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What is the relationship between muscle energy consumption, the period over which the contraction occurs and the mechanical work performed?
I'm asking this question with some basic knowledge of physics and general fitness.
Suppose you are lifting a still object with mass $m$ from height $h_1$ to height $h_2$ with an arbitrary (straight or curved) path. Let's ignore the movement of the body parts during the lift. Suppose you keep the object still at the final height $h_2$.
From physics, the object gains a mechanical energy equal to the variation of the gravitational potential energy during the movement:
$$\Delta E = mg(h_2-h_1)$$  [Joule]
Now, from what I can gather, such a quantity is absolutely not equal to the energy consumption of the muscles performing the lift, as:

Muscles fatigue more if they are shortened for a longer amount of time. That's the reason why lifting an object slowly is harder than lifting it fast. The previous equation does not consider the duration of the lift.

The previous equation ignores the object path because the mechanical energy gained by the object depends only on the vertical distance. But a curved and longer path may mean a longer duration of the lift. Hence it may mean more energy consumption, because of point 1.

Not sure of this, but I suppose muscles aren't 100% efficient. Hence, for each Joule (or Kcal) of input energy (in terms of ATP), they won't provide one Joule (or Kcal) of mechanical energy. I suppose some of that becomes heat.

So, I'd say that the previous equation provides the minimum amount of energy expended by muscles. It ignores the muscles inefficiency and the duration of the movement. But at the same time, the mechanical work does contribute to the energy consumption, since lifting an object is much harder that just keeping the muscles squeezed for the same amount of time.
Do you know some equations which take into account of these factors, and hence relate the mechanical work to these last two variables? Also some papers dealing with t

I suggest also posting this question in physics community

@RogerVadim Cross-posting is typically frowned upon. That said, similar questions have been asked at Physics so I'd strongly suggest OP to look for them there.

Welcome to Biology.SE. I've made some changes that I think make your question clearer, but please check to make sure I've not changed your meaning. In addition, note that your post stops mid-sentence. Also note that this may be too unfocused to be answered here — I would guess that there is a large literature on this subject. Some key words you can try to add to your searches: biophysics, kinematics.

Likewise I have edited your title so it employs standard scientific English. Check whether I have not inadvertently changed your meaning.

Does this answer your question? Why a continuous supply of energy is needed to support a weight?

This is at least partly duplicate from question https://biology.stackexchange.com/questions/35225/why-a-continuous-supply-of-energy-is-needed-to-support-a-weight/35290#35290 , although the question "what equation could model the extra energy spent due to other losses" is not in that one.


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What in the brain has gone awry during sleep paralysis?
I experience episodes of what I assume is sleep paralysis (lasting ~ 10-30 seconds) a few times a year, where I'm conscious of being somewhat awake but unable to move.  I can hear, but not see, and am quite focused on my breathing which feels labored and uncomfortable (can be accompanied by a feeling my face is covered by a sheet).  Sometimes, I've even been able to "jolt" myself awake if somehow muscle control is regained. Otherwise, I assume I drift off back to sleep.
Do we know yet what has gone wrong (if it can be assumed to be aberrant) and which neural circuits are involved? What i'm looking for is a specific explanation at the neural circuit level of how it can occur.
Is anyone aware of anyone conducting research into this or how it could be studied as it doesn't occur frequently and likely difficult to induce on demand?

Body paralysis occurs during REM sleep to keep your body from acting out your dreams.  You experience sleep paralysis when the mind awakens from REM sleep before the body paralysis has subsided.  I've had this happen before also, along with the "jolting" out of it you describe.  It usually happens when I'm very tired and trying to stay awake.  I try to stay calm but it's not easy as you know.  There is a good description at WebMD.

Thanks for sharing, @Kurt.  Yes, i'm aware of the general mechanism of muscle atonia during REM and that sleep paralysis is most likely to happen as you exit the ultradian sleep cycle.  What i'm curious about and after is a more specific explanation at the neural circuit level of how it can occur, and whether that is known/being researched (I can't find fMRI of an SP episode for example)? Is it a brain "snafu" or is a vestigial evolutionary-inherited trait that other animals have use for perhaps?

@Louis Leung.  Thanks for the clarification.  I have had trouble finding much more indepth research also.  I'll be interested to see what others come up with.

Sleep paralysis is  common, and associated with poor sleep
Isolated sleep paralysis is a relatively common parasomnia. Lifetime prevalence rates vary quite a bit from study to study, and between populations, but aggregating them gives a rate of about 7%. There are a number of associated conditions, many which are also associated with disturbed or irregular sleep in general (e.g., being an undergraduate student, shift worker, or having a psychiatric disorder).
Sleep paralysis also occurs in narcolepsy, but here it may be different
Sleep paralysis is a component of the overall clinical presentation of narcolepsy. It may have a similar but related mechanism, since these patients also experience cataplexy (muscle atonia in response to an emotional stimulus). Isolated sleep paralysis means sleep paralysis that isn't associated with narcolepsy. Some of our understanding of isolated sleep paralysis comes form studies of narcoleptic patients and animal models of narcolepsy. Because of the substantial differences in sleep patterns in narcolepsy, it's unclear if findings from these studies provide useful information for isolated sleep paralysis.
You can induce sleep paralysis by forcing sleep onset REM
You can induce isolated sleep paralysis in healthy volunteers by inducing sleep onset REM, a sleep period where REM sleep quickly follows sleep onset, instead of following a march through the phases of non-REM sleep. This was done in the linked study by, essentially, by waking the volunteers before the onset of the second REM period. Since sleep onset REM is more common in sleep deprived individuals or individuals with disturbed or irregular sleep patterns, this may be one of the reasons we see more sleep paralysis in these individuals.
Neural pathways involved in sleep are complicated, but REM doesn't directly inhibit arousal
The circuitry can be understood from studies of circuits involved in sleep in general and REM sleep in particular. You can read about this in Principles of Neural Science, Ch 47. It's quite complicated. One interesting note, though, is that the general cortical pattern for REM sleep, as measured, for example, by EEG, is more similar to waking that it is to non-REM sleep. Both states (waking and REM sleep) involve inhibition of a set of thalamic neurons that orchestrate the synchronous cortical firing seen in non-REM sleep.
Importantly, while the transition from waking to non-REM sleep involves a clear interaction between the neurons of the reticular formation that mediate arousal and non-REM sleep, there doesn't seem to be a direct pathway from REM-on neurons to inhibition of the reticular formation. It is not surprising that, during sleep onset REM periods, you could have dissociation of arousal (mediated by the reticular formation) and REM-on mediated hyperpolarization of motor neurons in the spinal cord. This review briefly discusses a possible mechanism of hyperactivity or hypersensitivity of REM-on neurons or weakness of the (still unknown) inhibition of REM.
Suppress REM and you reduce the frequency of sleep paralysis
Treatment focuses on reassurance and treatment of any underlying sleep irregularity and disturbances as well as any underlying psychiatric conditions, but when used, medications that suppress or inhibit REM in general reduce the frequency of sleep paralysis episodes.
It's probably not a big funding draw
There is, clearly, some research on isolated sleep paralysis outside of narcolepsy. It's an interesting phenomenon, but since it isn't dangerous or important clinically, I don't expect it gets much funding.

Thanks a lot for the info and particularly the link to ISP study in 1992, it was an interesting read.  I agree there seems intuitively a strong association with the epiphenomenon linked to REM states, so it would make sense to start any study with the major REM modulators.  Anectdotally, I've also noticed that my SP generally occurs in the early morning, which correlates to the time of more common bouts of REM sleep during the cycle.  As you rightly say, as it's not a major life-ruiner, there won't be much ISP study but we can leave this open until the answer is eventually found!

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Why aren't all infections immune-system resistant?
It's been less than a century since the widespread use of antibotics started, and already we're seeing bacteria that have evolved immunities to the antibotics we use.
On the other hand, we've been using immune systems to to fight bacteria for millions of years, and bacteria evolve much faster than humans do.  Why have bacteria not evolved immunities that let them completely overwhelm our immune systems and kill us all?

First of, not all infections are mediated by bacteria and not all bacteria are infectious. Also, not all parasitic bacteria lead to a strong infection or important health problem that cause any non-negligible selection pressure. Following the implicit logic of your post I will talk about infectious bacteria which cause "noticeable harm".
The mistake in your thinking is in the sentence

bacteria evolve much faster than humans do

While it is true that the mutation rate of base pair is higher and that the generation time is lower, the statement bacteria evolve much faster than humans do is made way too general and lead to your mistake here.
Infectious bacteria are selected to deal with the host immune system and the host is also selected to deal with the the parasite. Both virulence and penetrance evolve in this evolutionary arms race.
The evolution of host-parasite interaction is a very large field of study and it would take several books (and several books have been written on the subject; see this Amazon search) to summarize it. For some theoretical insights into the evolution of host and parasites, you might be interested in the book by Martin Nowak Evolutionary Dynamics: Exploring the equations of life
You will also note that a parasite does not have any "direct interest" in killing (or even harming) its host (thanks @jamesqf for his comment). You might want to have a look at the post Why do parasites sometimes kill their hosts?

Consider that an infection which kills off all its hosts is committing suicide :-)  From an evolutionary viewpoint, the ideal of bacterial survival would be to not harm the host at all, or even to benefit it - and indeed, there are many such bacteria living in your digestive system.

I'd like to add to @Remi.b's excellent answer with a few additional points
To quote Lewis Thomas in Germs

Disease usually results from inconclusive negotiations for symbiosis, an overstepping of the line by one side, a biologic misinterpretation of borders.

The human host is a complex ecosystem. Many "pathogens" live quite happily in one compartment, having co-evolved to the point where detection and attack by immune system mediators doesn't happen (the microbe avoids it) and is unnecessary (attacking the microbe provides no benefit to the host). For example, enterobacteriaceae have a capsule that allows them to avoid binding of IgA in the gut (see Murray Medical Microbiology, Chapter 30). Disease occurs when that otherwise commensal microbe is introduced to a compartment where it doesn't belong. Here, as it often is, disease may not be beneficial for either the host or the pathogen.
Two other small points to consider:

Antibacterial resistance is not new. The spread is new. In fact, resistance genes have been around for at least tens of thousands of years (see my answer to another question)
Again, a (human) host is a complex ecosystem. It is not an arms race between two species. A successful microbe must negotiate for space and resources with many other species, and may, in fact, be a host itself.

Every pathogen is resistant to immune responses. That's why they're pathogens. "Normal" bacteria, that don't have resistance adaptations, are immediately destroyed by immune responses; that's why we're not immediately infected by the vast cloud of microbes that surround us.
Individuals with weakened immunity (such as AIDS patients) are infected by microbes that normally aren't considered pathogenic. Such microbes don't have most of the immune-resistance armory that true pathogens or even opportunists have; but even they have some immune resistance capacity, as proven by the fact that even AIDS patients aren't infected with, say, plant viruses or the billions of soil bacteria that surround us, but that lack immune resistance altogether.
Although all pathogens and opportunists have immune resistance, few if any have complete immune resistance. Why not? Because the selective pressure on hosts to develop and maintain effective immunity is extremely high. Those hosts that failed to protect against some form of infection are probably extinct.

Immune-system resistance is especially difficult due to how immunity works.
First, I make 2 assumptions in my explanation:

the pathogen isn't specially designed to dodge the immune system and it isn't able to hide dormant in cells
the immune system is healthy and normal

When a pathogen is present, the immune system samples pieces of it (epitopes) and works on "randomly" putting together antibodies that bind to that epitope. Once a match is found, the qualifying antibody proliferates and is deployed in full force. Each copy of the matching antibody binds to the offending pathogen on contact with good probability - think of it as a microscopic football tackle. Cell-like pathogens (bacteria, fungi, and protozoa) thoroughly covered in antibodies can't consume nutrients, attack cells, and in extreme cases they can't excrete toxins because exocytosis proteins are blocked in antibodies. Viruses covered in antibodies have their surface structures blocked, thoroughly preventing binding to host cells.
The only reason why antibiotics are "easy" to gain resistance to by comparison is that they don't change on their own. The ones most vulnerable to resistance rely on tricking bacteria into eating them (endocytosis), which quickly selects for bacteria that work around the vulnerable protein channel. In other cases, bacteria develop something that inactivates antibiotics.
There has recently been work on antibiotics that force their way into bacterial cells, effectively punching large holes in the membrane. These would be difficult to develop resistance to, especially if they operate via electrical potential or grab onto a wide variety of bacterial epitopes.
Additionally, bacteria would be in a lot of trouble if humans developed antibiotic-generator implants that work as a secondary immune system. Consider a technology that scans for pathogenic bacteria, builds computerized 3D models of them, and then uses a biochemical 3D printer chip to construct custom antibiotics after preliminary safety checks to verify that the custom antibiotic in question wouldn't have dangerous side effects.

This answer has a number of misconceptions and speculation with no references.

Prove it. Your accusation provided no references. At least I'm contributing. How do I (or anyone else for that matter) know that you aren't #FakeNews? If you want to fact check, post a link in a comment and prove me wrong. Don't just downvote with no source, that's effectively trolling and abuse of the system.

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Why is Turner syndrome a problem?
Turner syndrome is a chromosomal disorder where one of the X chromosomes is missing. For more details visit the Wikipedia page
I don't understand why missing one X chromosome would be harmful. In normal females one of the two X chromosomes is inactivated at an early embryonic stage to a Barr body. For more details visit the Wikipedia page on this.
This X chromosome inactivation can be beneficial. For example, women are less prone to sex-linked genetic disorders due to this X chromosome inactivation.
My questions are:

If only one copy of an X chromosome is active in normal human females, why would having only one copy of an X chromosome cause a disorder?
What does it mean to deactivate parts of a chromosome
Why would it be essential to have two copies of a gene, as only the dominant one is expressed?

I've edited your question to improve the spelling, grammar, and style. Feel free to roll back or make further edits if you'd like. I'd note, it is best if you ask only one question at a time. I think @AliceD and my answers have addressed your main question (if X inactivation happens anyway, why is Turner syndrome a problem?). I've very briefly addressed what X inactivation is. If you have more questions about it, I would recommend asking another question. If you would like to know more about what having two copies of a gene accomplishes, that should probably be its own question as well.

If I do that people downvote and mark it as duplicate

Duplicates aren't bad. they mean you have asked a good question and we already have an answer for you. If a duplicate doesn't actually answer your question, you just need to articulate the difference between the duplicate and your question.

Short answer
Some genes on the X chromosome escape X-inactivation. Two copies of these genes are needed for normal development. These genes are also present on the Y chromosome. Hence, healthy males and females both have two copies of these genes. In Turner's, the SHOX gene seems to be one of the culprits, which is needed for normal skeletal development.
Background
It appears that both of the X chromosomes are needed for normal development in females, as some genes on the X chromosome escape X-inactivation. Many of these genes are located at the ends of each arm of the X chromosome in areas known as the pseudoautosomal regions. Although many genes are unique to the X chromosome, genes in the pseudoautosomal regions are present on both sex chromosomes. As a result, men and women each have two functional copies of these genes. Many of these genes are essential for normal development (source: Genetics Home Reference).
Which genes on the X chromosome are responsible is not yet known, but a gene called SHOX seems to be involved, which is important for bone development and growth. The loss of one copy of this gene likely causes short stature and skeletal abnormalities in women with Turner syndrome (source: NIH), see Fig. 1.
SHOX is a transcription factor of the homeobox family. It acts during early embryonic development to control the formation of the development of the skeleton. It plays an important role in the growth and maturation of bones in the arms and legs source: NIH).

Fig. 1. Some developmental malformations seen in Turner's syndrome. source: University of Chicago
FYI - I wrote an answer before checking for duplicates. I think my answer does add additional information (the SHOX gene is not mentioned in the linked question's answer

Rudimentary ovaries may be caused by wrong genome imprinting cause XI did not happen. We know that much better in 2022.

@AliceD's answer is excellent, but I thought it would be helpful to include an additional perspective.
The issue here isn't that monosomy X shouldn't be a problem because the majority of one X chromosome is inactivated. It is that monosomy X isn't as big a problem as any other monosomy because the majority of one X chromosome is inactivated. Monosomies generally lead to embryonic or fetal loss. There are a number of other disorders and reports that are described as monosomies, but they are partial monosomies (e.g., monosomy 10, monosomy 22). Monosomy X is the only complete monosomy that regularly produces a viable fetus, occuring in about 1 in 4000 live female births. It is believed to be present in 1-2% of all conceptuses.
There is an excellent overview of this topic in Chapter 5 of Thompson & Thompson Genetics in Medicine, with a particular discussion of Turner syndrome in Chapter 6.  There is also a review of the process of X inactivation, which involves usual strategies of silencing genes (conversion of a section of a chromosome to heterochromatin by covalent modifications of histone and DNA). It is just used more broadly on the X chromosome.

authors: Валерий Заподовников


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What is the difference between transport proteins and effector proteins in gram-negative bacteria?
When considering pathogenic gram-negative bacteria, is there any difference between the function of  transport proteins and effector proteins? Or are they of the same functionality? Any reference would be very helpful.

Any difference with what? Gram positive, non-pathogenic strains? Please  expand your question to make it more clear.

This is a pretty clear question. It's asking for the difference between two types of proteins involved in bacterial pathogenesis. They are often not well described in microbiology classes.

Is there any difference between the function of transport proteins and effector proteins?

Yes. In this context, the term "effector proteins" refers to proteins that are inserted into a host cell on infection to modulate host cell processes. Effector proteins are inserted into a host cell using a secretion system. The proteins involved in the secretion system are transport proteins, but the effector proteins themselves have a wide variety of functions. They include enzymes, transcription factors, and protein-protein interaction partners, and they have been shown to regulate many host cellular processes, from metabolism, to vesicular trafficking, cell adhesion, and apoptosis.
You can read more about this here.  This review has an interesting perspective, and the Wikipedia page on Bacterial effector proteins isn't bad either.


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How do we know that mild forms of rabies are nonexistent?
Wikipedia's rabies article says: "Death usually occurs 2 to 10 days after first symptoms. Survival is almost unknown once symptoms have presented, even with the administration of proper and intensive care."
I am wondering why we exclude the possibility of bite victims developing a mild form of rabies, in the same way that influenza can be mild or asymptomatic depending on the individual and the season. I noticed that rabies vaccines use an inactivated (killed) virus, while influenza vaccines can be attenuated, for example cold-adapted, so that a live virus may be used causing minimal symptoms. Clearly, for these vaccines to work, influenza infection must be able to proceed without symptoms. Similarly, the bubonic plague bacillus Yersinia pestis is endemic in many regions and presumably spread through asymptomatic carriers. Rabies vaccines are made from viruses whose infectivity upon intracranial injection is titrated according to a method of serial dilutions, suggesting that a harmless live vaccine would also be feasible at some level of dilution (barring, perhaps, the infeasibility of intracranial administration of such a vaccine).
What evidence do we have to suggest that rabies is different from influenza or plague, i.e. that it is not possible to have an infectious case of rabies with no or with mild symptoms?

There are many people worldwide who are exposed to rabies and don't die (they get treatment), but there are very few of these cases where people don't die after rabies has entered the central nervous system, and even fewer who didn't receive post exposure prophylaxis before the virus reached the central nervous system. Rabies isn't as rare as many would like to believe, unfortunately, with approximately 15 million exposures and 59,000 deaths a year, so data is available.
"Once symptoms have presented" in the Wikipedia article should probably be edited to "once central nervous system symptoms have presented". As discussed in this review rabies entry to the central nervous system is typically the "point of no return". One of the main challenges of rabies is that the virus hides from the immune system inside cells, making its way from muscle to peripheral nerves to the central nervous system before the immune system can mount a response. Once in the central nervous system, it has special protection from immune surveillance. The goal of post exposure prophylaxis is to allow the body to generate an immune response clear the virus before it gets to the central nervous system.
Generally, we say that central nervous system rabies is almost uniformly fatal without treatment because that is what has been observed and reported. *I'm not aware of any published epidemiologic survey looking for anti rabies antibody in healthy non-immunized adults. I know it's not very satisfying, but I would strongly suspect that someone has done a seroepidemiologic study and not published these results, since they're exactly what physicians have been taught since before Hippocrates: a dog bite followed by the characteristic illness leads (almost inevitably) to death. Other illnesses, on the other hand are observed to produce an antibody response in individuals' with mild disease. It is possible that there are unknown cases of mild non-encephalitic rabies that are self limited, but given the 150 years of intense study, I don't think it is likely there is a major aspect of the disease's natural history that hasn't been observed and reported.
Re: your idea about dilution of the vaccine suggesting you could dilute the virus, I think you may have a misconception about what that method actually involves. A killed virus vaccine cannot replicate, and so cannot cause rabies (though some forms of rabies vaccines used in the developing world have fairly high rates of nasty side effects).
Pasteur's risky rabies vaccine trial in 1885 may have involved a live vaccine, but he was notorious for incomplete documentation on his methods. It was essentially, a specimen of air dried rabbit spinal cord that didn't cause rabies in dogs. Here, his method was reported as drying spinal cord segments for longer and longer periods of time until the specimen did not produce rabies in dogs. This isn't a method that "dilutes the virus", but rather a method that attenuates the virus, making it less virulent. Pasteur didn't have methods for detecting what exactly that meant, other than that it didn't cause rabies, but did prevent the animal (or human child) from developing rabies after exposure to a virulent sample.
You can read more about rabies in Murray Medical Microbiology, Ch. 60
*Please see the link in @iayork's comment for a very interesting example of rabies serology in members of two communities in the Peruvian Amazon.

Evidence of Rabies Virus Exposure among Humans in the Peruvian Amazon found serological evidence of rabies exposure in people repeatedly exposed to vampire bats; other papers have found rare seropositive individuals among cavers and raccoon hunters, etc. However, that's not evidence of infection (could be exposure to inactivated rabies antigen floating in the air) or for that matter to rabies (could be a related lyssavirus with lower virulence, especially with the Peruvians and cavers).

@iayork fascinating read. Thank you for that!

Exposure events are very clear in the case of rabies. Unlike the flu, that one may catch without even knowing how or when, individuals at risk of developing rabies are usually clearly identified (for instance, people bitten by wild animals) and as a consequence they are carefully monitored. If they were to occasionally develop mild symptoms like fever, these would not go unnoticed.
In addition, it is very easy to take biological samples from these patients and check for the presence of virus using sensitive detection techniques; it turns out that no case of asymptomatic infection was ever documented, and at this stage it is reasonable to assume that if it had a signifiant risk of happening, we would have seen it by now.

Please would you provide references for your claims. Speaking personally, of the half dozen or so times I've been bitten by wild animals - and not felt well the next day - i ve not reported to anyone. Could you please be specific as to the provenance of your study?

Thanks @Duckisaduckisaduck. I have had similar experiences, but didn't want to describe them in the question, as I worried this would distract people from the question itself and make them want to blame me for not seeking out a painful course of rabies shots.


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How is it determined whether a chromosome is maternal or paternal for imprinting?
For imprinting, how does the cell determine which chromosome is maternal and which is paternal? For example, in the parental imprinting of insulin-like growth factor 2 (Igf2) on chr7 (autosome), how is it determined which is paternal and to be imprinted?

Imprinting occurs via DNA methylation in gametes. Different parts of the genome are methylated in either eggs or sperm, and this then marks those genes throughout the lifespan of the organism, inherited epigenetically across cell divisions. See:
Wood, A. J., & Oakey, R. J. (2006). Genomic imprinting in mammals: emerging themes and established theories. PLoS genetics, 2(11), e147.


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What prevents non-aminoacylated tRNA from binding to mRNA on the ribosome and disrupting protein synthesis?
Specific aminoacyl-tRNA synthetases catalyse a reaction in which a transfer RNA molecule with a given anticodon is covalently attached to its cognate amino acid (aminoacylated).
What factors favor the binding to the ribosome/mRNA of an aminoacylated tRNA molecule, rather than one without an attached amino acid?
Is it exclusively the presence of an exposed OH group on the end of the non-aminoacylated-tRNA molecule or is it possible that the tRNA molecule undergoes some degree of conformation change when the amino acid is enzymatically attached that makes the anticodon have a greater affinity for the codon?

I made a few edits that I think make your question clearer — please check and [edit] if you feel I have altered the question you are trying to ask. Note that binding and bonding are (in biochemistry/molecular biology) used differently — bonding suggests a covalent bond was made, while binding covers other interactions. Also, please make sure you're familiar with the steps of translation — this is covered in many textbooks (e.g. search the NCBI 'bookshelf'). I think you may find clues (if not a complete answer) by doing so.

Yes I am familiar with translation.  I think my question was overly developed.  What I really want to know is what mechanisms keep a t-RNA that is not bound to an amino acid from getting into the ribosome and sticking to the codon.  I have read that the exposed OH group on the non AA bound tRNA is repelled by the ribosome, but also hypothesize that the t-RNA may have its shape altered when it's bound to an AA to make the anticodon lock up tighter.

I think the question is good now.

Great. Do you have a reason to think exclusion must be happening? The reason I suggested reading up on translation is because IIRC the amino-acylation of a tRNA creates a "high-energy" molecule, which is required for the addition of the amino-acid to the C-terminus of the growing protein. If it isn't charged I suspect (haven't had time to check) the tRNA won't have a large effect on translation ...

@tyersome I am not asking why the uncharged, non amino acylated tRNA can't contribute to translation.  I am asking why an uncharged, non amino acylated tRNA molecule doesn't occasionally slide into the ribosome and bind to a codon.  It probably doesn't matter.  It would eventually detatch.   What actual changes occur in a t-RNA molecule when it gets charged?

I posted a (brief) answer below, let me know if it helps. The first reference is fairly readable, so (depending on your background) you may find it to be of some interest. If you could post where you read that the uncharged aa is repelled, I can have a look later — my "quick" literature search could easily have missed something important.

I have edited the question in the following ways. 1. I shortened title without changing meaning in any way. 2. I inserted precise biochemical terms where needed. In particular I replaced the word "bound" in relation to amino acids and tRNA by (covalently ) attached or aminoacylated. This makes a clear distinction with the non-covalent binding of the tRNA to the ribosome. 3. I also made clear that the tRNA binds to the ribosome as well as interacting with an anticodon, as was indicated to be the concern of the poster in a comment.

Short answer
The codon-directed non-enzymic binding of tRNA (aminoacylated or not) to the A-site of the ribosome is much weaker than the (normal) binding of aminoacyl-tRNA complexed to EF-Tu/EF-1, the tRNA-binding elongation factor (which discriminates against non-aminoacylated tRNA). Hence it is unable to compete effectively with the latter to disrupt protein synthesis.
Explanation
The stages in protein biosynthesis relevant to this question are shown below.

In stage 1 tRNAs are aminoacylated with their cognate amino acid in a reaction catalysed by a specific aminoacyl-tRNA synthetase.
In stage 2 aminoacylated tRNAs (except the initiator tRNA) are recognized by a single elongation factor (EF-Tu in prokaryotes, EF-1 in eukaryotes) and form a complex with it and GTP. The elongation factor will not form a complex with non-aminoacylated (also referred to as ‘deacylated’) tRNA, and this has been shown to be caused by structural differences from aminoacylated tRNA. This latter is particularly pertinent to the question, and will be discussed in more detail below
In stage 3 this complex binds to the A-site of the ribosome in a codon-specific manner. However it is important to understand the strength of the interaction between the elongation factor and the A-site of the ribosome compared with the tRNA–anticodon interaction alone. The latter is, of course, necessary for accurate protein synthesis, but may be regarded as preventing (or  more strictly delaying) dissociation of the complex.
Basis of the discrimination against non-aminoacylated tRNA
The discrimination occurs at the stage of binding by EF-Tu/EF-1. What is known about its structural basis? This appears not to be merely recognation of the amino acid, but involves indirect effects on the structure of the tRNA and its recognition by EF-Tu, as is discussed in the 1996 paper of the Aarhus group that elucidated the structure of the aminoacyl-tRNA.EF-Tu complex. I quote:

Deacylated tRNA binds to EF-Tu-GTP with an affinity which is approximately four to five orders of magnitude lower than that of aa-tRNA. Thus, the aminoacyl group is a primary discriminator in the ternary complex formation. It is impossible to explain this by the direct interactions with the aminoacyl group alone. Other structural features of aa-tRNA must contribute to the affinity.
There has been a long-standing research on the conformational changes of tRNA upon aminoacylation. Fluorescence studies… have indicated that conformational changes occur upon aminoacylation, though in a diverse manner among the individual acceptors.

One precise structural difference is discussed:

It is evident that aminoacylation of tRNA restrains the conformational space of the terminal A76 considerably. Compared to the crystal structure of the ternary complex, the residues A73 through C75 of deacylated tRNA-Phe (PDB entry code 4TNA) are in an equivalent conformation, though slightly shifted in their position relative to the acceptor helix. However, the terminal A76 residue in deacylated tRNAPhe adopts a conformation which is impossible in the phenylalanylated form (fig 7).

[Non-acylated free tRNAPhe (left) and acylated Phe-tRNAPhe of the ternary complex (right)]
It can be seen that the residues 73–76 are near the 3′ end of the tRNA where the phenylalanine (Phe) is attached.
Evolutionary perspective
One presumes that primitive protein synthesis did not involve elongation factors. It would have been important to prevent the unproductive binding of un-aminoacylated tRNA to the ribosome and the competition with aminoacylated tRNA postulated in the question. A first step towards this may have been the evolution of a ribosomal A-site that could discriminate between the structures of aminoacylated and non-aminoacylated tRNA. The development of tRNA-binding elongation factor, as well as making the process more efficient would have amplified this discrimination which is in the range of  10-200x, depending on the concentration of magnesium ions (which artificially enhance binding of non- aminoacylated tRNA).

In some bacteria, uncharged tRNAs have been shown to bind to the ribosome. In fact, that binding is responsible for the "stringent response" a mechanism that signals that the cell is running low on amino acids1,2.
From Raina & Ibba (2014):

RelA is a ribosome-associated (p)ppGpp synthase which senses the presence of uncharged tRNAs that accumulate at the ribosome A site as a result of amino acid limitation. The presence of the uncharged tRNA acts as an effector molecule, stalling protein synthesis and activating RelA which then synthesizes pppGpp and ppGpp by phosphorylation of GTP or GDP using ATP as the phosphate donor (Haseltine and Block, 1973; Sy and Lipmann, 1973).

A similar mechanism has been proposed to operate in eukaryotes1,3,4.
Again, from the same section of Raina & Ibba (2014):

It has been proposed that discrimination between the charged and uncharged tRNA by Gcn2p occurs via an analogous mechanism of RelA protein activation as observed in E. coli by the presence of uncharged tRNA at the decoding (A) site on translating ribosomes. The activation of Gcn2p by uncharged tRNA requires its association with the ribosome via its C-terminal region and also, interactions between the N terminus of Gcn2p and the Gcn1p–Gcn20p protein complex which is also associated with the ribosome.

And, from the last paragraph of the discussion in Dong et. al. (2000):

We have argued previously that uncharged tRNAs bound to the decoding (A) site of the ribosome and base-paired with their cognate codons in mRNA activate GCN2 (15).

References:

Raina, M., & Ibba, M. (2014). tRNAs as regulators of biological processes. Frontiers in genetics, 5, 171.

Haseltine, W. A., & Block, R. (1973). Synthesis of guanosine tetra-and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. Proceedings of the National Academy of Sciences, 70(5), 1564-1568.

Dong, J., Qiu, H., Garcia-Barrio, M., Anderson, J., & Hinnebusch, A. G. (2000). Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain. Molecular cell, 6(2), 269-279.

Ramirez, M. A. N. U. E. L., Wek, R. C., & Hinnebusch, A. G. (1991). Ribosome association of GCN2 protein kinase, a translational activator of the GCN4 gene of Saccharomyces cerevisiae. Molecular and cellular biology, 11(6), 3027-3036.

So what is the answer to the question — why doesn't this binding disrupt protein synthesis? And where in reference 3 (or 1) is there anything about the activation of GCN2 being due to binding of deacylated tRNA to ribosomes?

@David — You're right, my answer kind of went off on a tangent — your answer is (as usual) excellent. If you're interested I added a bit more detail clarifying what I was basing my (non-)answer on. I've also clarified that the eukaryotic relevance is speculative. ——— I'll probably delete this later, but I want to think about how the "stringent response" and EF-Tu based discrimination work together ...

— A long ago I worked on tRNA binding to ribosomes, so I am familiar with some of the literature. There is a relatively recent paper on the stringent response that is relevant: Nature 534, 277–280 (2016). One recurring theme is the recognition of different structures and conformations of tRNA by different proteins, and I may add a section to my answer to point this out. In the case of stringent control one has RelA discriminating between acylated and deacylated tRNA bound to the ribosome.


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Why do eubacterial DNA Ligases use NAD whereas eukaryotic and archaeal DNA Ligases use ATP?
DNA ligases in eukaryotes are ATP-dependent (as is the enzyme from bacteriophage T4) but in Escherichia coli the DNA ligase is NAD+-dependent. I cannot understand the reason for this.
An extensive literature search just left me with more confusion. (I read NAD+ dependent DNA ligase have BRCT domains and was wondering if it is in any way related to this)

This difference is certainly intriguing, but, like many other general ‘why?’ questions, can be approached on different levels.

Because they evolved differently.

is one answer, and not a trivial one because of the shared cofactors of archaea and eukaryotes. But I imagine that the poster would respond by asking why they evolved differently — whether there is some functional or structural difference that can explain this. There isn’t, and the question is avoided in the papers I have looked at, so the answer would seem to be

Nobody knows. If there is a reason it is not evident from the function the reactions perform (which is the same) or the structure of the enzymes (which is similar at the active site).

Let us look at the thermodynamics of the reactions. In both cases a phosphodiester bond is being formed, a reaction with a high +ve ΔG. In ATP-dependent DNA ligases an overall –ve ΔG is achieved by the hydrolysis of ATP to AMP and pyrophosphate; whereas in the NAD-dependent DNA ligases it is supplied by the more unusual, but equally energetic, hydrolysis of NAD+ to NMN+:

The overall structures of the two types of DNA ligase are different:

But the catalytic site for the ligation reaction is remarkably similar in both cases:

(Both diagrams from Structure 1999, 7:35–42)
So explanations in terms of mechanism of reaction would seem to be ruled out.
Coda
There are several analogous problems in biochemistry, e.g. why GTP is generated in the tricarboxylic acid cycle in most (but not all) organisms, and why NADP is the cofactor for a particular oxido-reduction reaction in bacteria, whereas NAD is used in eukaryotes. In general one feels (or at least I do) that the explanation must be something to do with compartmentation of cofactors or coupling reactions to their availability. Perhaps a particular choice was advantageous to bacteria early in evolution, but this was no longer the case in eukaryotes, and in fact the reverse became true. But without any evidence to support such arguments they are merely hand waving, which is why professional scientists generally tend to avoid them in their research publications.

This makes sense why authors have avoided the reason behind this. And I feel, with the answer you have provided (which i feel is explained much much better than what i could find in different literature sources) i need to make peace with the fact that some things have just happened due to reasons inexplicable. I hope if there's a concrete reason behind the utilisation of different cofactors we do find it soon.


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Why can't bacteriophages survive inside the human body thus negating the possibility of using them against bacteria?
I read about the therapeutic uses of bacteriophages in Pelczar's Microbiology. It was written that it is reasonable to think that bacteriophages could be used to kill pathogenic bacteria. However, the book also clearly stated that after a lot of research it was found that bacteriophages can't be used to kill bacteria in the human body because they can't survive inside the human body. But no reason was given why.

I think it's about a claim, that bacteriophages cannot survive in the human body and can therefore not be used as a treatment against bacterial infections. The question is fine, but it would be good to give the source of such claims. You say, you have done a lot of research. Showing your sources would help understanding the question.

It would be better to quote from the book verbatim, especially as English is not your native language. The misuse of the word "sustain" is critical here. I have edited it out, but it would be better to know what exactly was written.

Well the book actually wrote sustain, yes English is not my native language but I'm not blind.

This question cannot be answered, because the assumption behind your question is wrong. I haven't found a source to claim that bacteriophages cannot survive in the human body. Bacteriophages can and are, in fact, used as a treatment against human bacterial infections, it's called "phage therapy" (1,2,3).
This is, nevertheless, a rather uncommon procedure for a number of reasons:

Availability: Compared to antibiotics, which you can easily get from any doctor/pharmacy, phage therapy requires special facilities, because very specific phages need to be produced for each disease.
Safety and regulation: Virus handling requires special safety measures and using them in humans requires a lot of paperwork, safety tests and clinical trials.
Money: Due to the reasons above, phage therapy is a lot more expensive than antibiotics.
Lack of research: Thanks to the availability of antibiotics there was no urgent need to develop the application of phage therapy. We know comparably little about how the immune system might react to bacteriophages in the blood or bacterial toxins released by lysed bacteria. We haven't found a way to e.g. quickly engineer bacteriophages for diseases.

With a growing concern about multi-drug resistant bacteria, developing new ways to combat diseases has become more important. Maybe phage therapy will be one way to deal with this more regularly in the future.

Are the special safety rules for bacteriophage treatment really needed or only a matter of paranoid bureaucratic overhead? Intuitively, bacteriophages should be the safest viruses for humans to be exposed to considering they selectively infect bacteria (fundamentally different biological architecture from human cells). For bacteriophages to infect humans, first they need to figure out infecting eukaryotes, and then they need to adapt to the different ribosome structure (which also happens to be the reason why you can take macrolide antibiotics without shutting down your own ribosomes).

While most phages are no threat for human health, they are "biological agents" falling into the biosafety level 1 regulation. When they are modified in the lab, that level might even increase. So, your lab needs to meet all safety standards to be allowed to handle them. https://journals.sagepub.com/doi/pdf/10.1177/153567601001500106


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What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles?
As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of their evolutionary relationship.
To be more specific, I would like to know whether the use of tetrapyrrole in the blood and in photosynthesis can be traced to the earliest organisms in which tetrapyrrole had some function, and then the molecule evolved to be capable of the different functions it currently performs in animals and plants.

The general subject of your question is certainly on topic here, but a simple reference request is not, and at present it is unclear what your question is. Your title refers to evolution, yet the answer you say that you will probably accept says nothing about evolution. Is your question one of chemistry — why is the tetrapyrrole ring found in different functional molecules and how does it perform different functions? Or do you wish to know which tetrapyrrole is the most evolutionary ancient and whether others evolved from it? Please edit your question so that it asks a precise question.

@David Thank you, your second suggestion is the correct one. I tried to explain this but I certainly lack expertise to do it properly. Please edit the text accordingly if it contains any inaccuracies.

I have edited the question as you suggested, trying to condense it to its essentials to clarify it. Let me know if there is anything you object to.

@David Thank you very much! No objections, on the contrary, I think you improved the question a lot.

I've finally posted an answer of sorts. If you are a non-biologist, I assume that you have some chemistry. In any case answers on SE are not necessarily aimed at the poster, but at the question. However, if you wish clarification, do comment on the answer.

Preamble
I found this question interesting, so that, despite my general ignorance in this area, I have attempted to address the question of the evolution of tetrapyrroles rather than answer it. Additional contributions are welcome as comments. I apologize for the large graphic, which I feel is indispensable to my answer, however I have included a summary above it, so readers can decide whether they wish to read further.
Summary

There are four main types of tetrapyrrole associated with proteins
They share a common pathway from 5-aminolevulinic acid to uroporphyrinogen II
The unresolved question of which subsequent pathway evolved first is discussed in relation to their antiquity and complexity.
The possible evolutionary relevance of the two different pathways for the synthesis of  5-aminolevulinic acid — found in different organisms — is also discussed.

Tetrapyrroles in proteins — Diversity and Chemical Rationale
Although the cyclic tetrapyrrole structure looks complex, it appears to be very ancient, presumably because of the greater chemical versatility of its complexes with metal ions in proteins, compared with simpler proteins that contain metal ions. The ring provides a precise four-co-ordination which can be held in position to provide two additional co-ordination sites (at right angles to the plane of the ring) which can interact with protein side-chains or other molecules (such as oxygen). The combination of ion, substitution of the tetrapyrrole and interaction with the protein allows fine-tuning of the redox properties of the ion.
The diagram below (adapted from Zappa et al.) shows the four main types of tetrapyrrole in proteins and how their biosynthesis is related. The two mentioned in the question are actually both derivatives of protoporphyrin IX: chlorins, such as chlorophyll — with its role in photosynthesis — and haem proteins — with the examples of the cytochromes of the electron transport chain being more widespread than that of haemoglobin in eukaryotes. In addition, however, are the corrins — most notably in Vitamin B12 with a role in methyl transfer — and sirohaem — which occurs in certain sulphite and nitrite reductases.

Which tetrapyrrole is oldest in evolutionary terms?
How can we address the question of which tetrapyrrole was first to arise? This question is, in fact, which synthetic pathway — which series of enzymes — was first to arise. In my review of the literature I (like the poster) find this an area which angels are fearful of, but, being foolhardy, I suggest two criteria. The first is what we consider the relative ages of the functions the proteins subserve, and the second the relative complexity of the pathways needed to synthesize them.
The first criterion is subject to dispute. Unfortunately the easy comparison between haem as an oxygen carrier in eukaryotes and chlorophylls as ancient prokaryotic photosynthetic proteins is complicated by the more ancient role of haem in cytochromes. One might argue that cytochromes are a feature of aerobic metabolism that followed the emergence of oxygen generation by photosynthesis, but unfortunately the electron transport chain exists in anaerobic organisms, where the terminal electron acceptor may be nitrate, nitrite, ferric iron, sulphate or carbon dioxide. Given this, and the greater complexity of the pathway from protoporphyrin IX to bacteriochlorophyll a compared with that to protohaem (10 steps compared to one), one might argue that chlorins emerged after haems.
But what about the other tetrapyrroles? One approach to relative ages is to consider the biochemical processes that might have been present early after the emergences of life. One such analysis of this was made by Weiss et al. in a paper published in Nature Microbiology (2016) 1, 1–8, entitled “The physiology and habitat of the last universal common ancestor”. They drew the conclusion that the Last Universal Common Ancestor (LUCA) was an anaerobic autotroph that existed in a hydrothermal setting and obtained energy using a Wood–Ljungdahl pathway with hydrogen as the electron donor and carbon dioxide as the electron acceptor. The two types of tetrapyrroles that they postulate would have been present in the LUCA are corrin (as cobalamin for methyl group transfer) and sirohaem for sulphur metabolism (sulphite reductase) in the hydrothermal environment.  No mention of porphyrins! Given the complexity of the 16 step pathway to corrin, compared to the one-step pathway to sirohaem, one might suggest that the latter evolved first.
Synthesis of 5-aminolevulinic acid — evolutionary implications?
5-aminolevulinic acid (frequently referred to by its old name of δ-aminolevulinic acid) is the precursor of uroporphyrinogen II, the common tetrapyrrole precursor. However there exist two pathways by which this can be formed, of which, as I understand it, only one is present in any organism. One of these (at least to my thinking) could have evolutionary implications. These pathways are shown below in a figure adapted from a paper on prokaryotic haem biosynthesis by H. Panek and M.R. O’Brian (2002).

The intriguing aspect of this is that one of the pathways (the C5 pathway) involves reduction of glutamyl-tRNA, whereas the other (the Shemin pathway) is a conventional synthase reaction with substrates glycine and succinyl-CoA. Arguments supporting the RNA world hypothesis include catalytic RNA, and the presence of nucleosides in molecules such as NAD where there complexity belies the simplicity of their function. So, putting my head over the parapet again (to vary my metaphors), I would suggest that the use of glutamyl-tRNA for the synthesis of this ancient and important intermediate might be another fossil of the RNA world. (Perhaps not what the poster had in mind in posing his question.)

Note the molecules are not that similar, only one portion is similar.
The similar portion in each molecule is a cyclic tetrapyrroles. Cyclic tetrapyrroles and porphyrins in particular are a fairly common structure in biology they have several functional uses and are fairly easy to construct from existing simpler biological molecules. The fact that they are functionally good at binding metals makes them a reoccuring solution, although not all Cyclic tetrapyrroles bind metals. Many many biological molecules contain Cyclic tetrapyrroles.
Many biological molecules have similar structures to other molecules, especially ones that perform similar tasks, there are only so many shapes you can make with carbon atoms, the shape of a molecule affects its chemical properties and that shape is simple and has useful properties. Heme itself is a functional component of many proteins called hemoproteins, basically whenever they need to bind iron. Another cyclic tetrapyrroles would be cobalamin otherwise known as vitamin B12 which binds cobalt.
Its the same reason hammer handles look very similar even in very different cultures, just attaching a stick is a simple easy to discover solution, so it is the one that gets found most of the time. Functionally that is the shape that works. Or to put it another way they are only so many shapes you can make a wheel.
https://www.sciencedirect.com/science/article/pii/S0167488912001000
http://www.org-chem.org/yuuki/porphyrin/porphyrin.html
https://www.cpp.edu/~lsstarkey/courses/CHM-Lab/PorphyrinBasics.pdf
https://www.mdpi.com/journal/molecules/special_issues/porphyrin_chemistry
To address the updated question. I honestly don't know if they share an evolutionary origin. But given that they are synthesised in different organelles (mitochondria for heme and chloroplast for chlorophyll, I would guess no.

Many thanks for explaining this, and most probably I will accept your answer, but the references you provide hardly mention any evolutionary issues. In light of your answer, - could you possibly add a reference discussing earliest known occurrences of porphyrin in living organisms?

Also, could you name examples of other biological functions, aside of in blood and in photosynthesis, that porphyrin rings have?

Chemically you are incorrect. The similar portion of each molecule is a tetrapyrrole  — in one case a porphyrin, in the other a chlorin. If the question is about the relationship betweeen structure and function in tetrapyrroles, then I suggest it needs extending, but I would wait until the poster clarifies things first.

@მამუკაჯიბლაძე the earliest known occurrence would be an entirely different question.

@John I agree. Still, I believe telling about it in the answer would be relevant for the existing question, as it would provide some information about possible common precursors of hemoglobin and chlorophyll. Note that, as David points out, I should talk about tetrapyrrole rather than porphyrin in that comment of mine.

@David Yes your right, They are both cyclic tetrapyrroles, I forgot about that little extra ring on chlorophyll. I will correct this. But to be clear many paper still identify them as porphyrins

One more thing - it is true that only the tetrapyrrole portions are similar, but they are the main functional parts, performing metal binding, which is crucial both for photosynthesis and for oxygen transport in blood.

And also, I want to apologize for the unclear question. The word "evolutionary" was only mentioned in the title, not in the text. According to the suggestion by @David I have now added second paragraph trying to clarify the question.

@მამუკაჯიბლაძე I did mention that

authors: მამუკა ჯიბლაძე


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Obtaining protein atomic co-ordinates from dihedral angles
https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg
I've been reading on Protein Amino Acid Sequences and their 3D structure. It seems that the 3D structure is encoded by the three torsion angles as shown above. My professor said there is a 1-1 encoding between 3d cartesian coordinates and the torsion angles, but I cannot find any way to do this either in pyrosetta or biopython. Is there any formulas/packages that would be of use for this conversion?

Do you want to calculate the dihedrals from the coordinates? That's easy enough - use something like dang http://kinemage.biochem.duke.edu/software/dang.php. For the other way round, see https://www.rosettacommons.org/content/conversion-dihedral-angle-representation-cartesian-representation

Welcome to SE Biology. If your professor said really said that (and I imagine he qualified it in some way), he should be fired; and you should reconsider whether angles alone can determine (not encode) a structure in which there are different amino acid residues with bonds of various length. Do you actually have any imput data for the program you can't find? You should ask yourself what is the experimental data in the real world that would need computer processing. Are there experimental techniques for determining dihedral angles, or are they deduced from the determined 3D co-ordinates?

As I indicated in my comment:

You need the amino acid sequence and values for bond lengths before you could determine the atomic co-ordinates from the dihedral angles.
Originally the dihedral angles are calculated from the experimentally atomic co-ordinates (with the help of the sequence), so that what you propose is in its nature an academic exercise.

There is, however, a situation in which I have — in effect — done that, in exploring the structures that would be produced if the dihedral angles were varied. Rather than a command-line tool, there is a graphical tool that allows you to vary the angles interactively and see the results. This is the excellent Ramachandran Plot Explorer (Rama) by Bosco Ho. And yes, it can also generate the co-ordinates — you can save the results in PDB format to reopen or to visualize with other protein graphic software, such as JSmol.
The only problem is that the last version of this software was released in 2006, and is not 64-bit, so it will not run on the next version of Mac OS X (no idea about Windows). Bosco’s blog is still active, so perhaps he could be persuaded…


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Why is ATP synthase sometimes referred to as ATPase?
Quite a few times I have seen the term ‘ATPase’ used for what I would consider ATP synthase. For example, my text has:

“The phosphorylation of ADP to ATP is also catalysed by the enzyme ATPase.”

I don’t understand this. Surely the enzyme that catalyses the synthesis of ATP should be entitled ‘ATP synthase’, so why is ‘ATPase’ used in this case?

Welcome to SE Biology. Your question is quite reasonable (I had the same experience years ago) but I have edited it a little to give it a more formal and neutral tone, better suited to the question and answer nature of this site. It is generally useful if you could tell us the name of the texts you quote from, so others can check them.

The way we were
To understand why you may encounter ATP synthase referred to as ATPase, you need to be aware of the historical context — the experimental work that preceded the knowledge of the structure and function of the enzyme complex that we have today. In a nutshell:

Original studies of the components of what we now know to be a complex capable of synthesizing ATP could only be assayed by their ability to hydrolyse ATP. Even though these components (F1 and F1FO) were derived from a mitochondrial system that coupled electron transport to ATP synthesis, and the authors believed these components were responsible for ATP synthesis, they were obliged to refer to them by the activity they had assayed: hence F1 ATPase and F1FO) ATPase.

History lesson
It is instructive to consider a paper by Kagawa and Racker, published in 1966, and entitled:

Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation
  VIII. PROPERTIES OF A FACTOR CONFERRING OLIGOMYCIN SENSITIVITY ON MITOCHONDRIAL ADENOSINE TRIPHOSPHATASE”

This work demonstrated that a mitochondrial ‘fraction’ (FO — ‘F’ stood for ‘fraction’) when added to another ‘fraction’ (F1), previously shown to have ATPase activity, could confer sensitivity of the ATPase to inhibition by oligomycin, a compound that inhibits oxidative phosphorylation in intact mitochondria. The title shows clearly that they were aiming to understand ATP synthesis, but were at the stage where all they could measure was the ATPase activity of fractions. It was not until 1973 that Racker and Stoeckenius were first able to  synthesize ATP, and for that they had to use a different system — the light-activated purple membrane of Halobacterium halobium. The key was the incorporation of the membrane — without it there could be no proton gradient to drive the synthesis of ATP, and this was why the isolated F1FO) complex could never catalyse synthesis of ATP on its own.
Those days are gone now
The structure of the components of the ATP synthase finally started emerging in the 1990s, after which no doubt remained that the F1 and FO fractions were part of a synthase.

Therefore, in describing the enzyme complex as we now know it to be,
  there is no excuse to refer to it as anything other than ATP synthase. Moreover there is a particular need to avoid confusion with a membrane ATPase (below).

In my opinion, any textbook that refers to ATP synthase as ATPase is severely out of date and should be burned.
Of course, I exempt historical accounts, as long as the context is made clear.
The acid test
In some cells there are transmembrane complexes, structurally related to the mitochondrial (or bacterial membrane) ATP synthase, that are ATPases. These are the Vacuolar-type H+-ATPases (V-ATPase) which use the energy of ATP hydrolysis to transport hydrogen ions across the membranes of certain tissues and organelles. Another reason not to refer to the ATP synthase as ATPase!

The flagellar motor complex is also a good example of an ATPase that is structurally similar to the ATP synthase.


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How many molecules of ATP are actually produced in aerobic respiration?
I have been through the process of aerobic respiration a few times in different text books and almost every book quotes a different value for the number of ATP molecules produced. The consensus seems to be 30–32, but why is there disagreement and why aren’t the numbers exact?
The possible reasons I can think of are:

Phosphorylation of ADP is not directly coupled to redox reactions.
The number of ATP molecules produced depends on the shuttle used to transport electrons from the NADH in the cytosol to the mitochondria, i.e.  whether it’s FADH2 which enters the ETC or NADH. (I have a silly question on that, but I need confirmation, does the electron carrier chosen depend on availability?)
The proton-motive force can be used to drive other cellular processes other than the production of ADP? (I'm guessing.)

Are these suggestions correct, or is there some other explanation?

The discrepancy between 30 and 32 molecules of ATP quoted in the question may well arise from the two possible ways in which the reducing equivalents of the two molecules of NADH generated in glycolysis may be shuttled across the inner mitochondrial membrane into the mitochondrion (suggestion 2).
If one assumes that the malate-aspartate shuttle is used, then NADH is transported into the mitochondrion as such, and the yield of ATP is the same as for those molecules of NADH generated in the mitochondrion — 2.5 ATP per NADH from the most generally accepted measurement.
However, if one assumes the glycerol phosphate shuttle is used then the reducing equivalents are transferred from NADH to FADH2, from which only 1.5 molecules ATP is produced per molecule.
In summary, using the malate–aspartate shuttle a total of 5 molecules of ATP (2 x 2.5) will be produced from the two molecules of glycolytic NADH, whereas using the glycerol phosphate shuttle there will be only 3 molecules of ATP (2 x 2.5). This gives a difference of 2 molecules of ATP, which would cover the range in the question.
As the relative proportions of the two shuttles varies between tissues, a range of values is actually possible.

I have edited your answer to correct what I felt were ambiguities (initially I thought they were mistakes) and to give it greater overall clarity. (SE encourages improvement of answers.) However, if you don't like my edits you are free to revert them and I will include them in an answer of my own instead.

Thankyou @David for the changes, now it's more clear.

There is a fixed number of NADH and FADH2 produced per glucose oxidizes (assuming we are starting from the beginning of glycolysis) so reason 2 is unimportant for variability. The third reason you are right that the cell uses the proton gradient for additional purposes such as pumping ADP and Pi into the mitochondria by secondary active transport but we know that this requires 1 proton overall per ATP synthesised so this doesn't contribute to the variability in the number. The proton gradient may be used for other transport processes across the inner mitochondrial membrane and this might contribute to variability in the number as we aren't sure how much of the proton gradient is used by these other processes or if these processes are always active. The other reason (probably the most important reason) is that protons can leak back across the membrane without producing ATP and the extent of leakage measured depends on the quality of membrane preparation and the experiment performed (and the equipment used) so there is variation in the amount of leakage and hence the number of protons required per ATP synthesised, resulting in variation in the overall number of ATP synthesised in one round of aerobic respiration.

You are totally spot on with #1. ADP phosphorylation pump is driven by the proton gradient and ADP availability, while the the electron transport chain slows when it becomes too hard to pump protons.
Furthermore, other processes (mostly channels) may use up a proton from the gradient.
The different electron carriers have store different amounts of energy (NADH is more energetic than FADH) and differ in the uncatalysed energy required to release the electron pair, hence why there is not a one size fits all.
NADPH vs. NADH is a special case as NADPH is anabolic (builds), while NADH is catabolic (the electron pair is used for energy generation) and the enzymes in the cell keep it so that NAD+ levels are higher than NADH, and NADPH higher than NADP+. The passing of a pair from NADH to NADPH (a membrane bound transhydrogenase) actually utilises a proton off the gradient to drive it.


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Validity of the August Weismann mouse-detailing experiment refuting Lamarckism
Weismann conducted the experiment — described in Wikipedia — of removing the tails of 68 white mice, repeatedly over 5 generations, and reporting that no mice were born in consequence without a tail or even with a shorter tail. This was intended to refute the Lamarckian idea of of acquired characteristics.
However, surely five generations is too short a time to observe a change in an organ when the fossil record indicates that such changes in animals took millions of years. Was this not known at the time and does it invalidate the experiments?

This is not a site for discussions where people can exchange opinions, it is  site about biological questions, to which people give factual answers. Your question is particularly bad in that you give no literature reference to this experiment so if this question were on topic there would be no way for people to judge. And if this person (whom I know nothing about) was such a novice, why are you so concerned?)

@David It's a very famous experiment in evolutionary biology.

@BryanKrause — But it is not even referenced in the question and the OP is asking about a specific experiment. I am an intelligent scientist in a different area of biology and have never heard of this experiment and have no way of finding out from the question. Hence it is an unsatisfactory question on the basis of SE Biology.

@david "I am an intelligent scientist in a different area of biology" very honestly (no offence), that leaves you with very little right to say that the question is unsatisfactory for Biology.SE. I too belong to the field that you do, yet I know about this experiment. Also, how many questions have you seen on Biology.SE that are satisfactory to all the aspects of biology? As is clear from the wordings in question, it is about evolutionary biology, so biochemists, like both of us, are not supposed to answer this.

@BryanKrause — I am not interested in answering it, I am interested in understanding it. The question is incomprehensible to anyone unfamiliar with the experiment. I am fairly sure the experiment is within my comprehension, but, in either case the question does not allow me to find out. There is absolutely no justification for this and questions that ignore  whose posters ignore requests for clarification should be removed regardless of whether others recognise which Great White Chief is in the OP's mind. I am amazed that you can defend it.

@David That wasn't me you were responding to. My point in noting that it is famous is that if you Google, for example, "Weismann mice experiment" you will get dozens of results in the very top on exactly this experiment, even without any mention of tails, like referring to "Darwin's finches" or "Watson and Crick's (Franklin's) x-ray crystallography" - it's an experiment that many students of biology (even non-majors with just 1 bio course) would know, not just evolutionary biologists. You can still request the OP add some better referencing but your initial comment was quite abrasive.

@BryanKrause — Sorry. On my phone. But my initial comment was well justified. The whole tone radiated the arrogance of ignorance borne out by the poster's inability or unwillingness to document his question. And the title still presumes the answer in a most unacceptable manner. Why has nobody in the magic circle bothered to amend the question so it conforms to the SE model? I suppose I'll have to do it myself.

@another'Homosapien' — my comment to Bryan Krause was meant for you.

@BryanKrause — Actually see you have edited the question, presumably to describe the experiment. If so, well done. I'll fix the title and the last sentence when I have a moment.

I have started making your question acceptable by rewriting the title. Previously it was phrased in a manner that presupposed an answer ("Isn't" or "Wasn't") and involved a subjective emotive adjective — "senseless". As such it comes under the category of "What types of questions should I avoid asking?" — rant in disguise: “______ sucks, am I right?”. The revised version is neutral — "validity" — and actually indicates, for those not familiar with this Weismann, what the experiment was about.

I have now added a reference to the question (one shouldn't have to look for such in answers), added the purpose of the experiment and a link to Lamarckism, and phrased the query in a measured manner. If what I have written is not completely correct, could one of the elite take the trouble to amend it please. Rolling back to the previous version would do nobody a service.

@David I appreciate the changes you've made in the question. I'm just learning how to question at SE. Also, I'm an 11th grade student from India.

@David also, you'd find it surprising that this Germplasm experiment done Weismann is taught to every high school student here, right in the 11th grade. So, i presumed that it's famous enough (no offence)

@david oops, I wasn't defending the question. The question is, obviously, poorly written. All that I was saying is that 'I am an intelligent scientist in a diferent area of biology' doesn't necesaarily give an explanation for you saying that the question is about discussion and not factual answer. I didn't know I was indirectly defending the question (；一_一)

If you are reading this after 31st July 2017 it will seem somewhat disconnected from the question. This is because the question has been extensively edited since I wrote this answer.

Anyone who is interested in the work of August Weismann should start by reading the corresponding Wikipedia page.

Ernst Mayr ranked him as the second most notable evolutionary theorist of the 19th century, after Charles Darwin.

As far as the mouse tail experiment is concerned, we learn that Weismann was concerned with disproving Lamarckianism, and that:

Weismann was aware of the limitations of this experiment, and made it clear that he embarked on the experiment precisely because, at the time, there were many claims of animals inheriting mutilations (he refers to a claim regarding a cat that had lost its tail having numerous tail-less offspring).

My grandfather used to claim that his mother was frightened by a bear whilst pregnant, which was was why he was born with bare feet but that's more likely to be due to an epigenetic effect I suppose.

Added later in response to Remi.b
I see that Charles has already addressed this to some extent, but since I have already done the research I'll post what I found:
from August Weismann, Essays Upon Heredity. Clarendon Press, Oxford, 1889
(Volume 1, Chapter 8, p. 431)

But now, after this little digression, let us return to the transmission of mutilations.
We have seen that the rudimentary tails of cats and dogs, as far as they can be submitted to scientific investigation, do not depend upon the transmission of artificial mutilation, but upon the spontaneous appearance of degeneration in the vertebral column of the tail. The opinion may, however, be still held that the customary artificial mutilation of the tail, in many races of dogs and cats, has at least produced a number of rudimentary tails, although, perhaps, not all of them. It might be maintained that the fact of the spontaneous appearance of rudimentary tails does not disprove the supposition that the character may also depend upon the transmission of artificial mutilation.
Obviously, such a question can only be decided by experiment: not, of course, experiments upon dogs and cats, as Bonnet rightly remarks, but experiments upon animals the tails of which are not already in a process of reduction. Bonnet proposes that the question should be investigated in white rats or mice, in which the length of the tail is very uniform, and the occurrence of rudimentary tails is unknown.
Before this suggestion was made, I had already attacked the
problem experimentally. Such a course might, perhaps, have been more natural to those who maintain the transmission of mutilations, to which I am opposed. Although I undertook the experiments expecting to obtain purely negative results, I thought that the latter would not be entirely valueless; and since the numerous supporters of the transmission of acquired characters do not seem to be willing to test their opinion experimentally, I have undertaken the not very large amount of trouble which is necessary in order to conduct such an experimental test.

Nice quote +1. Would be great an original's Weissmann's quote as well. Also, you grandfather was a funny guy!

@Remi.b Thanks. I've added a quotation, as you suggested - it's rather long. The last sentence is a great put-down.

[D]oesn't it take around millions of years for an organ to disappear or appear

No, not necessarily. But whether this claim is true or not is not so much the point of your question.
False Negative Result
Weismann did not observe an effect of cutting a rat tail on the length of the tail of rats at birth. It is what we call in statistics a negative result. Any negative result can be a true negative (cutting rat tail really does not affect the length of the tails in the offspring) or a false negative (maybe Weissmann had too a small sample size or maybe the experience should have been conducted on a longer time scale).
This is true for any experiment. It is the basis of the philosophy of knowledge. You can't show evidence of absence, you can only show evidence of existence. So, if an effect does not exist (if the result should be negative), then the only thing one can do is to fail to show evidence for the existence of this thing.
So, Weismann was in no way naive. Just like any other scientist, he just accepted the very nature of how knowledge can be acquired about the world. Actually, from @AlanBoyd's answer, Weissmann did comment on the limitations of his study.
This section was more about philosophy of knowledge than about biology. You should maybe learn a bit more about philosophy of knowledge, philosophy of science and typically about some key concepts such as Russel's teapot and evidence of absence.
So was it a false or a true positive
It was a true positive! We today understand a lot about genetic mechanism of inheritance and know that modifying the phenotype will not affect the DNA sequence (although it may affect the surrounding of the DNA sequence but this is a story for another time).
Introduction to genetics
You might want to follow an intro course such as Khan Academy > Classical and molecular genetics, Khan Academy > DNA as the genetic material and Khan Academy > Central dogma.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Can people with AIDS/HIV be vaccinated?
If there is no immune system,it  seems like vaccines wouldn't do much since there is no adaptive immune system to develop antibodies and memory cells. But can people with AIDS/HIV still be vaccinated? It is expected that a normal person will have antibodies to attack the minimal infection produced by the vaccine and generate memory cells, but without an immune system I expect vaccines to be deadly.
Is that right?

Can people with AIDS/HIV be vaccinated?

Yes. Immunization is an important part of the overall treatment strategy for HIV positive individuals. HIV infection is a risk factor for a number of vaccine preventable infectious diseases. Immunization in these patients is particularly important because of their increased risk of developing disease. (See Cecil Medicine Ch 396)
Can the immune system still mount a response to the vaccine?
Yes. HIV infection does lead to a decreased immune response. Though the primary deficiency is a decrease in both CD4+ (helper) T-cell count and function, there is, perhaps consequently, B-cell dysfunction as well. This would suggest that vaccines are less immunogenic. When this is studied directly, as would be expected, we see that vaccines are less immunogenic, but they are still effective.
Which vaccines are given?
Specific recommendations are based on both the age of the individual and their immune status. As a rule, vaccines are more effective when given early in the natural history of an HIV infection or after immune reconstitution with HAART, but there is some effectiveness and little risk of heat killed or subunit only vaccines even in highly immunosuppressed individuals. While live attenuated vaccines are contraindicated in individuals with a CD4+ cell count below 200, these vaccines are given routinely to other HIV positive patients. Current guidelines are found here. Here is the main figure from those guidelines:

Can people with HIV still be vaccinated?

No (most of the time) if the vaccine is an attenuated vaccine, this means it contains living organisms that have been modified in order to reduce their virulence. The reduction would keep a healthy individual unharmed while still inducing an immune response to form antibodies, however it is considered dangerous to administer these kinds of vaccines to HIV positive people. Some physicians will decide to administer these kinds of vaccines if the patient has had excellent control of his/her disease and is strong enough to take for example, the influenza virus vaccine without any major complications.
Yes if the vaccine is not an attenuated vaccine. Being HIV positive doesn't mean "no immune system" right away. The damage to the immune system goes in function with the viral load and the CD4 count; if the viral load is low the HIV positive individual can still benefit from vaccination, moreover he should be vaccinated because he is more exposed to infections than an average person.

source: HIV InSite, University of California San Francisco.
I would suggest also reading more about CD4 count in HIV patients and viral HIV load.

I think I don't understand. If the vaccine is atenuated, they can't be vaccinated; but if the vaccine IS NOT atenuated they CAN be vaccinated? It's the opposite of what I would expect.

@Gabriel the missing information here is that the alternative to live attenuated is killed or antigen component only. Vaccines that are not live vaccines cannot replicate in the vaccinated individual. There are no non-attenuated live vaccines.

To clear things up vaccines that don't belong to the group of attenuated vaccines do not contain any sort of living organisms and use other agents to induce immunization (polysaccharides, inactivated toxoids, etc.) and hence are safer to use in an individual with a compromised immune system.

@DeNovo, there are no non-attenuated live vaccines any more.  The original vaccine for smallpox was the live cowpox virus.

@Mark vaccinia, in that instance was effectively an attenuated variola.

A person with AIDS cannot be vaccinated. The immune system is no longer functional and is unable to mount an immune response to your vaccine.
If the vaccine is a "live vaccine", the person will get a dose of viruses that body can no longer fight against. And the live vaccine would probably give the AIDS patient an infection of what the vaccine was suppose to protect against
However if the vaccine is an attenuated vaccine (which is the case for most vaccines made today), then all your be introducing into the body is parts and pieces of a virus or bacteria. These piece can trigger an immune response in a healthy person but as they just pieces, are not a live cell or a functional virus. So in a person with AIDS, the attenuated vaccine will be harmless.
A person with HIV can be vaccinated. The HIV virus is in the body multiplying. However the immune system while damaged is still functional.

"if the vaccine is an attenuated vaccine (which is the case for most vaccines made today), then all your be introducing into the body is parts and pieces of a virus or bacteria."

It sounds like the opposite of what the other answer said.

Most vaccines contain dead virus today. Attenuated viruses are alive (as far as you can say that for a virus) but usually do not cause full blown disease. An example for this is the oral polio vaccine.

With genetic engineering, its not possible for the immune system to be "completely" non-functional. This is because the body is constantly producing immune cells from non-terminal differentiated cells. These cells are almost never specifically targeted. Whatever is left can, with time, clean up the infection.


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Very frequent multiple births in humans
18th century Feodor Vassilyev is said to have had children by two wives, each of whom only ever had twins, triplets or quadruplets. His first wife has 16 sets of twins, 7 of triplets and 4 of quads; his second had 6 sets of twins and 2 of triplets. Is there any known plausible biological explanation for this, or do we have to dismiss it as a fabrication?
I could understand a woman's body being unusually susceptible to multiple births. I can't find information on whether these women tended to have monozygotic or polyzygotic offspring, but neither option seems unviable to me. However, since it's unlikely two of Feodor's sexual partners would share such a trait, one would think to attribute it to him. Presumably there would have to be a mechanism by which paternal DNA can trigger embryo fissions, in which case I imagine the offspring would be polyzygotic.

The probability of having twins is hereditary (see this non-peer review source of information)

Risk factors for dizygotic twinning are related to multiple follicular development, and include maternal family history, ethnicity, geography, maternal parity, maternal age, and, of course, use of assisted reproductive technology. There may be a genetic component to monozygotic twinning as well, but that rate is fairly consistent across populations. Other risk factors, such as diet and supplementation, have been proposed, but the data are less robust. There are some interesting studies demonstrating geographic clusters of twinning, but these tend to be demographic clusters that are associated with other risk factors.
Though a higher risk of twinning can be transmitted from a father to his daughters, the father's family history of twinning is not a significant risk factor (for his own children to be twins). To clarify -- if a man has a family history of multiple births, his children are no more likely to be twins than the general population, but his daughers are more likely to give birth to twins. This study is one example of the studies that have shown a significant independent association between maternal family history and twinning, with no significant independent association with paternal family history.
As far as the case of Feodor Vassilyev is concerned, many people have lived on this earth, making very unlikely events in a single instance more likely to have ever occurred. I would say this case is either a hoax or a rare chance event. There is no modern data I'm aware of that would support a paternal genetic reason that this particular man produced so many multiples.


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Which vaccines are damaged by freezing?
I have noticed that many of the freeze-sensitive vaccines are antigen only vaccines, for example Hib, pneumococcus, and tetanus vaccines. Why are these vaccines damaged by freezing? Are inactivated or killed vaccines like IPV damaged by freezing? How about live vaccines?

Are vaccines made of non-antigens too?

@Tytoalba some vaccines are made of purified antigen. Others are made from an entire pathogen. I expect the OP might actually mean inactivated/killed vaccines, vs. live attenuated vaccines (IPV is an inactivated vaccine, not a purified antigen). eyadoalshaikh, if you could edit your question to clarify, that would be helpful.

OP: I've edited this question to make it answerable and resolve the comment above. Feel free to roll it back or further clarify if you'd like :)

many proteins are damaged by ice crystal formation when they freeze in an aqueous solution.  https://www.ncbi.nlm.nih.gov/pubmed/12673768

In order for a vaccine to work, antigens in the vaccine must maintain their shape and charge. Freezing a vaccine, particularly vaccines that contain aluminum, can cause antigens or other important constituents of the vaccine to aggregate. This may be what prevents them from working correctly, though we don't know for sure, and it may be something else about the freeze-thaw process. The main thing that we know, though, is that (typically in animal models, as in the last reference) for certain vaccines, if you allow them to freeze, they don't produce a sufficient immune response.
You can look at this very large table of data about which vaccines are freeze stable and which are not.  There are a few patterns to this, as the OP seems to have noticed.

Aluminum adjuvant: Any vaccine that uses an aluminum adjuvant (a chemical used to enhance the immune response) will be damaged by freezing. Polysaccharide vaccines and other purified or recombinant antigens are more likely to require an adjuvant. This is one of the reasons antigen only vaccines are more likely to be freeze sensitive. Some antigen only vaccines can be frozen themselves, and reconstituted with the adjuvant prior to administration (for example, some Meningitis polysaccharide and polysaccharide protein conjugate vaccines).
Live attenuated vaccines: Almost all live attenuated vaccines are freeze stable (e.g., MMR, oral polio). The only ones that aren't, as far as I'm aware, are influenza vaccines: flumist and the live attenuated H1N1 influenza A vaccine. This may or may not just be a precaution, as I'm not aware of immunogenicity experiments that demonstrate freeze sensitivity.
Inactivated vaccines: Most killed or inactivated vaccines are sensitive to freezing. IPV is one of them. Rabies is an important counterexample. This is entirely speculation, but since many of these vaccines are formalin inactivated enveloped viruses or bacteria with cell membranes, freezing a perforated cell membrane may further damage it's antigenicity.

You can read about the basic principles of vaccination (e.g., how a vaccine works, what an adjuvant is, when you need it, etc) in Abbas Basic Immunology Chapter 8, and Murray Medical Microbiology Chapter 13.


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Can cerebrospinal fluid pass through the pia mater or ependymal cells of the ventricles?
During a lecture, a professor commented that the cerebrospinal fluid and interstitial fluid of the brain parenchyma have similar composition because they can exchange with one another. This struck me as surprising because I was always under the following impressions:

pia mater is essentially impermeable to fluid (therefore CSF from the subarachnoid space could not penetrate it to be in a passive exchange with the underlying brain tissue)
the ependymal cells of the ventricles (besides the choroid plexus where blood is 'pushed' through) is impermeable to fluid...i.e. CSF cannot leave the ventricles to be in passive exchange with the surrounding brain tissue.

Could someone please confirm if these two impressions are correct, and, further, if they are correct, could someone confirm the accuracy of the professor's claim and by what means it is true?

Both the blood brain barrier and the blood CSF barrier tightly regulate the CNS fluid interstitial fluid environment of the CNS. You, however, are talking about a different barrier, the barrier formed by the pia mater, sometimes called the brain/CSF barrier. This barrier is less well studied. It does appear to prevent transport of particulate matter and red blood cells, but allow the passage of immune cells and small molecules. In addition to your professor's statement that the composition of CSF and brain interstitial fluid is similar, intrathecal injection directly into the CSF in the subarachnoid space provides an effective way to deliver drugs with CNS action, suggesting the pia mater does not effectively restrict small molecules (see Goodman and Gilman's The Pharmacological Basis of Therapeutics Ch 2).

Well then, an even better question is, "Okay, so it makes it past the pia mater. How does fluid then make it past the glia limitans?"

@S.Cramer there's definitely a good question in there. I'd recommend writing it up and asking it. You would, of course, want to phrase it more specifically than "How does fluid make it past the glia limitans?"


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Occurrence of the theoretical thymine enol::guanine base pair in DNA
DNA polymerase has a proofreading exonuclease activity that can remove incorrect tautomers in the DNA template or incoming base. In theory the enol form of thymine can form three hydrogen
bonds with guanine. Why is this base pair not favored in nature?

This is surely just a chemistry question — "why is the keto form of thymidine more stable than the enol form?" If there is almost no enol form there can be almost no base pairing involving this form.  In which case your question should be migrated to SE Chemistry. Or do I misunderstand you?