text:
Iron absorption and oxidative stress
Fe2+ is more bioavailable than Fe3+, so it's absorbed more quickly. I read that, for this reason, Fe2+ doesn't give enough time to the organism to bind it to a protein then it stays longer in a damaging free form in blood.
So if we consider 2 persons absorbing (in blood) the same amount of iron via Fe3+ for one and Fe2+ for the other, will Fe2+ generate more oxidative stress?
In response to David:

The bioavailability of a drug product is known as the rate and extent
of its absorption.

https://www.ncbi.nlm.nih.gov/books/NBK557405/
So, high bioavailability means high rate of absorption which means that, for a given duration, a higher amount is absorbed, so it's absorbed more quickly.
By protein I meant ferritin or transferrin.

Ferritin preserves iron in a safe state; thus, it is a direct defense
molecule against redox-active iron.
Non-transferrin bound iron is a candidate for the redox-active iron in
extracellular space.
When a large amount of iron enters cells and overflows the capacity of
iron binding proteins, the iron behaves as a redox-active iron in the
cell.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9324531/
If iron can overflow the capacity of iron binding proteins, it means that it's about time since a slower absorption could help to prevent this overflow. As you can see, it's not a nonsense.
So, is Fe2+ more likely to cause such an overflow and thus more oxidative stress?

Welcome to SE Biology. Please either provide a link or quote the exact text and context of what you have read. That way we can check whether the author is correct and whether your understanding is correct. Statements such as "it's absorbed more quickly because it's more bioavailable" and "Doesn't give the organism time to bind the protein" are scientifically ambiguous at best and meaningless at worst. Which protein is "a protein", and could you check this is about affinity rather than the nonsensical "time to bind"? Are you just asking whether free ferrous ions cause more oxidative stress?

that info seems readily available online, did you check this list of findings: https://www.google.com/search?q=oxidative+stress+fe2+fe3&oq=oxidative+stress+fe2+fe3&aqs=chrome..69i57j33i160l3.7224j0j7&sourceid=chrome&ie=UTF-8

Most of the studies I found were about Fe2+ causing oxidative stress, and since Fe3+ has to be reduced to Fe2+ to be absorbed, Fe3+ may also cause oxidative stress. I didn't find any study comparing Fe2+ and Fe3+ intakes to confirm that Fe2+ generates more oxidative stress.

Please don't refer to me in your question. Edit it instead. 2. If you respond to a comment of mine, you need to leave a comment addressed to @david so I am alerted to it. (I don't have to do this to you as the poster or answerer always gets notified of comments.) Iron is a vital mineral not a drug, and your statements about bioavailability would seem to mean that ingested Fe2+ is taken up by cells less well than Fe3+.The question is why? Is it possible that it might be because transferrin only binds Fe3+. Check if/how Fe2+ can be taken up into cells and edit the start of your Q accordingly.

I know little about iron metabolism but I am an experienced biochemist/molecular biologist. I may be able to help you if you do the work to research your question in molecular and cellular terms. I have glanced very briefly at the literature and it would appear that bioavailability basically means absorption into the circulation. However it is absorption into cells that would appear of interest as that's where oxidative stress occurs. For Fe3+ this requires transferrin, interacting with receptors on the cell. If Fe2+ is not taken up the question is invalid. Is there a mechanism for this?


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Smallest animal that produces food for humans
I was thinking about how bees can produce honey and human can eat it. After that I came up with question. What are the smallest animal that can produce food for human?

It would depend on what you consider food, but if you consider things that contribute to food substances (e.g. food dyes) then cochineal scale mites are only about 5 mm (0.2 in) long and produce a red dye that is commonly used as a food colorant.
There are also several ant species of similar size that are eaten as food sources. For example, Liometopum apiculatum (6-7 mm adult) grubs are/were harvested as a food source in parts of the USA and Mexico.

I cannot find the size of Chaoborus edulis but they might be a contender: Kunga cake.

@Roland I knew of that one, but didn't know the name or which region of Africa it was from, so I didn't try to find it. You should write your own answer based on this. Bugguide.net suggests 8-10 mm for the genus.

I'll throw in my 2 cents and say fungi, especially yeast (or other fungi used for blue-cheese etc.), typically measuring 3–4 µm in diameter and could be perceived as 'producer' since it's converting sugars via fermentation..

@iLuvLogix That's not an animal as OP requested.

@bob1 Thanks for pointing that out - a quick search revealed that they seem to have a seperate kingdom of their own (besides plants and animals) - my bad..

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


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Methods of denaturing BL21 E.coli other than using lysis buffer and sonication
The goal is to try different denaturing methods for BL21 E.coli. However, finding detailed paper on this is challenging as most articles do not seem to include the details of their denaturing procedure. I am currently using lysis buffer and sonication but I would like to try something else. Any detailed suggestions with reason would be of help.

By "denaturing methods", do you mean lysis methods? "Denature" typically refers to the unfolding of structured macromolecules (protein, DNA) and not whole cells.

A detergent-containing lysis buffer along with sonication is basically the gold standard for E. coli lysis (which I'm assuming you mean instead of "denaturing", which is something different). Why do you need to try something else? What are you studying, or what are you trying to purify?

Yes you are right I am trying to alter various methods for the disruption, Lysis of E.coli BLC21 currently I am using sonication and a Lysis buffer that contains 20 mM Tris-HCl, 50 mM NaCl plus 10% lysozyme. But we are looking at a better way or alternative ways that may give similar or better results?

There's Ye Olde french press method. https://en.wikipedia.org/wiki/French_pressure_cell_press

https://www.google.com/search?q=methods+for+e+coli+cell+lysis THere are a large number of such detailed protocols described

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Can bottlenecked potato immunity defence be increased with knockouts?
I read in a Swedish newspaper advertisement some years ago that genetic intervention had been used to knock out part of the plant immunity defence. This advertisement was paid for by starch producer Lyckeby. The potato's own gene repair introduced variation in the resulting repaired genes, giving the plants a broader defense against various possible threats. What is the background to this story?
The reason given for why common agricultural potato varieties have low variation in their defence genes was genetic bottlenecking post-domestication (other potato strains in the endemic range retain substantial diversity).

Please provide a reference for this claim.

The rewrite of Maximilian Press goes beyond my intent in regard to how bottlenecking occurred. I see no need to mention it, especially since it likely occurred after domestication when the plant went to Europe. Is there any problem in removing it?

@DavidJonsson just fyi, you have to @ tag anyone so that they get notified that you respond. I don't now recall my chain of logic in introducing that edit, I think that I added it to provide more context. I will further edit to try to clarify what you mention in your comment.

This sounds to me like a CRISPR approach used to create S (blight susceptibility) gene knockouts that are then screened for blight resistance, though it's a little hard to know for sure due to the lack of a reference. CRISPR approaches do indeed exploit endogenous repair machinery to introduce mutations at targeted locations.
Here is one paper that follows that rough outline. The take home message is that, yes, you can use this kind of workflow to optimize resistance to particular blights. What it does not seem to address is the part of your question regarding the generation of variation at R genes via this approach, unless you refer to the specific variants introduced by such mutation. While such variants are not "unnatural", you cannot really replace population diversity removed by bottlenecks with CRISPR, they operate at different scales.
A more general review of CRISPR applications in potato is here, which may include more information if I have misunderstood something.
Another application that may be relevant is using CRISPR to modify the genes governing self-incompatibility in potato, which makes it easier to breed potatoes.


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How does an engineered supressive Lethal (when present in 2 copies) gene drive spread through a population until causing population extinction?
I understand that at the molecular level a CRISPR mediated gene drive works by copying the altered gene (and the drive containing CAS enzyme, and guide RNA) into the other chromosome containing the wild type allele through homology directed repair...Lets consider  a suppressive drive that is designed to be lethal when the altered gene is present in Both copies of the chromosome (for example maybe organism is likely to die of a heart attack before reaching reproductive maturity)..... In a  lethal suppression drive as described above, Where is this copying  and homology directed repair happening. In the somatic cells of one of the “parents”, or the germline cells of  the parents during meosis/gametogenesis?  What happens when a organism containing wild type allele mates with an organism containing the drive?
If the drive and altered gene is copied in the somatic cells of the organism that was inserted in, then wouldn't the organism perish before, being able to pass on the drive/altered gene (given how our suppression drive is designed being lethal if both copies of gene are present)?
Or is this copying happening during when the offspring is a zygote (thus all off offsprings somatic cells), or the germline of the offspring? If the copying is occurring in the Zygote stage, all somatic cells of the offspring will contain two copies of the altered gene and will be Homozygous recessive for the altered deleterious gene. Then how will the offspring be able to mate and SPREAD the drive before perishing (or not being able to reproduce).
How is it ensured that drive copying only occurs during gametogenesis and does not alter the somatic cells in either parent or offspring? Because it seems to me for the drive and the altered gene to spread it can only happen during meosis/gametogensis...

Have you read, for example, the Wikipedia article on gene drives, or review articles like this one or this one?

Yes I read the Wikipedia and review article Did not quite clarify where and when the homology directed repair/copying is occurring for a suppressive gene drive.., Let us consider a suppressive drive that is supposed to kill organism before reaching reproductive maturity.  Is this occurring during gametogenesis of the organism that contains the drive? Because in suppressive gene drives having TWO copies of the deleterious gene kills the organism, but one copy is benign. So if HEG/copying is happening in the somatic cells wouldn't the organism just die before able to pass gene?

Crossposted on Medical Sciences SE

I have closed the copy on Medical Sciences as I believe it is a better fit here.

@MattDMo I think an answer based on those sources would be excellent.


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Are CpG sites always palindromic? If so how?
I'm having a bit of difficulty understanding why CpG sites are said to be palindromes. In what sense are they palindromes? Like they always have this shape CGGC? (for example)

CpG motifs are always palindromic. A palindrome is something which reads the same way forwards as it does backwards. A palindromic sequence is a DNA sequence which gives you the same string of nucleotides regardless if you are looking at it on the forward or the reverse strand, so long as you are reading in the same (5' → 3') direction.
Notice that the nucleotide sequence of a CpG island is just CG. So on the forward strand you might denote the sequence 5' CG 3'. On the reverse strand, the sequence is 3' GC 5'. So long as you read both strands in the 5' → 3' direction, you end up with the same nucleotide string: CG. Therefore, because the nucleotide sequence is the same in both the forward and reverse strands, a CpG motif is a palindromic sequence.
An example of a sequence which is not palindromic might be 5' ATT 3' on the forward strand and 3' TAA 5' on the reverse strand. On the forward strand, the sequence is ATT. Reading 5' → 3' on the reverse strand, the sequence is AAT. Because ATT ≠ AAT, this sequence is not palindromic.

Gotcha! now it make sense :) thanks


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What keeps pyridoxamine phosphate inside the aminotransferase enzyme active site?
In the function of an aminotransferase enzyme after the first substrate (amino acid) has been deaminated there seem to be nothing binding the resulting pyridoxamine phosfate to the rest of the enzyme (thus defying the definition of prosthetic group).
So what keeps it inside the active site of the enzyme so that it is ready to donate the amino group when the second subtrate binds?
Bonus question: what keeps the lysine bound to the pyridoxal phosphate (internal aldimine) from losing a proton and becoming a quinonoid intermediate itself?

What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not simply to be an answer site, but rather a site that promotes self-learning with some expert help along the way.

Reading everything my course's book (Lehninger's Priciples of Biochemistry) has to say about aminotransferase enzymes in my opinion counts as an attempt to get an answer. And it seemed to me that the question was specific enough to show that I've done a bit more than little or no prior research. If this is not enough thanks for the info, I didn't know that.


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Does Ramon Margalef really stated in 1972 general criteria for Shannon-Wiener index interpretation?
I work as field biologist in Chilean System of Environmental Impact Assesment. Several reports made by colleagues use Shannon-Wiener index for characterizing the richness study area, with the following interpretation of the result:

H
Diversity

0
minimum

0.1 <= H <= 1.5
Low

1.6 <= H <= 3
Medium

H <= 3
High

The reference that "back up" this criteria is:

Margalef, R. 1972. Homage to Evelyn Hutchinson, or why is there an upper limit to diversity. In: Growth by Intussusception. Ecological Essays in honor of G.E. Hutchinson. E.S. Deevey ed. Trans. Connecticut Acad. Arts & Sci., 44: 211-235.

I didn't find the document, but I suspect that Margalef:
a) Never established these criteria
b) It is misinterpreted
c) Established these general criteria but without enough proof
My suspicion is based on the fact that in information theory, Shannon entropy does not have a straightforward interpretation.
So, does Ramon Margalef really stated in 1972 general criteria for Shannon-Wiener index interpretation? or:
Can Shannon-Wiener index value be used for assigning a "Richness Quality" to a Study Area without comparisions?

What do you mean "without proof"? These look to me like just labels - there's nothing really to prove.

I mean an argument, evidence or something convincing to the usage of those labels

Isn't that opinion-based? It seems like you just need help finding the document, have you tried asking your librarian?

A limited index of word occurrences for that volume of Transactions is available at hathitrust.org ; the cited paper appears present, but neither Shannon nor Wiener is shown present (but OCR could be an issue).  There are many other papers on the Shannon-Wiener index.

related discussion: https://www.researchgate.net/post/Does_anyone_have_experience_using_the_Shannon_Wiener_Diversity_Index_Score

To be clear, my suggestion to ask a librarian is not meant to be sarcastic or rude: this is part of a librarian's job. See for example https://academia.stackexchange.com/questions/134634/how-can-i-find-an-old-obscure-or-otherwise-inaccessible-paper-when-the-usual-m Librarians are trained professionals and an often underutilized resource.

Thanks for the aclaration and post Bryan, but I don't have an institution for asking a librarian. However, I will stop this search for the general (and more relevant question) about diversity index interpretation.


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Is there a way to isolate bacteria and viruses without a centrifuge?
Is there a way to isolate bacteria and phages from soil samples if you do not have access to a centrifuge? The purpose for which we need to isolate bacteria is for basic phage hunting.

Filtration? https://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_33-34/36462.pdf

Would be helpful if we knew for what purpose you need to isolate them.

Thank you. Please see edit.

In the seaphages discovery guide the protocol for direct isolation states:

Allow the sample to sit until particulate matter has mostly settled. This may take as few as 2 minutes or as many as 20 minutes. Alternatively, you can centrifuge these samples to hasten this process. To do this, balance the tubes and centrifuge at 2,000 x g for 10 minutes to pellet (i.e., force to the bottom of the tube) most of the soil.

So filtration is really doing most of the job in separating the phage from the bacteria. Centrifugation mostly just speeds up the process.

Filtration is the correct answer - the very first viruses were identified as being filtratable (using the technology at the time) agents that could pass through the filters when bacteria couldn't.
Basically for phage isolation from a mostly water sample you just need to get rid of the sediment and ideally any bacteria that might be there too. Sedimentation (i.e letting it sit, centrifuge to speed up, as in Johan Wikstrom's answer) works well, but the best non-centrifuge method is to let large particulate matter settle, then start with filter papers of different grades to remove particulate matter, fine sediments and then work up to 0.45 micrometre filters to remove bacteria.
Of course you also need suitable plates and liquid media with a suitable host bacterium. E. coli works well for many bacteriophages in the Lambda group, but many other species of bacteria have bacteriophages of their own.

Thank you to everyone!


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Production method of custom seed mir451? How to edit middle of a fragment?
I am trying to create a plasmid that produces mir451 targeting a new gene, so I need to alter the seed sequence. The seed sequence is 7 bp long, so I think that is too long for PCR mutagenesis. How do people generally alter sequences that would be in the middle of an amplicon? Buying it from gBlock or something is an option, but if I need to try multiple permutations that could get really expensive quickly. I haven't done any synthetic biology in a long time so sorry if this a basic question or it doesn't make sense. Thanks

I think 7nt is ok for site-directed mutagenesis, see older question here.
The size constraint comes largely from being able to have enough flanking homology 5' and 3' of the substitution on your primer (e.g. Figure 1 here). This provider suggests >=10nt of 3' homology, this other provider suggests at least 11nt on either side.
gBlock is almost certainly the fastest and removes the experimental error side, but if you need to screen a lot of combinations SDM seems workable.

Thanks that's helpful, I'll probably go with gblock first then maybe try SDM to test sequences if its cheaper


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How to figure out growth/culture conditions for a specific strain?
Specifically, I'd like to find out how to grow ME-3 L.Fermentum (DSM 14241) at home without any fancy equipment.
What food does it need? Sugar? Lactose? Something else? At what temperature does it grow? How fast?
How can I generally find answers to these questions? ME-3 is not the only strain I'd like to grow.
I know ME-3 grows in milk, but that doesn't work for me. Can I grow it in vegan milk? In just water with sugar?
I'm even more interested in finding ways to find out the answer to these questions. Where would you look to answer this? I tried to google it but it's hard. Is there not some cool data base that has growth conditions for every known strain?

Why not grow it in milk? Bacteria aren't vegan...

Another thing to consider is that, as an intestinal bacterium, L. fermentum is almost certainly anaerobic, meaning you need to culture it in conditions with little to no oxygen in the atmosphere. While not impossible, this is rather difficult to accomplish at home.

It's not anaerobic. ME-3 may not be vegan, but I am ;-) . That's why animal milk doesn't work for me.

I saw a paper where they were culturing it under anaerobic conditions. that's why I made the comment. Doing more research, I see that it's a facultative anaerobe, not obligate.

If you do not have any experience culturing microbes do not attempt this.
You are very very likely to contaminate your culture with things that could make you very sick or even kill you. Pathogenic microorganisms are part of our natural microflora and are a significant cause of hospitalizations throughout the world as a result of food poisoning. For this to work you would need some skills in both identification of microorganisms (to make sure you have the right one) and in sterile technique. Growing specific microorganisms is NOTHING like making yogurt or beer with high inoculums of culture organism that suppress the growth of contaminants, or even like starting a sourdough starter, where you have a relatively low inoculum but the right  the culture to the right bacteria/yeasts.
This would mean that you need, at a minimum, a microscope (with 40-100x objectives; for identification purposes), slides, a differential bacterial stain (e.g. Gram stain), sterilization equipment (for preparing media; this could be a pressure cooker), media and an incubator with the right conditions.
This organism needs some carbon, nitrogen and a number of elements to grow happily. I don't think you will be able to do this at home easily; it would require quite a bit of experimentation and you are likely to grow something nasty as a contaminant before you get a decent culture of your target organism.
The American Type Culture Collection recommends Medium 416 for growth of Lactobacillus group organisms. This medium is comprised of lactobacillus MRS medium from BD and contains:

Proteose Peptone No. 3 10g/L, Beef extract 10g/L, Yeast extract 5g/L, Dextrose 20g/L, Polysorbate 80 1g/L, Ammonium Citrate 2g/L, Sodium Acetate 5g/L, Magnesium Sulfate 0.1g/L, Manganese Sulfate 0.05g/L, Dipotassium Phosphate 2g/L.

Now this might look like a scary list of things, and fairly unobtainable, but beef extract is essentially beef broth, and yeast extract is hydrolyzed yeast. The Polysorbate is an emulsifier used to help solubilize the ingredients and as a carbon source. I don't know if it is obtainable outside of a laboratory setting. The other chemicals may be hard to find too, though citrate = citric acid (fruit acids, you can buy this in a supermarket), acetate = vinegar/acetic acid. Manganese and Magnesium might be obtainable as health supplement pills, but you would need to work out how much is in a pill and do some calculations to convert. As a bonus, supplement pills often contain calcium phosphate as a bulker/tableting agent. For the peptone you might be able to substitute milk powder or "protein shake" powder. You would need to know a bit of chemistry to for the citrate -> citric acid, acetate -> acetic acid, and etc. conversions.
The last problem is that the ATCC recommends that the organism be grown in 5% CO2 at 37 degrees Celsius (98.6 F). This requires a sealed incubator box, with a means to get the CO2 in there. You might be able to achieve this by chemical means, reacting some chalk (calcium carbonate) with acid, but it would take some experimentation to do so effectively. It should grow at lower temperatures too, but it will grow slowly, if at all. I don't know if the CO2 is a requirement or just something that helps with the growth. This is not an obligate anaerobe as suggested in the comments, but can grow anaerobically too (facultative anaerobe).

I don't know... I've made DIY yoghurt with all sorts of probiotics countless times and never got sick from it. Now I want to do the same with ME-3 yoghurt. It doesn't have to be a 100% only the ME-3 strain, i.e. it doesn't need to be sterile. As to avoid food poisoning, I just add some other standard yoghurt strains to the mix, e.g. L.Bulgaricus (found in most yoghurts) to create a stable environment. I've done this many times with cow milk. But now I want to do it without milk, i.e. vegan yoghurt. That's why I want to know what ME-3 (and other's that I want to grow as well) need to be happy.

The ATCC link leads to a a different L.Fermentum strain. Is this not strain dependent? ME-3 is DSM 14241, but somehow I can't find it in the DSM (why?). HOw would you find out the ATCC number of ME-3 ?

An MRS medium doesn't work for me, since my goal really is to make a vegan yoghurt that I can eat.

Also, I'm particularly interested in a general approach as to how I can answer these questions myself such I don't always have to ask this forum. I struggle with just googling it since I don't know what websites to go to. I take it from your answer that culture collections are the place to look for answers? Here I often struggle to find the type number of that strain. E.g. it took me a lot of googling to find out ME-3 is DSM 14241.  Is there not some great data base that has everything that there is to know about all known strains? What temperature, pH, salt content etc do they tolerate?

@AntonRodenhauser if you have an inoculum (i.e. the strain itself) this makes it a whole lot safer to do. Trying to isolate is a lot harder. If you do inoculate with other bacteria you will likely result in those dominating the culture, especially if they are ones that are already selected for growth in those media. You would have to do some relative growth rate experiments to work out how well it would work.

@AntonRodenhauser Not strain dependent as far as I can tell. Most bacteria of the same species will have no difficulty growing in the same medium.  ATCC may not have ME-3; as they are a public repository where things are "free" (you have to pay for shipping, handling and some recompense for time, reagents etc.) to the scientific community. ME-3 is patented, so can't be handed out for free.

@AntonRodenhauser for vegan substitutes - you would need to work those out for yourself. There is a whole community of scientists out there trying to make non-animal product derived substitutes for common lab reagents. Some have been worked out, but you would need to dig through the literature for that. You might need to look for individual components (e.g. beef broth = gelatin, minerals (particularly Ca I think), salts, collagen etc.).

@AntonRodenhauser Answering them for yourself can be difficult - we (microbiologists) have reference books and the like to work from, as well as received knowledge and the scientific literature. Culture collections are a good place to start. Generally what works for one strain will work for another within the same species, and even within genera, assuming no selective reagents added. Another place to look is pubmed - the scientific literature. Find a free paper (pubmed central...) and look at the materials and methods section. I don't think you'll find a giant tablulated database of any sort

@AntonRodenhauser as to why the DSMZ doesn't have it - probably similar to ATCC; patented so they can't supply it. It is registered with them as a strain though.

Thank you! That is all very helpful! I've marked your answer as "correct"


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Why does 360 degree rotation not seemed to ever have evolved?
Of the designs of species that have evolved, I am curious why a 360 degree rotation, like a joint that can spin, does not seem to have evolved, for example wheels or a propeller.
Like, is there some reason we would expect evolution to not be able to discover those forms, or does it mean that it didn't evolve because it never was that advantageous? Owls can rotate their heads very far but not over and over in one direction. It's hard to imagine that wheels or propellers would not give you an advantage considering cars, helicopters, etc.
I think it's a puzzle because I never thought there was any form that evolution could not produce, and it's hard to believe it could not evolve in a way that was advantageous. But I think the second option is the better of the two. Maybe rotational joints are structurally weak?

Does this answer your question? Why do some bad traits evolve, and good ones don't?

It's tough connecting a blood supply to something like a wheel or propeller- it would basically need to be dead. How do you connect muscles?

Those are bad examples. Would you replace your legs with wheels? Cars are pretty useless without roads. Also, helicopters are really big for something that hovers. Look at how big hovering animals are compared to animals that can't hover: hummingbirds and insects.  They guzzle fuel. You can't find that much food in nature to survive and even if you could you wouldn't be able to consume it fast enough. Hummingbirds drink sugar and barely eat fast enough to not starve to death. At the sizes flying animals exist at wings are more efficient.

It has. Look up ATP synthase. Or flagella

Actually there are propeller like features called flagellum (3) evolved on many organisms like plants, animal sperms (4), bacteria (1) and flagellates (2). There are known only one macroscopic form of such features in bivalves and gastropods (5) but it is used for digestion not for locomotion.
One reason why we don't see it everywhere is thought to be evolutionary constraints which means that some feature might give very big advantage but the evolution to this final working "product" goes through "valley" where half developed feature is discarded by selection as less advantageous to competing features (6). In case of rotating features there are thought to be too many physiological and physical "valleys" like nutrient transfer, friction, power transmission (6,7,8).
Second big reason is using wheel on terrain has many disadvantages like bad maneuverability and going over obstacles (7). Propellers in water have efficiency up to 60% and in air 80% but fish tails and bird wings are in range of 96-98% (9). Also there are known that even in human civilizations like in Mexico have discarded wheel as way for locomotion (10).
References.

Bardy SL, Ng SY, Jarrell KF (February 2003). "Prokaryotic motility structures". Microbiology. 149 (Pt 2): 295–304. doi:10.1099/mic.0.25948-0. PMID 12624192.
Silflow CD, Lefebvre PA (December 2001). "Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii". Plant Physiology. 127 (4): 1500–7. doi:10.1104/pp.010807. PMC 1540183. PMID 11743094.
Jarrell K, ed. (2009). Pili and Flagella: Current Research and Future Trends. Caister Academic Press. ISBN 978-1-904455-48-6.
Malo AF, Gomendio M, Garde J, Lang-Lenton B, Soler AJ, Roldan ER (June 2006). "Sperm design and sperm function". Biology Letters. 2 (2): 246–9. doi:10.1098/rsbl.2006.0449. PMC 1618917.
Owen, Jennifer (1980). "Filter-feeding". Feeding Strategy. University of Chicago Press. p. 89. ISBN 978-0-226-64186-7.
Gould, Stephen Jay (1981). "Kingdoms Without Wheels". Natural History. 90 (3): 42–48. ISSN 0028-0712.
LaBarbera, Michael (March 1983). "Why the Wheels Won't Go". The American Naturalist. 121 (3): 395–408. doi:10.1086/284068. JSTOR 2461157. S2CID 84618349.
Dawkins, Richard (November 24, 1996). "Why Don't Animals Have Wheels?". Sunday Times. Archived from the original on February 21, 2007.
Diamond, Jared (April 14, 1983). "The Biology of the Wheel". Nature. 302 (5909): 572–573.
Gambino, Megan (June 17, 2009). "A Salute to the Wheel". Smithsonian. Archived from the original on June 26, 2017.

Another problem is both parts need to be made of living tissue, which means it needs to have a blood/nerve supply, but can't have any connection or it wont be able oto rotate.

@John - "Nutrient transfer" covers blood. The nerves involved in locomotion are mostly proximal and end at the neuromuscular junction. Of course pain and proprioception are important, too, pain as a warning and proprioception for the cooperation of the whole, but... could they be done away with for specific joints? Probably part of what the OP was asking.

blood without blood vessels only works if the wheels are very small. diffusion scaleing the bane of weird biology.

This very question has been asked a number of times before. Maybe an answer to why this is not superior to legs (or any other appendage) is in order.
Your head, arms and legs don't move through magic. They move because they are attached to other bones by ligaments, muscles and tendons. There are ligaments surrounding each joint holding it in place, and blood vessels feed these living tissues as well as the bones themselves. When joints are forced beyond their anatomical limits, ligaments tear, tendons tear or snap, sometimes muscles tear, and blood vessels rupture. (That's why even a mild ankle sprain results in swelling.)
The closest thing to full rotation of the arms is found in gibbons (picture these animals gracefully swinging through trees.) The range of motion of their arms is amazing, and occurs due to elongated tendons, significantly different shoulder bony anatomy, and greater forelimb muscle strength. But it is not, cannot, and will never be 360 degrees, nor is there a need for it: they simply change hands to achieve their forward movement. If they need to change directions (go back) they pivot/turn around, not swing backwards.
An owl's head can rotate an astounding 270 degrees in either direction. Deceased owls were studied at Johns Hopkins to determine how they can do so without keeling over.

If humans attempted to turn their heads as quickly or as far as owls do, artery linings would tear, causing blood clots to form and potentially leading to a stroke not to mention broken necks, explained study author Dr. Philippe Gailloud in a statement.

To understand the details, read the link. It's short and of interest. Still, it's not 360 degrees. This is true for any joint in the body.
Why? Because it's physiologically impossible. Full rotation would tear apart the very things necessary for any motion at all in living animals. So no wheels or propellers, please. At the very first 360° rotation, the joint would be rendered nonfunctional, which would very likely result in a much earlier death.
People with Ehlers-Danlos Syndrome have stretchier ligaments allowing more extremes of motion, but that comes with its own problems. So it's not "better".


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Why does hemagglutinin transfection fail in HEK293 cells?
I have tried to transfect HEK293 cells with the Influenza A H1N1 PR8 Hemagglutinin expression plasmid.
https://www.sinobiological.com/cdna-clone/h1n1-hemagglutinin-ha-vg11684-ch
I used PEI MAX as the transfection reagent.
After two days of transfection, I lysed the cells and performed SDS-PAGE and CBB staining, but there were always no bands representing hemagglutinin compared to negative controls (cell lysates without transfection).
I followed the protocol below.
The same protocol worked previously for a different plasmid expressing a different protein.

One day before the transfection experiment, I placed HEK293 cells in a 6-well plate to reach a confluence of 50~70% the next day.
Mix 3.5 µg of the plasmid in 150µl of DMEM without serum
Mix 11 µg of PEI Max in 150µl of DMEM without serum
Mix mixture 2 into mixture 1 and wait for 20 minutes at room temperature.
Aspirate the medium from the 6-well plate and wash with PBS
Add Mixture 3 to the 6-well plate
Place the plate in a 5% CO2 37°C incubator for 2 days.
After 2 days, aspirate the medium from the dish
Detach the cells using a cell scraper and suspend in ice-cold 2ml of PBS by pipetting
(I have also tried detaching cells using trypsin, but it did not change the results.)
Centrifuge at 400g at 4°C for 5 minutes, and aspirate the supernatant
Resuspend in 1ml of ice-cold PBS
Centrifuge at 400g at 4C for 5min, and aspirate the supernatant
Resuspend in 100µl of RIPA buffer containing protease inhibitor cocktail
Vortex for 1 minute
Sonicate for 15 seconds
Keep on ice for 15 minutes
Centrifuge at 15,000g for 5 minutes at 4°C
Collect the supernatant
Perform SDS-PAGE and CBB-staining

How do you select for positively transformed cells?

I did not select positively transformed cells.

I performed transient transfection and lysed all cells on a plate.

So you have no control which cells where transfected?

Yes. I thought that there should be a band at about 60~70 kDa, which is the size of the protein. When I used a different plasmid, I could see the band.

Band after CBB-staining in step 18

“Yes. I thought that there should be a band at about 60~70 kDa, which is the size of the protein. When I used a different plasmid, I could see the band.” This might be confusing, but I don’t have positive controls.

I am asking about this because transfection efficiency is sometimes a problem. The plasmid carries a hygromycin resistance gene, I would select after the transfection. If this works, then there is another problem.

Selection by hygromycin sounds a good idea to check if there are cells that are successfully transfected.

Actually, it is not clear which is the problem: transfection, cell collection, or cell lysis. When I detached cells, I observed that cells adhered to the dish more strongly than the negative control or other plasmid-transfected cells. So, thinking that the cell collection method might be wrong, I tried trypsin and cell scraper, but the result did not change.

That's correct. The later two can easily be tested and optimized with any cell. In my experience these two rarely failed while transfection is more often a problem.


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Do afterload and stroke volume form part of a negative feedback loop in blood pressure regulation?
Blood pressure is the product of cardiac output and total peripheral resistance:
$\text{BP} = \text{CO} \times \text{TPR}$
Since cardiac output is the product of heart rate and stroke volume, we have:
$\text{BP} = \text{HR} \times \text{SV} \times \text{TPR}$
Stroke volume is determined by preload, contractility, and afterload. An increase in afterload leads to a reduction in stroke volume and thus a decrease in blood pressure. [1]
However, it then seems that hypertension, which increases afterload, would lead to a decrease in blood pressure and form a negative feedback loop. Is this in fact what happens in the human body?
Also, when total peripheral resistance increases, it seems to me that afterload should increase, leading again to a reduction in blood pressure. Nonetheless, peripheral resistance also directly determines blood pressure ($\text{BP} = \text{CO} \times \text{TPR}$). Which of these has a stronger effect?
1: http://pie.med.utoronto.ca/CA/CA_content/CA_cardiacPhys_strokeVolume.html

However, it then seems that hypertension, which increases afterload, would lead to a decrease in blood pressure and form a negative feedback loop. Is this in fact what happens in the human body?

Yes and no. If the only parameters affecting cardiac output were peripheral vascular resistance, then yes, a resultant decrease in blood pressure would occur initially with hypertension. And yes, that is what happens. However, it is quite temporary because there are numerous modulators of "blood pressure", as blood flow, especially to the head, is critical to survival.
There are baroreceptors located at points in the arterial vasculature  which, upon sensing a fall in blood pressure, cause the sympathetic nervous system to release positive inotropes, causing the heart to contract more forcefully to push out that increased afterload. There are cordioreceptors assessing the effect of every heartbeat; decreased BP causes an increase in heart rate.  Sensors in kidney arterial vasculature sense decreased blood pressure and preserve water and electrolytes to increase intravascular fluid volume. Etc, etc.
Which in the end boils down to

BP = CO x TPR

Thank you, can't upvote yet but I would. Is there a way to predict with any accuracy what the effect of changing one of these parameters (as in a pathological condition or upon administering a drug) would be? Right now, I feel like the answer is just "it depends on many variables", but I assume that wouldn't be of much help in a clinical setting.

Of course! These things are studied extensively in disease and drug trials. If we couldn't predict their effects, drug dosage recommendations and therapies for diseases would not be possible. I don't need mine to be the accepted answer, but if it was/is helpful, you certainly should upvote it.

Not really following your logic at all, but maybe it helps to think that the parameter that needs to be held constant to deliver sufficient/constant blood to tissues is cardiac output.
All you need is your first equation:
$\text{BP} = \text{CO} \times \text{TPR}$
to see that an increase in peripheral resistance will mean an increase in (mean) BP if CO is constant.
Anything else you argue from subsequent steps has to conform to this, or you've made an error someplace.

I agree that this would be the case if there were no feedback loops and the cardiovascular system could be modeled in a linear manner. However, why do you consider that first equation to be the 'primal' equation? For example, if you agree that increasing TPR increases afterload, which decreases SV and subsequently decreases CO, then surely increasing TPR both increases and decreases BP. I don't think we can simply assume that CO is constant.

@Quin No, you can't assume anything at all; for many possible parameters, the outcome is death and then you can simply assume everything drops to zero. I'm saying that what the body cares about is how much blood it gets, so generally that's the reference point it makes sense to consider from a perspective of homeostasis. From a perspective of illness, all bets are off, but it doesn't make any sense to assume homeostasis is absent, either.


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How to correct the different (background) fluorescence for different cell types?
I am differentiating mouse bone marrow macrophages in vitro. However, I found that the differentiated macrophages have higher background fluorescence (the unstained sample) in all channels, which includes both BV421 and AF-647. I also test this in single-stained cells and got similar results (therefore, I believe is not because of failed compensation).
I have these specific questions:

Is it common to see cells having different background fluorescence?
Are there any tools or algorithms to be used to correct such differences?
For publication/ presentation purposes, is it common to omit the plot of unstained control? I would like to know what is the convention.

I hope this is not caused by my experiment's failure. I found this thread, but the hyperlink does not work. Therefore, it would be great if you can also comment on what are the potential causes of this observation if you found that relevant.
Thanks!

Far from an expert here but I believe that there are many tools that can help you correct background fluorescence, here is one such.


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What retrospective analysis happens after a clinical trial fails?
After a failed pharmaceutical clinical trial, what retrospective analyses are typically performed to understand why the drug program failed the trial? For example, are further experiments done to determine whether it was due to inaccurately predicted pharmacokinetics versus whether the biological target was non-causal? Do such analyses look only at the data gathered in the clinical trial itself, or are there teams which do further experiments to understand the precise mechanism of the failure? Are there investigations to replicate and reproduce earlier data and reports that led to the green light for the clinical trial, in order to catch fraudulent data generated by company scientists?
Another way of asking this question: how do pharmaceutical and biotech companies internally implement the scientific method, given that they don't publish peer-reviewed biology papers with all their internal findings? In other words, to what extent do clinical trial failures advance our understanding of biology?
I am asking in particular about Phase 2 and Phase 3 trials, because they seek to answer whether Drug A improves Disease C. Typically, Drug A attempts to affect Drug Target B which was believed to play a causal role in Disease C, so I wonder whether there tends to exist a process for revisiting the hypothesized biology of Target B (and revisiting the process that led to hypothesis) after Drug A fails.

You mean as opposed to burying the results or falsifying them? Sorry, just being honest and cynical (it happens a lot. Remember, the majority of pharmaceutical companies are in it for the big bucks. Money spent with no profitable potential outcome is not to be followed by more, unless there are potentially REALLY BIG BUCKS!!! ahead.) This site, btw, expects you to show evidence of your research into answering your question before we do so. Strange for a Q&A site, but this is an advanced Q&A site, if you will.

I clicked the wrong close box, but I think that questions about clinical trials are not about biology. They may or may not be acceptable on SE Medical Sciences, but getting a useful answer depends on having a list member with experience in the pharma/biotech industry — not very likely.

I don't know what you mean with a trial 'failing'? I run clinical trials and to me, at least, a 'failed' trial is one where something went wrong enough such that it caused erroneous data (e.g., inappropriate test design for the specific outcome measure), no data at all (e.g., fatal technical failure that could not be resolved) or other causes (e.g., COVID regulations that restrict patient access). I bet that's not what you're after.

@AliceD -- I have reworded the question to clarify that I meant that the drug program failed in the clinical trial. This is of course the fault of the drug program, not the trial itself.

@AliceD - I suspect that the OP is asking what happens if a newly developed substance is tested and fails to have the desired effect, but I'm not sure, as a drug program isn't a term I'm familiar with.

Yes, that's exactly what I'm asking!

What phase of trial?

@BryanKrause - Phase 2 and 3. I added clarification and explanation in the original question.


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Research surrounding visualisation (inner eye)

Aphantasia is the suggested name for a condition where one does not
possess a functioning mind's eye and cannot visualize imagery.

I have self-diagnosed aphantasia, so I might be asking a question that is obvious to everyone, but completely alien to me. In that event, I am asking for a 2-3% minority of the population that have aphantasia.
I cannot visualise faces or people at all. When I close my eyes and try to visualise the rubics cube on my desk, at my worst, I don't see anything at all and at my best, I see something like each of the two images on the right (and that's really pushing it):

How are other people able to visualise a rubics cube, in how much detail? Is there research surrounding this?
Some people state, they are able to vividly visualise faces, people, their clothing etc. If they can visualise a face, with all it's details and complexities, how are they completely unable to visualise a simple string of numbers? Because if they could, they would be able to do complex arithmetic calculations inside of their head.
Since I am not (or barely) able to visualise I would like to comprehend how other people are able to visualise anything. For example, I can easily calculate something like this in my head:

If I was able to visualise things, what's stopping me from doing this in my head, and a lot more?:

Other people can't even do "5727:3". The article on wikipedia suggests that people with aphantasia often become mathematicians or engineers, which seems counter intuitive to me, as being able to visualise would give me a great advantage in either field. I cannot wrap my mind around how someone can visualise an entire face but fail to visualise a few numbers in a grid and failing basic arithmetics.

You might not get anything here, but our sister-stack [psychology.se] might be able to help. Be sure to take their tour, read their help centre etc, and be sure to include some instances of prior research to satisfy their standard requirement for it.

The question indeed is better suited for Psych & Neurosci. However, before migrating, I need a clear question from you. I cannot make up what you want to know. Literature on aphantasia? If yes, about what aspect? Or do you need a diagnosis of some kind? If yes, please seek professional help (self-help questions are offtopic here and on Psych&Neurosci). One way to bring focus to a question is by adding prior research efforts on your side. That can help to crystallize a focused question.


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What is the difference between growth hormone and growth factor
What is the difference between growth factor and growth hormone?
I am aware of the fact that hormones are directly poured into the blood stream and that the growth factors can be released by non endocrine organs.
But how else do they vary from each other ?
And are they functionally different and if yes how?

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not simply to be an answer site, but rather a site that promotes self-learning with some expert help along the way.

Plugging your exact question title into Google yields many helpful resources.


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How can a layperson get their hands on a specific strain that's not readily available commercially?
I'm mostly interested to get my hands on L.plantarum D-103, but there are a few other strains as well. D-103 is e.g. mentioned here https://meridian.allenpress.com/jfp/article/80/10/1682/199965/Degradation-of-Histamine-by-Lactobacillus . It's commonly found in miso. My understanding is that the usual way is to find out an active culture collection like the ATCC, and the number that strain hast at that culture collection. But how do I find out this number? (I think it's called the type number).
With D-103 specifically the problem seems to be that it's not available at any active culture collection. It's listed as IMAU70005 (I had to google for ages to figure this out, how would you guys figure this out?), but the IMAU is not an active culture collection. What do I do then?
I'm not a biologist, just a lay person.

Generally what happens in the scientific community is you go to a culture collection - there are lots of different ones around the world. If they don't have it available, then you write to the authors of a paper on it and ask if they can share some.
In the past this used to be simple; however, now that universities and similar institutes have become much more commercially focussed, they have started to put Material Transfer Agreements (MTA) on any product coming out of them. This means that if you write to an author, they may not be able to share things with you as they also received it under a MTA - though they might be able to direct you to their source. You would also likely have to sign a MTA with the supplying institute (even the ATCC and similar usually have MTA these days), which would restrict what you could do with the material and how long you can keep it and any derivatives for. You would need a lawyer to look over an MTA if you went down that route.
Another complicating factor is that they will be very reluctant to share anything with someone outside of a research institute, for biological safety reasons among many others.
Long story short: you probably can't get these sorts of things easily.


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Non-toxic reporter gene or other transgenic DNA integration verification method that does not kill/damage organism?
I have been thinking that I will just use EGFP to know whether my attempted transfection was successful, but I've been coming across some publications that over expression of GFP can cause cell death. I need to create a stable line of transgenic organisms that have rather delicate embryos, and the organisms themselves are mildly fluorescent, so I am concerned that I need to hit a sweet spot of fluorescence that may be difficult to achieve. Too much and my cells die and too little and its not detectable. Does anybody know of another method that doesn't require expression of fluorescent proteins and doesn't require me to kill my organisms for sequencing?  Thanks.

Have you investigated low copy expression vectors? If they are mildly fluorescent; which colour, and have you thought about RFP or another colour vs GFP?

beta gal, maybe? https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwi00O7ggN_8AhWVADQIHZTzAQEQFnoECBEQAQ&url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fam%2Fpii%2FS0141022921001435&usg=AOvVaw2eymUOIzNHuPITIS2yVzHp


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What happened to dead cells which still keep DNA information?
I heard that the destination of dying cells is either one of them: Apoptosis and Necrosis. Further I heard that apoptosis causes destroy of cell components and necrosis is caused by autolyses.
But we can do DNA profiling from supposedly dead cells. How is DNA stored in dead cells? Those cells not dead by any chance? Otherwise, the core occasionally remain safe even during such destroy process in Apoptosis or Necrosis?

In apoptosis, the nucleus falls apart, DNA is fragmented, and cell contents are packaged into vesicles which are then degraded by phagocytes. I suppose there might be fragments of DNA that could be sequenced before phagocytosis occurs.

@iowf Thank you for the insight. That makes sense to me. Cells are surely dead and destruction process happen but there are many cases that fragmented DNA components remain safe enough to investigate. Now this is my latest understanding.


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Antibody structural determinants of epitope size
I am curious whether there are structural correlates in antibodies that relate not to epitope sequence but to epitope size. Specifically, I imagine that the antibody-epitope interface size is constrained to some extent by the structure of the variable regions that confer specificity, which likely do not have any direct interaction with the epitope.
Put another way, taking this illustration below from this educational site, it seems to me that the $V_{H}$ and $V_{L}$ portions (including hypervariable regions) that are not necessarily part of the orange "hand" interacting with the antigen, but rather lead to the gross shape of this "hand", can significantly affect the size of the epitope independently of the epitope linear sequence (assuming a linear epitope).

I'm aware that epitope prediction is an extremely difficult computational task, so presumably there is not a straightforward structural encoding of epitope size. Nonetheless, I'm curious if anything is known.
I found this question pointing to a paper that indicates substantial variation in the size of the epitope, leading me to believe that such an epitope size-antibody conformation relationship might be possible. This possibly suspect company page indicates some very small possible epitope of 5 amino acids or less, which would suggest a high degree of constraint in the interface if true.

Slightly OT, but why do you think that page is "possibly suspect"?

@MattDMo It's a marketing page without supporting data, i.e. "trust us". I don't personally doubt that it's more or less true, but I've noticed that SE Biology tends to be pretty critical of such sources.

I agree. I used to work at an antibody company, and we had tons of internal data that we'd never release, because it's proprietary and gave us a business advantage. No so good for an open-access site like this, but good for the customers who believed the marketing (which was for the most part rather accurate, I must say).


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Do all animals with eyesight get an upside-down image on their retina, or is it right-side up with some?
here's as good an image as any for showing the thing about human vision that I am asking about:
So, our retina gets an upside-down image.
My question is, do all animals' eyes work this way? Or do some have their cells report the image as-is?

How do you know that ours don't? How would you tell if another animal does?

"Or do some have their cells report the image as-is?" You can't objectively make judgements about perception since perception is subjective. You might as well ask what the colour red looks to different animals. Think carefully about what you mean when you say "report image as is". Relative to what? Relative to your inner ear says is down? That's not going to change how you interpret the world because "down" in the image is still going to be perceived as "down" in your ear.

Look at your image (which is not quite right, btw.). Where, exactly, does the angle of light entering your eye change (there are actually three places). Any animal with a cornea and a convex lens will have an inverted image on their retina if their eyeball is deep enough. All you need to do is a search for which animals don't have the above to know if they have an inverted image on their retina or not.

https://www.cell.com/current-biology/pdf/S0960-9822(05)00441-0.pdf

@bob1 - Physics. Plain old physics. This has been studied extensively in almost every animal. Not sure exactly why, but it has, and it's interesting.

@anongoodnurse I was thinking along the lines of insects, crustaceans etc, where there is no lens etc. My point was to get OP to think.

"How would you tell if another animal does?" Ah, I didn't read this carefully enough. Thanks.


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Specific Heat Capacity and Thermal conduction of Blood
Is the specific heat capacity and thermal conductivity of animal blood (e.g., steer for beef) and bird blood (e.g., broilers, ducks) [e.g., immediately after slaughter] similar/same as human blood?
I found regarding human blood:
Specific heat capacity = $3300-3900$ Jkg$^{-1}$ $^\circ$C$^{-1}$ (average $3617$ Jkg$^{-1}$ $^\circ$C$^{-1}$) (https://itis.swiss/virtual-population/tissue-properties/database/heat-capacity/)
(For Americans that's $0.788-0.93$ BTUs lb$^{-1}$F$^{-1}$) (average $0.86$ BTUs lb$^{-1}$F$^{-1}$).
Thermal conductivity = $0.49-0.56$ Wm$^{-1}$ $^\circ$C$^{-1}$ (average $0.52$ Wm$^{-1}$ $^\circ$C$^{-1}$) (https://itis.swiss/virtual-population/tissue-properties/database/thermal-conductivity/)
(For Americans that is $0.2848-0.3248$ BTUs hr$^{-1}$ft$^{-1}$F$^{-1}$) (average $0.3$ BTUs hr$^{-1}$ft$^{-1}$F$^{-1}$).
Is this the same/similar for animals and birds? Where can I find this info?
Thanks a ton!

I have no evidence, but I'd suspect so, the compositions are very similar.


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Ducks highest body temperature
Normal body temperature for ducks are 106-108°F (41.1-42.2°C).
Young ducks 102-106°F (38.9-41.1°C).
How hot can a duck's body temperature get?
Possible causes are fever and viruses, as well as stress hypothermic response.
Will it ever reach 113°F (45°C)?
What will be the cause?
How common is it?
Thanks a ton!

Welcome to the site. Please visit the [help] and take a [tour] for more information on what we do here and what make a good question and answer. Please also note the homework policy. In that light - what have you found out about this. A quick search leads to some very relevant papers with great detail as the top links.

The only thing I found so far was temperatures caused by injecting the duck with different pathogenic constituents for testing purposes, it also says "When they were handled to apply treatments, the ducks developed stress hyperthermic responses", but not so sure how to read those charts, looks like it reached +-43°C due to the injection. Not sure how common this is. I heard that it can reach 45°C, but cannot verify it nor the cause.
https://www.researchgate.net/publication/51150900_Body_temperature_responses_of_Pekin_ducks_Anas_platyrhynchos_domesticus_exposed_to_different_pathogens

You can probably generalize from other birds - just as you can for most mammals. Max I have seen is 46 C being fatal.


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Why is random protein selection not used more often in biotech to create proteins with desired enzymatic activity?
mRNA/cDNA display allows random libraries of up to ~ 10^13 proteins to be subject to selection for binding to arbitrary binders. In the listed studies, proteins selected for ATP binding also had ATP hydrolysis activity. This likely means that selection for transition state analogue binding can create enzymes as well, or at least functional uniform binders. More stringent selection schemes with lower diversity can then be used to improve this initial activity.
Functional proteins from a random-sequence library
ATP selection in a random peptide library consisting of prebiotic amino acids
The question is, why isn't this process used more in biotechnology to create proteins with the desired enzymatic activity? Is scouring database for appropriate natural proteins that much more better, or are there technical barriers that I'm missing here?

Used more often in biotech to do what?

To create proteins with desired activity for what purpose? "Biotech" is extremely broad, covering everything from basic research to pharmaceuticals to food to engineering problems.

I have narrowed it down to enzymatic activity.

Think about it - if you can find an existing protein with [some of] the characteristics you desire, why would you go through the bother and expense of creating something from scratch?

I'm not sure if this is the kind of tools you are asking for. "https://pubmed.ncbi.nlm.nih.gov/16919347/". They uses an evolutionary algorithm to search proteins with high enzymatic activity.

Think about it from a numbers perspective. Briefly, $10^{13}$ is a very small number in the combinatorics of protein sequence space.
There are $20^{100} = 1.267651*10^{130}$ possible peptides of 100 amino acids, a rather small protein. That's more proteins than there are atoms in the universe by 50 orders of magnitude. If you like, here's a paper I found via google that happened to pick this same example, they also have some discussion of the sequence space of naturally occurring proteins.
Do you want to do $10^{117}$ such $10^{13}$-plex random peptide experiments to on average 1X sample that 100 amino acid sequence space, or do you want to do one single $10^{13}$-plex mutagenesis experiment on a known protein that kind of does what you want already, which will let you readily sample the local sequence space around that protein?
You can undoubtedly shave a few orders of magnitude off there by encoding your random peptide generative model with non-uniform aa sampling, structural motifs, sequence Markov models, or whatever. But that isn't going to help you very much. You could also argue that you don't have to exhaustively sample the space as long as you get in the locality of something useful. But a useful protein is almost certainly longer than 100 aas, so you still need to sample astronomical numbers of random proteins.
Even if you get lucky with your random polypeptide approach, you are almost certainly only sampling an unoptimized protein, so you will have to turn around and optimize whatever random polypeptide you find.
The existing protein can admittedly probably only get you to a local optimum. But the search for the global optimum is through an incredibly massive domain of possible proteins.

I was expecting more of a technical than theoretical answer. My intuition is that every approach will have pros and cons, and random protein generation has to have pros too. It would depend on the details of the process.

@symmetrickittens certainly, I've addressed the pro already: it's possible to search for a globally (or "less locally") optimal protein. That could readily be worth the search, we have no reason to expect that existing enzymes are globally optimal! As for theory vs. technical, search through sequence space is theory, on their own the numbers are pretty daunting. Empirically, consider the ratio of de novo gene birth vs. gene duplication as ways of generating useful genic sequence in genomes (a ratio of "very few" to "almost all"). If I have a little time later, I can try to add to question.

@symmetrickittens put differently: when the numbers are this far against you, the theoretical becomes the technical. My knowledge of the breadth of the Pacific Ocean is theoretical, but it gets technically useful when considering whether I can row to Australia from the N. American west coast.


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Can we improve the hemocompatibility of VAD by growing a single layer of endothelial cells on the surface?
Maglev centrifugal pumps have been used in the latest ventricular assist devices (VAD) and several experimental total artificial hearts (TAH). Compared to previous generation pumps, maglev pumps don’t have any moving parts (joints, bearings, etc.), which greatly reduces the risk of coagulation. However, the risk of blood clotting is still not eliminated. Normally the bloodstream is lined with vascular endothelial cells, which secret anticoagulants to prevent blood clotting in the vessels.
So I come up with an interesting idea. Can we prevent blood clotting by growing a single layer of endothelial cells on the surface of the stator and rotor? We have successfully cultured many animal cells. By adding a few animal cells and culture medium into a bottle, the cells will grow into a single layer of cells along the smooth surface of the bottle. Because there is no moving part inside maglev pumps, it would not be difficult for endothelial cells to adhere onto the surfaces. The blood can serve as an ideal culture medium which provides nutrition and carries away metabolic wastes. So if we can grow endothelial cells on VAD or TAH, will it eliminate the need to take anticoagulants?

"By adding a few animal cells and culture medium into a bottle, the cells will grow into a single layer of cells along the smooth surface of the bottle" - oh really? What makes you think that?

So what else does it take?

The answer to that question would fill textbooks.

I know there are many other things required like temperature, pH, disinfectants and growth factors, but I don’t think this is a big problem inside our own body.

Our body is the best cell culture.


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Which organ receives blood from arteries and veins at the same time?
This is a question in my exam paper.  I answered 'the heart' as it receives blood from venae cavae and the coronary arteries.  However the correct answer should be the liver.  How is that so?

The questions is not very good. The lung is another organ which receives blood from arteries and veins at the same time.

The liver gets all the venous return from the GI tract, so it may well be the largest organ getting venous blood. But the question is a bad one, as every organ needs arterial blood and a number of them deal with venous blood as well (liver, spleen, lungs and heart off the top of my head.)


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Estimates for the volume and mass of most ancestral multicellular organism, and a similar question for alive animals with radial symmetry
please I'm interested in an estimate for the volume and weight, the mass, of (most) ancestral multicellular organisms. Wikipedia has the article Multicellular organism, and my main interest are estimates for ancestral eukaryotic groups (the oldest and simplest of these fossiles) in the International System of Units.
Other question of my interest are the same estimates of volume an mass for alive animals with radial symmetry. I apologize if my question bother some user of the site Biology Stack Exchange, I'm not a biologist. Wikipedia has the article Symmetry in biology, and I clarify that the approximations/estimates are for a typical specimen of the cited in this paragraph: alive animals with radial symmetry.

Question. Please provide estimates for the volume and the mass, of (most) ancestral multicellular organisms, and for the volume and the mass of a typical animal (of our geological epoch) with radial simmetry. Many thanks

I'm motivated to ask these questions after I read the book by Walter Álvarez [1], and inspired in  a graphic, the Figure 2.1, that refers the book [2] by John D. Barrow. I know the Spanish editions of these books.
References:
[1] Walter Álvarez, A Most Improbable Journey: A Big History of Our Planet and Ourselves, W. W. Norton & Company, (2016).
[2] John D. Barrow, The Constants of Nature, Jonathan Cape; 1st edition (2002).

Please if my question isn't suitable for the site add a comment, I can to delete the question in next hours.

Welcome to the Biology Stack Exchange. Please take a [tour] and visit the [help] for more information on what we do here and what makes a good question and answer. Note that we usually ask that the OP make some attempt at answering the question for themselves. We also have a requirement for answers backed with references - which might be a challenge for this question. I would guess multicellular algae, <1 mm across and a few micrograms in mass.

Many thanks for you kind messages. I'm mathematician, I am not able to answer my question, I think that I'm not able to answer the kind of questions that I'm asking in this site Biology Stack Exchange, these are of my invention since I'm curious about from the books that I read @bob1 . I don't know how to search information related to Biology, and I add the encyclopedia Wikipedia as general reference for all users and because my English is bad. If you want, please expand you comment in an answer.

The browser of Google has an answer for "What is the oldest known fossils of multicellular eukaryotes?", but I don't know how to estimate the density and length/volume of a fossil (estimates for the organism corresponding to the fossil, when this organism was alive). I'm agree with the requirements of the site and I add the promise of make more attempt of answering my questions @bob1

I'll convert this to an answer...

So, it looks like it all depends on how you define multicellular - living in mats/biofilms, which are often mixed species, isn't necessarily a multicellular organism, even though it can behave like one, but might be one of the steps along the pathway to being multicellular.
In addition, organisms that live as a group/chain of cells (such as Spirogyra, or many bacterial species which grow in clumps or chains such as Staphylococcus aureus or Streptococcus pyogenes) are not necessarily multicellular organisms.
The earliest I could find that seem to fit the description of Eukaryotic and Multicellular is a report in PLoS Biology entitled: "Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae" (Bengtson et al, 2017). In this paper, they discuss fossils of a couple of thallate multicellular red alga from about 1.6 billion years ago (Palaeo–Mesoproterozoic).
They state that the structures are:

The 58–175 μm wide Rafatazmia tubes are up to ca. 2 mm in length

and

The thalli are megascopic, ranging from approximately half a millimetre up to well over 3 mm across.

So - pretty small. I don't know how this equates to mass, but I would guess a wet weight (i.e. living state with no additional water) of about 0.5 grams.
Full reference: Bengtson S, Sallstedt T, Belivanova V, Whitehouse M (2017) Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae. PLoS Biol 15(3): e2000735. https://doi.org/10.1371/journal.pbio.2000735

Thank you very much I will study your post. It looks like one of the most nice posts I've seen on these sites Stack Exchange. The origin of biofilms seems misterious and fascinanting (I didn't know this article of Wikipedia about biofilms). Many thanks for your work (your remarks  and bibliography) that will be interesting for your colleagues; next time I try improve my research about the questions that I'm asking, but your work is unbeatable. My main interest was the details that you've provided.


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Single-cell subcloning of BV-2 cells?
I am trying to knock-out genes in BV-2 cell line. However, the majority of protocols require cell subcloning and expanding. I tried to subcone these cells and grow clones in DMEM+10% heat-inactivated FBS+1% PS (usual media I am using)+Insulin-Transferrin-Selenium. My cells did not grow and eventually died. Maybe there are supplements that I can add to the media to promote cell growth from one cell? I am considering using conditioned media from the same BV-2 cell culture after culturing them for a few days. Should it work?

Welcome to the Biology Stack Exchange. Please take a [tour] and visit the [help] for more information about the site and what we do here. This isn't a simple question and answer site, so things are a little different to more conventional forums.

We would need a few more details on how you go about your subcloning to troubleshoot why it isn't working.

As always, consulting reference materials is a good idea: https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/cell-culture-and-cell-culture-analysis/mammalian-cell-culture/poor-cell-growth

I am growing these cells routinely in the lab, and they grow fine with usual media (cell thawing is always successful, they are not contaminated etc.). When I do subcloning i calculate cells so there is one cell in 100ul media. And then i seed them in 96-wp. After they attach i search wells where is only one cell in the well (subclone). And the next step would be expanding the subclones. I read articles where similar things were done and did not find any specific requirements for successful subcloning.

Are your knockouts lethal?

It shouldn’t be, I am knock-outing CB1 and CB2 receptors (separately).  There are also transgenic mice without CB1 (it results in 30% mortality in mice if knockouted in whole organisms). Mouse who doesn't have CB1 receptors in microglia cells are fine as far as know.


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Is there a name for this type of diagram?
Is there any commonly used name for this type of diagram / symbology? I have not been able to find them referred to by any name.

is this what you are looking for https://en.wikipedia.org/wiki/Block_diagram

The glyphs themselves come from SBOL visual: https://sbolstandard.org/visual-glyphs/. You could look in the spec to see if they refer to the diagrams as something other than an SBOL visual diagram.


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Can macrophages phagocytose viruses directly?
I've been reading that Macrophages, members of the innate immune system, can actively track bacteria and protozoa to devour and destroy them. In the same way, can macrophages devour free viruses, in blood for example, 'actively'? I can understand that random phagosomal uptake might contain virus particles, but by 'active' uptake, I mean the process by which it tracks bacteria to engulf them.
I guess not, but I need an answer. Would be grateful if a source, like a textbook, is provided as well!
Thanks in advance.

Welcome to the site. Please take a [tour] and visit the [help] for more information on this site and what we do here. In particular note that there is a homework policy that requires an attempt from the OP to answer the question for themselves. On that note - what do you know about the immune system and how it works to label foreign bodies?

If the viruses have been opsonized, macrophages will phagocytose them. I suspect that direct phagocytosis of non-opsonized viruses would depend on the type of virus and the surface molecules it expresses.

@MattDMo thanks for the response! Any example of viruses macrophages phagocytosing non-opsonized viruses?


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Sources of chlorophyll fluorescence
I have been reading this article recently, which claims that photoinhibition of photosystem II can have measurable impacts of chlorophyll fluorescence. This confused me, however, because photoinhibition (at least as the article describes it) occurs mainly in the PSII reaction center, and I had thought that the majority of chlorophyll fluorescence was caused by excitations that form in the antenna and don't reach the reaction center in time before they decay (after all, there are many more antenna chlorophylls than reaction center chlorophylls). With this in mind, how can it be that photoinhibition of the RC modifies the F0 value of chlorophyll fluorescence data?

Not an expert in this field, but a dig through the literature seems to indicate that the chlorophyll fluorescence that is generally referred to for measuring photoinhibition is indeed localized to or associated with the PSII reaction center. In case it is in question, there are estimated to be ~100 chlorophylls directly positioned within the PSII.
I don't know the basis of your supposition about the excitations that never reach the reaction center, so I'm not really sure how to address it. This paper writes that the efficiency of excitation reaching the reaction center is actually quite high in realistic physical simulations. A quantity of interest here is $L_D$, the parameter controlling how far an excitation can travel readily through a photosystem before being lost; I was not able to readily find their estimates for this value though:

Most of the LHCIIs in the mixed membrane are surrounded by PSII-S within a radius of $L_D$, which led to the 82% maximum quantum efficiency of the membrane upon uniform chlorophyll a (ChlA) excitation.

This review links chlorophyll fluorescence to PSII phenomenologically and theoretically but does not directly address the mechanism:

Changes in the yield of chlorophyll fluorescence were first observed as early as 1960 by Kautsky and co‐workers (Kautsky et al., 1960). They found that, upon transferring photosynthetic material from the dark into the light, an increase in the yield of chlorophyll fluorescence occurred over a time period of around 1 s. This rise has subsequently been explained as a consequence of reduction of electron acceptors in the photosynthetic pathway, downstream of PSII, notably plastoquinone and in particular, QA. Once PSII absorbs light and QA has accepted an electron, it is not able to accept another until it has passed the first onto a subsequent electron carrier (QB). During this period, the reaction centre is said to be ‘closed’. At any point in time, the presence of a proportion of closed reaction centres leads to an overall reduction in the efficiency of photochemistry and so to a corresponding increase in the yield of fluorescence.

In one rather blithe review, it is suggested that other sources of fluorescence are close to zero at relevant wavelengths, though they only mention PSI as a source:

At room temperature, we assume the variations in the fluorescence signal arise from PSII only and we ignore emission from PSI largely because the signal does not make a significant contribution below 700nm (Butler, 1978; Pfündel, 1998; Baker, 2008)

Looking into the Pfündel paper, they write in turn:

At room temperature, a small fraction of the absorbed light energy is re-emitted as chlorophyll a fluorescence. It is usually assumed that most of this
fluorescence is emanated by PSII, and that the PSI contribution is negligibly small (Krause and Weis 1991; Govindjee 1995)

Without following the citation trail any further, it seems that the general assumption in the field is that excitation "lost" to fluorescence of ChlA without a reaction center accepting the energy is pretty negligible. No one seems to be interested in distinguishing the total PSII fluorescence from the PSII fluorescence actually associated with reaction centers. This probably indicates that the two amounts are pretty close to identical.
For some validation of your intuition, this paper writes:

FV/FM works well for plants with Chl a/b antenna systems in which in vivo fluorescence is dominated by emission from Chl a associated with PSII. In phytoplankton, with their diverse antenna systems and thylakoid configurations, FV/FM must be interpreted with more caution [36], [52]. Taxonomic differences in FV/FM can result from contributions to the minimum fluorescence (F0) from pigments outside PSII (see e.g. [53]). Due to the fluorescence from such pigments, the measured values of FV/FM may depend on the excitation and emission wavelengths (unpublished data).

In other words, you need to be careful to account for fluorescence from non-reaction center-associated pigments but it's quantitatively not a large amount (though I haven't yet found a direct estimate despite a lot of looking!).


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What enzyme could you use to delipidate lipidated serine?
I have a protein with a serine modified with an O-octanoyl group (ester linkage). What enzyme could I use to remove this group? Could I use a lipase, such as pancreatic lipase?


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Can an amoeba go through states that would be analogous to pain?
Amoeba can move freely.  Would I be correct in assuming that this movement is not completely random?  Would it be correct to assume that an amoeba can seek out food and can attempt to avoid danger?
If this assumption is correct, would it be reasonable to assume that the amoeba has states which are roughly equivalent to being in pain? If this is not the case, what is it that motivates the amoeba to pursue food and avoid danger?  Or is it believed to be instinctual -- that is, fully scripted without a need to presuppose a pain state?

Update from a search on the web:
I did find this article which suggests to me that amoebas might also show avoidance behavior.

This question is about perception which can't be answered because perception is subjective.

I was thinking solely about behavior.  Does an amoeba ever move in a way that would indicate "avoidance" or in another way that indicates "targeting"?  I was thinking that the state that precedes avoidance or the state the precedes targeting might be analogous to a "pain" or "pleasure" state.  I agree that we can never know if a subjective state exists for an amoeba.

The second paragraph is not too different from asking whether free will exists, albeit at the level of an amoeba. "Pain" is a subjective state, if you take the subjective state out of pain you don't have anything at all. A chemical motivation to perform some behavior is, at a cellular level, no different than what happens in our own nervous systems.

See also https://biology.stackexchange.com/questions/36401/can-plants-feel-pain https://biology.stackexchange.com/questions/19446/can-insects-feel-pain https://biology.stackexchange.com/questions/60949/do-lobsters-possess-a-nervous-system-to-feel-pain https://biology.stackexchange.com/questions/60337/at-what-stage-is-the-nervous-system-developed-enough-to-interpret-neuronal-signa

@BryanKrause, I am unclear on your first comment.  Why does pain behavior presuppose a subjective state?  If an amoeba shows avoidance behavior, then there is a biochemical state that precedes it.  That's what I am interested in.  I call this "pain" only so much as :"avoidance" would suggest that state. If there is no such behavioral state of pain, what is motivating the avoidance?

@LarryFreeman I mean that pain is a label for a subjective experience. If you call anything else "pain", you should know that you are no longer using "pain" in the way it is used in the fields of psychology/neuroscience/biology. Avoidance doesn't require pain, nor does it require any preceding state: common avoidance and approach behaviors in single-celled organisms are directly chemically mediated. "Motivation" is similarly a fraught term.

@LarryFreeman Well, they do respond to stimuli in the environment if that's what you mean.


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What are the relative frequencies of dominance and codominance in genes underlying phenotypic characters?
Many questions already exist regarding dominance/recessive relationships, see e.g. here. I am asking this question because I have often wished to have it to refer to, and also genuinely curious whether someone has a clear answer grounded in evidence.
A common misconception that one encounters in genetics (especially as received from a high-school level class) is that all genes affecting a phenotype follow the classic Mendelian relationship of a dominant / recessive inheritance pattern yielded by diploid organisms. See for example this recent question.
It follows that many consider this relationship to be foundational to genetics rather than largely the result of ascertainment bias. In contrast, most quantitative genetics models perform well assuming linearity / additivity, i.e. "co-dominance". It is not clear whether this is an outcome of the real state of affairs, or simply that the additive model is "good enough" for summarizing the complex reality of underlying epistasis, dominance, etc (I believe "good enough", but that's somewhat philosophical).
My question is this: what proportion of variants with quantifiably large phenotypic effects fit a dominance model of inheritance?
The question is muddied somewhat by incomplete (but not co-) dominance, or the possibility of multiallelic loci with many alleles with a complex dominance hierarchy, as in this example. But I'd be satisfied with a rough quantitative estimate.
My vague sense is that most variants are better explained by an additive model, if only because their effects are rather small. In other words, I think that our fixation on dominance is a result of ascertainment bias inherited from Mendel. We then teach it to early students because it's simple and illustrates some important features of genetics. Am I wrong?

This seems like it would be exceptionally difficult to quantify. By far the most common cases of apparent dominance are going to be those involving enyzmes where a recessive allele is somehow non-functional, yet the product isn't limiting or negative feedback is present such that haplosufficiency is observed. Even then, though under some circumstances you may see some evidence of haploinsufficiency, or there may be some other allele that shares a phenotype with the "true" dominant allele, yet shows haploinsufficiency when paired with a true nonfunctional allele. How do you count that?

@BryanKrause I agree with the sentiment- it's hard! This is the kind of thing that variance partitioning claims to handle, but doesn't actually. Perhaps a more viable question would be something like how frequently variable characters segregate in a true Mendelian fashion following dominance, vs. complex, vs. additive or whatever. In which case, almost none would be dominant I'd bet! But it's highly contingent on the population and whatever other variation exists.

It is not clear whether this is an outcome of the real state of
affairs, or simply that the additive model is "good enough" for
summarizing the complex reality of underlying epistasis, dominance,
etc (I believe "good enough", but that's somewhat philosophical).

I think it is likely that it is both. Additivity is real biologically and isn't just convenient, but it is also true that if we had complete information about every genotype-phenotype relationship, we would improve our models a bit beyond the purely additive model (for many phenotypes).

My question is this: what proportion of variants with quantifiably
large phenotypic effects fit a dominance model of inheritance?
Proportion of variants in the genome would be hard to define. Most nucleotides are probably useless and don't significantly affect any phenotype, drastically reducing the proportion of dominant and additive alleles. The proportion of variants that effect a given trait is easier. This is different than "importance" of dominance/additivity: you can have a lot of dominant alleles with little affect, so the phenotype is overall additive but has more dominant alleles governing it, or vice versa.

We can try to get an idea of both the raw number and the variance explained. For a raw number, and picking educational attainment as an example, Okbay et al. 2022 looked at 2,574,253 people and found that their "dominance GWAS identifies no genome-wide-significant SNPs. Moreover, with high confidence, we can rule out the existence of any common SNPs whose dominance effects explain more than a negligible fraction of the variance in EA." The "combined variance explained by dominance deviations in common SNPs is negligible." Since they found thousands of additive alleles, the proportion of dominant alleles for this phenotype is zero. For other phenotypes, I'm sure someone has found non-zero dominance alleles.
It seems like the core of what you want is how much variance is explained by additive vs. dominance/epistasis effects. I don't like this too much for the reason you stated in your comment, but it's interesting nonetheless. There have been a number of estimates on this.
A study on 70 complex traits on 254,679 individuals "found strong evidence for additive variance," but negligible dominance variance" and "epistatic variance... not significantly different from zero." "Genetic variance for complex traits is predominantly additive." "Epistatic variance is likely to be extremely small in human complex traits." This replicated a similar earlier result that looked at 79 phenotypes. This was replicated again here with 50 phenotypes. Each time, dominance is negligible.
Hill et al. "evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close to 100%, of the total genetic variance."
Twin studies also support the additive model being predominant, with no effect of dominance for most phenotypes, but some effect for some phenotypes.
You wondered if it was the "the real state of affairs" or just "good enough." Here are some reasons why there might be real biological bias for additivity--though this isn't mutually exclusive with it being "just good enough."

Imagine if a gene for having a long neck was dominant in giraffes--it
would be impossible to eliminate the recessive allele from the
population (aside from genetic drift), as there is no phenotypic
difference between heterozygous and homozygous long-neck individuals.
Now imagine if there was simultaneously a different, additive pathway
to having a long neck. Selection would favor increasing neck length
via the additive pathway, as there would be decreased risk of one's
offspring having a short neck. In this case, selection inherently
favors additivity.
Mutations happen randomly. By definition, in
order for a new dominant interaction to occur, two mutations must
happen. If the mutations require each other to be useful, they'd have
to occur simultaneously to be selected for. On the other hand, a new
additive mutation being selected for only requires that a single new
mutation is beneficial.
Most
allele frequencies are biased towards one extreme or another.
Therefore, the remaining genetic variation between individuals is
likely to be of small effect and polygenic.
[Multilocus epistasis
itself mostly contributes to additive variance.][6]
The existance of polygenicity alone can be sufficient for a lack of dominance effects.

I like your list of arguments about "the real state of affairs", and it seems to be a good set of arguments that dominance is very uncommon, which is great because that's the point of the question. However, it is not a good set of arguments that additivity has a real biological basis- e.g. your point 4 is explicitly a "additivity is good enough" point. Overall, thanks for the comprehensive answer!

Right. I also agree that it is "good enough." However I do think at least points 1 and 2 are relevant to the biological basis of additivity.

Mm... I think that points 1+2 make arguments for the relative frequency of additivity under a toy model of selection. But they're not really biological arguments (as I usually think of them). They're saying effectively, "if additivity existed, then selection would like it." (A corollary of these is that additive variation would become fixed!) They're not saying "under the hood, there are biochemical, cytological, developmental, and ecological reasons why a certain genotype::phenotype map exists". The latter is more interesting to me, which shows my biases.

You may be interested in this paper: https://academic.oup.com/genetics/article/121/4/869/5997956

I don't have a citation for this, but I imagine a common biochemical reason as follows: imagine you have a typical protein-coding gene or promoter. You alter a random base pair. Odds are, the promoter or the protein is still going to function, just slightly better or worse as most amino acid sequence changes wouldn't have devastatingly large effects outside of specific critical regions (BRCA2 is a good example of this). You mostly modify the binding affinities by modifying a random base pair, which wouldn't result in dominance. If most mutations killed the gene, dominance would be more common