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Would intravenous insulin + glucose significantly accelerate glycogen synthesis?
Would an intravenous injection of insulin + glucose result in significantly quicker replenishment of exhausted glycogen stores than an injection of glucose alone?
This is a strictly theoretical question and I'm aware of serious dangers of intravenous insulin (Diabetes Spectrum). It is to help with writing a story in which a quick recovery from exhaustion is needed.
After heavy exercise, during which the glycogen stores are depleted, the glycogen can be replenished fully in about a day by consuming high-carbohydrate meals (PubMed).
According to one study, intravenous glucose stimulates glycogen synthesis, but there is no timing mentioned.
Would adding insulin into glucose injection further accelerate glycogen synthesis and for how much? Is there any minimal time needed for glycogen synthesis regardless of the amount of glucose and insulin available?
The added insulin would probably inhibit the natural secretion of insulin from the pancreas, so does intravenous insulin injection even make sense?

What is the mechanism you presume?  (Do you presume signaling in a feedback loop - or, what you mean is depletion of (elevated) blood sugar?

Concluding from this 1991 PubMed article, intravenous (or subcutaneous) insulin may not stimulate glycogen synthesis more than naturally secreted insulin.

Experiments carried out in man have suggested that insulin may play
  only a permissive role in the determination of splanchnic glucose
  uptake. In a study by DeFronzo et al. (5), in which the plasma glucose
  and insulin levels were raised via peripheral intravenous infusion to
  223 mg/dl and 55 μU/ml, respectively, net splanchnic glucose
  uptake was 1.0 mg/kg per min. The rate of glucose uptake did not
  change appreciably when the arterial insulin level was raised further
  to 191 μU/ml.

So, at insulin level 191 μU/ml, there was no greater hepatic glucose uptake than at 55 μU/ml and hence no further stimulation of glycogen synthesis.
According to Emedicine, insulin levels can increase to 276 μU/ml 1 hour after glucose administration.
Which means that even naturally secreted insulin can reach levels that no longer stimulate glycogen synthesis and there is no point to give insulin by injection to stimulate it.

does intravenous insulin injection even make sense?

No, it does not make sense for two reasons:

Half-life of insulin: Insulin has a half-life on the order of minutes. On the other hand, it takes much longer to remove the blood glucose and turn it into glycogen. This is why people with type 1 diabetes receive injections of microcrystalline insulin subcutaneously to form depots that are released into the blood stream at a slower pace.
The body is able to make its own insulin in time: We are used to large increases in glucose levels, and the pancreas is quick in responding with secretion of insulin. So you are trying to find a solution for a problem that does not exist. Of course, injecting glucose instead of eating carbohydrates raises the blood sugar level more quickly. However, the processes downstream of insulin mobilization take some time too. So it the glucose concentration administered intravenously is too high in the absence of extra insulin, extra insulin will not fix the problem (and the problem could be death).

Intravenous insulin injections exist and can be used to treat severe hyperglycemia https://emedicine.medscape.com/article/2049152-overview . They can be used in emergeny cases in hospitals and not by patients at home, because, yes, they can cause dangerous hypoglycemia.

You did not  integrate that "paradox" into your answer: how can hypglycemia by to much insuline occur if, according to answer, adding more insuline does not add to depletion of blood sugar?


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skin colouration in thalassemia
Now when i was studying about thalassemia, I read that anaemia is its major characterstic. I can understand that fact. But it was also written that the skin gets pale.

Wikipedia says that the skin turns yellowish.

I want to ask firstly is it that the skin gets darker when the affected person is exposed to sun and is otherwise pale?
And also why does the skin turn yellow/pale in the first place? Does that have to do something with Iron?

Thalassemia is a genetic disease, in which either the alpha- or the beta-globins are missing or mutated. The hemoglobin of the blood is a protein complex which in adults consists of 2 alpha- and 2 beta-globin subunits. The ratio of these proteins needs to be exactly right, if one of them isn't produced enough or even missing, this leads to non-functional hemoglobin and subsequently abnormal erythrocytes.
These are then removed and broken down in the spleen (which is often abnormally enlarged), which also leads to the breakdown of the non-functional hemoglobin. The main product of the hemoglobin breakdown is Bilirubin, which is yellow. The yellow skin is a sign of jaundice, which is caused by high levels of Bilirubin in the blood.
The cause for the high Bilirubin levels in the blood of Thalassemia patients is the abnormal high rate of Hemoglobin breakdown.

But how is it even related to thalassemia? @Chris

@Ishi It is. I will expand the answer.

@Ishi Is this clearer now?

This is such a great answer, thankyou so much, I understand it now ! @Chris

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Selective breeding fluorescent sheep - possible?
I got into a small argument :-)
Friends of mine try to draw fat line between "natural" selective breeding and applying molecular biology (CRISPR/Cas9) to put new traits in existing species. The line of their argument is "GMO is something different, because you can't (in reasonable timeframe, ~1000 years) breed a sheep that will glow in the dark.
Intuitively I think that doing so is possible even without molecular tools to "write" new genes, just using things like horizontal gene transfer and "standard" breeding (I reserve right to use all modern knowledge and tools to plan and monitor progress). I don't have much to substantiate this claim though.
In your enlightened opinion, who is correct?

We welcome new posters to SE Biology but ask them to read what sort of questions we encourage here, namely "questions about an actual problem you have faced", and those we don't, namely, questions the answers to which will be subjective. We are not here to arbitrate hypothetical arguments, even if we do have our own opinions, "enlightened" or otherwise.

Understood, and sorry if I did not adhere to guidelines - I can only say that is a community I trust to give me valid answers, hence I asked here.

Welcome to Bio.SE. Very interesting idea and I am definitely bringing this up at lunch! I think framing your question as a debate between GMO and selective breeding isn't clear. A more format friendly way of getting your answer would be "Has bioluminescence ever been selectively bred into animals or plants?" Remember to show evidence that you've attempted to answer the question yourself (maybe check google scholar).  Also, note that CRISPR is not the only way to introduce specific genetic changes into organisms.

Natural horizontal gene transfer in higher animals is possible, but still very rare.
If any transfer happens then it's usually from micro-organsims (viruses/bacteria) or parasites to the host animal (or the reverse). Transfer of genes from any other source to animals is almost unheard of, because the transfer needs to affect the germline (sperm / eggs) to last more than a single generation and anything that doesn't live inside an animal is unlikely to get there.
Therefore your example of getting GFP (or any other fluorescent gene) into a sheep is highly unlikely$^1$, even with a 1000 year timespan.
You'd need a virus or bacteria that has a fluorescent gene and naturally infects/lives in/on sheep. However, no natural bacteria or viruses have a fluorescent gene in the first place (they almost all come from corals or jellyfish). Another problem is that just having a fluorescent gene somewhere in the DNA, doesn't mean the any part of the organism is fluorescent; once its in the gene pool this should be achievable by breeding though.

You'd have to wait for HGT of a fluorescent gene from a source animal/life form to bacteria. (Time estimate is super hard, you can maybe house some of these jellyfish in a fish tank regularly sequence the bacteria that live with them to see if HGT happened.)
Then the genes needs to be transfered to a bacterial/virus strain native to sheep (This is relatively easy/fast, since bacteria are quite proficient at HGT between each other)
Lastly you need a 3rd round of HGT from the bacteria to the germline of the sheep. (Again this might take 'forever': most mammals don't like bacteria or viruses living in or near their reproductive organs. Also at least from this point on animal experiment laws will become a serious hurdle to your project).

1) This is a researchers highly unlikely: without trying this, its not correct to say impossible, but the chances are so low that for all practical purposes it might as well be impossible.

Great answer, thank you :-) I actually thought about using fluorescent bacteria to start with, but this only cuts time in half, not in orders of magnitude :D

Perhaps you can add that even if someone infects the animal with a bacteria/virus carrying a foreign gene, that is still artificial genetic modification (albeit an inefficient technique compared to CRISPR-Cas).

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Human Stem Cells and Disease
Can human stem cells be stored for use by future family members as a way to combat generational diseases like diabetes

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

Stem cells can be stored but that is an expensive alternative to generating them freshly. It has been shown that you can make stem cells from skin cells.
Theoretically, it would be much less expensive to store a piece of epidermis from a recently deceased relative than to make fresh stem cells and store those.
However, the research for generating stem cells from deeply frozen tissues is not there yet. Furthermore, the concept of using stem cells to 'combat disease' is not the right paradigm. It might even be said that some diseases (cancer) are the result of dedifferentiation gone awry.
Where stem cell transplants are used is in the replacement of bone marrow after total body radiation/chemotherapy to destroy marrow (in those cases where the disease has arisen in the marrow). In these cases we rely on the poorly defined process that allows cells to target their microenvironment.
For example, it would not work if marrow replacement cells decided to grow wherever they landed (lungs, liver,etc).
So stem cell storage is an option whose time has passed ,as our tech now allows us to make them.


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What sauropod genera had a double row of chevron bones in the tail?
I know that Diplodocus is marked by the feature of having a double row of or "double-beamed" chevron bones in the tail, but how diagnostic is this feature if several other sauropods have it? I mean, if there are other genera with the feature, which ones are they, so I know not to confuse them with Diplodocus?

It's fairly common. It is believed to have evolved two times independently, basically in both groups presumed to use their tails as weapons. Both Diplodocoidea and Euhelopodidae have species with forked chevrons and evolved it independently. It is fairly diagnostic since it is not seen outside these groups.
Source
Independent half chevrons (two rows of individual elongated splints of bone, one right, one left) pop up in many groups but double beamed chevrons are something different: the ends of the chevrons are joined, creating a single solid structure. In some parts of the tail they are separated into right and left halves (these are not very unique), but the joined ones are taxonomically significant. These are not chevrons dwindling into nothing along the tail but changing structure in a specific structurally significant way.

Thank you for your answer, but I am still not clear on something. Did you mean to say that ALL genera in Diplodocoidea and Euhelopodidae had double-beamed chevrons? I knew that at least some did, but I am trying to know which genera specifically so I can have a relatively quick and easy way to distinguish the specific genus Diplodocus from the rest of Diplodocoidea (e.g., Barosaurus and Galeamopus).

most Diplodocoidea do (it is lost on some of the Dicraeosaurus who re-evolve short tails) and only a few Euhelopus do it appears to be a an independent evolution. It is hard to say definitively because so many sauropods are known from only a few elements.  It is not a good distinguishing feature simple because it is one of the smaller more easily lost elements.


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What can eating pink mold do to a healthy person (someone whose immune system is not weakened)?
I've tried searching it up, but my research has yielded nothing very specific.
The following website was the closest I came to finding something about pink mold on bread. It, however, said nothing about the effects of eating pink mold (https://moldcleans.com/pink-mold-on-bread/)
I also found another website, https://lookmold.com/detect/type/pink-mold, which states that healthy (people without compromised/weakened immune systems) people don't get sick right away from exposure to pink mold. Other sources, however, claim that only people with compromised immune systems will get infected by a fungal infection. Hence my question: what can eating mold do to a healthy (healthy immune system) person?
Edit: Thanks to all who responded! The advice was very helpful. I have also edited my question to fit the rules, for I am still curious about the effects of pink mold on a healthy person.

Just fyi your second linked source says "It’s not actually mold! That’s right, it’s actually bacteria. For the sake of this article we will refer to it as pink mold. The name of the bacteria is called Serratia marcescens." It's great that you did some research before posting your question here. It may not be true that what you saw in the muffin is the same as what is commonly found on bathroom walls. You should save all traces of the muffin you ate and any other muffins and consider seeing a doctor. Stack Exchange is not the right place to ask real personal health-related issues.

Was the patch fuzzy? If not it wasn't mold. But it could be pink yeast which can be found in spoiled dood according to wikipedia. https://en.m.wikipedia.org/wiki/Rhodotorula_glutinis

I reopened this question because I had previously unilaterally closed it for being a request for personal medical advice. I still think it could use a bit more clarity and prior research to be a good Biology.SE question, but I'll leave it up to the community.


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Is DNA actually like source code repository?
So after reading articles like "People Use Just 8.2% of Their DNA" etc., and thinking a bit... I got this idea:
What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.
So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.
Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?
This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!
Also this explains why human embryo come though all this steps of been single cell, multi-cell, fish, amphibian, mammal etc.
I'm no expert in biology by any means, and I suspect that this idea was around for long time, but I'm not sure... What do you think?

Comments are not for extended discussion; this conversation has been moved to chat.

@BryanKrause — Let’s make it clear. I have no wish to discuss anything, only to use the comment box for it’s correct purpose to ask the poster for clarification: What is your biological question?

that seems to me like a very open-ended "discussion"-type question right now. How is it about biology?

@David umm... this hardly seems like the place to discuss it. Please take it to meta if you feel it's important.

@rotaredom — “Discuss”? I’m asking the poster to clarify his question. Poster, are you asking what junk DNA is, whether it’s the decaying remnants of duplicated genes, whether the expansion of the gene repertoire of organisms occurs/ed by duplication, whether duplicated genes can acquire different functions or what? But just one at a time, please. Biology is an experimental science. A lot of genomes have been sequenced and analysed and we can attempt to answer questions on the basis of this analysis. Proposition of theories by people, however much biology they know, is not a question.

I think this analogy is not actually that bad, but you are making some incorrect conclusions from it especially regarding 'junk' DNA and which parts of a repository DNA holds (which shows the limits of analogy!). Think instead of the DNA of an organism as a single local copy of a particular commit.
There is no remote to compare to and no list of historical changes, each organism just has its own local copy of the most recent source that can sometimes be merged with other local copies via sexual reproduction or horizontal gene transfer.
What you need to drop from the analogy
Get rid of any thought of a master branch or ideas that the repository contains backups of previous versions. These thoughts will only mislead you.
This statement:

original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

makes little to no sense in biology. There is no backup, except in that each organism is a branch of it's parent(s) source.
Where the analogy could work
Genomes of different species are all branches from some original source code. Therefore, you find a lot of commonality when you compare even very distantly related life, especially in the most key libraries that are involved. There is a ton of conserved sequence in the basic machinery for replicating DNA and producing proteins, for example.
This is why your statement:

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

is mostly correct.
Length of source
Your analogy has gotten some criticism for your conclusion:

Theoretically, the more primitive organism is, the shorter DNA it should have.

but I would argue this is actually a way in which your analogy works, yet your conclusion from it does not. Software development involves both adding new code and deleting obsolete code. Lines of code is a poor measure of how primitive some code is. Biology shows this well: all life is equally primitive in terms of years of existence, and single-celled organisms are much more advanced in terms of numbers of generations. If organisms contained some log of all the past changes (which they do not), the repository would be way way bigger in bacteria than in animals because of that large number of generations.
Summary
In summary, analogy can be helpful to wrap your head around some information, but be careful in taking it too far. Sometimes analogy is good for generating new hypotheses and for guiding your learning, but you need to verify those hypotheses in the actual biology (see Richland and Simms 2015 for one take on the usefulness of analogy as an educational tool).
I disagree strongly with the comment by @SPr stating "The analogy between the genome and source code repository is unhelpful and poor": even the imperfection in an analogy can be very helpful in that they help you build a relational map of the world by finding where analogies work and where they conflict.

Richland, L. E., & Simms, N. (2015). Analogy, higher order thinking, and education. Wiley Interdisciplinary Reviews: Cognitive Science, 6(2), 177-192.

Watch out with analogies. Even when they are somewhat helpful, they are only analogies. That being said, unfortunately, your analogy is completely unhelpful!

What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.

It is unclear what you would call "junk" here. Typically, if you include regulatory sequences in "junk" as it is often done by lay people (see @iayork comments below for more information), clearly they are being used and are essential. But anyway, seeing non-coding, non-regulatory sequences (such as the ALU sequences) as experiments would be very misleading. Large amount of repetitive DNA usually comes to existence through the work of transposons and retrotransposons. They are not attempts (clearly not with an intuition but even without intuition in mind) to make something "better"

So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

DNA get lost all the time. A mutation can alter the code, it can also duplicate sequences (or even whole chromosome or whole genome) and it can "remove" sequences (even "remove" whole chromosomes). Genome reduction is indeed not that uncommon.

Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?

"Old sharks that still survived from the Mesozoic era" are not more primitive than humans, E.coli or than the European green lizard. At least not in any way that "primitive" is easy or intuitive to define. Please have a look at the post Are we “more evolved” than present-day bacteria? for more information.

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

I am not sure I understand what you have in mind here.
Any two extant lineage share a common ancestor at some point in the past. Depending upon how recent is their Most Recent Common Ancestor (usually abbreviated MRCA), they are more or less likely to have similar genome.

Also this explains why human embryo come though all this steps of been single
  cell, multi-cell, fish, amphibian, mammal etc.

I am not sure I understand what you have in mind here.
There is MRCA of all living creatures on earth is called LUCA (Last Unversal Common Ancestor). We don't know much about LUCA but it was pretty clearly single celled and had a relatively short genome. Note btw that LUCA itself is not the very first cell though but that does not matter much for our discussion.

Typically, if you include regulatory sequences in "junk" (as it is generally done, I think) Not so. Although there are a lot of people who attack the concept of junk DNA with this as a straw man, regulatory sequences are not and never have been considered part of junk DNA. Doesn't change the rest of the argument, just a caution

I don't know what meant the first people who coined this term but my first 5 google results for "junk DNA" define it as "non-coding DNA". But yes, let's be cautious that it might not be what everyone mean at least. Answer edited. Thanks

The original definition did not use that - I agree it's often used that way, but actual researchers on the field are much more strict. See The Case for Junk DNA, especially the section The origin of “junk DNA”

I would compare DNA to a computer filesystem rather than a source code repository. Coding sections are "programs" that can be run to produce a protein product. An important difference, however, is alternative splicing, where a gene can code for multiple products. This serves as a form of "compression on disk", where repeated regions can be represented by a copy and pointers wherever the region is required.
The vast majority of what was previously called "junk" DNA instead turned out to be important for other purposes. For example, some serve as regulators or recombination faciliators (source - https://www.scientificamerican.com/article/what-is-junk-dna-and-what/), some serve important structural purposes (source - https://www.sciencedaily.com/releases/2018/04/180411131659.htm), and others serve as important binding sites for transcription control (source - https://ghr.nlm.nih.gov/primer/basics/noncodingdna)
Think of noncoding DNA as filesystem metadata - stuff like file allocation tables, master file tables, journaling, and the master boot record that doesn't represent actual data - although your computer will probably break if this data disappears. Again, the analogy doesn't fit too well considering only about 1.2% of the human genome is coding regions (source - https://www.bing.com/search?q=what+percentage+of+the+human+genome+is+noncoding&pc=MOZI&form=MOZSBR ). On the other hand, computer filesystems are generally designed to minimize the amount of metadata overhead since that costs you an extra storage space that could otherwise be used for files.
Further reading on "junk" DNA that really isn't garbage:
https://www.scientificamerican.com/article/what-is-junk-dna-and-what/
https://www.sciencedaily.com/releases/2018/04/180411131659.htm
https://ghr.nlm.nih.gov/primer/basics/noncodingdna


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Why are mules/donkeys aggressive when faced with predators but horses are not?
I came upon an interesting quote after going down the rabbit hole on a variety of subjects. While deep in the data, I came upon this quote

oat and farm animal owners likes to have mules with their herds because donkeys or mules will actually attack predatory animals such as foxes and coyotes.

Which raised quite a few questions in my mind. I was able to find additional sources as it relates to the predisposition of the given species.
Seemingly, donkeys and mules will act aggressively in confrontation with predators and attempt to attack to the point of killing many of them. Is there something about the physiology of a donkey/mule that makes them much less timid? Perhaps body structure? Seemingly a horse has equal or even better tools to try and defend itself.
Here are the sources (the first 2 are not the most authoritative by any means):

 Mule Behavior: Differences with horses and donkeys
Mule Facts
Donkey Behavior: A comparative study of donkey and horse behavior

I was able to find additional sources Can you please indicate these sources?

It has been completed

Different organisms evolve different behaviors, evolution is a whatever works kind of designer. it can influenced by all kinds of things, social behavior, what kinds of predators there are, offspring care needs, herd size, and a hundred other things.

We know what wild donkeys are like because they still exist in Africa, population 570, and they are more like small zebra's than horses.
Wild horses are from Eurasian grasslands and have all been captured for domestication and eaten, so current wild horses are feral.
The are completely different animals, they diverged 5-10 million years ago. They are much more genetically distant than a wolf, labrador and an alsatian, and their habitat and behaviours are completely different, including the dung strategy of donkeys and the semi-desert versus steppe habitat.

Horses have specialized in running away from predators, they are generally a bit faster than donkeys and today's horses tend to often be more slender, like deer.
Donkeys are more stout and probably adapted for different predators, terrains and climates, so they perhaps more likely to form group and kick rather then outrun the wolves/lions/tigers that would have preyed on them in the past.
It's probably best to post on a forum with people that have studied horses and donkeys for 20-40 years because they know a lot more about them.

I can’t speak for other mules but mine does not like dogs so I assume she would not like foxes or coyotes. I’ve seen her literally stomp a dog with her front hoofs. If the dog runs, I’ve seen her chase the dog and start stomping if she can get close enough to the fleeing animal. Our horse, well, he doesn’t give a hoot if a dog is nearby or not.

So horses, donkeys, and zebras are all of the genus Equus. Mules are not a species, since they are the product of the cross-breed between horses and donkeys, and are sterile (therefore do not comply with the biological interpretation of species).
Given that 2 out of the 3 species from the species of the genus Equus are aggressive against predators (zebras see reference and donkeys), it might be possible that the "aggressive" behavior is the ancestral trait of the genus, and horses evolved afterward the behavior of fleeing before fighting. Furthermore, it looks like the "aggressive" trait is dominant over the "fleeing" trait since mules (cross-breeds between horses and donkeys) inherit the aggressive trait. There are no sources that necessarily say that a dominant trait is associated with ancestral (common ancestor) provenance, but for the case of single genes, this is the most likely scenario.
So if we think that horses evolved the trait of fleeing before fighting (being the "aggressive" trait the ancestral one), then one should ask why did they evolve such behavior (why is a cringy word for evolutionary biologists, but serves the purpose here). And this is probably due to the exposure horses had to different types of predators. I wouldn't be surprised if horses had more contact with human beings than donkeys or zebras, thus they evolved this behavior as a way of coping with extensive hunting.
Alternatively, some traits are not "modular" traits that can evolve independently from other traits. More often than not, complex behaviors, like the "aggressive" trait, are determined by a large number of genes, some of which have phenotypical effects elsewhere. This means that if a species has a "selective pressure" for one trait, other traits can also be modified over time as a causal effect of this selective pressure. Horses were domesticated long before donkeys were, and zebras haven't been domesticated at all. Domestication is usually conferred by a process of selectively breeding individuals that express the least amount of aggressiveness, or show signs/traits of "neoteny". If horses were selected to produce neoteny in the species, the non-aggressive behavior might also have been selected as a causal effect of this selective-breeding.  This would explain why horses, which have been domesticated way before donkeys have, do not show aggressive behavior as donkeys or zebras do.


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Do tarantulas and humans have the same mechanism for growing hair?
There's hair on my arms.
Tarantulas also have hair on their arms.
Is this the same type of hair?

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

Arthropod hairs are called setae and are not homologous to human hairs. Each setae forms from a single cell called a trichogen. The hair follicles in mammals contain 20 different cell types and produce hairs made of keratin. Arthropod hairs are made of chitin rather than keratin.


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What is the smallest known viviparus
I want to know what is the smallest viviparus known at this time.
I was Googling, but I can discover this animal.
Thanks.


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At What Rate Do Ions Leak Out of a Plasma Membrane Segment That Has No Ion Channels?
In reading about the purpose of myelin during action potential propagation, I came across a point of confusion.
From what I understand, one of the primary "benefits" of myelin is that it aids in increasing the transverse resistance of an axon...which, biologically, is equivalent to stating that it minimizes the extent to which ions move out of or into the cytoplasm of the axon.
However, I feel as though I have always been taught that "the plasma membrane is impermeable to charged particles" and am therefore confused as to what additional benefit is conferred on the axon by the myelin.
Consider the following two cases:
Case A) The action potential starts at the axon initial segment. The subsequent segment is myelinated. The action potential, through passive diffusion, makes its way down the myelinated section until it reaches the 1st node of ranvier, where the action potential is subsequently regenerated.
Case B) The action potential starts at the axon initial segment. The subsequent segment is unmyelinated but contains no ion channels (or pumps). The action potential, through passive diffusion, makes its way down this unmyelinated section that has no ion channels (the same distance as in Case A) until it reaches a dense collection of voltage gated sodium channels.
In case B, will the action potential be regenerated? Or has the passive diffusion event suffered from too much "leakage"? If so, is it really true that:
(the plasma membrane + myelin) transverse resistance >> (the plasma membrane) transverse resistance alone

I'm going to mostly skip over the title of your question and focus on the confusion in the body, because the question in the title is a bit of an XY problem. It doesn't make much biological sense to think about a membrane that is truly that resistive (that is, I am unaware of any example neuron, or even any other cell, that has that property).

If there were truly no channels of any sort, you could indeed consider the resistance to be very high, at least as high as one could measure in patch clamp. Additionally, what matters is not the resistance itself but the ratio of the transverse to axial resistance; relative to the axial resistance the transverse resistance is already very high.

From what I understand, one of the primary "benefits" of myelin is that it aids in increasing the transverse resistance of an axon

Your understanding is not completely correct. The insulating benefit of myelin (ignoring other organizational benefits) is not only related to the transverse resistance, but importantly to a decrease of the capacitance of the membrane (see Moore et al 1978 or Richardson et al 2000 for some example simulations; also any reasonable neuroscience textbook will explain this). You can test this yourself in a simulation environment like NEURON.
Myelin decreases capacitance by effectively increasing the distance between the 'plates' of the membrane capacitor (see this answer).
In order to charge a long length of membrane with channels on only at short segments, you would need enough charges to come in within that short segment to charge the entire length of axon, and the potential would decay with distance.
Myelin does also affect resistance, but that's mostly important because the membrane does not consist only of a phospholipid bilayer and there is non-zero leak. For example, there are channels under the lipid bilayer that establish a resting potential (Chiu & Ritchie, 1984).

Chiu, S. Y., & Ritchie, J. M. (1984). On the physiological role of internodal potassium channels and the security of conduction in myelinated nerve fibres. Proceedings of the Royal society of London. Series B. Biological sciences, 220(1221), 415-422.
Moore, J. W., Joyner, R. W., Brill, M. H., Waxman, S. D., & Najar-Joa, M. (1978). Simulations of conduction in uniform myelinated fibers. Relative sensitivity to changes in nodal and internodal parameters. Biophysical journal, 21(2), 147-160.
Richardson, A. G., McIntyre, C. C., & Grill, W. M. (2000). Modelling the effects of electric fields on nerve fibres: influence of the myelin sheath. Medical and Biological Engineering and Computing, 38(4), 438-446.

For clarification, are you saying that there are leak channels present in the plasma membrane that directly underlays the myelin sheath? My understanding was that the plasma membrane that lays just beneath the myelin sheath is effectively "barren" of any sort of channel or pump.

otherwise it seems like the only energetically favorable purpose of the myelin is the reduced capacitance that you mentioned...because, if I'm the neuron...why don't I just create patches of plasma membrane that have no pump or channels. In which case, I don't understand why people even mention the fact that "increased transverse resistance" is an advantage of the myelin's presence.

Yes. See the Chiu paper for example (they talk about VGK channels but any channel means resistance isn't zero). There are also more recent papers that show the myelin itself contains channels. Also it's possible some people don't quite understand what they are saying, but in general I would agree with a statement that the capacitance reduction is most important.


text:
Why do chain identifiers in PDB have no standard starting chain id type?
At first I assumed that PDB chain identifiers are just uppercase letters (A, B, C,..) but found out there are protein chain ids that are numbers (0-9) and lowercase letters as well.
For example,

1NAL only has chain ids (1 - 4). It starts with chain '1' (number).
103L has chain identfier 'A'. It starts with chain 'A' (uppercase letter).
5afi's chain id's range from [a-zA-Z0-6] since it has 52 unique protein chains. It starts with chain 'a' (lowercase letter)

Can someone please explain? Or are id's just arbitrarily assigned?

Chain IDs are assigned by authors who submit the structure to the wwPDB.
According to the PDB spec:

Non-blank alphanumerical character is used for chain identifier.

Usually, the chains are assigned uppercase letters.
But since digits and lowercase letters are also allowed, some people will use it.
And a good reason to allow more characters is to accommodate for structures that have more polymer chains than there are letters in English alphabet. With lowercase letters and digits the limit is 62 chains.
Which is still not enough for some structures.
(Many programs can handle two-character chain IDs, but this common extension has not been embraced by the wwPDB.)


text:
Where is the cartilage plate in this electron microscope image of the trachea?
Also how could you tell? Assuming you were shown a photo of the cartilage only, how would you identify it?


text:
What phosphorylates tau protein & and what causes tau to be phosphorylated?
I want to know what phosphorylates tau protein and its 6 isoforms.
I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but when it is hyperphosphorylated it becomes the cis conformation of tau.
Do the same or different kinases cause the normal phosphorylation / abnormal hyperphosphorylation of tau? Is it completed by a single kinase or multiple kinases?
----Edit---
So I've done a lot of reading of many different papers and have uncovered that there two types of broad spectrum kinases classified as:
Proline-directed kinases, such as CDK5 and GSK-3beta
Non-proline directed kinases
Source: https://www.hindawi.com/journals/omcl/2015/151979/
But I read in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601591/
that Cdc2 can also phosphorylate tau
My new question is a follow up to my existing previous question, I guess why is tau phosphorylated at all? What causes tau to be phosphorylated at in the first place?
Thanks.

I recommend checking out PhosphoSitePlus's entry on tau protein. Click on the "Upstream" tab to see a list of confirmed (SRPK2, Syk) and putative kinases (PKA) and their associated phosphosites (i.e. the specific amino acid they phosphorylate). The Wikipedia page for tau protein also lists more kinases, as does this 2013 review by Noble et al. As for why Tau protein is phosphorylated, [its phosphorylation is a key


text:
Techniques of molecular medicine/biology for aesthetic medicine?
Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but actually all the problems of aesthetic appearance should be traceable to the genetic/epigenetic causes and that is why the molecular treatment at that level should be possible and optimal.
My question is can be considered also as a veterinary medicine question (aesthetics of pets) and that is why it is really a biology question.
https://journals.sagepub.com/doi/full/10.1177/2470289718787086 is the only more or less relevant article that I have managed to find.
Also CRISPR can be quite promising tool, but I have not managed to find scientific studies for aesthetic medicine of it.


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Are mitochondrial genes decoded in the same way as nuclear genes?
Mammalian mitochondrial genomes contain only 22 tRNA-coding genes, which is an insufficient number to decode mRNAs under the standard wobble rules.
How is translation of mitochondrial mRNAs achieved with this number of tRNAs?
The possibilities that occur to me are that certain genes encode multiple tRNAs (but this appears unlikely as each gene has its own promoter) or that mitochondrial tRNAs can adopt alternative three-dimensional structures, each with a different anticodon loop and hence a different anticodon.

Answer Summary

Translation in the mitochondria of mammals differs markedly from that
  in the cytoplasm. Although it has more similarity to translation in
  prokaryotes, it also shows significant changes from the latter. A smaller
  repertoire of tRNAs is able to translate a ‘simplified’ genetic code
  through structural alterations and base modifications that allow their anticodons
  to decode groups of synonymous codons, not possible according to the standard wobble ‘rules’.

Relationship to the eubacterial translation system
One of the pieces of evidence for the endosymbiotic theory of the origin of mitochondria was the fact that their translation machinery was more similar to that of prokaryotes than to that in the eukaryotic cytoplasm. The similarities to prokaryotes included the (smaller) size of their ribosomes, the susceptibility of their ribosomes to antibiotics specific for bacterial ribosomes, and the formylation of their initiator tRNA — fmet-tRNA.
Although in no way rebutting the endosymbiotic theory (which is widely accepted), mitochondrial translation shows several differences from that in prokaryotes. These include there being a single tRNA to decode methionine in both initiation and elongation (discussed below), the lack of leader sequences preceding the initiation codon, hence precluding a Shine & Dalgarno type of recognition by the ribosome, and additional ribosomal proteins which are thought to “provide a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain”.
Decoding with 22 mitochondrial tRNAs
General Review: Suzuki et al. (2011) Annual Review of Genetics 45, 299–329
As the question states, mammalian mitochondria encode 22 mitochondrial tRNAs, which would be insufficient to decode mRNAs using the standard genetic code and the wobble ‘rules’ that apply to translation in the eukaryotic cytoplasm and in prokaryotes.
One way out of the dilemma would be if some of the tRNAs were encoded in the nucleus and imported into the mitochondrion in a similar manner to that of nuclear-encoded mitochondrial proteins. Although this turns out to be true for certain organisms (although the import system is different from that for proteins), and important in some cases, this is not the answer for mammalian mitochondria. Thus, as reviewed in Current Genetics (2009), the mitochondrial tRNAs encoded in the nuclear genome of H.sapiens only duplicate the 22 mitochondrial tRNAs and their anticodons. (The one exception is an extra Gln(anticodon CUG) in addition to the Gln(anticodon UUG).)
Let us look more carefully at the problem. Although there are 61 codons specifying amino acids, because of wobble, fewer than this number of tRNAs are required to decode them. The left-hand frame of the figure below shows the standard genetic code, and the minimum number of tRNAs needed to decode it using the wobble ‘rules’ shown beneath, indicated by the colour-coded rectangles.
For those not familiar with the actual pattern of wobble (summarized in my answer to another question), in elongator tRNAs the 5′-position of the anticodon has some flexibility such that a G in that position can form base pairs with U or C in the 3′-position of the codon, an inosine (I) can pair with U,C or A, but an anticodon C can only pair with a codon G. The unmodified bases A and U are rarely found in anticodons, but a variety of different chemically modified Us are found (U* in the figure) which only pair with A. Thus, the minimum number of elongator tRNAs needed would be the number of coloured rectangles — 36 — and, as there are separate species of tRNAmet for initiation and elongation, the minimum number of tRNA species is 37.

When the human mitochondrial genome was sequenced, two anomalies stood together: the limited number of tRNA genes already mentioned and (more sensationally) changes from the standard genetic code (indicated in red on the right-hand side of the figure). It was immediately realized that these changes served to rationalize the code so that all synonymous codons were in groups of four or two. If it were assumed that the decoding specificity or wobble of mitochondrial tRNAs were different, then 22 tRNAs would be sufficient using the ‘wobble’ shown beneath the right-hand frame of the figure for groups of four amino acids (dark blue) and groups of two amino acids with codons ending in A or G (red).
One further requirement was that a single tRNAmet be involved in both elongation and initiation, a requirement the fulfilment of which has already been mentioned.
What features of the tRNAs could change the wobble ‘rules’ that have been conserved between prokaryotes and eukaryotic cytoplasm? There turn out to be two types of changes. The first, and most obvious, is the fact that certain (but not all) mitochondrial tRNAs have non-canonical cloverleaf structures, the most extreme being tRNAser in which the whole D-loop is missing. The second is the post-transcriptional modification of bases in the anticodon — just as is the case for tRNAs in the cytoplasm, this can markedly affect decoding specificity.
It is not yet possible to describe the codon–anticodon interaction in mitochondrial translation in the way that this has been done in for the cytoplasm or for prokaryotes. The problem would appear to be the difficulty of obtaining sufficient pure tRNAs. Whereas it is easy enough to clone and transcribe the tRNA genes, this is insufficient without the secondary chemical modifications of the bases which is key to the structure and function of the tRNAs.

Wow. Thanks for taking on the effort to write this! It’s been really helpful. May I ask a very dumb question? What do you mean by “the anticodon decoding both 3’A and G, or 3’ A,U,G and C.”?

@YamanKJ — I have revised my answer to explain the tRNA decoding better using a diagram of my own. I hope it's clear (and that there aren't any mistakes in the diagram.)

At first I thought that the "wobble pattern" was another name for the "Watson and Crick pattern" as I'm too naive with genetics, obviously. Your answer is indeed very informative, and you may have just made a frame-shift change (to use genetics' terms) to my level of comprehension of this topic. Every time I read your answer I understand one more detail. I think you need to edit "modified Us only pair with G (here I think it should be A instead of G?)."  and flip the colours here "groups of four amino acids (red) and groups of two amino acids with codons ending in A or G (dark blue)."

Forever grateful for this detailed explanation!

@YamanKJ — Thanks for pointing out the typos — one can go blind writing these things, especially when the output is out of view. Happy to help. I used to be more involved in protein synthesis, so I welcome the opportunity to check out how things have progressed in a particular sub-area. Of course, the danger is always that one gets an incomplete or distorted picture, but then one hopes someone will come along and point it out.

It turns out (and I’m not a 100% sure of this) that every tRNA-coding gene could give multiple variants of anticodons by different folding ways, so that you’d have enough anticodons in the end.

No, that's incorrect. tRNAs do not get their anticodon identity via folding. The anticodon is defined by the gene sequence.

@KonradRudolph That’s what I’ve been told when I asked my tutor. Do you have any idea about the answer to the aforementioned question?

Your tutor is definitely wrong (I should know: I literally wrote my PhD thesis on the topic). Unfortunately I don’t know the answer for mtDNA either but you forgot at least two possible explanations in your question’s list: (1) mtDNA only uses 22 different codons, (2) mtDNA co-opts nuclear tRNA for its translation. I suspect that the answer is a mix of these two explanations (i.e. mtDNA mostly uses a reduced pool of codons, and almost certainly uses nuclear tRNAs because these are abundant and the genetic code is almost the same as the nuclear one anyway, and translation happens in cytoplasm).

@KonradRudolph Well, I definitely trust Cambridge students more than I trust our university’s (he’s a great, great tutor nevertheless). I’d thought about what you’ve suggested beforehand but(1) is wrong because I’ve seen a table that contains every codon and its corresponding amino acid, they surely need more than 22 codons. (2) I thought it was not likely given the fact that mtDNA has 4 stop codons(only 2 of which are shared with nuclear DNA)so if the tRNA of nuclear DNA fits, the translation would not stop there. Could be that mtDNA shares SOME of the tRNA w the nuclear DNA. (2) makes sense!


text:
What is the meaning of expansion of T cells?
In immunology, what does it mean by the term 'expansion' of T cells ex-vivo and activate it (generally with reference to cancer immunotherapy)?

In immunotherapy, the T cells need to hit a therapeutic dose. The dose is normally determined pre-clinically or in a phase I or I/II trial. A good example is the YESCARTA label dose information:

YESCARTA comprises a suspension of 2 × 10^6 CAR-positive viable T
  cells per kg of body weight, with a maximum of 2 × 10^8 CAR-positive
  viable T cells in approximately 68 mL (3).

YESCARTA commercial label
Lets run through a hypothetical situation based loosely on information obtained in this publication.
So say you have a cancer patient that weighs 70kg on the day they obtain a leukapheresis for their starting material. The manufacturing facility is going to say okay, we need to produced 2E6 viable CAR+ cells/kg for a 70kg patient in 68mL per the label indication. So your final product needs to have 140 million viable CAR+ cells.
The patient leukapheresis can go wildly different on a patient-specific basis due to factors such as current treatment or disease. Your separation method can result in loss. Cells die in their initial culture period pre-transduction, and they can die post-transduction. So case study in point from the paper I linked:
Their patient 029-03 ended up with 0.494E+09 cells in their leukapheresis. Transduction efficiencies aren't published for a lot of these, but lentiviruses are typically employed and efficiencies can range from 1-90% depending on numerous factors. The manufacturer needs a target efficiency of ~28% to hit 140E+06 total cells if they manage to isolate every single CD3+ cell, but if they're 85% viable for example, they still wont hit the target dose. So you need to expand the cells aka make them divide so you hit the target therapeutic dose.
You typically culture your cells in IL-2, a potent T cell stimulator, but activation can improve transduction and stimulate cell division aka expansion. You can use something like CD3/CD28 beads, for example. These provide the so-called signals 1 and 2 that stimulate T cells in a similar way antigen challenge would.
Let me know if anything is unclear.


text:
Tiny huntsman found in Czechia?

I found this spider today and I'm curious to know what it was.
Discovered today at 14:27 CEST, about 200 meters from Hamr pond, Prague, Czech Republic. It may have been carried all the way from the pond.
Body length cca 5mm (cf. photo #2 - reference object is a 5 CZK coin, 23mm in diameter according to Wikipedia)
Initially swept off my shoulder (white T-shirt), to which it succeeded in attaching, and began descending on a thread. After it was placed on a small ledge, it began climbing the adjoining wall. After some convincing to stay in place (using my finger as an obstacle and a little physical contact with its legs), it lifted its four front legs, so I left it alone.
I didn't manage to get good sight of its eye pattern, but it did appear to be consistent with the eye pattern of huntsman spiders - the sides of its face were black with a brighter region between. I was unable to determine the quality of its eyesight either, though it did not object to placing the coin nearby to it.
Wikipedia page on huntsmen living in Europe lists nine species, but none of those that had photos included matched in appearance.

The spider in question is actually Xysticus Cristatus, also known as the common crab spider.
From Wikipedia:

The adult female reaches a length of 8mm and the smaller male 5mm. The colour varies from light cream, dark brown to greyish with a dark triangle on the carapace which ends in sharp, defined point. The abdomen has a broad middle band fringed by two darker rows of triangular marks which extends back to about two thirds of the carapace length from the posterior row of eyes. ... Active adults have been recorded from February to December, with a peak of male activity in May and June. ... The species has a Palearctic distribution, being found throughout Europe, including Iceland.

Arachnology.cz provides several photos of the species. The image below is a perfect match.
Copyright by Rudolf Macek; published at https://www.arachnology.cz/druh/xysticus-cristatus-800.html; page viewed in May 2019


text:
Is complete dominance actually a genotypic process?
An example often stated for codominance is blood groups, where both alleles version of the protein is expressed and can be found in the cell membrane.
An example of incomplete dominance often given is of red and white flowered snapdragons giving pink flowered offspring because enzymes for both pigments are transcribed and translated and the mixing of these pigments gives the intermediate phenotype.
In both these examples both alleles are transcribed and translated.
In the text-book mendelian situation of a dominant and recessive allele are there actually a cellular mechanisms by which a 'dominant' allele silences the 'recessive' allele and inhibits it's translation, transcription or both? If so are there any well characterised examples?
Or are all alleles actually codominant at the transcription/protein level? e.g like in many recessive gentic diseases where both the mutant and the normal protein are present (cystic fibrosis, sickle cell anemia etc) but the activity of the normal protein gives the 'healthy' phenotype.

Related: Evolution of dominance of alleles

I don't think dominance is subjective at all. Do you have any references for the claims you made? For example "for a physician the healthy allele is dominant".

As @Cell said, you seem to confound dominance with fitness. Make sure to clarify that. Many people also confound dominance and frequency. Make sure to understand that these concepts are very different.

@Cell I'll reword the question but I am paraphrasing from an example in my undergrad lectures

@Mirte It is a good question +1. Can you please make sure to cite your source (what text-book are you referring to) and eventually give a direct quote (although you don't necessarily have to).

"Or are all alleles actually codominant at the transcription/protein level?"
Yes this is the right idea. Generally all alleles are transcribed independently (with some exceptions like in females where one X chromosome is inactivated). And the dominant and recessive phenotypes are in a sense extreme cases of codominance. The terms are used for describing phenotypes and depend on thresholds of activity. In the snapdragons example we can associate 2 functional enzymes EE with the red phenotype and white (lack of red pigment) associated with 2 nonfunctional enzymes ee. But one E is not enough to make the red pigment so we see some red pigment and a pink phenotype.
Now consider a yeast cell with 2 hexokinase genes (H). With two inactive proteins (h/h), the cell will grow slowly. Now let's say that H is a very efficient protein and that glucose transport into the cell is rate limiting so one active H has the same phenotype as having 2 H/H, so H/H is the same as H/h thus H is a dominant allele and h is recessive because one H is past the threshold of activity for fast growth on glucose. h is recessive because h/h genotype is needed to see the h phenotype. Hope that helps.

An example of incomplete dominance often given is of red and white
  flowered snapdragons giving pink flowered offspring because enzymes
  for both pigments are transcribed and translated and the mixing of
  these pigments gives the intermediate phenotype.

White snapdragons are not making a white pigment.  A step in the pigment-making pathway fails, because a needed gene is broken.  A snapdragon with one working pigment enzyme allele makes some pigment, but not as much as one with two working enzyme alleles.
https://en.wikipedia.org/wiki/Haploinsufficiency
A blood does not react to A blood.  B blood does not react to B blood.  AB blood doesn't react to A or B blood.
One copy of the A allele does all the same stuff as having two copies.  One copy of a working pigment enzyme does not make as much pigment as two working copies.

In both these examples both alleles are transcribed and translated.

It is not at all clear to me that the broken pigment enzyme is necessarily translated at the same rate as the working one.  There are cellular mechanisms to clear away non-functional transcripts, the broken enzyme transcript might be subject to those processes.
https://en.wikipedia.org/wiki/Nonsense-mediated_decay
Or the defect in the broken allele might be in its promoter, preventing it from being transcribed at all.


text:
Is this an asian hornet
My mother found a hornet at home (in northern France) that is probably building a nest. Is that an asian hornet? If yes, how can I exterminate them?

I am not very good at species ID but it does not look like a Asian giant hornet to me. Asian giant hornets typically have wider dark stripes. It could be a European hornet. Where was the picture taken?

Yes, northern France to be precise

The OP is probably asking about the asian hornet (which is invasive in France) rather than the asian giant hornet (which is not), though this one looks like neither.

Yes I'm talking about the invasive asian hornet

This is not a hornet, this a wasp. See the yellow dots on the thorax ? They are typical of the Vespula genus. So is the yellow and black stripe pattern on the abdomen. Those wasps are smaller than hornets (1-2 cm for wasps, 3-4 cm for hornets). Picture from Wikipedia:

There are two common Vespula species in France  (V. vulgaris and V. germanica), but to identify yours, we would need a better view of the head and abdomen.
On the image below, you can compare it to the two hornet species you can find in France (source). The first one is a bee, the second one is a wasp (Vespula), the third one is the invasive "Asian hornet" (Vespa velutina) and the fourth one is the native "European hornet" (Vespa crabro).

So no extermination needed ;) You can find more information (in French) on how to recognize these species on the Natural History Museum website.
Sources:

Le Rucher des Plaisirs - French beekeeper website
Natural History Museum - hornet and wasp identification in France
Same source in English
Wikipedia page


text:
Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?
Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some CRISPR-like tools? I guess, that extensive databases of already performed experiments are available and human mind is required to select candidate genes for experiments. But maybe there are some methods, that allow computational select, planning of experiment, e.g. using: 1) already known biological pathways for different biological processes or incomplete pathways for the process under consideration; 2) protein-protein interaction models to predict some pathways and to select genes from them. Etc.
I am complete novice for this field, coming from computer science and only starting to read books about molecular cell biology, epigenetics and protein-protein interaction. Maybe there are special terms that allow me to Google for the subject of this question

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work with CRISPR-CAS9 is still limited to model organisms and tissue cultures.
Are you referring to Adiposis Dolorosa?  Apparently the cause is not actually known yet. It's thought to be heritable, but it isn't known to be associated with a single gene or family of genes. The most common technique for analyzing what genes and gene mutations cause disease is Genome Wide Association Studies (GWAS), so you might use that as a staring point for your searches.
There are several computer programs that try to model what pathological effects a given mutation will have, but these are pure research at this point, and typically require extensive training for each gene or protein product. Try searching for "sequence based pathology prediction". However you may not find much related to Adiposis Dolorosa since the causative genes are apparently not known yet.


text:
What is the difference in the electrical excitability between a "large diameter soma" and a "large diameter axon"
There are two stereotyped statements that I have seen during my coursework regarding electric properties of neurons:

Large diameter axons propagate action potentials more quickly than small diameter axons
Large motor neurons are the last motor neurons to be recruited

Separately, I have always understood these statements through the following lens:
Explanation for 1. (for arguments sake, lets talk about unmyelinated neurons...so, for example, a C-fiber with a small diameter and a C-fiber with a slightly larger diameter). The reason the larger diameter neuron will propagate its action potential more quickly is because, in a given cross section of the axon, there are more voltage gated sodium channels present along the circumference. Consequently, the speed with which the incoming sodium signal is generated is quicker. I am aware of "reduced longitudinal resistance" for larger axons, but I am purposely ignoring this...please continue reading.
Explanation for 2. Idealizing the soma of a neuron as a sphere, we know that capacitance increases with increasing radius (related to the distribution of charge along a 'longer' circumference). Consequently, for a large soma, the amount of charge required in order to observe a change in potential difference across the membrane is MORE than it would be for a smaller soma.
When treated individually, both of these statements are intuitively "okay". However, when I think of these two statements together, confusion arises:
A. Shouldn't the increased total number of ion channels observed in the larger diameter axon also be observed in the larger soma?
B. Shouldn't the capacitance increase observed in the larger soma also be observed in the larger unmyelinated axon?
If both of these statements are equivalently applicable in both cases, why do the two statements "1" and "2" seem fundamentally different?
The only rationale I can think is the following: The % of surface area occupied by ion channels on the soma membrane is significantly less than the % of surface area occupied by ion channels on the axon membrane. Consequently, the axon can offset its increased capacitance by the gain in additional ion channels. However, the soma cannot offset its increased capacitance because the % of ion channels occupying its surface is below this "capacitance offset" value.
Edit:
I have provided two pictures to help clarify my question:

As you can see from the above two images, the values in the two tables are the exact same. Summarizing, the larger soma and larger myelinated segment of axon both exhibit:

Less Longitudinal Resistance
Greater Capacitance
Greater Surface Area Available for Ion Channels

I have previously asked two separate questions:
Here_1: Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?
and
Here_2: Why do larger diameter myelinated axons have greater conduction velocities than small diameter myelinated axons?
The conclusions from the two questions were that larger somas take longer to depolarize and larger axons transmit electric signal more quickly.
Even though both 'entities' exhibit shared electrical properties, it appears as though the outcome of having these electrical properties is fundamentally different. In one case, the membrane is taking longer to depolarize...but in another case, the membrane is depolarizing quickly!
What am I missing that results in my perception that electrical properties are somehow being differently applied to the soma of a neuron and the axon of a neuron?
(Note that this question involves the myelinated section of the neuron so there is no need to talk about nodes of ranvier or any sort of "active" electric process)

Can you cite where your assumptions are coming from? I think you are taking things to be rules that are not rules. Also: where is the stimulus coming from? why are you talking about receptors on axons? why are you applying motor neuron ideas to C-fibers?

The "receptor" was a typo. I have corrected some other typos accordingly. My assumptions are coming from my own intuitive understanding of physics and other general sources. C fibers were chosen because they are unmyelinated...I didn't want to involve myelin in this discussion...and why should the electrical phenomenon affecting motor neurons not be extendable to the electrical phenomenon affecting any other sort of neuron?

Because the "size principle" is an experimental finding with motor neurons. It is not a rule for all neurons. Please separate out your question a bit too, there is far too much here to unpack, and ask a single answerable question.

From what I recall, isn't the intuition behind the size principle the very concept that I mentioned? Namely, that larger cell bodies have larger capacitance and therefore their membranes take more positive charge in order to depolarize?

I really think you'll enjoy the NEURON program (neuron.yale.edu) that I've recommended to you before if you want to test out some of your thoughts. In any event, the size principle is an experimental finding, not a physics one. That doesn't mean physical properties of size don't have an influence, but it also doesn't mean size is the only factor.

Hmmm. So, besides the size principle observed in motor neurons, you’re saying that neurons with larger somas actually fire with LESS total input than with neurons that have smaller somas (i.e. large somas are more sensitive to input than neurons with smaller somas?)

I never said that.

Then I do not understand any of your preceding comments. Why do you take issue with me generalizing the intuition behind the size principle of motor neurons to all other neurons? It seems to me that larger somas should therefore require greater input (as compared to smaller somas) in order for the axon initial segment to be sufficiently depolarized such that it initiates the action potential.

What I said is that size is not the only determining factor, and you should not assume that a larger cell is activated at higher threshold if you aren't talking about a motor neuron: that principle counts for motor neurons only, others you have to approach on a case by case basis.

If it's helpful, i've broken down my question into two other questions: https://biology.stackexchange.com/questions/82885/why-do-larger-diameter-axons-have-greater-conduction-velocities-than-small-diame and https://biology.stackexchange.com/questions/82883/are-large-cell-bodies-of-neurons-harder-to-depolarize-than-small-cell-bodies-of
hopefully that should "clean up" the question a bit...and my confusion regarding some of the general principles I often hear regarding the electric properties of neurons with different morphology.

Closed as too broad to allow the other two questions to remain.

Does the soma fires action potentials?

Depends on your definition of soma (AIS included?)...but no, it does not.

I don't see any difference between your soma and your myelinated axon.Then, they are fundamentally a nonconductive compartment. So if for the same entity you get two different results, there's something you`re not considering.


text:
Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?
In order for the axon to initiate an action potential, we know that the axon initial segment must be brought to threshold. So my question is as follows:
Say we have the minimum charge input, "X", necessary to depolarize the axon initial segment of Neuron 1.
Now, we have Neuron 2, which has a larger soma. Will this same input X be sufficient to depolarize the axon initial segment of Neuron 2?
I am trying to explore how physical concepts like capacitance manifest in biological systems. Neuron 1's soma (approximated as a sphere) presumably has a lower capacitance than Neuron 2's soma (approximated as a sphere), due to the difference in cross sectional area of the somas. Therefore, I would assume that Neuron 2's axon initial segment requires greater input to depolarize than Neuron 1's axon initial segment.
Is this simplistic idealization of somas actually observed in experiments?

Your intuition is correct, in order to attain the depolarization necessary to trigger an action potential you need more charge in the bigger neuron. This is simply because you have a larger capacitor.

Great! Knowing this, could you please explain then, WHY larger diameter axons convey action potentials more quickly than smaller diameter axons? (assume they are both equally myelinated) Shouldn't the larger diameter axons "require more charge to depolarize" and therefore actually take longer to convey an action potential?

Larger axons also have more sodium channels, so they move more charge. The reason why larger axons have faster conduction is because the have less internal resistance.

Can't I apply that exact same logic to the soma of the neuron? It has a larger diameter...therefore it has less internal resistance...it has a larger diameter, therefore it has more surface area available for ion channels to be present...etc
AND YET the conclusions are different between the two: big axon depolarizes more quickly but big soma depolarizes more slowly.

The soma doesn`t contain voltage dependent sodium channels, the voltage is propagated in a passive way. In the axons, conduction is active even though if you have an external input, larger axons need more charge. You can play with axon simulation in this web page http://nerve.bsd.uchicago.edu/nervejs/MAP.html you can change parameters of the axon such as the radius or stimulus amplitude and see how that affects the propagation of the action potential.

I will say that the main source of your confusion is between propagation velocity and charge needed for depolarization. They are related, but they don`t mean the same.

within the myelinated segments of an axon, however, the voltage IS propagated in a passive way. So I still fail to see how for the same conditions, different results are observed between axons and somas.

I really recommend that you run neuron simulations to see how the different parameters you`re interested affect conduction velocity. This program will allow you to play with myelination and axon diameter https://neuron.yale.edu/neuron/

Again, larger axons need more "stimulus" or charge to reach the threshold for the propagated axon. Nevertheless larger axons have more sodium channels in the node of ranvier, so the only difference will be the length constant. Somas don`t have sodium channels so you need more external stimulus to charge the membrane.


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Why do larger diameter myelinated axons have greater conduction velocities than small diameter myelinated axons?
A canonical statement I have frequently read is that "large diameter axons conduct action potentials at faster velocities than small diameter axons". After recently learning the effect of increased capacitance on the cell membrane (namely, that more charge is required for depolarization to occur...Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?), I find this canon to be rather confusing.
I have attached a picture to make my question clearer:
In the above picture, both neurons have the same myelin spacing. So, my question is why should the action potential in Axon B traverse the distance X1 to X2 more quickly than in Axon A. Shouldn't the increased capacitance of Axon B (due to its increased diameter) increase the time it takes for the action potential to travel between the two points?

Why should the action potential in Axon B traverse the distance X1 to X2 more quickly than in Axon A?
The larger the diameter of the axon, the less the longitudinal resistance, so the current can propagate along the axon more easily.
Shouldn't the increased capacitance of Axon B (due to its increased diameter) increase the time it takes for the action potential to travel between the two points?
Both, the capacitance and the number of ion channels increase quadratically whit the diameter. So the increase in capacitance is compensated by an increase in total ionic current.
Wiki cable therory


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DNA replication in $ E.coli $
$ E.coli $ has circular DNA which I guess implies one strand forms the outer circle and the other the inner one. So, is there a way to know if the replicated DNA forms the outer or inner circle?
In the image attached it is seen that the replicated DNA forms the inner circle. Also mentioned is the fact that it is not possible to make out individual strands by TEM.

The picture on the bottom is a simplified cartoon. The two strands make a double helix so they both alternate between top strand and bottom strand. Also plasmids aren't 2D circles in the cell; they twist and turn and rotate.


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Where does the gluteus medius attach to the greater trochanter compared to the gluteus minimus attachment?
Where does the gluteus medius attach to the greater trochanter of the femur  compared to the gluteus minimus attachment? Is it above, below, next to it, etc.? Ideally I'd like to know the distance as well and location relative to the greater trochanter.

What I have found so far: some diagrams place the gluteus medius attachment below the gluteus minimus attachment, some place it above and some place it next to it at the same height.
Example of diagram placing the gluteus medius attachment below the gluteus minimus attachment (image source (mirror)):

Example of diagram placing the gluteus medius attachment next to the gluteus minimus attachment (image source (mirror))

Example of diagram placing the gluteus medius attachment above the gluteus minimus attachment (image source (mirror)):

{1} greatly answers the question.
Regarding the insertion location (lateral view):

Note that unlike the gluteus minimus insertion, the gluteus medius insertion can also be viewed anterolaterally:

Table 2 contains more detailed insertion location data:

Regarding the insertion area:

Gluteus maximus: Average Area, mm^2 (95% CI): 473.4 (381.0, 565.8). Thick, muscular insertion along the posterior femur on the linea aspera
Gluteus medius: Composed of 2 contiguous rectangular footprints, the lateral facet oriented in the sagittal plane and the superomedial facet primarily in the transverse plane:

Lateral facet: Average Area, mm^2 (95% CI): 141.1 (117.7, 164.5).
Superomedial facet: Average Area, mm^2 (95% CI): 501.5 (442.8, 560.2).

Gluteus minimus: Average Area, mm^2 (95% CI):  280.9 (229.3, 332.5). Two morphologies noted: The majority (11/14) were long, thin, and crescent shaped and ran medial to lateral and concave facing inferiorly, while a few (3/14) were bowtie in shape.

Below are some actual pictures of the gluteus minimus insertion, the gluteus medius insertion to get another sense of their shape and location. Still  from {1}, this picture shows the gluteus medius (but not the gluteus minimus):

From {2}, this picture shows both the gluteus medius muscle and the gluteus minimus muscle:

I also find this picture good to give a better sense as to where the greater trochanter is located with respect to the human body (image source (mirror)):

References:

{1} Philippon, Marc J., Max P. Michalski, Kevin J. Campbell, Mary T. Goldsmith, Brian M. Devitt, Coen A. Wijdicks, and Robert F. LaPrade. "Surgically relevant bony and soft tissue anatomy of the proximal femur." Orthopaedic journal of sports medicine 2, no. 6 (2014): 2325967114535188. https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Surgically+Relevant+Bony+and+Soft+Tissue+Anatomy+of+the+Proximal+Femur&btnG= ; https://www.ncbi.nlm.nih.gov/pubmed/26535335 ; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555602/ ; https://doi.org/10.1177/2325967114535188
{2} Woodley, Stephanie J., Susan R. Mercer, and Helen D. Nicholson. "Morphology of the bursae associated with the greater trochanter of the femur." JBJS 90, no. 2 (2008): 284-294. https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Morphology+of+the+Bursae+Associated+with+the+Greater+Trochanter+of+the+Femur&btnG= ; https://www.ncbi.nlm.nih.gov/pubmed/18245587 ; https://doi.org/10.2106/JBJS.G.00257


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Why is sex hurtful for some animals but pleasurable for others?
Sex seems to be pretty hurtful for feline for example. On the other hand sex is pleasurable for humans. Why is sex pleasurable for some and not for others? How do these things evolve?

what makes you think it is hurtful?

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

There are various selection pressures that may lead to sex being more or less harmful. I don't think there is an easy way to summarize these selection pressures other than just going through load of examples. Here is an attempt to give you some notions of why can sex be pleasurable and/or painful. Note that I do not consider myself particularly knowledgeable in this field.
Why could it be pleasurable
We tend to seek for positive experiences. If we like sex, we have more sex. If we have more sex, we are more likely to have more offspring. Hence, the trait "liking having sex" is positively correlated with "fitness".
Why could it be harmful
Dick pics
In many species, the penis has spikes and stuff and is most definitely hurting the females. Here is a Drosophila penis

And here are penises of two dragonfly species

Here is a feline penis

By the way, according to wikipedia (could not find peer reviewed paper on the subject so take this with a grain of salt), some humans still have on remnants of those barbs you can still see on many feline penises left from our ancestor. They are called hirsuties coronae glandis. Here is a perfectly healthy (but I would tend to consider quite extreme) example of hirsuties coronae glandis

Some theory
There is a lot to say here and I only want to say a few words and hopefully you will go get more information by yourself.
So why do these species evolve these fancy and scary "armed" penises. In many species, it is a small investment for a male to make a baby (just mate and the job is done) but a big investment for the female (producing the egg, eventually even parental care, ...). Because the sex-ratio is always (assuming no group selection) pushed toward 0.5 (see this post and Fisher's principle), it happens that males end up with lots of free time looking for females (see Why are female not competitive for reproduction like males? and Bateman's principle). You might also want to read about sexual conflict.
Why would such penis evolve?
The reason vary among species. Here is a non-exclusive, non-exhaustive list of reasons:

In some species (e.g. nudibranch, damselflies)The goal is to remove the sperm from an eventual previous male so as to reduce sperm competition (Cordero-Riviera, 2016).

In some species, the goal is to damage the female reproductive track so that she will not subsequently mate with other males hence reducing sperm competition ().

In some species, the male can even leave toxic products in the female (Chapman et al., 1995).

In some species, females get severly harrassed by males for mating and rape is not unusual (e.g Drosophila). Some penile barbs and spikes can be used to get the female stuck in place. To avoid that the female can escape before the sperm has been delivered ()! That being said, in some circumstance such use of spiky penis might be beneficial to the female too. This non-peer reviewed article may bring some light.

In some species, the male can pierce through the female abdomen to deliver its sperm. This is called traumatic insemination.

In a classical experiment, Rice 1996 shows that there is an arm race between males and females. Race in which males increases their negative impact on female's reproductive organs and females protect themselves from it. The paper is free, is short, easy to read and has a pretty amazing experimental design. It is worth having a look at it.
Feeding the babies via the mother
I just want to point with other examples that sex does not have to be romantic in many species. In some species, the female eats the male after sex or even while having sex. To what I have heard (; please be cautious with this information), in some mantis prey, the male does not even release his sperm before the female has cut the male's head off. Why would the male do that?
A male that let himself get eaten by the females ensures that the female has lots of energy for taking care of her babies. Hence a male may increase his fitness by sacrificing himself to his partner.

Nice examples and good links! However, could you add some support for your first 2 bulleted points regarding reasons for armed penises (i.e., sperm removal and female injury). Thanks, @Remi.b!

Also note that your wiki link in support for a vestigial link to penile spines has no source/citation provided in the source text. Given my lack of knowledge of penile spines I can't be certain, but the remainder of your wiki link seems to suggest more of a glandular or sensory role which seems to deemphasize a spine origin. Could you dig a bit more to find more concrete support for this notion that HCG might have an evolutionary connection to spines. Thanks!

@theforestecologist Indeed, citations were lacking. It has been improved now (although some are still missing). I naively followed wikipedia's claim when talking about the evolution of hirsuties coronae glandis. I have now tried to find some peer-reviewed paper on that but could not find anything. I made sure to write "according to wikipedia (could not find peer reviewed paper on the subject)". Thanks


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Formula for Oxygen Consumption for Atlantic Salmon (Mathematical) - insecurities regarding variable

The oxygen is calculated in mg per kg per something, so what does $h^{-1}$ stand for? hours maybe?

The formula given below is an estimation of oxygen consumption for Atlantic salmon

\begin{equation}
        V_{O_{2}} (mg \cdot kg^{-1} \cdot h^{-1}) = 61.6(\pm6.6) BW^{-0.33(\pm0.11)} \cdot 1.03(\pm0.10)^{T} \cdot 1.79(\pm(0.10))^{U}
    \label{eq:salmonoxygenconsumption}
\end{equation}

Here is a link containing the scientific article describing the formula - ScienceDirect

Yeah, it's hours.
Further down in the paper, you can read,

The mass exponent was estimated to be −0.33 (b in Eq. (4)) for the specific metabolic rate \begin{equation} V_{O_{2}} (mg\space {O_{2}} \cdot kg^{-1} \cdot h^{-1}) \end{equation}

Rate by very definition implies an extent of time; since mg refers to oxygen and kg refers to water, the only variable left is h, which evidently refers to hours. Hours also jives well with the experimental design.

Source:

Grøttum JA, Sigholt T. 1998. A model for oxygen consumption of atlantic salmon (salmo salar) based on measurements of individual fish in a tunnel respirometer. Aquacultural Engineering 17(4): 241-251.

Thank you very much for your answer @rotaredom, very helpful!


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Is NMDA produced in the body?
On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA?
Also how is it possible that our body can produce something that is synthetic? I thought synthetic was man-made chemicals. Does that mean the NMDA receptors it binds to are also synthetic? How did this come to be?

(my comment reiterating the answer seemed useful, so I've reproduced it here)
There are "NMDA receptors" in our body. There is not NMDA naturally in our body*. "NMDA receptor" is just a name people gave to one of the receptors that normally binds glutamate. They could have called it something else, like the "slow glu receptor", or "Glutamate Receptor A", but they called it the NMDA receptor because they discovered it was different from other glutamate receptors in that it was activated by a chemical called NMDA in their experiments.

(original answer)
NMDA receptors are in fact glutamate receptors natively: there is no endogenous NMDA*. They are named NMDA receptors because experimentally they were differentiated from other glutamate receptors using the compound NMDA. At first glutamate receptors were known as "NMDA" and "non-NMDA" glutamate receptors, and later the non-NMDA sort were found to be sensitive to AMPA or kainate and named thusly.
Many other receptors are named this way: the nicotinic acetylcholine receptor is the receptor that nicotine is an agonist at, but the endogenous ligand is acetylcholine; muscarine is an agonist to the muscarinic acetylcholine receptor but the endogenous ligand is acetylcholine.

Watkins, J. C., & Jane, D. E. (2006). The glutamate story. British journal of pharmacology, 147(S1), S100-S108.

*In the comments, @gilleain pointed out some research suggesting that NMDA does exist endogenously, although in fairly specific areas and not disputing that glutamate is the primary endogenous agonist for NMDA receptors. This work was long after the NMDA-sensitive glutamate receptor was discovered and named, but is some interesting trivia nonetheless.

So does that mean the so called "NMDA" in our bodies is just a chemical scientists found that is similar to glutamate, and thus named it that way? I still don't understand why there is no endogenous NMDA, where does it come from in our bodies?

@user3665690 There are "NMDA receptors" in our body. There is not NMDA naturally in our body. "NMDA receptor" is just a name people gave to one of the receptors that normally binds glutamate. They could have called it something else, like the "slow glu receptor", or "Glutamate Receptor A", but they called it the NMDA receptor because they discovered it was different from other glutamate receptors in that it was activated by a chemical called NMDA in their experiments.

I see! ok that makes a lot of sense now, so basically NMDA is a synthetic chemical that mimics glutamate induce NMDA receptor activity. Is that the right interpretation?

@user3665690 Yes that's correct

It might be useful to mention that there is essentially no difference between a 'synthetic' chemical and one produced by the body. If they have the same atoms, arranged in the same way, then they are the same thing

@gilleain True, but NMDA is, to my knowledge, not found in any natural biological system, so it's appropriate to call it synthetic. There is no biologically produced molecule for it to be the same thing as.

https://www.ncbi.nlm.nih.gov/pubmed/11014243 : " we show that N-methyl-D-aspartate (NMDA) is present at nanomolar levels in rat nervous system and endocrine glands as a natural compound, and it is biosynthesized in vivo and in vitro. " but anyway that's beside the point - the question includes "Also how is it possible that our body can produce something that is synthetic?"

Perhaps that's just a different question entirely (probably already answered elsewhere) of the false split of natural/synthetic molecules

@gilleain Thanks for the reference! Quite interesting, I'll have to look into related work and possibly change my worldview a bit.

There is no clear-cut line between "synthetic" and "natural" substances.  They are made from the same kinds of atoms using the same kinds of covalent, ionic, and other types of bonds.  The fact that a substance MAY be produced by some organism by biological processes does not make it any different from the same substance made in a laboratory by a human chemist from non-living reactants.  What is relevant is the precise structure of the substance and the impurities that may be present in a particular sample of it.  Sometimes, because of the details of the kinetics and thermodynamics of biosynthetic and human laboratory synthetic processes, the relative isotopic composition of one or more of the elements may be different, but that can also be true of different "natural" processes and different "synthetic" processes.


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Is all of the DNA used by genes (encoding DNA)?
My intuition tells me no, since only 1.5-2% consists of exons, so this statement would be wrong.
The correct statement would have to be: only about 1.5-2% of the whole DNA is used by genes (encoding DNA).
Am I correct in this assumption?

Possible duplicate of Is most of the human genome functionless “junk DNA”?

The ENCODE consortium classifies human and mouse genome elements to try to answer this very question.
Work by ENCODE suggested up to 80% of the genome is functional in some way. In other words, by that upper-bound measurement, there is apparently more to DNA's role in biology than just encoding genes — there's a lot going on under the hood.

Case for Abundant Functional Genomic Elements.
Genome-wide biochemical studies, including recent reports from ENCODE, have revealed pervasive activity over an unexpectedly large fraction of the genome, including noncoding and nonconserved regions and repeat elements (58⇓–60). Such results greatly increase upper bound estimates of candidate functional sequences (Fig. 2 and Fig. S2). Many human genomic regions previously assumed to be nonfunctional have recently been found to be teeming with biochemical activity, including portions of repeat elements, which can be bound by transcription factors and transcribed (79, 80), and are thought to sometimes be exapted into novel regulatory regions (81⇓⇓–84). Outside the 1.5% of the genome covered by protein-coding sequence, 11% of the genome is associated with motifs in transcription factor-bound regions or high-resolution DNase footprints in one or more cell types (Fig. 2), indicative of direct contact by regulatory proteins. Transcription factor occupancy and nucleosome-resolution DNase hypersensitivity maps overlap greatly and each cover approximately 15% of the genome. In aggregate, histone modifications associated with promoters or enhancers mark ∼20% of the genome, whereas a third of the genome is marked by modifications associated with transcriptional elongation. Over half of the genome has at least one repressive histone mark. In agreement with prior findings of pervasive transcription (85, 86), ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome. [emph. added]

However, people outside the ENCODE consortium have criticised this research with very strong language, such as in this article by noted critic Dan Graur:

Actually, the ENCODE authors could have chosen any of a number of arbitrary percentages as “functional,” and … they did! In their scientific publications, ENCODE promoted the idea that 80% of the human genome was functional. The scientific commentators followed, and proclaimed that at least 80% of the genome is “active and needed” (Kolata 2012). Subsequently, one of the lead authors of ENCODE admitted that the press conference mislead people by claiming that 80% of our genome was “essential and useful.” He put that number at 40% (Gregory 2012), although another lead author reduced the fraction of the genome that is devoted to function to merely 20% (Hall 2012). Interestingly, even when a lead author of ENCODE reduced the functional genomic fraction to 20%, he continued to insist that the term “junk DNA” needs “to be totally expunged from the lexicon,” inventing a new arithmetic according to which 20% > 80%. In its synopsis of the year 2012, the journal Nature adopted the more modest estimate, and summarized the findings of ENCODE by stating that “at least 20% of the genome can influence gene expression” (Van Noorden 2012). Science stuck to its maximalist guns, and its summary of 2012 repeated the claim that the “functional portion” of the human genome equals 80% (Anonymous 2012). Unfortunately, neither 80% nor 20% are based on actual evidence.

Other critics, including Sean Eddy, focus a great deal on what is called the C-value paradox: Given a genome of a certain size, if it was all functional — or a lot of it functional, as the ENCODE consortium has claimed — then it would all be under evolutionary pressure, i.e., you'd expect certain mutation rates to occur, but they don't. Evolutionary biology would say about 5-10% is functional, I believe, based on how much selection takes place and where. So those critics would say (and have had indeed said) a lot of negative things about results reported by ENCODE.
I suspect that the true answer, if there is one, depends on what one defines as functional and as evolutionarily conserved, by what means you measure it, and what the balance is between functionality and conservation. You pick your definitions and processes, and you accept the compromises and limitations that go along with those choices.
Caveat: I am a contributing author to ENCODE papers released in Nature in 2012.

It's good that people of your experience are contributing to SE Biology, although you may do better to transfer your answer to one of the previous questions on this topic if it is judged a duplicate. Although your answer is extensive and interesting, I do feel that it might help readers if you summarized the way the ENCODE data supports a larger proportion of functional DNA. I believe that the data were mainly RNAseq, so would I be right in thinking the argument is based on the portion of the genome transcribed, together, perhaps with data on conservation?


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Is "muscular attachment" synonymous to tendon? (when talking about the insertion of glutei medius and minimus to greater trochanter of the femur)
I have read the following two terms in an MRI report (both points refer to the insertion of gluteus  medius/minimus to greater trochanter of the femur):

mild degeneration of the muscular attachment of the left gluteus medius
mild tendinosis of the left gluteus minimus

Is muscular attachment (to a bone) synonymous to tendon? Or does the muscular attachment designate the muscle part that attaches to the tendon? Or something else?

The tendon and muscle attachment are not the same. In your example, both are affected, so they are described separately.
A muscle extends into a tendon and this into an enthesis - an actual attachment site where the muscle is attached to the bone (PubMed).

Thanks! Just to confirm, it means that muscular attachment = tendon + enthesis?

No, the tendon is not really a part of the muscular attachment.

so muscular attachment = enthesis?

Yes, that's it. It also applies for the sites where ligaments are attached to the bone.

Thanks for confirming! Good to know about ligaments.