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What dictates which protein to synthesize at a given time?
I understand how DNA is replicated and how it directs the synthesis of proteins from amino acids through RNA polymerase, RNA and ribosomes. Now I want to understand how it works in the big picture.
With my current level of understanding, any protein can be synthesized at any time at any rate, but it looks to chaotic to work at all.
What dictates which protein to synthesize at a given time?

Regulation of gene expression and protein synthesis occur on multiple levels, and together these levels allow for fine control of when, and to what extent genes are active. It would be impossible to give a comprehensive answer for such a broad question. Here is a starter, beginning with the most important fact:
DNA is used as a template to make messenger RNA, which is exported out of the nucleus to produce proteins on structures called ribosomes in the cytoplasm.
One the level of DNA, there is a lot of regulation of which genes, and when, and to what extent, will be transcribed into messenger RNA. The name for this regulation is transcriptional regulation. For example, a network of proteins called transcription factors bind to DNA, regulating a gene's accessibility to transcriptional enzymes. Another example: the three-dimensional topography of DNA is also important. Epigenetic features may render some stretches of DNA inaccessible. The specific action of distal elements called enhancers can also affect a gene's level of expression. There are many things working in tandem on this level.
Once a messenger RNA is formed, it has to be exported out into the cell from the nucleus. In the cytoplasm it can be packaged, isolated from being translated into protein, degraded, accumulated, the list goes on. This is called translational regulation. Currently, there is a lot of focus in biomedical and basic research on microRNAs, which are RNA species which participate in regulating the amounts of messenger RNAs present in the cell. They are also found in the nucleus. Many biotechnologies are based on this concept; also, a common lab practice is to knock-down (reduce the expression of) genes of research interest by a technique called RNA interference.
Additionally, there's regulation of protein biosynthesis at the ribosome, which often complexes with other molecules in complicated ways to ensure an additional layer of tuning of how much protein is produced, and how quickly.
There are many, many other known levels of regulation. There also remain many unknown mechanisms of regulation, which scientists are busy with uncovering and understanding as we speak.
EDIT: What dictates which protein to synthesize at a given time? The history and present identity of a cell. By identity, I mean its state regarding regulation of its own gene expression, as well as other things.

Your asking how a cell or organism regulates protein synthesis. This is a complex question, with many different parts. It is well presented in Alberts Molecular Biology of the Cell, Chapter 7, on genetic switches. Here's an online section from that chapter in the 2002 edition.
There is a lot involved in regulating protein synthesis. As a general rule if you can imagine regulating it, it's regulated. Here's a figure from Alberts to get you started thinking about this:

There are some things that are required for all genes. General transcription factors, for example, and the Pribnow, or TATAAT box. The presence, absence, location, and accessibility of these things can regulate the levels of protein synthesis by the cell. Other things are going to discriminate between different genes. Under certain conditions, certain gene regulatory proteins will be produced, not destroyed as quickly, activated, allowed entry into the nucleus, etc, regulatory sequences will be exposed or not exposed, methylated or unmethylated... and transcription rates will change accordingly (increasing if those protein gene interactions stabilize assembly, binding, and transcription by the polymerase, decrease if they destabilize assembly, binding, and transcription by the polymerase).
This is just a taste of the wonderful world of gene regulation in the eukaryotic cell. As it says in Alberts, of the roughly 30,000 human genes, an estimated 5–10% encode gene regulatory proteins. And these are just the proteins that directly regulate transcription.


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Can immunity to diseases vary by populations?
A common explanation for the massive population decreases of isolated societies upon contact with Europeans during the Age of Discovery is that the natives lacked immunity to newly introduced diseases.
What does this actually mean?
Is it just a shorthand for "the adult population was not subjected to these pathogenes during childhood and is therefore more susceptible to them" or is there maybe a certain genetic component to it?

This is a very interesting question. 1) You might want to narrow your question down to a single disease (such as smallpox for example) because otherwise the question might be too broad. 2) You might also want to consider the possibility of a cultural difference in response to specific diseases. Maybe in Europe, the people knew how to deal with a specific disease they were used to encounter (quarantine, specific treatments, ...) but the native, having never encountered this specific disease, did not know how to deal with it.

Related posts: Why was disease transfer to the Americas one-way? and Why Can't The Immune Systems of Uncontacted Tribes Handle Our Common Colds?. This second post might actually be a duplicate. You might want to address this other post in your question.

@Remi.b I'm a complete layman and really wouldn't know which disease would be suitable for narrowing down the scope though.

@Remi.b I don't think this is a duplicate. This question, to me, focuses on the heritable vs. non-heritable factors in susceptibility in general. The proposed duplicate, to me, reads as a question about how the common cold can be relatively innocuous in one population but fatal in another. That's a different question entirely (and is poorly answered right now). Both are questions about host-pathogen interactions on a population level, but I read them as very different.

It would also help to consider the response of European populations to newly-introduced diseases.  For instance, bubonic plague killed tens of millions of Europeans in several episodes.  Yet now it's endemic amoung rodents in the western US, yet only about 10 human cases per year are reported: https://www.livescience.com/51792-plague-united-states.html  Similarly the Antonine Plague (either smallpox or measles).

Is it just a shorthand for "the adult population was not subjected to these patogenes during childhood and is therefore more susceptible to them" or is there maybe a certain genetic component to it?

It's a little of both. You can read some of the math behind this in Infectious Diseases of Humans: Dynamics and Control, by Anderson and May.  Chapter 2 gives an overview. The behavior of an epidemic depends a great deal on the specifics of the host-pathogen interaction, but generally you can say that the epidemic curve in a a naive population will have a larger and sharper upswing than in a previously exposed population. You can attribute some of this different behavior to lack of adaptive immunity in the adult population. Again, depending on the pathogen, you can also attribute some of this different behavior to lack of selective pressure in the naive population on highly variable loci involved in the immune response.
To address more directly what seems to be your primary question: yes, there is a genetic component to the susceptibility of a host (e.g., a human) to a pathogen (e.g., a microbe that can cause disease).
Non-heritable aspects:
There are certain aspects of what we call the adaptive immune system in jawed vertebrates that are not directly heritable. You are a jawed vertebrate, and the DNA in each of your B-cells and T-cells that produces B-cell receptors (BCR) and T-cell receptors (TCR) goes through a number of changes outside of the germ line. You can read about these changes in, for example, How the Immune System Works, Chapter 3, by Lauren Sompayrac. It's an excellent introduction if this is new to you.
In addition to the exact set of BCRs and TCRs in the pre-immune state, your current repertoire of cells and molecules is determined by your history of exposure. While some of this can be vertically transmitted, the majority of it is not. This is one of the reasons why, when you look at this repertoire, much of the variability is attributable to non-heritable factors. A not insignificant proportion is attributable to heritable factors, though. So if TCRs and BCRs are not encoded in your germ-line, and your environment obviously has a strong influence on your current immune state, where does the heritable component come from?
Heritable aspects:
All of the other proteins involved in the immune system response are encoded in the germ line, and are thus heritable. Some of them are highly variable, and since they are very important they are under strong selective pressure. You can see important changes in the population distribution of these loci over a relatively small number of generations. There are many other heritable components of an individual or population's susceptibility to infectious disease. There is a great deal of work on this. Casanova has a great article about this in PNAS, which I've linked to in another answer to a related question. A more traditional review of his is here. Of course, he's not the only one working on this. I just like the way he writes. Here's a good one by Baker and Antonovics.
A simplified and speculative example
Re: your comment about measles in the Polynesian islands, we don't have scientific consensus about the relative importance of non-heritable and heritable factors for this particular case. Instead of getting into the nitty gritty details, I'll walk you through a hypothetical:
Imagine an isolated population with a lot of variability in germline genes that code for a special protein that helps their immune system mount a full response to viruses.
A very nasty, very contagious virus is introduced to this previously isolated population. The characteristics of the population help determine the outcome of their interaction with this new virus. Here are 3 important characteristics:

Because nobody has ever been exposed to this virus, nobody has neutralizing antibodies or the rapid immune response that happens the second time you're exposed to a pathogen.

Some versions of that special protein with all that variability don't do a good job of helping the immune system mount a response to this new virus.

Luckily though, some other versions of that special protein with all that variability do an especially good job of helping the immune system mount a response to this new virus.

Because of (1) the disease spreads broadly throughout the population. Because of (2), a specific group of people get especially sick, die, and (because they are dead) don't reproduce, and don't pass on their version of the gene that codes for special protein. Because of (3) a specific group of people do very well, are only sick for a little while, and do an especially good job at generating long lived immunity, and (because they are alive and well) reproduce a lot, and pass on their version of the gene that codes for that special protein.
The epidemic is eventually controlled. Years go by, and the virus starts circulating again.
Now the characteristics of the population are quite different, so the dynamics of the host-pathogen interaction will be different.
Many of the people that were alive during the first epidemic now have neutralizing antibodies and a memory response, so this second epidemic will not spread as quickly or as broadly. This is a non-heritable factor. Previous exposure to the virus has changed the repertoire of cells and molecules in people's blood.
Among the younger generation, more of them have the helpful version of the special protein that helps the immune system generate a response, so not as many of them will die. This is a heritable factor. Previous exposure of the population to the virus has exerted selective pressure, changing the frequency of the helpful and unhelpful alleles in the population.

Thank you. I'm still having trouble reconciling my (naive!) ideas of how evolution works with the phenomenon at hand. Say, after 40% of Polynesians were wiped out after the first wave of (e.g.) measles, were the surviors genetically "hardier" to the germ? I understand that most likely the best answer is "go read a textbook" (thank you for the references), but maybe you could address this point (more).

@TNierath It's very plausible that those who survived were genetically more resistant to measles (on average). Don't think of this as an on/off switch, more on a gradient. People can be more likely to survive for many reasons. Perhaps some people had stronger lungs (partially for genetic reasons, but also partially due to non-genetic reasons). Perhaps some people had a stronger immunity system. All kinds of factors can be involved, and all these factors may influence how much at risk any individual is.

@TNierath I've added a hypothetical example that may help you understand.

Thank you again for taking the time. I understand the evolutionary logic (I think), but have trouble with some of the terminology and concepts: What are germline genes and how are they different from other genes? The "same" protein can have varieties? Are proteins themselves uniform across human populations and only differ in their varieties coded by genes? What is a "memory response"?

@TNierath Germline genes are passed on to your children. My first paragraph on non-heritable factors talks about how some genes involved in the immune response are changed outside the germline, so can't be passed on to your children. Variability is what makes evolution work. Genes are not uniform across human populations, they are variable. The proteins they code for are not uniform either. Different versions of a gene (and the protein it codes for) are called alleles. Small differences in a protein may not have an impact in certain conditions, but will in other conditions. This is an example

@TNierath the memory response is a specific property of the adaptive immune system. When you're exposed to a pathogen the second time, your immune system remembers it and can mount a quicker more effective response.

@De Novo Ah yes, so the "germline" is what laymen usually just think of as "genes" (information transferred to offspring). I assume there must be utility in making a conceptual distinction between "having antibodies" and having a "memory response", but that it may nevertheless not be esp. relevant in the current context?

@TNierath yes. Having antibodies can be just a passive response. You've already made them. This can be helpful for neutralizing and preventing an infection. A memory response is more than just ongoing production of antibodies. It's reactivation of memory cells, and a rapid increase in many different effector mechanisms of the immune system.

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Pox virus infection process
How does Pox virus duplicate it's genome? Does it bring DNA polymerase or RNA polymerase into the host cell?

Poxviruses, such as variola (the causative agent of smallpox) and vaccinia (the active constituent of the vaccine that eradicated smallpox), are very large, complex DNA viruses that replicate in the cytoplasm, rather than the nucleus. Because of this, they must carry enzymes with them to accomplish tasks that occur in the nucleus of the eukaryotic cells they infect. This includes all the proteins necessary for mRNA synthesis (e.g., a DNA dependent RNA polymerase). The enzymes for DNA replication are encoded in the poxvirus genome and are transcribed and translated as part of the "early" stage, directly after adsorption and penetration.
So, yes, poxviruses bring their own preformed RNA polymerase with them. They don't bring their own DNA polymerase with them, but they do produce it shortly after infecting a cell.
You can read more about this in Murray Medical Microbiology Chapter 54.

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Can vaccines move from person to person?
Can someone who has been given a vaccine "infect" another person with the virus used in that vaccine? For example, let's say Bill is vaccinated against tuberculosis. If Frank is exposed to Bill, is there a chance he could "catch" the tuberculosis vaccine, and become immune?

So, A got a vaccine but still got infected by the virus (which is totally possible). And then, you are asking if A can transmit the virus to B? Is that your question?

Here are a few things that can help you clarify the question. Who is "they" in the first sentence? Does it refer to "another person" (but then it should be "he/she")? What do you mean by "contacted"? By "become immune", do you mean after the infection happen? If not, why would there be a need for the first person to be infected? Or maybe when you said "infected from viruses", you refered to the neutralized form of the viruses that were injected in the vaccine?

I think Jossie is assuming the antigen in vaccines can can be transmitted and infect other people like an ordinary pathogen.

OP, I've edited your question to try to clarify it. Feel free to roll back or further edit if I've misunderstood or missed anything.

@Jossie, in simple terms: vaccines only contain parts of "dead" pathogens that trigger an immune response to those parts inside the body of the person who was vaccinated. There's nothing to pass on (via a sneeze, cough, etc.).

A weird analogy I'm making up as I type (& as I eat): Imagine wanting to know what vanilla ice cream (IC) tastes like. You could taste vanilla extract & your taste buds would know what vanilla tastes like. You'll not have eaten vanilla ice cream, but if you ever do eat vanilla IC, your taste buds will know the IC is vanilla flavored. This is because your taste buds had previously been exposed to the parts of vanilla IC (i.e., vanilla) that could inform your brain of the sensed flavor. However, someone else could only know what vanilla tastes like if they sampled their own vanilla extract.

Most immunizations are not transmissible. A few are. To be transmissible, an immunization would have to be a live attenuated vaccine (i.e., a vaccine that can reproduce in the host, but doesn't cause disease), AND have the necessary reproduction rate and virulence factors that would allow for person to person transmission. There are many live attenuated vaccines in use today, but only one that is transmissible, Oral Poliovirus Vaccine, or OPV. OPV is currently not in use in the US, but is used in the developing world, and can circulate in communities. Some would argue that this is a good thing, as it further disseminates immune protection to the population, but it is a little problematic, because it is not without risk, including reversion to a virulent type that can cause Vaccine associated Paralytic Poliomyelitis.
On editing your question, I'm reminded that your example was of TB. I would note that BCG, the vaccination against Tuberculosis, may be a particular case, and I'm not as familiar with it except as a complicating factor in interpreting the results of a TB test in U.S. immigrants. BCG is a live attenuated strain of Mycobacterium bovis, can (rarely) produce disseminated disease itself, and the mycobacterium itself can be isolated in the blood of individuals some time after vaccination. There is also a possible report of vertical transmission of the mycobacterium (from mother to child), but these results use novel methods, and I'm unfamiliar with this group's work. Whether this would lead to immunity of the child is definitely an open question. BCG even when administered in the standard way (as in intradermal inoculation) isn't particularly good at producing immunity, though it is good at preventing meningitis and miliary TB in young children. I'm not aware of any documented case of horizontal person-to-person transmission, but wouldn't declare it impossible.


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Why did humans lose their tail during evolution?
Most mammals seem to have tails. Even human embryos start out with a tail. But here we are with nothing but a tail bone that hurts when we trip over backwards. What is it good for? Why don't humans have a tail to wag around?
Some science fiction (like Avatar) even portrays a tail as something sexy. And we all have experienced that a third arm of some kind would be very useful once in a while. Especially since humans stand up a lot of the time it could help us keep balance.
Is there any utilitarian evolutionary explanation for why we don't have tails any more? Is it only because we try to be different?

The tail serves a variety of complex balance tasks in locomotion, turning, jumping, aerial balance, hanging, and most mammals have a tail, save for other examples, i.e. rabbits, pigs, capibaras, manx cats, seals and bats, lemmings and hamsters have mini tails.

All the previous large apes related to humans lost their tail millions of years ago. The reason why that occured are multiple and mixed. Multiple good explanations have been suggested.
Gibbons are some of our most monkey-like ape cousins. If you see how they move, they run on two legs rather than 4. Monkeys with tails are less adapted to walking and their pelvis is angled differently. https://www.youtube.com/watch?v=b9Pt2qgSqJw
Large animals with small tails, such as caribou, hippos, elephants, deer, seem to keep some kind of tail, however with chimpanzee type animals, once the tail became small it didn't stay on as a mini-tail. So would it make sense for chimpanzees/humans to have small tails like hippos or very long ones? If a chimp can run on 2 legs, that leaves it two hands to catch the tail of another competing chimp.

The big apes move differently to small apes: big apes live on the ground more, they don't run in trees as much, they move differently, they are larger, they have completely different body ratios for arm and leg size, and there have been a wide variety of propositions for hundreds of years on this topic without a particularly clear reason being accepted for which great apes don't have a tail.

My take away is that three is company. Two hands outcompeted the tail. I suppose the tail would just get stuck in all sorts of stuff anyway. Unlike our very sensitive fingertips.

@LocalFluff: OTOH, consider elephants, who seem to do quite well by putting their "tail" (AKA trunk) at the front.

And then there's this, from the news today: http://www.sciencemag.org/news/2017/07/watch-robotic-appendage-give-humans-third-arm  Mount it a little differently, and there's your prosthetic tail :-)

In 2021 an elementary genetic point mutation was found to coincide with the presence or absence of the tail about 25 million years ago, so it's not a complicated feature that takes millions of years, it's a basic random mutation that can happen in 1-2 generations in a population. It happened at the same time as there was a dramatic change in monkeys towards apes that have good bipedalism and inhabit a new ecological niche. The tail mutation could be a cause and/or a consequence. The corresponding animals are: Gibbons.

Gibbons are close to the oldest human ancestors that lost their tail. They branched off from monkeys ~20 million years ago and they have even more impressive climbing skills, they are entirely arboreal and run waving their arms around in a clumsy way. Gibbons don't have a quadrupedal running gait like big babboons and squirrels, who run like small dogs and cats.
If you study these videos of gibbons, think... Would a tail benefit or hinder these animals?
They are some of the most impressive climbers of all because their opposeable thumbs are well developed and their arms and legs are more ambidextrous than running animals.
So if you think back in time, for the point genetic mutation, potentially there was a family of monkeys living together that had individuals with tails and individuals without tails.
image of the latest primate phylogeny

(+1) A likely tale!

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Why are there so many carbonic anhydrase structures in the Protein Data Bank?
I've been looking through PDB — the Protein Data Bank — and I noticed that the protein with the most structures is human carbonic anhydrase II (UniProt: P00918), with over a thousand X-ray structures.
This seems surprising to me, as carbonic anhydrase is a zinc-containing enzyme which catalyses a really simple reaction, and doesn’t seem to be part of any key signalling pathways.  In terms of relevance to disease or as a drug target, all I could find was on DrugBank was a few glaucoma drugs which have this as their target (diclofenamide, methazolamide, acetazolamide), and those are really old (60 years).
So, what is it about carbonic anhydrase that makes it so interesting?  Is it that more or better drugs are needed to target it? (For what disease?)  Is it that it’s a really interesting scientific model of a metalloenzyme?  Or something else?

Answering this question really needs some hard work, and we expect the poster to make a start looking through the PDB entries in terms of date/CA type/species/whether they have an associated paper/whether they relate to a complex with another molecule. Have you looked at some of the recent and older papers in which the work is reported to see how they justify their work and who funded it? Please do, and let us know what you find.

It certainly is related to disease! There are tons of inhibitors (as David mentioned in the comments Aslam & Gupta 2022 ). The reaction is simple but maintaining the pH of your blood is essential (keep a perfect equilibrium between $CO_2$ and $CO_3^{2-}$). It's essential because pH determines if hemoglobin binds/releases $O_2$.
It's so famous because every beginner biochemistry course will talk about carboanhydrase at some point. The enzyme is very stable and can be purified relatively simply from blood, which was possible even 60 years ago. It helped early biochemists understand enzyme kinetics. Carboanhydrase in particular was interesting, since it has a ridiculously fast turnover rate ($10^6$  molecules per second). That makes it perfect to describe enzyme kinetics ($K_m$ and $k_{cat}$) and also chemical equilibria in general.
Bob1 pointed out that some courses even require you to crystallize, make an x-ray structure of carboanhydrase and submit the result. So carboanhydrase is like the absolute tutorial enzyme of biochemistry, which explains the inflated structure count.

It certainly is related to disease. I had a look at the hits on PDB, and a huge number are of inhibitors of CA. I searched for "Carbonic Hydrase Inhibitors" and found a short piece on this topic on NCBI Bookshelf that starts: "Carbonic anhydrase inhibitors are a medication used to manage and treat glaucoma, idiopathic intracranial hypertension, altitude sickness, congestive heart failure, and epilepsy, among other diseases." Why else would you determine the structure of protein that has already been done, and who would fund you?

@David True, I found a few links to diseases too but the number of structures still seems like way more than the disease relevance would suggest.  Surely not enough to be the most studied enzyme - still somewhat puzzling

@AlexI I think you will find that as per the second part of Markur's answer, a number of courses for biochem will have "purify, grow crystals, X-ray diffract and submit structure" as part of the course requirements.

@AlexI — This was a comment/criticism of the first sentence of this answer. It was not an answer to your question. I do not answer questions in comments. When/if I have considered the matter I will give you a balanced answer.

Carbonic Anhydrase is heavily researched because of carbon dioxide capture.
It’s hoped to be used in getting $CO_2$ from combustion exhaust to hydrogen carbonate, and thence to other capture reactions in industrial settings.
Also for possible more efficient plant $CO_2$ capture, so plants can grow better with less water loss.

This is very interesting, but would mainly make sense if those were (eg) extreme thermostable or pH-stable versions; rcsb.org has 1000 structures of plain old human CA2, so I feel this can't be the whole answer


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What is the purpose of gluconeogenesis?
The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?
Can someone explain why we have gluconeogenesis and when it is used?

Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as their energy source. These include the brain (although ketone bodies can be used here as well), erythrocytes, testes and the kidney medulla.
Usually the glucose for the supply of these tissues comes directly from carbohydrates in food or storage carbohydrates as glycogen or starch, but when these are not available, the body has another way to get around this problem and to avoid the starvation of these tissues. See for example here and here.

fatty acids are not a substrate for gluconeogenesis.

@AliceD Fatty acids are no direct source for gluconeogenesis, but where does the necessary Acetyl-CoA come from? For example from the beta-oxidation of fatty acids.

I thought the backbone of the glucose as the end product is not structurally related to fatty acids, but to the substrate of GNG such as amino acids. As the answer is formulated it reads like fatty acids are converted to glucose, which is not the case. I thought an essential feature of metabolism in general was that sugars can be converted to fatty acids, but not the reverse. Hence the problems people have to reduce bodily fat. GNG doesn't take fatty acids in as a substrate. Correct me if I am wrong.

I will make the answer clearer later today.

@AliceD In a way, we are both right. Odd chain fatty acids can be oxidized to propionyl-CoA which is then converted into succinyl-CoA and further into pyruvate, which can enter the glucneogenesis pathway. Even chain fatty acids are oxidized to Acetyl-CoA which enters the TCA cycle but cannot be used for making glucose. It's good to have the thick biochemistry books at hand :-)

Before discussing gluconeogenesis it is necessary to be clear on the following:

What organism you are considering
Under what physiological circumstances gluconeogenesis is occurring
What is the substrate for gluconeogenesis

and, if one is considering mammals:

Which tissue is performing the gluconeogenesis
Which tissue(s) will consume the glucose produced

because these latter two are never the same,
or in other organisms:

What is the glucose produced actually used for

MAMMALS
Gluconeogenesis is performed almost exclusively by the liver, which is able to provide the NADH and ATP for this process from its oxidative metabolism. (The kidney also has a small capacity for gluconeogenesis, but the reason for this is another question). The tissues consuming the glucose are predominantly erythrocytes, brain and nervous tissue and muscle, depending on the circumstances.
Resting post-absorptive ‘lactate recycling’
Erythrocytes have no mitochondria so can only respire by anaerobic glycolysis, reducing the pyruvate to lactate (in order to regenerate NAD+). The lactate goes into the blood, and is taken up by the liver and oxidized to pyruvate. Gluconeogenesis converts the pyruvate to glucose which passes back into the bloodstream, restoring that used by the erythrocytes. (The brain also uses glucose here but I’ll deal with it below.)
‘Lactate recycling’ in exercise
Muscle has a certain aerobic capacity depending on type. However in vigorous exercise the skeletal muscle becomes anaerobic and obtains ATP for muscle contraction from aerobic glycolysis, again producing lactate. The liver glycolysis recycles this lactate to maintain the blood glucose, as in the previous section. (This overall co-ordination between tissues is often called ‘Cori Cycle’ in text books. However the name can be misleading, as it is not a chemical cycle like the tricarboxylic acid cycle or the urea cycle.)
Starvation
In starvation the net supplies of energy will fall. However the one tissue that must be kept supplied with a glucose is the brain (even though it can obtain part of its energy requirements from other sources). Liver gluconeogenesis provides this, but substrates other than lactate are need to restore the glucose lost by net consumption after the liver glycogen reserves have been depleted. The main gluconeogenic precursors are a subset of amino acids from protein breakdown (the so-called glucogenic amino acids) which feed in at different parts of the pathway. Glycerol from the breakdown of triglycerides can also be used, but fatty acids themselves cannot, because they are converted to acetyl CoA, which condenses with oxaloacetate to feed into the tricarboxylic acid cycle, and produces no net carbon skeleton that could be used for glycolysis.
PLANTS
I am not a plant biochemist, so I am happy to be corrected if wrong, but I understand that gluconeogenesis is important after seed germination for production of hexoses for use in cell wall polysaccharides during growth. Seeds contain reserves of fat, which on germination is oxidized to acetyl CoA which passes into the tricarboxylic acid cycle. However plants (and some bacteria) are able to convert this to pyruvate by means of a pathway mammals lack — the glyoxylate cycle (http://www.ncbi.nlm.nih.gov/books/NBK22383/). So in plants the glucose produced is not being used to provide energy by oxidation, but as a biosynthetic precursor.
BACTERIA
Gluconeogenesis is present in certain bacteria, where the pathway presumably arose (rather than in mammals). So it is of interest to consider its role there. Again, I am no bacteriologist, but the glyoxylate cycle is also present in bacteria, and it is likely that one function of gluconeogenesis would be to allow growth on fatty acids, with the glucose produced being required for synthesis of cell-wall polysaccharides.

Gluconeogenesis occurs during prolonged starvation or overnight fasting, mostly in liver and kidney to provide glucose to brain and RBCs. As brain and red blood cells require continuous glucose for their activity, this process comes in handy. The steps involved in gluconeogenesis are different from that of glycolysis, it is not the reverse of it. You can get more details 1 and 2.

Could you expand on the linked articles please? I also don't think this answers the question

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Does using the human genome as a reference influence the chimpanzee genome's similarity to the human genome?
It is often stated that human and chimp genomes are 98% similar, e.g. this is included in an article on the American Museum of Natural History website.
I also see in the release notes for the NCBI chimp genome:

Contigs were assembled using the human genome as a guide, and are therefore "humanized" in their construction. This is an important distinction, as some sequences, such as insertions, deletions, and gene duplications, may not be accurately represented by the current chimpanzee assembly.

So, does building the chimp genome using the human genome as a scaffold affect the figure of 98% similarity? If so, do we know how much?
(A previous question on this list mentioned a 2018 assembly independent of a human scaffold. Has this resulted in any revision of the figure?)

@David I fixed the link, chopped an 's' off the end.  Perhaps the question I linked to has the answer I am looking for, but the technical language is beyond what I know.  I cannot derive a 'yes' or 'no' from the answer to that question, nor understand if 'yes' to what degree.

I have edited your question so that it appears as a valid independent question, not starting with an oblique reference to another question. I have included that at the end. I have also tidied up the presentation of the links so that the text is more readable.

The similarity IS high
The main thrust of the question is the high similarity (98–99%) between human and chimpanzee genomes. The concern is that the use of the human genome as a scaffold for assembling part of the chimp sequences in the whole  chimp genome project, published in 2005, is a possible source of error in this figure so that the similarity is actually signficantly less.
The answer is an unequivocal NO because:

The high similarity was known before the chimp genome project was published.

The figure refers to comparable portions of the two genomes, excluding insertions and deletions. The use of the human genome as a scaffold only introduces uncertainty into the latter, not the former, as will be explained in the next section

Thus, even before DNA sequencing, DNA hybridization methods indicated an approximately 98.5% similarity of single-copy DNA. As one would imagine, before the technology for whole genome sequencing was developed many individual chimpanzee genes were sequenced using ‘traditional methodology’ that depends on mapping and constructing overlaps, and only subsequently comparing the sequences with the corresponding human genes. This methodology also revealed insertions/deletions of the genomes relative to one another, and led Britten to estimate on overall similarity of 95%, with 1.4% divergence due to base substitution and 3.4% difference due to insertions and deletions. Furthermore the whole of chimp chromosome 22 was determined without reference to the human genome. Finally, in the whole genome sequencing project, part of the sequence was determined assembling the shotgun fragments both with and without use of a human scaffold in order to validate the former approach.
The use of the human scaffold does NOT prejudice the base reads
Comments to my initial answer on this point and my assertions in reply appear not to have been understood. I have therefore constructed a diagram (below) to explain this more clearly.

The left-hand side of the diagram shows a much simplified schematic of steps in ‘traditional’ directed sequencing. This can start with a focus on a particular gene or region of the genome from which large clones (BACs or bacterial artificial chromosomes were used for chromosome 22) and, after mapping, smaller overlapping fragments were generated, sequenced, partially assembled and further overlapping fragments generated and sequenced. In this way the assembled sequence is gradually extended. When complete (it may be joined by overlap to other large fragments) it is compared with the corresponding region of the human genome and base differences, insertions or deletions noted catalogued.
The second approach, using a human genome scaffold, relies on, and is justified by, the prior knowledge of the very high similarity between the two genomes. The approach here is to generate and sequence millions of random fragments, but as they are small the overlap tends to be small and not unique in the way that they are in the directed approach. Thus the second step is to arrange these small fragments in groups by their similarity to the human genome. I emphasize that this is done — as it must — after the chimp fragments have been sequenced. What this step does is place the fragments at co-ordinates on the human genome so that they can be located relative to one another. That’s it for the human genome — the method doesn’t need it any more. The placed fragments are then stitched together computationally into an assembly on the basis of small overlaps that would not have been meaningful without the initial alignment. Because of chimpanzee polymorphism there will be redundancies at particular positions. I read in the supplementary data to the paper that if this was greater than two, the situation would be reviewed for artifacts and dealt with.
As the disclaimer the poster quotes makes clear, the use of a human scaffold can miss duplications, but it cannot and does not change the chimp base calls. One of the key reasons for sequencing other primate genomes is to have a precise knowledge of how they differ from ours. It would have negated the whole purpose of the project (not to mention being unethical) to choose between two possibilities on the basis of which was the same as the human (as the poster suggested might occur). This was not done. Problems with the data were subject to rigorous critical review. If the sequence of a region was uncertain it was marked as such.
And, of course, having this initial sequence allowed the uncertainties regarding insertions, deletions and duplications to be specifically addressed in subsequent work.
Appendix: The 2005 report in context
The paper describing the “Initial sequence of the chimpanzee genome and comparison with the human genome” was published in 2005. It is 18 pages long (plus appendices) and contains no sequence data and was the work of a consortium of about 70 highly skilled workers at 24 different institutions with a spectrum of different skills, including informatics and statistics. There is no mention in the abstract of the overall percentage similarity, which was already known. This work was preceded by other work on this topic over a number of years (as mentioned) and was not intended as an end in itself — it was intended to lay the foundations of further work to find the effects of the differences between chimp and human genome of the type discussed in the more recent paper mentioned in the question. Work of this type has been assisted by the vast technological advances that have occurred over the last 16 years. This is the way contemporary science works.

I have now revised my answer completely. I have therefore deleted all my responses to your previous comments. This should suffice.

Thank you very much! I probably need to rework my question to make it clear where I see a specific technical problem as I'm afraid I still don't understand from your answer how they avoid the source of bias I pointed out in my previous responses.

To elaborate, in the arrangement step, they start with a bunch of very small pieces, many of which have errors.  An error that matches the human genome will produce a better alignment score than a piece without that particular error.  Since they don't know beforehand which pieces have the errors, how do they make sure they are only aligning error free segments?  If they cannot say which pieces are error free, then I fail to see how the alignment step avoids the bias problem I point out.

A second, related, issue is that with many small pieces, even without errors, there is the possibility that pieces from entirely unrelated portions of the chimp genome are aligned to the human genome because they get better matches.  I am also curious how they avoid this source of bias.

@yters 1. The fragments selected from the BLAST alignment will have a cut-off that allows for the human-chimp divergence, e.g. 95% identity, so WILL also include fragments with random errors in whatever direction. No chimp fragments will be excluded. The assembly is done after the fragments have been positioned. Because of the multifold (e.g. 10X) coverage, random errors will show up as e.g. 1/10 and be discarded, regardless of their relationship to the human genome. 2. Pieces from other regions of the genome that BLAST matches will represent duplications, for which bias is a admitted.

So it sounds like there could be a bit of bias at the nucleotide level from using human scaffolding, but I suppose you are claiming it is not significant enough to affect the similarity score.  I understand there are alternate ways the similarity has been calculated, which also show a very high similarity, but I'm interested in focusing just on the nucleotide to nucleotide comparison.  Has anyone attempted to calculate how much bias could be introduced by the errors and duplication?

@yters — Error frequency is generally estimated and quoted in such papers. For details you would need to check the original — which, incidentally I highly recommend, even if you don't understand the details. As I mentioned, the differences between the human and chimp caused by duplication etc was estimated by Britten. But, as I keep saying, the percent difference between chimp and human is known independently of the whole genome project paper which did not even report it and any numerical changes from subsequent correction of mistakes are minuscule and of little interest.

Thanks, I really appreciate the time you put into this question and researching it.

I see in the 2005 paper it says "About 98% of the chimpanzee genome sequence has quality scores of at least 40 (Q40), corresponding to an error rate of ≤10-4." So, I think that answers my question about whether base errors can create bias.  If each read is 100 bases long, and each read is duplicated 10 times, then the Q40 number means the expected number of errors is 0.1 per section read, if I am understanding correctly, which means adding only 0.1% bias in the worst case scenario.  That does seem insignificant.  Please correct me if I am misunderstanding.

You can look at the sequence similarity between homologues yourself.  Here's just one example.
http://uswest.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog/Alignment?db=core;g=ENSG00000138650;g1=ENSPTRG00000016444;hom_id=55568071;r=4:133149294-133208606;seq=cDNA
Those sequences are 99% similar, and that's not because they used human reference a assembly guides.  It's because the sequences really are that alike.

Are you saying this chimpanzee sequence was not assembled using a human reference?

The base by base alignment of that those homologous genes is not affected by the use of any reference-guided assembly which might have been used to stitch larger pieces together.

The chimp genome is 3 billion bases long, so there are 6 to 30 million pieces in that case.  Additionally, my understanding is there is a fair bit of error in the piece generation.  In that scenario, it isn't obvious to me using a human reference won't bias piece selection.


text:
Will new proteins incorporating new amino acids trigger an immune response?
This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done were able to produce new proteins using the newly added bases. The article quotes the scientists as saying that the extra amino acids “might become building blocks for new drugs and novel materials”.
My question is that if new proteins are made from amino acids that don’t naturally occur, won’t the body reject them?

The body's mechanism for detecting foreign object has a built-in failsafe that minimizes the likelihood of misinterpreting a self-derived antigen as foreign.

Immunologic tolerance (unresponsiveness) normally prevents reactions
  against self-antigens; if immunologic tolerance is broken, autoimmune
  reactions may occur. Much of the development of tolerance occurs in
  the thymus by the elimination (clonal deletion) or inactivation
  (clonal anergy) of self-reactive clones of T cells. Other mechanisms
  of tolerance occur extrathymically and include activation of
  antigen-specific T suppressor cells and clonal deletion, which results
  in the elimination of self-reactive B cells or T cells, and clonal
  anergy.

https://www.ncbi.nlm.nih.gov/books/NBK7795/
Basically, before a T cell starts looking for potential antigens, it generally first spends some time in the thymus being tested against antigens which are native to the body. If it responds to such an antigen, the T cell will either be destroyed or deactivated.
Having unnatural amino acids as part of this process is unlikely to change its efficacy. T cells which would target peptides with these unnatural amino acids will still be checked against the body's cells before being sent out to do their work; the mechanism would work the same way. I suspect that the rate of autoimmune diseases would be unchanged compared to normal organisms.

@Astrolamb The question asks whether the body will reject proteins containing unnatural amino acids. Your answer focuses on the mechanism of tolerance, indicating that this will continue to operate as normal and that synthetic proteins will be treated by the immune system as non-self, a conclusion that few would disagree with. However it does not address the concern of the poster that synthetic proteins would be rejected by the body, implying that their use as "new drugs" would be doomed to failure. Please provide more information on this point. Does your argument imply rejection or not?

Introduction
This question has two components. The first is the near rhetorical question whether proteins with unnatural amino acids will be considered by the immune system as ‘non-self’. Unless, by chance, the unnatural amino acid resembles some normal macromolecular component, the answer is obviously that it will be regarded as ‘non-self’.
The second question is, to my mind, much more interesting, but does not appear to be considered (or has been taken for granted) in the answer by @Astrolamb. This is whether the immune response would cause such artificial proteins to be eliminated, if  administered therapeutically. It is important, at this juncture, to emphasize that proteins containing unnatural amino acids as the result of expanding the genetic code do not, in principle, raise any problems of immune ‘rejection’ that have not already been seen in ‘unnatural’ proteins containing normal amino acids. Any immune response should therefore be regarded as being to ‘non-self protein’ and rather than to ‘non-self amino acid’.
As there have been many such studies with the latter proteins (and with proteins containing unnatural amino acids introduced by chemical modification) there are extensive studies on which to base an answer. An immunologist would be a better person to do this, but in the absence of any “immune response” I will attempt an answer from my perusal of the literature, leaning particularly on:
K. Wals and H. Ovaa “Unnatural amino acid incorporation in E. coli: current and future applications in the design of therapeutic proteins” Front. Chem 2, 1–12 (2014)
and
B. Leader  et al. “Protein therapeutics: a summary and pharmacological classification” Nature Reviews Drug Discovery 7, 21–39 (2008)
I welcome comments suggesting improvements or corrections.
Summary
The question asks:

“if new proteins are made from amino acids that don’t naturally occur,
  won’t the body reject them?”

which I take to mean:

“if new proteins are made from amino acids that don’t naturally occur,
  won’t they induce an immune response which will render them
  ineffective?”

The brief answer to this is:

It depends — the immunogenicity of foreign proteins varies.
Even if an immune response is elicited this may not necessarily render such proteins ineffective.
In some cases the therapeutic intention is actually to provoke an immune response — to make a weakly immunogenic protein more so.

Foreign proteins vary in immunogenicity
The crux of the answer to this question lies in the following:

The fact that a protein used for therapeutic purposes differs from
  those in a human subject does not in itself mean that it will invoke
  an immune response.

Let us consider two examples to illustrate this.
The first is the case of porcine insulin, which has been administered to patients for many years, but has one amino acid different from human insulin. Regarding such non-human insulin this review states that “severe immunological complications occur rarely, and less severe events affect a small minority of patients”.
The second example is taken from more recent work by D-A. Silva et al. in designing artificial proteins. (See also Nature News & Views summary). They designed mimics of the cytokines, interleukin-2 and interleukin-5, that had extensive differences in helix organization and amino acid sequence from the native proteins. However they reported that “Immunogenicity against the de novo designed proteins appears to be low”.
It turns out that  a wide variety of factors affect the immunogenicity of foreign macromolecules, so that even if a therapeutic protein elicits an immune response it may be weak enough to allow the therapeutic action to occur. In the work just cited, Silva et al. suggest that the reason for the low immunogenicity might be “the small size and high stability” of the proteins on the basis of previous work they had performed with 20,000 mini-proteins.
Admittedly, in some cases a strong immune response will occur and can obviously be a problem, so that measures need to be taken to reduce the immunogenicity. This is widely recognized and discussed in the following paper:
V. Brinks et al. “Immunogenicity of Therapeutic Proteins: The Use of Animal Models” Pharm Res (2011) 28:2379–2385
Sometimes chemical modification of proteins can actually reduce their immunogenicity, as is the case for polyethylene glycol in relation to interferon (B. Leader et al. review, cited above).
Use of therapeutic proteins to provoke an immune response
One use envisaged for modified proteins is in cancer immunotherapy. In brief, the objective is to try to make the body mount an immune response against cancer cells, which may exhibit ‘foreign’ tumour antigens. However, in many cases these differences from normal cells are not sufficient to provoke an adequate immune response. It is has been shown that modifying retinol binding protein by introducing an unnatural amino acid can help overcome the self-tolerance to tumours in mice, suggesting a possible use in cancer immunotherapy  (J. Grünewald et al. “Mechanistic studies of the immunochemical termination of self-tolerance with unnatural amino acids” PNAS (2009) 106, 4337–4342).
Conclusion
Proteins containing unnatural amino acids as the result of expanding the genetic code do not, in principle, raise any problems of immune ‘rejection’ that have not already been seen in ‘unnatural’ proteins containing normal amino acids or chemically modified amino acids. The problem of potential immunogenicity is widely recognized and has been extensively studied by those wishing to develop the considerable therapeutic potential of all such proteins.

This is a lovely answer, and I'm not sure why someone downvoted it.

I think this answer is good, but sort of following from the cleaned up discussion in the comments, the problem I see is that you don't answer the interesting part of the question until your conclusion. The key important concept here, in my opinion, is that Proteins containing unnatural amino acids as the result of expanding the genetic code do not, in principle, raise any problems of immune ‘rejection’ that have not already been seen in ‘unnatural’ proteins containing normal amino acids. If there is an immune response issue, it's with non-self protein, not with non-self amino acids.

@BryanKrause — Thank you for your suggestion. I have edited my answer accordingly.


text:
Why is the hippocampus considered to be a cortical structure but not the amygdala?
I'm having some trouble understanding the anatomical differences that classify the hippocampus as a cortical structure but not the amygdala. I have included the screenshot of a diagram from Gray's Clinical Neuroanatomy.

Medial aspect of the left cerebral hemisphere demonstrating some limbic structures (yellow). The anterior nuclear group of the thalamus is coloured orange, and the rest of the thalamus is magenta. The approximate position of the brain stem is outlined in a heavy interrupted line.

I have suggested an edit to your question that corrects the link to the figure. However, I am not sure that the figure adds anything to the question. If anything, it shows that the hippocampus and the amygdala are both areas of the limbic system. You may want to have a look at the Wikipedia page on allocortex and if that does not satisfy your curiosity, maybe read the Cortex: Statistics and Geometry of Neuronal Connectivity.

You can't distinguish cortical from deep structures from a picture like the one you reference in Gray's Clinical Neuroanatomy. The hippocampus is a cortical structure because its cell bodies are in the outer layers of the cerebrum. The amygdala is a deep structure because its cell bodies are in nuclei. I'm not sure if your textbook has stained sections, but if it does, that should help clarify the difference between the two structures.
In this sagittal section you can see both. Notice the hippocampus (at both ends) follows the bumps and grooves of the cortex where the amygdala is a circular/almond shaped cluster of cells.


text:
Do decibels matter if the sound is outside human hearing?
I bought a dog training device that emits sound at 25K hertz and 130 dB. Can this damage anyone’s hearing since they can’t hear it?  Also is it possible for an infant to hear in the 25K hertz range?  Thanks

Your dog training device produces what is called ultrasonic noise. Children can hear in the 25 kHz range, though they may not develop that ability until they are school aged.
This review has a good overview of the literature around ultrasonic noise. They draw the conclusion that it's hard to isolate the effect of a particular frequency or frequencies exactly, but there is some inconclusive evidence that noise at the frequency and dB of your dog training device could cause hearing damage and have other negative effects. In several countries, you're above the admissible range, but this is for longer term exposure.

We are starting a Bioacoustics Stack Exchange for people interested in the studies of non-human animal sounds and the impacts of sounds on animals. Please join us!
https://area51.stackexchange.com/proposals/126698/bioacoustics?referrer=YjZmYjUxYzJkNDI1YmY5NDk3NzdhMzViMmZlNzI4ZDdiYTAyMWQxNTM5ZWFiNzRhODNkMmFiMzIxZjI3MmY1N_gFvrICTvBsmYNJ2ptRM6lIZEAV-VGkXtIwNyVDja680


text:
Osmosis in red blood cells and bacteria
This is a question from an exam in my biology course.
Bacterial cells and human red blood cells were inserted into one solution. Upon testing one hour later the blood cells exploded, while the bacterial cells stayed intact. What answer explains the findings:
A. The bacteria cell walls prevented their explosion.
B. The blood cell walls didn't prevent their explosion.
C. solute concentration in the solution is equal to the blood cells and bacteria solute concentration.
D. solute concentration in the solution is higher than the blood cells solute concentration.
My lecturer said the right answer is B. I thought the right answer is A.
What would be the correct answer and why?
To my understanding, red blood cells don't have a cell wall, but rather a membrane, which is why in my opinion you can't say that it prevented the explosion if it doesn't exist. On the other hand, bacteria does have cell wall, that's why I thought this answer is the correct one.

Do you have any proposals for what would distinguish the two answers?

To my understanding, red blood cells don't have a cell wall, but rather a membrane, which is why in my opinion you can't say that it prevented the explosion if it doesn't exist. On the other hand, bacteria does have cell wall, that's why I thought this answer is the correct one.

I edited your question to include your reasoning. When you have a homework or exam related question, you should include this kind of information in your question

Absent a very specific learning objective, if (B) is correct, this is a poor question. In a high-school or undergraduate introductory biology course, I would say:

(A) The bacteria cell walls prevented their explosion

Would be the correct answer, because of exactly your reasoning. This is what you're taught in introductory biology. You're taught that animal cells don't have cell walls. Bacteria and plant cells do have cell walls.
See The Cell

animal cells are not surrounded by cell walls

Under this concept of a cell wall, red blood cells certainly don't have them.
However, red cell osmotic fragility testing comes out of a tradition that uses the phrase cell wall strength to describe the response of a red cell to osmotic stress. See Orcutt

It appeared logical to us that a model based on a distribution of cellular wall strengths ought to reproduce the experimentally observed variation of degree of hemolysis as a function of osmotic stress.

All the same, if you were operating from that perspective, how would you distinguish between (A) and (B)? Here, we're not even taking into account the fact the primary mechanism for responding to osmotic stress in most animal cells, including the human erythrocyte, is regulation of ion flow, not the pressure of a rigid extracellular matrix. If the solution contained ouabain, which certainly does lyse human RBCs, would it be best to characterize the problem as "The blood cell walls didn't prevent their explosion"?
I would ask your lecturer to clarify the learning objective behind the question. As an interpersonal note, I'd point out that this is very different from asking him or her to justify the correct answer. Some (many...) teachers are oddly sensitive to any suggestion that they need to justify their expertise, especially when it comes to exam questions. If you make it a question about the learning objective, this should help you avoid triggering that particular sensitivity.


text:
What exactly does Curare do to the peripheral nervous system?
so, I was told:

If you give them the right dosage it'll wear off within an hour or two.
  It was used for veterinary stuff until they tried it on a human and realized it only paralyzed you and didn't block the pain. I don't know the exact dosage but if you go over the limit it'll start to relax the lungs
  So the exact dosage will be exactly enough to paralyze them without injury.

SO, naturally, I was wondering, what exactly does Curare do to the peripheral nervous system?

Curare is a plant alkaloid originally used as a poison on darts and arrows used in hunting. It is a competitive antagonist for the nicotinic acetylcholine receptor, which is found in the neuromuscular junction and autonomic ganglia.  We know a lot about this receptor and it's blockade by curare, so most good basic pharmacology textbooks devote a fair amount of space to it and you'll find mention in many physiology and neuroscience textbooks. I'd refer you to Goodman and Gilman Chapter 11 for a general reference.
The basics are as follows:
Curare is a quaternary amine. This means it has a charge on it and cannot cross the blood brain barrier. This was confirmed in 1947 by Scott Smith (pubmed link), an anesthesiologist, who administered very high doses of d-tubocurarine to himself (while under mechanical ventilation), resulting in complete paralysis but no central CNS effects. It's an interesting read if you get the chance, and records very carefully details of the minute by minute response for 4 hours of a series of administrations and reversals (with an acetylcholinesterase inhibitor).
What you get, as reported by Smith and confirmed by others, is blockade of motor outflow with skeletal muscle paralysis (including respiratory muscles) and also probably some ganglionic blockade (this is supported with further research since 1947). There are no changes in sensory inflow or any central effects. The blockade of the nicotinic acetylcholine receptors is reversed with an acetylcholinesterase inhibitor by increasing the amount of acetylcholine in the cleft to the point where it overcomes the competitive inhibition by curare.

+1 Were the reversals self-administered as well? ;-)

@uhoh that would be a real trick, wouldn't it.

The paper can be downloaded from the journals website. And since I am at home right now, there should be no paywall.

@Chris thanks for the non-paywall link. I added it to the answer.

Nice finding btw.


text:
Is every neurotransmitter receptor an ion channel?
This is a rudimentary question--perhaps the answer is well known to biologists, but is every neurotransmitter receptor also an ion channel?
For example, NMDAR is a glutamate receptor and cation channel and GABA_A receptors are gated ion channels.  Is this true generally?  If not, is there a classification of neurotransmitter receptors according to abstract function (e.g. all gated ion channels would form one class, then perhaps there are others)?
Thank you in advance!  I am a mathematician just getting interested in some biology problems and trying to organize the basic knowledge in this area.  I appreciate any insights here!

is every neurotransmitter receptor also an ion channel?

No.
There are two general types of receptors for neurotransmitters, ligand gated ion channels and receptors that activate second messenger systems, for example, G protein coupled receptors. They are sometimes referred to as ionotropic and metabotropic receptors. This figure from Principles of Neural Science, Ch. 10 illustrates the difference nicely:

Very clear!  It's interesting that although not every neurotransmitter receptor is an ion-channel, every receptor does control an ion channel.  Perhaps this is too broad a question for a comment, but do metabotropic receptors have any other effects on neuronal signaling apart from affecting the post-synaptic cell's membrane potential through control of ion channels?  In other words, is the control of ion channels all that really matters for neuronal signaling via neurotransmitters?

@user334137 good question. It turns out, sgnaling at the synapse is as complex and varied as signaling in any cell. Both types of receptors can result in many downstream effects beyond immediate changes in permeability to specific ions. The main difference is in the control of the time course of the response.


text:
Endogenous retroviral insertions as evidence for evolutionary relationships among primates
A synopsis of a 2005 paper in PlosBiology by Yohn et al. states that:

Searching the genomes of a subset of apes and monkeys revealed that
  the retrovirus had integrated into the germline of African great apes
  and Old World monkeys—but did not infect humans and Asian apes
  (orangutan, siamang, and gibbon). This undermines the notion that an
  ancient infection invaded an ancestral primate lineage, since great
  apes (including humans) share a common ancestor with Old World
  monkeys.

Also, Micheal Lynch writes :

"Remarkably, we have found many cases of parallel intron gains at
  essentially the same sites in independent genotypes," Lynch said.
  "This strongly argues against the common assumption that when two
  species share introns at the same site, it is always due to
  inheritance from a common ancestor."

Since shared ERVs in humans and chimps is touted as one of the proofs of humans and chimps sharing ancestry (like by Ken Miller here), does the above paper (and quote) undermine this line of reasoning?
Is there any good (recent) source which discusses proof of common descent using ERVs?

I have changed the first sentence of the question so as to provide a reference to the actual paper, rather than just the synopsis. I have changed the title so that it indicates the area of biology the question is about and spells out endogenous retroviral for general comprehensibility and indexing. In relation to the original title ("Does this paper show…") would point out that it is scientific facts established by observation or analysis that may or may not show something, not the papers.

The Yohn et. al. (2005) paper (from Evan Eichler's lab) is describing a single type of endogenous retroviral element (loosely think of it as a 'species'), called PTERV1. They show that there were multiple independent infection events that resulted in permanent integrations in the ancestors of modern species (~3-4 MYA in the ancestors of gorillas and chimps, ~1.5 MYA in the ancestors of baboons and macaques). This in no way contradicts the notion of common ancestors among the apes/monkeys; indeed, they state this as a given in their analysis (emphasis mine):

A total of 275 of the insertion sites mapped unambiguously to
non-orthologous locations (Table 2), indicating that the vast majority
of elements were lineage-specific (i.e., they emerged after the
divergence of gorilla/chimpanzee and macaque/baboon from their common
ancestor).

The presence of an ERV (or intron, or any general genomic synteny), can be used as evidence to support a particular model of common decent. Changes in genomic architecture are stochastic processes, and the work you cite by Li et. al. (Lynch lab) is showing us that ERV placement can occur at a similar, or nearly identical, location at a much higher rate than previously thought. We therefore need to take this into account when calculating how strongly a shared ERV increases our confidence in a given phylogenetic model.
The video you linked to uses a completely random (i.e., very simple) model of ERV integration, setting the chance of an insertion at a given location at 3.3e-10. The findings by Li tell us that this is incorrect. In daphnia, at least, ‘hotspots’ may account for nearly 25% of new intron gain. The video also failed to include all of the instances of ERVs that are not shared between humans and chimp (back-of-napkin, this could account for differences of ~0.3% between their genomes, see Mun et al. 2014). This will increase the probability of an exact match occurring by chance (e.g., put two people in a room, what’s the chance of them having the same birthday? Put 100 people in a room, what’s the chance of any of them having the same birthday?).
So, let’s be extremely conservative and say that the chance of the same insertion at a given location in both chimps and humans is one in one thousand (1e-3, seven orders of magnitude more probable than in the original model). Sixteen shared ERVs are identified in the video; if each is considered an independent event because of no shared decent, we are still looking at odds around 1e-48 (1e-3 ^ 16). An alternative could be that they are derived from insertions that predate the split from a common ancestor. Given Li et. al., maybe each event should be given a probability of only 0.75 instead of 1.0 (as per the video) because up to 25% of them could be from hotspots. In this scenario, the probability is 0.01 (0.75 ^ 16). Therefore, the second hypothesis is 46 orders of magnitude more probable than the first. In my mind, this is extremely compelling evidence that humans and chimps share a common ancestor, using only ERV data.
I want to be clear, I am fudging these numbers extensively towards not supporting common descent. The real odds will be much higher in favour of common descent.
For further reading, Welkin Johnson wrote a comprehensive review on ERVs in 2015 (paywalled, so you may need to search for Alexandra Elbakyan's scientific literature retrieval method if you don't have institutional access).

References
Johnson WE. (2015). Endogenous Retroviruses in the Genomics Era. Ann. Rev. Virology. doi: 10.1146/annurev-virology-100114-054945
Li W. et al. (2009) Extensive, Recent Intron Gains in Daphnia Populations. Science. doi: 10.1126/science.1179302
Mun S. et at. (2014) Chimpanzee-Specific Endogenous Retrovirus Generates Genomic Variations in the Chimpanzee Genome. PLoS One. doi:  10.1371/journal.pone.0101195
Yohn et. al. (2005). Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol. doi: 10.1371/journal.pbio.0030110

I wasn't saying that these quotes contradict common descent. I was asking if, in the light of the quotes I mentioned above, ERVs can be presented as evidence of common descent of man and chimp (as many, like Ken Miller, have done).

Yes, they absolutely can be used as evidence. This is just one class of ERV, and the authors clearly explain why this class presents as non-orthologous copies in different taxa.

Ok. I got that this paper was talking of only one type of ERVs, but Michael Lynch's statement above says that even if we find ERVs (or generally, introns) at the same site in multiple lineages, it doesn't serve as proofs of common descent. If this is the case, then how can ERVs be used to prove common descent (especially, human/ape common descent)?

I've modified my answer to better address our discussion.

@Bond....SteveBond You have a cool name. And on top of that you write good answers +1. Good to have you active on Biology.SE!

Thanks a lot. Have marked the answer as accepted. Just one more point. How many ERVs are found among humans and chimps at the same location? Different sites seem to be giving different answers. This one says there are 40 such ERV families : https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-6-r51
This one says there are 14 shared ERVs : http://scienceblogs.com/erv/2009/06/19/charles-jackson-expert-on-ervs/


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In DNA repair, how is it determined which strand contains the error?
DNA replication is more accurate than transcription (or RNA replication) because mechanisms exist for proof-reading and repair of DNA, but not for RNA.
Consider a segment of a DNA strand, AGTC. Its complement is GACT. Now suppose its complement is mutated to TACT — the DNA repair system will replace the wrong T by G. Why isn’t A in the original strand replaced by C? How does the system determine that the first strand is correct and its complement is incorrect?

I've edited this question, removing anthropomorphic "know" and the implication that the DNA, rather than enzymes, did the repair. Although the question was answered some time ago, this makes it more useful for indexing and reference.

The reason the fact it isn't realistic is important. DNA repair machinery works by repairing common errors that occur due to common mutational pathways. The enzymes are specific for this, for example one particular enzyme targets mutations caused by UV and itself is activated by sunlight thus it's specificity makes it repair the correct chain. Also during replication, newly synthesised DNA lacks methylation. The repair enzymes thus know which chain is correct.

There are many types of DNA repair. Let us limit to the following three different types to answer this condition.
1. UV damage
Exposure of a cell to UV light can result in the covalent joining of two adjacent pyrimidines (usually thymines), producing a dimer. These thymine dimers prevent DNA polymerase from replicating the DNA strand beyond the site of dimer formation.
In such cases, UV-damage specific endonucleases cleave both the 5' and the 3' end of the lesion. Along, with the lesion some normal DNA is also lost as an oligonucleotide. Here modifications are being made only on one strand, the other is taken as a template (correct) and the DNA in the lost part is replaced.
The UV-damage may occur on both the strands but locally, one is affected and the other is the template (since you can't have thymine both sides)
2. Base Excision
Normal DNA bases can get deaminated spontaneously or on insult to an abnormal base (not on DNA).The abnormal base is excised by glycosylases and gap is later filled by considering the other strand the template.
3. Mismatch repair
What you are talking of in your example is not a case of deamination or UV damage but a mismatch repair. There can be errors in replication too where such a case could set in. There are specific enzymes for this repair, but discrimination is based on the degree of methylation. GATC sequences, which are found approximately once every thousand nucleotides, are methylated on the adenine residue. This methylation is not done immediately after synthesis, so the newly synthesized DNA is hemimethylated (that is, the parental strand is methylated but the daughter strand is not). The methylated parental strand is assumed to be correct, and it is the daughter strand that gets repaired.
The above said mechanism of discrimination is only in the gram negative bacteria. To quote Wikipedia,

However, in other prokaryotes and eukaryotes, the exact mechanism is not clear. It is suspected that, in eukaryotes, newly synthesized lagging-strand DNA transiently contains nicks (before being sealed by DNA ligase) and provides a signal that directs mismatch proofreading systems to the appropriate strand. This implies that these nicks must be present in the leading strand, and evidence for this has recently been found.

There are other cases where there is damage occuring to both strands that I'd suggest for further reading.
References

Lehninger's Principles of Biochemistry, Ed. 6
Lippincott's Illustrated Reviews, Biochemistry, Ed. 5
Wikipedia. DNA mismatchrepair

Your specific scenario is not realistic, thymine is a pyrimidine base while guanine is a purine base. They are very different chemically and can't spontaneously convert into each other. So this is a type of damage that only occurs during the replication of DNA.
The typical damage that occurs and can be repaired is oxidation, methylation and hydrolysis of DNA. This kind of damage results in modified or missing bases and can be detected due to that.
You might also be interested in why thymine is used in DNA instead of uracil, as uracil can be easily damaged in a way that would not be detectable.

Perhaps it is not realistic, but talk theoretically, if this kind of error happened, can it get auto repaired?

This kind of error can totally happen in a laboratory setting - true, it's maybe not a natural context, but it's not unimportant

To solve the problem of which strand is edited to correct mistakes, immediately after DNA replication, the original strand is methylated to prevent correction on this strand.Thus only the newly synthesized strand is searched for errors for correction. In short methylation prevents the template strand from being edited error and correction.

Could you add some references to this, please?


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How did viruses acquire the ability to utilize the cellular machinery?
As I understand it, viruses can infiltrate a cell, take it over and multiply. A virus has projecting fibers whose ends are shaped as a kind of a "key" to a mobile sentry on the cell membrane so it can be permitted access into the cell. When it enters the endosome of a cell, a protein pump blows an acidic gas onto the virus to break it down, as if it were a special nutrient. But the virus is adapted to this of course, and when the protecting fibers break off (and so too the body of the virus) proteins are released that rip apart the skin of the endosome so the virus can escape.
These are just two of many things the virus does to compromise a cell. Its entire existence is for the sole purpose for infecting a cell, and it seems adapted to do that perfectly. How did the virus evolve the capability to do things like this?

Do you have a specific virus in mind?  This is incredibly broad, and we'll honestly never know; we weren't there to study most evolution.  The short answer is "over many years."

@Amory Lets just say the common cold.

It's a numbers game.  Viruses can produce thousands, millions, even billions of copies every day, and only one of them needs to be slightly better to get ahead.  Rhinoviruses make roughly one error every time the genome is replicated; over many, many replications a single change can arise giving an advantageous effect.  As another example, it's been said that HIV mutates every single spot on its genome every single day.  Evolution is simply a waiting game.
This article is a pretty cool write up detailing the process.  It says exactly what I said: large numbers, high mutation rate.  Besides, the virus only has to take advantage of cellular processes, not make new ones every time.  That's much more efficient.  It also details some specific changes that explain some differences between similar viruses.  It's amazing, but a single base change can mean a single protein is different which can mean a different receptor is used for binding, which can make all the difference.
And there's this cool quote:

[T]here may well be more viruses in a single common cold infection than there have been primates in the entire history of life on Earth.

Scientists are unsure, but it seems that viruses have been around a very long time, and have been specific to every domain of life and possibly even may have infected the last common ancestor. It isn't impossible to imagine a co-evolving arms race that makes both viruses and cells as complex as they are today.

You are making the mistake of looking at modern viruses, which are the result of millions of years of selective pressure. Its like looking at a modern car and asking how humans could have built that from scratch, they didn't.
There are 2 leading ideas.
Viruses arrising from simpler self replicating RNA and/or DNA. Look at viroids instead which are just strands of RNA that infect plant cells, and it is easy to see how the the first of such infectious agent could have arrise from simple mutations in the host genome. it makes eaven more sense when you see how readily some single celled organsms exchange plasmids to see how n infectious one could arrise. https://www.nature.com/scitable/topicpage/the-origins-of-viruses-14398218/#:~:text=Viruses%20may%20have%20arisen%20from,the%20evolution%20of%2C%20cellular%20life.
The other idea is that the first virus may have arrisen from prasites that evolved to get simplier and simpler eventually giving up all unneeded materal. simplification of parasites occurs often enough since they are relying on the host for so much already offloading more can be benefical as simplicity leads to faster replication.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7609044/
https://www.sciencedirect.com/book/9780123741530/origin-and-evolution-of-viruses


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Calculating gene separation -a genetics problem
I am really struggling with genetics. In particular, I have the following question

Now I am OK with calculating the separation of genes in centrimorgans when I have data like so:

But in the first question, I am not sure if this is even possible. I gone through many books to no avail.
The conclusions I have been able to draw so far are:

these mutations are carried on X due to similar proportions of males and females exhibiting the characteristics.
the order of genes seems to be white, miniature, forked due to white miniature and forked miniature occurring much more frequently than white forked. Also it seems that white and miniature genes are close than miniature and forked as the former is a more commonly exhibited phenotype.

All of this is alluding to me somehow being able to figure out the separation of the genes, but I do not know how. Or if this is at all possible in this problem..

Text on images are not very welcome. These texts are not searchable and cause problems for people with visual impairments.

Your second image appears completely black on my browser. @Remi.b is right, you should take the trouble to set out your question properly otherwise I shall vote to close.


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Does a large effective population size result in faster decay of linkage disequilibrium (LD)?
I am thinking about an invasive species that was introduced into North America just a few (<20) generations ago. Using microsatellite genotypes (105 loci), I have identified almost no significant linkage across the genome. I'm tempted to speculate that this has something to do with rapid population expansion that has caused LD to decay that quickly, but I'm not sure whether this is a reasonable train of thought. Can anybody think of why this might or might not be the case?

It is certainly possible as yes, rapid population growth will reduce LD.  From Slatkin, 1994:

In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid.

Or Nature Reviews, 2002

Przeworski... showed that population growth tends to decrease the extent of LD, especially for longer periods of growth. By contrast, population subdivision tends to increase the extent of LD, especially when a sample contains individuals from several strongly differentiated subpopulations.

See also box 1:

Rapid population growth decreases LD by reducing genetic drift.


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Free software for measuring parts of an image?
Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? Would the software be able to export these data to a spreadsheet?

I'm voting to close this question as off-topic because this question is about software not Biology.

ImageJ is all you need. Particularly see the documentation sections on setting the image scale and measuring.

This is great! Thanks! It even continues to add values from new images into the table. Awesome!

see also Fiji for a distribution of ImageJ with more plug-ins

WebPlotDigitizer is an online application that can also be used to make distance and angle measurements in an image.

Looks interesting. I will try it at the next chance.


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How do muscle relaxants work?
Do they act directly on the muscle and actually relax muscle tissue and ease spasms, or do they just prevent your brain from receiving signals that inform you of tight muscles?
In the latter case, it seems like your brain would sort of become "immune" to the pain even though the muscle is still in a spasm.
I'm obviously not a biologist, just curious about this.
How do muscle relaxants work?

Check out the muscle relaxant article on Wikipedia, it's pretty straight forward.  In short, there are two main types: Neuromuscular blockers, than act at the junction between the neuron and the muscle; and spasmolytics/antispasmodics, which (mainly) act on the central nervous system to reduce excitation or increase inhibition.  Most of the ones I've heard of, such as diazepam, are in the latter category.


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Identification of this plant?
Photographed in Rocky Point, Mexico. Any ideas about this plant? Thank you!

Could you give an indication of its size? It is hard to judge with no reference. Also, when was the picture taken?

[Not really a precise answer (and I'm not a botanist after all).]
It's likely a lycopodiophyte. Looks like a Huperzia species, but it's impossible to tell exactly from the provided photo [if the species is not familiar, of course]. Of great help would be general appearance of the plant and form of sporangia.
You can try this key: Lycopodiaceae of North America.

Lycopodiophyta was definitely my first idea as well, but beyond that I have no clue.


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When did birds and mammals diverge?
Which was the most recent common ancestor between mammals and birds?
Form a rapid google research I could not find good answers. This site seems to imply it was at least 250 milions of years ago. This scientific article mentions 600 milion years but the sentence is a little unclear.

You can check it easily in the timetree website:
http://www.timetree.org/
Put a mammalian species as taxon 1 (Homo sapiens) and a bird as taxon2 (Gallus gallus) in the first pair of boxes and hit run.
You will see a compilation of studies, with their references, with different calculations about the time when the last common ancestor of both species lived. A median and a mean are also provided.
In this case the values are
Median Time:
320 MYA
Estimated Time:
312 MYA
CI: (297 - 326 MYA)

Useful tool for the timing! Any Idea about which one is so far the recognized  MRCA?

The Most Recent Common Ancestor (MRCA) of birds and mammals was the first amniotes.
Fossil record
The latest known fossil of amniotes are 312 million years old (Bentou and Donoghue, 2007).
Genetic data
From EOL, using data from The Paleobiology Database, the first amniote is in between 314.6 and 323.2 million years old. Those results are a little bit older than the latest known fossil which very much makes sense.
The (apparent) contradiction in the sources you found

This site seems to imply it was at least 250 milions of years ago.

They actually say 250 to 320 millions years. This broad estimates match the above studies and data.

This scientific article mentions 600 milion years but the sentence is a little unclear.

It is actually a news feature published by a science writer (former neuroscientist according to her twitter account), not a researcher. She indeed made the claim (Even so, 600 million years of evolution and radically different brain architectures separate birds from humans.). There is no reference for the claim and based on above evidences, it appears at first to be a mistake. It is not impossible though that she considered the evolutionary time in both branches in her statement but that would be very unusual If two lineages diverged $t$ years ago, then they both evolved for $t$ years and it could arguably be said that they are separate by $2 t$ years of evolution. If this is what she meant, then the claim is correct but quite misleading.

Scientists do not use the convention of measuring time on both branches, between endpoints, although maximum likelihood methods of estimating nucleotide states do measure both branches. So 600 million years is an error. Also, the first terrestrial ecosystems were little more than some plants surviving on the seashore, about 450 million years ago. The Earth was an inhospitable place with nothing to eat (Misof et al., 2014); no way could amniotes precede plant life.  The first tetrapods were much later, which preceded the first amniotes.

Also, the "first" amniote was not the MRCA of birds and mammals, as it is most likely that amniotes survived for a time, and diversified before branching off into synapsids and diapsids.


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Relationship between inbreeding and sterility in humans
In general, inbred individuals tend to be at increased risk of sterility as shown in cows (Gonzales-Recio, 2007) or in leghorns (Nordskog and Cheng, 1988) for examples. I only have very quickly looked at a few abstract but it seems that this effect is a bit controversial in humans with two studies showing a negative relationship between consanguinity and sterility (Rao and Inbaraj, 1979; Bittles et al., 2009) and one showing a positive relationship (Ober et al., 1999).
What is the relationship between the inbreeding coefficient $F$ and the (relative or absolute) risk of sterility in humans?
For a definition of the inbreeding coefficient, please see here, here and there or just google inbreeding coefficient.
I am looking for some function, linear or not, that describes the probability of being sterile ($P_s$) as a function of the inbreeding coefficient $F$ in humans. I am aware such measure might differ among human populations but I'll be interested in whatever we can find.

I'd note that two of the three human studies you cite re: inbred individuals are at increased risk of sterility actually show the opposite. The 1999 Ober study demonstrates decreased fecundity (not sterility) in a subset of Hutterite women, but generally, larger population based studies (Bittles is a good example) show the opposite (no decrease in fecundity, or general production of offspring). The concerns that do hold up are increased rate of major birth defects and childhood death. Once these individuals in these communities reach reproductive age, if anything, they produce more offspring.

@DeNovo Oops! Indeed! +1. I rephrased my post.


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Nomenclature of enzymes involved in synthesis of glutamine
I am considering nitrogen fixation and in my lecture notes, there is the statement

The glutamine synthetase- glutamate synthase system requires use of an ATP molecule as well as reducing power. Although it is energy intensive compared with glutamine synthase, the Km of glutamine synthetase is much lower than that of glutamate dehydrogenase. When NH3 is scarce, the additional ATP investment is worthwhile.

Try as I might, I can't find anything about glutamine synthase. Searches online seem to only return results for glutamine synthetase. I was wondering if this is a mistake in my notes? If so, I can only think that this should be 'glutamate dehydrogenase', in which case the statement is about comparing the method used by animals and fungi (which use glutamate dehydrogenase to fix nitrogen via a Schiff base) compared with plants and other microorganisms  (which use the glutamine synthetase glutamate synthase method).
This is my first exposure to learning about nitrogen fixation, so I would very much are coated any clarification.
Also, I was wondering what the general difference is between a 'synthase' enzyme and 'synthetase', if there is one.

I think you are correct, "glutamine synthase" must be wrong, and "glutamate dehydrogenase" makes sense in the context. Glutamate dehydrogenase does have a much higher Km for ammonia (about 1mM, https://en.wikipedia.org/wiki/Glutamate_dehydrogenase) than glutamine synthetase. Why don't you check with your teacher and then you can answer the question yourself :)

I have changed the question so that it refers to the general topic in the question rather than the mistake in nomenclature. As an original question that was fine, but it has now had all the impact it is likely to have, and by making it more general it — and the answers — will be of more general use.

Probably a mistake in your notes, or in the lecture notes for the class, but not a very important error in either case aside from the confusion it has caused you.
See the wikipedia article on Synthase and on wikipedia article on Ligase for a note on the terminology: historically synthetases use ATP, synthases do not, but this terminology is not adhered to strictly, and the current standard is that the terms are essentially synonymous; in my experience, however, a particular nomenclature dominates the literature even if the synonym is technically correct.

I'll deal with the second question first. There is a difference between synthetases and synthases, but because of the confusion the International Enzyme Commission now discourages the use of the term synthetase. The section on ligases states (my emphasis):

Class 6. Ligases. Ligases are enzymes catalysing the joining together
  of two molecules coupled with the hydrolysis of a diphosphate bond in
  ATP or a similar triphosphate. The systematic names are formed on the
  system X:Y ligase (ADP-forming). In earlier editions of the list the
  term synthetase has been used for the common names. Many authors have
  been confused by the use of the terms synthetase (used only for Group
  6) and synthase (used throughout the list when it is desired to
  emphasis the synthetic nature of the reaction). Consequently NC-IUB
  decided in 1983 to abandon the use of synthetase for common names, and
  to replace them with names of the type X-Y ligase. In a few cases in
  Group 6, where the reaction is more complex or there is a common name
  for the product, a synthase name is used (e.g. EC 6.3.2.11 and EC
  6.3.5.1). It is recommended that if the term synthetase is used by authors, it should continue to be restricted to the ligase group.

But the old nomenclature dies hard.
As regards your first question, this is an obvious mistake, as others have pointed out. For the record, I post diagrams from my own lectures of the two alternative methods of aminating ketoacids (oxo-acids).

As this question has been reposted (or whatever) for clarification I have given an extensive answer. The shorter answer from Bryan Kause is also correct, so I have given it a vote so this question has at least one approved answer. I suspect the original poster may have lost interest by now.