text:
The parts of the phylogenetic nomenclature that need to be "unique"
I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be globally unique in the name of a species.
I understand how to construct a name using the Binomial Nomenclature, and am under the assumption that this "uniquely defines a species" (for simplicity, not considering all of the variations of subspecies and sub-x ranks). But I am not sure what exactly "uniquely defines" means. In addition, I am not sure if the names of all the different ranks are globally unique, and how the rank names are defined (if they are defined differently from the binomial nomenclature-defined species names) (but this is probably a separate question). This makes it hard to figure out what actually needs to be unique, and what is unique, in these names.
So to start from the top, we have Domains. Wikipedia shows 3 (Archaea, Bacteria, Eukarya). I have seen more in other places, but not too concerned with that currently. First question is, if these names are globally unique. Second (related, possibly separate) question is, if these names are decided according to the same codes as the binomial-nomenclature defined genus/species names, or if they have a different process. I'm not sure if a domain (and later, the kingdoms, phyla, etc.) is associated with one single specimen. I read that for at least the Genus', they have individual specimens that act as the model or reference point for the Genus (not sure if I can call a Genus a clade). So I'm wondering if this technique/requirement/workflow is applied to domains/kingdoms/phyla/etc. That is, there is an individual specimen in some museum somewhere that serves as the type / model for that clade (domain/kingdom/phylum/etc.). That would be interesting and helpful for better understanding how the uniqueness requirement works in the terminology.
So following domains we have Kingdoms. Wikipedia shows 7 of them. Same thing, if these names need to be unique from the Domain ones, and if they are chosen the same way.
Then Phyla has approximately 32 for Kingdom Animalia, 14 for Kingdom Plantae, etc. Same questions here, if these names need to be unique from Domains/Kingdoms/Orders/etc., and if they are chosen the same way (and have the model specimen in some museum somewhere).
Oh, in regards to that model specimen. If it turns out that each clade indeed does have a model specimen in some museum somewhere, that means it must have a genus/species name. This is a big part of the question: wondering if that means that a Kingdom like Plantae actually has a specimem along the lines of Plantae plantae. That would make me confused as to how the clade then gets its name. If there is a thing/specimen called Plantae plantae (used as the model/type representing that clade), then it seems almost circular. Plantae plantae is the name of a species, but it is also somehow [partially] defining the Kingdom Plantae! That is where I get confused. Anyway, back to the other big half of the question, about each level.
So then we have Class, Order, and Family. I see some naming rules now starting to pop up. For example, in botanical nomenclature, they have "-aceae" as the ending of the names for the most part. So this to me says that, yes, they are using the standard binomial nomenclature codes to construct the name of the Family. But there again I am confused, because the Family is only 1 word, whereas binomial nomenclature is 2 words. So don't see how those two fit together. But anyways, Class, Order, and Family start having custom endings to the words in some cases, so it seems to use binomial nomenclature codes.
Then Genus is where it starts to get a little bit more familiar. Still I don't know how the genus names are constructed (that will probably be answered with the above stuff), but I at least know that the Genus is the first part of the binomial nomenclature name.
Then Species has a name, but I guess the "full name" (as opposed to the "relative name") is <Genus> <Species>, rather than just <Species>.
So to summarize, I am wondering
What needs to be globally unique, and in reference to what. My first guess as of now is that Domain, Kingdom, Phylum, ..., Family, Genus, Species, all with 1 Latin name, are all globally unique. So you can't have a Species named the same thing as a Family or a Kingdom. But wait, no that doesn't make sense. So everything from Domain-Genus needs to be globally unique, but Species is only unique relative to the Genus. So you can have Volpus volpus (for example). But you can't have an Order named Foo and a Kingdom named Foo, that wouldn't work (that is my understanding at this point).

Many of the problems you are discovering are the basis for phylogenetic classification. Without necessarily answering each of your question specifically, I'll mention some of the basics of phylogenetic classification as compared to traditional Linnean classification:

Species are the main "currency". We classify species and species alone.
All taxonomic groups higher than the species level are arbitrary. The Linnean system of Kingdom - Phylum - Class, etc. has no biological meaning. For example, Reptilia and Aves can't both be classes, because birds are reptiles (a class within another class).

These two points alone address most of the questions. There are no general rules (and lots of arguments) for naming clades above the level of species. Clades are names following the main rule of "the most recent common ancestor of [taxon] and all of its descendants". This conveniently does away with all the business about "Supraclass" and "Infraorder" and such.
The implication of this scheme is that there are no (extant) species at the bifurcations, so there is no taxon that is not assignable to a "tip" on the tree. In other words, "we do not find direct ancestors in the fossil record", which basically answers your third question.

Binomial nomenclature does not uniquely define a species unfortunately, there are several duplicates.
The Wikispecies directory shows 5 duplicates: each of this is with an organism from kingdom Animalia and another from either Plantae or Fungi.
Therefore, you could conclude that binomial nomenclature is a unique identifier within a kingdom.


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How to reduce the quantity of (carcinogenic) mycotoxins in oatmeal?
Like all cereals, oat is commonly (nearly systematically) contaminated by several types of mycotoxin (produced by molds) known to cause cancer{1}. Oat is one of the most infected cereals{2}. Unless the package looks or smells bad (which is unlikely, and even dangerous to touch since some mycotoxin can penetrate through the skin), there is no way to know its level of toxicity.{3} Eating a large quantity of oatmeal (eg 250g/day) could thus be problematic, especially in a country that doesn't take this kind of food contamination seriously (even if the customer store the oats in a dry environment, it's too late: the molds have already grown (eg. while stored in a humid silo or warehouse, or during transportation).
There isn't much information about how to reduce mycotoxin in oat specifically but some studies done on other cereals suggest some procedures:

"Heating and cooking under pressure can destroy nearly 70% of aflatoxin in rice compared to under atmospheric pressure only 50% destroyed (37)".{4}

According to several studies, mycotoxins can be totally eliminated by cooking it at 160-180°C for 30 minutes {5}. But it doesn't make sens "Since [...] long-time cooking and overheating would destruct essential vitamins and amino acids in treated food".{4} (And it would not be easy to do: is it possible to reach such temperature in a pot ? Won't it burn? Plus this is quite an energy-intensive process and thus not ecologically responsible nor economically interesting).

Another study{6} mentions a more practical option: they reduced the quantity of mycotoxins (till 70-87%) by adding sodium bicarbonate. The study focuses on corn: they add 9 gr of sodium bicarbonate per liter. But the paper doesn't describe well the procedure: they wrote "the results obtained in this work correspond to an aqueous solution", which suggest they mixed some water, the corn (as flour?) and the sodium bicarbonate, but what quantity of water/corn, what temperature and for how long...?

And these pieces of information don't provide a practical way to reduce the mycotoxins in oats :
Oats aren't cooked like rice which needs to stay 10 (or more) minutes in boiling water. To cook oat, I simply pour boiling water on it and wait 15 min. It probably doesn't reduce much the aflatoxin (how many percent?). What about adding bicarbonate with the boiling water? (how many percent reduction?)
Is there a better way, or other steps that would decrease the amount of mycotoxins in oatmeal?
1:
https://www.tandfonline.com/doi/abs/10.3109/15569541003598553?journalCode=itxr20
2: https://www.sciencedirect.com/science/article/abs/pii/S2214799317300152
3: Aflatoxin is colorless and completely invisible. The loss of the nuts smell, which happens when the oats start to turn bad (just before they start to smell and then taste bad) is probably the only indication our senses can detect.
4: http://www.fao.org/3/x5036e/x5036e0q.htm
5 https://link.springer.com/article/10.1007%2FBF03032339
6: https://onlinelibrary.wiley.com/doi/abs/10.1002/jsfa.11001

Very difficult question. This review article discusses all of the above including oats (cereal). Can you buy whole hulled oats instead? Irish and UK oats seem to be lowest of European oats for mycotoxins. Just imho, trying to prevent cancer this way will be crazy-making. Carcinogens are absolutely everywhere.

Your refs 1 and 2 are behind paywalls and so generally unavailable. Can you remove them or at least extensively quote from them? Alternatively, @anongoodnurse provides a good review that's accessable.

@Armand do you know sci-hub?

@JinSnow Yes; Personally, I don't think that's an appropriate reference for questions here, but ymmv.

The methods adequately describe the NaHCO3 process - whole grains - how many or what weight is not described. "Solutions of sodium bicarbonate at 0.4, 1.2, and 3.0 g L−1 were added to the PDA culture medium. The inoculated corn grain was deposited in the center of the PDA, and it was incubated at 22 °C, measuring mycelial growth in millimeters, at 48, 72, 120, and 168 h." BTW this process sounds like nixtamalization - a process often used for corn products to increase availability of essential amino acids.

@bob1 What you quoted is the "Evaluation of mycelial growth inhibition of Aspergillus niger in corn with sodium bicarbonate" and not the "Evaluation of aflatoxin reduction". In other words, the goal (at our consumer level) is not to stop the growth of the mycotoxins (because it's too late, even if stored in a dry environment), but to destroy/reduce them.

Indeed it was - my apologies. The reduction section works with certified standard aflatoxin incubated (unknown time) with 9 g/l HCO3: "standard of aflatoxins (Trilogy TSL-108, USA) with a certified concentration of 2 μg mL−1 AFB1 and AFG1 and 0.5 μg mL−1 AFB2 and AFG2". So basically it is a vial with aflatoxins at the specified concs and the specified conc of HCO3 in water. There is no grain or flour/meal substrate in there.

This redearch is about rapid detection methods https://www.google.com/url?sa=t&source=web&rct=j&url=https://www.olmix.com/sites/default/files/document-2-article-9-mycotoxin-analysis.pdf&ved=2ahUKEwj7vc_KkofzAhVJXRoKHSsWC04QFnoECCsQAQ&usg=AOvVaw0OQfUQr3jkhxTlCwL_w1WI

I’m voting to close this question for the reasons outlined in this meta post.

So far, the applications for the control of aflatoxins in food are experimental; and they require further evaluation by researchers. However, the use of basic products has been used and tested in Mexican tortillas through the nixtamalization process, which is part of the production of this food. I share a part of a review that I am writing that could help you:

"Since aflatoxins are susceptible to alkaline hydrolysis, the addition
of bicarbonate salts promotes their reduction. Nixtamalization can inhibit some
percentage of aflatoxins because it is a thermal alkaline process (Torres, et al. 2001)".

Torres, P.;  Guzmán-Ortiz, M.; Ramírez-Wong, B., Revising the Role of pH and Thermal Treatments in Aflatoxin Content Reduction During the Tortilla and Deep Frying Processes. J. Agric. Food Chem. 2001, 49 (6), 2825-2829. doi: 10.1021/jf0007030

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Boost of Janssen COVID-19 Vaccine increasing Immune Response to Vector
I have been looking for published, or even pre-print, data that evaluates the serological response to a boost of the Janssen COVID-19 Vaccine against the adenoviral vector Ad26 rather than the intended SARS-CoV-2 spike protein target.
Vector-targeting immune responses are a generic and known issue with adenovirus vectors. Janssen has made the claim that Ad26 is superior to Ad5 in this regard, but while increased response to the target epitopes is obtained in boost (though slight in my opinion), a frank discussion or display of differences in anti-vector response is not covered in any of the references:

In contrast to Ad5-based vaccines, a similarly clear impact of
natural- or vector-induced pre-existing immunity to Ad26 on vaccine
immunogenicity has not been observed to date in clinical studies.
Results from clinical trials assessing repeated administration of
Ad26-based vaccination approaches showed that a second or subsequent
dose of study vaccine was able to boost humoral and cellular immune
responses to HIV antigens (Ad26.EnvA, study IPCAVD001; and
Ad26.Mos.HIV, APPROACH study; even in the presence of high Ad26
neutralizing antibody titers induced by the first dose.
Similarly, naturally occurring Ad26 neutralizing antibody titers or
Ad26-targeting T cell responses at baseline were not associated with
decreased immune responses against the vaccine antigen. (DOI)

Not destroying your target immune response with a boost is not the same thing as a meaningful boost to response or a lack of boost to vector.
I was hoping to find a report on changes (or lack there of) reaction to any Ad26 proteins via Western, ELISA, or any acceptable protein interaction assay for individuals after both prime and boost with Jansen vaccine.  Generic reaction to the vector, even related ones, would be apricated if a clear division in prime and boost responses were present.
Most studies that use the vector (an example with RSV that I know had the problem but was unreported) seem to avoid discussing it altogether.

For ChAdOx1 https://www.thelancet.com/article/S0140-6736(20)32466-1/fulltext#figures  (should be quite similar for Ad26)

@reuns I was looking at that, with figure 7 being on point but not clearly to me showing if 7a actually covered the significant difference at boost (would love to see that data broken down by the cohorts in #1).

I think figure 7a is after first dose because at day=0 there is no neutralization

@reuns D0 is definitely the prime/first dose. The schedule was to get boost at D28, and considering it goes to D56, one presumes it covers the boost.  The problem is that they didn't divide out by which group was boosted, so any difference on that division is hidden.

@armand I wasn't meaning to reject your edits, I was already editing it myself.  Concerning the meta question, I can understand taking out the first paragraph, but I do not think it is unsupportable opinion

Re: "Similarly, naturally occurring Ad26 neutralizing antibody titers or Ad26-targeting T cell responses at baseline were not associated with decreased immune responses against the vaccine antigen" I interpret this to mean that the vaccination response (e.g. higher Ab levels) against the vaccine antigen was not weaker even in those with pre-existing naturally occurring anti-Ad26 responses. What wording underlies your "Not destroying your target immune response with a boost ..." comment?

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What is difference between High quality and low quality proteins
I have seen in news that some bodybuilder died of taking steroids; when I went through details I learned that  "low quality proteins" contributed to their death. I have studied about linkages in proteins but I don't understand what makes them stronger or weaker. So what is the difference between high quality proteins or low quality proteins? How does low quality protein affect muscular activity or growth?

I'm voting to close this question as off-topic because it belongs to fitness.SE not biology.SE.

@Remi.b I tried to save this question for the OP - I think there is an on-topic question contained there once the personal health component is removed. There might be an additional question to send to fitness.SE about how/whether to use protein supplements that wouldn't be appropriate here.

Without a link to the news story, and subsequently the investigation into this individual's death, it's impossible to know what exactly "low-quality" means in this context. It could be what @BryanKrause talks about in his answer, or it could mean "low-quality" as in it was procured from a disreputable source that didn't take adequate care to verify the protein's purity, or adulterated the product somehow like the melamine scandal regarding milk powder in China beginning in 2008.

"Low quality" vs. "high quality" protein does not refer to anything about the linkages between amino acids in proteins. Instead, these terms are used in a nutritional context to refer to whether an individual protein source is sufficient as a sole source of protein in someones' diet.
Essential amino acids are the amino acids that humans cannot synthesize; other amino acids can be synthesized from these, but they do not need to be part of the diet. Not all sources of protein have sufficient quantities of all of the essential amino acids. Low-quality protein sources are also referred to as "incomplete" and high-quality sources as "complete."
Meat products are typically "high quality" because they contain all of the essential amino acids together. Therefore, if you subsisted on various foods but only got your protein from one animal source, you would be okay.
Some plant products do not have all the essential amino acids in large concentrations. However, if you combine protein sources from different "low quality" plant sources that together cover these deficiencies, there is no disadvantage compared to a single "high quality" source.
In the digestive process, all you take out of the proteins you eat is the individual amino acids (generally): that means that only the amino acid composition matters, not the strength or quality of the bonds between amino acids. If someone tries to tell you otherwise, they are probably just trying to sell you something.
Here is a paper that talks about some of these issues, and addresses some of the myths about balancing proteins. The quick summary is that problems develop if you get your sole protein from a source that is low in a particular essential amino acids over a long time period, but there is no need to ensure every meal contain all the amino acids.
It is possible for people on unusual protein diets, either because they are avoiding animal products or using incomplete protein supplements, to develop a particular amino acid deficiency. Otherwise, as long as all amino acids are supplied, there is no difference on health or muscles to consuming "low quality" vs "high quality" proteins.

References:
Young, V. R., & Pellett, P. L. (1994). Plant proteins in relation to human protein and amino acid nutrition. The American journal of clinical nutrition, 59(5), 1203S-1212S.

My understanding is that amino acids are not generally stored. Say you eat just corn which is first-limiting in lysine. Once you've built what proteins you can before the lysine is exhausted, the remaining amino acids are further metabolized, mostly for energy, as opposed to being incorporated into proteins. My source dates to my Biochem degree in the '70s, and textbooks from the '90s. Maybe something new has been discovered about storage of amino acids? (Still, +1 on your post.)

@bpedit Thanks, I think that's a good point, to my understanding you are correct that amino acids aren't "stored" the way fats are (at least not in humans) - and I didn't say anything about storage in my answer. However, you have a huge storage of amino acids in the form of all the proteins in your body. When proteins are degraded they aren't just junked, you can reuse a lot of the amino acids. The lysine you take in from a single meal is just a fraction of your total body lysine. So, it takes awhile for the shortage to catch up and cause problems.

@bpedit ...From the source I linked and just a general survey of "advice on the internet" it seems like a general guideline for vegetarians is to try to get a complete protein intake within the timeframe of a day, rather than worrying about being complete at each and every meal. I'm sure there is no immediate problem missing a day or two at a time, either, because fasting on those timescales isn't harmful (to my knowledge).

@bpedit You mention "many" but only gave one example. Many cultures have also suffered from things like rickets and scurvy at various points. I'm not sure what your perspective is, but I'd caution against the logical fallacies that people in the modern "paleo" movements employ, assuming that cultures they are less familiar with must have it all "figured out." Surely there are good evolutionary/anthropological reasons why there aren't extant cultures that subsist solely on corn with no other protein source, but I wouldn't read much further than that.

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Is Sda a protein, or is it a protein domain of DnaA?
I initially thought that a domain was a specific part of a protein, with it given tertiary structure, to which a given molecule is able to bind. (I think I recall phrases such as "the haem binding domain of protein X..." being used in lectures?)
Having consulted Wikipedia on protein domains, I see the definition is a bit more subtle:

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

I can understand this, however the reason why I started questioning what a 'domain' actually refers to was because if it's use in reference to Sda in control of endosporulation of bacteria. In my lecture notes, it is stated that "KinA is bound and destabilised by Sda, a DnaA target,"
From this I was under the impression that Sda is a protein (although to the best of my knowledge DnaA only binds DNA, so I do not know why Sda would be target of DnaA. Anyhow,) on the other hand Wikipedia states "the protein domain Sda is short for suppressor of dnaA or otherwise known as sporulation inhibitor A.", which seems to me to suggest that Sda is a part of DnaA whose modifications allow DnaA suppression?
Also, on Wikipedia, it is later written "Sda protein domain is a checkpoint which prevents the formation of spores." How can a protein, if Sda is one, be a checkpoint?
On the other hand my lecture notes later talk about the regulation of Sda levels, so it again is referred to as a separate protein!
I would very much appreciate if someone could explain what 'domain' means in this context.

There is nothing in the idea of a domain that requires it to bind a particular molecule. The definition in Wikipedia sounds reasonable enough — domain doesn't mean anything else in a protein context. So I am unclear what your question is. Are you asking us to clarify the use of this word in a text to which you don't give a reference and may be poorly written and use words loosely? Surely not. Or are you asking us to explain a scientific description of a DNA-binding system in sporulation? If so you need to present it more clearly with references and do a little more research yourself.

Short answer
Wikipedia has unnecessarily made an already confusing situation much worse. Sda is its own protein, it is regulated by DnaA, and it prevents sporulation.
Full answer
I don't think your misunderstanding is based on the meaning of 'domain' - the definition you give sounds quite reasonable - but rather the use of the term domain with respect to Sda and the naming of Sda itself, which I agree is quite confusing and made much worse by Wikipedia in this case.
Sda is a protein that inhibits KinA activity (Burkholder et al., 2001) and is a completely separate protein from DnaA. I don't see where you jumped from your notes to the idea that Sda is a domain of DnaA except for from Wikipedia: I don't know why Wikipedia thinks Sda is a protein domain, it is a protein. It is a very small protein, so perhaps it would be appropriate to think of it all as one domain, but there is not a single result for "Sda protein domain" on Google Scholar - no one else is using this terminology. A full Google search only returns a few (~150) results, most of which are direct copies/translations from Wikipedia, or Wikipedia is a direct copy of them. Wikipedia can be useful, but if it starts to cause you confusion, don't assume it is correct.
The phrasing "KinA is bound and destabilised by Sda, a DnaA target" means that Sda binds KinA and destabilizes it, and notes that Sda is a target of DnaA; since DnaA is a transcription factor, you can infer that this means that DnaA controls expression of Sda in some way.
In biology a checkpoint just refers to a place that a process can be halted/arrested, often in reference to the cell cycle. Sda is considered a checkpoint because when Sda is expressed, it prevents cells from sporulating by indirectly preventing activation of Spo0A (Burkholder et al., 2001).
Another source of confusion is that the name "suppressor of dnaA" on Wikipedia is WRONG, but further, molecular biologists sometimes have an impenetrable way of naming things, owing to the complexity of control of gene expression and the circuitous way that new proteins are identified and understood.
The correct name for sda is "suppressor of dnaA1". dnaA1 is NOT DnaA - dnaA1 is a MUTANT ALLELE of DnaA that results in cells that are completely unable to sporulate. But! sda is also NOT Sda: sda is a MUTANT ALLELE that produces non-functional Sda (the protein).
I'll quote from the title of the table in Burkholder et al:

sda Mutations Suppress the Sporulation Defect of dnaA1 Mutants

Or, stated again, in dnaA1 mutants, there is a defect in DnaA which prevents sporulation. The researchers searched for mutations that would reverse this effect. They found one, and named it sda, because it reverses (suppresses) the effect of the mutation they were studying. The dnaA1 mutant's effects on sporulation seem to be caused by an increased expression of Sda, which is why the sda mutant reverses the effect.
References

Burkholder, W. F., Kurtser, I., & Grossman, A. D. (2001). Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis. Cell, 104(2), 269-279.

+1 at least for this: molecular biologists sometimes have an impenetrable way of naming things, though the whole answer was great.

@canadianer Seriously, I mean come on.

Ha! That was the exact example I was thinking of as I typed that comment.

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text:
Is the offspring of two-sex plants a clone or a child?
Many common plants e.g. tomato, pepper; produce both male DNA carriers and female embrions. In the case that the plant is confined alone, do the resulting seeds carry a carbon copy of the DNA of the parent like when rooting a broken branch in water or do they experience some profound mutations beyond the usual UV induced ones?

A child, in that it's produced by fusing the parent's gametes.
Note that many agricultural and decorative strains derive from "true breeding" or purebred plants - terms that predate a modern understanding of genetics but indicate that the plants are likely homozygous at all the alleles relevant to the observed/desired traits. When you self-fertilize a homozygous plant, the genotype will be the same as if it were cloned. You will still have the plant going through meiosis and therefore recombination processes will still be acting, but there is no variation to yield novel combinations, so in principle it is not much different from a clone (assuming that everything is indeed homozygous).
See also Growing peaches from (supermarket) bought seeds - in many cases, there are actually separate true breeding strains that are then crossed (rather than selfed) to produce the strains you're familiar with. In that case, even in self-fertilizing plants, you can't expect to get similar traits out of the selfed offspring. I believe most commonly used garden tomatoes and peppers are hybridized, so you typically won't want to plant the seeds of the next generation if you're looking for optimal production. Heirloom tomatoes are an exception that tend to be closer to true-breeding as they've been self-crossed for generations.
Some quotes from: https://open.lib.umn.edu/horticulture/chapter/14-4-plant-breeding/

Inbreeding is producing seed by selfing over 5–7 generations to develop plants that are highly homozygous at most loci in their genomes. Homozygosity results in identical plants propagated by seed. This is done so the resulting progeny look more and more alike until, after 4–6 years, plants grown from seeds harvested off the same plant are indistinguishable from each other.

Most new commercial tomatoes, including new garden tomatoes, are F1 hybrids. The seeds you plant in the field are the result of crossing two parents, as described above. (...) Garden catalogs will tell you whether the seed you are buying is hybrid. If you are getting your fruits from the store, you can count on them being hybrids unless they are marked as heirloom.

A lot of big words for my small brain: I wish I had paid more attention during Biology classes at school. Learned so much by reading the basic definitions. Thanks!


text:
Do humans produce rennin?
At school, we've been taught that human infants produce rennin/chymosin (which aids in the digestion of milk). More specifically, it is the peptic cells in the stomach which secrete prorennin, the inactive form of rennin (in addition to pepsinogen, the pepsin proenzyme).
User @another'homosapien's answer here also seems to concur with this (excellent answer by the way, I enjoyed reading it).
However
According to Mod. @AliceD's answer here (yet another excellent answer):

...in humans there is only a chymosin pseudogene present...

Which (probably?) implies that humans (infant or otherwise) do not produce rennin.
I managed to get my hands on the Textbook of Medical Physiology (Guyton and Hall, South-Asian edition), and according to the book (Chapter Gastric secretions, page 406) peptic cells produce a large quantity of pepsinogen. There is, however, no mention of prorennin. I even flipped over to the Appendix at the back to look up "Rennin", but it turns out there is absolutely no mention of rennin in the book.

My questions,

Some sources claim that rennin is produced in human (infants). Is this true?
Other sources claim that rennin is not produced in humans ( we have a pseudogene for it though). Is this correct (I mean the "rennin-is-not-produced" bit, not the "pseudogene" bit)?
If rennin is produced in humans only during infancy, what stops it from being produced as we mature? (I'm asking this because every source I've seen that claims that rennin is produced in humans, explicitly states that is done so during infancy...which would suggest that rennin is not produced in adults)

2 things: 1) Existence of a pseudogene doesn't necessarily mean a non-functional protein product, it just means that it differs from the gene being referred to. 2) Rennin exists to curdle milk and slow digestion (like in the answer you linked), it is not necessary for digestion of milk otherwise.

@Bryan Ah, thanks! Being the idiot school-boy I am, I assume "pseudogene" = "No proteins translated". ;P Also, I just want to know if rennin is produced at all. Thanks for the pointer anyway!

I clarified below and decided to turn my comment into an answer. It's quite possible someone will come up with a better answer but that was all I found so far.

Also, as sort of a tongue-in-cheek answer: actually humans (presumably primarily adults) produce tons of rennin, via recombinant expression in bacteria. It is quite important for producing most cheeses, and a lot more convenient than isolating from animal sources. :)

Scanning various reviews it seems that everyone who mentions the possibility of a human chymosin refers to a single paper. So for example this 2014 review has a single reference to a human chymosin:

Henschel et al. detected a
  protease in the gastric aspirates of newborn infants within 6–10 h postpartum that was not
  pepsin [62]. The electrophoretic mobility and immunoreactivity are similar to that of calf
  chymosin, a protease that cleaves κ-casein and causes casein curdling. This protease is
  unique in that it disappears from gastric fluid at 10 days postpartum and is not found in adult gastric fluid.

I don't have access to the Henschel et al. paper (from 1987) but here is the abstract:

The electrophoretic mobilities of proteases present in gastric juice taken within 10 h of birth from 5 healthy, premature infants were compared with calf chymosin, pig pepsin A and human adult gastric juice. The juice from 2 infants contained predominantly a chymosin-like enzyme, another had almost exclusively pepsins similar to those of the adult juice, while the other two contained a mixture of both. The pepsins consisted of two elements, probably pepsin A (EC 3.4.23.1), and pepsin C (EC 3.4.23.3). Single radial immunodiffusion gave a definite reaction to calf anti-chymosin serum in five samples taken from a further 17 infants. These results indicate that some human infants secrete chymosin. The reaction in the immunodiffusion assay indicated a much lower enzyme activity than that implied from electrophoretic separations. It is suggested that species differences resulted in poor cross-reactivity of the antiserum.

Now, obviously, without seeing the data it isn't possible to be conclusively critical, but the quality of the evidence seems to be rather weak, being based upon similar electrophoretic mobilities and an immunodiffusion assay (why not a Western blot?) with an overt apology for weak cross-reactivity of the antiserum used.
However, leaving all of that to one side, the strangest thing about this is the sporadic appearance of the proposed chymosin: although 4/5 were scored as chymosin positive in the 1st experiment, is it likely that 2 of these would apparently contain little pepsin? And in the second experiment (the immunoassay) only 5/17 scored positive for chymosin.
Evidently no-one has ever reproduced this result, and the evidence for the pseudogene (but no active gene) is very strong. I vote that humans do not produce a chymosin.
Update
Having read Bryan Krause's answer: if the human gene product was lacking an exon's worth of amino acid sequence then presumably it wouldn't have an electrophoretic mobility that was closely similar to the calf protein.

I think the answer is really that is isn't clear, though I only searched a bit and found mostly old papers.
It seems like people have found immunoreactivity to anti-rennin antibodies in human infants, but that doesn't necessarly mean rennin is present, just something similar (which could even be a totally unrelated protein).
On the genetics side, humans have a pseudogene for rennin (known as prochymosin), but if you take the same exons from that gene that are used to make rennin in cows, the protein would be truncated because one of those exons has a frame-shift mutation (this is why they are calling it a pseudogene). However, it is possible that there is a functional protein produced by that gene if that 'exon' is excised from the transcript (see the paper below).
Örd, T., Kolmer, M., Villems, R., & Saarma, M. (1990). Structure of the human genomic region homologous to the bovine prochymosin-encoding gene. Gene, 91(2), 241-246.

The psuedogene is not functional, according to Wikipedia: "Humans have a pseudogene for chymosin that does not generate a protein, found on chromosome 1." The reference for this says " Thus, this genomic sequence apparently represents a human prochymosin pseudogene. No functional gene was identified."

And yet some people claim that human infants do have rennin: if they do, it has to come from a gene, and this is the only candidate. It's pretty hard to prove definitively that it doesn't, which is why the statement is "apparently." I agree that it seems the most likely conclusion is that it does not produce a protein (note that the actual source for that statement in wikipedia on the pseudogene is the reference in my answer).

Ok.. I noticed the reference... I thought you were making the point that a protein was produced, although it is most likely not true...

Yeah, sorry, I was just trying to note that the answer by @AliceD about the presence only of the pseudogene does not by itself totally rule out the possibility of a human rennin. I think the other papers failing to find it is better evidence.

you mean @Alan Boyd...

@TanMath No I meant AliceD - the post the OP referred to. Oops - I had tracked down that quote to its actual post and meant to edit the OP to fix it. OP quoted from an answer but then linked to a different answer twice.

@Bryan Thanks for the answer! That the "answer isn't really clear" (though it's quite likely that we don't produce typical calf-rennin) became apparent after I read Alan's answer. Plus, the excerpt from the paper (Henschel et al.) in his answer made for an interesting read. Hence I've "accepted" Alan's answer. Your answer was very insightful, and I appreciate that you took the time to post an answer. Thanks a ton! ^_^

Way back in 1964 I was asked a question about Rennin in a physiology class. Perhaps you are not searching back far enough for information. Also, if the infant was not nursing on human milk there may not be a substance present to cause rennin production, if nursing on cows milk the substance that causes the production is not the same as in human milk so no rennin is produced. If all other mammals produce rennin it would seem that humans would also produce unless after several generations no stimulation has resulted in functional loss. One assumption you can always make is the body knows what it is doing. We discover scientific facts:God creates them.

Welcome to Bio.SE!  We're glad to see you here.  It would be much better if you could add some sources for your answer: as it stands it's a bit anecdotal and subject to removal.


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What Software could I use to create Diagrams of Biochemical Processes like these?
Cross-posted at GraphicDesign.SE here
Is there any software software that I could use to (closely) create pathways as depicted in these diagrams?

Or does anyone happen to know what software was used for these diagrams specifically? [Sourced from Harper's Illustrated Biochemistry (31e) and Murray's Medical Microbiology (8e) respectively]
I would like to be able make alterations such as adding extra steps, changing color, including newer pieces of data and such-like for the purpose of making my own notes.
I assume that knowing which software was (or can be) used to create these, I'd have greater versatility making the edits I need, or creating something in similar from scratch for other processes/pathways.

I've cross-posted on Graphic Design SE (since it seems like another good place to ask); however I'm under the impression there are Users here on Bio.SE that may have better recommendations, since I want to create/recreate pretty much only biochemical and biologic processes; there might be software for this very purpose popular among people in the field :-)

Cross-posting is typically frowned upon, see https://meta.stackexchange.com/questions/64068/is-cross-posting-a-question-on-multiple-stack-exchange-sites-permitted-if-the-qu I'll let each community decide whether this one is okay with them or not.

By posting to this forum, I presume the question is whether the illustrators of this and other biochemistry books used software specifically designed for the purpose of drawing reaction pathways, or, if not, whether such software exists. From my experience of using such illustrations in my own teaching over the years, I believe that the answer is probably no (although there are a couple of what I would consider ‘almosts’ mentioned below.) The main reason I would not expect this is that it would not seem commercially viable (biochemistry teachers and book illustrators are hardly a huge market) and you can get by with more generic pre-existing applications.
The class of application I consider best for this is termed a vector graphics application (popularly known as a ‘drawing’ application), as opposed to a bitmap or raster graphics application (popularly known as a ‘paint’ application). Although today there are applications that combine both functions, vector graphics applications have the advantage that they are more easily editable and they scale to any print resolution. The professional applications in this area can be very expensive and have a steeper learning curve than bitmap graphics applications (such as Adobe Photoshop). Moreover, they may lack features needed for biochemical use. It is therefore be worth exploring cheaper offerings, or investigating specialist vector graphics applications more focused on engineering or computing diagrams.
For biochemical work I personally would require software to be able to provide the following:

Controllable geometric lines (Bezier curves)
Customizable arrowheads
Text control that at least allows subscripts and
superscripts, and ideally both simultaneously, e.g. for a charged
phosphate species.
Rotatable text (as in the upper example)
Basic graphic primitives (as in the lower example)
Export to vector formats accepted by other applications (PostScript or PDF) to allow output in formats and at resolutions required for print publication.

How do different applications satisfy these criteria? They all support basic graphic primitives, and most allow export at least as PDF, if not the more flexible PostScript.
Surprisingly the creation of a line with an arrowhead is not straightforward as one is dealing with a combination of two separate objects. Although all applications tend to provide straight lines with arrowheads, curved lines with arrowheads tend to be absent from the general applications (even the most sophisticated) because a curved line is not really a line as such, but is generated as an oval segment with a stroke (visualization of its drawn edge) but no fill (the body is transparent). I have tended to use this sort of application (going back to MacDraw II of the Classic Mac) and fudge the arrows on them by combining them with straight lines of the same length as the arrowhead. However they are provided by more specialized diagramming software like OmniGraffle (mentioned in another answer) or the dedicated ChemDraw (which I find too limiting to use other than for export).
Text handling is the other problem. Placing a superscript directly above a subscript is a page layout operation that only dedicated mathematical software (e.g. MathType) is likely to support. Microsoft Word’s equation editor will do this, but export is only as PDF, and import into other applications varies in effectiveness. If you work in a generic application you will have to fudge it yourself with separate text boxes.
What are the choices for generic vector drawing applications? Adobe Illustrator is the most sophisticated, is used by most professional illustrators, but is very expensive (it is now subscription only). Other vector drawing applications that I am aware of but have not used include the commercial Corel Draw (cheaper than Illustrator) and the even cheaper Affinity Designer. As mentioned in a comment, there is also the free application, Inkscape. Free trials are available with most applications, so I would recommend seeing what is the best solution for your personal situation.
Addendum
I have just had a quick look at BioRender, which was mentioned in another answer. It has many different modules, including ones for biochemistry (including a Glycolysis pathway template) and seems quite attractive. However if you want to use the results for publications you need a $35 per month personal academic subscription (or your institution to buy a site license). I guess you tend to get what you pay for.

I find the absence of any "dedicated" software for the job a bit disappointing. Your answer's fairly comprehensive, and it didn't immediately occur to me to use ChemDraw, but I guess I could  use something similar (MarvinSketch) to craft some elements of the diagram. And thanks for the last bit about transferring vector graphics between apps; my brain was fixated on finding the One Perfect App, that it didn't occur to me. Thank you very much! +1

You’re welcome. I was going to extend and reorganise my answer a bit but have been tied up this morning. Will probably do it later.

Have done a 'final' tidy up, reorganizing a little, adding a few more titles, and explaining some of the technical stuff.

In the scientific community, we mostly use a couple tools to draw publication-quality pathway figures:

OmniGraffle
BioRender

These tools are optimized for making the kinds of figures shown in your question.
Others have also used Adobe Illustrator, Inkscape, or PowerPoint.
Like OmniGraffle, Illustrator and Inkscape can export resolution-independent vector graphics, ideal for publication on screen and paper. They do not make it easy to draw pathways, because unlike OmniGraffle, they lack "magnetic" points to lock arrows, lines, text, and other elements.
In Illustrator and Inkscape, you have to do a lot more work by hand with these tools to make nice figures. Tweaking the appearance of some element over in one layer will force you to spend a lot of time cleaning up other layers.
Microsoft PowerPoint is good for making slide decks, but it is not ideal for publication-quality work. It can be used to draw the kinds of primitives in the example figures in your question, but it exports high-resolution TIFF files, and these are very large files and so are difficult to distribute.

I've had a look at BioRender, and it looks like a tool that's very close to what I'm looking for. In addition, it looks like it'll help me with a whole bunch of other things as well. Great find! (That and the Nature article you linked).

I've accepted @David's answer because it provides me with general guidelines on using multiple apps to be able to create the diagrams I want (i.e: It gives better versatility than any one app). However, I'm still very pleased that you recommended BioRender to me. I to hope award a bounty on your answer for that (when the bounty window opens). Thanks!

I have used Draw.IO for similar tasks involving flow charts from scratch.
I've also used Adobe Illustrator, usually to modify figures when I have them in a compatible vector graphics format.
Finally, I've often made similar graphics directly in PowerPoint when I needed them only for a slide presentation and not a paper-quality figure.
As @David mentioned, you're unlikely to find any purpose-built tools, but there are a whole array of vector-based graphics programs. My main advice would be to try to pick one and use it, these are tools with massive feature sets that you tend to learn gradually. You can do a lot with just the basics, but the more you learn about a specific tool the faster your workflow will be.

I spent a few hours fiddling with draw.io the other day, it was considerably frustrating (primarily because it was my first time using it). The thought of using PPTs to recreate something  like this scares me (aesthetics matter to me, I'm afraid). I might give draw.io another shot later on; and @David's suggestions look promising. Thank you! :-D


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Why does inbreed produce a higher percentage of abnormal babies?
The babies of close (say, brother and sister, or cousin and niece) family members have a higher chance of being born with an abnormality than babies from non-family related men and women. Why?

Who says this is a homework question?

Please do not edit in content to questions that is not part of the question. The homework policy here doesn't only cover assignments specifically given as homework, it covers other types of school work as well as questions that need further research effort. "This isn't homework" does not make a question subject to different rules.

Many disease/abnormality causing alleles of a genes are maintained in populations through their recessive nature. That is to say, in order for the disease to manifest itself in offspring they must in have TWO copies of the disease causing allele - they must be homozygous for the disease causing allele. Inbreeding leads to a far greater chance of being homozygous at a disease locus if a recent common ancestor of the parents was affected or a carrier. The likelihood of this occurring is measured by the Inbreeding Coefficient.


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Which organisms require the least fluctuation in ambient temperature?
Note that I am NOT asking "which organism can survive the most extreme temperatures." Many extremophiles like the tardigrade can survives extreme heat, but also extreme cold. Many heat adapted animals like the camel can also tolerate fairly cold conditions. I want to know what species that are adapted to hot climes are hot climate obligates (or the corollary for cold climate obligates) and which extreme temps-obligates have the narrowest tolerance.

the icefish must have a pretty narrow band of temp tolerance since they have no hemaglobin and the really cold antarctic water is loaded with O2

I don't have a precise answer for this, but if you want to do some more research on your own to try to find answers, I have two guesses for directions to take: 1) Parasites of warm-blooded hosts. I would expect these to have some mechanism for survival between hosts, like a spore or egg phase, but they would do all their growth, reproduction, etc, inside a nice, comfy host and they would have enzymes adapted for the host condition. 2) Extremophiles, like you mention, that are so adapted for strange conditions such as ocean vents that they cannot survive outside these areas.

(also, if you are wondering about animals you really need to specify animals; otherwise, unless you are talking about sizes of individuals or something like that, "what is the most" or "what is the least" questions have a high probability of leading to bacteria/archaea, or if you need a eukaryote then protists)

@BryanKrause obligate-symbionts is a really good thought since their host takes care of providing a homeostatic environment. Thanks for that thought!
I thought about ocean vents, but in reality, those environments fluctuates quite a bit since the temp varies wildly at the boundary layer between deep-ocean cold water and magma-hot water.
Also, just to note, I'm not specifically asking about animals, but I suspect sedentary organisms probably adapt for greater fluxes since they cannot cope with temp changes through vagility.


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Is the information in the brain stored in the connections rather than neurons?
Can I imagine the difference between the model of the grandma neuron and the model of interconnected neuron network so that the information isn't primarily stored in the neurons (respectively in their states) but in the connections between them.

Also in discussions of neural networks we don't use the term "parent" or "child" when describing a network. So your term "grandma neuron" is not something that is commonly used. Instead use terms like "sender" and "receiver".

Would the connections be the same as the axons? Since an axon is either charged or discharged, the information (1 for charged, 0 for discharged)  could be said to be stored in the axion which is a part of a neuron.

@GabrielFair The question asker is probably referring to the "grandmother neuron" in the context of the famous papers by Quiroga et al or more generally, rather than in terms of hierarchy. "Sender" and "receiver" are also not terms typically used in neuroscience, instead words like "afferent" and "efferent" or "presynaptic" and "postsynaptic."

This article says that memories are not stored in synapses: https://www.scientificamerican.com/article/memories-may-not-live-in-neurons-synapses/

Is the information in the Brain stored in the connections rather than
  in the neurons ?

It depends on what information you are referring to.
The brain does not just store one type of information,the model of a grandmother cell and the model of an interconnected neuron network are 2 subsystems of a greater system working together perhaps in a competitive or complementary arrangement. The purpose of this system is to extract information from the environment and identify it again for the organisms benefit. 1.
So let's say we see something that will benefit us in the future or that we might want to avoid. This is a simplification, but as you see that something, neurons in your neocortex light up specifically in region V1 in the back of your head, they arrive there after a lot of computations along the way from your retina, but also project to other parts of your brain where they are perhaps processed consciously,they fire in an orderly fashion, in a map, this bouncing around of electrical signals represents your conscious, and unconscious processing of the image, so the information exists as a network of electrical signals. 2.
During recollection, ( there are different types of memories so the structure in charge could be the neocortex,basal ganglia, hippocampus or even a muscle)3. this same map ( or a smaller subset ) gets replayed. The mechanism(s) by which this information is first encoded and later retrieved is still not entirely understood, but it involves a map and a getaway or switchboard.4. This switchboard ties together different percepts ( a smaller network of electrical signals), so in a way the information is represented at the switchboard level, if you disable this switchboard, you can't make new memories or lose previous ones.
A grandmother cell in the scheme of what I just explained, is the result of another subsystem that helps recognize something. Once you successfully encode a percept ( thing we want to remember seeing) you might want to associate it with something ( good,bad,delicious,etc), at the top of a series of associations lies a grandmother cell, which in turn is a handy evolutionary way of signaling back to other systems when some previous information has been experienced. So in this way the information of whether a subset of relationships in between networks of electrical signals has been experienced and encoded lies here.
References/Sources:

The idea of grandmother cells and object recognition in general is summarized in the Object Recognition chapter of ( Cognitive Neuroscience,Gazzinga-3rd ed 222-225) along with the problems a grandmother cell introduces in object recognition (ie if you lose the grandmother cell you would lose all the information about your grandmother)
Koch( Quest for Consciousness-2004) chapters on vision provide a very readable account of how the information goes from retina to v1. Vision Science (Palmer) is a more thorough account.
The chapter on learning and memory (Cognitive Neuroscience) gives an overview.
(Gluck -2001-Gateway to memory) presents different models of this arrangement.

The physiology of memory is still poorly understood, but there are some generalizations we can work with:
There are four "types" of memory which the human brain works with.
Sensory memory is very short-term (milliseconds), cannot be consciously accessed (it's used by the sensory processing centers of the brain for things like tracking moving objects), and is stored in the activation state of neurons (ie. which neurons are firing at any given time).
Working memory is short-term (it lasts up to 30 minutes), and stores "what you're thinking about now". It is not yet fully understood exactly how it works. However, we know that drugs which interrupt neuron state can "delete" working memory to some degree; this suggests that working memory is stored at least partially in the activation state of neurons.
Long-term memory is persistent and lasts, in theory, until the end of a person's life. It has been well established that long-term memory is stored in the connections between neurons.
Intermediate memory is a relatively new theory of memory which operates somewhere between working memory and long-term memory. As far as I'm aware, we don't yet understand many of the mechanisms behind it.

I don't see where you have tried to answer the question

Grandmother Cells vs Distributed Representations
The idea of a "grandmother cell" is effectively the ultimate in sparse representations: that there is one, single neuron in your brain that represents your grandmother, and that everything you know about your grandmother is associated with that cell through connections.
At the other end of the spectrum is a "distributed representation," where a network of simultaneously active cells represents a concept, and that these cells are connected to each other and to related concepts (see here, here, and here). These networks could be highly overlapping, and could potentially overlap more when you are talking about related concepts: i.e., "dog" and "cat" might overlap more than "fish" and "squirrel" because the former are both 4-legged animals that live on land and are kept as pets - lots of similarity.
Realistically, no one in modern neuroscience is truly arguing for the existence of "grandmother cells" but there are certainly arguments about sparse vs. distributed representations, and now large or small the cell assemblies or networks are that reflect particular concepts, and what the importance of context is. The main arguments you will see today concern the extent of distribution across brain areas: that is, are there brain areas that contain somewhat-distributed representations of abstract concepts, or are those concepts distributed across modalities (where your concept of 'baseball' includes a synthesized visual representation in visual cortex, the texture of the seams in somatosensory cortex, the sound of ball-on-bat in auditory cortex, the motor plan for throwing the ball in motor cortex, etc).
Evidence for Grandmother cells?
Despite what I just said, there were some interesting papers from human subjects published several years ago, especially this one. These papers showed neurons in a particular area of the brain that had invariant responses to particular concepts, perhaps most famously "Jennifer Aniston" cells and "Halle Berry" cells that responded not only to various pictures of each actress but also to other more abstract representations such as their written name. Clearly, these are not the cells typically described in the primary visual cortex that respond to stimuli like bars and edges.
These papers were reported in the lay science and general press as evidence or proof of the "grandmother cell" theory. Some were more responsible and included some of the authors own words (see also here): essentially, what the authors are arguing is that cell assemblies might be pretty small (but not too small - the authors only recorded from a few cells yet found dozens that responded to Jennifer Aniston, not just one, for example).
Information in cells or connections
To get back to your original question: you asked about whether the difference between a grandmother cell and a neuronal network is whether the information is stored in the cells vs. the connections. I would argue that, although in the "grandmother cell" model there is a lot of importance placed on individual cells, in both cases the information is stored in the connections.
Even if you assume the extreme case of the "grandmother cell", where one cell is the hub that alone represents your grandmother, the information isn't stored as "grandma", it's stored as the associations you have with her: maybe smells of cookies, the shape of her face, her name signed on a birthday card. If you pulled someone's grandmother cell out of their brain network and interrogated it, you wouldn't be able to learn anything at all about their grandmother.
The difference between the "grandmother cell" and a more distributed network is that in the "grandmother cell" case, we would expect to find another cell that represented specifically the cookie smell, yet another that represented the shape of her face (and only her face), and so on. In a more distributed network, each of those related concepts would be encoded by their own network, and those networks might overlap somewhat where the concepts are closely related: that is, part of your representation of "grandmother" is the smell of her cookies.

I would love an explanation for the downvote - I am happy to update my answer if it would help in any way.

I think you went for the tree while ignoring the forest :) , I upvoted though.

@Keno Ironic, because that's sort of what a "grandmother cell" theory does ;)

From what I can gather, the short answer is that we don't have the full picture of how biological neural networks store information.
If you are willing to relax the constraints of your question to extent to artificial neural networks, then your answer becomes significantly easier to answer in part because we understand them much better. Artificial neural networks do store information as synaptic weights which is the only part that changes during the training of a network. The rest of the network such as the topology and the activation function remains unchanged.
Image classifiers are a convenient example of information as synaptic weights since we can see what the neural network 'sees' by maximal activation of neurons. It is immediately obvious that there is a lot of information stored in the weights of a network. The image below is taken from Understanding Neural Networks Through Deep Visualization

Some feedback as to why this is being down-voted would be nice.


text:
Is there a measurable variance in neuronal transmission speed and fidelity?
My understanding of how neurons transmit signals is pretty basic - dendrites receive signals (both excitatory and inhibitory), transmitting them to the cell body where, if a sufficient depolarization builds up, the axon fires an action potential, sending the signal along. This entire process is carried out by various ion channels, especially voltage gated ones. My question is this - do we know how sensitive the speed and reliability of the process are to genetic variations that control how these ion channels are built? Is it robust enough to permit small variations, or is any change catastrophic? If it permits small variations, do we know how variable the human population is for features like signal fidelity (low rate for failing to fire when the neuron should, and low rate for firing in the absence of stimulus) and transmission speed?
Considering the difficulty of studying humans, is this sort of information known for mice, rats, primates, or etc?

Action potentials are pretty robust in most circumstances, but minor tweaks at various stages of the process, whether conduction, neurotransmitter release, or post-synaptic responses, sometimes affecting only certain populations of cells, are thought to be behind many neurological disorders and conditions, including schizophrenia, autism, epilepsy, multiple sclerosis, and some peripheral neuropathies. Of cousre many of these conditions have both environmental and genetic influences, so it is often difficult to attach a specific genetic cause.

There is a certain amount of variation in the genes that regulate ion channel/receptor structure, much of which has little/no affect on neuronal function. But as @BryanKrause says, many are known that do cause neuronal disorders. A very interesting question, but I don't know the genetics well enough to provide a decent answer.

@OliverHouston What I was trying to get at, although maybe not too clearly, is that a lot of the variation in those genes does not deterministically cause disorders, but that variation may predispose certain individuals to those disorders. For Sean: it isn't directly related to your question, but on the issue of robustness you could read some papers on multiple sclerosis. MS is a demyelinating disorder, which eventually impairs conductivity, but it actually takes quite a bit of demyelination before the symptoms are noticeable.

@BryanKrause My main interest is less in disorders and more in variations and trade-offs in how these things affect performance. For instance, I could imagine that tuning the depolarization needed to trigger down could lead to faster nerve conduction, but also less reliable signalling. Another way to imagine it is the extent to which a plurality of strategies in the trade-off spaces manifest themselves.

Got it - based on your SE background I see you are mostly a physics/math person. I would highly recommend the "NEURON" simulation which is freely available and documented in various places. There are pre-existing models that you could tweak to test some of your hypotheses. For example, if you are talking about conduction, rather than action potential initiation, you will find that one of the important factors in both threshold and reliability is voltage-gated sodium channel concentration. However, more Na+-VGCs will mean both a lower threshold and more reliable signalling.

Also note that in biology if you ask about variability: "do we know how sensitive the speed and reliability of the process are to genetic variations" - the answer is almost always going to depend somewhat on the phenotype. If a variation doesn't cause any disorder, there is no selective pressure to prevent that type of variation, so over generations that variation will tend to increase on average. The presence of some low-efficacy genetic causes for some of the disorders I mentioned is good evidence that there is some variability in the population, though.


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Why aren't drugs delivered directly into arteries, rather than veins?
Normally when drugs are administered to the blood of a mammalian subject, it is done intravenously--the needle being inserting into a vein. One potential problem with this is that the veins contain the exhausted blood which is returning to the liver and spleen. This is potentially disadvantageous because these organs could absorb the drug or be damaged by it.
It would seem more advantageous to introduce a drug to the arterial system, such as the aorta, so that the drug flows outwards to all parts of the body before returning to the filtering organs of the body.
Is this type of drug administration a known procedure. If so, why is not more generally used?

Because of the risks of putting a needle in an artery. Additionally: After a few heart strokes the drug is distributed in the blood and it is going through the liver anyway, most drugs are processed there.

Seriously, the aorta? It's not accessible, and you don't want to mess with it. Veins are used because they are low pressure and low risk. You can't administer a drip into a high pressure artery; the blood would back up into the tubing; in fact, there is enough pressure in just the radial artery to push a plunger up as it fills the syringe. Also, it would keep bleeding as long as there was a needle or tube in it. Damaging a vein is no big deal, damaging an artery is. Finally, regarding metabolism, just give enough drug to minimize the effect of first pass metabolism.

Further, most IV drugs are given through easily accessed veins such as in the arm: these return to the heart before any pass through the liver or spleen. Unless you were trying to deliver the drug to the arterial circulation of that particular hand, it's going to circulate before it gets to the target organs. And if your drug is going to damage the liver, why don't you think it's going to be dangerous for anything else? The liver isn't particularly vulnerable, quite the opposite.

Although this is a fairly basic question, I realized three very active users here put our answers in comments. Let me summarize:
1) It is risky to poke holes in any artery, let alone the aorta. Arteries are full of blood under high pressure. When you poke a hole in one, there is always some risk of serious bleeding. You also have to push against the arterial pulsatile pressure, making it more difficult to administer slow drips of drugs, as is often done with I.V. administration: either you are going to get high flow during diastole with high pressure, or you are going to get backflow of blood into the catheter during systole, or both. On the venous side, there is a lot more collateral circulation, too, so in an emergency you can usually close most veins without severe effects. Some drugs can be toxic to the local vascular environment, as well, which is again safer in a vein should it occur. Note that for some special procedures, such as angioplasty/stenting, arterial access is necessary, but this isn't true for drugs. (Thanks @Chris and @anongoodnurse)
And the aorta? Depending on body fat and where on the aorta you want to target, you are talking about a needle inches long, poking into a vessel you can't see, after passing other organs and tissues, versus veins, some of which are specially located near the surface.
2) IV drugs aren't "delivered" specifically to particular targets in the first pass: they dissolve in the blood, flow around the circulation, diffuse in and out of tissues, and eventually partition according to their binding affinity, hydrophobicity, etc. Therefore, drugs are going to go through the liver anyways. In fact, many drugs are metabolized by the liver, and some aren't even delivered in their final active form: metabolism may be required for activity, and often the liver is involved. Essentially, if a molecule isn't stable enough to make a pass through the liver, it won't be a useful drug or needs to be given in a higher dose to account for the high rate of metabolism. (thanks @Chris and @anongoodnurse)
3) Further, most IV drugs are given through easily accessed veins such as in the arm: these return to the heart before any pass through the liver or spleen. Unless you were trying to deliver the drug to the arterial circulation of that particular hand, it's going to circulate before it gets to the target organs. And if your drug is going to damage the liver, why don't you think it's going to be dangerous for anything else?

The question is not just about human beings, but about any mammal.

@ImprisonedRhesus That changes little if any of my answer - which parts do you think are human specific?

Not all mammals have "arms" for starters. Also, when the researchers give me injections, they never put the needle in my arm.

Forelimbs might as well be arms in this context. Are you getting IV injections? The veins of the arm, or hand are by far most common. If there are other targets I presume that's either directly related to the research or they are not IV.

(Still none of this affects substantially my answer - unless you are getting injections into the veins in your digestive organs or spleen that drain to the portal system, none of the blood is going directly to the liver)

@ImprisonedRhesus - Vets often do use the veins in the animal's foreleg to administer IV meds; other meds are subcutaneous or intramuscular. In humans, IM usually involves the upper arm (deltoid area) for small amounts of drugs, the buttocks or thigh for larger amounts. IV could be any vein; before picc lines, we'd even use the veins of the scalp for neonates or between the toes for adults.

A couple of things to add:

(Most important) The 'exhausted blood' in the veins isn't going directly to the liver or metabolic organs - it's going directly to the heart, to be pumped through the lungs and then returned to arterial circulation. First-pass metabolism by the liver is a concern for oral delivery, since a substantial fraction of blood goes directly from the absorptive digestive tissues (e.g. intestines) to the liver through (IIRC) the hepatic portal circulation. This isn't an issue for drugs administered IV.
In addition to the relative safety of venipuncture vs. arteriopuncture, there's also the small point of pain. Arterial puncture is done when necessary - for example, when you need a sample for blood gas analysis. This procedure is quite painful. I have had it performed on me, and I have performed it on animals when I worked in veterinary practice. So in addition to venipuncture being safer, it's also much more comfortable for the patient/subject.
What you describe in your last paragraph is kind of done, although not into the aorta. When large boluses of drugs need to be given frequently, and/or the drug in question might seriously irritate peripheral veins, you sometimes see devices like a PICC line used - a percutaneous indwelling central catheter - or for shorter durations a temporary jugular central line. These are used to deliver the drug into the vena cava - the venous analog of the aorta, if you will. Just as in conventional IV administration the blood goes through the heart, through the lungs, and back into arterial circulation, but this time it's administered in a large enough volume of blood to avoid adverse effects of dilution (large/fast bolus) or irritation.


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Ecology of the environment for the ruffed grouse
I live in a coastal New England town and while reading a local history I noticed frequent mention of the "partridge" as being a commonplace bird in the area. Now, however, this bird which is more specifically the ruffed grouse, Bonasa umbellus, is completely absent in our community and not to be seen at all. There are many turkeys, however. I am trying to understand what happened to them.
I read that apparently the critical ecological prerequisite for the grouse is "young stands of forest". For example, from one report: "Though grouse use all age classes of forests, they cannot do without thick stands of young forests 5 to 25 years old for cover, food, brood rearing and courting."
Our community used to be gentleman farming town and was mostly cleared for agriculture, except for a town forest, before 1950. Since that time it has evolved into quasi suburban town with a mix of conservation land, large 3 acre residential lots, and a few farms left over from the old days.
I don't quite understand how there could have been lots of grouse in the farming days, but none now. First of all, in the farming days, more or less the whole town was agricultural fields, so that hardly seems like grouse habitat. Secondly, how could grouse even exist in the pre-colonial times, because the habitat at that time would be primordial forest. When the first settlers came here in the 17th century the whole area was covered in 100 foot eastern pine trees, which were farmed for masts for the English navy.
So, should I presume that the grouse first came into the area when the farmers started cutting down all the trees, thus allowing "young stands" to arise; then the grouse population collapsed when most farming ceased in the 1950s?
If the grouse need "young stands", how do grouse even exist in areas without humans where no clear cutting occurs? I have read claims that "forest fires" clear areas naturally, but that is not the case in New England where it is too wet for forest fires to occur. For example, in Maine the ruffed grouse is abundant, but only in the "transitional zone" between unoccupied forest lands and abandoned agricultural lands where humans have cut down the trees and then left the land unoccupied. There are no "forest fires" to speak of in Maine, so the grouse apparently live only in areas modified by humans. However, this raises the question of how the grouse lived before there were farmers with axes.

It's "ruffed" not "ruffled". A common error. Ruffed is pronounced as a single syllable.

@MTA In New England they are actually ruffled grouse. They wear little lace Elizabethan collars around their neck. It's very cute.

When I am curious how things were with American birds back 200 years ago, I read Audubon.
https://www.audubon.org/birds-of-america/ruffed-grouse

Although these birds are particularly attached to the craggy sides of
mountains and hills, and the rocky borders of rivers and small
streams, thickly mantled with evergreen trees and small shrubs of the
same nature, they at times remove to low lands, and even enter the
thickest cane-brakes, where they also sometimes breed...
The charming groves which here and there contrast so beautifully with
the general dull appearance of those parts of Kentucky and Tennessee,
to which the name of Barrens is given, are sought by the Ruffed
Grouse. These groves afford them abundant food and security. The
gentle coolness that prevails in them during the summer heat is
agreeable and beneficial to these birds, and the closeness of their
undergrowth in other spots moderates the cold blasts of winter. There
this species breeds, and is at all times to be found.

Audubon goes on to note that ruffed grouse occurred everywhere in the US but most of all in the northeast.
There were always edge spaces - for example on hillsides where big trees lose their purchase and fall, or by water and in cane breaks as Audobon notes.  I think the barrens her describes had to do with the geology of Kentucky and Tennesee but there were no doubt equivalent open spaces for various reasons in the Northeast.  I can imagine that ruffed grouse did better when humans showed up and farmers increased edge spaces by clearing forests.
A question analogous to yours pertains to chimney swifts - how did those birds live before people put up chimneys?>  The answer is "probably not in such large numbers as they did after the chimneys went up".  So too the grouse and early farmers.
Chimneys and edge spaces are now both less common, as are swifts and grouse.  There are people who manage the forests they own for hunting, and increase edge spaces because deer and game birds like grouse like those best.
I am not so much for hunting, but I would like to put up a large chimney because I love the swifts!

Ok, but why are there zero grouse now? There should be some habitat somewhere.

Maybe they have just not found their way back yet.  You could help them.  https://www.purelypoultry.com/red-ruffed-grouse-hatching-eggs-p-1447.html


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Why summation takes place at Initial segment?
I know that many EPSPs summate at initial segment to produce action potential.
But I don't understand why if EPSP can travel from dendrite to initial segment, then why it doesn't travel further?
What halts it there and make it to wait for other EPSPs to come and add to make Action Potential?
Why does it can't propagate as such and cause release of small amounts of neurotransmitters?

Why don't EPSPs travel passively through axons?
EPSPs decay over distance. The decay is described by the length constant, which can be calculated based on the electrical properties of some compartment (i.e., a length of dendrite or axon). By definition, the length constant is the distance at which the amplitude of the signal will decay by about 37%. If you are familiar with the concept of a "time constant," the math is exactly the same.
There are two main factors that influence the length constant: the number of open channels (i.e., how "leaky" the membrane is) and the diameter of the neurite. The "leakiness" of different parts of the cell is often modulated by inhibition. Preventing EPSPs from reaching the soma or decreasing their amplitude by increasing leak is called shunting inhibition. However, for your question, it is the diameter and overall length that is important.
Dendrites tend to be a bit bigger than axons, so they have a longer length constant: that is, EPSPs travel further. Dendrites are also not entirely passive: dendrites can actively propagate signals (see review by Yuste and Tank) using voltage-gated channels to boost EPSPs, especially in cells that have a long distal dendrite, such as the deep-layer pyramidal cells in neocortex. These voltage-gated channels give the dendrite a longer effective length constant
The most important thing is that even relatively short axons are just way too long for passive conduction: that's the reason for action potentials. Length constants depend greatly on the size of the neurite, but you can expect the distances to be on the order of millimeters to 10s of microns.
That said, it isn't ever true that a subthreshold EPSP won't flow into an axon: it just will get weaker and weaker with distance. Neurotransmitter release depends on a substantial depolarization which opens voltage-gated calcium channels; a small little EPSP that has decayed several-fold from the soma has no chance to cause calcium influx and subsequent vesicle release.
Spatial and temporal summation
EPSPs don't 'wait' anywhere, the EPSP is constantly decaying because all membranes are somewhat leaky, and current isn't restricted to any compartment. Current is constantly flowing out of the membrane and out into all the other processes of the neuron (and then out through those parts of membrane too!). In fact, if you are talking about passive conduction of EPSPs, you are really talking about a form of "leak", not through the membrane but through the cytosol! The EPSP isn't traveling to the soma in any directed way, there is current "leaking" in all directions, and some of it happens to go towards the soma. To get summation at the soma or anywhere else, EPSPs have to arrive both close enough in time and close enough in space.
EPSPs can sum with each other in the dendrites if they occur close enough in space, but of course that also only works if they occur around the same time. Similarly, at the soma, an EPSP slightly depolarizes the soma but only for a brief time. If one EPSP has an amplitude of, for example, 5 mV, and another EPSP has an amplitude of 3 mV, they will only sum to close to 8 mV if they occur simultaneously. If the 3 mV EPSP comes a few milliseconds later, the peak voltage might only be 6 mV, or if they are separated even more in time, there may be no summation at all.
Why do spikes start at the axon hillock?
The axon hillock is a special part of axon, right at the beginning of the axon. This area is more than just the first section of axon, it also typically has the lowest threshold for initiating an action potential due to a greater density of voltage-gated sodium channels. Sort of by definition, a cell's threshold is going to be the threshold for whatever part of that cell has the lowest threshold (at least near the soma, which is so big compared to axons/dendrites that it is nearly isopotential).
For example, take an example cell whose overall threshold is at -45 mV. If you were to somehow remove the axon hillock, leaving just the rest of the soma and the dendrites, the threshold wouldn't be -45 mV anymore, it would be much higher, maybe -10 mV. Even if you had some really huge EPSP (or manually injected some current) to bring the cell towards -10 mV, the axon hillock would still hit its threshold first and start the action potential well before the EPSP reaches a peak sufficient to start a spike in the soma proper.
If it helps you could think of a balloon analogy. The EPSP is air flowing into the balloon, and the action potential is the balloon popping. If one part of the balloon is thinned/weakened, that part will always be the site where the popping starts. It doesn't matter if you put in enough pressure to cause the thick part of the balloon to pop, because before you can possibly get it to that pressure the weak part has already burst.
Also note that for this analogy to fit with all the rest of this answer, it has to be a leaky balloon, so it only pops if you put enough air in fast enough before it has a chance to leak out.

References
Yuste, R., & Tank, D. W. (1996). Dendritic integration in mammalian neurons, a century after Cajal. Neuron, 16(4), 701-716.


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What is the degree distribution of synapses per neuron in the human brain?
I believe the mean number of synapses per neuron in the human cortex is around 6000.  What is the distribution around that average, either for the cortex or for the whole human brain?  E.g., is it normal, power law, etc.?

For a given class of cells, I'd expect it to be roughly normal, possibly gamma, but the distribution across all neurons is likely to be somewhat polymodal. You have extreme cases where there is effectively only 1 synapse, for example, and cells vary greatly in size both across and within brain regions. It's certainly not power law.


text:
Why do large neurotransmitters travel faster down the axon?
I understand that with large neurotransmitters, like neuropeptides, the precursor neurotransmitter and the enzymes are produced in the soma and quickly travel down the axon to be modified in the axon terminal.
With the small molecule transmitters, the enzymes are made in the soma and then transported slowly down the terminal to the terminal where they synthesize the small transmitters.
Why is it that the precursors and enzymes for large neurotransmitters travel fast down the axon, whereas the enzymes for the small transmitters travel slowly? Is there a specific reason?

is their a molecular weight for "small" and "large" transmitters that you can reference? Can you add a general reference that talks about this question?

@VanceLAlbaugh I edited the question a big to what I assume the OP was getting at, and already included some clarification in my answer. Textbooks often distinguish two major categories of neurotransmitters: small molecules vs. peptides.

I presume you are referring to fast versus slow axoplasmic transport.
I presume by "small neurotransmitters," you are referring to "small molecule" neurotransmitters like GABA, glutamate, acetylcholine, and the catecholamines like dopamine.
For the "large" neurotransmitters, I assume you are referring to peptides.
(for a quick reference on these two categories you can see this book blurb)
Although local protein synthesis is possible outside the soma, particularly in dendrites, and there is even evidence for protein synthesis in axons, including neurotransmitter peptides, most protein synthesis still seems to occur in the vicinity of the nucleus, at the soma. Synthesis anywhere else means you need to transport the mRNAs and translation machinery instead, since the mRNA needs to be made at the nucleus. Even the "large" neurotransmitters, which are peptides, need to be synthesized just like bigger proteins.
Back to axoplasmic transport... There are two main mechanisms for moving things down the axon. The faster version of this transport is really for the transport of vesicles. To transport a neurotransmitter peptide in this fashion, you fill a vesicle full of the peptide and send it on its way along the microtubules via kinesin and dynein motors.
Larger, non-membrane bound proteins, however, are often not transported in vesicles, but by the slower transport mechanism. Note that this transport is still pretty fast, way faster than simple diffusion, it just isn't as fast as the "fast" transport. The exact mechanisms of slow transport are still an active area of research and not fully understood.
To get back to your question, "is there a specific reason?" The reason isn't so much about the speed, but about the mechanism of transport. Small peptides and membrane-bound proteins move in vesicles via fast transport. Large proteins not bound in membranes move via slow transport. The enzymes that synthesize the small neurotransmitters fall into this latter category. Importantly, although the neurotransmitters may be small, the enzymes themselves can be big, at least certainly bigger than the small peptides that are equivalent to the "large" neurotransmitters.

Absolutely fantastic answer. Thank you so much for this! Thanks to the links as well haha, I understand everything about the answer I was looking for. Thanks again.


text:
How is the beginning of an episodic memory encoded in the brain?
before asking how information is stored, I need to understand

how does episode start and end are determined by the brain ?
how do i remember a movie ?

can you suggest a link to article addressing this issue
thanks

We don't know; it also isn't necessarily true that it is necessary for episodic memories or experiences to actually have any distinct start and end.

thanks. how can the brain recall an episode if it's not bound by some way like start/end "flag" or by special "sub circuit" (hard wired)

If it’s associative memory the chances of ‘multiple recalls’ is high without some boundaries that reduce its ‘fuzzy level’

Two answers to that comment: 1) Think a bit about your own memory. Are you really able to remember your whole life in sequence without interruptions or getting distracted? 2) The 'boundaries' you are talking about can be fairly subtle: just an increase in connectivity that causes an increase in probability of states progressing in the order of the original memory. There is actually a lot of research on just how poor our memories are, as well as how poor our estimates of how good our memories are (we think we remember well when we don't).

We don't have a full understanding of how episodic recall really happens in the brain, but there are theoretical approaches to understanding memory that are supported (but not shown definitively - it is really difficult to design appropriate experiments that are not beyond current technological capabilities) by experimental evidence. These approaches don't require any sort of hard "start" or "end" signal for episodic memory to work. In these approaches, an episodic memory is thought of as a sequence of brain states that correspond to previously experienced states.
The sequence occurs because connectivity promotes the network to progress from State A to State B to State C, etc. Additionally, all of the states consisting of that one "connected" memory are also associated, so that they prime one another.
To recall, you don't need to start at State A - you can start anywhere in the chain, and just recalling State C will prime you to also recall State A and B, so you can mentally "rewind" the memory a bit (we have no idea how exactly this type of conscious control works), even though it progresses most clearly in the A->B->C sequence.
The point of entry that allows you to initially get in to this chain might not be part of that episodic memory, either. For example, maybe you see a cat, and this leads to to an episodic memory of one event you shared with your own cat 5 years ago.
Brains are very dynamic, they do not behave like a feed-forward computation you might implement in a simple computer program. It is possible that there are "start" or "end" signals for episodic memories that we haven't found yet, but they may not be necessary at all.
For some further reading you could look for references on attractor networks, pattern separation and pattern completion, and theories of memory formation.
The book by Dayan and Abbott on theoretical neuroscience is also a good approach to some of the more basic background and includes an introduction to biologically-inspired models of learning and memory.

thank you Bryan. let us assume i have 5 cat's episodes. i might be confused if all are recalled. may be i have 1000 episodes with my family - all are recalled ...i'll be lost :)

You might be interested in reading about "attractor networks" and how they work - TL;DR version is that a network is structured so that there are stable states that are associated with particular memories or concepts. Thermodynamic analogies are appropriate to attractor networks, so the way you would think about it is that the 5 cat episodes are each stable attractors, with a relatively low energy barrier to passing between them.

Could you add some references to your answer? I'm not well enough versed in the area to judge whether or not it's a good answer, so some basic background references, links to wiki pages, good reviews in the literature, etc. would be much appreciated.

@MattDMo I'll try to come up with some basic references at least for further reading...this is the sort of thing people write books about that contain a fair bit of speculation and hand-waving, and far from settled knowledge, so it's a bit difficult to point to a particular authoritative source.

OK, thanks. If the science is totally settled, you probably want to mention that some way in your answer - "One hypothesis is ..." or "Many scientists seem to think that ..." etc.

@MattDMo The first sentence of my answer was "We don't have a full understanding of episodic recall, but let me try to answer from just a theoretical perspective" - by this I meant to convey that we don't have answers as to how episodic recall really happens but there has been a decent amount of educated speculation. I'll try to clarify a bit.

I want to hypnotize that the “end of memory item” is associate with inhibitor triggered; are there  any supportive evidence ?


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What could cause sudden deafness and deliriousness on a boat adrift?
I'm reading a completely nonfiction book  called In the Heart of the Sea, and in it, the characters are lost at sea without food and they are starving. They cast lots to see which crew member will be eaten, and it lands on one of them. He asks for the night to resign himself to his fate, and the other members accept. However, by midnight, he'd become deaf and by morning he was delirious. Why would this happen? It wasn't starvation-induced because they'd used up the very last of their rations that night in a large meal. So why did the threat of death induce deafness and deliriousness?
Edit: And it was 100% true: not only was the book nonfiction, there are accounts from the surviving crew members of the event.

Maybe because the author wanted it to? I think it will be difficult/impossible to get a biological explanation for every event in a work of fiction, and psychosomatic reactions aren't all that well understood (and can be a matter of some debate).

@BryanKrause: No- it was completely nonfiction, but even speculation would help.

Ah I see - could be psychosomatic, could also be that he ingested seawater, maybe trying to kill himself so his crewmates wouldn't have to do so: dehydration could cause both of those symptoms. Could also be that the emotional stresses interacted with dehydration he was already experiencing, or the anxiety caused nausea/vomiting/diarrhea. It's also possible the accounts from the surviving crewmembers were not entirely accurate.

Also depending on what food they were eating and their metabolic state, that large meal could have contributed as well. I edited the title to something more appropriate in case others think this can be saved, but I still think it's too speculative a question to be on-topic for biology.SE.

sounds more like dehydration, eating will only exacerbate that especially a protein heavy meal. digesting protein uses more water than digesting anything else. a sudden switch from carbohydrate rich biscuits to solid proteins would require much more water, so if they are rationing water someone with marginal dehydration could be pushed over the edge unless they take more water rations as well.

He probably had hypernatremia: salt toxicity from drinking seawater.  That definitely can cause delirium.  It was harder to nail down that hypernatremia could cause deafness specifically but I found that for pigs.
http://www.merckvetmanual.com/toxicology/salt-toxicity/overview-of-salt-toxicity

Affected pigs may be blind, deaf, and oblivious to their surroundings;
  they will not eat, drink, or respond to external stimuli.

It would be easy to think a person was deaf if he were altered / delirious / encephalopathic.  His brain does not process what he hears and so he is oblivious - like these pigs.


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Are there mammalian species in which the male makes no contribution after coitus?
It seems that live bearing is very high cost relative to egg laying. Therefore, I would expect that in a live bearing species the male would always have a post coital role.
Is this the case?

Are you claiming that, say, polar bear and tiger fathers help to raise their young?

I am not claiming I'm asking what advantage live bearing has over egg laying?

Can you clarify your question? The question you're explicitly asking here ("are there mammalian species in which the male makes no contribution after coitus") has clear answers, but in the comments you say that you want to know what advantage live bearing has over egg laying - which is a different question.  Can you be more explicit about the steps in your logic and say more precisely what your question is?

and, FWIW "sociality" (as in your title) is yet another topic - usually refers to associations of unrelated or distantly related individuals (not parent-offspring or parent-parent interactions)

there are two very different questions here, I suggest asking them separately .  And a better way to frame your first questions is what allowed eusociality to evolve in mole rats  the only vertebrate that is eusocial. its not insects and mammals it is insects and one mammal. Also I suggest you first ask what the benefits of live birth are because there are some pretty solid benefits.

I've adapted the question closer to what it originally said plainly and fitting the answer given. Eusociality is really a different thing altogether; I'd recommend asking that as a separate question as others have suggested, perhaps framing it on what you can learn from Ben's answer. Probably worth reading generally about eusociality before asking, too, in order to frame a clear question. "what advantage live bearing has over egg laying" is a third separate question, also only barely related to the others.

Narrowly speaking, the answer to your question is "yes, most of them".  West and Capellini (2016) analyze a data set comprising 529 mammalian species, of which only 65 have any form of male care of offspring. This figure from their paper shows that it is common in some primates and some carnivores (I haven't zoomed in to see exactly which clades these are), and otherwise rare.

West, Hannah E. R., and Isabella Capellini. “Male Care and Life History Traits in Mammals.” Nature Communications 7, no. 1 (June 14, 2016): 1–10. https://doi.org/10.1038/ncomms11854.

I'd think it would depend on how you define "care".  Is it just male-female pairings, or herd/pack animals, where the male(s) protects the entire group, including young?