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How does the white blood cell ‘hunt’ the bacterium?
There's this mildly viral video which reportedly shows a white blood cell hunting a bacterium:
https://www.youtube.com/watch?v=JnlULOjUhSQ
What I don't understand is - at this scale, how does the white blood cell "know" to chase the bacterium and where to go? How does the bacterium "know" to run? Are they constantly shedding some bacterium-specific molecules that the white blood cell reacts to? Wouldn't the bacterium soon run out of molecules that way? Is there some other mechanism? What's going on here?
Note - I'm a total newbie; my own biology/chemistry knowledge is high-school level at best (and even then I graduated 16 years ago), so please try to explain it simply. :) I'm OK with looking up unknown terms on Wikipedia, but I probably won't be able to comprehend too much jargon. Thanks! :)

Sadly if you want a scientific answer, the question is too broad. We would have to delve into motility, immune and non-immune signaling, membrane biology of pathogens and commensals, the repertoire of immune cells, and the entirety of many kinds of response. For a rudimentary answer, try finding inspiration here, an article in Scientific American from 1998, and here on proteins that work as scouts.

@SPr - So... the gist that I get from these three links is that the invading cells do shed material all the time, and it's this material which leaves a "trail" for the white blood cell to follow. The invading cell in the video is probably not "running away" but rather moving randomly, and perhaps being pushed a bit (via fluid dynamics) by the following white blood cell.

@SPr - The exact details of losing the material and detecting it are, of course, complicated (and it seems there are many variations when it comes to the technical details), but that's the general principle.

Water (or viscoelastic fluids like blood) is not static; water molecules are constantly moving or vibrating. That poor little diplococcus isn't swimming away from the white blood cell; it's simply being moved by kinetic forces. The bacteria in this video are being pushed by the fluid in front of the moving phagocyte, making it appear to be 'running away'. The WBC is capable of movement and what you're seeing is chemotaxis. While it's more complicated than this, no, the bacterium won't run out of whatever it is that the WBC is responding to.

@anongoodnurse - That poor little diplococcus isn't swimming away from the white blood cell; it's simply being moved by kinetic forces. Yes, I suspected as much.


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Share immunity by kissing?
How can you get a cold by kissing someone who already has it, but you can't get their antibodies by kissing them after they recover? Or can you?

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

Some questions to ask yourself: What are antibodies and where are they found? What causes colds and how are they spread? From the answers to these basic questions you should be able to see that the answer to your question is relatively straightforward ...

Antibodies are in the blood, not in the saliva, whereas herpes virus is secreted to saliva so you get infected through the contact with mucosa.

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What is an allele?
According to the entry for allele in Wikipedia:

“An allele is a variant form of a given gene, meaning it is one of two or more versions of a known mutation at the same place on a
  chromosome.”

However on Nature Scitable the definition of allele it states:

“Humans are called diploid organisms because they have two alleles one
  from each parent.”

These definitions disagree: one states alleles arise due to mutations on a chromosome, whereas the other states that they are the forms of a gene on a  homologous pair of chromosomes.
So what is the correct definition of an allele?

I have edited your question, especially to include links to the sources of your quotations. In future questions be sure to do this yourself. Also please complete the Tour and read the Help on asking questions.

The Wikipedia definition is poorly worded, but I don't see a contradiction — alleles are specific instances of genes. This is analogous to isotopes in nuclear chemistry — every atom exists as a specific isotope. I'm voting to close because this seems to me like a very basic question that could be answered by looking at any decent undergraduate textbook or on a site like Khan Academy.

@tyersome — Correction. You are not voting to close, because you have not yet accrued the privilege (3000) to do so. You are suggesting that the question should be closed.

The question takes one sentence in the Nature Scitable article about alleles out of context. The statement:

“Humans are called diploid organisms because they have two alleles one
  from each parent.”

is not the actual definition of allele in the article, which is in the first sentence:

“An allele is a variant form of a gene.”

Rather, it is part of an explanation of the situation for variants in humans. (It is not meant to be a definition of diploid, either.)
This is perhaps clearer in the definition for allele given in the respected undergraduate text, Alberts’ Molecular Biology of the Cell, where the same two ideas follow one another directly.

Allele
  One of a set of alternative forms of a gene. In a diploid cell each
  gene will have two alleles, each occupying the same position (locus)
  on homologous chromosomes.

The first sentence is the definition, the second sentence provides an example of the variants in diploid cells.
As the Wikipedia entry explains, the word allele is derived…

…from the Greek prefix ἀλληλο-, allelo-, meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, allos (cognate with Latin alius), meaning "other".

Thus it encompasses the idea of variation or difference (rather than gene homology) which is what it was coined to describe.
FOOTNOTE
It is possible to refer to alleles that are identical, but only in a context where variation is possible. Consider the four possibilities for the mutation, m, of a wild type gene, wt.
1. wt wt
2. m  wt
3. wt m
4. m  m

We can refer to 2 and 3 as having one mutant and one wild-type allele, and 4 as having two mutant alleles (or both alleles mutant). But what about 1? It is natural to refer to this as saying both alleles are wild type, and indeed almost impossible to avoid referring to them as alleles. They are both normal, and therefore not strictly variants, but they are alternatives to the mutation at this same position.

I'm clearly missing something, but I don't see the problem.  My understanding is that an allele is a specific instance of a gene.

Apologies for missing the quotation out of context in the question. I have recast my answer extensively to address this. The person that upvoted the original answer is welcome to retract his vote.

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Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?
I read this article https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/ and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the very same thing that micro RNA and short interfering RNA does- cleaves synthesised mRNA strands by attaching to the complementary part of the mmRNA strand, and the restrictive enzymes combine to this RNA and cleave it. I don't see how the CRISPR system is any different or better...
Thank you in advance :)
EDIT: Also, does anyone know whether Cas 9 cuts both DNA strands at the same place, or whether it leaves 'sticky ends'? Thank you.

answer is that CRISPR targets DNA, while siRNA targets RNA. siRNA is incapable of creating mutations

@aaaaaa Thank you for your reply! I see why CRISPR is important in terms of it targeting DNA rather than RNA now! But I was wondering if you could elaborate on siRNA being incapable f creating mutations... From what I understand, CRISPR only cuts DNA at a specific location, and a different system has to be used to insert a new gene section...

@21joanna12 the CRISPR/Cas9 systems being used commercially and in academics have been cobbled together to cut the DNA and deliver a new template sequence into the cut, not only allowing for sections to be removed, but sections added or mutated as well. That is why it's so revolutionary - it's all based on the gRNA. Just change its sequence, and you change your target. (Hopefully)

The CRISPR Cas 9 system is used to introduce insertion or deletion in a genomic sequence not mRNA.
https://www.addgene.org/CRISPR/guide/

this is not an answer. CRISPR/Cas9 system originally is sort of immune response

@aaaaaa The article that 21joanna12 shows mentions the CRISPR/Cas9 system as a research tool to edit genomic DNA, doesn't it?

Whatever Cas9 is, it was and is never relevant to the cleaving of RNA, only DNA. This is a perfectly valid answer.

this is not high-quality answer

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Is phosphofrucrokinase1 PFK1 found in the liver?
I am trying to understand glycolysis control. One thing I am stuck on is whether there is PFK1 in the liver, or only PFK2.
Edit: As far as I am aware, there is no pfk2 in muscle cells, only pfk1. This is entirely under allosteric control of ATP/AMP ratio to control the rate of glycolysis compared with gluconeogenesis. In the liver there is pfk2 which ensures that there is hormonal control of the rate of glycolysis. However is there also pfk1 so that there is a rate of glycolysis sufficient for liver cells to survive, irrespective of the hormone signals?

What research have you done on your own to try and answer this question? A simple Google search using the title of your question will quickly answer it. Homework questions and questions that show little or no prior research effort are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.

I have read quite a lot about this, but Google was not answering my specific question. I will edit my question with the research I have done so far and the specific point of my confusion.

If you read the Wikipedia article on PFK1 that came up at the very top of the Google search I mentioned previously, the very first paragraph in the body of the article answers your question.

PFK2 (PFKFB2) doesn't appear to be present in the liver. The two sources I have used agree that PFK1 (PFKL) is present in the liver. They diverge regarding the levels of expression of PFKL.
This is the expression of the three 6-phosphofructo-1-kinase and one 6-phosphofructo-1-kinase genes according to the Human proteome map (mass spectrometry).

I can't see a huge dynamic range across the proteins in the liver, although the liver specfic gene (PFKL) is the 'winner' there.
The Human protein atlas (immunohistochemistry) is also a useful source for information and it provides a very different answer. Using immunohistochemistry it shows robust signal for PFKL but not for PFKFB2 in the liver.

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Ingredients in Pfizer vaccine
The ingredients in the Pfizer vaccine have been listed in a number of websites, including government healthcare ones. This site claims that the list includes ALL of the ingredients of the vaccine. Considering that things like sodium chloride have been included on the list, that would seem to suggest that it is indeed comprehensive. The ingredients list is the following:

mRNA
Lipids (including ((4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis(2-hexyldecanoate), 2 [(polyethylene glycol)-2000]-N,N-ditetradecylacetamide, 1,2-Distearoyl-sn-glycero-3- phosphocholine, and cholesterol)
Potassium chloride
Monobasic potassium phosphate
Sodium chloride
Dibasic sodium phosphate dehydrate
Sucrose

I cannot help but feel suspicious about whether this truly is the full list. For a synthetic medicine, I would expect a much longer list with stabalisers, peservatives, adjuvants etc.
So my questions are: Is it reasonable to assume that this truly is the entire contents of the vaccine, sans water? And, where are the adjuvants? There is no aluminium here.
EDIT: I feel like I have been downvoted because my post gives the impression that I am an anti vaxer. I emphasise I am not. I just really wish to know what is inside these vaccines and how they work, and why the things that I expect to be inside are not. Because vaccine are such a sensitive topic now, it makes sense for anyone posting iformation about them to be very careful about what they include. This extends to publishing incomplete ingredients lists, which are not explicitly said to be complete (so there is no legal repurcusiion) although the wording makes it seem like such. I have no issue with some aluminium being present in vaccines. People consume aluminium all the time when drinking soda pops from cans. But, I do want to be fully aware of everything that is inside of them and how they work, and I think it is reasonable to when you are putting something inside of yourself. As someone with a family history of severe autoimmune conditions, I am also concerned about the presence of other adjuvants and I think justifiably so. Again, this is just to say that I am not an anti-vaxxer at all, but I am all for knowing what is inside a vaccine and how they work. And unfortuantely the scare around vaccines means that it can be hard to get complete information about them, because people with little scientific background may be scared by what they see in a complete list as they don't understand it. Thus it is discretely censored, and I understand why.

An adjuvant increases the immune response to some antigen. No one wants any immune response to any component of these vaccines; including an adjuvant would be silly. I don't see how this question can be answered with any biology, though - you're basically just expressing skepticism about a manufacturer's ingredient list. They'd get in quite a bit of trouble with regulators if it's incomplete.

@BryanKrause I assume you downvoted, which I think is unjustified. I am not skeptical about the manufacturer's ingredients list. I have not seen this published by Pfizer themselves. Rather, by other websites. The reputable ones have not claimed that this is the entire list and could merely be listing the things that they believe are important and/or would not scare the public. Only a non-reputable one has claimed that this is the entire list.

Secondly, I think it is perfectly valid to question why there are not more preservatives/stabilisers (the lipids are some stabilisers, and I think the sucrose acts as a preservative or stabiliser here too). AND, why there are no adjuvants I recognise. As is mentioned in the website below, "many vaccines contain aluminium salts... they act as adjuvants" https://vk.ovg.ox.ac.uk/vk/vaccine-ingredients#Added%20ingredients

The point is that one wants to amplify the immune response such that there is one towards a small amount of viral material. Now I do not know whether the white blood cells directly detect the viral mrna and create some protein/rna 'antibody' against this, or whether the mrna gets into cells and is expressed as an antigen which the white blood cells make antibodies for. I presume it is the latter, since the mrna encodes the viral protein spike specifically. In any case, since little material is injected, amplifying the immune response would be beneficial.

@Meep, I've answered your question. Though it seems like a better question to ask (and the crux of your inquiries) is "Why do mRNA vaccines not require adjuvants, but other vaccine types (like inactivated influenza vaccines) often do?"

@acvill Thank you for the suggestion. It seems like this may be a better way to go, as I think I am getting downvoted as people think I am just another anti vaxer looking for reasons to scaremong people. Not the case at all!

@Meep You do not want an immune response to the lipids or mRNA or any ingredient in the injection. You ideally want the mRNA to enter cells without the immune system knowing anything about it, you only want an immune response to the spike protein that can be used to identify active virus particles. You may not be an anti-vax person but you are really carrying a lot of their baggage.

@BryanKrause Ok thank you for telling me that the immune response is meant to be towards the expressed antigens and not the mrna (I would never have thought of the lipids triggering immune response). This may be why the mrna vaccines do not require adjuvants, just a longer amount of time to create enough antigens from the mrna templates to have a sufficiently large immune response.

@BryanKrause Also, yes it may be the case that I carry anti-vax baggage. I come from a family of scientist turned anti-vaxers. However I am trying to educate myself. My questions are ones of genuinely trying to understand vaccines, and formulate my own opinion as to whether they may be harmful in certain circumstances or no (obviously mass use of vaccines rules out severe harmful effects in the general population). Being attacked like this makes me scared to ask whether it is harmful to the cells which the mrna enters and which express the antigens. From my knowledge of the immune response

these would be detroyed by the white blood cells. I think it is a valid question to ask. I know it is no issue to lose a few cells, but if the mrna gets into many cells, or the immune response goes awry because some cells are expressing thsi antigen, then it can be harmful.

I don't see the point of posting a likely disreputable site and essentially asking "is this right", when one can just access the official materials descriptions from the FDA, the manufacturer, and so forth.  You also baselessly claim "Thus it is discretely censored, and I understand why"  Those are the reasons for my downvote.

@Meep Being destroyed by the immune system is the fate of every infected cell that is recognized as such cell. So you lose a few cells because of the vaccination, however these are easily replaced. The same process (but on a ways bigger scale) happens throughout your whole body (and not only around the injection site) when you are infected with SARS-CoV-2.

@Meep Generally, there is no need for an immune response against mRNA. Free ssRNA is very unstable in cells because of RNAi. There are plenty RNA-dependent RNA polymerases floating in cells that detect (both endogeneous and exogeneous) free ssRNAs, such as mRNAs. These synthesise the complement, and the dsRNA is then rapidly degraded because dsRNA is never functional in human cells. In fact, this system probably evolved as a defense mechanism against infections from ss/dsRNA viruses.

@Meep And, if anything, the production and publication process around vaccines effective (or non-effective) against SARS-CoV-2 shows that there is no discrete, indiscrete or whatsoever censorship. The fact that potential side effects are widely publicly discussed that even occur less often in the vaccinated population than in the non-vaccinated population suggests that there could not be more transparency. In fact, I consider the development and publication of these vaccines to be examplary for a very transparent process (at least on the side of scientists).

@Meep For your interest in scientific evidence on the subject of vaccinations, I suggest you have a look at this excellent blog: https://www.skepticalraptor.com

The source for the linked  article is this FDA factsheet, which gives the following description for the Pfizer-BioNTech COVID-19 Vaccine (emphasis mine):

The Pfizer-BioNTech COVID-19 Vaccine is supplied as a frozen suspension in multiple dose vials; each vial must be diluted with 1.8 mL of sterile 0.9% Sodium Chloride Injection, USP prior to use to form the vaccine. Each dose of the Pfizer-BioNTech COVID-19 Vaccine contains 30 mcg of a nucleoside-modified messenger RNA (modRNA) encoding the viral spike (S) glycoprotein of SARS-CoV-2.
Each dose of the Pfizer-BioNTech COVID-19 Vaccine also includes the following ingredients: lipids (0.43 mg (4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis(2-hexyldecanoate), 0.05 mg 2[(polyethylene glycol)-2000]-N,N-ditetradecylacetamide, 0.09 mg 1,2-distearoyl-sn-glycero-3-phosphocholine, and 0.2 mg cholesterol), 0.01 mg potassium chloride, 0.01 mg monobasic potassium phosphate, 0.36 mg sodium chloride, 0.07 mg dibasic sodium phosphate dihydrate, and 6 mg sucrose. The diluent (0.9% Sodium Chloride Injection, USP) contributes an additional 2.16 mg sodium chloride per dose.
The Pfizer-BioNTech COVID-19 Vaccine does not contain preservative. The vial stoppers are not made with natural rubber latex.

The factsheet does not mention adjuvants.

Thanks very much for this. The wording is quite waffly though. They do not claim to list all of the ingredients, just other stuff that the vaccine contains. Considering the concern over aluminium in vaccines, they might have reason not to mention it, but have themselves covered by not claiming it isn't there.

You expect a statement like "This is a comprehensive list of ingredients."? No one does that. The wording is succinct, not waffly. The FDA has no reason to exclude ingredients from their fact sheets (e.g. note the mercury content of Fluzone is clearly stated).

I am not. At all. But I do expect more explicit wording. Thank you in any case.

I've edited my comment, sorry for the presumption of anti-vax sentiment. We get a lot of that here. Additionally, the hep A vaccine factsheet clearly states its aluminum content.

Note that the temperature handling requirements act as a preservative, as likely does the sucrose content of the vaccine (dilution occurs only just before administration).  The reason for the lack of adjuvants is covered in the comments under the question.


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Schiff Base in Enzyme Mechanisms
Can a schiff base stabilize the transition state and form an intermediate as in covalent catalysis with a substrate in the same reaction? Basically I'm wondering if a schiff base creates a ping pong reaction.

I think the answer to this one is a most definite 'yes'.  Almost all aminotransferases proceed via a ping-pong mechanism where a schiff base involving pyridoxal phosphate is an obligate intermediate, and where  the 'half-reation' modified enzyme form has often been isolated. An example is aspartate aminotransferase.
Let's also remind ourselves that a transition state is not an intermediate on the reaction pathway (in the TS bonds are in the process of being broken and formed), but may resemble one.


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Where do gut bacteria come from in different organisms
We know that some of the bacteria in our gut come from the food we eat and our environment. I want to know if there is evidence of bacteria being transferred from the mother to her fetus or from the mother to the eggs.
I'm currently working with insects that have plastic-eating bacteria in their gut. They are raised in isolated spaces so those bacteria would have to come from the bran they eat or from their mother. I'm a physics student interested in biophysics so my biology knowledge is still a work in progress. Thank you.

Human babies get coated in birth canal fluids and vaginal microbes as their first encounter with the microbial world, and they absorb 40% of gut microbes from milk.,,, Insects come from eggs and may have no contact with the parents, so you should say which insects you are working on.

For technical information on the subject, perhaps start with "vertical transmission insect symbionts" on google, which will lead to you to a variety of info's. Studies for symbionts of lice, fruit flies, mosquitos, termites, isopods, stinkbugs, butterflies and planthoppers.
Insect Symbiosis Vol 3 page 145 states:
Insects have been shown to use transovarian, egg smearing, and coprophagy, transmission, else entirely from the environment at every generation. There is a list of summaries of different insects that use different methods.
this also has masses of information:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2967712/
Samples for large insects are taken with tweezers, small insects can be dunked in alcohol and then microbes are extracted.
Microbia RNA can be checked for evidence if the symbionts come from the parents. You can probably figure out a variety of methods for transmitting your insects symbionts, simply applying the wanted gut bacteria to the substrate of new cultures. I expect it can work in between species. you can try smearing eggs too.


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Is copy number variation dynamic?
Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need to make is that it is static.

the answer to this question depends on the scale you're looking at: individual cells? tissues? organisms? tumors?

@MichaelKuhn Good clarification point, thanks for bringing it up. I'm thinking of changes in the output of whatever technique is measuring CNV--e.g., in situ hybridization, etc.--in a given organism. I assume that data is averaged over multiple cells, but I'm not taking about variance due to the averaging process. You're tumor point is good as well, as I'm interested in variation the cancer genome. Does that help?

Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, ("Is there any evidence showing that [the rate of] copy number variation changes over time?"), then yes, there is indeed.
The rate depends on many factors including which mechanism and which organism and which region of the organism's genome and as @Michael wrote, also what scale (et. al.) is under consideration too.
So your assumption that the rate is static should probably be stated explicitly.
Nature Reviews Genetics 10, 551-564 (August 2009) | doi:10.1038/nrg2593

Thanks, Kevin! That's mostly what I was looking for, and it looks like this review will give me some more information as to how it works. As a side note, I'm interested in modeling regulatory relationships in time series of expression data, but was curious as to whether, if I could get CNV data for my model as well, if those data could be assumed to be fixed over time, or if that would just have to be a limitation of my approach.


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Neuroscience of temperature regulation and perception
The hypothalamus is known to be important in the regulation of body temperature, but I'm curious whether anyone knows about the neurocircuitry of perceived temperature. It seems like there could be a difference between how warm/cold someone feels and the temperature to which their body is trying to adjust. Intuitively, I'd imagine that any apparent difference in these  has to do with some sort of delayed feedback that is experienced before the autonomic nervous system can kick in. Does anyone know something more about this?

I've found a good resource for this--an open-access review by Nakamura, "Central Circuitries for Body Temperature Regulation and Fever." In it, the author provides a nice summary figure of the circuitry involved in temperature regulation (see below). As I suspected, the hypothalmus is pretty central to temperature regulation. I had forgotten about the involvement of the peripheral nervous system in responding to environmental temperatures, which, now that I think about it, makes some amount of sense, but is still pretty interesting. It appears that there's a difference in the specific circuitry and neurotransmitters used in responding to warm and cold temperature (especially GABA v. 5-HT), so I think a reasonable hypothesis regarding the basis of individual differences in the perceived temperature of an external environment might be differences in peripheral 5-HT systems (in addition to differences in body composition). Perhaps someone with a background in the peripheral nervous system could speak to this better than I can, but single nucleotide polymorphisms (SNPs) leading to differences in central 5-HT systems has been an active area of research in the neuroscience community of late (e.g., Nordquist & Oreland, 2010, Gonda et al., 2010), which I think lends some face validity to this idea.

Nice schematic!

@nico Thanks, I thought so too! Sadly, I cannot take credit for creating the figure!


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Significance of the resequencing of the chimpanzee genome
Introductory remark: I am not a biologist, but a somewhat knowledgeable layperson.
I have been told that sequencing of chimpanzee DNA until recently has been done almost exclusively using human DNA as a “template” to help piece together short DNA sequences. The similarity that emerges to human DNA could then perhaps be somewhat misleading, as the structure of human DNA affects the end result obtained for chimpanzees.
However, recently (2018) a new study was performed in which the assembled DNA fragments from various apes were assembled completely separately from human DNA, giving a better estimate of the similarities and differences between the DNA of humans, chimpanzees and other apes (Kronenberg et al. Science vol 360 issue 6393, eaar6343).
What new information has emerged and to what extent does it alter previous results?

Welcome to Biology.SE! Please edit to include complete references to reliable sources for the assertions you are making. I'm also pretty sure that "shotgun sequencing" is integral to modern methods for generating whole genome sequences. I think the question you are trying to ask is really about genome assembly methods. If so it would help to clarify your post. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

@tyersome I've done that for him. I'll answer the question later if nobody else does.

Many thanks, @David. I had this from a panel discussion from a creationist only. even though my source was bad (and in Swedish) it tickled my curiosity. I was not even sure if there was any merit at all to the assertion.

I've added an answer and edited your question. The distinction wasn't whole genome v. shotgun — both sequences were whole genome — but method of assembly of the fragments.

The effect of re-sequencing the great ape genomes (orangutan as well as chimpanzee) without the use of a human genome as a guide to assembly has in general been to correct mistakes and improve the ape genome sequences so that they can be compared better with the human genome.
As far as I am aware, it appears that in a broad sense the same genes are present in humans and great apes, i.e. each will have a similar (orthologous) gene for, e.g. insulin, trypsin, keratin, generally at the same position on the chromosome. As the species are different these differences are thought to come from differences in these orthologous genes or in the regions of the genome that control their expression as RNA and then protein. The differences could also affect their activity, where they are expressed in the body or whether different variants occur (by differential splicing of transcripts).
So with improved and independent genome sequences it was possible to identify a greater number of variants in these orthogonal genes.
The focus of this work was on genes that are expressed in brain cells, because a key feature that distinguishes man from the great apes is brain size. The interest was in genes that were found in separate experiments to have significantly different expression when glial or neuronal cells of human or non-human species were compared. The authors report mutational variation in 252 genes with such differences in glial cells and 123 in neuronal cells.
To quote the discussion:

These improved genomes yield a comprehensive view of intermediate-size
  structural variation among apes. As we focused on SVs (structural
  variants) that potentially disrupt genes or regulatory sequences, we
  began to address potential functional effect. Differential gene
  expression, especially in cortical radial glia, has been hypothesized
  to be a critical effector of brain size and a likely selective target
  of human brain evolution. Nearly 41% of the genes down-regulated in
  human radial glia, when compared to chimpanzee radial glial analogs
  from cerebral organoids, associate with an fhSV (fixed human-specific
  structural variants) and most often as a deletion or a retroposon
  insertion. These findings are consistent with the “less-is-more”
  hypothesis, which argues that the loss of functional elements
  underlies critical aspects of human evolution.

So, they haven’t found what makes us human yet, but have laid the foundations for studies that may at least find out why we have bigger brains.


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Why is ATP used as a source of energy rather than glucose?
I'm struggling to pinpoint a misconception, but I don't think I understand why ATP is used as an energy molecule instead of glucose. I understand that glucose is respired, oxidised or combusted and produces energy in the form of ATP so I guess what I don't understand is why glucose isn't hydrolysed (like ATP is) when energy is needed instead of having to convert its energy to ATP first.

Well the mechanics of this can actually get pretty complicated, depending on how far into the biochemical weeds we want to go, but there are a couple of very simple reasons at the core... Well they actually aren't that simple, but they can at least be analogized in simple ways.  The first, and easiest to illustrate is this.  This is a glucose molecule:

And This is an ATP molecule:

If you want to get some energy out of an ATP molecule, all you have to do is break off one of those phosphate groups.  If you want to add more, you just stick another phosphate group back on.  This can be done without significantly changing the structure of the molecule itself.  That Adenosine base never gets touched.  Only the chain of phosphates is manipulated.  It is much more energy efficient to add and remove those phosphate groups than to add and subtract elements from a glucose molecule, as there is no way to effectively break it down without significantly changing its structure, which makes it harder to build back up.  We want a molecule that it is just as easy to add energy to as it is to pull energy out.  The glucose molecule just doesn't have a chain sticking off that's easy to remove and put back at will.  The CH2OH group on the end looks like an attractive energy sink on its face but getting the whole thing off isn't nearly as easy as it looks, and it doesn't contain as much energy as a phosphate group either, which brings us to the second easy to illustrate reason ATP is more attractive than glucose as an energy carrier.
If you look at that chain of phosphates, you will notice that they are each separated by an oxygen atom.  There are also a bunch of convenient hydrogens and OH groups floating around that make hydrolysis and dehydration very easy.  Where would you hydrolize the glucose molecule to produce a low energy molecule that can be converted back to glucose more efficiently than ADP can be converted back to ATP?  Just compare this process:

To this one:

The ATP hydrolysis looks more like the breaking down of polysaccharides into glucose than the catabolism of glucose itself, and this is at the core of the difference between the two molecules.  It is always easier to add and subtract links from a chain than it is to make direct modifications to one of the links themselves.  Glucose is great for energy storage.  You can pack a lot of energy into a glucose molecule, but once you get it out, it's very hard to put it back.  It's much easier just to throw out the waste and start over by making or eating another one.  We don't have this luxury with ATP.  It has to be able to drop off its energy load and go pick up more.  For this, the structure of ATP is much more appropriate than the structure of glucose.

Why was this answer downvoted? It appears to be correct and is close to what I would have written.

Lol I have no idea.  Maybe they wanted to answer it.  Maybe they didn't like my simplification.  Maybe they thought this question just shouldn't have been answered at all for one reason or another.  Downvotes without comments can mean anything and often indicate an opinion too poorly thought out for me to even bother wondering about.  If there is a real, concrete problem to be addressed, it should be pointed out.  Otherwise I just tend to ignore it and briefly assume some sort of misanthropy on the voter's part before forgetting it altogether.

To understand this answer to the question one needs to have an elementary acquaintance with glycolysis and the concept of free-energy change in chemical reactions. This can be obtained from biochemical texts such as Berg et al.
Energy Currency
If biochemical energy is stored predominantly in a particular molecule, that molecule acts as “currency” which can be used for a variety of biochemical requirements. The general idea is that the (negative) Gibbs Free Energy change of the conversion:
                            Loaded-Purse —> Empty-Purse

is used to drive some chemical reaction or process such as ion transport, light emission, muscle contraction etc. that requires energy. For a chemical reaction, this would be:
                    Low-energy-compound —> High-energy-compound

There needs to be some way of recharging the unloaded-purse with energy.
In cellular metabolism ATP is the loaded purse and ADP — and sometimes AMP — the empty purse. The question is why ATP, and not glucose.
Desirable Properties for an Energy Currency
Here are some. You may be able to think of others.

It can be used in a wide variety of chemical processes in the cell.

It can store and release energy in amounts that are sufficient for most reactions, but not too large to be wasteful.

Its removal and regeneration will not disrupt important metabolic pathways.

It can be made available to different types of cells and organelles in a variety of circumstances.

How do the candidates fulfil the requirements?
If we look at glucose as such, it immediately fails the test on count 2, because the energy released by its oxidation to carbon dioxide and water is much more than is needed to drive most chemical reactions: approx. 30x that for the hydrolysis of ATP, which turns out to be of a more suitable magnitude.
But, let’s not give up on glucose yet. We could take just one of the intermediate steps of glycolysis where a suitable free energy change does occur. A prime example is the oxidation of  glyceraldehyde 3-phosphate. In glycolysis the energy change is used to phosphorylate the oxidation product (phosphoglycerate), but in a different universe we might imagine glyceraldehyde (with or without the phosphate) to be the energy currency, and the free energy of its oxidation coupled to other reactions.
This has one chemical problem: what is happening to glyceraldehyde (and glucose as a whole) is oxidation — not hydrolysis as the question states — so it would only be suitable for driving reduction reactions. It fails on count 1.
“High energy” redox intermediates have their place in metabolism — NADH etc — but this is clearly limited, which is why the energy of their oxidation is used to regenerate the more general currency. In practice this is ATP. Although one can argue whether Nature could have adopted some other molecule which had a high negative free energy of hydrolysis, that is not the question here. (It does in some cases.)
There is no real need of either of points 3 and 4 to rebuff the glucose argument, but there is no harm in addressing them. Could an intermediate in the oxidation of glucose be used without disrupting the process of glycolysis? Perhaps — ATP is used for RNA synthesis. But what would be the advantage anyway? Glucose is not the only cellular source of energy — Why not an intermediate in the oxidation of fatty acids? And if you accept that the currency would have to be an intermediate, the availability of glucose is less relevant, because  the purse would not need remaking all the time, just refiling, in a similar way that adenosine synthesis is low compared with the phosphorylation of ADP.
Reference
There is a specific section in Berg et al. on ATP as an energy currency, which used to be freely available on NCBI bookshelf, but is no longer so. If the reader cannot afford the latest edition an old edition covers these basics just as well, and can probably be picked up cheaply second-hand (e.g. on eBay).


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Why might a cell have no respiratory reserve capacity?
I am trying to understand why a cell might have minimal respiratory reserve capacity in the presence of unlimited substrate supply. This essentially means that the oxygen consumption rate (OCR) of the cell does not increase from its basal rate when oxidative phosphorylation is uncoupled — i.e. the reactions of the electron transport chain are uncoupled from ATP synthesis. What factors might conspire to cause this? I am thinking specifically of the photoreceptors1.
I am interested in all logical possibilities here e.g.
(1) mitochondrial ATP production is barely meeting demands at basal level.
(2) oxidative phosphorylation may already be physiologically uncoupled.

Is this a question about trouble shooting an experiment, or a theoretical question?

Welcome to SE Biology. I assume that you are trying to understand the results in the paper you cite. I do not wish to be discouraging, but few people will read that paper (questions here should be self-contained), and the key term it uses — respiratory reserve capacity — is one that I, as a biochemist, am unfamiliar with, and find difficult to understand from a brief perusal of the paper. If you understand it yourself it would be helpful if you could edit your question to expain it.

Thanks for the responses. It's a theoretical question, the answer to which I was hoping might shed some light on the Warburg effect in the retina. I have some experience with metabolic assays but was hoping someone more experienced might be able to enlighten me.


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Who created the codon wheel chart (not as a table)?
I'm trying to find out who created or first used the codon wheel chart as far as we can know.
I don't mean the tabular format.

Perhaps better asked on the History of Science & Math StackExchange.

I am Rosemarie Swanson, still alive, and yes, the Gray code representation  of the codon wheel was my idea.  I was trying to develop a linear similarity scale for amino acids.  On Thanksgiving of 1977, I suddenly realized that instead of a linear scale, a circle gave a better representation of the similarity of amino acids.  Later, I thought to look at codons.  When I realized that a 2-bit gray code representation of codons approximately matched my amino acid similarity circle, I was excited.  I worked very hard on writing up the idea, but had a hard time getting it published, until the editor of Bulletin of Mathematical Biology said he would like for me to submit the manuscript in 1983.

Amazing. What made you look into circular representation?

It is very difficult to answer this one for certain but I think the codon wheel representation is sometimes attributed to Rosemarie Swanson who represented the amino acid code using Gray code (or reflected binary code).
Swanson's work actually went quite a bit deeper than the simplified codon wheels you find in ordinary textbooks (ordering by size of the amino acid and position within the chain as well). You can have a look for yourself here in her 1984 article A unifying concept for the amino acid code in Bulletin of Mathematical Biology.
DISCLAIMER: I do not claim that I know the answer to this question for certain nor can I. However, I cannot find official publications earlier than Swanson's 1984 paper showing a circular representation of the amino acid code.

Even if she was not the originator, your answer takes this back far enough to deserve upvoting.

Nice but as you say it still does not mean it is her idea. I wonder if she is still alive and can be asked

 This answer *pre-dates* the others' focus on Rosemarie Swanson

The German Wikipedia article for the "code-sun" credits this circular diagram to Carsten Bresch and Rudolf Hausmann1.
 1. Bresch, C. and R. Hausmann. 1972. Klassische Und Molekulare Genetik. Springer-Verlag, Berlin / Heidelberg / New York 1972, ISBN 3-540-05802-8.
Below is a screenshot of page 243 from a supposed 1970 edition2 of the text that introduces the "code sun":

Interestingly, this source is 14 years earlier than Swanson's paper3 (and even 7 years earlier than she claims to have come up with her version (which, for those who have not clicked on the link to her 1984 paper in Johnny's answer, looks quite different)).
What remains unclear to me (due to the lack of availability of additional pages of an online version of this text and my own lack of access to other versions):

if this idea in Bresch and Hausmann is original or from an alternate earlier source.
whether this wheel (or "sun") was depicted in earlier versions of this text (e.g., first version was in 1964)
how this version relates to Swanson's ideas years later...

 1. Bresch, C. and R. Hausmann. 1972. Klassische Und Molekulare Genetik. Springer-Verlag, Berlin / Heidelberg / New York 1972, ISBN 3-540-05802-8.
 2. Bresch, C. and R. Hausmann. 1970. Klassische Und Molekulare Genetik. Springer-Verlag, Berlin / Heidelberg GmbH 1970, ISBN 978-3-662-23449-5.
 3. Swanson, R., 1984. A unifying concept for the amino acid code. Bulletin of Mathematical Biology, 46(2), pp.187-203.

Interesting. I also asked ChatGPT and it claims that the codon wheel was developed by a team at the University of Wisconsin-Madison in the 1970s. I couldn't find a source though.

@JonathanSisam do yourself a favor: don't ask ChatGPT questions. It doesn't actually know the answers

@rosemarie-swanson, can you comment on the similarities/differences/history comparing your representation and that of Bresch  & Hausmann? Thanks :)


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Can more concentrated tomato products increase stomach acidity?
It appears from Internet sources that tomatoes have a pH of 4-4.5, as does tomato puree/paste.
I’m wondering about the fact that paste is more concentrated.  Will eating say a teaspoon of tomato paste cause a greater acidity/lower pH than eating one whole tomato?
If you consider a soup made with a tomatoe base(say 15 crushed) tomatoes and a soup with more alkaline vegetables and two tomatoes I guess the acidity in the later will be brought down by the more alkaline vegetables and so will definitely be higher than 4.5. What might the acidity be of one serving of the tomato-based soup?

Rather depends on what's in the tin. Citric acid as an acidity regulator/ripening agent is added in some cases. Species of tomato used (and ripeness) would make quite a difference too. Only way to be sure is to measure it.


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Does biofilm formation hinder photosythesis?
In photosynthetic bacteria such as Cyanobacteria, Synechocystis sp. PCC 6803, the bacteria need access to both light, CO2, and water to perform photosynthesis.
However, in thick biofilm structures (e.g. a sphere or any 3D shape), I feel that physiologically the cells inside the biofilm 3D structure won't have direct access to sunlight, due to the outer cells forming layers blocking sunlight. Moreover, the inner cells are less likely to have the same access to carbon dioxide and water as the outer cells of the 3D construct.
So, Does the biofilm formation affect the viability and efficiency of the photosynthetic bacteria? or Do the bacteria have a mechanism to transfer the photons of light, gas, and moisture inside the biofilm?

Interesting question, In addition I wonder if the Cyanobacteria in a biofilm perform any activity normally seen in eukaryotic organisms. Namely nutrient transfer

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Most of the constituents of Phototrophic biofilms are transparent by which light can easily pass. Phototrophic biofilm are very essential for the growth of photosynthetic microbs (colonies).Due to the presence of glycolipids the 3D structure act as lens which evenly distribute the light in the Phototrophic biofilm.

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Even if lights pass, does the wavelength delivered get affected. Furthermore, How about the nutrient and gases transfer?

It is well known and established that cyanobacterial biofilms are permeable to small molecules including both CO2 and O2. More generally bacterial biofilms per se allow diffusion of small molecules, including gases like CO2. For more information, refer to studies on microbial biofilm permeability, reviewed by:
Flemming, H.C., & Wingender, J. (2010). "The biofilm matrix." Nature Reviews Microbiology, 8, 623–633.
Specific reviews on gas exchange in cyanobacterial biofilms include:
Frontiers in Climate. Recent advances in engineering fast-growing cyanobacterial species for enhanced CO2 fixation (2024). by Kim et al.
Note "Moreover, not all cyanobacteria readily form biofilms." direct citation from Kim et al (2024). This reference will tell you all you need to know about the subject - recommended.
Note2 Cyanobacteria use a complex carbon dioxide concentration mechanism even when concentrations of CO2 are low.


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Database of Medical Assertions
Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be in some sort of structured format, or be in free text.

What an interesting idea for a database! Do these type of databases exist for other fields? I've never heard of something like that until now. I'd love to browse such a resource. Looking forward to answers!

@A.Kennard: they definitely exist for computationally-driven domains that are narrow in scope! For example, the Neuroinformatics community is actively creating knowledge bases of Neuroscience-related information, and the Bioinformatics community has been active here for some time. I don't know about clinical findings, though, which would be handy for some machine learning experiments I'd like to try!


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How long will norovirus live?
I hope this is the right place to ask. I subscribe to several Stack Exchange threads, and regard them as the best internet forum for genuine and credible answers.
I spent last evening talking to friend, at an Amateur Radio Club, who told me he has recently recovered from the norovirus. I was demonstrating an oscilloscope to him, and he also handled the handbook. All this is now in the holdall I used to carry it to the Club. I took all the precautions I could, like washing my hands and not getting them near my lips, nose etc. So, my question is: how long should I wait before opening my holdall, to be sure any infection there is dead?

Well, for him the virus is already likely at minimum levels within his body. If he's recovered (pass the fever phase) then his immune system has already dealt with the majority of the viral bodies in his system, since the peak of the immune response comes after the peak of the viral infection density (ignore B):

How much of the virus was left in his system to actually spread is hard to guess. Sometimes infections never truly go away, but merely become undetectable by conventional testing. However, if we're to assume that there's at least some norovirus left to transfer to you then you should realize that the greatest chance for exposure has already come and gone.
The moment you were in the same room together, talking in close proximity, shaking hands (if you did), or generally being close is the most likely source of any infection you could have picked up. However, while most virii don't survive well outside of the body, the norovirus notably bucks that trend. The Hawaiian Department of Health (PDF) notes that the virus can definitely survive outside the body for several days on hard surfaces (though it will not grow), can survive being frozen, and that it only takes about 100 viral units to cause an infection (which could fit a few thousand times over on a grain of salt). Scientific American also notes that norovirus can survive for months or years in sources of drinking water.
What you've already done is pretty much what you should do to avoid infection. You've washed your hands, refraining from mucous membrane contact, etc.
Ultimately how long you should wait depends on where the norovirus currently resides. A week should be sufficient if all of the norovirus is contained on the book or on other surfaces that you're not making contact with. However, if it's already had contact with your skin or mucous membrane, then you're either already fighting it off or you're about to become ill. Unfortunately it's a lot easier to expose yourself than contain something you can't see, as the Mythbusters have done a good job of showing (Video).
In all likelihood if he was still infected enough to transmit the virus to other people by the time you two started handling the same equipment and you didn't use gloves, you've probably been exposed. However, exposure doesn't automatically mean you get sick. If you're not sick within a week afterwards, you've successfully fought it off. So, congratulations, perhaps!

Thank you @MCM very much for that comprehensive answer. A bit reassuring, but it seems that really I must just wait and see. As a supplementary question: is my wife at risk (she did not come with me) assuming I do not show symptoms? Unfortunately I do not have enough "reputations" to vote your answer up, as I would like to do.

@HarryWeston - "Is my wife at risk if I don't show symptoms?" Yes. Whether or not you show symptoms after having contracted any infection depends on your immune system's response. If you've seen a similar strain (or the exact same strain) before, then there's every chance you won't show symptoms but still be a carrier. If your wife hasn't encountered the strain, she could still get sick and invoke the normal immune response. This is all contingent on whether or not the guy passed it on to you, though.

Thank you again @MCM, so it is just a question of wait and see, though much much better informed now.


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How do warm-blooded animals keep their temperatures constant?
Warm blooded animals like us keep their temperature constant irrespective of their surroundings. But how do they do that? Energy should be supplied from the inside. I assume that reactions like making ATP from glucose are exothermic. That means in winter our body reacts more. Water is absorbed by those reaction.We should need more water in winter. Which is contradictory with our real life experience.
On the other hand what prevents cold blooded animals from making heat? Don't they need ATP? Do they use different types of reactions to make energy? Do they have different evolutionary path? They don't seems very different from us.

It's a process called homeostasis - have a look at this Wikipedia entry: http://en.wikipedia.org/wiki/Homeostasis

Since there seems to be several distinct sub-topics in your question, I will answer them one-by-one:
1). There are a variety of mechanisms that allow endothermic animals to maintain thermal homeostasis in a cold environment. The main ones are:
a). The shivering response: When the core body temperature of a endotherm drops below a critical value (36.8C in humans), it causes the posterior hypothalamus to stimulate certain skeletal muscle groups (especially around vital organs) to start to "shiver" rapidly, generating heat.
b). Compared to ectotherms, endotherms have more mitochondria per cell, thus allowing them to have a higher metabolism. Since metabolism always generates heat, an [general] increase in cellular metabolism will cause an increase in body heat.
c). Many endotherms have layers of insulating matter, such as fur, blubber, feathers…etc, allowing them to preserve body heat. In addition, endotherms can also route blood away from  capillaries via vasoconstriction of arterioles, reducing the area in which heat can be lost.
d). As mentioned by Memming, brown adipose tissue also plays a role in temperature regulation. Thermoregulation-based metabolism in brown fat causes the P+ in the electron transport chain to go through thermogenin instead of ATP synthase. This process generates heat, but no ATP.
e). Some endotherms, such as penguins and arctic wolves have countercurrent exchange in their capillaries. This is when warm arterial blood "passes" some of its heat to cooler veinous blood. This feature allows some of the heat normally "wasted" into the air to be recycled back into the body.
Note: Though it is true that endotherms are able to keep their body temperature constant irrespective of their surroundings (ignoring extremes), they do this at a cost of requiring significant amounts sustenance. Most endotherms require much more sustenance than ectotherms.
2). Your second sub-question is very interesting. Though it is true that generating heat will require substantial amounts of carbohydrates/fats/...etc, it does not necessarily mean that the net consumption of sustenance in cold environments is greater than that in normal environments. In most cases, endotherms in cold environments will have exhibit significantly less activity than when in an optimal environment. The decrease in activity when in a cold environment will likely balance out the increase in thermo-regulation based metabolism. This likely explains why people tend to drink equal or slightly less amounts of water when in cold environments. One more thing: some reactions heat-generating reactions (like the alternate ETC pathway) do not require water. Glycolysis and Krebs actually generates water (not to say that there is a net gain in the body :))
3). In truth, nothing "prevents" ectotherms from generate heat. They simply do not have the cellular "machinery". Ectotherms metabolize in ways very similar to other organisms, using molecules like ATP, glucose, fat…etc. Unlike endotherms however, they spend very little of their energy on temperature regulation. As a consequence, their overall metabolic rates are dependent on the external temperature. The point is this: A substantial portion of endotherm sustenance is used to generate heat. Only a small (if any) portion of ectotherm sustenance is used to regulate heat. As a result, endotherms require much more nourishment than ectotherms.
4). I am not entirely certain what you mean by "evolutionary path", but I will just say this: In many ways, endotherms and ectotherms are organisms that have found different ways to the same problem; how to regulate body heat for maximal survival and reproduction. Basically,
ectotherm- more dependent on environmental temperature, requires less sustenance
endotherm- less dependent on environmental temperature, requires more sustenance
5). You are quite correct. The cellular and genetic components are very similar. Some morphological aspects seem to be shared as well.

Sources:
Cambell & Reece (2010) Biology (9th ed)
Swan, K. G.; R. E. Henshaw (March 1973), "Lumbar sympathectomy and
  cold acclimatization by the arctic wolf", Analysis of Surgery 177 (3):
  286–292,
Guyton & Hall (2006) Textbook of Medical Physiology. (11th ed)
Romanovsky AA. (2007). Thermoregulation: some concepts have changed.
  Functional architecture of the thermoregulatory system. Am J Physiol
  Regul Integr Comp Physiol. 292(1):R37-46.

Here answers a part of your question. Warm blood animal burns more food in the winter, so they can keep their body warm. They are not consuming much more ATP in the winter, just a bit more. Usually they have mechanism to reduce the heat loss, like growing hair. How do you know that you need to drink more water? You should know that you area also sweating less in the winter.
The cold blood animal has a mechanism encoded in their gene to prevent them keep warm in the winter. It is a evolution result so that they dont have to consume much foods and so ATP in the winter. It means that they belong to a different branch of phylogenetic tree thus has a different evolution path.

There's always shivering, and also the brown adipose tissue that generates heat to keep the core temperature regulated. Extra mitochondria in brown adipose tissue can be used to generating heat without producing ATP. As @jackweirdy mentions, this is a negative feed back involving hypothalamus.


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Calculating sequence divergence score for a protein from identity or similarity score?
I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue is that I wanted to have divergence scores instead. So in order to calculate divergence scores, I first looked for the conventional method to calculate divergence score from protein alignments. But turns out, most of the methods/tools calculate % identity and % similarity scores instead of divergence scores.
(1) So I wonder what is the conventional method to calculate divergence scores from protein alignments.
(2) Could I simply calculate % sequence divergence as 100 - % identity or 100- % similarity score? If that's ok, should I prefer 100 - % identity or 100- % similarity?
Any suggestions from experts are welcome.
Update: As suggested in a comment below, I should mention that the average % identity score is more than 70. I hope this information would be helpful.

It depends on how similar your proteins are, the quality of the alignements. Measuring distance between distant sequences is harder than for very similar sequences.

The sequences of the proteins very similar. Average % identity is >70. Thanks for suggesting, in the updated question, I mention this. Also, I started the bounty, in case you may know the answer!

Since you don't want to use similarity or identity calculating divergence as 1-(similarity | identity) won't do what you want. What exactly you want to find? Why you can't use similarity or identity

@Hachiloni, yes, indeed the answer of @Mike Serfas below, suggests that the 100 - (% identity) may not be the right way to calculate the % divergence. However, similarity score could be used, if some condition is met.
Well, that's what I was asking i.e. if I could calculate divergence score from similarity|identity scores.

This is a very tentative answer as I haven't done anything like this, but it's a learning experience for me and I hope it could be helpful to get a more knowledgeable response started.
I don't think you can do this.  Per Wang, 2009 and Yona, 2002, divergence scores could be Kullback-Leibler divergence or Jensen-Shannon divergence, but both papers opt for the latter.  Divergence scores are based on "empirical probability distributions between the 20 amino acids".  BLOSUM or PAM matrices may be used.  Simply counting the identical or similar residues wouldn't contain as much information.  Wang, 2004 compared JensenShannon to numerous other scoring methods in the context of PSI-BLAST.
The similarity score is related to the divergence score:  Score = 0.5(1-D)(1+S) where D is the divergence score and S is the significance score. It is equation #15 in Wang, 2009 paper.  If you could safely assume the significance score for some alignments was near 1 (no chance similarities) then maybe you could say D = 1 - similarity score.  Unfortunately, judging by the glossary because I haven't downloaded any of the datasets, for the Ensembl data similarity is merely "How well one sequence matches another determined by calculation by an alignment program of identical and conserved residues/nucleotides."  So from that I take it they may just be counting up the "conserved" amino acids in the old fashioned way, but don't know that.

thanks for the answer, it indeed clears things out. Especially the equation i.e. Score = 0.5(1-D)(1+S) seems to be very relevant to what I wanted to do. I wonder if the condition i.e. significance score for some alignments was near 1 (no chance similarities) is satisfied in the case of the alignments I have. Could you please point to a reference where I can get more details regarding this equation?

It's equation 15 from Wang, 2009 above, which goes through the derivation.  But I don't know if/when you could actually assume significance score near 1, though small deviations from that wouldn't affect the value of D very much.

Thanks! I just added source of the equation in your answer. I am indeed not sure if/when I could assume significance score near 1. I wonder what makes you believe that small deviations in that won't change D much.

I don't see your edit - I'd thought my hyperlink to Wang 2009 would be enough, given the context.  My comment about the significance score was trivial - since it's added to 1, a variation in that score only affects D half as much.

I think my edit which may not be that helpful indeed, will be checked by moderators I think before it shows up publicly.
Ok, indeed variation in D may not have much effect. Thanks for the clarification.


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Why did women historically have such a high mortality rate during birth?
Historically women had a relatively high chance of dying while giving birth.
At first thought it seems to me that this would be a disadvantage for the species for the obvious reason that a dead person can no longer give birth (and can't care for her offspring).
Is this outweighed by some advantages? I can imagine that there would be some evolutionary advantage to have the "weaker" women die during child birth and let the "stronger" ones live to produce more children with "stronger" genes.
Or is the high mortality rate in humans during child birth a result of civilization (pre-moderne civilization of course, with the general lack of hygiene/medical knowledge)?
What is it like for the relatively un-civilized tribes around the world?
How is it compared to other closely related mammals?

Dying during or shortly after birth has two main reasons: First is bleeding to death when the big blood vessels which support the developing embryo are not closed correctly or if the placenta gets stuck. The other are infections to wounds that occur during birth as tetanus infections. While the second is mostly a problem in less developed countries, the first still happens and can be very dangerous. The death rate went down pretty much, when doctors and midwifes started taking basic hygienic measures.

That's an interesting question. And it is also a common misunderstanding of evolutionary processes.
Thanks to @Chris comment, we know/can assume that high mortality rate is not a consequence of industrialization but has ever been before the era of modern medicine.
Women don't let themselves die in order to improve the species. Those women that carry a gene forcing them to commit suicide in order to improve the species won't pass on their genes, and in consequence no women will ever suicide in order to improve the species. In other words, altruistic behavior cannot appear and spread over time. This is the standard view of selection (and probably the good explanation in our case).
Now, I have to say that I lied in the previous paragraph! There is a field of study called social evolution which aims to study social traits. Social traits are those traits which influence not only the fitness of the individual carrying the trait but also the fitness of other individuals in the population. Theoretically all traits are somehow social traits! Typically altruistic behavior is among those social traits that cause a decrease (a cost) in the carrier fitness for an advantage (a benefit) for one or several other individuals in the population. There are several models (which are still debated in particular concerning the assumptions of these models) to explain the evolution of such traits. The most famous, most commonly used and most theoretically studied one is Kin selection/Hamilton's rule. You'll find some explanations about this rule on this post. The concept of population structure is key in the understanding of Hamilton's rule. Also important are the concept of levels of selection, which gives a possible explanation for the evolution of altruism, the concept of lineage selection, and finally the concept of reciprocity (but that doesn't make much sense in the current context!). Some people would not classify these models as I did, some would add other models, some would melt two models into one…
For one of these models to be correct we would need high lineage split and extinctions in human history which I don't think is really the case. Or we'd need that the death of a woman is particularly benefit to her family. I don't think first human were cannibals. Women were probably very often pregnant and males had to fight to be the father. So dying would probably not free much opportunities for the sisters and brothers…. One would need to write some equations and gather more information than what I have but intuitively I don't think that high mortality rate in women while giving birth is an altruistic behavior.

Human females have one of the worst  chidbirth experiences. This is because of our extremely high cranial capacity compared to the apes. This had an obvious evolutionary advantage and made us what we are today. However this creates problems as the braincase has to pass the pelvic cavity during childbirth. The wider hips in women compensate for this but still it is much harder than in case of other apes. Shorter women are in greater danger. Much easier for our closest cousins the chimps or gorillas. Compared to tribal women the civilised lineages have survived with more assistance...


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What does "tumour budding" mean?
tumour budding, lymphocytic infiltration and resection margins are established factors that influence the outcome of colorectal cancer (1)
In this context what does "tumour budding" mean?
Reference
(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. Chirurgia (2012) 107:555-563. Introduction/0

Tumor ‘budding’ is loosely defined as the presence of individual cells and small clusters of tumor cells at the invasive front of carcinomas. A study of the measure of budding can give an insight into how fast the disease might propogate.
Reference


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Will ants arriving with travel luggage form a new colony?
I have found a few dozens of ants in my luggage after arriving back from holiday. Am I at the risk that they will form a colony in my home? Are those ants able to form colonies that are normally gathering food? Will any other kinds of ants be present in the luggage? What will happen to these ants after they start exploring my flat (which is distant from their original colony)?

typically only if the queen is in the luggage. ants definitely arrive with cargo and colonize new continents, so its not unheard of however unlikely it will happen

If they're bringing luggage, they're moving in...

An ant colony is started by a queen ant (reference). Worker ants are sterile, and cannot start a new colony (reference). The ants in your luggage are worker ants (unless you have a colony in there :) ). The original queen ant never leaves her colony, but during a nuptial flight, new queen ants will land in (hopefully) good nesting sites.  (reference) These ants can be told by their wings, which are non-existent in worker ants.
The worker ants have an average life span of 45-60 days (reference), so the ants in your luggage won't be around for very long.
Also see:

If a worker ant gets separated from its colony, it's doomed. No other colony will take it in, and it can't start its own colony--only queens can do that. It might be able to live for a while, but generally not that long--a lost worker is generally more concerned with hunting for its colony than with feeding itself, and its energy reserves are fairly small (depending on the ant species--some have workers that are adapted to taking long foraging trips). A few ant species, however, have "supercolonies," where neighboring colonies are established by queens directly related to one another. When queens are close relatives, their workers tend to have similar chemical profiles, meaning they can move from colony to colony without triggering the usual colony defenses against intruders. (Intruders are recognized by their chemical profile--their odor--and not by appearance, ID card, etc.) In such cases, workers routinely transfer between colonies, so a worker may end up working for its grandmother or, forgive me, its aunt. (From this page)


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How do liver and lung metastases cause death?
Metastasis to the liver and lungs are the main causes of death in colorectal cancer.(1)
I understand that colorectal cancer may have metastases. But how do these metastases cause death?
Reference
(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. Chirurgia (2012) 107:555-563. Introduction.

As I understand metastasis doesn't cause death.. it just spreads the cancer to new sites and the body is parallely invaded at several areas.. worse than a single locus.. moreover it would be difficult to surgically remove the cancer in such conditions.

Metastasis is the spreading of cancerous cells to a new site within the body where they form a secondary tumour.  There is nothing special about how these metastases cause death, they do so in the same ways as the primary cancer eventually might:

Replacing functional cells with non-functional cancerous cells
Eroding into other tissues and disrupting normal body architecture
Causing haemorrhage
Putting pressure onto other structures

If we apply those principles to lung and liver secondary tumours, it is easy to see why they are likely to contribute significantly to mortality.
Cancerous masses in the lungs reduce the surface area available for gas exchange, reducing oxygen saturation of the patient.  The tumour may also erode into a primary bronchus, which if obstructed would cause lung collapse, or into the mediastinum.  If the mediastinum is involved then the great vessels or heart may be invaded into with significant consequences.
Liver metastases are more likely to cause problems due to the reduction of liver function as the cancer grows. This causes a plethora of problems as the liver is involved in so many pathways within the body.  Examples of serious effects would include the patient becoming coagulopathic due to a reduction in production of clotting factors, making bleeding much more severe.  The liver can begin to fail to clear toxins from the blood, leading to the risk of acidosis or hepatic encephalopathy (leading to coma and eventual death).  If the tumour were to invade the portal vein, this can cause portal hypertension, which in turn shunts pressure into the systemic venous system.  This can cause oesophageal varices which are prone to spontaneous and catastrophic bleeding. Similarly a tumour invading the common bile duct (or other part of the biliary tree) can cause obstructive jaundice and associated problems.
The reason your quote suggests that most deaths are from metastases than the primary tumour is probably because tumours in these locations have greater negative effects at a smaller size because they are in crucial tissues.
There may be another contributing factor in the form of data interpretation, however.  Tumours are often 'staged' via the TNM staging system, the last component of which is the presence of metastases.  The presence of distal metastases automatically makes colorectal cancer Stage 4.  This is often considered not to be curable, meaning a move to more palliative treatment options.  This may affect the survival curves for those with distal metastases and those without.

Fabulous explanation, thank you! Yes, the same paper states that these metastases occur in up to 25% of patients at presentation.


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How to measure the pH of a bacterial species?
I would like to calculate the pH of a certain bacteria species before after an experiment. I was reading about the pH cell of bacteria and I found out about Bacterial Intracellular pH which I different than the pH level outside the cell. I plan to measure the pH Outside of the cell as a method to represent the pH of the bacteria.
My experiment:
I am soaking a piece of paper into a bacteria solution (bacteria + media). After that, I am exposing the piece of paper to different parameters. I would like to measure the slight change in pH if any, due to the exposure. In sum, I would like to measure the pH level of the bacteria on paper before and after exposing it to different parameters to compare the change.
My idea:
For before and after exposure, I will submerge the paper in a neutral liquid suck as DI water or a new sample of the bacteria media for an hour and measure the pH of the solution.
Is that a valid method to measure the pH change or do I have to use a dye to see the color of the cell to quantify the pH?

I think that the only way you'll find this out for this system is to try it. Why not measure the pH directly in the solution rather than putting the bacteria on paper? It may be very hard to get reproducible amounts of bacteria by soaking the paper.

@bob1 Aren't nutrient solutions for bacteria usually pH buffered?

@bob1 I do not know how to take the measurement for the Bacterial Intracellular pH. Therefore, I can not validate my measurement if I took it for the solution or the paper. I was wondering if someone has done both and notice any ddifference.

@AnwarElhadad I don't think this is a great way to measure external pH (just pH the media), and I don't think any measurement of external pH would be a reliable proxy for cytoplasmic pH unless it was first validated in that specific organism. Different bacteria can have dramatically different pH homeostasis mechanisms. For example, E. coli can maintain its cytoplasmic pH within a range of pH 7.4–7.8 over an external pH range of 5.0–9.0. This review discusses some of the measurements and homeostatic mechanisms. https://www.sciencedirect.com/science/article/pii/S0065291109055015

@MikeyC I was thinking of having a very high-density bacteria solution to come close to the PH of the outer layer of the cell

The pH level of the Bacterial Intracellular structure is different from the pH level on the eternal side of the cell. Moreover, there are no studies that suggest that a change in the external pH of the cell will have a linear impact on the Intracellular pH. Therefore, the best methods to measure the Intracellular pH of the bacteria cell are:

microelectrodes ( Escherichia coli intracellular pH, membrane potential, and cell growth. J Bacteriol 158:246–252)

radiolabeled membrane-permeant probes (Escherichia coli intracellular pH, membrane potential, and cell growth. J Bacteriol 158:246–252)

pH-sensitive fluorescent probes (Noninvasive measurement of bacterial intracellular pH on a single-cell level with green fluorescent protein and fluorescence ratio imaging microscopy)


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Phenotypes caused by mutations in mitochondrial DNA?
Will mutations in mitochondrial DNA necessarily affect phenotypes?
I have some cursory knowledge of serial endosymbiotic cell theory, and find it difficult to consider that the DNA of the former cell — now organelle — would affect anything outside of the mitochondrion itself, although I can imagine the alteration of mitochondrial processes having an indirect effect on non-mitochondrial processes associated with certain phenotypes.

I have edited your question slightly. It's best to make titles short and punchy and ensure that the body is self-contained (i.e. comprehensible without reference to the title). One thing I had difficulty with was your phrase "mitochondrial process as a catalyst for certain phenotypes". Catalyst means one thing in biochemistry, and this is not it. I have replaced it by "having an indirect effect". Is this what you meant? If not, try to phrase precisely what you do mean.

Assuming that I have understood (and reworded) the question correctly, I find the logic strange. It is the disruption of or change in process that produces phenotypic changes following a mutation in the gene, so if the process is critical for life — like those occurring in the mitochondrion are — what difference does it make where it is encoded?
Perhaps the problem is the endosymbiotic theory of mitochondrial origin. Yes, most of us believe that, but, whatever it was millions of years ago, the mitochondrion is an integral part of modern eukaryotes. Extensive changes have occurred, the most relevant to clearing up this way of thinking is the fact that most human mitochondrial genes are now encoded in the nucleus. Would you these genes would be any more or less likely to produce phenotypes on mutation? Hardly.
Now to the facts. There are certainly mutations in mitochondrial genes that are associated with disease in man and hence produce phenotypes. Some are listed in the table below, taken from a review by Taylor and Turnbull in 2004.

An account of Mitochondrial DNA and Mitochondrial Diseases written for less advanced audiences is this Scitable article.

No, it will not necessarily affect phenotype. Of course silent or inconsequential mutations are possible in mtDNA just as they are in genomic DNA.
But, for example: In some cases, inherited changes in mitochondrial DNA can cause problems with growth, development, and function of the body’s systems. These mutations disrupt the mitochondria’s ability to generate energy efficiently for the cell.
(https://ghr.nlm.nih.gov/primer/mutationsanddisorders/mitochondrialconditions)


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Cheap enzyme assay for a high school lab
At the moment, I'm designing an experiment for a high school lab with no financial resources. I need to assess the impact of a variety of factors on a specific enzyme's reaction with its respective substrate and determine the rate of reaction. Normally this would require some combination of an assay kit and a plate reader. Though cheaper versions of the former are within my budget, the latter is not.
What are the cheapest ways you can think of to:
1) Get access to enzymes and the substrate;
2) Make them react in a controlled manner;
and 3) Assess the rate of reaction from the resultant substance?

Do you have a specific enzyme and substrate in mind?

No specific enzyme or substrate in mind. The only condition is that it can't be amylase.

There is the classic potato starch/iodine/amylase experiment:
http://dailynexus.com/2016-08-31/chemistry-101-the-classic-potato-iodine-blueblack-experiment-finally-has-an-explanation/
From memory, when you add iodine to a small piece of potato, the potato starch reacts to produce a dark blue/black colour.  The amylase enzyme in human saliva can break down the starch and remove the colour, which is effected by spitting into the test tube.
You might need to try titrations to work out how to do number 3.

How specifically would I use titrations?

That's a good question.  Now I think about it, I don't know how you would be able to assess the rate of reaction. My thought was to try increasing amounts of saliva until some kind of threshold was reached, but I don't know if that helps at all.

In order to set up an enzyme assay that allows quantitative kinetic analysis three key requirements come to mind:

The assay should be sensitive
A plot of velocity versus enzyme concentration should be linear and through the origin at both high and low substrate concentrations.
The initial rate should be measured.

Spectrophotometric Assays
Spectrophotometry is a very versatile method for measuring changes in absorbance with time, and if an enzyme produces a product that differs in absorbance (at a given wavelength) from that of the substrate, this can be the basis of a very convenient assay: NAD(P)H absorbs at 340nm whereas NAD$^+$ does not, for example
Furthermore, if the extinction coefficient is known (6220 M$^{-1}$ cm$^{-1}$ for NADH), initial rates may be quantitatively expressed as micromoles of product formed/minute (rather than change in absorbance per min).
Things are even easier if the chromogen absorbs in the visible region.
The p-nitro-phenolate anion is yellow, for instance, and any enzyme that produces p-nitro-phenol from a colorless (or near colorless) substrate at relatively high pH may be assayed by monitoring the increase in absorbance at about 400nm.
A further advantage is that the extinction coefficient is high (Dawson quotes a figure of 18000 M$^{-1}$ cm$^{-1}$ for p-nitro-phenol at pH 8-9 and 400nm, making this assay method roughly three times more sensitive than NAD/NADH).

If spectrophotometry is the chosen method, a valid assay requires that The Beer-Lambert law be obeyed within the absorbance range of the experiment.

Possible Examples
Alkaline phosphatase may be assayed with p-nitrophenylphosphate as substrate, producing yellow p-nitro-phenol as product. Thus recording the  increase in absorbance at about 400nm with time is the basis of a valid, sensitive assay.
In addition, many proteases and esterases may be assayed with p-nitro-phenylacetate, where the action of the enzyme also produces p-nitro-phenol as product. This includes chymotrypsin.
Both p-nitro-phenylphosphate and p-nitro-phenylacetate these are relatively cheap.
Another possibility is mushroom tyrosinase, which may be assayed spectrophotometically by measuring the decrease in absorbance at  475nm due to the formation of DOPA-quinone from L-DOPA, and there is a very concise and detailed description available.
There are many other possibilities.
Smartphone 'Spectrophometer'
The problem with spectrophotometry is that equipment is expensive.  However, a number of authors, have shown that smartphones may be used as 'spectrophotometers' in the visible region.
A very simple and effective method has been described by Kuntzleman & Jacobson (2016), and Kuntzlman has posted an outstanding blog which includes a YouTube video that describes the method in detail.
To understand the method, we need to be aware that a colored solution absorbs light in the region of its complementary color. A solution appears red (to us humans) because green light is absorbed. A yellow-orange solution absorbs (mainly) blue light.  (Complementary color may be obtained by consulting a colorwheel)
The method uses a  smartphone camera, together with an App to give average red, green and blue (RGB) values for pixels found in a 'detection circle'.
Light reflected from a background complementary to the color of the solution of interest is passed through the solution and is detected by the camera by noting the decrease in either the R, G or B value.
Other than a smartphone, all that is needed is a cardboard box with holes cut to accommodate a cuvette or other vessel and a sheet of paper or cardboard colored in the complementary color, which is placed behind the cuvette (to reflect light of the appropriate wavelength through the solution).
In the video example, red light is detected by using a green background and recording the decrease in G value.   The Beer-Lambert law was then be used to convert G values to absorbance. (The video even includes a spreadsheet example showing how to do this).
It should be easy to adapt this method for use in enzyme assay. Use of a timer is all that is required to record changes in absorbance with time, thus allowing the initial rate to be estimated.
There is one caveat.  The App by Kuntzleman is colorometer and this does not seem to be available for iPhone 7 and higher.  However, it appears that the App is still functional on Android devices.
References

Use Your Smartphone as an "Absorption Spectrophotometer" [Tom Kuntzleman blog]
Kuntzleman,TS & Jacobson, EC (2016) Teaching Beer’s Law and Absorption Spectrophotometry with a Smart Phone: A Substantially Simplified Protocol J. Chem. Educ. 93, 1249-1252 [ACS Site]
Smartphone "Spectrophotometer" [YouTube]
Rodriquez, MO & Flurkey, WH.  (1992) Biochemistry Project To Study Mushroom Tyrosinase. Enzyme Localization, Isoenzymes, and Detergent Activation J. Chem. Educ. 69 767 [ACS Site]

So, using a the colorometer, how would I ascertain the hydrogen peroxide content of a given solution?

Someone has already mentioned catalase and potatoes, but another way to do it would be to use hydrogen peroxide. The students could cut the potato up smaller to investigate the impact of surface area, heat/cool the mixture using a beaker with water in and a thermometer, and change the amount of potato used. So a few variations of conditions for a fairly low cost!
To measure rates, you can pop a bung attached to a tube and gas syringe onto the test tube when the potato is added, and record the volume of oxygen evolved within a given period of time, or the amount present at different time points (say, every thirty seconds). Lots of fun graph drawing for the students, and they can work out the initial rate of reaction etc! :)
If you're looking for a qualitative result, this experiment produces bubbles and foams up so you can go for which reaction produces the greatest height of bubbles in the tube. Perhaps the students could measure this height with a ruler to get quantative data?
I hope this is helpful!

Catalase from blood. Prick your finger,  collect a small amount of blood. Add some hydrogen peroxide to the blood, it will foam as the catalase decomposes the hydrogen peroxide. Obviously there are biohazard considerations when dealing with human blood. Some plants, notable horseradish also contain peroxidase if you wish to avoid pinpricks.

NO. You can’t do this sort of thing anymore! Not in Britain at least. We used to have medical students do blood glucose on themselves after fasting. That was pre-HIV. Not now. Don’t go there.

So, what substrate would you recommend I use? Additionally, how would I assess the rate of reaction?

The substrate is the hydrogen peroxide, the enzyme is contained on blood, horseradish, and a number of microorganisms. You can assess the rate of reaction by observing the bubbles produced, or collecting the oxygen in an inverted jar filled with water. David: calm down. What happens when someone gets a bloody nose or scrapes their knee? Do we call a hazmat team and incinerate the waste? No, we throw them in the trash and move on. Certainly the teacher could prick their own finger to obtain less than 20uL of blood for the sake of an experiment.

In theory you could buy some blood from a local butchers' so it's not that bad of an idea. But you'd have to check with health and safety due to the risk of blood borne diseases and religious concerns. Surely if you can dissect kidneys in class, you can use a test tube of blood though