of centiMorgan (cM), because the Morgan has a more intuitive meaning than one-hundredth of its value.</p>\n\n<p><strong>Morgan</strong></p>\n\n<p>If two loci are at distance 1M, it means the expected number... | [
{
"answer_id": 68404,
"pm_score": 0,
"text": "<p>1 centimorgan is equivalent to the percent recombination frequency for 2 genes during the crossing over step of meiosis. You can calculate it with</p>\n\n<p>(number of recombinant offspring)/(total number of offspring) * 100%</p>\n\n<p>and the result will... |
69,232 | <p>What is the current value of 'r' (instrinsic rate of natural increase) in India? How do we calculate it? </p>
<p>My book says that In 1981, the r value for human population in India was 0.0205. But this link (<a href="https://www.google.co.in/amp/knoema.com/atlas/India/topics/Demographics/Population/Rate-of-natural-increase%3fmode=amp" rel="nofollow noreferrer">https://www.google.co.in/amp/knoema.com/atlas/India/topics/Demographics/Population/Rate-of-natural-increase%3fmode=amp</a>) says it was around 22.50 in the year 1981. Such big discrepancies are a query. </p>
| [
{
"answer_id": 69234,
"pm_score": 3,
"text": "<p>From the <a href=\"https://esa.un.org/unpd/wpp/DVD/\" rel=\"nofollow noreferrer\">UN database</a> (this info is also reported on <a href=\"https://en.wikipedia.org/wiki/Demographics_of_India\" rel=\"nofollow noreferrer\">wikipedia</a>), the growth rate in... | [
{
"answer_id": 70947,
"pm_score": 2,
"text": "<p>It the most basic form, the intrinsic rate of increase, $r$, is defined as:</p>\n\n<p>$\\frac{dN}{dt} = rN = (a-b)N$</p>\n\n<p>where $a$ is the birth rate per unit time and $b$ is the death rate per unit time. So $r$ is the birth rate minus the death rate... |
69,267 | <p>In a related question, I ask how to <a href="https://biology.stackexchange.com/questions/69186/trick-fruit-trees-into-flowering-later-prolong-frozen-ground-conditions">trick fruit trees into flowering later in the spring by prolonging frozen ground conditions</a>.</p>
<p>However, I'm starting to realize that I don't actually understand what triggers plants to flower in the spring in the first place. Possibilities include:</p>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Photoperiodism" rel="nofollow noreferrer">Photoperiodism</a></li>
<li>Air temperature</li>
<li>Soil/root temperature</li>
</ul>
<hr>
<p>It seems to me that this is a simple enough question. I'm guessing that plants in a certain genus would have a fairly specific genetic program that would stipulate when they should flower.
For example:</p>
<p><code>If root temperature is greater than X (for greater than Y duration), and daylength is greater than Z, then initiate flowering.</code></p>
<p>I'm <strong>not</strong> looking for the specific values (example <code>x</code> = <code>10 degrees C</code>); the values would likely vary by species or even by plant. I'm just wondering what the <strong>primary variables</strong> are.</p>
| [
{
"answer_id": 69332,
"pm_score": 2,
"text": "<p>An answer provided by the <strong>University of Guelph Plant Sciences Department</strong> (they specialize in Malus):</p>\n\n<blockquote>\n <p>Flowering of Malus and Prunus is driven primarily by air temperature. Provided sufficient winter chilling has a... | [
{
"answer_id": 69269,
"pm_score": 2,
"text": "<p>Here’s how it works. Every morning when the sun breaks over the horizon — no matter what time of year it is — a clock starts ticking inside the trees. After a specific number of hours, the plants’ cells start producing high levels of a molecule known as t... |
70,874 | <p>Gnathostomates are vertebrates having jaws. But when I search on the internet for Gnathostomates, I always find out that they are sharks and fish-like organisms.</p>
<p>But are humans not also Gnathostomates? Don't we have jaws?</p>
| [
{
"answer_id": 70875,
"pm_score": 5,
"text": "<p>Absolutely, humans belong to the superclass Gnathostomata. It's simply the class of jawed vertebrates, and includes 99% of vertebrates. It also includes the class Mammalia, which includes humans.</p>\n\n<p><a href=\"https://i.stack.imgur.com/n3SwN.png\" ... | [
{
"answer_id": 70878,
"pm_score": 2,
"text": "<p>Yes of course Humans are Gnathostomes. Under division Gnathostomata you have 2 Superclasses that include Pisces and Tetrapods. Under Tetrapoda are 3 classes- reptiles, Aves, mammals. So Humans are indeed Gnathostomes. </p>\n"
},
{
"answer_id": 708... |
72,559 | <p>In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors?</p>
<p>I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly the same function, but are named differently. For example,</p>
<ul>
<li>Replication activator <em>protein</em></li>
<li>Replication licensing <em>factors</em></li>
<li>Replication <em>protein</em> A</li>
<li>Replication <em>factor</em> C</li>
<li>Transcriptional <em>factor</em></li>
<li>Eukaryotic translation initiation <em>factor</em></li>
</ul>
| [
{
"answer_id": 72562,
"pm_score": 5,
"text": "<p><strong>TLDR:</strong> As far as I know, there's no specific reason some proteins are called \"factors\"; it's just a matter of what name was chosen.</p>\n\n<hr>\n\n<p><em>\"Protein\"</em> is a specific term meaning a long chain of amino acids. They are t... | [
{
"answer_id": 72561,
"pm_score": 4,
"text": "<p><strong>Short Answer</strong></p>\n\n<p>There is no agreed upon naming convention for proteins - there are some rough standards because in language people usually try to convey their ideas in a way others can understand, but that doesn't necessarily mean ... |
73,675 | <p>Most dinosaurs were terrestrial, but there were a couple of groups of arboreal and <a href="https://biology.stackexchange.com/q/17546/42780">flying dinosaurs</a> (microraptors, birds etc).</p>
<p>I have read that the theory that Brachiosaurids were aquatic has been largely discredited<sup>1</sup>, but that Spinosaurids <em>were</em> probably semi-aquatic<sup>2</sup>.</p>
<p>Excluding modern marine birds (e.g. penguins etc.), <strong>were there any other marine/aquatic dinosaurs?</strong></p>
<hr />
<sup>
<p><strong>Note:</strong> I am aware that the marine reptiles <em>mesosaurs, phytosaurs, mosasaurs, dolichosaurs, Icthyosaurs, thalattosaurs, Sauropterygia</em> (<em>placodonts, nososaurs, plesiosaurs</em> etc), <em>Choristodera</em> were not part of Dinosauria.</p>
</sup>
<hr />
<p><em>References:</em></p>
<sup>
<ol>
<li>
<ul>
<li><a href="https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?referer=https://www.google.com/&httpsredir=1&article=3285&context=gbn" rel="nofollow noreferrer"><em>Three new sauropod dinosaurs from the Upper Jurassic of Colorado</em></a>, Great Basin Naturalist.</li>
<li><em>The Physiology of Dinosaurs: Circulatory and Respiratory Function in the Largest Animals Ever to Walk the Earth</em>, Respiratory Care</li>
<li><em>A note on the habits of sauropods</em>, Annals and Magazine of Natural History</li>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810024" rel="nofollow noreferrer"><em>Tipsy punters: sauropod dinosaur pneumaticity, buoyancy and aquatic habits</em></a>, Proceedings of the Royal Society of London</li>
</ul>
</li>
<li>
<ul>
<li><a href="https://pubs.geoscienceworld.org/gsa/geology/article-abstract/38/2/139/130188/oxygen-isotope-evidence-for-semi-aquatic-habits?redirectedFrom=fulltext" rel="nofollow noreferrer"><em>Oxygen isotope evidence for semi-aquatic habits among spinosaurid theropods</em></a>, Geology</li>
<li><a href="http://www.sciencemag.org/content/345/6204/1613.abstract" rel="nofollow noreferrer"><em>Semiaquatic adaptations in a giant predatory dinosaur</em></a>, Science</li>
<li><em>Convergent evolution of jaws between spinosaurid dinosaurs and pike conger eels</em>, Acta Palaeontologica Polonica</li>
<li><em>Functional Morphology of Spinosaur 'crocodile-Mimic' Dinosaurs</em>, Journal of Vertebrate Paleontology</li>
</ul>
</li>
</ol>
</sup>
| [
{
"answer_id": 73678,
"pm_score": 4,
"text": "<p>There are a couple of specimens of a dinosaur species named <em>Liaoningosaurus paradoxus</em> that have been found with fish in their stomachs and skeletal features suggesting it was at least semi-aquatic. It is a member of the ankylosaurian dinosaurs f... | [
{
"answer_id": 73677,
"pm_score": 1,
"text": "<p>The only example I could find for the moment are <a href=\"https://en.wikipedia.org/wiki/Hesperornithes\" rel=\"nofollow noreferrer\">Hesperornithes</a>. Hesperornithes are actually part of the <em>Aves</em> clade (see <a href=\"http://tolweb.org/Aves/157... |
74,157 | <p>I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently.</p>
<p><strong>what I already did</strong>
I already looked up the programs most used for this and they point me to JMol and Yasara but the download files are .bin files and the like and I don’t I don’t understand which file is the one I should download and how to install it.</p>
<p>Can someone help me please ?</p>
| [
{
"answer_id": 74168,
"pm_score": 4,
"text": "<p><strong>Jmol: how to install</strong></p>\n\n<p>Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC). </p>\n\n<ol>\n<li>Download Jmol from<br>\n<cod... | [
{
"answer_id": 74158,
"pm_score": 2,
"text": "<p>You could use an online molecular viewer for this. A fairly complete list is <a href=\"https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems#Web-based_systems\" rel=\"nofollow noreferrer\">available in Wikipedia</a> as well as in <a href=\"http... |
74,513 | <p>What did the evolution of multicellular animals look like? </p>
<p>Aspects of this question include:</p>
<p>(1) Are there any living organisms that might be helpful in visualizing "transitional forms" between unicellular organisms and multicellular animals? E.g. I have heard of slime molds as one example. Would love to hear of as many good examples as you can come up with. Not looking for strict hereditary relationships here, and I am fine with plausible but unproven theories. E.g., mudskippers might help a person visualize the evolution of amphibians, even if they aren't in fact closely related to amphibian ancestors. </p>
<p>(2) Do we think that the first animals evolved into sponges, or cnidarians/ctenophoroans, or something else? Did sponges and cnidarians/ctenophoroans evolve multicellularity separately? As this is probably a big topic, feel free to just post a link or two.</p>
<p>(3) For any examples that you can think of for #1, would love to hear of any good citations of articles or books for me to read, but keep in mind that I am not a scientist and not looking for anything extremely technical. </p>
| [
{
"answer_id": 74550,
"pm_score": 3,
"text": "<p>Evolutionary biologists have frequently cited volvocine green algae, which include both unicellular and multicellular members, as a useful model system (your point #1), e.g. see <a href=\"https://www.nature.com/scitable/topicpage/volvox-chlamydomonas-and-... | [
{
"answer_id": 74517,
"pm_score": 1,
"text": "<p>Choanoflagelates are single-celled eukaryotes that are almost identical to the flagellated cell type in sponges, and are thought to be the sister taxon of Metazoa (Multicellular animals) <a href=\"http://www.ucmp.berkeley.edu/protista/choanos.html\" rel=\... |
76,358 | <p>It's been less than a century since the widespread use of antibotics started, and already we're seeing bacteria that have evolved immunities to the antibotics we use.</p>
<p>On the other hand, we've been using immune systems to to fight bacteria for millions of years, and bacteria evolve much faster than humans do. Why have bacteria not evolved immunities that let them completely overwhelm our immune systems and kill us all?</p>
| [
{
"answer_id": 76359,
"pm_score": 3,
"text": "<p>First of, not all infections are mediated by bacteria and not all bacteria are infectious. Also, not all parasitic bacteria lead to a strong infection or important health problem that cause any non-negligible selection pressure. Following the implicit log... | [
{
"answer_id": 76362,
"pm_score": 2,
"text": "<p>I'd like to add to @Remi.b's excellent answer with a few additional points</p>\n\n<p>To quote Lewis Thomas in <em>Germs</em></p>\n\n<blockquote>\n <p>Disease usually results from inconclusive negotiations for symbiosis, an overstepping of the line by one... |
76,461 | <p>After searching "do antibiotics impact the immune system" I found out that antibiotics target <a href="https://en.wikipedia.org/wiki/Prokaryote" rel="nofollow noreferrer">prokaryotic</a> cells. It all made a lot of sense thinking about all those yogurt recommendations you get after taking antibiotics: the collateral damage is on the prokaryotic cells that live with us, but are not "us" as such.</p>
<p>Except I remembered human red blood cells don't have nuclei, so where's my confusion?</p>
<p>(I'm only a biology enthusiast.)</p>
| [
{
"answer_id": 78883,
"pm_score": 4,
"text": "<blockquote>\n <p>Are red blood cells prokaryotic?</p>\n</blockquote>\n\n<p>No!</p>\n\n<ol>\n<li><p>There are many more differences between procaryotes and eukaryotes than just the presence of a nucleus. See DeNovo's answer for more information.</p></li>\n<... | [
{
"answer_id": 76462,
"pm_score": 4,
"text": "<p>No. Prokayotic cells are full organisms with their own DNA, red blood cells are not.</p>\n"
},
{
"answer_id": 76465,
"pm_score": 5,
"text": "<p>When differences between prokaryotes and eukaryotes are taught in an introductory biology cour... |
76,566 | <p>Theoretically, is it possible to obtain the original gene from the protein’s amino acid sequence as its “template”, as in, the reverse of how gene’s codons were “templates” for the amino acid sequence of the protein?
I’m curious to know if it’s possible to use enzymes such as reverse transcriptase to obtain DNA from a protein in a reversed central dogma model. </p>
| [
{
"answer_id": 76580,
"pm_score": 5,
"text": "<p>Let’s first consider what the Central Dogma<sup>[<a href=\"https://paperpile.com/app/p/03df3adf-1e0f-0db9-ba1f-caa0b9d3d72c\" rel=\"noreferrer\" title=\"Francis Crick, Central Dogma of Molecular Biology, Nature (1970)\">1</a>]</sup> actually says. It is p... | [
{
"answer_id": 76569,
"pm_score": 2,
"text": "<p>Contrary to my belief, it may be possible.</p>\n\n<p>The main concern we must look at is Protein to RNA, as we know RNA to DNA can be done through reverse transcription. </p>\n\n<p>Some evolutionary scientist believe that reverse translation may be a proc... |
78,135 | <p>Here is a question from the book <em>SAT II Success Biology E/M</em> (where the SAT is the exam taken by the American high school students):</p>
<blockquote>
<p>Which of the following statements is true about mutations?<br>
(A) Rates
tend to be very high in most populations.<br>
(B) generally lethal<br>
(C)
irreversible<br>
(D) Only certain gene locations are affected.<br>
(E) source
of genetic variation</p>
</blockquote>
<p>In my opinion, we can definitely eliminate A, B, and D.<br>
Then, I struggle between C and E since I think mutations are definitely a source of genetic variation but are <strong>as well</strong> generally irreversible (I've found evidence on different websites, including this <a href="http://hawaiireedlab.com/wpress/?p=154" rel="noreferrer">http://hawaiireedlab.com/wpress/?p=154</a> where the author writes that only <strong>some</strong> mutations are reversible).<br>
In the end, I think I should have probably gone with E because C can be seen as having some exceptions.<br>
Then, here is the book explanation for this question:</p>
<blockquote>
<p><strong>The correct answer is (C).</strong> These recent conclusions about
mutations—recall that Darwin did not know of mutations—are all the
reverse of those listed in the choices, with the exception of choice
(C), the correct answer. Rates, in fact, tend to be below in
populations, mutations are generally not lethal, any gene location can
be affected, and they are felt to be the source of genetic variation.
Darwin felt over-production of offspring was the source of potential
variation.</p>
</blockquote>
<p>The answer is C here. However, I didn't particularly understand why E wasn't considered a correct answer.<br>
Could you please explain why C, and not E, is correct?</p>
| [
{
"answer_id": 78138,
"pm_score": 6,
"text": "<h1>Going through the possible answers</h1>\n<blockquote>\n<p>(A) Rates tend to be very high in most populations.</p>\n</blockquote>\n<p>This is a very unclear statement. What does "high" mean? In humans, the average mutation rate per reproduction ... | [
{
"answer_id": 78137,
"pm_score": 2,
"text": "<p>It depends. A mutation in somatic cells is not a source of genetic variation because they are not inherited by offspring. But mutations in the sex cells are a source of variation. Your answer key does not appear to be sure of the correct answer because it... |
78,927 | <p>In my textbook, it is written that the binomial name of mango is <em>Mangifera indica</em> and the binomial name of a bee is <em>Apis indica</em>. Now in the name the second part is the name of species. But mango and bee are not the same species. One is a tree and the o,ther is an animal. Then why is their second name the same?</p>
| [
{
"answer_id": 78929,
"pm_score": 6,
"text": "<p>In short, we do not think about the uniqueness of the second part of the binomial (the species epithet) but about the uniqueness of the binomial itself (the genus and the species epithet). Thus, the unique <em>binomial</em> of mango is <em>Mangifera indic... | [
{
"answer_id": 78932,
"pm_score": 4,
"text": "<p>That is the species name it is often the same for unrelated organisms, that is why we use a two name system. Binomial nomenclature (literally, two term naming system) goes <em>Genus species</em> respectively.</p>\n\n<p>The first part of the binomial ident... |
79,381 | <p>Protein life times are, on average, not particularly long, on a human life timescale.
I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/minutes/days passed from the moment that given protein was translated. I am not sure is the same thing as asking which human protein has the longest half-life, as I think there might be "tricks" the cell uses to elongate a given protein's half-life under specific conditions.</p>
<p>I am pretty sure there are several ways in which a cell can preserve its proteins from degradation/denaturation if it wanted to but to what extent? I accept that a given protein post-translationally modified still is the same protein, even if cut, added to a complex, etc. etc.</p>
<p>And also, as correlated questions: does the answer depend on the age of the given human (starting from birth and accepting as valid proteins translated during pregnancy or even donated by the mother)? What is the oldest protein in a baby's body and what is in a elderly's body? How does the oldest protein lifetime does in comparison with the oldest nucleic acid/cell/molecule/whatever in our body?</p>
| [
{
"answer_id": 79383,
"pm_score": 7,
"text": "<p><strong>Crystallin proteins</strong> are found in the eye lens (where their main job is probably to define the refractive index of the medium); they are commonly considered to be non-regenerated. So, <strong>your crystallins are as old as you are</strong>... | [
{
"answer_id": 79399,
"pm_score": 5,
"text": "<p>I like Mowgli's answer, because it is a non-obvious example. However I would also point out that there are many, many protein-based structural components in the body that we know do not regenerate due to associated pathologies; so presumably these structu... |
81,975 | <p><a href="https://en.wikipedia.org/wiki/Natural_selection" rel="nofollow noreferrer">Natural selection</a> is the differential survival and reproduction of individuals due to differences in phenotype. </p>
<p><a href="https://www.britannica.com/science/natural-selection" rel="nofollow noreferrer">Natural selection</a>, a process that results in the adaptation of an organism to its environment by means of selectively reproducing changes in its genotype or genetic constitution.</p>
<p><a href="https://www.britannica.com/science/evolution-scientific-theory/The-science-of-evolution#ref311587" rel="nofollow noreferrer">Natural selection</a>, then, can be defined as the differential reproduction of alternative hereditary variants, determined by the fact that some variants increase the likelihood that the organisms having them will survive and reproduce more successfully than will organisms carrying alternative variants. </p>
<p>Darwin's definition of natural selection his book "On The Origin Of Species By Means Of Natural Selection or the Preservation Of Favoured Races In The Struggle For Life" is:</p>
<blockquote>
<p>The preservation of favorable variations and the rejection of injurious variations</p>
</blockquote>
<p>In Evolution 101, natural selection is not defined, but rather the concept "<a href="https://evolution.berkeley.edu/evolibrary/article/evo_25" rel="nofollow noreferrer">evolution by natural section</a>" is characterized as the outcome of variation, differential reproduction and Heredity, and a clarifying example is provided.</p>
<p>Clearly, the wording in each of the above is different!</p>
<p>I searched Biology StackExchange for any explicit statement of the definition of natural selection, I couldn't manage to find one. There are some discussions about whether it is a tautology or not, but even in <a href="https://biology.stackexchange.com/questions/67494/is-natural-selection-a-tautology-and-therefore-not-truly-falsifiable">those</a> discussions, the definition of natural selection was not quoted.</p>
<p>I tried to search tags "natural selection" and "definitions" of biology StackExchange, and yet I didn't see any particular wording mentioned as the official definition of natural selection. </p>
<p>Actually, the tag [natural selection] mentions this definition in the tag information itself:</p>
<p><a href="https://biology.stackexchange.com/questions/tagged/natural-selection://">Natural Selection</a> is a mechanism of evolution that leads to non-random spread of genes due to the effect that genes have on reproductive success</p>
<p><a href="https://phys.org/tags/natural+selection/" rel="nofollow noreferrer">Natural selection</a> is the process by which heritable traits that make it more likely for an organism to survive and successfully reproduce become more common in a population over successive generations.</p>
<p>Is there an official definition of natural selection that is adopted by biologists nowadays? and what is that definition exactly?</p>
<hr>
<p>[EDIT] It came to my awareness that this question might be a possible duplicate of the following question: "<a href="https://biology.stackexchange.com/questions/60587/how-is-selection-best-defined">How is Selection best defined</a>", and indeed in the answers provided to that question the topic of definition of natural selection has been addressed.</p>
<p>I didn't know of this posting. I simply surfed for "natural selection", and not just for "selection", and I didn't notice it. But indeed what's presented in the answers does cover the question present here.</p>
<p>However there is some difference in the question itself from that present here. Here I wanted to know of what I thought would be an official definition, and I was asking in particular about "natural selection", while in the referred question, the question is more general, it's about what qualifies "any" force (apparently he means related to biology and especially evolution) to be labeled as "selection", including artificial selection, sexual selection, etc.., so it's a wider topic, at least as far as terminology is concerned. </p>
<p>Here in this question I've quoted the main results that one would see upon surfing the web for "definition of natural selection", and I wanted to know which one would be the official or as @Remi.b had put it, the most commonly used or referred to in biological research.</p>
<p>I still think, that for precision purposes, exact wordings are important, and such an extremely important concept like "natural selection", it would have been expected that it had an agreeable, kind of, official definition, by some convention or the alike. </p>
<p>Anyhow, I think, whether this question is a duplicate or not, can be better assessed by experts in evolution field present in this website, like those who provided answers, and others.</p>
<p>Thanks. </p>
| [
{
"answer_id": 81977,
"pm_score": 5,
"text": "<p><strong>Official definition</strong></p>\n\n<blockquote>\n <p>Is there an official definition of natural selection that is adopted by biologists nowadays? and what is that definition exactly?</p>\n</blockquote>\n\n<p>I don't think there is such a concept... | [
{
"answer_id": 81979,
"pm_score": 3,
"text": "<p>I've adapted your definitions to another process that I think will be less controversial to you.</p>\n<blockquote>\n<p>Eating is the intake of food by taking into the mouth, chewing, and swallowing.</p>\n<p>Eating, the process that results in digestion by... |
84,525 | <p>This question: <a href="https://biology.stackexchange.com/questions/21827/can-you-get-enough-water-by-eating-only-fish">Can you get enough water by eating only fish?</a> asks if a person could survive on fish alone. <strong>Can a person survive on fish and/ or blood alone of any species if stuck at sea or animal blood as a last resort where there is no water or fire?</strong> </p>
<p>Obviously if it was a fresh water fish there is water, but there are fresh water mud skippers that can breathe air and the water to tainted to drink in that case a fresh water fish blood maybe safer than the water. <a href="https://chemistry.stackexchange.com/questions/115901/what-can-i-eat-that-will-help-metabolize-blood">https://chemistry.stackexchange.com/questions/115901/what-can-i-eat-that-will-help-metabolize-blood</a></p>
<p>Desalination would be the best way to process the blood but this is in emergency situation scenario.</p>
<p>From @PTwr Comment's Link: <em>If you drink blood regularly, over a long period of time the buildup of iron in your system can cause iron overload. This syndrome, which sometimes affects people who have repeated blood transfusions, is one of the few conditions for which the correct treatment is bloodletting.</em> <a href="https://what-if.xkcd.com/98/" rel="nofollow noreferrer">https://what-if.xkcd.com/98/</a></p>
| [
{
"answer_id": 84811,
"pm_score": 3,
"text": "<p>You'd have no problem substituting blood for water, provided:</p>\n\n<ol>\n<li>You allowed it to coagulate first, and</li>\n<li>You prevented it from evaporating</li>\n</ol>\n\n<p>Fresh blood has a high concentration of protein, certainly, but it's not a ... | [
{
"answer_id": 84533,
"pm_score": 4,
"text": "<p>You can drink blood of course to a minimalistic amount (eg- a few teaspoons ) and also if blood is free from pathogens. But it should always be in very small amounts and from suitable donor. Here's why </p>\n\n<blockquote>\n <p>The strange fact is, blood... |
86,370 | <p>Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations</p>
| [
{
"answer_id": 86379,
"pm_score": 4,
"text": "<p>The premise of the questions suggests that mutations cannot take place in the mRNAs of higher eukaryotes. \nTo answer your question I think it is important to consider two viewpoints:</p>\n\n<p>First, from a theoretical point of view, since DNA and RNA ar... | [
{
"answer_id": 86382,
"pm_score": 1,
"text": "<p>Additionally DNA is inherently more stable due to the removal of the hydroxyl group from the C2 carbon on the ribose making it less reactive. This could be pointed to as an example of the limiting factor in the inherent complexity of any organism that use... |
86,581 | <p>We know that the DNA copying mechanism that replicates DNA during cellular division is not 100% accurate and the resultant errors are the source of variation in the members of a population.</p>
<p>At the same time, we are also aware of the benefits of variation - how it is useful in ensuring the survival of a species over time <strong>and leading to evolution</strong>.</p>
<hr>
<p>I would however like to know if 100% accurate DNA replication is possible (even if hypothetically) - because in my opinion, organisms can surely survive (atleast individually) without variation or evolution.</p>
<p>If it is so, <em>is it possible that <strong>organisms with 100% accurate DNA replication</strong> did exist, but eventually their populations died out (due to natural selection) and we were left only with organisms that showed variation</em>?</p>
<hr>
<p>Putting in simpler terms, it is possible that <strong><em>evolution itself is the cause of variation that now causes further evolution?</em></strong></p>
| [
{
"answer_id": 86590,
"pm_score": 3,
"text": "<p>You're asking if cells arose with 100% replication accuracy and if lower accuracy was selected for under a feedback loop. Maybe there was a sweet spot for DNA replication accuracy in terms of efficiency, but it's highly unlikely that our ancestor cells ha... | [
{
"answer_id": 86588,
"pm_score": 2,
"text": "<p>There is previous research for that field of macroevolution.... Horse shoe crabs change slowly and tropical fish change fast. </p>\n\n<p>You are right, it's not just random variation, it's fine tuned by DNA transcription processes which are too developed ... |
86,613 | <p>All humans have the same sort of proteins in our bodies. Take haemoglobin for example. </p>
<p>Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations in the nucleotide sequence? </p>
<p>Are there examples of proteins that are always completely conserved at the population level? </p>
| [
{
"answer_id": 86643,
"pm_score": 6,
"text": "<h1>Humans have many variants</h1>\n<p><strong>There is variation.</strong> The project I use to help understand this natural variation is <a href=\"https://gnomad.broadinstitute.org/\" rel=\"noreferrer\">gnomAD</a>.\n<strong>Using <a href=\"https://academic... | [
{
"answer_id": 86614,
"pm_score": 3,
"text": "<p>At the whole-gene level, there is <em>likely</em> no absolute conservation of any human protein-coding gene at the population level, though there might be complete conservation between individuals. Keep in mind that most human genes are on the order of te... |
87,965 | <p>As a botany amateur, I know that mushrooms (which are of course studied in field of mycology and not botany) are dependent in trees or shrubs (and maybe also bushes) and that there are generally strong symbiotic relations between trees and mushrooms.</p>
<p>If mushrooms are strongly tree dependent and appear <strong>per tree species</strong>, is it true to say that the genome of trees includes the genome of mushrooms by some mechanism?</p>
| [
{
"answer_id": 87969,
"pm_score": 4,
"text": "<p><strong>No.</strong> </p>\n\n<p><strong>Evidence:</strong> If you go to the <a href=\"https://treegenesdb.org\" rel=\"nofollow noreferrer\">TreeGenes</a> site and examine those tree genomes that have been sequenced you won’t find any fungal chromosome se... | [
{
"answer_id": 87970,
"pm_score": 3,
"text": "<p>A symbiotic relationship is entirely unrelated to the genetic origins of the participating organisms. Symbiosis only requires that the organisms interact in a manner that benefits both parties. There is nothing that requires any genetic similarity between... |
87,992 | <p>The cells of some organ or tissue are dividing and also dies (apoptosis). But this happens in somehow controlled manner so that the total size of the organ is approximately preserved or the total number of cells approximately stays the same. As far as I understand, this is somehow collective process, because cells in one side of the tissues should somehow coordinate the division/apoptosis processes with the cells of the far side. I have read in one book about cells, that such controlling mechanisms are purely undesrtood even today. Of course, such mechanisms work only approximately (or - to be more precise - they are more complex than just static preservation of the size/number), e.g. numberadipose cells can increase with time.</p>
<p>But anyway - my question is - what is the name/term for such controlling mechanisms and what are other important keywords/terms which I can use for searching more research papers about this theme?</p>
<p>I have specific interest in the control of those processes, e.g., with the aim to bound those processes for adipose cells and to encourage those processes for the muscle cell.</p>
<p><strong>"cell cycle control" and Hippo-pathways</strong> mechanisms can be the answers, but I am still searching for the matter.</p>
| [
{
"answer_id": 87969,
"pm_score": 4,
"text": "<p><strong>No.</strong> </p>\n\n<p><strong>Evidence:</strong> If you go to the <a href=\"https://treegenesdb.org\" rel=\"nofollow noreferrer\">TreeGenes</a> site and examine those tree genomes that have been sequenced you won’t find any fungal chromosome se... | [
{
"answer_id": 87970,
"pm_score": 3,
"text": "<p>A symbiotic relationship is entirely unrelated to the genetic origins of the participating organisms. Symbiosis only requires that the organisms interact in a manner that benefits both parties. There is nothing that requires any genetic similarity between... |
88,137 | <p>I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:</p>
<blockquote>
<p>Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to protein folding; computational protein design calculations completely ignore the order of synthesis which hence cannot be critical to protein folding.</p>
</blockquote>
<p>I was wondering, how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein? What I mean, is in case I look at mirror image of a protein, would it fold the same? if I consider for example the sequencers: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)</p>
<p>Can anyone provide evidence that this is, in fact, so. Or do I misunderstand the section quoted?</p>
<p>link to the paper: sci-hub.tw/10.1002/pro.3588</p>
| [
{
"answer_id": 88168,
"pm_score": 3,
"text": "<blockquote>\n<p>how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein?</p>\n</blockquote>\n<p>The quote by the researcher says that the form is unrelated to the di... | [
{
"answer_id": 88145,
"pm_score": 2,
"text": "<p>I suspect the author meant something a little different. It's not just that it doesn't matter if a protein is synthesized from N- or C-terminus it's also not important for the end result of folding that the synthesis is gradual at all.</p>\n\n<p>When desi... |
89,120 | <p>For instance, after starting <a href="https://www.ncbi.nlm.nih.gov/m/pubmed/26324274" rel="nofollow noreferrer">zidovudine</a> monotherapy against HIV, resistance develops against the drug because of a point mutation in the RNA transcriptase enzyme to which the drug binds.</p>
<p>So how does the virus ‘know’ to mutate this particular enzyme? </p>
| [
{
"answer_id": 89121,
"pm_score": 5,
"text": "<p>This is molecular evolution and is completely undirected.\nMutations happen all the time, most of them disappear without anyone noticing, since they have no evolutionary advantage to permeate. </p>\n\n<p>This is different when you treat the cells and put ... | [
{
"answer_id": 89122,
"pm_score": 6,
"text": "<p>It doesn't. Viruses don't \"know\" anything. <a href=\"https://www.khanacademy.org/science/biology/biology-of-viruses/virus-biology/a/evolution-of-viruses\" rel=\"noreferrer\">Mutations occur at random. Most of them don't do anything, or have a slight neg... |
89,123 | <p>What Im getting at is something totally impossible, but im making some mental experiences. </p>
<ol>
<li><p>Assuming I have a machine that can produce a living being just from a DNA code (like in the movie The Fly). If I make a DNA sequnce, that has mothers and fathers cromosomes identical, would such a being be a monstrosity or a human being when it got out of the machine.</p></li>
<li><p>For such a person, when DNA recombination between 2 eqal cromosomes is done, it will just be creating clones if itself.</p></li>
<li><p>Now we introduce a new monstrosity, a male twin male version of the identical-cromosome woman, that only hase the Y Chromosome altered. His sperm cells too will all be the same.</p></li>
<li><p>when theese 2.people mate, it will produce a clone.</p></li>
</ol>
<p>EDIT:
To clarify my question number one.. Chromosome pair 1 has 2 chromosomes, one from father, one from mother. If theese two would be identical.</p>
| [
{
"answer_id": 89121,
"pm_score": 5,
"text": "<p>This is molecular evolution and is completely undirected.\nMutations happen all the time, most of them disappear without anyone noticing, since they have no evolutionary advantage to permeate. </p>\n\n<p>This is different when you treat the cells and put ... | [
{
"answer_id": 89122,
"pm_score": 6,
"text": "<p>It doesn't. Viruses don't \"know\" anything. <a href=\"https://www.khanacademy.org/science/biology/biology-of-viruses/virus-biology/a/evolution-of-viruses\" rel=\"noreferrer\">Mutations occur at random. Most of them don't do anything, or have a slight neg... |
89,218 | <p>I've heard of parasites that can live in the human body and do a lot of damage to the host. There are even safer forms of worm-like parasites inside the intestine, but some parasites can live in the blood vessels or even in the brain or eyes.</p>
<p>Parasites are, in my opinion, the most disgusting creatures there are, so I wondered if they could be killed with intoxication.
Would it be possible to get rid of worm parasites in the blood by increasing the amount of alcohol in the blood to a level that humans can tolerate but parasites can't?
Could you also eliminate brain parasites with hangover-related brain dehydration? </p>
<p>That the dead parasites remain in the body may not be good or advisable. In addition, eggs, which are usually a little more resilient, should rather be removed from the body by antibiotics or proper medication. But is it at least theoretically possible to do something with alcohol against parasites?</p>
| [
{
"answer_id": 89223,
"pm_score": 6,
"text": "<p>In <strong>summary,</strong> there is no convincing evidence to say that alcohol intoxication helps to treat or prevent parasites in humans.</p>\n\n<p><strong>1) The evidence from in vivo human studies does not support the idea that alcohol consumption he... | [
{
"answer_id": 89247,
"pm_score": 2,
"text": "<p>The answer to your question depends on the <strong>kind of parasites</strong> you're focusing on.</p>\n\n<p>Looking at <strong>bacteria and gastro-intestinal infections</strong>, I found three articles (one based on a model stomach, a second one based on ... |
89,793 | <p>I got to know about an organism called "Tardigrade(water bear)" which is an extremely hardy organism and can survive in most conditions. </p>
<p>My question is that if the aim of life in general is to ensure the continuity of the species, why have we not simply stayed as tardigrades? it seems like they are the perfect candidates for survival purposes- ensuring(to a degree) that the species does not get wiped out as easily as dinosaurs. </p>
<p>Does that mean that life has a more different incentive--not to just only survive? or it doesn't have any? Could this be the reason of our incapability to make a superhuman intelligence, because our imitation of learning is to reach a certain objective when life does not have any distinct goal? Or am I missing a key point here? </p>
<blockquote>
<p>BTW I am an amateur in Machine Learning where we basically try to mimic the learning of phenomenon of nature through 'evolution'. So I would appreciate answers with minimum of abbreviations and as simple as possible :) </p>
</blockquote>
<p><strong>Edit:</strong><br>
<em>I am overwhelmed by the response I have received but seeing the answers and communincations, I have inferred that my question may be very basic and vague to biologists. The person who can answer would be the one who has studied both subjects(Deep learning and Evolution). But even then I thank you all for devoting you precious time to attend to my question. Cheers! <strong></em>:)</strong> </p>
<p>Also I wonder if there is some paradox somewhere here - in Machine Learning when we simulate some environment the agent, just like evolution figures how to survive it. But when more factors are present, the intelligence doesn't increase after a certain point. Could this Thus be that there is something ethereal unexplainable by science (like soul) which actually gives us a more-than-enough complex brain to further increase our intelligence? Or is this a baseless thought?</p>
| [
{
"answer_id": 89810,
"pm_score": 3,
"text": "<p>The key point you're missing is that perfection is a variable, or perhaps more accurately, a function of many variables that depend on environmental factors and the actions of other species. Even tardigrades have evolved a multitude of different species*... | [
{
"answer_id": 89794,
"pm_score": 0,
"text": "<p>I'm sure you understand natural selection. But there are many different forms of evolution (well 4 main ones). One is based on absolute chance. For example dinosaurs were just unlucky when the asteroid struck; it wasn't as if they weren't adapted. This is... |
91,094 | <p>Multiple groups of scientists are trying to develop a coronavirus vaccine but they are not yet being fruitful. What challenges or difficulties are there in the process that slowing down and/or causing failure in development of vaccine?</p>
| [
{
"answer_id": 91108,
"pm_score": 5,
"text": "<p>There are multiple challenges presented, and many of those are not limited to coronavirus vaccine.</p>\n\n<p>As mentioned above, it just takes time. Before a vaccine can be used in patients, clinical trials must be performed to validate the safety and eff... | [
{
"answer_id": 91107,
"pm_score": -1,
"text": "<p>A vaccine needs to be able to neutralize the virus (bind to it and masking from entering the cell) with high affinity. Now the virus is a large complex structure, so it is not immediately clear how to design a vaccine that can achieve that.</p>\n\n<p>Scr... |
93,337 | <p>While there are many gene regulation mechanisms from the cell itself, I was wondering whether it is possible to increase the gene activity in a living cell permanently (so that the protein that it codes for is produced in higher amounts) using methods of biotechnology (i.e. no external factors)? Are there any studies or experiments regarding this topic?</p>
| [
{
"answer_id": 93345,
"pm_score": 3,
"text": "<p>There are technologies available for inducing higher (or lower) gene expression in cultured mammalian/human cells as well as in bacteria. The state of the art is CRISPR-mediated gene activation/repression, where you fuse a transcription activation domain ... | [
{
"answer_id": 93340,
"pm_score": 0,
"text": "<p>It can be done. I've found <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922510/\" rel=\"nofollow noreferrer\">this article</a> which describes how cou can use a modified CRISPR-Cas9 mechanism to either repress or activate transcription.</p>\n"
... |
96,774 | <p>Prokaryotes and eukaryotes are unicellular, made of one cell. Great. Eukaryotes are unicellular or multicellular. But the typical examples of multicellular eukaryotes we have are made of, often, trillions of cells, like us humans. Ants must still be made of many millions of cells. Are there known eukaryotes with <em>very few</em> cells that make them up? Like, 5, or something? Or maybe a dozen cells making up the whole organism in its fully developed state?</p>
| [
{
"answer_id": 96801,
"pm_score": 4,
"text": "<p>There's <a href=\"https://en.wikipedia.org/wiki/Trichoplax\" rel=\"noreferrer\"><em>Trichoplax adhaerens</em></a>, a Placozoa, made of a few thousand cells. Then there is <a href=\"https://pubmed.ncbi.nlm.nih.gov/21506842/\" rel=\"noreferrer\"><em>Dicyema... | [
{
"answer_id": 96784,
"pm_score": 3,
"text": "<p>This nematode always has either 959 or 1031 cells.</p>\n<p><a href=\"https://en.wikipedia.org/wiki/Caenorhabditis_elegans\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Caenorhabditis_elegans</a></p>\n"
},
{
"answer_id": 96822,
"pm_score":... |
96,777 | <p>I am reading a <a href="https://www.sciencedirect.com/science/article/pii/S1769721214002092?casa_token=-catzBqPvHgAAAAA:ciaQZfNhNy_qyMAlmrYIXS4PRNwaou9THLV59mzPEQ9yLcuJZ7aiuRGEP30e-Zeucnv27QKo#bib4" rel="nofollow noreferrer">journal paper</a> about the relationship between the protein NCAM2 and autism, and I have come across the following statement:</p>
<blockquote>
<p>We report three patients affected with neurodevelopmental disorders
and harbouring 21q21 deletions involving NCAM2 gene.</p>
</blockquote>
<p>I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21.
However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.</p>
| [
{
"answer_id": 96801,
"pm_score": 4,
"text": "<p>There's <a href=\"https://en.wikipedia.org/wiki/Trichoplax\" rel=\"noreferrer\"><em>Trichoplax adhaerens</em></a>, a Placozoa, made of a few thousand cells. Then there is <a href=\"https://pubmed.ncbi.nlm.nih.gov/21506842/\" rel=\"noreferrer\"><em>Dicyema... | [
{
"answer_id": 96784,
"pm_score": 3,
"text": "<p>This nematode always has either 959 or 1031 cells.</p>\n<p><a href=\"https://en.wikipedia.org/wiki/Caenorhabditis_elegans\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Caenorhabditis_elegans</a></p>\n"
},
{
"answer_id": 96822,
"pm_score":... |
96,941 | <p>In the last few weeks, Pfizer/BionTech, Moderna and AstraZeneca have each released preliminary estimates of the efficacy of their SARS-COV-2 vaccines.</p>
<p>But what do their respective efficacy percentages actually mean? Is the Pfizer/BioNTech vaccine 95% effective in any person? Or is the success of provoking the desired immune response limited to 95% of the population?</p>
<p>Put very simply: is it 100% effective in 95% of the population, or 95% effective in 100% of the population?</p>
| [
{
"answer_id": 96944,
"pm_score": 6,
"text": "<p><strong>Vaccine efficacy</strong></p>\n<p>Pfizer's target measures for efficacy (see the study on <a href=\"https://clinicaltrials.gov/ct2/show/NCT04368728\" rel=\"noreferrer\">clinicaltrials.gov</a>) seem to be:</p>\n<blockquote>\n<p>Confirmed COVID-19 i... | [
{
"answer_id": 96942,
"pm_score": 2,
"text": "<p>Vaccine efficacy is the percent change in the percent of individuals who test positive in the vaccinated group versus the placebo group in a trial. The CDC website explains it <a href=\"https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section6.html\" rel=\"... |
98,613 | <p>I've been working on a protocol standardization project where, among other things, we want protocols to be able to be run equivalently by both humans and robots.</p>
<p>Something that I've noticed in doing so is that there's a radically different amount of information typically assumed needed by a human vs. a robot when it comes to pipetting.</p>
<p>With a robot, it is generally recommended to understand the nature of the liquid thoroughly, specify the liquid class (which includes information on viscosity, volatility, polarity, etc), and do quite a bit of quality control to make sure than when you want to pipette 100 µL you actually get 100 µL. A typical example is shown on <a href="https://www.hamiltoncompany.com/automated-liquid-handling/everything-you-need-to-know-about-liquid-handling/5-steps-for-setting-up-automated-liquid-handling" rel="noreferrer">this page by Hamilton</a>.</p>
<p>With a human experimenter, however, the protocol pretty much always just says "pipette 100 µL" and assumes that the human can figure out all of the potential issues that we have to be so careful for with robots.</p>
<p>Is this actually a safe assumption, or just something that we don't typically check during protocol development for humans? Is it really intuitively obvious for nearly all liquids, or should our protocols be providing more guidance for humans as well?</p>
| [
{
"answer_id": 98614,
"pm_score": 6,
"text": "<p>In my experience it is very rare to see a protocol for humans that describes how to pipette a certain liquid, but I don't have as many years pipetting as others do.</p>\n<p>In general, it is left to the experimenter to observe the behavior of the liquid a... | [
{
"answer_id": 98626,
"pm_score": 5,
"text": "<p>I work on software that controls one model of robotic pipetter. There are a few reasons why we use complex liquid class definitions:</p>\n<ol>\n<li><p>One of the selling points of using a robot is high speed. You can handle a wide range of viscosities i... |
98,656 | <p>I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me if any point is wrong or otherwise unclear. Assume we're working with humans, since the following will change depending on the species. (Assume all cases of interest are biallelic.)</p>
<p>When a locus has an allele on least one chromosome, the measurement <em>AA, Aa, or aa</em> is called a SNP (pronounced "snip"). <strong>Therefore, using statistical language, SNPs are three level factors--this is the data associated with a SNP</strong>. As said earlier, if the factor has 1 level (ie it's only aa or only AA) then it's not a SNP.</p>
<p><strong>Sometimes for humans it seems like people say a SNP is actually just one allele (so a two level factor, a or A).</strong> How is this possible? Do people sometimes only measure one allele instead of both to get the genotype?</p>
| [
{
"answer_id": 98670,
"pm_score": 2,
"text": "<p>I think the prevuious answers provide lots of valuable and relevant information, but let me add additional prospective:</p>\n<ul>\n<li>As noted, SNP is a <em>single nucleotide polumorphism</em>, whereas notation AA, Aa, aa, etc. may refer to many other ty... | [
{
"answer_id": 98666,
"pm_score": 2,
"text": "<p>SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single letter in a specific position in DNA sequence. It depends ... |
98,729 | <p>We're considering organizing some interlaboratory work on calibrating luminescence reporters (e.g., <a href="https://en.wikipedia.org/wiki/Luciferase" rel="noreferrer">luciferase</a>), and one of the key questions I don't know the answer to is whether most plate readers can measure luminescence or not.</p>
<p>From a first principles perspective, any fluorescence plate reader ought to be able to measure luminescence as well - just don't turn on the excitation light source. Thus, I would expect that a typical fluorescence reader should also be able to measure luminescence.</p>
<p>On the other hand, searching online, I am swamped by manufacturers eager to sell me specialized luminescence readers that emphasize their sensitivity, which leads me to think that maybe typical fluorescence plate readers can't measure luminescence.</p>
<p>My question, then, is this: should I expect that a typical current fluorescence plate reader will also be able to measure luminescence, or is this a much more specialized capability?</p>
| [
{
"answer_id": 98749,
"pm_score": 4,
"text": "<p>As the other answers here say, technically plate readers which are capable of fluorescent measurements can also make luminescent readings, but the sensitivity may be low (<a href=\"https://www.biotek.com/resources/technical-notes/use-of-the-fluorescence-o... | [
{
"answer_id": 98730,
"pm_score": 2,
"text": "<p><em>A priori</em> what you say about the fluorescence and luminescence readers is correct, even <a href=\"https://en.wikipedia.org/wiki/Plate_reader#Fluorescence\" rel=\"nofollow noreferrer\">wikipedia states this directly</a>:</p>\n<pre><code>Luminescen... |
100,082 | <p>Why aren't there any competing biologies on Earth? I read sci-books about life based on silicon and I've read <a href="https://www.extremetech.com/extreme/301888-researchers-find-more-than-1-million-alternatives-to-dna" rel="noreferrer">an article that said that other structures than DNA can encode genetic information</a>.</p>
<p>So does physics allow for many competing biologies? What makes DNA-based biology the dominant biology on earth according to known laws of physics?</p>
| [
{
"answer_id": 100089,
"pm_score": 6,
"text": "<p>There are indeed almost certainly other potential alternatives to DNA-based biology and the <a href=\"https://en.wikipedia.org/wiki/RNA_world\" rel=\"noreferrer\">RNA-based biology</a> that may have predated it, which could be used to form viable organis... | [
{
"answer_id": 100095,
"pm_score": 3,
"text": "<h1>Carbon</h1>\n<p>jakebeal's answer is very good, but the Wikipedia article on <a href=\"https://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry\" rel=\"noreferrer\">DNA alternatives</a> is also very thorough. In particular, when astrobiologists... |
101,429 | <p>I am reading <a href="https://rads.stackoverflow.com/amzn/click/com/1944228004" rel="nofollow noreferrer" rel="nofollow noreferrer">Anti-Tech Revolution</a> by <a href="https://en.wikipedia.org/wiki/Ted_Kaczynski" rel="nofollow noreferrer">Theodore Kaczynski</a>, in the second chapter the author talks about how technology will cause problems in society and before he begins the discussion, he introduces proposition. Here is the first:</p>
<blockquote>
<p>Proposition 1. In any environment that is sufficiently rich, self propagating systems will arise, and natural selection will lead to the
evolution of self-propagating systems having increasingly complex, subtle,
and sophisticated means of surviving and propagating themselves.</p>
</blockquote>
<p>This I felt was an additional assumption one would make after accepting the Darwinian proposition of natural selection... so I wondered.. does there exist any fleshed out sub field of biology which have axiom systems from which experimental predictions can be worked out from?</p>
<p>Definition of an axiomatic system:</p>
<blockquote>
<p>An axiomatic system is any set of axioms from which some or all axioms can be used in conjunction to logically derive theorems.</p>
</blockquote>
| [
{
"answer_id": 101468,
"pm_score": 3,
"text": "<p>In a way, all biological research is based on certain axioms, just as all scientific study is bound certain foundational principles. The proposition you shared sounds like something straight out of General Systems Theory (GST), an inherently interdiscipl... | [
{
"answer_id": 101433,
"pm_score": 0,
"text": "<p>I am not completely sure, but I think mathematical biology, bioinformatics and/or computational biology are what you are looking for. However, the assumptions in these fields are not always fundamental "truths" like with mathematical axioms or ... |
101,696 | <p>I know that proteins perform a lot of functions and as a result there are a lot of different types of proteins in our bodies. When I eat food that has x grams of 'protein', what is this? A homogenous mix of proteins? A heterogenous one? Is it specific set of them that are general enough to be used by my body despite coming from a different organism? How can it be sure that my body can use the kind of protein in the food?</p>
| [
{
"answer_id": 101697,
"pm_score": 6,
"text": "<p>When we say <a href=\"https://en.wikipedia.org/wiki/Protein_(nutrient)\" rel=\"noreferrer\">"protein" with respect to food</a>, what is generally meant is material that contains amino acids. Every protein is, at its heart, a long string of ami... | [
{
"answer_id": 101698,
"pm_score": 4,
"text": "<p>It's a mix of all the proteins in whatever organism the food is coming from. Some (especially vegetable/grain) sources might have fairly specific proteins present because you are eating a specific part of that organism which is enriched in that particula... |
104,655 | <p>Looking at the microbiome analysis literature there seems to have been a shift away from 16S rRNA sequencing analysis toward shotgun sequencing of the whole genome. While the motivation given is typically that there is more information obtained by the latter, I am curious about the actual limitation of 16S rRNA analysis. Is the problem that:</p>
<ol>
<li>There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis.</li>
<li>There is some variation that would be useful, but the noise in the current sequencing methods and the capacity of the current computational analytic techniques are not able to capture it.</li>
<li>There is some variation that would be useful, but it is not clear how this correlates with the phenotype it would predict therefore scientists prefer to use shotgun sequencing to investigate causal relationships between genome and phenotype.</li>
<li>Something else (please explain!)</li>
</ol>
<p>Thank you very much</p>
| [
{
"answer_id": 104658,
"pm_score": 4,
"text": "<blockquote>\n<p>There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis.</p>\n</blockquote>\n<p>The amount of sequence variation depends on the region of the 16S... | [
{
"answer_id": 104659,
"pm_score": 3,
"text": "<p>In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help elucidate causal mechanisms. 16s is mostly limited to pro... |
104,682 | <p>Humans and many animals have multiple teeth consisting of separate pieces of bone embedded in the jaw. For humans, this arrangement has some disadvantages:</p>
<ul>
<li>teeth are quite fragile when impacted and break easily</li>
<li>gaps between teeth are difficult to clean and risk decay</li>
</ul>
<p>Why don't we have a single piece of bone in our mouth (possibily with an uneven surface to aid crushing food)? Is there any evolutionary advantage to having multiple separate teeth, or does it simply not matter because by the time problems arise we have already reproduced?</p>
| [
{
"answer_id": 104658,
"pm_score": 4,
"text": "<blockquote>\n<p>There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis.</p>\n</blockquote>\n<p>The amount of sequence variation depends on the region of the 16S... | [
{
"answer_id": 104659,
"pm_score": 3,
"text": "<p>In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help elucidate causal mechanisms. 16s is mostly limited to pro... |
104,688 | <p>Someone I know has done an experiment using pure culture and given it to me for rna-seq analysis.</p>
<p>But there are a few problems</p>
<ol>
<li>the bacteria she gave me as reference was initially a Staphylococcus sp. but it turned out to be Bacillus sp. Upon my analysis.</li>
<li>upon analysis I could only find ribosomal RNAs for Bacillus sp.</li>
</ol>
<p>So my question is does a bacteria that is grown on a wrong culture media produce any proteins even in small amounts?
Will it have a lot of rRNA transcripts? Because I see all the sequencing reads map to ribosomal region. Are those not dependent on growth conditions? Or is it that Bacillus can survive on different media in a vegetative state and thus have a large number of ribosomal RNA?</p>
| [
{
"answer_id": 104658,
"pm_score": 4,
"text": "<blockquote>\n<p>There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis.</p>\n</blockquote>\n<p>The amount of sequence variation depends on the region of the 16S... | [
{
"answer_id": 104659,
"pm_score": 3,
"text": "<p>In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help elucidate causal mechanisms. 16s is mostly limited to pro... |
105,239 | <p>A simple mental model of a viral infection is that an infected cell emits a lot of virions and eventually dies. The emitted virions have a chance of infecting other cells. Nearby cells are at a higher risk of infection.</p>
<p>Based on this model, if one cell in my nose gets infected, I would expect a large part of my nose to be destroyed, as the infection spreads and destroys more and more cells in the same area.</p>
<p><a href="https://i.stack.imgur.com/OenIR.gif" rel="noreferrer"><img src="https://i.stack.imgur.com/OenIR.gif" alt="simple infection model" /></a></p>
<p>This does not happen! I survived a number of infections and still have my nose. Why?</p>
<p>I know there are "flesh eating" bacteria. Why isn't this the norm for infections? Does a common cold virus or SARS-CoV-2 not infect a lot of cells within the same area?</p>
| [
{
"answer_id": 105240,
"pm_score": 6,
"text": "<p>A virus does not destroy that many cells before it is exterminated by the immune system or before the host dies.</p>\n<p>Perhaps even more crucially, viruses typically target a very specific type of cell — those on the inner mucal surface of the nose in ... | [
{
"answer_id": 105248,
"pm_score": 4,
"text": "<p>The innate immune system is remarkably good at providing a first line of defense. Viruses don't just march into your body uncontested. They basically have to fight for every square centimeter of ground they claim, and even then, it's a race against tim... |
105,271 | <p>I read the generalization that life originates from a cell, and from my understanding animals, they originate from a single cell, produced as a result of sexual reproduction. And then life begins to develop from there on. But when it comes to botany, I stumble upon this doubt because of plant seed varieties. During any stage of seed production, can the seed be designated as having come from a single cell. Can i use the following generalization and correct me wherever i am wrong.</p>
<pre><code>every life is made of cells, and every life comes from a single cell
</code></pre>
| [
{
"answer_id": 105240,
"pm_score": 6,
"text": "<p>A virus does not destroy that many cells before it is exterminated by the immune system or before the host dies.</p>\n<p>Perhaps even more crucially, viruses typically target a very specific type of cell — those on the inner mucal surface of the nose in ... | [
{
"answer_id": 105248,
"pm_score": 4,
"text": "<p>The innate immune system is remarkably good at providing a first line of defense. Viruses don't just march into your body uncontested. They basically have to fight for every square centimeter of ground they claim, and even then, it's a race against tim... |
107,815 | <p>I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein.
However, when I look it up online, there is no clear organized data on different documented isoforms <em>(at least not for the one I am looking for...)</em> (For example, entries at NCBI Protein database do not match with those at ENSEMBL).
It would be great if someone can suggest a more systematic way (or previous such studies) to find out the sequences of different isoforms of a protein.</p>
<p>To elaborate, here the link at <a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000160183;r=21:42371887-42396091" rel="nofollow noreferrer">ENSEMBL database</a> (9 transcripts, of which 5 are protein coding, of which 2 have identical AAs seq) and here's what I found at <a href="https://www.ncbi.nlm.nih.gov/protein/NP_001243246.1,NP_076927.1,NP_115780.1,NP_115781.1" rel="nofollow noreferrer">NCBI Protein search</a> (4 isoform and a <a href="https://www.ncbi.nlm.nih.gov/protein/49481858" rel="nofollow noreferrer">5th one</a> from literature). It is evident that there are discrepancies between the two.</p>
| [
{
"answer_id": 107826,
"pm_score": 4,
"text": "<p>As will be clear from the question and various replies, there are several different repositories for data emerging from the various nucleic acid sequencing projects. The two main gene oriented ones — NCBI and ENSEMBL — are funded by the US government and... | [
{
"answer_id": 107816,
"pm_score": 2,
"text": "<p>I would suggest using the UCSC genome browser for the organism in question (assuming that they have your organism loaded), and use either the GUI or otherwise to pull out the transcripts you are interested in after searching the gene. For example, <a hre... |
108,749 | <p>If, as a physicist, I were to be told that quarks have never been isolated, and so they are not actually real particles, it would take some effort to respond. I'd have to talk about the Standard Model and Asymptotic Freedom, and thus admit that they do have some properties that are not like other particles.</p>
<p>If faced with insistance that this proves the case, that they are actually some sort of epiphenomenon of particle accelerators, I might have some difficulty knowing how to proceed. It's true that they manifest an as yet new characteristic, and so perhaps we have to expand our conceptualizaiton of what a particle is.</p>
<p>That may not be a perfect analogy for my question, but I have a medical friend who would like to tell me that no virus has ever been isolated, and that as opposed to some kind of transmissible, infectious organism, they are actually some kind of waste product of cells. I am told that any attempt to satisfy Koch's postulates involves the injection of materials in addition to the viruses at issue, and the claim is that it's these combination of materials that is making the animal sick.</p>
<p>I see a lot of varied "viruses don't exist" claims around the web, focused on HIV, measles, and CV19, and associated with names like Drs. Stefan Lanka, Andrew Kaufman, Tom Cowan, etc. Associated claims are that in any context that involves supposed exposure to a virus, less than 100% of the animals get sick, and so whatever may be going on, it's the animal itself at issue. In some quarters this is called "Terrain Theory." I would like to not have to dig too far into this.</p>
<p>How can I respond in a coherent way that doesn't require becoming a virologist?</p>
| [
{
"answer_id": 108750,
"pm_score": 6,
"text": "<p>It is very easy to disprove their claims, but the burden of proof doesn't lie with you, it lies with the person making the claim. If they want to claim that there is a "cell waste product" that causes the widely varying symptoms and viral effec... | [
{
"answer_id": 108754,
"pm_score": 5,
"text": "<p>This may be too brief or simplistic, but a short discussion of electron microscopy might be in order; the different viruses are consistent in morphology in the diseases they cause (e.g. Ebola virus, smallpox, COVID, etc.)</p>\n<p>It’s hard to argue with ... |
111,411 | <p>The Wikipedia article on the <a href="https://en.wikipedia.org/wiki/Life" rel="nofollow noreferrer">definition of life</a> states that there is no consensus for the definition of life with at least 123 definitions being proposed.</p>
<p>I am unclear why this is the case.</p>
| [
{
"answer_id": 111419,
"pm_score": 3,
"text": "<p>Here is a question, at what point in organisation, from molecules to cells, does 'life' suddenly appear?</p>\n<p>We can rephrase the question, what is the difference between 'life' and 'non-life'?</p>\n<p>The takeaway is, that the definition of 'life', a... | [
{
"answer_id": 111437,
"pm_score": 2,
"text": "<p>Because life is just one type of chemical process.</p>\n<p>There is a whole spectrum of chemical processes with complex life on one end of it and simple one way one off reactions on the other. Where a humans choose to draw a line and say "life above... |
2 | <p>Does anyone have any suggestions to prevent RNAse contamination when working with RNA?</p>
<p>I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered pipette tips.</p>
| [
{
"answer_id": 12,
"pm_score": 5,
"text": "<p>You need to be careful about everything that comes in contact with your samples. Every spatula, beaker and every magnetic stir bar need to be RNAse-free. </p>\n\n<p>For metal- and glassware we usually put everything into a drying closet at 200-250 °C for a f... | [
{
"answer_id": 14,
"pm_score": 4,
"text": "<p>Here are some tips from what I routinely do:</p>\n\n<ul>\n<li>wipe all the surfaces (including pipettes and gloves) with RNAse Away or similar</li>\n<li>do everything on ice</li>\n<li>use a RNAse/DNAse free tubes. Use also commercial RNAse free water (it's w... |
4 | <p>Various people in our lab will prepare a liter or so of LB, add kanamycin to 25-37 mg/L for selection, and store it at 4 °C for minipreps or other small cultures (where dosing straight LB with a 1000X stock is troublesome). Some think using it after more than a week is dubious, but we routinely use kan plates that are 1-2 months old with no ill effect.</p>
<p>How long can LB with antibiotic such as kanamycin, chloramphenicol, or ampicillin be stored at 4 °C and maintain selection?</p>
| [
{
"answer_id": 105,
"pm_score": 5,
"text": "<p><a href=\"http://bitesizebio.com/articles/ye-olde-antibiotic-plates/\">This Bitesize Bio article</a> is very informative on this issue. <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC376956/\">The 1970 study</a> they cite found negligible reduction ... | [
{
"answer_id": 62,
"pm_score": 2,
"text": "<p>As far as I know, that is fine. Thats the temperature that Amp is regularly stored at. I always do a negative control anyways to ensure that my antibiotics are still lethal. Just don't stick it in the microwave to make plates</p>\n"
},
{
"answer_i... |
5 | <p>Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or alternative splicing.</p>
| [
{
"answer_id": 24,
"pm_score": 5,
"text": "<p>I don't have any literature to back this up but I doubt that it occurs (at least frequently). </p>\n\n<p>For example, imagine a simple three exon gene. Upon splicing <code>exon 1</code> to <code>exon 3</code>, <code>exon 2</code> would be excised as part of... | [
{
"answer_id": 30,
"pm_score": 4,
"text": "<p>After performing a quick literature search, I am, as with GWW, unable to provide any literature against this occurring, although this paper by Black (2005) states that exons in multi-exon pre-mRNAs are always maintained in order.</p>\n\n<p><a href=\"http://d... |
8 | <p>I'm looking for resources or any information about the formation of dendritic spines and synaptogenesis, especially in relation to how new connections are formed on a daily basis.</p>
<p>Does the electrotonic signalling along the axons and through the spines cause new connections to be made based on some kind of spatial condition (maybe an electrical or chemical attraction), or is there some larger heuristic here?</p>
| [
{
"answer_id": 48,
"pm_score": 5,
"text": "<p>Spine formation (spinogenesis) is almost certainly due to chemical, rather than electrical, signalling between neurons. Although there are exceptions (gap junctions, for one), most forms of inter-cellular communication are mediated by chemicals released by o... | [
{
"answer_id": 25,
"pm_score": 4,
"text": "<p>Dendritic spines are thought to grow and recede under LTP and LTD, respectively. See <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/21963169\" rel=\"nofollow\">(Bosch and Hayoshi 2011)</a> for a review. </p>\n\n<p>From there, much of the synaptogenesis occurs... |
10 | <p>I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you may insert the gene for fluorescence next to your gene of interest so you know if it is transcribed or not by whether the organism's cells are fluorescent and to what degree they are fluorescing at.</p>
<p>I have noticed in some experiments that have multiple versions that in one case they use the fluorescent gene and in the next a different gene (for example lactose). Both portions of the experiment use almost the exact same steps so why would they not choose the same reporter gene?</p>
| [
{
"answer_id": 22,
"pm_score": 5,
"text": "<p>Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different... | [
{
"answer_id": 1872,
"pm_score": 1,
"text": "<p>Reporter genes are also used when the experiment is trying to distinguish the effect of that gene that the scientist introduces (exogenous) and the same gene that the cell already has (endogenous). Ideally, one would like to choose a cell system that does ... |
23 | <p>The whole question is</p>
<blockquote>
<p>What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer.</p>
</blockquote>
<p>I remember it has something to do with the average length of alpha-helix. More specifically, 3 on both side of a site. So in total the frame length should be 7. But I can't remember the reason behind the argument.</p>
<p>What do you think?</p>
<hr>
<p>According to what my professor said in class, 2nd and 3rd generation of protein secondary structure reconstruction relies on statistics data of several consecutive residues. I guess what he meant by "frame size", is how many adjacent residues we should take into account in the algorithm.</p>
| [
{
"answer_id": 26,
"pm_score": 5,
"text": "<p>By frame size, do you mean sliding window?</p>\n\n<p>I know that if you want to predict a secondary structure of a transmembrane protein, then your window size should be 20 amino acids (this is the average length of 1 transmembrane alpha helix spanning throu... | [
{
"answer_id": 40,
"pm_score": 2,
"text": "<p>I found that 13 worked best for Neural Nets and SVM performance of secondary structure information when I ran this in R.</p>\n"
},
{
"answer_id": 1262,
"pm_score": 2,
"text": "<p>OK, so 2 responses, each concerning different protein segments ... |
29 | <p>I recently downloaded gene annotations for <em>Homo sapiens</em> from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have as many as 250. I know enough about gene annotation to take these predictions with a grain of salt, but it got me thinking...what are the biologically relevant factors that might limit the length, exon number, etc of a gene? Is there any real possibility for a gene to have 50 exons? 100 exons? 250 exons? From a biological standpoint, where is the line drawn and why?</p>
| [
{
"answer_id": 41,
"pm_score": 4,
"text": "<p>This question drops firmly into the lap of molecular evolution and the constraints that are placed upon genes by the forces of mutation, selection, drift and recombination.</p>\n\n<p>There are numerous situations, particularly gene duplication, that can resu... | [
{
"answer_id": 43,
"pm_score": 2,
"text": "<p>I doubt there is really any direct limitation; the best test would be to check if the size matches, i.e. that 1kbp gene with 100 exons would rather have to have way too short introns. </p>\n\n<p>Quick search over NCBI Genes show even a <a href=\"http://www.n... |
33 | <p>I know the basics of epigenetics, but I do not know how epigenetic mechanisms are transmitted from parents to children (or if there is even enough literature to derive a consensus). My question is relates to surrogate motherhood, in which an egg is fertilized <em>in vitro</em> and then implanted in the womb of a woman other than the egg donor. </p>
<p>Are all the factors that affect epigenetic mechanisms encoded in the genome? Is it possible for the surrogate mother's epigenetics to influence the epigenetics of the child/children?</p>
| [
{
"answer_id": 44,
"pm_score": 5,
"text": "<p>Epigenetic information is information that can be inherited through cell division that is not encoded in the DNA sequence. This includes, but is not limited to, DNA methylation and histone modifications (there is also non-chromatin based epigenetic informati... | [
{
"answer_id": 45,
"pm_score": 3,
"text": "<p>The idea of epigentics is that there is more info in chromatin than just in the DNA sequence it contains and that this info can be altered <em>in vivo</em>.<br>\nThus, one cannot inherit epigenetic changes from a surrogate (which brings no new physical genet... |
115 | <p>Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?</p>
| [
{
"answer_id": 137,
"pm_score": 5,
"text": "<p><a href=\"http://www.wiley.com/WileyCDA/WileyTitle/productCd-3906390500,subjectCd-CH83.html\">Origin of Life: Chemical Approach</a> is an edited volume by Piet Herdewijn and M. Volkan Kisakürek.</p>\n\n<p>here is the book's description from the webpage:</p>... | [
{
"answer_id": 154,
"pm_score": 3,
"text": "<p>I quite like the account given in <a href=\"http://www.biology-direct.com/content/6/1/36/\">Early evolution without a tree of life</a>, where alkaline hydrothermal vents (like \"<a href=\"http://en.wikipedia.org/wiki/Lost_City_%28hydrothermal_field%29\">Los... |
171 | <p>What is the advantage gained by the substitution of thymine for uracil in DNA? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of DNA, which seems fine in theory, but why does the addition of a simple methyl group make the base more well protected?</p>
| [
{
"answer_id": 172,
"pm_score": 8,
"text": "<p>One major problem with using uracil as a base is that <a href=\"http://en.wikipedia.org/wiki/Deamination#Cytosine\">cytosine can be deaminated</a>, which converts it into uracil. This is not a rare reaction; it happens around 100 times per cell, per day. Th... | [
{
"answer_id": 174,
"pm_score": 6,
"text": "<p>The existence of thymine in DNA instead of uracil is apparently due to evolution process which made DNA more stable.</p>\n\n<p>Thymine has greater resistance to photochemical mutation, making the genetic message more stable. A rough explanation of why thymi... |
175 | <p>I am currently doing an experiment on cells to test the internalization of a protein.
Normally, I seeded my cells the day before the incubation. This worked well for Hela, CHL or PANC1 cells. However, when I did the same with INS1-E and MIN6 (both beta-cells) after the incubation and the washing step the majority of the cells were gone. This was better in the control where I did not put in the compound, but still a lot of cells were detached.</p>
<p>Therefore, I wonder if I should seed the INS1-E and MIN6 cells earlier, more like 2-3 days before. Do these cell lines need more time after splitting to attach again?</p>
| [
{
"answer_id": 172,
"pm_score": 8,
"text": "<p>One major problem with using uracil as a base is that <a href=\"http://en.wikipedia.org/wiki/Deamination#Cytosine\">cytosine can be deaminated</a>, which converts it into uracil. This is not a rare reaction; it happens around 100 times per cell, per day. Th... | [
{
"answer_id": 174,
"pm_score": 6,
"text": "<p>The existence of thymine in DNA instead of uracil is apparently due to evolution process which made DNA more stable.</p>\n\n<p>Thymine has greater resistance to photochemical mutation, making the genetic message more stable. A rough explanation of why thymi... |
193 | <p>I've read that the amoeba is capable of learning. Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the evolutionary distance.</p>
<p>How does this species learn? I would presume that there is a complicated chain of receptor mediated transcription regulation, but what are the specifics? What types of receptors does an amoeba have to sense its environs?</p>
| [
{
"answer_id": 256,
"pm_score": 5,
"text": "<p>I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for \"adaptive anticipation\" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system. </p>\n\n<p>In the ... | [
{
"answer_id": 1124,
"pm_score": 3,
"text": "<p>In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory.</p>\n\n<p>It is possible to design various <a href=\"http://en.wikipedia.org/w... |
264 | <p>For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?</p>
| [
{
"answer_id": 275,
"pm_score": 4,
"text": "<p>I understand that Robin Holliday was the first to discuss the possible role of DNA methylation \nin the control of Gene expression. In his paper \"<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/3310230\">The inheritance of epigenetic defects</a>\"\nhe present... | [
{
"answer_id": 270,
"pm_score": 2,
"text": "<p>I found two nice review papers focused of epigenetics and human disease, one from <a href=\"http://dx.doi.org/10.1146/annurev.genom.5.061903.180014\" rel=\"nofollow\">2004</a>, and one from <a href=\"http://dx.doi.org/10.1503/cmaj.050774\" rel=\"nofollow\">... |
280 | <p>Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. That being said, there is a clear emphasis in genome projects on nucleotide (genome and transcriptome) sequencing, with much less (if any) effort put into proteomics work (correct me if I'm wrong there).</p>
<p>Let's assume we're sequencing the genome of a new organism and we're focusing completely on genome and transcriptome sequencing--no proteomics. Let's also assume this organism has slight variations to the standard genetic code. Would it be possible to annotate this genome (for protein-coding genes) completely incorrectly since the gene prediction software does not take into account these variations, or would it be pretty obvious? What would you expect to see in this case?</p>
| [
{
"answer_id": 508,
"pm_score": 4,
"text": "<p>If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms.\nIn reality, the most commo... | [
{
"answer_id": 282,
"pm_score": 2,
"text": "<p>The short answer is yes, you could end up with many errors. See here for more detail:</p>\n\n<p><a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi\" rel=\"nofollow\">NCBI: \"The Genetic Codes\"</a></p>\n"
},
{
"answer_id": 288,
"... |
286 | <p>I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).</p>
<p>Does anyone know a good protocol which involves using only the supernatant, without purification of the enzyme? What is the preferred buffer for the reaction?</p>
| [
{
"answer_id": 508,
"pm_score": 4,
"text": "<p>If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms.\nIn reality, the most commo... | [
{
"answer_id": 282,
"pm_score": 2,
"text": "<p>The short answer is yes, you could end up with many errors. See here for more detail:</p>\n\n<p><a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi\" rel=\"nofollow\">NCBI: \"The Genetic Codes\"</a></p>\n"
},
{
"answer_id": 288,
"... |
304 | <p>I wonder what are examples of organs/structures/behaviours/cooperation that evolutionary biologists themselves find most difficult to explain -- to explain how they could appear evolutionarily -- within known mutation rates, generation frequency, and known time frames.
Excluding issue of appearance of life itself.</p>
<p>Knowing rates of mutation and generation cycle (and population size), it would be possible to estimate time needed for appearance of new feature. </p>
<p>Thus it would be possible to spot counter-examples, such examples that are probabilistically beyond possibility to appear in given evolutionary time. Are such examples known ?</p>
<p>I might be naive, but I think some rare behavioral trait can be a candidate, behavior that does not trigger even once in a lifetime of organism, on average, that triggers really rarely.</p>
| [
{
"answer_id": 397,
"pm_score": 4,
"text": "<p>I won't claim that these are <em>the most difficult</em> things to explain evolutionarily, but these two are hard:</p>\n\n<ol>\n<li>Host-Pathogen dynamics. They start out easy enough, but the interaction between a pathogen and its host is intensely complex.... | [
{
"answer_id": 312,
"pm_score": 3,
"text": "<p>The Nautilus eye used to be (still is?) a \"problem\" and became a poster boy for creationist arguments. It has a pin-hole camera eye, which is the highest resolution non-lens eye. However, I understand that several genera arose during the Cambrian and the... |
345 | <p>The standard protocol for a person experiencing chest pains is to <strong>chew</strong> a 300mg aspirin tablet, the argument being that chewing rather than swallowing the tablet results in the aspirin entering the blood stream faster. </p>
<p>From a biological standpoint, why is this the case? Given that the stomach and GI tract are specialised tissues to allow for maximum diffusion, why would it be faster to pass aspirin across the gums (<em>bucaal administration?)</em> tongue and cheeks which are not specialised for this purpose? </p>
<p>It is not just a special case for aspirin either, as Hypostop<sup>TM</sup>/Glucogel<sup>TM</sup> (acute treatment for hypoglycaemic shock, essentially concentrated sugar) is applied directly to the gums or cheek with a similar argument that in critical situations it is faster. </p>
<p>The only suggestion I could find was very vague from the "<a href="http://www.merckmanuals.com/professional/clinical_pharmacology/pharmacokinetics/drug_absorption.html" rel="nofollow">Merck Manual</a>":</p>
<blockquote>
<p>The stomach has a relatively large epithelial surface, but its thick mucous layer and short transit time limit absorption
Which I assume could mean that it is the reduced absorption rate in the stomach that makes the oral membranes faster, yet it also says that the delay in the stomach is brief. </p>
</blockquote>
<p>I'd be really interested to know the biology behind this!</p>
| [
{
"answer_id": 376,
"pm_score": 6,
"text": "<p>There are several issues here:</p>\n\n<p>1) <strong>Any mucous membrane is a specialized tissue for absorption.</strong></p>\n\n<p>Mucous membranes are indeed not so good for passive diffusion, that makes them absolutely perfect tools for active absorption ... | [
{
"answer_id": 469,
"pm_score": 4,
"text": "<p>It would also be logical to note that a chewed tablet increases its surface-area-to-volume ratio for absorption relative to an intact tablet, for any absorptive tissue.</p>\n"
},
{
"answer_id": 43126,
"pm_score": 0,
"text": "<p>From an engin... |
393 | <p>Forgive me if my question does not belong here or if I'm using incorrect terms, but I'm not educated in biology at all. I'm investigating the workings of the <a href="http://en.wikipedia.org/wiki/Biological_classification" rel="nofollow">biological classification system</a>.</p>
<p>I was wondering if there is a list somewhere of all kingdoms, orders, classes, etc., both in Latin and common names?</p>
| [
{
"answer_id": 395,
"pm_score": 4,
"text": "<p>The <a href=\"http://tolweb.org/tree/\">Tree of Life</a> project has a browse-able tree of all major taxa, but not necessarily all species. You can start at the <a href=\"http://tolweb.org/Life_on_Earth/1\">root of the tree here</a>. Tree of life uses moder... | [
{
"answer_id": 394,
"pm_score": 2,
"text": "<h1>Kingdoms</h1>\n\n<p>The UK accepted system has five kingdoms, for some it's hard to describe a single word common name so I hope you don't mind that I have written brief summaries too:</p>\n\n<ol>\n<li><strong>Animalia</strong> are multi-cellular organisms... |
406 | <p>This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.</p>
| [
{
"answer_id": 407,
"pm_score": 6,
"text": "<p>In 2010, Dr. Craig Venter actually used a bacterial shell and <a href=\"http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form\" rel=\"noreferrer\">wrote DNA for it</a>.</p>\n<blockquote>\n<p>Scientists have created the world's first... | [
{
"answer_id": 430,
"pm_score": 5,
"text": "<p>In principle it is possible. Life doesn’t contain some divine or intrinsically spiritual element that we would have to add to our <em>artificial organism potion</em> to breathe life into it. At this moment we are limited by gaps in our knowledge and by the ... |
445 | <p>The most annoying thing for me about being cold is a runny nose. Is there an advantage to having a runny nose when cold? What does having a runny nose achieve?</p>
| [
{
"answer_id": 449,
"pm_score": 6,
"text": "<p>There are two reasons for this:</p>\n\n<ol>\n<li>Nasal mucus helps warm inhaled air before it reaches the lungs. In cold weather, the mucus tends to dry out, so the membranes increase their production.</li>\n<li>At the same time, exhaled air is warmer than ... | [
{
"answer_id": 26331,
"pm_score": 2,
"text": "<p>Rhinorrhea, or runny nose is a response used by our nasal membrane to get rid of foreign particles including pollen dust and infection. As such we get runny noses when we have a cold, allergy or are exposed to high densities of air-born particles. Cold ai... |
537 | <p>My 2008 biology book (1) states that some 10% of the human genome consists of relatively short (~300 nucleotides long) <em>Alu</em> elements which do not code for proteins but many of which are transcribed into RNA. Do these <em>Alu</em> elements have any function in the cell?</p>
<p><strong>(1) Biology, 8th ed., Campbell & Reece, 2008</strong></p>
| [
{
"answer_id": 542,
"pm_score": 4,
"text": "<p>Alu elements are a type of transposable element. They possess the means for their own duplication and movement. Alu is a SINE-like element that is transcribed by RNA Pol III, and so a single DNA copy can make multiple RNA copies, each capable of inserting ... | [
{
"answer_id": 539,
"pm_score": 0,
"text": "<p>I've really not studied this, however <a href=\"http://en.wikipedia.org/wiki/Alu_element\" rel=\"nofollow noreferrer\">wikipedia</a> does a good job talking about some of the functions, particularly the associated diseases that result from changed in those ... |
543 | <p>What specific biochemical processes are involved in inducing meiosis rather than mitosis? Why are gonadal cells the only cells in the human body which do undergo meiosis? </p>
| [
{
"answer_id": 545,
"pm_score": 4,
"text": "<blockquote>\n <p>What specific biochemical processes are involved in inducing meiosis rather than mitosis?</p>\n</blockquote>\n\n<p>It's a difficult question because every step in the development of a germ cell is ultimately necessary for the final different... | [
{
"answer_id": 544,
"pm_score": 2,
"text": "<p>Let's start by answering the second part of your question first. I can ask you a similar question like \"Why do parietal cells secrete HCl?\" or \"Why are skeletal muscle cells multinucleated?\". The reason why the cells in our body carry out different func... |
576 | <p>When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction</p>
<hr>
<p><strong>ATP + H<sub>2</sub>O → ADP + P<sub>i</sub></strong> ΔG˚ = −30.5 kJ/mol (−7.3 kcal/mol)</p>
<hr>
<p>that 30.5 kJ/ mol is conferred by ATP molecules physically bumping around the reactants X and Y, the kinetic energy of the above reaction being what does it?</p>
<p>I mean, is the energy coin of ATP conferred to reactions by molecular collisions, or is it an electric field effect in the spatial geometry the way the ATP molecule tends to break apart?</p>
| [
{
"answer_id": 591,
"pm_score": 5,
"text": "<p>Usually in biology (and being ATP, it most probably is biology), it's one of two things.</p>\n\n<p>The gamma-phosphate (the third one, the one farthest from the adenosine) is very unstable, meaning the phosphoanhydride bond is easy to break. The cell \"all... | [
{
"answer_id": 81328,
"pm_score": 0,
"text": "<p>Chemical reactions are based on collisions, but only those with the right amount of <strong>energy</strong> and the proper <strong>orientation</strong> give rise to them. If just one of these parameters deviates enough, the reactants will just bounce off.... |
653 | <p><a href="https://biology.stackexchange.com/questions/651/minimal-number-of-amino-acids-required">This question</a> got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 20 amino acids (or 22 if you include <a href="http://en.wikipedia.org/wiki/Selenocysteine" rel="noreferrer">selenocysteine</a> and <a href="http://en.wikipedia.org/wiki/Pyrrolysine" rel="noreferrer">pyrrolysine</a>), so many of the amino acids are coded by multiple codons.</p>
<p>Is there any hypothesis as to why there are only 22 amino acids and not 64? Is it possible that there were 64 (or at least more than 22) at an earlier time?</p>
| [
{
"answer_id": 662,
"pm_score": 7,
"text": "<p>Brian Hayes wrote a very interesting article from a mathematical point of view:</p>\n\n<p><a href=\"http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code\">http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code... | [
{
"answer_id": 661,
"pm_score": 5,
"text": "<p>The <em>first</em> position of the anti-codon, the \"Wobble\" position, forms hydrogen bonds less well than do the second two. This means that the <em>last</em> position of the codon has less coding potential than the first two. The reason is that the ant... |
669 | <p>Can pollution and things in an organism's environment serve as hormones?</p>
| [
{
"answer_id": 672,
"pm_score": 5,
"text": "<p>A hormone <a href=\"http://en.wikipedia.org/wiki/Hormone\">is defined</a> as \"a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism\" (I'm just taking Wikipedia definition)... | [
{
"answer_id": 673,
"pm_score": 1,
"text": "<p>Yes, they can.</p>\n\n<p>An example of a man-made chemical byproduct affecting hormone signaling is <a href=\"http://en.wikipedia.org/wiki/Bisphenol_A\" rel=\"nofollow\">Bisphenol A (BPA)</a>. \nThere is a vast body of evidence linking BPA to all manners of... |
740 | <p>A while back there was a lot of noise about resveratrol, a naturally occurring phenol which was touted as a potential anti-aging drug due to its role in regulating the SIRT 1 gene. A number of studies suggested that it could extend the lifespans of model organisms such as <em>D. melanogaster</em> and <em>C. elegans.</em></p>
<p>Has there been any follow up on this? Have there been any human trials?</p>
| [
{
"answer_id": 742,
"pm_score": 5,
"text": "<p>It's worth noting that earlier this month a large body of resveratrol research was retracted:</p>\n\n<blockquote>\n <p>The University of Connecticut, in what clearly seems like an attempt to get ahead of damaging news, has announced an “extensive”\n inves... | [
{
"answer_id": 741,
"pm_score": 3,
"text": "<p>If you search clinicaltrials.gov (maintained by the NIH) for \"resveratrol\", you'll find <a href=\"http://clinicaltrials.gov/ct2/show/results/NCT01010009?term=resveratrol&rank=4&sect=X3015#evnt\">44 clinical trials</a>, many of them ongoing or not ... |
768 | <p><strong>Question</strong>: From a physiological point of view, when sex is <a href="http://en.wikipedia.org/wiki/XY_sex-determination_system">determined</a> in a human fetus, is it equally likely to be male or female?</p>
<p>Studies in this area typically measure age at birth, where the data would have already been biased. There's a slight imbalance in the <a href="http://en.wikipedia.org/wiki/Human_sex_ratio">human sex ratio</a>, in that there's an overall tendency towards males. However, this could be accounted for in numerous ways, such as abortion.</p>
<p><a href="http://en.wikipedia.org/wiki/Fisher%27s_principle">Fisher's principle</a> suggests there would be an evolutionary tendency towards 50:50 chance.</p>
| [
{
"answer_id": 770,
"pm_score": 5,
"text": "<p><strong>The Fisher's principle is not applicable to the fetuses</strong> because it has been formulated for parental expenditure and basically states that the ratio of male to female parents (implying that both parties have reached the age of fertility) wil... | [
{
"answer_id": 780,
"pm_score": 3,
"text": "<p>The following paper(1) studies the trends in male to female ratios among newborns over the period 1950-1994 in 29 countries (20 major European countries, USA, Canada, Japan, and others). In all countries at any time point, the male to female ratio was alway... |
775 | <h1>Background</h1>
<p>I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work.</p>
<h1>Context & what I think I understand</h1>
<p>In digesting all I have been reading, I am beginning to understand that there are layers to neural networks. A front-line layer of neurons may receive, for example, a visual stimulus such as a bright light. That stimulus is taken in by the front-line neurons, each of which produce a weighted electro-chemical response that results in a binary decision to pass an electrical charge through its axon to the dendrites of the tens of thousands of neurons to which it is connected.</p>
<p>This process repeats through layers channeling the electrical signals and focusing them based on their permutations until ultimately a charge is passed to a focused response mechanism such as the nerves that control shrinking of the pupils.</p>
<p>Hopefully I got that correct.</p>
<h1>Preamble to the question ;)</h1>
<p>Assuming that I am not completely off-base with my basic understanding of how a biological neural network operates, I am beginning to grasp how an input (stimulus) results in an output (response) such as motor movement or reflexes. That would just seem to be basic electricity of open and closed circuits.</p>
<p>HOWEVER, what confuzzles me still is how a memory is stored. The analogy to an electrical circuit breaks down here, for in a circuit I can't really stop the flow of electrons unless I dam up said electrons in a capacitor. If I do that, once the electrons are released (accessed), they are gone forever whereas a memory endures.</p>
<h1>So. . .</h1>
<p>How the heck are memories constructed and stored in the human brain? Are they stored in a specific region? If so, where?</p>
| [
{
"answer_id": 778,
"pm_score": 6,
"text": "<p>Unfortunately, we are all still \"confuzzled\" by how memory works. We are far from a complete understanding of how memory is stored and recalled. Nonetheless, we do know a <em>little</em>, so read on.</p>\n\n<p>Your understanding of basic neural function i... | [
{
"answer_id": 1196,
"pm_score": 3,
"text": "<p>I would like to point out some ways your understanding is wrong. \"Neural networks\" are usually a computer science term, only very, very loosely based on actual neural networks. The idea of layers in a neural network is pretty much an invention of compute... |
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