qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
78,018 | <p>For example, how much loading buffer (6X) do I need for my PCR reaction with a volume of 25 μl? What is the general way to calculate it?</p>
| [
{
"answer_id": 77930,
"pm_score": 4,
"text": "<p>A mature human sperm has some mitochondria, a nucleus, an acrosome, and a flagellar apparatus. That's it. Because of the lack of other organelles in the sperm, they have to be kept in a kind of 'cold storage' so that they are viable for at least some time... | [
{
"answer_id": 77931,
"pm_score": 2,
"text": "<p>To keep sperm viable in natural body conditions, they are kept at a relative lower temperature than the body temperature, and this can achieved by the scrotum. As sperm is produced in testis, and testis are situated in the scrotum outside the main part of... |
78,036 | <p>I would like to investigate the dynamic of the number of cells over time as the embryo grows. I am interested in any multicellular animal species for which we can have some data. How does the number of cells change over time in an embryo?</p>
<p>I welcome any graphs, empirical data and/or mathematical expression for this dynamics.</p>
| [
{
"answer_id": 77930,
"pm_score": 4,
"text": "<p>A mature human sperm has some mitochondria, a nucleus, an acrosome, and a flagellar apparatus. That's it. Because of the lack of other organelles in the sperm, they have to be kept in a kind of 'cold storage' so that they are viable for at least some time... | [
{
"answer_id": 77931,
"pm_score": 2,
"text": "<p>To keep sperm viable in natural body conditions, they are kept at a relative lower temperature than the body temperature, and this can achieved by the scrotum. As sperm is produced in testis, and testis are situated in the scrotum outside the main part of... |
78,093 | <p>One of the major results of the Human Genome Project (HGP) was that humans have far fewer separate genes than previously thought. From <a href="http://news.mit.edu/2004/humangenome" rel="nofollow noreferrer">a 2004 article about the HGP</a>:</p>
<blockquote>
<p>Francis S. Collins, director of the National Human Genome Research Institute (NHGRI), said, "Only a decade ago, most scientists thought humans had about 100,000 genes. When we analyzed the working draft of the human genome sequence three years ago, we estimated there were about 30,000 to 35,000 genes, which surprised many. This new analysis reduces that number even further [to 20,000-25,000] and provides us with the clearest picture yet of our genome."</p>
</blockquote>
<p>What was the old estimate of 100,000 based on? I assume that in 1994 no one had sequenced the entire proteome...</p>
<p>As Remi.b points out, the 100,000 gene estimate may be based on the <a href="https://en.wikipedia.org/wiki/One_gene%E2%80%93one_enzyme_hypothesis" rel="nofollow noreferrer">one gene–one enzyme hypothesis</a>. If that's true, did people before the human genome project think that there were 100,000 distinct enzyme activities? If so, what experiments/data were used to establish that number?</p>
| [
{
"answer_id": 78163,
"pm_score": 4,
"text": "<p>There's actually no need to speculate on the answer to this question since scientists have published their estimates and methodology, as is their way. The following paper is a good review:</p>\n\n<p><a href=\"https://www.nature.com/articles/ng0794-345\" r... | [
{
"answer_id": 78094,
"pm_score": 2,
"text": "<p>I don't know much about the evolution of thoughts on the subject but I would suppose that the estimate of 100,000 genes is probably caused by the <a href=\"https://en.wikipedia.org/wiki/One_gene%E2%80%93one_enzyme_hypothesis\" rel=\"nofollow noreferrer\">... |
78,215 | <p>I don't mean if a bacterium can be the cause of cancer inside a human. But can actually a bacterium changes in the way as normal cells change into tumor cells?
So gaining such characteristics of a tumor cell and if inside human body create a tumor mass?</p>
| [
{
"answer_id": 78223,
"pm_score": 4,
"text": "<p>You ask two questions:</p>\n\n<ol>\n<li>If a bacteria can get the same characteristics as tumor cells. </li>\n<li>If such \"bacterial tumor cells\" actually can form a \"tumor\" within the\nhuman body.</li>\n</ol>\n\n<p>I assume that your question is not ... | [
{
"answer_id": 78219,
"pm_score": 2,
"text": "<p>No - when bacterial cells grow in an invasive manner in the body, this is termed a bacterial infection. When one’s own cells grow in an invasive and uncontrolled way, it is termed cancer.</p>\n"
},
{
"answer_id": 78293,
"pm_score": 1,
"tex... |
78,383 | <blockquote>
<p>An unrelated couple has a daughter and a son with the same rare condition. Neither parent has any obvious signs of the condition, but the father's mother (paternal grandmother) and her brother have the same condition. Select the most likely mode of inheritance:</p>
<ul>
<li>A. X-Linked</li>
<li>B. Autosomal recessive</li>
<li>C. Autosomal dominant</li>
<li>D. Multifactorial</li>
<li>E. Mitochondria</li>
</ul>
</blockquote>
<p>The correct answer is C. But I'm confused why it would be autosomal dominant when neither parent has the phenotype. I thought it might be autosomal recessive, even though this mode usually does not have a family history, just because of the fact that the paternal grandmother and her brother both had the disease, and this is consistent with the horizontal pattern associated with autosomal recessive inheritance. For it to be autosomal dominant, the disease would have to be incompletely penetrant, which seems like a less likely scenario than it being autosomal recessive.</p>
<p>Can someone explain why it is dominant, not recessive? </p>
<p>Thanks!</p>
| [
{
"answer_id": 78411,
"pm_score": 3,
"text": "<p>I think this question is not possible to answer without knowing the frequency of the deleterious alleles in the population. There's no way to assess whether incomplete penetrance is more or less likely than an undetected mutation in the mother's side. S... | [
{
"answer_id": 78387,
"pm_score": 2,
"text": "<h1>Possible answers</h1>\n\n<blockquote>\n <p>A. X-Linked</p>\n</blockquote>\n\n<p>It is possible. However, it is unlikely. The condition is claimed to be rare and as the daughter carries it, it means that the mother must have been a carrier. As the patern... |
78,792 | <p>If a cancerous cell enters the body of a healthy person from someone else's blood or something, will that healthy person get cancer? In human beings.</p>
| [
{
"answer_id": 78800,
"pm_score": 6,
"text": "<blockquote>\n <p>Can a cancer cells from someone else's body cause cancer in a healthy person?</p>\n</blockquote>\n\n<p>No. Cancer cells from another person cannot cause cancer in a healthy person. The rare cases of transmissible tumors all involve unhealt... | [
{
"answer_id": 78798,
"pm_score": 5,
"text": "<p><em>Before OP edited his/her question, it was a little unclear whether the question was only about humans. The following answer is more general than asked as it also considers cancers in non-humans</em></p>\n\n<hr>\n\n<p>Most cancers are not transmissible... |
78,946 | <p>If there is no immune system,it seems like vaccines wouldn't do much since there is no adaptive immune system to develop antibodies and memory cells. But can people with AIDS/HIV still be vaccinated? It is expected that a normal person will have antibodies to attack the minimal infection produced by the vaccine and generate memory cells, but without an immune system I expect vaccines to be deadly.</p>
<p>Is that right?</p>
| [
{
"answer_id": 78961,
"pm_score": 4,
"text": "<blockquote>\n<p>Can people with AIDS/HIV be vaccinated?</p>\n</blockquote>\n<p>Yes. Immunization is an important part of the overall treatment strategy for HIV positive individuals. HIV infection is a risk factor for a number of vaccine preventable infectio... | [
{
"answer_id": 78947,
"pm_score": 3,
"text": "<blockquote>\n <p>Can people with HIV still be vaccinated?</p>\n</blockquote>\n\n<ul>\n<li><p>No (most of the time) if the vaccine is an attenuated vaccine, this means it contains living organisms that have been modified in order to reduce their virulence. ... |
79,097 | <p>Many parasites infect multiple host species, with one host species being the definitive host (where the parasite reproduces), and the other host species being the intermediate host (where the parasite grows to maturity). (Further details described as "complex life cycle" at <a href="https://en.wikipedia.org/wiki/Parasitic_life_cycle" rel="noreferrer">https://en.wikipedia.org/wiki/Parasitic_life_cycle</a> ) Why is this complex life cycle so common? Why wouldn't more parasites adopt a simpler life cycle of just one host? </p>
<p><strike>I knew that there were some parasites that infected more than one kind of host species, but now that I am looking into it, it seems like a majority of internal parasites have this kind of life cycle. Does anyone know why?</strike></p>
| [
{
"answer_id": 82900,
"pm_score": 3,
"text": "<p>Several reasons have been proposed.</p>\n\n<blockquote>\n <p>We suggest that complex cycles in helminths without penetrative infective stages evolve by two essentially different processes, depending on where in the cycle a new host is inserted. In ‘upwar... | [
{
"answer_id": 79121,
"pm_score": -1,
"text": "<p>I assume that by internal parasites you mean animals like tapeworms etc?</p>\n\n<p>They can infect several species simply because they are not picky. These parasites do not rely on precise molecular hijacking mechanisms like intracellular parasites (e.g.... |
79,162 | <p>I've heard that wombat scat is cube shaped, but I don't understand how that can happen. Has anyone studied the phenomenon? What would the evolutionary pressure have been to cause this?</p>
| [
{
"answer_id": 98189,
"pm_score": 3,
"text": "<p>Although the OP might no longer be active, I'm comming back to this question, because there is a new study on this released in "Soft Matter". With simulations <a href=\"https://pubs.rsc.org/en/content/articlelanding/2021/sm/d0sm01230k#!divAbstra... | [
{
"answer_id": 79164,
"pm_score": 5,
"text": "<p>I'm almost certain that your question is based on the press that <a href=\"https://pyang.gatech.edu/\" rel=\"nofollow noreferrer\">Patricia J Yang's</a> <a href=\"http://meetings.aps.org/Meeting/DFD18/Session/E19.1\" rel=\"nofollow noreferrer\">research</... |
79,521 | <p>I recently read Arthur Koestler's 1967 book <a href="https://en.wikipedia.org/wiki/The_Ghost_in_the_Machine" rel="noreferrer"><em>The Ghost in the Machine</em></a>. In it, Koestler criticises the neo-Darwinian theory of evolution—beneficial random mutations preserved by natural seleciton—as insufficient to explain the formation of complex forms like eyes and eggs. The issues Koestler has with the theory are ones that I've been trying to wrap my head around since before I read the book, but I'm aware that:</p>
<p>a) the book is half a century old;</p>
<p>b) Koestler was not a biologist or scientist; and</p>
<p>c) neo-Darwinian theory/the modern synthesis seems to have stood the test of time</p>
<p>so I'm wondering how accurate Koestler's account of the theory is, and if he is wrong what the retorts to his claims are. Here are two examples he gives of complex forms:</p>
<blockquote>
<p>[The giant panda] has on its forelimbs an added sixth finger, which comes in very ‘handy’ for manipulating the bamboo-shoots which are its principal food [but] that added finger would be a useless appendage without the proper muscles and nerves [and t]he chances that among all possible mutations those which produced the additional bones, muscles and nerves should have occurred independently are of course infinitesimally small.</p>
</blockquote>
<p>and</p>
<blockquote>
<p>The decisive novelty of the reptiles was that, unlike amphibians, they laid their eggs on dry land...[b]ut the unborn reptile inside the egg still needed an aquatic environment...[i]t also needed a lot of food...[s]o the reptilian egg had to be provided with a large mass of yolk for food, and also with albumen—the white of egg—to provide the water. Neither the yolk by itself, nor the egg-white itself, would have had any selective value...[e]ach change, taken in isolation, would be harmful, and work <em>against</em> survival.</p>
</blockquote>
<p>Instead of random mutations and external selection, he suggests that ‘internal selection’ works at all levels, from chemical upwards, to correct ‘misprints’ long before the developed organism is exposed to any sort of external selection. The implication that there must therefore be some plan towards which embryonic development works is supported by two examples:</p>
<blockquote>
<p>the growing eye-bud of the embryo is an autonomous holon, which, if part of its tissue is taken away, will nevertheless develop into a normal eye</p>
</blockquote>
<p>and </p>
<blockquote>
<p>[the fruit fly has a recessive gene that when paired with another in a fertilised egg will produce an eyeless fly.] If now a pure stock of eyeless flies is made to inbreed, then the whole stock will have only the ‘eyeless’ mutant gene, because no normal gene can enter the stock to bring light into their darkness...within a few generations, <em>flies appear in the inbred ‘eyeless’ stock with eyes that are perfectly normal</em>.</p>
</blockquote>
<p>His other main point is that evolution takes a zig-zag path, evolving down until reaching an evolutionary dead-ends before retracting to ‘an earlier or more primitive, but also more plastic and less committed stage—followed by a sudden advance in a new direction’. For example:</p>
<blockquote>
<p>[A]mphibian...ancestry...goes back to the most primitive type of lung-breathing fish; whereas the apparently more successful later lines of highly specialised gill-breathing fishes all came to a dead end.</p>
</blockquote>
<p>and </p>
<blockquote>
<p>...the human adult resembles more the embryo of an ape than an adult ape</p>
</blockquote>
<p><strong>Is Koestler's science just faulty, or are these valid criticisms that've been resolved since?</strong></p>
| [
{
"answer_id": 79522,
"pm_score": 4,
"text": "<p>Maybe both. Certainly his understanding of limb developement doesn't match modern understanding. The quote you provide seems to indicate that he thought the appearance of an additional digit would require a multitude of coordinated mutations. Our current ... | [
{
"answer_id": 96382,
"pm_score": 3,
"text": "<p>Koestler's entire argument can be summed up is an argument of <a href=\"https://en.wikipedia.org/wiki/Irreducible_complexity\" rel=\"noreferrer\">irreducible complexity</a>, which always stems from a lack of understanding of the biological systems. All hi... |
79,633 | <p>So throughout my education and research career I have been taught that all enzymes are proteins. This makes sense when you consider enzyme denaturing and folding/shape etc. However, I was recently told by a biology professor that in fact, not all enzymes are proteins -- and he alluded to the RNA world hypothesis and rRNA's. </p>
<p>Could someone explain further how exactly an rRNA (or similar) could be (or not be) considered an enzyme, and whether or not all enzymes are proteins etc?</p>
<p>Thank you!</p>
| [
{
"answer_id": 79770,
"pm_score": 3,
"text": "<p><strong>Disclaimer</strong></p>\n<p>I voted to close this question as it struck me that the by giving the poster the magic word ‘ribozyme’ he could easily verify for himself that the answer to the question in his title was “No”. However, as this question ... | [
{
"answer_id": 79645,
"pm_score": 3,
"text": "<p>Until the late 1980's all enzymes* were believed to be proteins, and were often <a href=\"http://www.cnrtl.fr/definition/enzyme\" rel=\"nofollow noreferrer\">defined</a> as protein catalysts, often in textbooks which are often not perfect representations ... |
79,940 | <p>For example let's take two sentences; "engineer made a design for camera", "evolution made an X for eye". What is the best X that could be used? </p>
<p>I need it for an essay about evolution.</p>
| [
{
"answer_id": 79942,
"pm_score": 5,
"text": "<p>Although not ideal, \"adaptation\" is more appropriate than \"design\" as a noun describing something that has come about in an evolutionary context, even though not all evolution is adaptive.</p>\n\n<p>In writing, though, I would not phrase it as you hav... | [
{
"answer_id": 79944,
"pm_score": 0,
"text": "<p>How about \"strategy\"? For example, elephants, giraffes and koalas all need to eat leaves from tall trees, but they have evolved very different strategies to accomplish that goal.</p>\n"
},
{
"answer_id": 93109,
"pm_score": 0,
"text": "<... |
80,144 | <p>ADP has two phosphate groups, and can be hydrolysed to AMP in a reaction which involves a similar free energy change to that of hydrolysing ATP to ADP. </p>
<p>Why is the latter reaction, <em>rather than the former reaction,</em> coupled to energetically unfavourable reactions to provide an overall reaction with a negative change in Gibbs Free Energy?</p>
| [
{
"answer_id": 80173,
"pm_score": 4,
"text": "<p><strong>Summary</strong></p>\n\n<p>The original question was edited — with the approval of the poster — so that in brief it now asks:</p>\n\n<blockquote>\n <p>Why is ATP hydrolysis to ADP, rather than ADP hydrolysis to AMP, the\n normal way in which cel... | [
{
"answer_id": 80150,
"pm_score": 3,
"text": "<p>It <em>can</em>, and a very famous example is <a href=\"https://www.qmul.ac.uk/sbcs/iubmb/enzyme/EC2/7/7/8.html\" rel=\"noreferrer\">polynucleotide phosphorylase</a>, an enzyme of great historical importance in the <a href=\"https://profiles.nlm.nih.gov/p... |
80,353 | <p>I have seen in textbooks referring to ds RNA and ssDNA.
How a RNA can be double stranded and likewise how a DNA can single stranded and if they do exist why are there names not interchanged?</p>
| [
{
"answer_id": 80355,
"pm_score": 3,
"text": "<p>The main differences between RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) is that DNA contains a hydrogen atom where RNA has a hyroxyl (-OH) group and RNA's uracil is substituted for DNA's thymine. The below image shows several deoxyribose mole... | [
{
"answer_id": 80418,
"pm_score": 2,
"text": "<p><strong>Complementary base-pairing is possible for RNA</strong></p>\n\n<p>As the poster is no doubt aware, the <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK22415/#A143\" rel=\"nofollow noreferrer\">double-stranded structure of DNA</a> is stabilized by ... |
80,619 | <p>Neurons and muscle cells in adult humans do not have the ability to divide by <em>mitosis</em>, so they can not repair themselves and their cell cycle remains in the interphase. I’m looking for more cells with this feature. Are there other cells with this inability to undergo mitosis in humans or in plants?</p>
<p>In an adult human:</p>
<ol>
<li><p>Do nervous cells ever undergo mitosis?</p></li>
<li><p>I wonder if all muscle cells do not undergo mitosis or if this inability only applies to cardiac and skeletal muscle cells.</p></li>
</ol>
| [
{
"answer_id": 84520,
"pm_score": 4,
"text": "<p>To answer the numbered questions:</p>\n\n<ol>\n<li>In general, neurons never divide by mitosis. However, I believe you may have unintentionally misphrased your question; there are functional neural stem cells in the adult human brain as well, and these ar... | [
{
"answer_id": 80620,
"pm_score": 1,
"text": "<p>Yes, nervous cells never undergo mitosis coz they lose their centriole thereby they are present permanently in G0 phase of cell cycle in which a cell doesn't divide,rather it just carries out it's day to day metabolism.</p>\n\n<p>As far as plants are conc... |
80,634 | <p>As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of their evolutionary relationship.</p>
<p>To be more specific, I would like to know whether the use of tetrapyrrole in the blood and in photosynthesis can be traced to the earliest organisms in which tetrapyrrole had some function, and then the molecule evolved to be capable of the different functions it currently performs in animals and plants.</p>
| [
{
"answer_id": 84520,
"pm_score": 4,
"text": "<p>To answer the numbered questions:</p>\n\n<ol>\n<li>In general, neurons never divide by mitosis. However, I believe you may have unintentionally misphrased your question; there are functional neural stem cells in the adult human brain as well, and these ar... | [
{
"answer_id": 80620,
"pm_score": 1,
"text": "<p>Yes, nervous cells never undergo mitosis coz they lose their centriole thereby they are present permanently in G0 phase of cell cycle in which a cell doesn't divide,rather it just carries out it's day to day metabolism.</p>\n\n<p>As far as plants are conc... |
80,685 | <p>Something that doesn't quite make sense to me is why lots of insects like ants, bees and wasps have a such a small petiole when it connects many major organs to the rest of their body from a suddenly much wider abdomen.</p>
<p>Normally from an engineering standpoint, you don't increase the width of a cantilever from a joint because the torque applied to a joint already increases with the length of an overhanging segment, so increasing the width would only multiply the torque that joint or opposing segment needs to balance. </p>
<p>It could have something to do with ants being so small that large torque isn't an issue in proportion to their body size, but if it wasn't, then why do their legs also get thinner as they measure further in length from their body? </p>
| [
{
"answer_id": 80724,
"pm_score": 4,
"text": "<p>This thin waist is called <a href=\"https://en.wikipedia.org/wiki/Petiole_(insect_anatomy)\" rel=\"nofollow noreferrer\">petiole</a> (aka. wasp‐waist).</p>\n\n<p><strong>How many times did the petiole evolve?</strong></p>\n\n<blockquote>\n <p>Why did a ... | [
{
"answer_id": 80694,
"pm_score": 1,
"text": "<p>Apocrita insects (i.e. the clade containing bee, wasps and ants) are supposed to have evolved a thin waist because it gives them more flexibility to manoeuvre their abdomen. Most Apocrita are parasitoids and they need this flexibility to parasitize theirs... |
80,886 | <p>I was trying to understand DNA transcription from <a href="http://ocw.metu.edu.tr/pluginfile.php/1184/mod_resource/content/0/Schedule/reading/ch06final.pdf" rel="noreferrer">this chapter</a>, and there seems to be no explanation on how exactly the proteins, enzymes and other molecules manage to find each other inside the cell. How do they get attracted to each other in order to start reactions or transcriptions? </p>
<p>Same way, when the body secretes a Follicle Stimulating Hormone, how does it reach the follicle instead of losing its way in the bloodstream and ending up in a woman's feet or getting excreted out of the body? In minute 20 <a href="https://www.youtube.com/watch?v=r0rRgvhNy1U" rel="noreferrer">of this video</a>, the person speaks of how medicines are first "sent" to the liver, but <a href="https://engineering.mit.edu/engage/ask-an-engineer/how-do-medicines-know-where-in-the-body-to-start-working/" rel="noreferrer">this MIT article</a> says that medicines go all over the body. </p>
<p>At least for a wound it's an understandable process. An artery of vein is severed and any blood that was supposed to flow through it now can't, so there's an accumulation of white blood cells and antibodies there which can disable any intruders (though I'm sure they wouldn't be able to see an intruder and move toward it, but rather just probabilistically bump onto the intruder), and if the intruder enters the bloodstream it would probabilistically bump into other WBC's or antibodies and get killed. Else there's always fever to kill them. </p>
<p>Similarly, one study says <a href="https://www.sciencedaily.com/releases/2003/02/030203071703.htm" rel="noreferrer">sperm use heat sensors</a> to find the egg. Another <a href="https://www.livescience.com/794-sniff-swim-sperm-find-eggs.html" rel="noreferrer">assumes it's a chemical signal</a>. </p>
<p>I went through the information about <a href="https://en.wikipedia.org/wiki/Cell_signaling" rel="noreferrer">cell signalling</a>, <a href="https://en.wikipedia.org/wiki/Signal_transduction" rel="noreferrer">signal transduction</a> and <a href="https://en.wikipedia.org/wiki/Allosteric_regulation" rel="noreferrer">allosteric regulation</a>, but although they speak about receptors, they don't explain how the chemicals manage to find those receptors. It's like saying that I entered a huge college campus and found the secret place where my friends were meeting and they receive me when I met them, but there's no explanation on how I knew which way to travel in that huge campus to reach my friends. Given how accurately DNA transcription happens and how viruses know to shed their shell on entering a cell and make use of the cell's transcription mechanism, I believe there has to be a specific process through which these molecules "know" how to find these receptors. Is there any research that could throw light on it?</p>
| [
{
"answer_id": 80897,
"pm_score": 4,
"text": "<p>The answer given by Sadegh gives a general correct broad view. But one part of the puzzle is missing, which is <a href=\"https://en.wikipedia.org/wiki/Molecular_recognition\" rel=\"nofollow noreferrer\">molecular recognition</a>.</p>\n\n<p>Molecules bind ... | [
{
"answer_id": 80893,
"pm_score": 3,
"text": "<p>It's both simple and complex. The simple answer is <strong>Brownian motion</strong>. All the particles in the cell do have mobility which is related to their mass. A small particle like a soluble enzyme undergoes random walks through the cytoplasm or nucl... |
81,499 | <p>It seems our most common everyday O<sub>2</sub> molecule happens to be a <em>paramagnetic</em> one (see <a href="https://en.wikipedia.org/wiki/Oxygen" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Oxygen</a>).</p>
<p>But, does this have a biological relevance as well? In other words, Do any chemical processes occurring within the physical volume of any entity considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties? </p>
<p>(It seems to me the answer would be "no", but I am no expert in this field!)</p>
| [
{
"answer_id": 81526,
"pm_score": 3,
"text": "<p>The answer to your re-phrased question </p>\n\n<blockquote>\n <p>\"Do any chemical processes occurring within the physical volume of any entiy considered \"living\" depend in any way, shape, or form on oxygen's paramagnetic properties? </p>\n</blockquote... | [
{
"answer_id": 81522,
"pm_score": 2,
"text": "<p>It sounds a bit like chem exam question to be honest... Or at least the answer does... namely that O<sub>2</sub> being paramagnetic creates a <a href=\"https://en.wikipedia.org/wiki/Spin-forbidden_reactions\" rel=\"noreferrer\">\"spin barrier\"</a> that p... |
81,535 | <p>I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site located on my insert, and since I am using 2 restriction enzymes in my digestion, I had little choice in choosing my restriction enzymes. The only two restriction enzymes that will work for me are Xmal and KpnI. XmaI uses CutSmart buffer while KpnI uses NEB buffer. The efficiency of XmaI in CutSmart buffer is 100% while the efficiency of KpnI in CutSmart buffer is 50%. Would it be easier to perform a double digestion using CutSmart buffer and 2x KpnI than to perform two consecutive digestions? </p>
| [
{
"answer_id": 81526,
"pm_score": 3,
"text": "<p>The answer to your re-phrased question </p>\n\n<blockquote>\n <p>\"Do any chemical processes occurring within the physical volume of any entiy considered \"living\" depend in any way, shape, or form on oxygen's paramagnetic properties? </p>\n</blockquote... | [
{
"answer_id": 81522,
"pm_score": 2,
"text": "<p>It sounds a bit like chem exam question to be honest... Or at least the answer does... namely that O<sub>2</sub> being paramagnetic creates a <a href=\"https://en.wikipedia.org/wiki/Spin-forbidden_reactions\" rel=\"noreferrer\">\"spin barrier\"</a> that p... |
81,609 | <p><strong>Warning:</strong> I have almost no knowledge of biology past the high school level.</p>
<p>Viruses generally have three components: the DNA, the virus protein coat, and an outer membrane "decorated" with these surface marker glycoproteins. I am thinking that a virus would want to infect as many hosts as possible, so that it would reproduce as much as possible, why would a virus just infect one group of organisms.</p>
<p><strong>What evolutionary advantage do viruses have in host specificity?</strong></p>
| [
{
"answer_id": 81610,
"pm_score": 4,
"text": "<p>It is true for any living creature, that it would be great for it if it could thrive in all environments. Any creature would do better if it had a greater ecological niche while remaining as competitive in each of these niches. However, competition, preda... | [
{
"answer_id": 81616,
"pm_score": 0,
"text": "<p>I would more specifically address the advantage/benefit, in that even though a virus may be host specific (or not, since it really doesn't matter in terms of gain), even the most virulent of viruses throughout history have not killed off entire species, s... |
81,639 | <p>My question here is about evidence for evolution from Embryology and from Genetics.</p>
<ol>
<li><p>Mammals do have similar Embryos, but is it the case that for each species there is an embryonic development that occurs in earlier species, has such relationship been observed?</p>
<p>What I mean for example if we generally conceive of having species<span class="math-container">$Sp_1,Sp_2,...,Sp_n$</span> where each <span class="math-container">$ Sp_{i+1}$</span> being evolved from <span class="math-container">$Sp_i,$</span> then is it the case that the embryonic development stages of <span class="math-container">$ Sp_{i+1}$</span> contains some of the embryonic development stages of all of its ancestor species.</p>
</li>
<li><p>Similar question to 1 but regarding Genetics, is it the case that every species has a genetic thumbprint of its ancestors that lie there in the non-functional sections of its DNA, i.e. is it the case that all the genetic history of our evolution is recorded in the non-functional section of our DNA. So do human DNA have some portions of the DNA of some dinosaurs for example?</p>
</li>
</ol>
| [
{
"answer_id": 81642,
"pm_score": 4,
"text": "<p>Question 1 asks whether <strong>ontogeny recapitulates phylogeny</strong>. It is striking that the when observing e.g. human embryo development, the embryo seems to go through stages that its ancestral species would go through, but where those 'lower' spe... | [
{
"answer_id": 81645,
"pm_score": 2,
"text": "<p><strong>Question 1</strong></p>\n\n<blockquote>\n <p>Mammals do have similar Embryos, but is it the case that for each species there is an embryonic development that occurs in earlier species, has such relationship been observed?</p>\n</blockquote>\n\n<p... |
81,775 | <p><a href="https://en.m.wikipedia.org/wiki/Sexy_son_hypothesis" rel="nofollow noreferrer">Sexy son hypothesis</a>.</p>
<p>It states that females are attracted to certain traits in males, because these traits will be attractive in her sons either. But isn't this circular?</p>
<p>Like "I'm attracted to that male because he is the son of an [formerly] attractive male". And you can repeat the process infinitely, going through granddad, great-granddad and so on. Doesn't this hypothesis presuppose some sexy traits that are sexy with no cause?</p>
| [
{
"answer_id": 81785,
"pm_score": 4,
"text": "<p>The process is self-reinforcing but the argument is not circular (no tautology implied).</p>\n\n<p>As soon as some male traits are considered more sexy than others, then there is selection for females to like those traits even more, which causes those tra... | [
{
"answer_id": 81786,
"pm_score": 2,
"text": "<p>Taken by itself I can agree that it might seem circular. However, in practice, all traits act and occur in a pre-existing background, i.e. in organisms with their genetic background and their living environment. All that is needed is a preexisting differe... |
82,136 | <p>I just want to understand the concept of natural selection and its relation to evolution. </p>
<p>Evolution by natural selection occurs when we have hereditary trait(s) that causes an effect on reproduction rate of a population, either towards the positive, and thus deemed as beneficial or towards the negative and thus labeled as harmful. </p>
<p>Evolution by natural selection would result in keeping the beneficial trait(s), and wiping out the harmful ones.</p>
<p>The idea according to Darwin is that the slightest harmful effect a hereditary trait(s) would bring to a population then with time it would result in extinction of the population with that trait(s). [On the origin of Species, p.78, chapter: natural selection: "On the other hand we may feel sure that any variation in the least degree injurious would be rigidly destroyed"].</p>
<p>Therefore natural selection could be viewed to result ultimately in washing out of injurious traits, and only promoting beneficial traits. So natural selection can be the cause of extinction of some genotypes, and ultimately of some species. </p>
<p>In this sense natural selection can be considered as a creative natural tool, like a rubber wiping bad intermediate solutions, and only keeping the correct steps, thereby facilitating reaching into a solution.</p>
<p>Now suppose that we have a population of living subjects with varying heritable traits on an Island, and those had equal fitness over a very long period of time, so they were pretty much adaptive to their environment. Now suppose a volcano erupted or a big comet stroked that island that ended all life in it. Lets suppose that the genotypes of that population is not present outside of that Island. So these genotypes became extinct. </p>
<p>Here this event doesn't have the same functional genre that natural selection had, it actually didn't act in a differential manner promoting those genotypes with better fitness and wiping out those with lower fitness. No it actually was NOT fitness dependent at all, it simply squashed all life forms without regards to whatever feature was brought up by the different genotypes, all were simply extinguished.</p>
<p>Now can we label this event of indiscriminative extinction to be the work of natural selection also? Or we just label it as inadvertent environmental factor?</p>
<p>If the latter, then are those inadvertent environmental factors part of the mechanism for evolution?</p>
<hr>
<p>Let me give another example:</p>
<p><strong>The beetles stochastic example</strong></p>
<p>Suppose we have a population of brown and green beetles, now suppose that we divide the place they live in into two territories A,B, now suppose that the movement of beetles across those territories is random, so at some moment of time all brown beetles happen to be in territory A, other times they have different distribution, and as said the movement pattern is totally random, i.e. there is no significant difference in the pattern of movement of both genotypes of beetles across territory A and B. Now suppose by the act of randomness a moment came where all brown beetles were located at Territory A, while some of the green beetles were in territory A and others in territory B, and suddenly came a big comet and hit territory A at that time that caused all the brown beetles to die, and also caused all green beetles on territory A also to die, but since territory B was not hit, the green beetles in B remained a life.</p>
<p>Now a moment of evolution did occur, since a change in the heritable characteristics of the beetle population did occur. But that change was merely accidental, there was no role attributable to fitness of the green beetles that resulted in their survival, it was a mere random event that caused all of the brown beetles to die. In some sense it's a kind of a stochastic environmental factor that caused that extinction. Fitness of the green beetles didn't have any role in that case of differential survival. </p>
<p>This can be called selection, it is environmental kind of selection, BUT it is NOT the outcome of differential fitness of the genotypes in that environment. </p>
<p>Now this moment in evolution is it described as an event of evolution by natural selection? </p>
<p>More broadly speaking, is it the case that any point of change in the heritable characteristics of a population (i.e. evolution) that is <em>merely</em> due to an environmental factor [like the above example], would qualify as a case of <em>evolution by natural selection</em>? or only those points where the resultant change is attributable to fitness differential that is genotype determined? </p>
| [
{
"answer_id": 82142,
"pm_score": 3,
"text": "<blockquote>\n<p>Is a change in allele frequency resulting from a catastrophe evolution by natural selection?</p>\n</blockquote>\n<p>The catastrophe itself is an example of a change in environment that brings with it a change in selective pressure. The event... | [
{
"answer_id": 82137,
"pm_score": 3,
"text": "<blockquote>\n <p>The idea according to Darwin is that the slightest harmful effect a\n hereditary trait(s) would bring to a population then with time it\n would result in extinction of the population with that trait(s).</p>\n</blockquote>\n\n<p>Citation?... |
82,339 | <p>The BBC News article <a href="https://www.bbc.com/news/world-australia-47742473" rel="nofollow noreferrer">Pink lake in Australia attracts and delights tourists</a> describes an artificial salt lake in Westgate Park, Melbourne, Australia that tuns pink around February and then in "late Autumn, until cooler temperatures restore it back to blue."</p>
<p>I am not sure about the autumn part as it's in the southern hemisphere, but my question is about the color change.</p>
<ul>
<li>Could they mean <a href="https://en.wikipedia.org/wiki/Beta-Carotene" rel="nofollow noreferrer">bet<strong>a</strong> carotene</a> rather than <a href="https://en.wikipedia.org/wiki/Beto_O%27Rourke" rel="nofollow noreferrer">beto</a> carotene? </li>
<li>And if so, does the pigment stay inside the algae or is it released into the water to produce this color change?</li>
<li>And why pink, rather than the orange color we associate with carrots?</li>
</ul>
<hr>
<p><a href="https://i.stack.imgur.com/md8jL.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/md8jL.jpg" alt="enter image description here"></a></p>
<blockquote>
<p>In those conditions, the lake's algae produces a red pigment called beto carotene</p>
</blockquote>
<p><a href="https://i.stack.imgur.com/8dY8N.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/8dY8N.jpg" alt="enter image description here"></a></p>
<blockquote>
<p>The lake's pink colour typically lasts through to late Autumn, until cooler temperatures restore it back to blue.</p>
</blockquote>
| [
{
"answer_id": 84469,
"pm_score": 3,
"text": "<p>The \"beto\" is a typing mistake. Beta is an organic chemistry label referring to a beta-ring of 6 carbons that exists at either end of a carotenoid polymer C40-Hx.</p>\n\n<p>It is localized in the chloroplast. The plants don't really have a mechanism to ... | [
{
"answer_id": 82356,
"pm_score": -1,
"text": "<p>Not sure which kind of microorganism they talk about, but bet<strong>a</strong>-carotene is a red-orange~ish pigment (as you pointed out, also produced by carrots). The pink coloration I would assume is the product of the color mixture of the pigment wit... |
82,344 | <p>Photo taken in a garden in Singapore. The organism is attached to a stone, close to water. Many of these were there.</p>
<p>Size approx 3cm. </p>
<p>The shell of this eggs is very soft. When touched, a pink colored liquid drops out.
<a href="https://i.stack.imgur.com/5yrWq.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/5yrWq.jpg" alt="Photo taken in a garden in Singapore. Size approx 3cm."></a></p>
| [
{
"answer_id": 84469,
"pm_score": 3,
"text": "<p>The \"beto\" is a typing mistake. Beta is an organic chemistry label referring to a beta-ring of 6 carbons that exists at either end of a carotenoid polymer C40-Hx.</p>\n\n<p>It is localized in the chloroplast. The plants don't really have a mechanism to ... | [
{
"answer_id": 82356,
"pm_score": -1,
"text": "<p>Not sure which kind of microorganism they talk about, but bet<strong>a</strong>-carotene is a red-orange~ish pigment (as you pointed out, also produced by carrots). The pink coloration I would assume is the product of the color mixture of the pigment wit... |
84,084 | <p><a href="https://i.stack.imgur.com/8Rd5U.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/8Rd5U.jpg" alt="Part of plant"></a></p>
<p>I found this plant in Rajasthan, India.
This sample is 4-5 cm long.
This is an ornamental plant. It was a potted plant.
I put my fingertip in the photo to give an idea of size of the specimen.
I can't figure out which plant this part belongs to.
Please give the species name if you can.
I would be very thankful to anyone out there who will help me.</p>
| [
{
"answer_id": 84087,
"pm_score": 3,
"text": "<p>This is a bit hard to say exactly, since there is a number of possibilities. We can be pretty sure that these sample is from a <a href=\"https://en.wikipedia.org/wiki/Cypress\" rel=\"nofollow noreferrer\">Cypress</a>, belonging to the family of <a href=\"... | [
{
"answer_id": 84085,
"pm_score": -1,
"text": "<p>It is called Leyland Cypress. For more details, refer the following link. <a href=\"https://en.wikipedia.org/wiki/Leyland_cypress\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Leyland_cypress</a></p>\n"
},
{
"answer_id": 95018,
... |
84,106 | <p>When I am learning about evolution I barely see any source that explains how insects, mammals, reptiles and fish came to be. Can someone show me a source where I can learn about this? Especially insects and mammals - I want to know how those 2 distinct group came to be.</p>
<p>And I have a related question: can a fly evolve into a rabbit given enough time with the necessary condition? (I know the question sound stupid but please can someone explain me that)</p>
<p>I have a layman understanding of evolution. So please can any of your source or explanation be simple? Thank you.</p>
| [
{
"answer_id": 84120,
"pm_score": 2,
"text": "<p>Re a fly evolving into a rabbit, theoretically yes, practically no. Insects (and invertebrates in general) made some evolutionary \"choices\" like having an exoskeleton & breathing through trachea that put serious limits on their maximum size. (And ... | [
{
"answer_id": 84109,
"pm_score": 2,
"text": "<p>Insects and mammals diverged from one-another over 500 million years ago. For most of Earths 4.5 billion year history, life was single-celled, or organized into colonies of single-celled organisms. Likely sometime shortly before the Cambrian, multicellula... |
84,129 | <p>After performing a PCR, I ran the products (700 bp) in an agar gel electrophoresis along with a Genedirex ladder (100 bp), but the transilluminator did not reveal them.</p>
| [
{
"answer_id": 84120,
"pm_score": 2,
"text": "<p>Re a fly evolving into a rabbit, theoretically yes, practically no. Insects (and invertebrates in general) made some evolutionary \"choices\" like having an exoskeleton & breathing through trachea that put serious limits on their maximum size. (And ... | [
{
"answer_id": 84109,
"pm_score": 2,
"text": "<p>Insects and mammals diverged from one-another over 500 million years ago. For most of Earths 4.5 billion year history, life was single-celled, or organized into colonies of single-celled organisms. Likely sometime shortly before the Cambrian, multicellula... |
84,132 | <p>All around us we hear and read articles which suggest that soft drinks or carbonated beverages are acidic and damage our body but we still consume them (or atleast a significant proportion of us do). Why doesn't consuming such drinks during a bacterial infection in stomach help to kill all the bacteria?</p>
| [
{
"answer_id": 84178,
"pm_score": 2,
"text": "<p>I don’t know if soft drinks can help ward off bacterial infections in the stomach, however if you’re not taking antibiotics, other acidic compounds can be helpful for that. One of these is apple cider vinegar, you will find many videos on youtube about it... | [
{
"answer_id": 84137,
"pm_score": -1,
"text": "<p>Carbonic acid (H2CO3) itself in the human body is not stable and falls apart to water and carbon dioxide. When you consume anything by eating/drinking it and swallowing it via the gastro-instestinal tract, it does not enter your bloodstream directly but ... |
84,483 | <p>If mitochondria exist at random within a cell, isn't there a possibility that cell division will result in a daughter cell with no mitochondria? If not, what is the process for guaranteeing at least one is present in each daughter cell? If so, what happens to that cell?</p>
| [
{
"answer_id": 84484,
"pm_score": 6,
"text": "<blockquote>\n <p>Isn't there a possibility that cell division will result in a daughter\n cell with no mitochondria?</p>\n</blockquote>\n\n<p>Yes, there is always the possibility. However, there must be a strong negative selection pressure against eukaryo... | [
{
"answer_id": 84493,
"pm_score": 4,
"text": "<p>In addition to S Pr's excellent example, I wanted to point out that some very recent research describes some special behavior in oocyte development specifically related to mitochondria selection.</p>\n\n<p>Here's a easy-to-read version:\n<a href=\"https:/... |
84,485 | <p>I am trying to determine the bare minimum nutritional requirements to survive as a human, ignoring energy (caloric) requirements. Another way to ask this question is: What elements can humans not live without? I am not inquiring solely about <strong>what</strong> nutrients are needed, but also their approximate amounts.</p>
<p>Imagine pills that a person can take that covers all their base nutritional needs and that after taking this pill the person can eat whatever they want to meet their caloric requirements. Hypothetically, this pill could have some amount (how much?) fat, carbohydrates, protein, fiber, minerals, and vitamins, and the person could subsequently eat any other food to meet their caloric requirements knowing their nutritional needs would already be otherwise met. Lets ignore the possibility of the person suffering from health issues due to eating too much of any specific food to meet their caloric requirements (e.g., taking the magic pills and then eating only butter).</p>
<p>A person in this situation could think "Ok I've got most of my bases covered, now I just need to ingest another 1000 calories of (almost) anything I want).</p>
<p>What nutrients are absolutely necessary for humans to survive indefinitely, and how much of these nutrients are required?</p>
<p>I am hoping for a complete list with approximate amounts (e.g., 20g fat, 20g carbohydrates, 1mg Vitamin X, .05mg Vitamin Y, 10mg mineral X).</p>
| [
{
"answer_id": 84513,
"pm_score": 4,
"text": "<p><strong>Essential nutrients</strong> include (<a href=\"http://www.nutrientsreview.com/glossary/essential-nutrients\" rel=\"nofollow noreferrer\">NutrientsReview</a>):</p>\n\n<ul>\n<li>Water</li>\n<li>9 amino acids: histidine, isoleucine, leucine, lysine,... | [
{
"answer_id": 84486,
"pm_score": 2,
"text": "<p>You are not going to get an exact number because of variation in body mass, age, sex, and metabolism. life style also has a huge effect,what someone doing hard labor needs is vastly different that what a comatose person needs. Minimums are harder because... |
84,670 | <p>I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?</p>
| [
{
"answer_id": 85078,
"pm_score": 3,
"text": "<p>Artifacts are variations introduced by non-biological processes. Sequencing involves a lot of chemical reactions, and changes in nucleotides that can seem like mutations are really introduced somewhere in the processing of the sample. That's what we call ... | [
{
"answer_id": 85074,
"pm_score": 2,
"text": "<p>I believe an artifact is something that appears in the first analysis but is not actually present in the sample. You would want to sort out all of the artifacts so that your final analysis is accurate. </p>\n"
},
{
"answer_id": 85087,
"pm_scor... |
84,786 | <p>Crows are surprisingly clever with tool making/use and even understanding displacement water <a href="https://www.youtube.com/watch?v=ZerUbHmuY04" rel="nofollow noreferrer"><em>over sand!</em></a> Clearly there's some relatively high level cognitive processes going on up in those avian brains.</p>
<p>When I stumbled across a video of what appears to be <a href="https://www.dropbox.com/s/be1fifxwg27wu5n/grieving%20bird.webm?dl=0" rel="nofollow noreferrer">a bird grieving over its mate</a> (shown in clip below), I wondered how far animal emotion and psychology goes.</p>
<p><a href="https://i.stack.imgur.com/H9ccT.gif" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/H9ccT.gif" alt="enter image description here"></a></p>
<ul>
<li>Is that bird in the video grieving? (and shaking because of stress?)</li>
<li>What species of bird is this?</li>
</ul>
| [
{
"answer_id": 84802,
"pm_score": 4,
"text": "<p>Your "grieving bird" is a video of a <strong>peregrine falcon <a href=\"https://en.wikipedia.org/wiki/Peregrine_falcon\" rel=\"nofollow noreferrer\">(<em>Falco peregrinus</em>)</a></strong> and its (nearly?) dead chick on a hot summer day in Pho... | [
{
"answer_id": 84826,
"pm_score": -1,
"text": "<p>There seems to be a long folk tradition that birds do grieve:</p>\n<blockquote>\n<p>“All the birds of the air fell</p>\n<p>a-sighing and a-sobbing</p>\n<p>when they heard the bell toll</p>\n<p>for poor Cock Robin”</p>\n</blockquote>\n<p>See the Wikipedia... |
85,237 | <p>In the <a href="https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data" rel="nofollow noreferrer">price curve of the genome, from NIH</a>:</p>
<p><a href="https://i.stack.imgur.com/tQeTv.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/tQeTv.png" alt="price curve"></a></p>
<p>NIH explained the abrupt drop at 2008 thusly:</p>
<blockquote>
<p>beginning in January 2008... the sequencing centers transitioned from Sanger-based (dideoxy chain termination sequencing) to 'second generation' (or 'next-generation') DNA sequencing technologies.</p>
</blockquote>
<p>The NIH did not give any details as to why there was a similarly precipitous drop in 2015, or why there was such a saddening (for me!) plateau after that. Please explain them to me?</p>
| [
{
"answer_id": 85359,
"pm_score": 4,
"text": "<p>This graph from the <a href=\"https://www.broadinstitute.org/blog/opinionome-can-dna-sequencing-get-any-faster-and-cheaper\" rel=\"noreferrer\">Broad's <em>Opinionome</em> blog</a> (ugh) is somewhat more annotated:</p>\n\n<p><a href=\"https://i.stack.imgu... | [
{
"answer_id": 85241,
"pm_score": 2,
"text": "<p>The graph is in contradiction with the data in the Excel spreadsheet the same webpage provides (<a href=\"https://www.genome.gov/sites/default/files/media/files/2019-06/Sequencing_Cost_Data_Table_Feb2019.xls\" rel=\"nofollow noreferrer\">https://www.genom... |
85,457 | <p>Is the term "cistronic", meaning an ORF on a mRNA, still commonly used in modern genetics? I´ve seen "polycistronic" being applied to prokaryotic mRNA in old textbooks, but I´ve rarely stumbled upon this in recent papers, except for research focusing on plasmid engineering.</p>
| [
{
"answer_id": 85464,
"pm_score": 4,
"text": "<p>The thing that I think biologically interesting about this question has perhaps not been emphasized sufficiently in the answers so far which document <strong>that</strong> the term is still in use. This is <strong>why</strong> the term is still in use. As... | [
{
"answer_id": 85458,
"pm_score": 3,
"text": "<p>Yes, it's still used. </p>\n\n<p>If you search <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=polycistronic\" rel=\"nofollow noreferrer\">Pubmed for \"polycistronic\"</a>, it offers you a chart showing the counts of the term by year (top right). Dow... |
85,476 | <p><a href="https://i.stack.imgur.com/CVh6s.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/CVh6s.jpg" alt="wasp picture"></a></p>
<p>Yesterday while moving a chair in my garden I got stung by a group of wasps. During the night I went hunting for their nests and managed to neutralize 3 of them: one was in the chair's legs, about the size of a child's fist and with a dozen on them inside. It was made of grey hexagonal cells, similar to paper in appearance.</p>
<p><a href="https://i.stack.imgur.com/xo9qQ.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/xo9qQ.jpg" alt="Nasty"></a>
(Sorry for the blurry image, I was a bit scared :-P)</p>
<p>Then I've found another one in a water hose tube that was slightly smaller, but quite active.</p>
<p>And finally a third one in a vase, it was very small, only had a couple of cells in it and wasps were working on it, almost as if they were building it from scratch.</p>
<p>Given the number and size of the nests I'm afraid that they could be spreading in the garden. I have already noticed that a couple of them survived the massacre of last night and I'm worried that unless I kill every of them they might keep nesting.</p>
<p>I don't know much about the hierachical society of wasps, but I was not able to identify the queen (although I haven't checked every single one I've killed). Reading online I've found that killing the queen might mean that the worker would eventually die.</p>
<p>So what kind of wasp is this? What can I do to make sure that they do not keep bothering me?</p>
<p><strong>EDIT</strong>: by the way, I live in northern Italy</p>
| [
{
"answer_id": 85478,
"pm_score": 5,
"text": "<p>These are <a href=\"https://en.wikipedia.org/wiki/European_paper_wasp\" rel=\"nofollow noreferrer\">European paper wasps</a>. </p>\n\n<p>(They look very similar to <a href=\"https://en.wikipedia.org/wiki/Yellowjacket\" rel=\"nofollow noreferrer\">yellowja... | [
{
"answer_id": 85488,
"pm_score": 0,
"text": "<p>To keep these pests away from your house and other areas, on the underside facing up use a sky blue paint, along soffits, including the bottom of some patio furniture. When these see the sky blue they think its the sky and will go some place else to build... |
85,643 | <p>I've heard most non-subsaharan africans have neanderthal DNA with it being more prevalent in northern regions, that sometimes 1-4% of the DNA has neanderthal origins. </p>
<p>Speaking strictly scientifically, would it be possible through selective breeding to breed an individual where the majority of the DNA is neanderthal? </p>
| [
{
"answer_id": 85644,
"pm_score": 4,
"text": "<p>No, it is not. As you said only 1-4% of non-subsaharan africans' genome is from Neanderthal and it is more or less the same sequences. The entire Neanderthal genome is not present in modern day humans, it is only a small set of sequences.</p>\n"
}
] | [
{
"answer_id": 85645,
"pm_score": 2,
"text": "<p>Selective breeding will select for genetics that are already present in your population, but won't introduce new DNA sequences that aren't carried by any of the population members. It would technically be possible if everyone carried a different 1-4% of t... |
85,723 | <p>And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ?</p>
<p>Moreover, I've read that knowing the structure of a protein helps predicting its function, but is the prediction [Structure -> Function] reliable ? Should't we predict directly the function if that's our interest (I don't mean we should not take into account predicted structure, but I don't understand why the structure IS the purpose instead of the function)
I also read the structure helps predicting affinities with other proteins and how it will bind : same question here, is this prediction [Structure -> Affinity] reliable and why don't we predict directly affinities.</p>
<p>To sum up a bit, I have the impression that the structure in itself is not important to know except that it is a good predictor of other protein properties (like function of affinity) and that the structure is kind of an 'intermediate' ? What am I missing ?</p>
| [
{
"answer_id": 85727,
"pm_score": 3,
"text": "<p>How do you want to predict function and binding partners without knowing how your protein looks like? The sequence itself contains only limited information. Similar sequences might fold into similar structures with similar functions. These <a href=\"https... | [
{
"answer_id": 85724,
"pm_score": 1,
"text": "<p>There are several reasons why understanding protein structure is useful; the most obvious is that drugs that interfere with a specific protein can be deliberately designed based on the protein structure.</p>\n\n<blockquote>\n <p>Today, even though there ... |
85,915 | <p>In <a href="https://apps.who.int/iris/bitstream/handle/10665/149782/9789241549028_eng.pdf" rel="noreferrer">this paper</a> of the WHO, it is claimed that we should limit our consumption of free sugars:</p>
<blockquote>
<p>WHO recommends a reduced intake of free sugars throughout the
lifecourse. [...] <br/> Free sugars include monosaccharides and
disaccharides added to foods and beverages by the manufacturer, cook
or consumer, and sugars naturally present in honey, syrups, fruit
juices and fruit juice concentrates.</p>
</blockquote>
<p>At first, I was wondering if the sugars in a fruit can be different from sugars in a juice. According to the answer to <a href="https://chemistry.stackexchange.com/questions/118451/what-is-the-difference-between-the-sugar-in-a-fresh-fruit-and-the-sugar-in-a-jui">my question here</a>, the sugar molecules are exactly the same in both (in the case of a 100% pure juice).</p>
<p>So, why this recommendation? Why doesn't our body digest sugars from fresh fruit the same way as sugars from juice? To make it simple, my question only concerns 100% pure juice with no added sugars.</p>
<p>I tried to find an answer and, according to the answers of <a href="https://biology.stackexchange.com/questions/38739/how-is-sugar-in-fruit-metabolized-or-digested-and-used">this question</a>, because our body is slow to digest sugars from a fruit, it assimilates it better. Is it right? And, if it is the case, if we eat fiber and starch with our fruit juice, it should be the same as a fresh fruit, right?</p>
| [
{
"answer_id": 85916,
"pm_score": 7,
"text": "<p>Sugars in 100% natural fruit juices are chemically the same as in whole fruits. They mainly include glucose, fructose and sucrose:</p>\n\n<ul>\n<li><a href=\"https://nutritiondata.self.com/facts/fruits-and-fruit-juices/1809/2\" rel=\"noreferrer\">Apple</a... | [
{
"answer_id": 85941,
"pm_score": 3,
"text": "<p>Drinking the juice without the fruit can easily lead to over-consumption. It is after all harder to eat four apples than drinking 500ml apple juice.\nAs the liver breaks the fructose through <a href=\"https://www.health.harvard.edu/heart-health/abundance-... |
85,983 | <p>At about 11 pm, I heard a loud impact on the nearby glass door to a second-floor balcony. I thought it might be an acorn but it'd be a very unlikely angle - it'd have to be thrown from below or be a very strange ricochet.</p>
<p>So I looked and encountered this rather impressive creature recovering on the balcony:
<a href="https://i.stack.imgur.com/kmD3W.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/kmD3W.jpg" alt="enter image description here"></a>
Those planks are six inches wide.</p>
<p>I've never seen one of these before. What is it? Are those giant serrated appendages on the front mandibles or antennae? </p>
<p>I expect it's not as hazardous as it looks, but is there any risk of it biting people or pets?</p>
<p>Do they routinely launch themselves two stories into the air, or would it have crawled up and then just bounded from the balcony floor?</p>
<p>Location: Southern Oregon, USA.</p>
| [
{
"answer_id": 85916,
"pm_score": 7,
"text": "<p>Sugars in 100% natural fruit juices are chemically the same as in whole fruits. They mainly include glucose, fructose and sucrose:</p>\n\n<ul>\n<li><a href=\"https://nutritiondata.self.com/facts/fruits-and-fruit-juices/1809/2\" rel=\"noreferrer\">Apple</a... | [
{
"answer_id": 85941,
"pm_score": 3,
"text": "<p>Drinking the juice without the fruit can easily lead to over-consumption. It is after all harder to eat four apples than drinking 500ml apple juice.\nAs the liver breaks the fructose through <a href=\"https://www.health.harvard.edu/heart-health/abundance-... |
86,022 | <p>In my city park there are mostly two types of bird:</p>
<ul>
<li>Mallard ducks</li>
<li>Rock doves (pigeons)</li>
</ul>
<p>When I feed pigeons, they approach me very closely. Sometimes they peck the food that fell on my feet. If I hold my hand with food in the air some pigeons will land on my hand and eat.</p>
<p>In the same park there are Mallards, who are always very cautious and they try to maintain about 1-1.5 meters distance from me. They also run away when they see some rapid movement of mine.</p>
<p>Why are ducks more cautious? Why are pigeons more careless?</p>
| [
{
"answer_id": 89757,
"pm_score": 2,
"text": "<p>A possible reason is that pigeons in a city <a href=\"https://www.audubon.org/field-guide/bird/rock-pigeon\" rel=\"nofollow noreferrer\">live there year around</a>, while <a href=\"https://www.audubon.org/field-guide/bird/mallard\" rel=\"nofollow noreferr... | [
{
"answer_id": 97271,
"pm_score": -1,
"text": "<p>This could be due to the fact that mallards are wild animals, whereas, although they may appear to be, ferral pigeons/rock doves, are not. They are, as the name suggests, ferral. Meaning they were once domesticated and then their ancestors were set free ... |
86,309 | <p>It's a reasonably well-known fact that insects grew to massive sizes due to the excessive concentration of oxygen in the prehistoric-Earth's atmosphere.</p>
<p><strong>If one were to try to recreate this high-oxygen environment in a lab setting, would insects reared within grow to massive size?</strong></p>
| [
{
"answer_id": 86330,
"pm_score": 4,
"text": "<p>While @CalendarJ comments \"Yep!\" above, a quick search suggests that experimental hyperoxia typically only increases insect body sizes <em>slightly</em>. Everything below is from VandenBrooks et al. 2012 (of course there could be other sources that cont... | [
{
"answer_id": 86310,
"pm_score": 2,
"text": "<p>The latest documentary I watched about the Meganeura (a giant Dragonfly from Pre-Cambrian) seems to confirm your intuition.</p>\n\n<p>Based on experiments by John VandenBrooks at Midwestern University, with bugs in conditions A with less oxygen than curre... |
86,417 | <p>Are there any studies that point out that we could have a device in the future or drug that could give us endless amount of pleasure by stimulating or blocking processes in the brain or nerve system? </p>
<p>Drugs and alcohol end up saturating receptors in the brain. Is it known inside out how this mechanism of rewards / saturation / abstinence work in the brain and how it relates to consciousness? </p>
<p>It is well known that you cannot have the same amount of pleasure by repeating the same action over and over again but is it truly known how that works? Would it be possible to reset the receptors in the brain to accomplish this?</p>
| [
{
"answer_id": 86442,
"pm_score": 3,
"text": "<p>Of course. </p>\n\n<p>There is a famous set of experiments (<a href=\"https://web.stanford.edu/group/neurostudents/cgi-bin/wordpress/?p=3733\" rel=\"nofollow noreferrer\">Milner & Olds</a>) in biology that basically started modern behavioral research ... | [
{
"answer_id": 86421,
"pm_score": 1,
"text": "<p>What we call pleasure is effectively the way that we have evolved brains that learn to do what promotes survival and reproduction. Animals get pleasure when we do things that contribute to our survival and reproduction, like eating certain foods or mating... |
87,718 | <p>Everywhere I look online says the brain is about 60% fat. But when it comes to water, I see numbers like 70-75%. One webpage even makes both those claims back to back! That doesn't make any sense. So what is it, really?</p>
| [
{
"answer_id": 87721,
"pm_score": 4,
"text": "<p>Whenever you see a percentage, you should think \"Percentage of what?\". Not doing this is usually at the root of the trouble people get into with percentages.</p>\n\n<p>The water and fat percentages mentioned in the question are certainly not percentage... | [
{
"answer_id": 87727,
"pm_score": 0,
"text": "<p>mgkrebbs is totally right. It's standard in biology to evaporate the water to get the wet/dry weight, and then to see for the rest. This study is old so it may lack accuracy:</p>\n\n<p><a href=\"https://i.stack.imgur.com/EsA1u.jpg\" rel=\"nofollow norefer... |
88,338 | <p>It is an often-repeated claim that human, and in fact all animal blood is salty because we evolved from aquatic organisms, and that blood has a similar concentration of salts as ocean water, or at least as primordial ocean water. </p>
<p>Is any of that true? Does science know what the salinity of the oceans was billions of years ago, and was it indeed similar to the blood of today's organisms? Does that knowledge prove anything about evolution and the origin of life?</p>
<p>I am wondering, because I tried to Google for the answers, and unfortunately all I could find were creationists referencing each other how it couldn't possibly be true because evolution is a lie in the first place etc., and they claim that there is no empirical research that would compare salinity levels of organims' cells and ocean water.</p>
| [
{
"answer_id": 88339,
"pm_score": 7,
"text": "<p><strong>Short answer</strong><br>\nEarly sea water had a very different <a href=\"https://en.wikipedia.org/wiki/Plasma_osmolality\" rel=\"noreferrer\">osmolality</a> than blood plasma.</p>\n\n<p><strong>Background</strong><br>\nThe reference range of seru... | [
{
"answer_id": 88355,
"pm_score": 2,
"text": "<p>Even shorter answer: This can be easily (well, not <em>that easily</em> since you need to convert mols to milligrams) answered by looking at your last lab result.</p>\n\n<p>Say you had <code>Na: 135 mmol/ml</code> on there which would be a plausible value... |
88,417 | <p>In "The Red Queen", Matt Ridley frequently argues that evolution is a means to an end, without providing much explanation for such a big statement.</p>
<p>Is this a fact in biology? Do species mutate their genes so they can reach an optimum state, like the coelacanth fish that (allegedly) remained unchanged for the last 300 hundred million years?</p>
| [
{
"answer_id": 88424,
"pm_score": 4,
"text": "<p>Good question--I think the first point to address is \"a means to an end\" seems to imply <em>willful action</em>. That is, evolution (according to Ridley) would be a conscious effort by a species to optimize the gene pool for survival of future generatio... | [
{
"answer_id": 88431,
"pm_score": 2,
"text": "<p>In a comment I ask you for specific passages that give you this impression (since when I read The Red Queen I came away with the opposite impression). You provided the following quote.</p>\n\n<blockquote>\n <p>in my 2003 copy published by Harper Perennia... |
89,056 | <p>What is meant by functional unit of a system?</p>
<p>Like when we say that the neuron is the basic unit of neural system, do we mean that all those things that are performed by neural system can be performed by an isolated neuron?</p>
<p>If yes, how? And if not, then why do we call it as functional unit of neural system?</p>
<p>Like we say hepatic lobule functional unit of the liver is not hepatocytes, because we say that liver has complex functions, and single hepatocytes cannot perform it. So the functional unit of liver is the hepatic lobule.</p>
<p>Basically I am asking can a single neuron perform the most complex functions of neural system: like memory storage, control and coordination (to a smaller extent) regulation of a cell.</p>
<p>How can a single neuron control or regulate another cell, because wouldn't it need other neurons for processing of stimulus?</p>
<p>Can an isolated neuron process any stimulus and make other cell to respond in some way? If not so why we call it the functional unit of neural system?</p>
| [
{
"answer_id": 89060,
"pm_score": 4,
"text": "<p>In biology, <strong>functional unit of a system</strong> refers to the smallest structural element that is capable of performing the tasks typical for that system (<a href=\"https://books.google.com/books?id=4Gr43yYwauMC&pg=PA131&lpg=PA131&dq=... | [
{
"answer_id": 89061,
"pm_score": 2,
"text": "<p>\"Functional unit\" doesn't have a very specific meaning. It's mostly a term used to help biology students imagine organs as collections of parts.</p>\n\n<p>The entities named functional units in a textbook don't typically perform every single function of... |
89,382 | <p>At the moment I'm especially interested in the question of whether biological sex is really a spectrum. Unfortunately I could not find any good answers on the Internet. Therefore I hope that some of you might be able to present the current state of science here and whether it is already generally accepted in biological science that sex is a spectrum.</p>
<p>What I am confused about here is for something to be a spectrum it must have some some sort of distribution along a parametrised scales. For example, it would be daft to think height to be binary even though there are tall people and short people. Tall and short are relative; height is defined by a continuous factor, length, measured (for example in cm) from foot to head. There is no such parameter that can be used to show that male and female are relative in the way that tall and short are. There is no scale. What I thought is that it relies on the binary to classify gonads as either male or female. So, people with disorders of sex development are still either male or female due to the presence of gonads (which define sex) if I understood correctly. There are only two gonad types since this is the fundamental feature of what sex is. I hope someone can correct me here, if this is wrong.</p>
| [
{
"answer_id": 89393,
"pm_score": 1,
"text": "<p>Scientists Fred P. Thieme and William J. Schull of the University of Michigan wrote about sexing a skeleton in 1957: “Sex, unlike most phenotypic features in which man varies, is not continuously variable but is expressed in a clear bimodal distribution.”... | [
{
"answer_id": 89397,
"pm_score": 4,
"text": "<p>First gender and sex are not the <a href=\"https://www.who.int/genomics/gender/en/index1.html\" rel=\"noreferrer\">same thing</a>; as an old teacher of mine glibly put it, \"sex is plumbing, gender is clothing,\" and even that is a gross generalization. T... |
89,492 | <p>Let’s say you have the following DNA sequence fragment: </p>
<pre><code>5’-ACCAGTACTTCGT-3’
3’-TGGTCATGAAGCA-5’
</code></pre>
<p>Is there any way to determine which strand is the template strand and which is the coding strand for RNA synthesis solely from the above information?</p>
| [
{
"answer_id": 89502,
"pm_score": 3,
"text": "<p>Given a DNA sequence alone, you can annotate <a href=\"https://en.wikipedia.org/wiki/Open_reading_frame\" rel=\"noreferrer\">open reading frames</a> (ORFs) in order to identify the coding strand, with the caveat that not all ORFs are genes. ORFs are sequ... | [
{
"answer_id": 89501,
"pm_score": 1,
"text": "<p>I don't know about your specific example (perhaps look for triplets that code start codons?), but machine learning has been used to predict promoters from sequence information (from promoter regions, you get downstream initiation of transcription of DNA t... |
90,095 | <p>A number of countries are using test kits for detecting new cases of nCoV (2019-Coronavirus) and apparently China is running low. </p>
<p><strong>What exactly is in a nCoV "Test Kit" — How does it work?</strong></p>
<p>(Surely they also differ, so in which way do they differ?)</p>
| [
{
"answer_id": 90096,
"pm_score": 7,
"text": "<p>The CDC has made available online its <a href=\"https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html\" rel=\"noreferrer\">nCoV test kit</a>. Briefly,the kit contains primers and probes for real-time reverse-transcriptase PCR, a... | [
{
"answer_id": 90134,
"pm_score": 5,
"text": "<p>There are actually 3+ types of test kits widely used to diagnose diseases caused by viruses. We can check for the nucleic acid of the virus, the antigen of the virus that would cause an immune response or the antibody produced during the immune response o... |
90,752 | <p>I am confused about the needed ratio of bleach to water required to disinfect COVID-19 from surfaces.</p>
<p>The guide on CDC states that: <a href="https://www.cdc.gov/coronavirus/2019-ncov/community/home/cleaning-disinfection.html" rel="nofollow noreferrer">https://www.cdc.gov/coronavirus/2019-ncov/community/home/cleaning-disinfection.html</a></p>
<blockquote>
<p>Diluted household bleach solutions can be used if appropriate for the surface. Follow manufacturer’s instructions for application and proper ventilation. Check to ensure the product is not past its expiration date. Never mix household bleach with ammonia or any other cleanser. Unexpired household bleach will be effective against coronaviruses when properly diluted. </p>
<p>Prepare a bleach solution by mixing: </p>
<p>5 tablespoons (1/3rd cup) bleach per gallon of water or </p>
<p>4 teaspoons bleach per quart of water</p>
</blockquote>
<p>This is a 2% ratio. My problem is that it is not clear what "bleach" means. Chemically I guess it's <a href="https://en.wikipedia.org/wiki/Sodium_hypochlorite" rel="nofollow noreferrer">Sodium hypochlorite</a>. What's not clear is that what is the strength of the solution I can buy in shops.</p>
<p>Wikipedia states that bleach in stores can be anything between 3-25%.</p>
<p>Does CDC recommend the final strength of Sodium hypochlorite : water to be 2% or "bleach in stores" : water to be 2% (which can be anything between 0.06% - 0.5%</p>
<p>Disregarding this confusing CDC direction: <strong>What is the scientific recommendation for the required sodium hypochlorite : water ratio needed for disinfecting COVID-19 from surfaces?</strong></p>
| [
{
"answer_id": 92189,
"pm_score": 3,
"text": "<p>Perhaps I can help answer your microbiology question which is really about SARS-CoV-2 which is an enveloped mRNA virus. There is a lot of misunderstanding about SARS-CoV-2 and the medical disease it causes, COVID-19. The confusion is understandable as thi... | [
{
"answer_id": 90760,
"pm_score": 3,
"text": "<p>I have also been frustrated by use of percentages in protocols when making dilutions of stock bleach. It's helpful to look at the product labels, as they often have dilution factors for different uses as well as concentrations in parts per million. </p>... |
90,793 | <p>A couple of colleagues suggested in a discussion that the virus that causes COVID-19 appears to be made by humans, since nature could not have produced such an efficient virus — that spreads so fast and whose patients are contagious quite some time before showing signs of infection.</p>
<p>Since my knowledge of biology is very limited, my only counterargument for such a conspiracy theory was along the following lines:</p>
<ul>
<li><p>there is a consensus that the most probable source of the first infection was in an animal market in China.</p></li>
<li><p>since that animal market was actually composed of a plethora of animals belonging to various species (mixed with humans), a virus had a bigger chance of evolving a mutation that might infect an individual from another species (a thing that is way less unlikely in the wild since many of those animals do not sit close to each others or next to humans).</p></li>
</ul>
<p>Clearly, I have made a little story that might be quite far away from how SARS-CoV-2 infected humans, so I am interested in a scientific arguments to support my cause.</p>
<p><strong>Question:</strong> What are the main scientific arguments that can be used to debunk COVID-19 being engineered by humans?</p>
<p>Answers that also include explanations more accessible to laymen are greatly welcomed.</p>
| [
{
"answer_id": 90796,
"pm_score": 8,
"text": "<p>At the moment, there is very little scientific literature about this, but I found two papers that address the problem and are fairly easy to understand. You can find them in the references. Reference 1 is probably the most interesting and is the basis for... | [
{
"answer_id": 90903,
"pm_score": 5,
"text": "<p>If you need more [counter]evidence, there's a <a href=\"https://www.nature.com/articles/s41591-020-0820-9\" rel=\"noreferrer\">newer paper</a> "The proximal origin of SARS-CoV-2" by Andersen et al. (March, 17) that touches on the same topic.\nTh... |
90,912 | <p>All news I can see scientist telling that the SARS-CoV-2 virus survive more in <strong>cold and dry weather</strong>. I can understand cold as hot weather will desiccate virus, but why dry weather.</p>
<p>Would not dry weather dry droplets of saliva sooner also desiccate virus, would not humid weather support virus?</p>
| [
{
"answer_id": 91129,
"pm_score": 2,
"text": "<p>So I found this information regarding humidity from an article by MIT on corona:</p>\n\n<p>1) <strong>High humidity</strong> leads to condensation of sneezing cough saliva particles sooner, so it does not spread to farther distance</p>\n\n<p>2) <strong>Lo... | [
{
"answer_id": 90926,
"pm_score": 3,
"text": "<p>I found an answer to this mystery in the literature, but it is a somewhat tentative explanation from a relatively recent (2012) <a href=\"https://doi.org/10.1371/journal.pone.0046789\" rel=\"noreferrer\">paper</a> by Yang et al. In a nutshell, [respirator... |
90,962 | <p>Can one be immune to the new coronavirus?</p>
<p>Another question is what is the exact definition of "being immune". Does it mean that even when the virus enters my system, it cannot multiply?</p>
| [
{
"answer_id": 90969,
"pm_score": 6,
"text": "<p>It is hypothesized that exposure to and recovery from SARS-CoV-2 (as with other coronaviruses in humans) would generally result in short-term immunity to this strain, but we do not yet have data on this:</p>\n<blockquote>\n<p>However, according to Dr Step... | [
{
"answer_id": 90965,
"pm_score": 3,
"text": "<p>No, you cannot be immune to the virus, if you haven't been in contact with it before. You are also not immune to the influenza viruses (flu), you just happened to not contract any of them.</p>\n\n<p>Simply speaking, being immune means that your immune sys... |
92,436 | <p>It was recently reported that a handful of tigers and lions tested positive at the Bronx Zoo for SARS-CoV-2 (see <a href="https://www.bbc.com/news/world-us-canada-52177586" rel="nofollow noreferrer">here</a> and <a href="https://www.forbes.com/sites/judystone/2020/04/05/nadia-a-tiger-at-the-bronx-zoo-is-ill-with-covid-19/#40c93a066ac2" rel="nofollow noreferrer">here</a>). Does this imply that the SARS-CoV-2 strain in humans mutated into a form that can infect these other species? I thought these sorts of mutations required a long time and prolonged contact between the species (which I wouldn't have thought would be present with such large cats).</p>
<p>Alternatively, is it possible that a single strain of the virus is capable of infecting multiple species?</p>
| [
{
"answer_id": 92458,
"pm_score": 5,
"text": "<p>A partial answer, to the question of how the virus might spread to animals I found several references</p>\n<ul>\n<li><p>The <a href=\"https://www.nature.com/articles/s41586-020-2334-5_reference.pdf\" rel=\"nofollow noreferrer\">HongKong dogs</a>, the New ... | [
{
"answer_id": 92448,
"pm_score": 1,
"text": "<p>A single strain of virus (such as rabies) can infect multiple species of hosts.</p>\n\n<p>The big question is whether domestic cats also get infected? \nIf they do, two main problems.\nThere would be a reservoir of virus circulating in cats allowing reinf... |
92,444 | <p>I was watching a <a href="https://www.youtube.com/watch?v=7Hk9jct2ozY" rel="nofollow noreferrer">DNA transcription video</a> when I realized that cells basically create copies of DNA all the time in our body. There may be a few mutations/errors, but it works out fine. However, when the haploid DNA in sperm combines with the one in the egg, there's so much extra work to be done to avoid errors. It's like if I write some software in one project and try to combine it the code I've written in another project, it's easier for me to do it because my coding style is similar and I know the code. But if I have to merge somebody else's code into my code, there would be a heck of a lot of merge conflicts and errors. Sure, I may learn better programming from the other person's efficient code, but the amount of bugs, testing etc. will be much more cumbersome. </p>
<p><a href="https://en.wikipedia.org/wiki/Inbreeding#Overview" rel="nofollow noreferrer">Some research</a> says: </p>
<blockquote>
<p>Malformations or harmful traits can stay within a population due to a
high homozygosity rate, and this will cause a population to become
fixed for certain traits, like having too many bones in an area, like
the vertebral column of wolves on Isle Royale or having cranial
abnormalities, such as in Northern elephant seals, where their cranial
bone length in the lower mandibular tooth row has changed. Having a
high homozygosity rate is problematic for a population because it will
unmask recessive deleterious alleles generated by mutations, reduce
heterozygote advantage, and it is detrimental to the survival of
small, endangered animal populations. When deleterious recessive
alleles are unmasked due to the increased homozygosity generated by
inbreeding, this can cause inbreeding depression.</p>
</blockquote>
<p>But <a href="https://en.wikipedia.org/wiki/Inbreeding#Wild_animals" rel="nofollow noreferrer">bed bugs for instance</a>, have managed with inbreeding without any problem (goddamned creatures!). </p>
<p>The question I'm asking is from the perspective of how the DNA combination and copying happens. Since the regions chosen during meiosis is random, shouldn't a similar DNA from sperm and egg resulted in a more stable genetic code since they are similar? I'm not looking for simplistic answers like "because Nature wanted diversity" or "because recessive alleles are unmasked". </p>
<p><strong>I'm looking for a more fundamental explanation about the property of DNA, or the process of copying/merging these complex structures. Why does merging two similar things cause more problems than merging two dissimilar things?</strong> </p>
| [
{
"answer_id": 92461,
"pm_score": 3,
"text": "<p>I suspect your problem is grasping what is a deleterious recessive allele. Wikipedia and textbooks explain it much better but I will try to illustrate with respect to your question.</p>\n\n<blockquote>\n <p>I have to merge somebody else's code into my co... | [
{
"answer_id": 92467,
"pm_score": 1,
"text": "<blockquote>\n <p>Why does inbreeding cause genetic defects, but cell division in one's own body does not?</p>\n</blockquote>\n\n<p>Inbreeding does not cause genetic defects, it just makes already existing ones more likely to be problematic.</p>\n\n<blockqu... |
92,447 | <p>The ancestral solution to oxygen transport is with hemoglobin (or, similar proteins) dissolved in blood (or, "hemolymph", but, basically, dissolved in water. ) What was the advantage of enclosing the oxygen-transport proteins in cells?</p>
| [
{
"answer_id": 92461,
"pm_score": 3,
"text": "<p>I suspect your problem is grasping what is a deleterious recessive allele. Wikipedia and textbooks explain it much better but I will try to illustrate with respect to your question.</p>\n\n<blockquote>\n <p>I have to merge somebody else's code into my co... | [
{
"answer_id": 92467,
"pm_score": 1,
"text": "<blockquote>\n <p>Why does inbreeding cause genetic defects, but cell division in one's own body does not?</p>\n</blockquote>\n\n<p>Inbreeding does not cause genetic defects, it just makes already existing ones more likely to be problematic.</p>\n\n<blockqu... |
92,614 | <p>In flying vertebrates, almost all have only two wings (with the exception of <em><a href="https://en.wikipedia.org/wiki/Microraptor" rel="noreferrer">Microraptor</a></em> and its close relatives). This makes some sense because you need some way to walk also, and a wing isn't very good as a leg, hence why bats are so bad at walking. Of course, bats do demonstrate that being able to walk well is not necessary to be a successful clade.</p>
<p>As far as insects are concerned this might seem like an odd question, since most insects technically have four wings. But among the four largest insect orders (which together make up a sizeable majority of insects), Coleoptera, Lepidoptera, Diptera, and Hymenoptera, all of them functionally have two wings. In Diptera and Coleoptera, only one pair of wings is used to fly. In Hymenoptera and Lepidoptera the two pairs are attached and don't move indepedently. </p>
<p>So my question is, why is two-winged flight so much more common than four-winged? If two-wingedness is advantageous, why do other insects retain four-winged flight (most notably Odonata)?</p>
| [
{
"answer_id": 92627,
"pm_score": 4,
"text": "<p>Note you are talking about two very distinct conditions</p>\n\n<p>In vertebrates, 4 \"wings\" only evolves once in vertebrates (in early birds) and only one set function as wings the others \"wings\" are control surfaces for low speed stability, they gene... | [
{
"answer_id": 92622,
"pm_score": -1,
"text": "<p>This is far from being the complete explanation (which I don't have). But:</p>\n\n<p>From a molecular standpoint, the symmetry between left and right is achieved often by presence / absence of gene expression of certain developmental genes.</p>\n\n<p>In ... |
92,644 | <p>It's possible that this is offtopic here; if so, please let me know.</p>
<p>I'm wondering what technologies exist that rely on evolution being a correct model; I'd like to be able to offer examples of that to people who find it to be "just a theory". As an example, I can point out lots of technologies for which our models of electromagnetism have to be correct to an immense accuracy for them to work - computers, any electrical wiring, electrical motors, light bulbs, electrical ovens, etc. etc.</p>
<p>The best I could find as examples of technologies that require our models of evolution to be fundamentally correct are things like pharmaceutics that work against germs that have developed a resistance against other pharmaceutics.</p>
<p><strong>What are some good examples of technologies that require our models of evolution to be fundamentally correct for those technologies to work?</strong></p>
| [
{
"answer_id": 92627,
"pm_score": 4,
"text": "<p>Note you are talking about two very distinct conditions</p>\n\n<p>In vertebrates, 4 \"wings\" only evolves once in vertebrates (in early birds) and only one set function as wings the others \"wings\" are control surfaces for low speed stability, they gene... | [
{
"answer_id": 92622,
"pm_score": -1,
"text": "<p>This is far from being the complete explanation (which I don't have). But:</p>\n\n<p>From a molecular standpoint, the symmetry between left and right is achieved often by presence / absence of gene expression of certain developmental genes.</p>\n\n<p>In ... |
93,746 | <p>I've tried to research this online and looked through my textbooks as well. This is something that has been on my mind for a bit. Will it just mean that the organism is more simple? Or would it mean they are less efficient? I'm not sure. </p>
| [
{
"answer_id": 93748,
"pm_score": -1,
"text": "<p>The organism would be unlikely to grow any \"useful\" tissues, and if the appropriate growth factors were still present (with differentiation blocked) there would be a higher chance of cancer.</p>\n"
}
] | [
{
"answer_id": 93747,
"pm_score": -1,
"text": "<p>Then you'd have lumps of unspecialized stem cells. Differentiation means that most of the genome has been turned off and only a subset of the genes is active. Makes IMHO sense in the light that different cells make use of the same signalling pathways dow... |
93,815 | <p>In essence - <a href="https://www.theclevercarrot.com/2019/03/beginner-sourdough-starter-recipe/" rel="nofollow noreferrer">to make a sourdough starter</a>:</p>
<ol>
<li>Put flour and water in a jar, and leave it in a warm place overnight</li>
<li>Divide the remaining mixture in half, throw out half, add half as much flour and water again. </li>
<li>Repeat for 7 days. </li>
</ol>
<p>I don't see why you couldn't just add all the ingredients required at the start, open it once a day to let more yeast drop in and give it a stir, and keep in a warm place every day. </p>
<p>The vague idea comes to me that throwing out half the mixture every day has a Darwinian element, but it doesn't involve any 'selection', you're simply casting out half, regardless of adaptability. </p>
<p>My question is: <strong>Does the process of making a sourdough starter involve Darwinian selection?</strong></p>
<p>EDIT: There is no 'choice' involved in throwing out half the sourdough. It is entirely arbitrary - and both halves look equally the same. </p>
| [
{
"answer_id": 93819,
"pm_score": 2,
"text": "<p>Yes, continually diluting the mix like this encourages the organisms (bacteria, yeasts, fungi) to have more constant conditions (maximum nutrients, fewer waste products) and be in log phase growth. The mix selects for particular faster-growing organisms. ... | [
{
"answer_id": 93820,
"pm_score": -1,
"text": "<p>That is not Darwinian selection, because you are not selecting anything. As you mention yourself, it doesn't matter which half you discard and which half you keep. In fact, you can keep the entire thing. Discarding just makes it more practical.</p>\n\n<p... |
93,993 | <p>Information given at this resource <a href="https://predictioncenter.org/" rel="noreferrer">https://predictioncenter.org/</a> is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict tertiary protein structure now - I would be grateful.</p>
<p>Also would love to hear your thoughts on 'why a cell can make exactly the same protein structure thousands of time using known to us physical laws, but we have to guess it using machine learning'? Why is it difficult?</p>
| [
{
"answer_id": 93995,
"pm_score": 4,
"text": "<blockquote>\n<p>what is the accuracy we can predict tertiary protein structure</p>\n</blockquote>\n<p>That depends on the protein. If the primary sequence closely matches the sequence of a protein for which the structure is already resolved, then <strong>t... | [
{
"answer_id": 96337,
"pm_score": 2,
"text": "<p>The predictioncenter.org runs an open contest every two years - Critical Assessment of Structure Prediction (CASP). CASP 14 is underway now.</p>\n<p>The best programs for <em>ab initio</em> folding are highly augmented molecular dynamics with machine lea... |
93,996 | <p>I'm doing a presentation on the replication of SARS-CoV-2 for my chemistry class, and I found that to replicate its RNA, the virus uses RNA-dependent RNA polymerase, which is primed by a VPg primer. Since the presentation is for a chemistry class, not a molecular biology class, I would like to know the chemistry behind the way that primers work. </p>
<p>I've tried searching the information on the internet, but could not locate the information I need. </p>
| [
{
"answer_id": 93995,
"pm_score": 4,
"text": "<blockquote>\n<p>what is the accuracy we can predict tertiary protein structure</p>\n</blockquote>\n<p>That depends on the protein. If the primary sequence closely matches the sequence of a protein for which the structure is already resolved, then <strong>t... | [
{
"answer_id": 96337,
"pm_score": 2,
"text": "<p>The predictioncenter.org runs an open contest every two years - Critical Assessment of Structure Prediction (CASP). CASP 14 is underway now.</p>\n<p>The best programs for <em>ab initio</em> folding are highly augmented molecular dynamics with machine lea... |
94,077 | <p><strong><a href="https://graphicdesign.stackexchange.com/questions/138042/what-software-could-i-use-to-create-diagrams-of-biochemical-processes-like-the">Cross-posted at GraphicDesign.SE here</a></strong></p>
<p>Is there any software software that I could use to (closely) create pathways as depicted in these diagrams?</p>
<blockquote>
<p><a href="https://i.stack.imgur.com/AogXQ.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/AogXQ.jpg" alt="enter image description here"></a>
<a href="https://i.stack.imgur.com/RDjwu.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/RDjwu.jpg" alt="enter image description here"></a></p>
</blockquote>
<p>Or does anyone happen to know what software was used for these diagrams specifically? [Sourced from Harper's <em>Illustrated Biochemistry</em> (31e) and Murray's <em>Medical Microbiology</em> (8e) respectively]</p>
<p>I would like to be able make alterations such as adding extra steps, changing color, including newer pieces of data and such-like for the purpose of making my own notes.
I assume that knowing which software was (or can be) used to create these, I'd have greater versatility making the edits I need, or creating something in similar from scratch for other processes/pathways.</p>
| [
{
"answer_id": 94080,
"pm_score": 4,
"text": "<p>By posting to this forum, I presume the question is whether the illustrators of this and other biochemistry books used software specifically designed for the purpose of drawing reaction pathways, or, if not, whether such software exists. From my experienc... | [
{
"answer_id": 94082,
"pm_score": 2,
"text": "<p>In the scientific community, we mostly use a couple tools to draw publication-quality pathway figures:</p>\n\n<ul>\n<li><a href=\"https://www.omnigroup.com/omnigraffle/\" rel=\"nofollow noreferrer\">OmniGraffle</a></li>\n<li><a href=\"https://www.nature.c... |
94,096 | <p>My 9 year old niece asked me this when I was explaining some stuff to her about the coronavirus. She asked "What does this virus taste like? Can I tell whether my sandwich is contaminated for example?"</p>
<p>That sounded like a silly question and I immediately responded by saying that they are too small to have any taste, and even if you manage to eat a whole lot of viruses it would taste like water.</p>
<p>The day after, I searched a bit just to make sure that I haven't fed the wrong information to the kid. As I expected, there wasn't a single page mentioning this question (except <a href="https://www.quora.com/How-is-the-taste-of-bacteria" rel="nofollow noreferrer">this quora post</a> with a vague answer). Now it may sound like I am overthinking and the question is too naive and isn't worth the time, but then again, I thought what's the harm in asking?</p>
<blockquote>
<p>Has there been any research on the likely taste or maybe smell of a specific virus or bacteria?</p>
</blockquote>
| [
{
"answer_id": 94100,
"pm_score": 6,
"text": "<p>As you could imagine, a systematic cataloguing of bacterial or viral flavor profiles would violate a number of biosafety protocols. However, in a laboratory setting, different bacteria definitely have <a href=\"https://microbeonline.com/pathogenic-microbe... | [
{
"answer_id": 94099,
"pm_score": 5,
"text": "<p>So I think this is a more conversational kind of question. I will address some misconceptions you have, and I will try to keep it brief, considering the nature and depth of your question. One could comment on the question very deeply, so I'll stick to add... |
94,382 | <p>I read a lot of articles on this and all seem to agree that the brain storage in neural connections is tremendous but that doesnt explain why we forget things so easily and have such a modest memory in our subjective lives and we use much humbler devices to store information, i specifically wanna know if we can really store this information but the problem is we cant acces them as efficiently as a computer can or the whole process of storing this information is different than a hard disk on a computer.
None of the articles i have read make any comments addressing this question.
Links to relevant information on memory processing and storage will be appreciated.</p>
| [
{
"answer_id": 94385,
"pm_score": 4,
"text": "<p>The brain is trained to remember patterns and predictable associations. Randomness is the absence of patterns, so it's the exact opposite of what the human brain is for. A human can remember random numbers to about 67,890, which is the world record digits... | [
{
"answer_id": 94383,
"pm_score": 2,
"text": "<p>Our brains usually make associations to different words including images, sounds, emotions, etc... which help reinforce the neurological patterns required to memorize sentences, etc...</p>\n<p>To remember something, it must also be repeatedly 're-thought'... |
94,499 | <p>Small birds (sparrows, robins, jays, finches) and mammals (squirrels, rats, opossums, raccoons) are a common sight in many urban and suburban communities with green space. However, I observe carcasses of these animals relatively infrequently.</p>
<p>I imagine that the following are some of the most common causes of death:</p>
<ul>
<li>Predation (the species I mention are small, and somewhere in the middle of the food chain)</li>
<li>Age-associated decline in foraging ability, leading to starvation</li>
<li>Disease</li>
<li>Fatal contact with infrastructure (collisions with buildings or wind turbines, contact with electricity lines)</li>
</ul>
<p>I can think of two reasons why we don't see carcasses very often:</p>
<ul>
<li>predation is the most common cause of death</li>
<li>individuals that succumb to disease/starvation end up in their nests/dens</li>
</ul>
<p>Is this plausible? Has this been studied systematically, e.g. in populations of birds with tracking bands?</p>
| [
{
"answer_id": 97352,
"pm_score": 3,
"text": "<p><strong>Cats, windows, and cars</strong> appear to be the leading causes of <em>avian</em> (bird) deaths:</p>\n<p><a href=\"https://i.stack.imgur.com/sFyj3m.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/sFyj3m.png\" alt=\"enter im... | [
{
"answer_id": 94513,
"pm_score": -1,
"text": "<p>The overwhelming cause of death of small animals ( and deer) that I see is that fearsome predator , the Toyota, Ford, Chevy, etc; AKA roadkill. I am in suburban E.TX. Other than that ,Coopers Hawks are common here and take many small birds. Also barred O... |
94,501 | <p>From a DNA extraction procedure description (an in-house pharma document I'm translating into Russian):</p>
<blockquote>
<p><strong>Preparation of Standards</strong></p>
<ul>
<li>All the <strong>standard reactions</strong> should be prepared at least in duplicates. The template DNA stock (CHO cell genomic DNA) should not be less than 100 ng/μL concentration.</li>
</ul>
</blockquote>
<p>Does "standard reactions" here mean what it says, or does it really mean "reactions <strong>with</strong> standards" (reactions using standard samples)?</p>
<p>P.S. It is part of a qPCR procedure to quantify host cell DNA content. The company is producing a monoclonal antibody drug and is describing its internal procedures. As a translator I cannot disclose the document in full.</p>
| [
{
"answer_id": 97352,
"pm_score": 3,
"text": "<p><strong>Cats, windows, and cars</strong> appear to be the leading causes of <em>avian</em> (bird) deaths:</p>\n<p><a href=\"https://i.stack.imgur.com/sFyj3m.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/sFyj3m.png\" alt=\"enter im... | [
{
"answer_id": 94513,
"pm_score": -1,
"text": "<p>The overwhelming cause of death of small animals ( and deer) that I see is that fearsome predator , the Toyota, Ford, Chevy, etc; AKA roadkill. I am in suburban E.TX. Other than that ,Coopers Hawks are common here and take many small birds. Also barred O... |
94,746 | <p>I have read that during the Second World War, some mosquitoes got trapped in the London underground railway system. The mosquitoes never got out and eventually they became a new species by themselves.</p>
<p>I had a similar thought. In the next few centuries, if humans could, in theory, colonize other planets like Mars, Proxima Centauri and beyond, then the environments there are not the same as Earth. So, in the long term, humans who would be born and who would grow up on Mars, for example may become more and more suited to Martian conditions than Earths.</p>
<p>Now, when early humans explored and ventured into new geographical areas, they did change characteristics, but we are still one species <em>Sapiens</em>. But living extraterrestrial, is a whole new thing. The gravity alters, the entire atmospheric composition does. So that is going to have some significant changes on humans.</p>
<p>So, my question is: is it possible that in millions or even billions of years, if humans expand to space, there may arise separate species of humans? And would this new emergence of human species actually result in humans moving one step up the taxonomical ladder: becoming a genus?</p>
<p>EDIT: To avoid confusion and create speculations at the answers, I should specify that I am talking about a very particular case: if <em>Sapiens</em> are living in different planets, then is there a chance that <em>Sapiens</em> will become a new genus, and that <em>Homo</em> can be taken one step higher in the taxonomical order? There would still be <em>Sapiens</em> on Earth, but considering the environmental changes that could happen here too, humans then can be drastically different from humans now. So the question is: can '<em>Sapiens</em>' become a genus?</p>
<p>Thanks to @tyersome and @jamesqf for pointing this out.</p>
| [
{
"answer_id": 94749,
"pm_score": 6,
"text": "<p>The concept you are referring to is <strong>speciation</strong> and it has been well studied in a wide variety of different natural organisms. I suppose here we are talking about the <a href=\"https://www.sciencedirect.com/topics/earth-and-planetary-scien... | [
{
"answer_id": 94784,
"pm_score": 0,
"text": "<p>As others have noted, the key concept is speciation. Imagine some H. sapiens living on Mars. How are they going to breathe? Presumably we have a nuclear reactor generating power, which in turn is used to make oxygen. What is it breaks down? Those who can ... |
94,805 | <p>I'm a 5th-year PhD student in chemical biology. I've mostly been doing computational work, so my bench skills are rusty. To help me, I'd like a handbook of common techniques -- transformations, ELISA, protein purification, DNA extraction, SDS-PAGE, column chromatography, etc. I'd especially like a collection of recipes for buffers, etc.</p>
<p>I can find some protocols, but it's hard to find ones covering the more basic methods, and I'd like something cohesive. And there's something satisfying about an actual book.</p>
<p>I found these (and browsed through them in an HHMI library once):</p>
<ul>
<li><a href="https://rads.stackoverflow.com/amzn/click/com/0879697083" rel="nofollow noreferrer" rel="nofollow noreferrer">https://www.amazon.com/Kathy-Barker/dp/0879697083/</a></li>
<li><a href="https://rads.stackoverflow.com/amzn/click/com/1936113791" rel="nofollow noreferrer" rel="nofollow noreferrer">https://www.amazon.com/Lab-Ref-Handbook-Reagents-Reference/dp/1936113791/</a></li>
</ul>
<p>But they're pretty out of date! Most of the techniques are still valid, but I know many have been superseded. There are still a lot of radioligand assays (which are now uncommon in most labs).</p>
<p>So, can anyone recommend a book that could help someone relearn basic techniques?</p>
<hr />
<p>My experience is that techniques are almost most often taught by hands-on, one-on-one training -- you find someone who knows the technique and ask them to show you, but COVID-19 distancing protocols make that nearly impossible. (The good news is that I often have the lab to myself and an underused supply of chemical stocks and reagents.)</p>
| [
{
"answer_id": 98338,
"pm_score": 3,
"text": "<p>The extremely old-school answer here would be Maniatis' <a href=\"http://www.molecularcloning.com/\" rel=\"nofollow noreferrer\">Molecular Cloning</a>. They put out a new edition every decade or so, there is one from 2012 that is updated.</p>\n<p>To get a... | [
{
"answer_id": 95840,
"pm_score": 2,
"text": "<p>I know you are asking for books, but for up-to-date basic overview of how some methods work - I would try websites or YouTube instead of textbooks...</p>\n<p>One good website is <a href=\"https://bitesizebio.com/webinars/\" rel=\"nofollow noreferrer\">Bit... |
94,937 | <p>I took these photos around noon in late July in Hsinchu county Taiwan. This particular stick in this particular pond is visited by many dragonfly species. This one was very high energy and nervous but taking my time and waiting for it to return each time I spooked it I eventually got almost (but not quite) close enough to take a decent photo with my phone.</p>
<p>Its body is about 5 cm long and mostly jet-black. However it has a bright, solid white or blue-white band about 1 cm long behind the fat part of it's body along the long "tail section".</p>
<p>I'm showing the two best photos below, for the darker one I lowered the brightness of the photo on my phone before taking it so that the band wouldn't be saturated but it is still extremely bright. It may in fact be slightly blue-hued or that could be an effect of the phone's camera.</p>
<p>Is it possible to identify this particular species of dragonfly?</p>
<p><a href="https://i.stack.imgur.com/s3Oto.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/s3Oto.jpg" alt="dragonfly in Hsinchu County Taiwan July 2020" /></a></p>
<p><a href="https://i.stack.imgur.com/ubGcS.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/ubGcS.jpg" alt="dragonfly in Hsinchu County Taiwan July 2020" /></a></p>
| [
{
"answer_id": 94951,
"pm_score": 4,
"text": "<p><strong>update:</strong> A week later on August 7th I revisited the same pond and it's drangonfly stick and photographed what appears to be the same species, but this time it was perched at a different angle and I was able to photograph the "white fo... | [
{
"answer_id": 94939,
"pm_score": 2,
"text": "<p>Looks like this species is <a href=\"https://eol.org/pages/131385\" rel=\"nofollow noreferrer\"><em>Orthetrum triangulare</em></a> commonly known as blue-tailed forest hawk.\nIt is an Asian fresh water dragon fly species.</p>\n<p>As you mentioned that the... |
96,163 | <p>There are various reasons such as intake of neurotoxins, and possibly traumatic injuries, that can cause neurons to die.</p>
<p>After several hundreds, or thousands of our neurons die, how does our body remakes them?</p>
| [
{
"answer_id": 96314,
"pm_score": 3,
"text": "<p>Evolution set us humans up to not regenerate our neurons on the whole, which is a pity since we can regenerate our liver cells, so it's not an impossible feat. If neurons die because you drank too much, banged your head, or just because they got old, they... | [
{
"answer_id": 96277,
"pm_score": 1,
"text": "<p>Disclaimer: I'm not an expert, but my recent reading on this topic is fresh in memory, so I'm typing up something of an answer.</p>\n<p>The body does not remake any individual cells that die. In case of cells that regenerate, their place is simply occupie... |
96,371 | <p>I am concerned by the fact that babies cant walk because the muscles in their limbs arent developed and tuned to give directional control, it takes years before babies gain mobility and dexterity. So technically the neural nets in the motor cortex requires years of training before that capability is achieved.</p>
<p>However, when the babies are born they dont need training for ocular muscles for directional control of their eyeballs (which is quite computationally challenging problem due to high degree of freedom compared to hinge movement) . Do biological neural network for occular muscles come pre-trained while the neural network for limb muscles come untrained by birth?</p>
| [
{
"answer_id": 96377,
"pm_score": 4,
"text": "<p>Biological neurons function in a very different way, as compared to the simplistic artificial neural networks of machine learning. For example, see how <a href=\"https://www.youtube.com/watch?v=LosTnvwt794\" rel=\"noreferrer\">real neurons work</a> and ho... | [
{
"answer_id": 96372,
"pm_score": 3,
"text": "<p>Some babies start walking by 12-15 months, so it's not exactly years before they can do it. They can also grasp things with their hands from birth. When first born they still don't have <em>full</em> ocular control, and especially can't focus except on st... |
96,401 | <p>My friend's argument against evolution goes like this:</p>
<p>It is extremely unlikely that life as we know it evolved from a random mutation process because every organism is like a machine, in that one "mistake" could render the whole machine unworkable. What makes this even more unlikely is that harmful mutations are more likely to occur than beneficial ones. If evolution were true, it would not last very long, most likely.</p>
<p>My rebuttal goes like this:</p>
<p>While it is true that evolution is influenced by a random mutation process, this process is not random in the sense that all mutations are equally likely. When evolutionary biologists say mutations are random, they mean that the environment has no influence on the type or frequency of mutations. They do not mean that all mutations are equally likely to occur. In fact, if you look at certain mutations in humans, you'll see that mutation rates for certain phenotypes are not equal, which means we have unequal probabilities. Also, while it is true that harmful mutations are more likely to occur than beneficial ones, neutral mutations are the most likely of all. Another issue I have is that it only appears unlikely if we are just working with one organism, but if we have a whole population of organisms, mutating and reproducing, then your argument seems to be undermined by this fact.</p>
<p><strong>Was my rebuttal good? Is there anything wrong with my friend's argument against evolution?</strong></p>
| [
{
"answer_id": 96410,
"pm_score": 3,
"text": "<blockquote>\n<p>It is extremely unlikely that life as we know it evolved from a random\nmutation process because every organism is like a machine, in that one\n"mistake" could render the whole machine unworkable.</p>\n</blockquote>\n<p><strong>Gar... | [
{
"answer_id": 96632,
"pm_score": -1,
"text": "<p>I will henceforth use the word <em>"unfortunately"</em> to describe the predicament of a person who denies evolution.</p>\n<blockquote>\n<p>Is there anything wrong with my friend's argument against evolution?</p>\n</blockquote>\n<p><em>Unfortun... |
97,583 | <p>Full disclosure; no biology since 9th grade, so please go easy on me!</p>
<p>XKCD's <a href="https://xkcd.com/2406/" rel="nofollow noreferrer">2406</a> shows a literal wooden <a href="https://en.wikipedia.org/wiki/Trojan_Horse" rel="nofollow noreferrer">Trojan Horse</a> outside a castle, but instead of bringing it inside the castle walls, the soldiers <em>recognize</em> the shape as horse-like:</p>
<blockquote>
<p>Look! It's a statue of that horrible animal that trampled Steve!</p>
</blockquote>
<p>and the soldiers decide to destroy and dispose of it rather than to let it in.</p>
<p>The title of this XKCD is</p>
<blockquote>
<p>Viral Vector Immunity</p>
</blockquote>
<p>with the subtitle</p>
<blockquote>
<p>How <strong>Vaccine Failure</strong> Due to Viral Vector Immunity Works</p>
</blockquote>
<p>Wikipedia's <a href="https://en.wikipedia.org/wiki/Viral_vector#Vaccines" rel="nofollow noreferrer">Viral_vector; Vaccines</a> explains the basic idea, which is (I think) that the viral vector's genome is modified so that it includes a new protein on its surface that serves as an antigen, and the host builds and learns an immune response to this antigen that will then immunize the host against an infection by another organism that also presents this antigen.</p>
<p><strong>Question:</strong> The XKCD shows recognition and an analogy of an immune response, so why does the subtitle call this a "Vaccine Failure"?</p>
<p><a href="https://i.stack.imgur.com/Hv3h1.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Hv3h1.png" alt="https://xkcd.com/2406/" /></a></p>
<p><a href="https://creativecommons.org/licenses/by-nc/2.5/" rel="nofollow noreferrer">XKCD image License</a></p>
| [
{
"answer_id": 97599,
"pm_score": 3,
"text": "<p>Yes, the cartoon is a description of immune action.</p>\n<p>Traditionally shown is first exposure being a vaccine, and the second exposure being the bad virus being destroyed.</p>\n<p>However, this cartoon is describing viral vector immunity.</p>\n<p>The ... | [
{
"answer_id": 97585,
"pm_score": 2,
"text": "<p>Viral vector only serves to deliver to cells the proteins/mRNAs necessary for triggering the immune response. In this sense it is like a Trojan horse - it is not supposed to cause suspicion, since otherwise it fails.</p>\n<p>In this case the immune system... |
97,635 | <p>I was discussing with a colleague about using dark-mode vs. light mode and remembered <a href="https://www.linkedin.com/pulse/astigmatism-part-1-starry-effects-olivier-sannier/" rel="noreferrer">an article</a> arguing that humans vision is more adapted to light-mode rather than dark-mode:</p>
<blockquote>
<p>I know that the trend “du jour” is to have a dark mode for pretty much
everything, but look around the world is not dark with a bit of light,
it’s actually the contrary. And <strong>as the human has evolved its vision to
adapt to this reality, it’s asking extra efforts on many people.</strong></p>
</blockquote>
<p>Unfortunately, no reference is provided to support this claim, so I am wondering if this is just an opinion or there are some studies to support this.</p>
<p><a href="https://en.wikipedia.org/wiki/Adaptation_(eye)" rel="noreferrer">Wikipedia</a> seems to confirm this somewhat since we are adapting much faster to "light mode" transition than to dark mode one:</p>
<blockquote>
<p>This adaptation period is different between rod and cone cells and
results from the regeneration of photopigments to increase retinal
sensitivity. Light adaptation, in contrast, works very quickly, within
seconds.</p>
</blockquote>
<p>Also, <a href="https://www.nngroup.com/articles/dark-mode/" rel="noreferrer">some studies</a> confirm that working using light mode is on average more efficient than using dark mode:</p>
<blockquote>
<p>light mode won across all dimensions: irrespective of age, the
positive contrast polarity was better for both visual-acuity tasks and
for proofreading tasks.</p>
</blockquote>
<p>I am looking for arguments coming from evolutionary biology to confirm (or not) the assumption that human evolution favors light mode.</p>
| [
{
"answer_id": 97639,
"pm_score": 6,
"text": "<p><a href=\"https://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont\">A question that requires quite a lot of guts to ask on this site</a> :) Nonetheless, and risking sparking a debate, there are a few arguments th... | [
{
"answer_id": 97856,
"pm_score": 3,
"text": "<p>Both.</p>\n<p>More specifically, we're a kitbashed light-mode version of a primarily dark-mode group of animals. Mammals famously have terrible color vision, most mammals are dichromats (red color-blind) whereas most other animals like fishes, amphibians,... |
98,047 | <p>I understand that we have 46 DNA molecules in the nucleus of our cells, arranged in 23 pairs: 22 autosomal and 1 sex chromosome pairs.</p>
<p>I have read in different sources that the pairs contain nearly identical members, excluding any mutations. I have also read that the pairs contain 1 member we inherited from our mothers and 1 we inherited from our fathers, which are different due to inheritance.</p>
<p>This seems contradictory, given that genealogical companies match up on the differences on these chromosomes.</p>
<p>My understanding was that meiosis creates sperm and egg cells that each carry 23 chromosomes - they are haploids. During the first steps of meiosis that creates the reproductive cells we have a combining of the parent's chromosome pair from their parents to create 4 daughter cells, each independently viable, where the recombination of the chromosome pair has occurred at somewhat predictable spots (for you perhaps :-) ) and that these spots can be related to genes. It is this step that give us our genetic variation between siblings for example. A new person's DNA is partially formed from any one of these highly varied daughter cell possibilities.</p>
<p>Fertilization combines the reproductive cells to produce the 46 chromosome zygote with is again diploid.</p>
<p>I think this understanding supports the second interpretation that our chromosome pairs are not 2 nearly identical DNA molecules but are distinct.</p>
<p>Have I got this right? Is there a missing process or a misunderstanding in my interpretation?</p>
| [
{
"answer_id": 98050,
"pm_score": 4,
"text": "<p>Homologous chromosomes (those that are paired up), excluding the sex pair are almost identical in size, shape and genes (members as you called them) present in them.</p>\n<p>Genes determine traits and each homologous chromosome controls the same traits. T... | [
{
"answer_id": 98060,
"pm_score": 1,
"text": "<p>Two major resources of genetic variation between siblings:</p>\n<p>1- Random segregation of chromosomes during meiosis I. consider only mother: the mother has 46 chromosomes, 23 from grandmother and 23 from grandfather. during meiosis anaphase I, pairs of... |
98,595 | <p>All protein coding sequences in the <a href="http://parts.igem.org/Main_Page" rel="noreferrer">iGEM Registry</a> are supposed to <a href="http://parts.igem.org/Help:Protein_coding_sequences/Design" rel="noreferrer">end with a double stop codon</a>. Presumably, this is to decrease the potential for read-through, which could be problematic if one is putting together a polycistronic design.</p>
<p>If the design is intended to have only one CDS, however, and is targeted at a prokaryote (<a href="https://science.sciencemag.org/content/354/6318/1437" rel="noreferrer">which have "backup" ribosome release mechanisms</a>), then is there any problem with using only a single stop codon?</p>
| [
{
"answer_id": 98596,
"pm_score": 4,
"text": "<p>The impact of any read-through from a leaky stop codon in an expression unit with only one CDS would probably depend on a few things, mainly (i) where is the next in-frame stop codon, (ii) what are you trying to express, and (iii) how leaky is the stop co... | [
{
"answer_id": 98854,
"pm_score": 3,
"text": "<p>Perhaps I could add for eukaryotic systems which terminate all stop codons by a single protein, eRF1, this study by <a href=\"https://pubs.acs.org/doi/abs/10.1021/ja5069728\" rel=\"noreferrer\">Schmied et al.,</a> showed readthrough of all stop codons to ... |
98,834 | <h2>Background</h2>
<p>I've always been told that DNA assembly can be tricky when using very small DNA parts due to low efficiency. I've also seen this when using 3A biobrick assembly to assemble promoters and RBSs together. However, there doesn't seem to be any information that I can find which definitively shows what the minimum DNA part size is that can be used before the efficiency becomes so low that assembly is unfeasible. The most I can find are warnings that small DNA parts are problematic (e.g. <a href="https://blog.addgene.org/plasmids-101-golden-gate-cloning" rel="noreferrer">https://blog.addgene.org/plasmids-101-golden-gate-cloning</a>).</p>
<h2>The Question</h2>
<p>What is the minimum DNA part size that can be used in DNA assembly before it becomes unfeasible? I'm specifically interested in Golden Gate assembly, but information for other digest-ligate assembly methods could also be helpful.</p>
| [
{
"answer_id": 98987,
"pm_score": 5,
"text": "<p>Purely going off experience here having used golden gate assembly methods for 5+ years now, there is a definite lack of literature regarding small part assemblies. In my current lab, we use CIDAR MoClo (a golden gate method) and have assembled 100's of co... | [
{
"answer_id": 98855,
"pm_score": 3,
"text": "<p>It may also be worth considering how you are amplifying and isolating your small part. Gel extraction kits sometimes have an optimum DNA size ranges that may prevent recovery. Or if your part is similar to your primer length you may see considerable conta... |
98,865 | <p>I am hoping to mutate the active site of the enzyme I am researching that has 5 residues in proximity with the substrate. I am wondering how many colonies I'll have to assess to theoretically sample all the possible mutant combinations?</p>
<p>I am guessing that just screening the number of possible combinations will not be very successful because I am likely to sample a particular mutant more than once?</p>
<p>I have been looking at 'NNK Saturated Mutagenesis' which uses the redundancy in the genetic code to be able to create all residue encodings where N = A/G/C/T and K = G/T, while limiting the number of repeated residues from synonymous codons.</p>
<p>Are there any other ways of performing this sort of mutagenesis with better codon compression?</p>
| [
{
"answer_id": 98874,
"pm_score": 4,
"text": "<p>This sort of method is indeed quite useful and frequently used in synthetic biology: I've used a similar approach before to <a href=\"https://doi.org/10.1371/journal.pone.0176013\" rel=\"noreferrer\">generate 5' insulators for promoters</a>.</p>\n<p>Calcu... | [
{
"answer_id": 98903,
"pm_score": 0,
"text": "<p>CyberDope was first written at MIT, then again at Kairos, then again by me (privately) in Mathematica. The program gives the best "dopes" for a target set of amino acids. You will need someone who has Mathematica to view this program in "... |
100,146 | <p>I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the <a href="https://www.thermofisher.com/au/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html#:%7E:text=Protein%20expression%20refers%20to%20the,latter%20meaning%20of%20protein%20expression." rel="noreferrer">Thermo Fisher Scientific</a> website it states that <em>"Protein expression refers to the way in which proteins are synthesized, modified and regulated in living organisms"</em>. However, on the <a href="https://www.cancer.gov/publications/dictionaries/cancer-terms/def/protein-expression" rel="noreferrer">National Cancer Institute website</a> it states that protein expression <em>"Refers to the production of proteins by cells"</em>.</p>
<p>I was wondering, between these two definitions, which one is more correct? Can protein expression also be used to refer to how proteins are regulated (e.g. can you use the term protein expression when discussing how one protein regulates the activity of another)? Any insights are appreciated.</p>
| [
{
"answer_id": 100155,
"pm_score": 5,
"text": "<blockquote>\n<p>There are <strong>no</strong> formal definitions accepted in science for ambiguous\nphrases such “protein expression”.</p>\n</blockquote>\n<p>If you wish to know what a particular author who uses such a shorthand phrase means you need to ex... | [
{
"answer_id": 100152,
"pm_score": 3,
"text": "<p>The Thermo Fisher definition is more explicitly accurate, although one could argue that the term "<em>production</em>" in the NCI definition implies regulation and post-translational modification (PTMs) as well. Either way, <em>protein expressi... |
100,216 | <p>I saw a <em>Thought Emporium</em> video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique.</p>
<p>I am curious to know if plant derivatives like saffron (or its flavour), rubber, or even substances like quinine, tetrahydrocannabinol and cocaine, can also be produced by this same technique. From the information I have found, it seems that some plant derivatives are being manufactured in genetic engineered micro-organisms, but most are not.</p>
<p>Some of these derivatives are very expensive, so I would imagine such techniques could be used to mass-produce them more cheaply. If so, what is stopping industry from doing it? If not, what is the problem?</p>
| [
{
"answer_id": 100355,
"pm_score": 3,
"text": "<p><strong>General Considerations</strong></p>\n<p>The question asks specifically why certain plant products are not produced commercially in genetically modified micro-organisms. There are some general reasons, illustrated in some of the examples mentioned... | [
{
"answer_id": 100220,
"pm_score": 3,
"text": "<p>In principle, any biological product should be able to be developed through microbial synthesis, with the appropriate choice of chassis. Indeed, this was the goal of the DARPA "1000 Molecules" program, which did indeed <a href=\"https://doi.org... |
100,242 | <p><strong>How likely is a lack of DNA match with a distant relative?</strong></p>
<p>I have recently gotten interested in ancestry research and have had a DNA analysis performed by a prominent commercial provider.</p>
<p>I've been working on my family tree for a few months now and have gotten into contact with a lot of distant relatives of mine, which has generally been quite delightful. In one particular case, we discovered that we actually have a double-relationship about 5-7 generations back in time, depending on how you count (common links go back to about ~1790).</p>
<p>We found this quite interesting, and this distant relative had a DNA analysis performed on their own genome as well.</p>
<p>Much to our surprise, however, we didn't find any commonalities in our DNA, which seems odd given the double-relation, and the fact that we have what we believe to be original and authentic documents of all the relatives forming the link.</p>
<p>Of course, we began speculating about the possible reasons for this. Maybe a misattributed child somewhere in the family tree? However, this seems unlikely, given the double nature of the link - most likely, we would need two misattributed children to explain the lack of any commonalities.</p>
<p>The other explanation would of course be that the DNA analysis provided by these companies is less reliable than we think, and that just by random mutations and "unlucky" inheritance, any common DNA might have been lost or scrambled beyond recognition.</p>
<p>I would like to calculate the probabilities of this happening in order to judge whether it makes sense to dig further into the original documents to try and clear up this mystery, or whether a mismatch by chance alone is sufficiently likely to explain this oddity. Of course, I don't need super precise numbers, but a back-of-the-envelope estimation would be nice - are we talking a few percent, or one in a billion? Also, I would be curious anyway on how to calculate probabilities like this, given the publicly available data on these tests.</p>
<p>What are the relevant quantities for this calculation (number of SNPs, I suppose), and how would one define and calculate a probability like this?</p>
<p><strong>About myself</strong></p>
<p>I'm a physicist with a strong background in data analysis with some basic understanding of biology and genetics. Don't be afraid to hit me with those numbers and probabilities, but please explain any genetics jargon you're going to use!</p>
| [
{
"answer_id": 100257,
"pm_score": 6,
"text": "<p>First, if you haven't read it already, I highly recommend Carl Zimmer's "She has her mother's laugh." for anyone interested in ancestry/genealogy.</p>\n<p>In it, he presents the following figure showing the probability of sharing <em><strong>an... | [
{
"answer_id": 100248,
"pm_score": 4,
"text": "<h2>5-7 generations is a long time</h2>\n<p>Mother and child or brother and sister each share 50% of their DNA. If you find a link between two people that is five generations back, that means you take 50% of 50% of 50% ... for five generations. For <em>bo... |
101,350 | <p>Thanks for looking.</p>
<p>Firstly, I am nowhere near biologist, just a student, so my apologies if this isn't a "good" question.</p>
<h1>Background:</h1>
<p>So I was searching about intelligence, brains and computers, and noted 2 videos, one where <a href="https://youtu.be/V2YDApNRK3g" rel="nofollow noreferrer">a person tries growing human neurons to be connected to a computer</a>, and <a href="https://youtu.be/1QPiF4-iu6g" rel="nofollow noreferrer">a mouse brain connected to a supposed robot car</a>.</p>
<p>It made me curious, if there's any major difference between neurons between species.</p>
<h1>Question</h1>
<p><strong>Is there a difference between a human's brain cells compared to other species?</strong></p>
<p>For the sake of the question, it will be limited to a mouse or a dolphin's, but if you can bring more info from another kingdom, it would be really welcomed.</p>
<p>I'll be really grateful if you coupled it with some illustrations!</p>
<h1>Note:</h1>
<p>This question is NOT about brain-size, but rather, a single unit of whatever that makes a brain, brain.</p>
| [
{
"answer_id": 101362,
"pm_score": 3,
"text": "<h2>Not really.</h2>\n<p>There really is little difference in neurons in mammal and indeed not much change across vertebrates. You have to go back all <a href=\"https://pubmed.ncbi.nlm.nih.gov/7833621/#:%7E:text=At%20the%20ultrastructural%20level%2C%20many,... | [
{
"answer_id": 101351,
"pm_score": 1,
"text": "<p>As you mentioned yourself, there are differences in brain size, form and structure. This difference also affects the size and shape of cells, i.e. you won't find meter-long neurons in mice, but rather in bigger animals. However, the types of cells are ov... |
101,455 | <p>I know that there are some efforts from scientists working with bladder cancer to perform liquid biopsy from urine for detection and monitoring of the cancer such as <a href="https://pubmed.ncbi.nlm.nih.gov/31803629/" rel="nofollow noreferrer">this one</a>.</p>
<p>I've been searching online - but the "wastewater" search term gives me tons of hits about "microbiome" and several types of pathogens.</p>
<p>But I'm really interested in sequencing the sewage to find and analyze <strong>human DNA</strong>. I have been wondering about liquid biopsies to get an estimate of the cancer status of a population.</p>
<p>I immediately think of several problems:</p>
<h3>1. Technical Feasibility</h3>
<ul>
<li>Would we expect to find enough human nuclear DNA within the samples (taken across several days)?</li>
</ul>
<blockquote>
<h3>2. Law and Bioethics</h3>
<ul>
<li>Is it legal in the US or European Union?</li>
<li>It could be difficult to get informed consent of all people who are connected to a certain sewage system. You may get informed consent from all residents but what about visitors?</li>
<li>It could be difficult to opt out of such study the
wastewater without a) moving to a different place b) using a septic tank.</li>
<li>I only found <a href="https://massivesci.com/articles/wastewater-environment-disease-epidemiology-covid19-privacy/" rel="nofollow noreferrer">this</a> elaborating <strong>other</strong> privacy issues: its just about Cov-19 and drug testing; both of which are <strong>not</strong> able to identify individuals at a genomic level.</li>
</ul>
</blockquote>
<p>I'd appreciate your experience and thoughts and <strong>references</strong>!</p>
<p>[Edit] as suggested in the comments: I have posted part 2 of the question to the law stack exchange <a href="https://law.stackexchange.com/questions/67264/would-it-be-legal-to-sequence-human-dna-from-wastewater">here</a></p>
| [
{
"answer_id": 101457,
"pm_score": 5,
"text": "<p>As it turns out, you are not the first to have this idea. Prior research claims that it is, at least in principle, possible to conduct <a href=\"https://doi.org/10.1021/acs.analchem.7b02257\" rel=\"noreferrer\">epidemiology of cancer by sequencing on was... | [
{
"answer_id": 101475,
"pm_score": 3,
"text": "<p>As already hinted in the answer by @jakebeal, the low concentration (high dilution) of human DNA in waste water would mean that we need huge sequencing depth in order to detect something. This is not the case when dealing with urine or feces. This is als... |
101,824 | <p>This question has a specific context, a religious one, and so I'm not sure this is the right place to ask, but I can't think of a better place. I would like as objective and unbiased an answer as possible. I hope the religious context doesn't make this an unsuitable question. I'll explain the religious context:</p>
<p>There is a religion that believes that a small number of Jews left Israel circa 600BC and sailed to the Americas, where they multiplied and built their own new civilization(s). This religious organization also has a history of teaching Native Americans that they are the descendants of this population, so therefore that their ancestors are Jews from 600BC.</p>
<p>But we're quite lucky in the modern age that we can do genetic testing! And they have done, and of course they've found no signs of a genetic relationship between any Native American tribes and any known Israeli or Jewish populations. The organizations response to this is that, after 2600 years, you wouldn't expect any genetic similarities between the two populations - if they've been physically separated for so long, all genetic markers of a relationship would have disappeared.</p>
<p>Is that correct? Would 2600 years be enough time to erase all genetic evidence that this population originated from Israel Jewish people?</p>
| [
{
"answer_id": 101825,
"pm_score": 6,
"text": "<p>If we assume a population of 100 individuals migrated from the Middle East to Central America 2600 years ago and, even if they underwent admixture from the local population, then there would be extremely clear genetic signal that those individuals were f... | [
{
"answer_id": 101827,
"pm_score": 4,
"text": "<p>From the point of view of genome comparison the signature would be unmistakable, as @user438383 has pointed out in their answer. There may be however other methodological issues undermining this study:</p>\n<ul>\n<li><em>Scientific</em> - one need an att... |
103,022 | <p>If one is given the complete genome of some unknown organism, would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a repository of genomes of known living organisms)?</p>
<p>In another words, do we currently have a model capable of translating any random genome of an organism to a graphical representation of the organism and information on its behaviour?</p>
<p>Are there such 'genome-structure' or 'genome-behaviour' relationships known to us that would enable us to accomplish such a task?</p>
| [
{
"answer_id": 103029,
"pm_score": 4,
"text": "<p>As you specifically state:</p>\n<blockquote>\n<p>Would it be possible to systematically deduce what this organism looks like and behaves like <strong>without reference</strong> to anything else (ex: a repository of genomes of known living organisms)?</p>... | [
{
"answer_id": 103024,
"pm_score": 3,
"text": "<p>No, current technology is nowhere near what is required to deduce the form of a species from its DNA alone without comparing it to the DNA of the same or similar species.</p>\n<p>The reason for this is that genes in the DNA generate proteins and these pr... |
104,526 | <p>As I understand it, <em>co-dominance</em> is when both genes in an allelomorphic pair produce both their effects <strong>equally</strong> on the organism in question whilst <em>incomplete dominance</em> applies to an instance where a mix of the effects of two alleles are present — i.e. where one allele is not completely masked by the other.</p>
<p>However, I had this notion challenged by the following paragraph I obtained from a reputable online source:</p>
<blockquote>
<p>Carnation plants show co-dominance for the anthocyanin gene. There are two alleles:</p>
<p><span class="math-container">$F^A$</span> – allele for anthocyanin pigment (red flowers)</p>
<p><span class="math-container">$F^N$</span> – allele for no anthocyanin pigment (white flowers)</p>
<hr />
<p><strong>[...] a carnation plant heterozygous for this gene would yield pink flowers [...]</strong></p>
</blockquote>
<p>Shouldn't the phenotype of the flower be <strong>red and white</strong> as opposed to being <strong>pink</strong>, as the alleles have been said to exhibit co-dominance? Anything I am probably missing out on?</p>
<hr />
<h2>EDIT</h2>
<p>I have bountied this question because I think I have a major hole with my understanding on this topic somewhere; to give you some perspective, I am a High-School Sophomore currently on an introductory course in Mendelian Genetics/Inheritance.
I read through @swbarnes2's answer where they say:</p>
<blockquote>
<p>In the case of flowers, <em>if you have two different alleles for the same pigment gene, you <strong>will</strong> see a blending</em>, because all the pigment-making cells will produce from both alleles.</p>
</blockquote>
<p>In such a case (if this always happens), where do the ideas of codominance and incomplete dominance come in? According to my textbook, the following terms are defined as:</p>
<blockquote>
<p>If both genes of an allelomorphic pair produce their effects in an individual (i.e neither allele is dominant to the other) the alleles are said to be co-dominant.</p>
</blockquote>
<p><a href="https://i.stack.imgur.com/NWrss.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/NWrss.png" alt="codominance" /></a></p>
<blockquote>
<p>Incomplete dominance applies to a case where the effect of the recessive allele is not completely masked by the dominant allele (in this case, I assume, a blending would occur)</p>
</blockquote>
<p><a href="https://i.stack.imgur.com/8RlVo.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/8RlVo.png" alt="enter image description here" /></a></p>
<p>(I do get that this may not apply to carnation plants, but would it be safe to follow the phenotypes predicted by my textbook definitions for all other cases?)</p>
<p>Hope someone could clear my doubt; I am extremely confused to read (in the comments section) why co-dominance would not mean both colors/phenotypes are shown simultaneously — like being red and white (as opposed to them mixing into pink).</p>
| [
{
"answer_id": 104530,
"pm_score": 4,
"text": "<p>Unfortunately, that nomenclature is kind of old-fashioned; it predates our understanding of what's going on at a molecular level. Don't get hung up on the language. Lots and lots of genes and alleles just don't fit into the paradigm of dominant and rec... | [
{
"answer_id": 104531,
"pm_score": -1,
"text": "<p>Friend..you got the meaning of co dominance and incomplete dominance correct... but let me make co dominance easy... its just like mixing colors on a color plate...think it just like that.... otherwise in real sense both colors are indivisually expresse... |
104,960 | <p>Are there examples of new ORFs in SARS-CoV-2 created by mutations?</p>
<p>The ORFs should not be present in the reference virus, but they should occur in a lineage occurring in the wild (at best, being part of the definition of the lineage). Of course those ORFs will somehow overlap with the well-known ORFs of the virus, potentially frame-shifted.</p>
<p>Bonus: Is there evidence that a protein is produced from the newly emerged ORF?</p>
| [
{
"answer_id": 104982,
"pm_score": 3,
"text": "<p>There is surely better but</p>\n<ul>\n<li><p>A few sequences have G881T which extends MKIFKKTGTLNIAVVLPVNSCVSLTEGHTLAMSITTSVALMATLLSALKTF\nto MKIFKKTGTLNIAVVLPVNSCVSLTEGHTLAMSITTSVALMATLLSALKTFYHVLVKLHALCPNNWTLLTLRGVYTAAVNMSMKLLGTRNVLKRAMNCRHLLKLNWQRNLT... | [
{
"answer_id": 104973,
"pm_score": 2,
"text": "<p>The answer to this is both yes and no.</p>\n<p>The reason I say yes and no is that SARS-CoV-2 exists as what is known as a <a href=\"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008271\" rel=\"nofollow noreferrer\">quasispecies... |
105,119 | <p>I’m a student in the Biochemical Engineering field and the professor at the department just told us in a lecture that if we want to use a <strong>full-antibody structure</strong> for simulation purposes there aren’t very many of them. He suggested that we start with 1hzh.pdb.</p>
<p>So I wondered whether he was correct and, if so, why there wasn’t anyone using crystallisation or NMR to look into the structures of the antibody drugs that have come onto the market. Perhaps it costs too much and it’s very time-consuming? But, even so, I imagine that it would still be worthwhile.</p>
| [
{
"answer_id": 105168,
"pm_score": 3,
"text": "<p>The more flexible a molecule, the more difficult <a href=\"https://www.cambridge.org/core/journals/mrs-bulletin/article/abs/shape-change-in-crystallization-of-biological-macromolecules/63327B810503E63A4A154BAE643F010D\" rel=\"nofollow noreferrer\">it is<... | [
{
"answer_id": 105120,
"pm_score": 1,
"text": "<p>There are thousands of structures in the PDB of neutralizing antibodies against all sorts of viruses using all sorts of methods (NMR,x-ray,electron microscopy) as complex or stand alone. I guess your professor has certain requirements that are rarely met... |
107,021 | <p>I don't have a background in biology, but is trying to learn more about genetics; I have watched many videos about SNPs and still feel confused about the concept of a single nucleotide polymorphism. According to wikipedia, a SNP "is a germline substitution of a single nucleotide at a specific position in the genome". What I am most puzzled by is the concept of a 'specific position in the genome', if chromosome lengths differ, how can we talk of a 'specific position'?</p>
<p>For example, if we have two arrays of items that are of the same length:[A,C,C,C,A,T,G] and [A,C,G,C,A,T,G] then it is straightforward to that the entries at the third position of each array are different. But with chromosomes, their lengths differ, so it might look like: [A,C,C,C,A,T,G] and [A,C,C,C,A,A,T,G], now how can we say what corresponds to what? Do we say there is a SNP at the fifth/sixth base pair?</p>
<p>What about something more different like [A,C,C,C,A,A,T,G] and [C,C,A,A]? How do we know what corresponds to what? What are the SNPs?</p>
<p>What if two individuals each has a chromosome 1 that differ by many base pairs, how do we know what corresponds to what?</p>
| [
{
"answer_id": 107023,
"pm_score": 4,
"text": "<p>The reason we can compare SNPs between different people is because sequencing reads are aligned to a reference genome with a fixed set of coordinates for each chromosome (local alignment), rather than aligning the entire chromosomes of two different peop... | [
{
"answer_id": 107024,
"pm_score": 2,
"text": "<blockquote>\n<p>so it might look like: [A,C,C,C,A,T,G] and [A,C,C,C,A,A,T,G], now how\ncan we say what corresponds to what? Do we say there is a SNP at the\nfifth/sixth base pair?</p>\n</blockquote>\n<p>We say the second one has an insertion at 5.</p>\n<p>... |
108,104 | <p>I am looking for information about the use of glucosamine and chondroitin for treatment of back pain and disc degeneration. A paper published in <a href="https://academic.oup.com/milmed/article/164/2/85/4832145" rel="nofollow noreferrer">Military Medicine in 1999</a> reported some beneficial effects, but newer papers (references needed) do not support these conclusions.</p>
<p>How do I search for more recent papers that cite this older paper, to decide what the current medical consensus is?</p>
<p>Glucosamine trial (negative results):</p>
<p><a href="https://smallpdf.com/result#r=a595b512d3b25e41aabe7f3179ba8a4b&t=share-document" rel="nofollow noreferrer">https://smallpdf.com/result#r=a595b512d3b25e41aabe7f3179ba8a4b&t=share-document</a></p>
<p>Chondroitin Sulfate trial (negative results):</p>
<p><a href="https://smallpdf.com/result#r=b82b6b31030bfb6dffd6261a48153fe7&t=share-document" rel="nofollow noreferrer">https://smallpdf.com/result#r=b82b6b31030bfb6dffd6261a48153fe7&t=share-document</a></p>
<p>Glucosamine and Chondroitin Sulfate(good results but not conclusive)</p>
<p><a href="https://smallpdf.com/result#r=626038b39e87cc64baab274e1d053871&t=share-document" rel="nofollow noreferrer">https://smallpdf.com/result#r=626038b39e87cc64baab274e1d053871&t=share-document</a></p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165439/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165439/</a></p>
| [
{
"answer_id": 108113,
"pm_score": 4,
"text": "<p>Papers provide <em>evidence</em> for or against various hypotheses, but no one paper is ever a definitive statement on an issue. It is expected that different trials will have different outcomes, both due to differences in the studies themselves (differe... | [
{
"answer_id": 108111,
"pm_score": 2,
"text": "<p>Use google scholar and have a look at the papers that have recently cited it by filtering for the year the citing paper was published.</p>\n<p><a href=\"https://scholar.google.com/scholar?cites=17068797659415407733&as_sdt=2005&sciodt=0,5&hl=e... |
109,168 | <p><em>Reader :</em> please consider that I don't know anything about biology, which is the case by the way.</p>
<p><strong>Context :</strong> I am currently preparing a presentation for a research grant application, which I will submit to a jury of mathematicians for their decision. My first slide aims to highlight the fact that human beings have a natural reflex to classify the objects around them, and to do this I consider the case of two objects that are a priori <em>distinct</em>, but which are <em>equivalent</em> by convention: they are just two apples (image). To be clear, I need to say <em>why</em> they are equivalent.</p>
<p><strong>Question :</strong> Biologically speaking, what justifies that these two <em>a priori</em> distinct objects are indeed two apples, and therefore biologically equivalent? As a biologist, what is the justification you would give to say these two things are quite the same?</p>
<p><a href="https://i.stack.imgur.com/8Scyu.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/8Scyu.png" alt="Two distinct apples :)" /></a></p>
| [
{
"answer_id": 109169,
"pm_score": 4,
"text": "<p>Biologists aren't the people who decided what an "apple" is, the general population of users of language are.</p>\n<p>You could try back-create a definition that is biologically relevant based on descent, for example "fruit of plants in th... | [
{
"answer_id": 109170,
"pm_score": 1,
"text": "<p>My answer: based on DNA similarities I can confidently tell you whether two "things" are so similar they merit similar names.</p>\n<p>Other points to mention: We might call two things similarly without necessarily implying that they are the sam... |
110,447 | <p>I have searched through various websites, however, I am still rather confused with the difference between 'genotype' and 'alleles' since each site seems to be contradicting another site.</p>
<p>I would be much grateful if someone could please give me a concise and clear differentiation between 'genotype' and 'alleles'.</p>
| [
{
"answer_id": 110450,
"pm_score": 4,
"text": "<p>Please note that opinions on the exact wording of the following can differ a lot. You will have to find one for yourself that works best for you.</p>\n<p><strong><a href=\"https://www.nature.com/scitable/definition/gene-29/\" rel=\"nofollow noreferrer\">... | [
{
"answer_id": 110449,
"pm_score": 2,
"text": "<p>An allele is a variant of a gene, while a genotype is an (arbitrarily) specified combination of alleles, mostly stating the homo- or heterocygous presence or absence of certain mutation(s) in a certain gene or combination of genes. E.g. Genotype A: Gene ... |
110,819 | <p>It is my (very basic) understanding that neither plants nor animals utilize the nitrogen in the atmosphere. Humans do not make use of atmospheric nitrogen through respiration and plants do not extract nitrogen from the air, but rather from the soil. First of all, am I correct in this understanding?</p>
<p>If I'm right so far, then what role (if any) does the nitrogen in our atmosphere play, biochemically speaking?</p>
<p>I understand that it plays a significant <em>physical</em> role, contributing to air pressure, allowing light to permeate, allowing liquids to exist on the surface, burning up incoming meteors thus protecting life, and basically being a physical gas that is not oxygen or carbon dioxide thus keeping the concentration of those gasses low. But I'm interested in the <em>biochemical</em> use of atmospheric nitrogen if any. So, is nitrogen a necessary atmospheric component for life, in terms of its chemical reactions with living things? Or is the atmospheric nitrogen essentially unused in the chemistry of life?</p>
| [
{
"answer_id": 110820,
"pm_score": 6,
"text": "<p>To get soil nitrogen in the first place, <a href=\"https://en.wikipedia.org/wiki/Nitrogen_fixation\" rel=\"noreferrer\">nitrogen fixation</a> is necessary which takes atmospheric N<sub>2</sub> and converts it into biologically useful forms.</p>\n<p>Nitro... | [
{
"answer_id": 110830,
"pm_score": 2,
"text": "<p>While atmospheric nitrogen is definitely necessary for keeping up the ecosystem of Earth as we know it (as Brian Krause has already pointed out), it is not really a necessity for some life form on earth, especially among the <a href=\"https://en.wikipedi... |
111,146 | <p>The majority of western nations have lifted most if not all COVID restrictions, however we are not seeing a massive rise in serious cases of COVID-19.</p>
<p>Why is it different in China? Do they have a different strain?</p>
| [
{
"answer_id": 111147,
"pm_score": 6,
"text": "<p>There are a number of different reasons, all adding up to the current situation.</p>\n<ol>\n<li><p>The strain: There is not a special strain going on in China, according to different references it is mostly the Omicron BF.7 substrain. This strain is high... | [
{
"answer_id": 111172,
"pm_score": 1,
"text": "<p>1/ China hasn't built up natural herd immunity, only 0.1% has had it.</p>\n<p>2/ Restrictions are lifting in winter, the worst time to lift them for a low immunity nation.</p>\n<p>3/ Some Chinese populations are frustrated by extreme and unreasonable cov... |
111,169 | <p>I was reading the paper "A survey of methods and tools to detect recent and strong positive selection" (2017) and came across this:</p>
<blockquote>
<p>Upon fixation of the beneficial mutation, elevated levels of LD emerge
on each side of the selected site, whereas a decreased LD level is
observed between sites found on different sides of the selected site.
The high LD levels on the different sides of the selected locus are
due to the fact that a single recombination event allows existing
polymorphisms on the same side of the sweep to escape the sweep. On
the other hand, polymorphisms that reside on different sides of the
selected locus need a minimum of two recombination events in order to
escape the sweep. Given that recombination events are independent, the
level of LD between SNPs that are located on different sides of the
positively selected mutation decreases.</p>
</blockquote>
<p>I am having trouble understanding how this works. If I am understanding this correctly, if you took two sites on the <em>left side</em> of the beneficial mutation during a selective sweep, you would see high LD between them. The same goes for taking two sites on the right side of the beneficial mutation. (Provided they are close enough to the mutation site of course.) However, if you took one site 300 bp to the left of the mutation, and another 300 bp to the right of it, you may not see the same rise in LD. I am not sure why this would be the case: wouldn't the entire region linked to the beneficial mutation, regardless of which side of the mutation it occurs to, be co-inherited and thus display similar high LD across the board, provided it is overall close enough to the site of beneficial mutation?</p>
| [
{
"answer_id": 111147,
"pm_score": 6,
"text": "<p>There are a number of different reasons, all adding up to the current situation.</p>\n<ol>\n<li><p>The strain: There is not a special strain going on in China, according to different references it is mostly the Omicron BF.7 substrain. This strain is high... | [
{
"answer_id": 111172,
"pm_score": 1,
"text": "<p>1/ China hasn't built up natural herd immunity, only 0.1% has had it.</p>\n<p>2/ Restrictions are lifting in winter, the worst time to lift them for a low immunity nation.</p>\n<p>3/ Some Chinese populations are frustrated by extreme and unreasonable cov... |
111,196 | <p>In the answer(source - Campbell Essential Biology with Physiology, self-quiz question), it's given that "if the change doesn't affect the protein's shape in any way then it's possible to do so". But practically, is it possible to amend a protein without changing its shape?</p>
| [
{
"answer_id": 111147,
"pm_score": 6,
"text": "<p>There are a number of different reasons, all adding up to the current situation.</p>\n<ol>\n<li><p>The strain: There is not a special strain going on in China, according to different references it is mostly the Omicron BF.7 substrain. This strain is high... | [
{
"answer_id": 111172,
"pm_score": 1,
"text": "<p>1/ China hasn't built up natural herd immunity, only 0.1% has had it.</p>\n<p>2/ Restrictions are lifting in winter, the worst time to lift them for a low immunity nation.</p>\n<p>3/ Some Chinese populations are frustrated by extreme and unreasonable cov... |
111,225 | <p>It is always told that eating meat is bad for our climate. This is most often explained by mentioning following reasons (<a href="https://en.wikipedia.org/wiki/Greenhouse_gas_emissions_from_agriculture" rel="nofollow noreferrer">Source</a>):</p>
<ul>
<li>Methane is produced when digesting the food and also the faeces of cows produces greenhouse gasses afterwards</li>
<li>Fertilizers produce greenhouse gases</li>
<li>The processing of food with machines produces CO2</li>
<li>The farming of land with tractors etc. produces CO2</li>
</ul>
<p><strong>The last three points I can understand. But I have some problems understanding the first.</strong> My questions in this regard are:</p>
<ol>
<li>Cows emit methane. But the methane is produced by digesting plants. The plants themselves got the carbon from the atmosphere. So at least this is a closed cycle and no net greenhouse gases are emitted. <strong>Isn’t livestock therefore climate neutral?</strong></li>
<li>It may be that especially for factory farming, forests are cut down. This produces a lot of CO2. But <strong>I also heard that the plants that are grown may store more carbon then the trees that were there before. Is this true?</strong> If no, is this really the only reason meat is not carbon neutral?</li>
<li><strong>How is the carbon footprint of livestock even determined?</strong> Is it really determined by the forest which was cut down in order to produce food or is just the methane exhaust of the livestock measured?</li>
</ol>
<p><strong>Own research</strong></p>
<p>In <a href="https://civileats.com/2018/04/10/can-responsible-grazing-make-beef-climate-neutral/" rel="nofollow noreferrer">this</a> source it is stated that grass feed cows may be carbon neutral in the long run (under optimal conditions) and may even increase carbon capture in the short run. Nevertheless, nothing is stated why this is not true for crop feed cows (how do crops and grass differ in this regard?)</p>
<p>On <a href="https://www.earth.com/news/trees-grass-carbon-sink/" rel="nofollow noreferrer">this</a> site it is stated that “[Only] In a stable climate, trees store more carbon than grasslands”. But what’s about crops like wheat? They have more biomass and deeper roots than simple grasses. Also there may be several wheat plant on the area one tree takes. I found nothing regarding this on the web.</p>
<p>Ps. I am not a biology professional so please forgive me if I misuse some terminology and do not cite scientific papers.</p>
| [
{
"answer_id": 111241,
"pm_score": 3,
"text": "<h4>Short Answer</h4>\n<p>I'll address the first two of your three subquestions:</p>\n<ol>\n<li><p>Livestock are <strong><em>not</em> climate neutral</strong> because different processes of the <a href=\"https://en.wikipedia.org/wiki/Carbon_cycle\" rel=\"no... | [
{
"answer_id": 111232,
"pm_score": 1,
"text": "<p>I have found an answer for your first question. The <a href=\"https://en.m.wikipedia.org/wiki/Global_warming_potential\" rel=\"nofollow noreferrer\">Global Warming Potential</a> of methane is much higher than that of carbon dioxide. Because methane stays... |
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