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Are there any proteins not found in the brain that are affected by prions?
A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–Jakob disease. These are both diseases of the brain. Are there any non-brain proteins that also have corresponding prions that can cause disease, or do prion diseases only affect the brain?

Yes, malformed prion proteins can affect tissues outside of the brain.
Via: https://www.merckmanuals.com/home/brain,-spinal-cord,-and-nerve-disorders/prion-diseases/overview-of-prion-diseases

Another familial prion disease has been recently discovered. It differs from other prion diseases because it causes diarrhea and affects nerves throughout the body years before symptoms of brain malfunction develop. It is described as prion disease associated with diarrhea and autonomic neuropathy.

Via: https://www.merckmanuals.com/home/brain,-spinal-cord,-and-nerve-disorders/prion-diseases/prion-disease-associated-with-diarrhea-and-autonomic-neuropathy

Symptoms begin when people are in their 30s. People have persistent watery diarrhea and bloating. They may lose weight. Because the nerves that control body processes are affected, people may not be able to pass urine (called urinary retention) or may lose control of their bladder (urinary incontinence). Their blood pressure may drop when they stand up, causing them to feel dizzy or light-headed (called orthostatic hypotension). People may lose sensation in their feet. Later, when people are in their 40s or 50s, mental function deteriorates, and seizures may occur.

Although it may hadn't be described, I think that nothing chemical or physical would be an impediment to affect other organs, so, said this, in my opinion they could exist.
I found this one affecting outside the brain
 https://www.nejm.org/doi/full/10.1056/NEJMoa1214747 , I hope that this it's useful to you.
Héctor.

Prion disease is caused when cellular prion protein (PrPc) is misfolded to form abnormal prion protein called scrapie prion protein (PrPSc). These newly formed abnormal prions can't be degraded by enzymes so they keep on accumulating and are responsible for stimulating other normal proteins to fold improperly and form protein aggregates.
Accumulation of these amyloids cause diseases and these misfolded prions can't be converted back to normal prion protein.
Via: https://ghr.nlm.nih.gov/condition/prion-disease#genes
These prion proteins (PrPc) are present throughout our body but in lesser proportion as compared to brain cells and  recent studies have shown the possibility of this protein aggregation the cause of diseases outside the brain,
Via: https://www.ncbi.nlm.nih.gov/pubmed/21481020
MAVS, RIP1, and RIP3 are other prion-like proteins which are found in other parts of the body. These are not responsible for causing any disease. These proteins aggregate into filamentous amyloid and lead to cell death to prevent the spreading of viral infection.
Via: https://www.nature.com/articles/s41418-018-0172-x


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Coagulation of protiens of different products
Protein of egg coagulates on 60 degree but proteins of milk do not coagulate at high temperatures..why?
What is the main reason behind all this?

Milk coagulates at a temperature below 18 degrees is what I do know.

I'll look into it for you.

source: Stack Exchange

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

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What happens when the conductance of a sodium channel increases?
My intuition is that, since the concentration of sodium within a cell is higher than the extracellular concentration, when conductance increases, this corresponds to the channel being open and means sodium will enter the cell. Is this correct? And what impact will this have on the membrane potential?

No, not quite. You are on the right lines, but incorrect in thinking that intracellular sodium concentration is higher.
At the resting phase of a neuron, there is less sodium inside the cell and more sodium outside the cell. An ATPase sodium potassium pump is constantly pumping 3 sodium ions outside the cell for every 2 potassium cells that enter the cell.
For voltage gated sodium channels to open, there must be a significant change in voltage, which can be triggered by the binding of neurotransmitter to receptors for example. This triggers the sodium channels open and sodium will flood into the cell due to a high concentration gradient (because there are more sodium outside than inside) but also due to an electrical gradient (the neuron is more negative on the inside; positive sodium ions will be attracted to the inside).
Because sodium is flooding into the cell, this will cause the membrane potential to become more positive (depolarised) and will eventually reach an action potential (30mV). After an action potential, the channels will become de-activated and shut. After a period of hyperpolarisation, the neuron will return to a resting state.
Source: https://en.wikipedia.org/wiki/Action_potential

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


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Can primers for PCR be duplicated?
Complete beginner question here, don't laugh:
If I have some primers that have been synthesized, and I am close to running out of them, is there any way to duplicate them / amplify them / synthesize more of them myself? I don't know the sequences.
Or is my only option to buy more?
Thanks

Short answer: You need to buy some more, but you need the sequence also for ordering.
Long answer: The Taq polymerase needs a piece of DNA (or RNA) to prime the reaction and be able to enlarge the DNA chain, this is why we use primers in the first place (also to ensure reaction specificity to the region we want to amplify). To enable the reaction you would need a primer complimentary to the one you used of about the same length (or at least not much shorter), so this actually doesn't really make sense, because you would have to have a primer to make your primer. Since primers are cheap today, order some more.

Thank you for your help


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Why does brain invert the image formed on retina?
I have been studying about the human eye and it's working in school for some time. I came across something. I have been taught that the image formed on the retina of the eye by the lens is inverted and the image is made erect by the brain so as for correct perception. But how does the brain know what is erect or inverted? Why doesn't it just keep the image as it is? Please note that I am asking why the brain reverses the image and not about the nature of image formed on retina.

No. My question is completely different

https://psychology.stackexchange.com/questions/337/why-would-the-brain-flip-the-images-perceived-by-your-eyes is also relevant and may be helpful though it repeats from the duplicate marked here.

Thanks I got the answer


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A biological system to measure time
First of all I am a physicist, so I apologise for my non-existent understanding of basic biology. However, I have what I think is an interesting question and this seems like a good place to ask it...
I’ve recently been thinking whether there is a way to measure time using biological processes. In other words some system, a characteristic of which can be correlated to elapsed time. One example I can come up with is counting the number of divisions of a cell. I guess this can be done, but will most likely be highly inaccurate…
So this is my question: Do you know of any papers even tangentially related to the idea of a biological system that can be used as a clock?
Any ideas will be greatly appreciated!

I don't think circadian rhythms are accurate enough to be used as a clock.

What kind of time frame do you want to measure time on? If you want centuries / millenia / millions of years, you can look at the accumulated mutations in the noncoding sections of DNA; it's how we measure how long it's been since the last common ancestor of related species.

Fascinating question, thanks for asking! Welcomg to Bio.SE!

@Orange_Striped_Gecko I was hoping for minutes (or even seconds).

There are lots of biological clocks, or clocks made of biological components. The circadian clock is an important, though complicated, example. There are excellent engineered clocks that form some of the neatest examples of systems / synthetic biology. See for example Elowitz & Leibler's "repressilator" (link, link). The basic idea in all of these is to have gene regulatory circuits with feedback that lead to oscillation of the gene expression dynamics. Books on systems biology, or Philip Nelson's Physical Models of Living Systems (aimed at physicists), are good places to read more.

Thanks! I will look into this.


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Can monoclonal antibodies be used to transport insulin
Quick question
Monoclonal treatments in cancer require the drug attached to the antibody which then attaches itself to the neoantigen on a cancerous cell, would it be possible to
transport insulin in the same way?

There are no quick questions on SE Biology, only good questions and bad questions. Good questions are on topic, explain the problem clearly, and demonstrate an attempt to research it yourself. Your question does not explain the problem, and is really focused on your own answer. Where do you wish to deliver insulin to? Why do you think it cannot reach there already? What problem is doing so going to solve? Unless you edit your question accordingly it is likely to be ruled “off-topic” as “unclear what you are asking”.

Thanks I'll keep that in mind

Technically you can link two proteins together, but why would you want to do this?
Antibody drug-conjugates are used to specifically target cells which can be differentiated from the healthy cells by their cancer neoantigens. This provides a high specificity of the drug delivery and also limits side effects on healthy cells.
For insulin on the other hand this is not necessary, since insulin receptors are ubiquitous thoughout cell surfaces in the body, hence supplementing insulin is enough.

I think “most likely yes” is a comment rather than an answer. As the question is unclear I would suggest it comes under the category of “not all questions should be answered”.


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Does it make sense to make my own DNA copy (kind of backup) while I am young?
As I understand, when I am getting older DNA becomes more and more damaged in my body.
Does it make sense to make my own DNA copy (kind of backup) while I am young (38 years old or for my kids) in case that in future there will be the technology which will make possible to restore damaged DNA from this copy and make me younger?
Or it does not make sense, because original not damaged DNA always can be found in some places of my body?
If it makes sense, what is the best way to do this DNA backup? Cut a piece of hair or nails or freeze a piece of saliva?

While your DNA gets damaged, not every single cell will have the same damage.  Your consensus DNA sequence will not change.

I still did not get from your answer if it make sense to make DNA backup or not.

No, it does not make sense. When you ask: "in future there will be the technology which will make possible to restore damaged DNA from this copy and make me younger?" I can confidently say that there won't be such technology, for the following reasons.
1) DNA is only one component of your body's cells; important of course, but not really the 'master regulator' of everything about you (in fact, practically all cellular functions are performed by proteins and other molecules, not DNA). This belief (that DNA can determine every aspect of life) is called 'genetic determinism', and it is known to not hold even in trivial cases.
2) Your environment (diet, air, sun, family, friends, society, random events) plays a major role in who you are and how you age. Even if you were to repair all DNA damage as soon as it occurred (which, by the way, your cells do quite efficiently anyway), you could still not control for all there is outside of you, and thence you could not really 'rejuvenate' with the magic DNA pill. Most people tend to ignore this when fantasizing about DNA's healing powers: there is a world outside.
3) DNA is not something you drink or take as a 'medicine', not now, not in the future. The technology needed to rejuvenate all of your cells will likely not include 'DNA repair'. It might have to do more with metabolism than anything else (also, mutations occur all the time and not all of them are bad, so in fact 'repairing' DNA with your 'juvenile' DNA might not even be good long term).
4) It might make sense to freeze some of your cells for other applications (like tissue regeneration for you/your children), but it is quite expensive at the moment and usually requires a sample of your umbilical cord. I presume the technology to de-differentiate adult cells to totipotential cells is quite feasible, so in the future this application might be accessible, buy still unrelated to rejuvenation (unless there is something like 'whole body' tissue replacement).
As for the previous answer, "Your consensus DNA sequence will not change" makes no scientific sense. Your DNA sequences (of all of your cells) change all the time, and there is no 'average', or 'consensus' inside of you (the term consensus is simply a convention used in molecular biology for simplification).

Thanks for the answer. Let's think that theoretically there will be technology to recover DNA. In this assumption does it make sense to make DNA backup or original not damaged DNA always can be found somewhere in the body?


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Can someone identify the species of this frog/ toad?
Location: Tirupati, Andhra Pradesh, India
I found it at night time near a lake
It was quite small in size ( 5-6 cm Approx.) having dark brown spots all over its body and three prominent green stripes running along the length of its body and 2 stripes running across its upper body ( one crossing over its eyes).

Looks to me like an Indus Valley bullfrog (Hoplobatrachus tigerinus).
Your specimen would be a bit small, but the species is nocturnal, the area fits and the patterning looks like a decent match as well:

(taken from the Wikipedia page)


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What are the appendeges behind a crane fly's wings?
I noticed that crane flies have strange appendages behind their wings. The appendages look like a pair of antenna or a pair of vestigial wings. In the following picture I marked these appendages with arrows.

The specimen in the picture sat on my window this morning. I looked through the genera on Wikipedia, that is, on the images if there were any. All crane fly species seem to have these appendages.
While the appendages are clearly visible in most images I couldn't find a description of them. I've never seen anything like them and would like to know:

What's the name of these appendages?
What are they good for? Are they vestigial wings, antenna, or some sort of counter weight to stabilize the flight?

They are the halteres. These structures help the flies to perceive body rotation and maintain balance.


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The shape of mRNA
I was wondering about the shapes assumed by mRNA. I have read some sources quoting that it is linear (quora, so not very reliable) and also a source that says a hairpin shape is common (nature, so I would rather go with this one).
I was also wondering what additional factors or features ensure the mRNA has this shape. For instance, the first source says that the mRNA 'is linear so that the ribosomes can bind to it'. But, clearly, all that is required for this is that the ribosome binding site is exposed. In that case, the remainder of the mRNA may either spontaneously unravel as it is being translated, or there may be something slightly more specific taking place catalysed by the ribosome, or there may be an additional enzyme that associates and catalyses the unfolding of the mRNA as it is being translated.
The thing is, I just find it difficult to belive that the mRNA would not fold up on itself, but on the other hand if it did, perhaps it would be too stable and would not be degraded sufficiently easily. We would have accmulation of mRNA in the cell, unless there was a protein that specifically degraded it.
My only other hypothesis, if it truly is the case that the mRNA does not fold up, is that it is down to the DNA in the nucleaus being 'too dense' to permit the mRNA folding in the nucleus, and once it exits via a nuclear pore it is immediately being translated and forming a polyribosome complex. So then it can no longer fold.
I do not think that the DNA content in the nucleus is sufficiently dense for steric effects like this. I have seen electron micrograph images in a book (Molecular Biology of the Cell) of mRNA exiting a nuclear pore. It seems quite coiled up. Unfortunately, I have been unable to find a clear representative image online or the associated paper. But perhaps the mRNA can coil up in the nucleus, but is straightened out as it is pulled throught the nuclear pore. Proteins and factors associated with the nuclear pore may catalyse the breaking of the hydrogen bonds.
Any details on this would be much appreciated.

Possible duplicate of What stops messenger RNA from binding to itself?

Unfortunately it is often taught that mRNA is linear, but this is not true at all. Nucleotides within mRNA can form intra-molecular hydrogen bonds with other nucleotides, creating secondary structures, interactions between these secondary structures results in tertiary structures. mRNAs have highly variable secondary structures, primarily due to differences in the sequence of the ORF, so there is not a consensus structure adopted by mRNAs. However, codon degeneracy is important in producing more ordered and stable mRNA secondary structures in ORFs, resulting in increased mRNA half-life. Nucleotides in positions one and two in codons are the most conserved, whereas the third nucleotide position is the least conserved and has elevated GC content, thus making the greatest contribution to the stability of the secondary structure. The 5’ UTR typically contains lots of secondary structures, which may help in modulation of translation initiation, whereas 3’ UTRs contain fewer secondary structure, resulting in structural instability around binding sites for proteins and miRNAs, enhancing miRNA and protein binding. The start and stop codons are less frequently base-paired than the rest of the mRNA, suggesting they exist in local secondary structures which lead to efficient initiation and termination of translation. However, the sequence immediately downstream of the stop codon has a high GC content and an in increase in frequency of base pairing. It has been hypothesised that this strong secondary structure is present to interrupt post-termination ribosomal scanning. Whilst increasing stability of mRNA increases half-life, low secondary structures around binding sites within the mRNA suggests that thermodynamic stability of mRNA is optimised and not-minimised in all scenarios.
With regards to translation initiation there is quite a lot of cool work on dynamic secondary RNA structures for regulating translation initiation, this work primarily revolves around riboregulators and riboswitches. I won't go into detail about them here, but for a great paper on riboregulators see: Green, A. A., Silver, P. A., Collins, J. J. & Yin, P. Toehold switches: de-novo-designed regulators of gene expression. Cell 159, 925–39 (2014)
References:
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res. 32, 1774–82 (2004).Shabalina, S. A., Ogurtsov, A. Y., Rogozin, I. B., Koonin, E. V & Lipman, D. J.
Duan, J. & Antezana, M. A. Mammalian Mutation Pressure, Synonymous Codon Choice, and mRNA Degradation. J. Mol. Evol. 57, 694–701 (2003).
Shabalina, S. A., Ogurtsov, A. Y. & Spiridonov, N. A. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res. 34, 2428–2437 (2006).


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The genetic code and the effect of point mutations on proteins
I was asked a question, "Considering degenerate and non ambiguous nature of genetic code, Why is that certain mutations don't disturb the protein synthesis leading to synthesis of functional proteins where as certain mutations cause synthesis of non functional proteins or diseased proteins?"
My argument was that according to Wobble hypothesis, the tRNA carries anticodons that have A,U,G,C,I where I is inosine (sugar phosphate with hypoxanthine) that can bind with A,C,U of the codon and also G binding with U and vice versa is possible. Then, I gave the example of serine -AGU- whose anticodon is -UCI- for instance and after mutation say, -AGU- becomes -AGC-, it still codes for serine and -UCI- stills agrees to bind with -AGC- giving us serine as before and hence no disturbance is brought up leading to synthesis of functional protein. But suppose -AGU- got mutated to -CGU- , then the anticodon -UCI- no longer can bind with the codon and hence another tRNA molecule with anticodon of that of arginine gets attached and hence leading to interruption in the amino acid sequence which ultimately leads to non functional protein.
But my professor disagrees with my argument and says I am not clear with the concept. Can anyone please help with where I am going wrong ?

Nonambiguity refers to the fact that codon X will always code for the same amino acid.
Degeneracy refers to the fact that an amino acid can be coded for by many codons.
I rephrase the question to get to the gist of things:

Why do certain mutations cause no difference for protein synthesis, while others make a big difference?

Certain mutations can change the codon but still code for the same amino acid, so the resulting peptide sequence is unaltered (synthesis of a functionally identical protein). This is due to degeneracy, explained above. Certain other mutations change the codon in a way that produces a completely different amino acid, and these result in the synthesis of a different, distinct peptide that may be dysfunctional. This due to nonambiguity of the code. Simple!
It's best to refer to our translation guide, the codon table. If you know your codon table, you might have noticed that within a codon frame, changing the 3rd nucleotide often has no effect on the translated amino acid (see outer ring, below). Changing the 1st and 2nd nucleotide produces a more drastic effect in the translation of the codon.
That means that the position of a nucleotide mutation within the reading frame is key to the effect of the mutation on protein synthesis.

Where I am going wrong?

You are complicating the picture needlessly. You fail to explain that the resulting amino acid depends on its codon, and that the effect of changing the codon in different places (position 1, 2 or 3) has different outcomes. You also have to think about different kinds of mutations; we are discussing substitutions, but you must also consider what deletions and insertions of nucleotides do to the translation of the peptide! You may also get bonus points for discussing the start and stop codons... they are special cases.

OK, I completely agree that I haven't been specific to the point considering the degeneracy and non-ambiguity, but I need some clarification. Does the point about wobble hypothesis explain the concept of synthesis of functional and non-functional proteins ?

@SurajS — The wobble hypothesis is irrelevant to the question you have been asked. That answers how the degenerate genetic code operates. If the answer were through 61 different tRNAs it was make no difference to the effect of the degeneracy on the likelihood of a mutation having a detrimental effect. The genetic code diagram in this answer may look pretty, but I think you would do better looking at the standard tabular presentation found in text books and Wikipedia. This makes it easier to see how mutations would affect both the amino acid encoded, and the “type” of amino acid encoded.

@David Oh, now I get it. Thanks a lot


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What is the difference between sieve cells and sieve-tube elements?
I looked it up and I'm still confused. Apparently, sieve cells lack sieve plates? What does that really mean? It's difficult to find a good picture of either.

All plants have sieve cells, but not all plants have sieve tube elements because they evolved after the plant family tree had started to branch. Only angiosperms have sieve tube elements.
Sieve tube elements are more specialized for their job as transport cells, and can transport more nutrients faster than sieve cells. During their development, the meristem cell divides into two cells: the sieve tube element and the companion cell. The sieve tube element loses its nucleus, vacuoles, and ribosomes when it matures in order to make it easier for its cytoplasm to flow, and so it relies on its companion cell for proteins and carbohydrates. The porous plates between sieve tube elements provide little resistance to water and nutrient flow, and so flow through the sieve tube is more rapid than it would be if there were cell membranes or small pores for it to pass through. The sieve tube elements are wide to make wide tubes, which provide less resistance to fluid flow.
Sieve cells evolved before sieve tube elements, and are a bit less specialized for their job. They still have all their organelles, and are long and thin. Some plants, such as seedless plants and gymnosperms, don't have any sieve tube elements and rely solely on sieve cells for nutrient transport.
References:
Organelles present in sieve tubes
https://en.wikipedia.org/wiki/Sieve_tube_element


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Why are protein-coding regions rich in GC?
I have been searching for an answer for this question and have some possible solutions, but I am not sure. GC regions are more stable as there are 3 hydrogen bonds instead of 2 with AT, however I am not sure if this would influence the number of protein-coding genes in GC regions? Protein-coding regions would have to be less condensed than noncoding regions so transcription factors could access them. Would a high GC content influence this as well?

Do you have a reference to support your statement that protein coding regions have more GC?

Transcription factors generally bind to promoters, enhancers, silencers, and other regulatory regions that lie outside coding regions, through there are "duons" which code for amino acids and also bind TFs to regulatory effect. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967546/
One paper suggests GC content helps balance recombination events with genetic stability, and so there may be an evolutionary benefit from organisms that undergo sexual reproduction having GC-rich coding regions. https://www.frontiersin.org/articles/10.3389/fpls.2016.01433/full

In eukaryotes, meiotic exchange of genetic information, or recombination, between homologous chromosomes is a critical step in generating genetic diversity required for adaptation. Recombination is also a crucial tool in plant improvement efforts. Local genome architecture is sculpted by the recombination process, and genome architecture, in turn, drives recombination. This interplay helps to create variability in genomic space, defining relatively stable and plastic genomic regions. This fluctuation in genomic stability is critical for balancing adaptation and stability on the phenotypic level.
Recombination has direct implications for GC patterns and vice versa. GC content refers to the percentage of guanine and cytosine bases in a DNA sequence, as opposed to adenine and thymidine bases. There have been many studies substantiating the positive correlation between recombination and GC content (Ikemura and Wada, 1991; Eyre-Walker, 1993; Fullerton et al., 2001; Galtier et al., 2001; Marais et al., 2001; Duret and Arndt, 2008; Haudry et al., 2008; Escobar et al., 2010; Muyle et al., 2011). Crossovers have been found to be correlated with high GC content in rat, mouse, human, zebrafish, bee, and maize at a broad scale (Jensen-Seaman et al., 2004; Beye et al., 2006; Gore et al., 2009; Backstrom et al., 2010; Giraut et al., 2011), while other studies detected strong correlation only at a fine scale (∼5 kb for yeast, ∼15–128 kb for human) and rather weak correlation at a broad scale (∼30 kb for yeast, ∼1 Mb for human; Gerton et al., 2000; Myers et al., 2006; Marsolier-Kergoat and Yeramian, 2009).

GC-richness may offer the ability for organisms to create offspring that evolve to changes to the environment and fend off parasites, while also being viable enough to procreate, themselves.


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What is the name of this plant with a compound leaf of 8 leaflets?
this plant is present in my lawn and I don't know it's name. It is actually diseased and I'm trying to figure out what it is.

Can you please add some geographic location of your garden? Also information if this plant is native there or just planted would be helpful.

Is this related? https://gardening.stackexchange.com/questions/30373/what-disease-is-causing-raised-blisters-on-the-leaves-of-my-plant

I think it's [ https://en.m.wikipedia.org/wiki/Rauvolfia_caffra ] Still not sure, but it's worth giving a try... :)


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Can Chilopoda "vocalize" or produce sound for the express purpose of communication, as opposed to sound as a byproduct of other movements?
Is there any species of Chilopoda that can "vocalize" or or otherwise produce sound for the express purpose of communication, as opposed to sounds it might create  as a byproduct of other movements and body functions?
An example of non-communication sound in other arthropods would be insects wings causing "buzz" sounds while in flight.
An example of a communication sound in other arthropods would be crickets (and others) rubbing their legs together to "chirp".
Do any Chilopoda intentionally create sound for the purpose of communication?

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

@ASimonis Can you please stop to write your comment under each seamingly fitting question? In this frequency this can be seen as spam. Most of these questions (if not all) are old anyways and your comment will be useless.

I have been trying to help the Bioacoustics community grow and thrive, and I am sorry if the comments were inappropriate. I recently learned about the Chat space, so I'll try to direct some recruitment effort over there.  :-)

@ASimonis Unfortunately I cannot, in good conscience, indicate that I will commit to use that new Bioacoustics Stack Exchange, as I don't believe I would use it for anything other than attempting to get a single answer to this same question I've posted here.  My interest in bioacoustics is limited to this one specific use case.  If the stack exchange does gain enough support to be fully created, I will likely repost this question there, but that will likely be the full extend of my use of it.


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How big can a colony/society get?
I hope this is the appropiate place for this question, asked from a math/physics perspective with little to no training in biology.
Bacteria are very small and live in huge colonies, ants are bigger (but also very small) and live in smaller colonies (but also very big). Ignoring the human species, I can't think of any big animal living in big colonies
Is there any name for this relation? I want to study it from two perspectives: first, why? (this may be easy to explain in terms of resource supply or energy available) and second, what is the precise relation? (clearly inverse, but linear, logarithmic...?)
Thanks!

You should know the word "colony" means different things when referring to ants and bacteria. Bacterial colonies arise because bacteria divide faster than they can move (if they can even move). An ant colony is more of a social structure. Not really comparable.

It is not trivial to define a "colony/society". Sure, you can say "this bacterial blob is a colony", or "this ant nest is a colony", and so on, but these would be your own definitions. These systems you mention don't have definite boundaries (temporal or spatial). Although physicists like to do gross approximations to things in nature (and I'm pretty sure there is already some paper 'answering' your question), I'm not sure anyone can get a "precise relation" for a concept that even biologists struggle with (that of a "colony"). This is because at core, what you are really asking, is what is a biological individual and how can I measure it? (the individual ant, the individual colony, etc); and that's something we have no answer for. For what is worth, I recommend you read about the problem of biological individuality, which will give you no answer to your question but at least can tell you why you can't really answer it: https://link.springer.com/article/10.1162/BIOT_a_00068


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Why do we define anaerobic respiration as not requiring oxygen, while utilization of the Krebs cycle and electron transport chain both require oxygen?
We have an electron transport chain with the final e- acceptor as SO4 2-. We say this is an anaerobic process, or specifically a case of anaerobic respiration. Elsewhere, as with fermentation and glycolysis, we have anaerobic processes that do not require oxygen. Would it be more appropriate to call these processes with the final e- acceptor as anything other than oxygen to be pseudo-anaerobic?  I say this as it seems misleading to call a process anaerobic that inherently is composed of aerobic processes.

Does this organism grow in the absense of molecular oxygen in the environment?

Okay, thank you user1136. I was misled by the book I read. "The Krebs cycle and the electron transport chain both require oxygen to produce ATP and are collectively known as aerobic cellular respiration." Which I interpreted as the Krebs cycle and the electron transport chain always require oxygen, whether the end process is dubbed anaerobic or aerobic depending on the final e- acceptor.

Because oxygen is not the majority of the energy.
Krebs cycle relies on sugars. Other processes use oxygen but can do without it or primarily use carbon fuels. So they are called anaerobic.


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Why do our eyes not have interference from other sources of light?
When one looks forward at a glass of wine, one is seeing it via the reflection of light off of the glass. But if you have a person to your right, looking to the left side of you (still in front of your face), he can see objects across the room that are not in your peripheral vision. Considering that the light which is reflecting off of the object to your left is passing directly in front of you to your friend to the left, why are we unable to see that reflection?
In other words, why can we only see the light reflections of objects in front of us, but not the light reflections of objects which pass our eyes from our left or right?

I'm voting to close this question as off-topic because this is a better fit for the physics stack since it about basic optics and not biology.

You can see those objects not in your vision range on a mirror because it reflects the light rays coming from that object perfectly towards our eyes instead of scattering it in all direction. It is simple ray-optics and I agree with @John that this is a physics question but I guess it may to too trivial over there so I don't know if migration would be suitable.

You can't see light that goes past your eyes, only light that goes into your eyes.
Every seen a movie where there's a laser grid that's only visible when smoke is blown over it?  You can't see the laser until a photon is deflected towards your eyes by hitting the smoke particle.

Perhaps a better question for the Physics site, but light is composed of particles called photons.  (I'm ignoring the wave-particle duality for the sake of brevity, and because it doesn't really apply at this scale.)  A photon doesn't react with anything (like the light-sensitive chemicals in your eyes) unless it hits it.  So your question is like asking why, if someone throws a rock from right to left in front of you, you don't feel the rock hit you.


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Can undigested food proteins enter the bloodstream?
I know that food proteins in our digestive system are denaturated and broken down into amino acids or very small peptides that are then absorbed in the small intestine. If some proteins stay undigested they move to the large intestine and either gut flora eats them or they are excreted.
But lately, I've been hearing a lot of stuff like "if you eat a lot of eggs there will be egg proteins in your blood" or "drink liquid collagen and it will travel to your skin through the blood". It seems really stupid to me. I imagine if all sorts of food proteins entered our blood they would wreak havoc there catalyzing random reactions, triggering immune responses, etc. So it cannot be a very frequent event. But I've been wondering if some of the food proteins can on occasion end up in the blood of relatively healthy people. Does this ever happen? With food allergens maybe?

Possible duplicates/related: https://biology.stackexchange.com/questions/56131/can-proteins-peptides-pass-through-the-intestine https://biology.stackexchange.com/questions/36050/how-does-botulinum-toxin-enter-the-blood-stream-from-the-digestive-tract https://biology.stackexchange.com/questions/84089/why-are-prions-in-animal-diets-not-destroyed-by-the-digestive-system

Does this answer your question? Can proteins/peptides pass through the intestine?

Sort of.
Proteins can enter the body through the intestines by exploiting a few transport mechanisms, They are not truly crossing the cell membrane but are transported across the cell in vesicles. Though not into the bloodstream but into the lymph system.
M cells in particular will move antigens across the intestinal wall, a few more durable proteins (like prions) have been shown to piggyback on this system to cross in tiny quantities. Some viruses also exploit it. Collagen definitely does not enter this way but there are likely egg antigens that may.
Note this is very rare for non-antigens, the vast majority of food you eat will not contain anything that can exploit this although they may contain antigens that get passed to the immune system.
Source
Source 2

That's impossible, if it has to pass through your cells membrane , check this small protein of 3 amino acids (Garcia, A., Eljack, N. D., Sani, M. A., Separovic, F., Rasmussen, H. H., Kopec, W., ... & Clarke, R. J. (2015). Membrane accessibility of glutathione. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2430-2436.)
Although going through cells intermembrane... I think that's possible in theory, but even if that's happens so few protein concentration would reach other places.


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What are "feeder cells"?
What exactly are "feeder cells"? A paper I'm reading says they harvested the cells and then plated them onto feeder cells. What is the purpose? Is in order to promote growth?

Cultures of growth-arrested feeder cells have been used for years to promote cell proliferation, particularly with low-density inocula. Basically, feeder cells consist in a layer of cells unable to divide, which provides extracellular secretions to help another cell to proliferate.

From this paper's abstract:
Feeder Layer Cell Actions and Applications


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How does the descending branch of the loop of Henle equilibrate concentration?
I'm learning physiology and I have a hard time figuring out how the cortico-papillary gradient is created.
Most explanations go as follow:
1) Sodium is pumped out the ascending branch into the interstitium until a 200 mOsm/L gradient is established between the tubular fluid and the interstitium.
2) Water passively flows from the descending branch into the interstitium to equilibrate osmolarity between the tubular fluid and the interstitum.
3) The tubular fluid flows, moving everything towards the ascending branch.
1 bis) Sodium is again pumped out until the 200 mOsm/L gradient is established
Reapeating this steps over and over again creates the vertical gradient.
This is illustrated here

Ok, so far, so good; here comes my question :
In step 2, how comes the final concentrations in the interstitium and the tubular fluid in the descending branch are equal to the initial concentration in the interstitium?
I would expect the final concentration to be the mean of the two. In the examples above, starting from 400 mOsm/L in the interstitium and 300 mOsm/L in the descending branch, I would expect 350 mOsm/L at the end, not 400 mOsm/L.
How is that possible? Is this because at every moment, when water flows into the interstitium diluting its content, the ascending branch keeps pumping sodium to maintain the 200 mOsm/L gradient?
Thanks a million to whoever will answer this question!


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Why do women process oxygen faster than men?
https://www.newsweek.com/women-are-better-athletes-men-study-about-gender-fitness-says-736047 is the source that I use. Is it reliable?
Why did men and women evolve that way? What's the evolutionary advantage to women being naturally more fit?
Does childcare and gathering fruit require being athletic? I would have thought that hunting animals and fighting enemies would require being athletic.
So, how did natural selection favor women that are more naturally fit and not favor men that are naturally fit?

Beware of claims made by single tiny preliminary studies  blown out of proportion by the science ignorant media. the study only included 18 people.

Additionally, be wary of the word choices, they stand on very shaky ground. Women are clearly and demonstrably not more fit than men, nor are they more athletic. The claim is that they oxygen consumption and extraction (loosely 'oxygen processing') is faster in the 9 tested women than the 9 tested males. That could be due to lung and body size, (e.g. smaller creatures like mice in comparison to elephants probably process oxygen more quickly; and there exists a body size discrepancy between human males and females). Or it could be a host of other reasons that confound the study results.

remember that sexist and racist news headlines bypass your rational brain and aim straight for the limbic system in the brain: i.e. when you read them, your emotional state reacts faster than your concious self which then reads the headline and understands it's meaning. so, mostly those headlines are nonsense, they just illicit instinctive attention.

There doesn't seem to be anything wrong with the paper, but as pointed out in the comments (and in the press release itself), the study was small, so any conclusions should probably be tentative. Adding a little more detail from the link:

For the study, which was very small, researchers recruited nine young males and 9 females, all roughly in their mid-20s. Females and males were of similar weights within their own genders. Everyone participated in the same exercise—walking on a treadmill—and scientists compared oxygen consumption and extraction in both genders during the workout. They found that the women were consistently more efficient than men, as they processed oxygen 30 percent faster.

Beltrame, Thomas, Rodrigo Villar, and Richard L. Hughson. “Sex Differences in the Oxygen Delivery, Extraction, and Uptake during Moderate-Walking Exercise Transition.” Applied Physiology, Nutrition, and Metabolism 42, no. 9 (2017): 994–1000.
A few more details from the paper itself:

you have to be very careful about interpreting what "faster" means in this case. The paper says:

The greater maximal aerobic power [VO2max] of men compared to women is well recognized (Cureton et al. 1986).

For example, "good" VO2max for 20-29 year old males is 42.5-46.4 mL/kg/min: for 20-29 year old females it's 33.0-36.9 mL/kg/min. This means that at peak intensity, men can process oxygen faster than women.

In contrast, the focus of this study is how fast women and men ramp up their O2 metabolism as they exercise.

Here's Figure 2 from the paper:

based on the figure and on table 1, the "mean response time" is about 50 seconds for women, 60 seconds for men.

the other caution about this study (besides the small number of participants) is that the authors appear to have tested 32 different parameters of oxygen uptake metabolism, for both men and women; many researchers would recommend a multiple comparisons correction in this case, to account for the fact that it is more likely for some comparisons to appear significant by chance when making many comparisons.

Finally, it would be hard to be do much evolutionary speculation for the reasons behind these sex differences ... one might want to start by doing a comparative study, to find out if these differences are unique to humans or whether they also appear in our close relatives (chimps, gorillas, etc.)

It is incredibly hard to know for sure which evolutionary preasuress in our past led to specific taits we see today - in completly different enviroment - but my bet is on surviving childbirth in prehistoric conditions. Also note that women used to spend significant portion of their adult life pregnant, and so any form of resistance to exhaustion would be quite benefitial for them.
Some sources:

... increased aerobic fitness was associated with shorter labor in nulliparous women who started labor spontaneously.

https://obgyn.onlinelibrary.wiley.com/doi/full/10.1080/00016340903093583

... moderate-intensity exercise performed throughout pregnancy was associated with a reduction in the rate of cesarean, instrumental deliveries...

https://www.tandfonline.com/doi/abs/10.3109/14767058.2012.696165


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Which proteins are most sensitive to electric fields?
Many Proteins have ionic charges that can attract each other (e.g. Formation of salt bridges) or repel each other. On the other Hand, Proteins are mostly immersed in water that screens most of the Electric charges of the proteins. The reason is that water is a dielectric, the H2O-molecules can be polarized easily. So the Electrostatic Forces are reduced in aqueous solution.
Now I am asking which Proteins can be easily affected when applying an Electric field? That means which Proteins will Change their conformation substantially even when weak Electric fields are applied?
Can some proteins immersed in water also be dependent on external Electric fields?

There are various proteins sensitive to changes in electric field. More precisely, they are activated by changes in voltage (surrounding the protein), and immersed in water, as all cells are mainly composed of an aqueous solution. You are correct that most charges in the side chains of the proteins' amino acids are 'masked' by the dipole character of water molecules, but the electrochemical potential of the cell is primarily due to ions, and not to the interaction between side chains in a protein. However, it is important to note that within these proteins sensitive to changes in the electrochemical field, there are domains that contain charged aminoacids (i.e. not covered by water), very important to be able to 'sense' the changes in voltages.
You can check out some of the voltage-sensitive ion channels, which participate in different cellular pathways, including the generation and transmission of the action potential in neurons:

Wikipedia has a good entry about them.

As you mentioned water is a dielectric and because of that and the presence of ions in  solution, electrostatic forces have a very short range inside a cell.
If you apply a potential difference (voltage) in solution, you will generate a constant electric field between the two electrodes. Proteins will respond to this electric field by moving towards the anode or cathode depending on the charge of the protein. This is what we know as electrophoresis (note that for the electrophoresis of proteins you usually need tens to hundreds of Volts)
Now, when you have the same voltage difference but there is an electrical insulator in the middle, most of the electric field will be concentrated within the insulating material.
This is what happens in the cell membrane which insulates the small voltage difference between the inside and outside of the cell (-40 to -90 mV depending on the cell). This small voltage difference generates a huge electric field with the membrane which now can be sensed by charged residues of proteins within the membrane such as the arginines in the voltage sensor of a potassium channel. The electric fields sensed by these channels are in the order of 10^8 to 10^9 V/m.


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Insect Egg Case, and if so, What Insect?
Observed this object today (early October) in Sabino Canyon, on the north side of Tucson AZ, in a riparian area.  It's attached to a mesquite tree (Prosopis spp).  It's attached to one side of the branch, it does not wrap around the branch.  About 1.5 - 2 cm along the maximum dimension.
Looks like some kind of insect egg case and I'm curious if anyone can confirm and knows the insect.

A local graduate student relayed the answer to me.  It is an ootheca of a praying mantis.  There is some additional background on the egg life history here.  Wikipedia reports there are three mantid species.  The upper-left picture of the ootheca here is essentially what I observed, so we may be looking at the genus Stagmomantis.  There are some other great pics at that last site.

Hi Bryan, self answers are great but we like answers to have some support and a bit more information than one line. If someone gave you a tip, now you could write a good answer by using that tip to find a reputable source that describes a praying mantis ootheca that looks like yours, include a cited picture, and maybe even get a guess at a particular species based on your location, if possible.

I shall expand the answer in a few minutes.


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How do different genes on human genome express themselves?
It is said that human genome  contains over twenty five thousand genes, How many of these (can) express themselves as an external or internal trait in human beings (for e.g. like eye-colors, hair colors, earlobe-assosiation etc.). Other genes are responsible for (mostly) what functionalities?

Where is this said? References would help. There are a little over 20,000 genes in the human genome, so itś not clear what you mean by genomes in genomes.

The human genome doesn't contain 30000 genome, rather it contains 30000 genes, as the HGP has said us. Human gene is split gene,i.e., long sections of non-coding DNA is present in between short sections of actually coding DNA. Thus there is a lot of junk present. Different genes express themselves by a two step process, the first being transcription, where DNA is converted first into a mRNA, which undergoes splicing and then finally that mRNA is converted into protein and this is the second step which is known as translation. Thus it is by the conversion of DNA segment into proteins that helps the various genes in expressing themselves.
As for what the other genes do, not all genes are busy in determining phenotypic traits. There is a lot other things also going on.. the various biochemical reactions in our body need to be regulated by enzymes and the production of these enzymes are controlled by these genes. For more knowledge about this field... Google lac-operon concept or the tryptophan operon concept.

What is meta genome ? it is said that it governs activation and inactivation of certain genes in the genome.


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What is the genetic reason that this flower has petals of two different colors?
I have two different varieties of the flower, portulaca: one is bright pink, the other is pure white with pink specks at the centre. Recently a flower bloomed which had 50% of the former and 50% of the latter: both traits in the same flower. Is this an example of co-dominance or is there some other reason for it?

This can be a result of a somatic mutation, especially if the other flowers on the same plant don't have the same color pattern. Somatic mutations are not inherited for parent organisms but occur spontaneously in one of the cells in the body. If that cell then proliferates all of its descendants will have the mutation and new phenotype associated with it.
Look for example at Fig. 1 (c, d) in this article. Those peach flowers have similar coloration to the one on your photo.


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What function does a mane serve in animals that possess it?
Horses, Donkeys, Antilopes and Bovines grow masses of hair on top (and sometimes below) the neck. What function does it serve? Is that to hinder predators biting?

Keep in mind there is not much to the mane in wild equids it is only the human bred populations that have large manes. Also since you are talking about very different groups with very different mane structure the answer may be different for each. I suggest moving antelope and bovids to a seperate question.

Perhaps it can prevent predators from wrapping the claw over the top of the neck while biting the throat, except that predators often bite anywhere on the side and hind and ears and whatever they can catch to ground the zebra first. Perhaps it's to do with amplifying the size to make them look taller and stronger. strong animals have very strong necks.

@John Todays Eqids have dense standing manes, as had undomesticated wild horses (see https://en.wikipedia.org/wiki/Chauvet_Cave#/media/File:Chauvethorses.jpg ). Similaritys with those of e.g. sable antelopes look like convergent evolution and may well be the point.

@HannesH except you don't know if it is convergent evolution. manes vary a lot in size, placement, and stiffness across all those groups while equid manes are all almost identical outside domestication. .

I am not aware of the evolutionary advantage of the mane in the animals that you mention. In fact, the only reference I could find talks about a predator, not a prey, and thus it might indicate that mane is not mainly an adaptation against predation. I also want to mention that not every trait in every animal is advantageous at the current moment, many traits are 'vestiges' from previous adaptations (or maladaptations). In this case, however, the widespread appearance of the trait in different animal groups might indicate that it is in fact adaptive.
The evolution of mane in the lion seems to be related to sexual selection, as only male lions have mane, but there are competing hypothesis too, in that it appears that the ancestor of the lion was mane-less, and thus the appearance of mane only in lions (and not in other felines) might have been a product of drift (maybe through a bottleneck).
The evolution of mane in other groups of animals might have also been relevant for sexual selection, as it seems that the ancestors of horses had no mane, and thus something that most 'maned' animals have in common is the selective pressure to reproduce and have the mane perhaps as a secondary sexual character indicative of sexual maturation -as it occurs with lions- (I clarify that this is only my own speculation).

I believe the reason male lions have a mane is to protect their neck from damaging bites from other males (males fight over territory and females). Given that the manes of other animals, such as horses are also on the neck, a region that large predators often seem to target, I wouldn't be surprised if they are for the same purpose - i.e. - to protect against bites.

@TimFoster except the horses mane is the least useful place for stopping bite damage to the neck.

@John, not sure what you mean, a dorsal neck bite is a common predator strategy, you see it on nature programs all the time

@TimFoster a "dorsal" neck bite is not biting through the top of the neck, it is biting the sides of the neck.

@John based on a bit of Googling, it looks like biting the back of the neck in order to break or damage the spine is pretty common.

@TimFoster for small prey sure, not horses.

@TimFoster, when you say "I believe...", what is your source? I provided some sources in my answer, but I think you are just going with a 'gut feeling' with no supporting evidence, at least not one I can find.

@ lions are suffocation killers not bone breakers, they bite the front of the neck in large prey. a horse mane is pointless to defend against lions. https://www.sciencedirect.com/science/article/pii/S0003347205809078

Do not horses nip each other on the neck? Could it be a social adaptation?

The horses mane main purpose is to be braided by equestrianists.. ;)


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Why spin live fruit flies in centrifuge?
I was reading this article about the evolution of monarch butterflies’ resistance to cardiac glycosides: These Butterflies Evolved to Eat Poison. How Could That Have Happened?
And this passage made me curious:

The researchers put the mutant flies in a centrifuge and spun them for ten seconds. Afterward, the flies were overwhelmed by seizures for several minutes.
Ordinary flies, by contrast, immediately walked away from the laboratory carnival ride. Flies with the other two resistance mutations were also unharmed by the procedure.

Given that normal fruit flies are usually unharmed by the centrifuge, what made the researchers decide to spin the flies? I’m not a biologist, I’m a software engineer. So I’m just guessing that it might be a standard lab procedure when studying fruit flies. Assuming the researchers didn’t know the flies with mutation 122 alone would experience seizures, what do researchers usually expect to gain from spinning live flies in a centrifuge?

Correction of Poster’s Source
The article cited mistakenly refers to centrifugation, however the actual procedure used in the work — Karageorgi et al. Nature, 2 Oct 2019 — is vortexing, as illustrated in Fig. 3 of the paper below.

What is meant by standard lab procedure?

There is no such thing as standard lab procedure. There are standard
  lab procedures for performing certain kinds of experiments or processes.

In studying the effect of mutations on the behaviour of live fruit flies one devises laboratory procedures that are, if at all possible, cheap and easy to perform on many animals. All laboratories have vortex mixers of the type illustrated, as these are used to speed up dissolution of solutes and to disperse (resuspend) solids which have been precipitated by centrifugation — perhaps the source of confusion as the flies would likely have been put in centrifuge tubes as these would be appropriate (although the flies were not subjected to centrifugation).
Why vortex flies?
The vortexing is what is apparently called a ‘Bang’ assay — a means of testing flies for neurological seizures. The authors state:

To investigate this, we phenotyped monarch lineage knock-in flies for neurological seizures upon shaking (bang sensitivity), a common phenotype in hypomorphic Na+/K+-ATPase mutants29,30

Without consulting references 29 and 30, it seems clear that the authors were expecting cardiac glycosides to produce neurological seizures, and used a simple technique that had been used previously by others to assay this.
So, yes, if you are interested in these aspects of fly physiology vortexing may be a standard laboratory technique, but, no, other fly labs (e.g. those studying the gut) don’t start the morning by saying:

“Lets take the new mutant for a spin”.

Awesome! I did pull up the actual paper and tried to find the word “centrifuge” (and related forms). No wonder I couldn’t find it!

I don't know the exact history, but I wouldn't be surprised if this started as "shake them in the tube a little bit" maybe even initially as a complete accident, and the mechanical option was an attempt to standardize a bit.

In the field of Drosophila neuroscience, vortexing is also a standard treatment to disorient flies, for some decades already. It is, for instance, used in assays for measuring motor functions following a 'reset', or looking at orientation based on mechanosensation, vision and olfaction, and also as a punishment or an aversion stimulus in classical conditioning/learning studies. Vortexing is an easy and reproducible way to standardize what is essentially just vial shaking. Also crucially, centrifuging is a very common lab misnomer for vortexing (source: my experience in quite a few labs).

@SPr — I've never encountered the confusion you mention. I suppose it depends on the type of lab and perhaps nationality. In the biochemical labs I worked in the use of ultracentrifuges and large centrifuges was so central (long before the small desktop centrifuges were developed) that nobody would refer to a vorted mixer (the original was a "whirlimixer") as a centrifuge. It only appeared in the early 60s, whereas Morgan reported the use of the centrifuge to inflict changes on Drosophila eggs in 1902.


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Characteristics of a giant squid’s skin
Is the skin of a giant squid/colossal squid similar to the common squid? Does it possess chromatophores to change color? Or did it lose that ability because of the depth at which it resides or due to the comparative lack of predators?


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Do pale skinned people show other low light adaptations?
So, pale skin is, fundamentally, an adaptation to living in low light conditions. Pros: reduce energy spent on producing melanin, increase vitamin D production. Cons: more vulnerable to sunburns and skin cancer.
Do populations with this sort of adaptation have an increased rate of other low light adaptations? Specifically, I'm thinking of vision in low light situations. Examples of possible adaptations: increased rod count in the retina (pro: better low light vision, con: worse bright light vision), or faster production/resetting of rhodopsin (pro: better low light vision, con: greater energy expenditure).

Light intensities that are "low" for vitamin D production are still far more intense than needed for vision.  Indeed, one might reasonably regard the evolution of dark skin as an adaption to living in light that's too intense.

@jamesqf That seems to be a semantic difference, to me. Though it suggests another possible adaptation: greater light transmission through lens/fluid in eye. Pros: more sensitivity, cons: more vulnerable to retina burn/snow blindness, possibly also cataracts.

Not really semantic, just looking at the question from a different angle.  Why do dark-skinned people native to tropical countries wear sunglasses?


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Why have we evolved to snore yet find snoring so annoying?
Human's snore. I doubt this is a new occurence over the last millenia. I find it hard to believe that for the past million years, no human ancestor has been a snorrer.
And yet, the sound of snoring is incredibly irritating to humans.
Could there be any evolutionary basis for these two facts?
One thing I could think of is perhaps snoring serves a purpose of making adult males seek out their own homes and families.
A male child may be inclined to be so annoyed by his father's snoring that he goes off into the world to seek his fortune.
If it didn't serve a useful purpose, surely it would have died out, simply because other humans would be so annoyed by snoring that they would murder snorrers in their sleep and hence reduce the genes for snorring.

Possibly relevant: https://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont

We didn't evolve to snore, snoring is a byproduct of other traits, mostly the ones that allow for speech.

Who is "we"?  Not all humans snore.  Snoring is basically a symptom of illness.  We cough and sneeze as well, and sniffle when we have colds, all of which many people find annoying.

Human are not the only animals that snore.

So humans are not the only animals that snore and also snoreing is a symptom of illness? So does that mean only ill animals snore? So are you saying there is a trade-off between speaking and snoring. If so, why haven't we evolved to not find snoring so annoying?

A very common misconception about evolution is that traits are directed toward a function. It a trait exists, it must be adaptive. This is false. As for snoring, people generally do not snore until they are past the age humans evolved to survive (about 35). To be selected against, those who snore would have to be less fit (fitness defined as the number of offspring produced). Traits that develop after an organism has reproduced have absolutely no bearing on selection. Similarly, we don't evolve resistance to heart disease, or cancer, because these diseases occur after we reproduce.

But we do have some degree of resistance to heart disease & cancer, enough that our odds of getting those things are a good deal higher if we adopt lifestyles that we would have been unlikely to encounter during evolutionary history.

Yes.And this is another example of an anachronism when it comes our best options today vs. 10,000 years ago. Our genes lag far behind the present conditions.

Where do you get that we evolved to survive to 35? That sounds doesn't sound true.  Just thinking about the Native American tribes, there are lots of photos of them with very old people. Many people believe we evolved to live long lives and be grandparents to pass on our wisdom. If you're thinking of average life expectancy don't forget to remove all the humans that died in childhood. Those that survived childhood tended to live long lives.

Perhaps snorring is annoying to make females mate with males under 35! If you think about it, what young human female wants to mate with a middle aged snorring man. Snoring could indicate bad health or age like you say.


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Is glutamate always involved in the deamination and amination of the other amino acids?
For example, are there pathways for the deamination of phenylalanine that simply produce ammonia or pathways for it to be synthesized from phenylpyruvate with ammonia being utilized to form the amine group?
Preferably, I want to know how it is with human metabolism mainly.

What research of your own have you done to answer this question? Amino acid synthesis and degradation are covered on numerous internet sites and in texts on NCBI Bookshelf. Please consult the Help on asking good questions to find out what is expected from posters of questions. (And also include the question in the main body so that it is complete in itself.)

I'm not going to give you the answer, but Berg et al. Biochemistry on NCBI Bookshelf is a good starting point for any biochemical questions. Search for deamination and read the whole section. Tell us what you find — you could even make it an answer to help others and get yourself some credit.

For most amino acids, the removal of the α-amino group involves α-ketoglutarate and glutamate. The amino group is first transferred to a-ketoglutarate by transaminases, and the resulting glutamate is then deaminated (via glutamate dehydrogenase) to yield ammonia.

The same is true for amination. Glutamate and glutamine are the two major amino group-donors. Most ketoacids are converted to their respective amino acids by transamination involving glutamate or glutamine. Glutamine can be synthesized by amination of glutamate with ammonia without transamination (via a synthetase enzyme) and glutamate can be aminated with ammonia too.
Exceptions do exist, of course. For example, Not all transaminations involve glutamate/glutamine (as this user has replied), and serine and threonine can be directly deaminated (via dehydratase enzymes, as opposed to the dehydrogenase used for glutamate).


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DNA Inheritance- Math vs. Biology
After doing some statistical analysis of the raw math involved in DNA contributions, I would like to understand the scale of the biological factors.  I know that 99% of the human genome is identical in all human beings, so genetic recombination and gene conversion should be irrelevant in those areas.  I know that recombination occurs at different rates depending on the chromosomes and loci.  But what is the average order of magnitude?  That is, if I know that a chromosome mainly came from Grandma, how much of it is likely to be from Grandpa?  .1%, 1%, 10% ?  And, does the age of the male affect the rate of recombination to a measurable degree (in spermatozoa only, as body cells would not affect inheritance).

What do you mean by "the scale of the biological factors"? And what do you mean by "the average order of magnitude"? As you just said, differences are tiny between any two randomly drawn humans (in DNA sequence), so if this is your 'metric' there can't be any differences in 'orders of magnitude'. If you only ask about the fraction of the particular DNA (in chromosomes) that was copied into your own genome from your ancestors, then it is roughly half from your parents, a quarter from your grandparents, and so on.

DNA tests are done only on the variable segments:  It would be pointless to say "you're a 99% match to this other sample, it must be your identical twin."  Using the "average" of the actual distribution is misleading.  Only 32.24% of people inherit between 23.91% to 26.09% from a grandparent while 90.69% inherit somewhere in a range of 17.39% to 32.61%.

Agree, so, what is that you are asking then?

DNA testing is in its infancy, and different labs use different protocols for their tests and different models to report results.  2 samples from ME will not show a 100% match to MYSELF.  The zygote that turned into my mother, say, had 23 intact chromosomes from each of her parents.  When my zygote was formed, recombination may have occurred in the specific ovum that made me.  Take chromosome 1- the main body of which came from her father.  Is it likely to be 99.9% grandpa with .1% recombined from grandma, or more in the 90% grandpa 10% grandma range?

So, at core (it seems) you are interested in the rate of recombination events and the magnitud of their occurrences. This would be the only source I can think of that would give you information about the 'composition' of one chromosome (other than brute-force sequencing).
As you seem to know, recombination is an important factor that 'shuffles' some specific areas of the chromosomal DNA during meiosis (process needed to produce gametes). There is a technique developed by T. H. Morgan almost a century ago, that measures the rate of this 'recombination' events by comparing how two (or/and more) particular loci co-ocurr across generations (when recombination occurs, it is more likely to break co-occurrences of distant loci, as opposed to close loci). Thus, we can use this distance measure as a measure of recombination. In fact, in honor of Morgan, the units used to measure recombination rates are called 'centiMorgans', and abbreviated cM. A cM is the probability for a particular loci (it can be a gene or a smaller sequence) to co-occurr with another loci (to be 'linked' to). Thus, is a relational measure: every particular sequence is related to another, and by transitivity (if A and B are close, and B and C are also close, then A and C will probably be close -this is a generalization-). When done in chromosomal or genomic scale, we can build linkage maps.
In modern times, there's quite more resolution, from whole genome studies at gene/chromosome resolution, and even higher resolutions (remember that a 'loci' can be any unit of your interest in the DNA).
Being all that said, recombination rates, and thus the probability of inheriting certain DNA features from parents/ancestors based on recombination, vary quite a lot. There are many 'hot-spots' and other regions seem to be 'protected' from recombination (for instance, regulatory DNA). According to the work I cite here, the probabilities of recombination can vary within about an order of magnitude (the most likely recombination occurring at 10 times higher probability than the less likely), but this varies a lot.
I hope this helps a bit. I am still not sure what do you mean by "biological factors", but for sure recombination is one of the important factors influencing the identity of each chromosome across generations (others are, of course, point and chromosomal mutations).

I reviewed my understanding of centiMorgans.  It appears to be the measurement of a rate, but the units used are a distance.  To me, this is like estimating travel time by considering only the distance, with no regard as to terrain, weather or traffic.  As you said, there are known hot-spots in the genome.  With a cM being a .01 probability, and rounding to about 7,000 cMs in a human, that would be an average of 70 instances of genetic recombination in a single generation, and that's a non-directional switch, as opposed to conversion.  With variables you point out, only general ranges matter.

It gives a rate because the probability of 'linkage' between any loci can only be in the [0,1] range. So, even though it is thought of as a 'distance', in reality (both as conceived by Morgan, and in real 'physical' terms) it reflects the frequency of recombination events. So, to me, it is a bit like the inverse of your metaphor: we get traveling times, yet we like to talk about it as a 'distance traveled'; the weather, traffic, etc, are implicit to the traveling times observed (the linkage).


text:
is there any kind of paw/pads lines or paw muscle anatomy in animal hands?
just like in the title my question is, is there any kind of paw/pads lines or paw muscle anatomy in animal hands? or its pretty much random?
example like mammary lines as bilateral structure that rules where mammary tissue can develop. is there similar thing like this for animal paw/pads? especially comparable to human hands?
prefferably include image (example like this mammary lines) if possible.

Do hands have developmental pathways, yes there are a lot of them, listing them all would be pushing it for a single question.

@John a link is fine too

try starting here https://www.ncbi.nlm.nih.gov/pubmed/19553860 and https://emedicine.medscape.com/article/1287982-overview

@John so far as i read and search the link you provide, none of them talk or has anything resemble about paw/pads though, im not talking about the hands generally but specifically about the paw/pads but not exactly about human palm either if its not clear.

human hands and forepaws are the same thing, there really is no formal distinction.  they are all controlled by the same developmental pathways.


text:
By what mechanism do our nerves lengthen as people get taller?
How do nerves get longer as kids grow taller?  I searched for an answer but I can only find information on the formation of nerves in embryos.

They grow
Nerve axons can grow rather quickly as long as the body of the cell is intact, quickly as in the mm/day range. This is also the basis of how nerves can regenerate.


text:
What determines the influx of calcium ions in the voltage-gated ion channels?
Calcium channels play a crucial role in neuronal signaling by helping the synaptic vesicles to fuse through the synaptic active zone and release their neurotransmitters. My question is, at a given moment, what determines the influx of calcium ions in these channels? Where are the ions coming from and what is their source? Is the influx determined by the source by changing the ion flow, or the ion flow is constant and the influx of ions into the synapse is only regulated by opening/closing of the channels?

Short Answer
Extracellular calcium ions’ “source” are probably cells called astrocytes that connect to both neurons and blood vessels.
Calcium ions outside the pre-synaptic neuron are high in concentration, but since they are polar molecules they cannot passively diffuse in, where they are low in concentration, so they stay stuck outside the neuron.
Voltage-gated calcium ion channels are closed at rest. These channels will open when depolarization occurs, as the membrane reaches a high-enough voltage threshold. Calcium ions rush in when these channels open. These voltage-gated channels are the primary regulator of calcium ion pre-synaptic neuron influx.
Calcium ions, once inside the neuron, will be used to release neurotransmitters into synaptic cleft.
Long Answer

What determines the influx of calcium ions in these channels?

Whenever dealing with flux, it’s helpful to start with what determines the flux rate of anything:
Rate of flux ∝ gradient / resistance

The calcium ion (Ca2+) gradient is established by an extracellular concentration > intracellular concentration (at rest) across the neuron’s cellular membrane at the terminal end (pre-synaptic neuron). Le Chatelier’s Principle (equilibrium) indicates that potential energy will build from the unresolved Ca2+ gradient, which will drive flux from high to low when given the chance.
The Ca2+ resistance is established (mainly) by voltage-gated Ca2+ (VG-Ca2+) channels. These are also on the terminal end of the neuron (pre-synaptic), and resistance is determined specifically on if channels are open or closed (closed at rest), AND the number of VG-Ca2+ channels present on the membrane.
To create an influx, gradient has to become > than resistance. Once an action potential travels down the axon and depolarization occurs at our local site, the increase in membrane potential (voltage) opens the VG-Ca2+ channels, thus decreasing resistance. Influx of Ca2+ into the axon terminal occurs.

Where are the ions coming from and what is their source?

Neurons are the flashy & exciting (no pun intended) cells in the nervous system, but to answer this question we must acknowledge that glial cells exist.
Neuroglia, glia, or glial cells
are cells that DO NOT produce electrical impulses, but are cells within the nervous system.
One type of glial cells are called astrocytes, or astroglia, and a couple of their many functions includes distributing nutrients to nervous tissue, and maintenance of (neuronal) extracellular ion concentrations, including Ca2+. Astrocytes also have access to blood vessels, giving them access to nutrients (supposedly like calcium ions).
Research on the specifics is very up-and-coming, so it is difficult to find much on it. We know calcium is coming from blood (crossing the blood-brain barrier), glial networks (including astrocytes) distribute nutrients, and astrocytes specifically are tied to extracellular neuronal ion homeostasis.
If you are interested in researching this further, the connection (and network) of a neuron to its blood supply is called neurovascular coupling.

Image: a neurovascular coupling

Is the influx determined by the source by changing the ion flow, or the ion flow is constant and the influx of ions into the synapse is only regulated by opening/closing of the channels?

Ion flow from source is fairly constant (in a healthy individual), the biggest regulator of ion flux into the pre-synaptic neuron will be the actual VG-Ca2+ channels.
Ca2+ outside of the (pre-synaptic) neuron’s axon terminal will influx when depolarization reaches the axon terminal, as that decreases Ca2+ resistance across the membrane:

Action potential travels down axon
Depolarization occurs at axon terminal
Increase in membrane potential (voltage)
VG-Ca2+ channels open
Ca2+ flux down its electrochemical gradient (influx, pre-synaptic neuron)

Ca2+, once inside axon terminal, interacts with SNAP and SNARE proteins to shuttle vesicles containing neurotransmitters to the synaptic cleft (Ca2+ - regulated exocytosis).

Sources

Image
University of Texas: Astrocytes
Astrocytes-Endothelial Reactions at the Blood-Brain Barrier
Wikipedia: Astrocytes

I have edited your answer 1. to remove the internet slang heading — we use standard English here as it is understood by most users 2. marked up the superscripts for the calcium ion by using HTML markup Ca2+. giving your answer a more professional look. (There are also other ways of doing superscripts.)

So, let's use a neuron to neuron connection as an example.
Calcium is released into the neuron when voltage gated ion channels, specific to calcium, open. These channels can only open when there is a significant depolarisation in the axon terminal of the neuron.
Where do the calcium ions come from? The majority of them are outside of the cell by the plasma membrane and adjacent to the synaptic vesicles.
I'm not too sure what you mean when you ask what the calcium ion's "source" is. It is common for calcium ions to sit outside the cell, not just in neurons, to help maintain potential difference for example.
And yes, the influx of calcium in a neuron is determined by the opening of voltage gated calcium channels.
Sources: https://web.williams.edu/imput/synapse/pages/IIA1.htm , https://en.wikipedia.org/wiki/Calcium,  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249630/


text:
What happens if an enzyme stops working in the body?
For example, if the enzymes in the digestive system stop working will the digestion still occur as enzymes are only catalysts for the reactions.
Thank You

It depends on what particular enzyme 'stops' working, and what reaction it catalyzes. For one, the human genome (and that of most organisms) has many genes encoding for enzymes with partially (or fully) redundant functions, and this can mitigate the damage to a particular biochemical pathway in the case that an enzyme within the pathway stops working.
That being said, if the reaction facilitated by the particular enzyme is fundamental for the cell/body physiology, then the embryo/organism would not be viable and thus we would not observe these variants. Thus, whenever a mutation with a 'loss of function' phenotype is observed in an organism, it probably is not essential for its existence (although it might affect a lot the proper functioning).
Enzymes accelerate reactions in various orders of magnitude, and therefore, without them, most of the reactions would not occur fast enough to be useful physiologically. So, yeah, they are 'just' catalysts but quite fine-tuned for physiological needs by millions of years of evolution.


text:
How do mutations and protein synthesis link to cancer?
How do mutations and protein synthesis link to cancer?
I know that a mutation in DNA can cause the triplet code on the mRNA to change so different amini acids are made and a different order means a different protein is made but how does it link to cancer when cancer is caused by uncontrollable mitosis.
Thank You
This question is at GCSE level so freshman/sophomore level.

Mutation in DNA can be beneficial, harmful, or may have no effect. This is dependent on the gene location where this mutation has occurred.
Various genes linked to cancer are:
Tumor suppressor genes: These genes regulate cell growth by keeping check on cell division, repairing mismatched DNA  and regulating cell death.  Mutation in this type of gene leads to unregulated cell growth and lead to formation of tumor.
Examples:

TP53 is most commonly mutated tumor suppresor gene. More than 50% of
cancers are caused due to mutation in this gene.
Mutation  in BRCA1 or BRCA2 genes is responsible for breast and
ovarian cancers. It  may also increase the risk of pancreatic cancer
and melanoma.

Proto-oncogenes: These genes help cells to grow normally. Mutation in this gene cause its permanent activation and unregulated cell growth takes place and lead to cancer. This abnormal gene is called oncogene.
Examples:

HER2 is responsible for breast and ovarian cancer.
RAS family of genes, responsible for cell communication, cell growth,
and cell death.

DNA repair genes:  These genes play role in repair of DNA, which is mismatched during replication.   Defect in DNA repair gene, leads to synthesis of incorrectly formed DNA and eventually incorrect protein synthesis.

Genes and proteins regulate mitosis.  The most common example of a protein that regulates the cell cycle and prevents cancer is P53.
If you want to learn more, look into cell cycle checkpoints.


text:
Why does protein folding not depend on the order in which it is synthesized?
I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:

Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to protein folding; computational protein design calculations completely ignore the order of synthesis which hence cannot be critical to protein folding.

I was wondering, how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein? What I mean, is in case I look at mirror image of a protein, would it fold the same? if I consider for example the sequencers: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)
Can anyone provide evidence that this is, in fact, so. Or do I misunderstand the section quoted?
link to the paper: sci-hub.tw/10.1002/pro.3588

Welcome to SE Biology. I've tidied your question a little. Some tips on using the site. First, please finish the Tour. It  would be useful also to read the Help on asking good questions. One way your question could be improved is to cite the article you quote from, preferably with a link, so we can double-check it. Second, I am not clear what  you mean by "the order of amino acids". Do you mean that you would expect those synthesized first to fold first and independently of those later in the chain?

@David thank you for your remarks. I've edited the question, I hope Iv'e managed to better explain what I mean.

how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein?

The quote by the researcher says that the form is unrelated to the direction of synthesis (N->C rather than C->N). It implies that all that matters is the amino-acid sequence that constitutes the protein, and that protein folding is driven by thermodynamic stability rather than by kinetics.

in case I look at mirror image of a protein, would it fold the same?

Yes, if you had an exact mirror image of a protein alone in solution it would adopt the same fold but mirrored. The N and C-temini would be on the same amino acids but all amino acids would be D rather than L chirality. This molecule would not generally be found in biology, since typically life uses L-amino acids. It would have different enzymatic behaviour on chiral molecules.

if I consider for example the sequences: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)

These are not mirror images, they are entirely different molecules. They are not chiral counterparts (L and D). In general they would not fold to the same structure as the CO and N groups in the backbone are flipped, see more on reddit. However this is a topic of research and some reversible sequences have been found, see Zhang2016 and Mittl2000.
On a deeper level, the researcher's claim that synthesis direction (and hence synthesis broadly) is unimportant is not clear cut. For designed proteins it may be true but these are small and hyperstable. For larger proteins and protein complexes kinetics play more of a role, and chaperones may be used to protect a growing chain as it comes off the ribosome. See for example discussion in Sorokina2018 and Deane2007.

Thank you for your reply. could you please further explain what's the difference between mirror image and reversed order of the protein? I thought that the two sequences I mentioned were mirrored.

Sure. A protein is just a molecule, and it is a molecule with chirality: https://en.wikipedia.org/wiki/Chirality_(chemistry). This means that the mirror image of the molecule is a different molecule, but the connection between everything is the same. You can also, separately, reverse a protein sequence, though calling this "mirroring" is a bit confusing as you are not reflecting anything in 3D space. In this case you get a molecule that actually has different connections: the termini are in different places and the C and N in the backbone are flipped when you reverse the sequence.

I suspect the author meant something a little different. It's not just that it doesn't matter if a protein is synthesized from N- or C-terminus it's also not important for the end result of folding that the synthesis is gradual at all.
When designing proteins de novo they model the folding on a computer. The gradual addition of amino acid residues to the protein is not part of these models, the computations are made on the entire sequence at once. Still, when the designed proteins are synthesized on ribosomes they fold correctly. So the fact that the proteins are built step by step shouldn't influence how they are folded very much. As long as there is a sufficiently low free energy state it will be achieved.
Also, N-ser-gly-ala-glu-pro-asp-C and N-asp-pro-glu-ala-gly-ser-C are not exactly the mirrored images of each other. They just have terminal amino and carboxyl groups swapped. I imagine this can influence folding a bit.

In addition to what is already said, I want to mention something more subtle. What other people have commented here is about an old 'dogma' due to Christian Anfinsen, which postulates that all that matters is the sequence of aminoacids + the microenvironment (pH, temperature, etc).
However, I think you might be confounding two other layers of biochemical complexity. One, L versus D aminoacids. If all the machinery of protein synthesis (including the ribosome and the messenger RNA!) was perfectly specular (i.e. D-amino acids and L- sugars, and the corresponding RNA sequence), everything else being the same, then the folding would be expected to be the same (although in practice, this is a new field of molecular engineering that is not that advanced). In fact, it is not clear why we have a particular chiral form of sugars and amino acids, and might as well be an accident of evolution.
The second thing that might be confounded in your question is the order in which a particular amino acid is added to a newly synthetized protein. Even though the previous answers seems to dismiss this as unimportant; it is in fact very important. Amino acids at the beginning of a protein chain are being folded as soon as they exit the ribosome. Thus this is quite an important process, as proteins aren't just 'waiting' to be completely synthetized for the folding to start: they are continously interacting with the environment (including chaperones!), so the folding does depend also in the order of synthesis.

You're probably right that the order in which amino acids are added is important. It's just that the article quoted in the question seems to says that it isn't (in most cases).

Except aren’t there chaperones to PREVENT such initial inappropriate folding?

The question is asking if the order of the protein affects the native structure of the protein. Amino acids do begin to interact and form structures as soon as they are incorporated into the growing peptide, but as the paper you referenced states "in no case has a protein domain been shown to be able to fold into its native structure while still inside the ribosome", this is because although the amino acids fold, they form kinetically trapped intermediates and not the native structure. The native state is generally formed once all amino acids are present, so it it independent of order.

The quote is getting at protein structure is generally thermodynamically driven and not kinetically driven. The structures would be different if you took a mirror image of the sequence that you showed as the amino acid at the n and c terminus are different as is the orientation of all the other amino acids. However, if the ribosome were to be able to translate in the direction of c to n terminus rather than n to c terminus then the structure of the protein formed would be the same, that is what the quote is getting at. This is because like I say protein folding is typically thermodynamically driven, even though some amino acids come out of the ribosome first and form a structure (the kinetic structure as these amino acids came first) the structure with the lowest free energy is formed. This occurs because typically there is not a large energetic barrier for the protein to overcome to refold to find it's minimum free energy structure and so the thermal energy is sufficient to allow for the activation energy to be overcome and hence the process is thermodynamically driven to minimise the free energy of the protein.

Thank you for your reply! I guess my problem is that I don't quite understand the difference between thermodynamically driven process and kinetically driven one. I'll make sure to read into that.


text:
What is a partial regulator?

Source: MY textbook-NCERT 12th Biology-Ch: Organisms and Population
(Pg 7 of pdf/Pg 223 of the book)
Is this graph for Partial regulators correct? Isn't it that animals tend to be regulators first and then when they can't maintain homeostasis anymore, they tend to conform aka adapt themselves to the surrounding for better survival?
So shouldn't the graph for Partial Regulators first be a straight-line parallel to the axis (signifying constant internal environment aka Homeostasis) upto certain External surroundings level and then be the inclined straight line when it behaves as conformer ?
I would like to know where I am wrong in my logic or Is it that The graph is wrong in my book ?

Why initial should be regulation? Upto a certain level? When the text says: Some species have evolved
the ability to regulate, but only over a limited range of environmental
conditions, beyond which they simply conform. Could it not be like confirming at both sides of limited range, ie conforming at low and high conditions.

I haven't really encountered this term before and it seems there are not many original sources of this term; I cannot find any scientific article that uses this term. So this term is apparently not a standard one. Also, as pointed out by @JM97, most organism can achieve homeostasis only in a limited range and it doesn't have to be limited at one specific end of the spectrum.

I think, the graph you indicated, might saying the following matter:
Let's take an example. " Some snails and fish  go into aestivation  to avoid summer-related problems-heat and dessication."  Now, when summer comes after the season Spring, the temperature gradually rises. The fishes can generally  withstand upto a threshold limit of temperature, and conforms upto this threshold limit. When their   comfortable weather breaks due to rising temperature, then they enter Aestivation and the graph now starts paralleling the X-axis.
Look, the graph doesn't parallel to the " Conformers' line" from the origin, but deviates with a little angle from that line : that implies the organism was trying to regulate against the external environment at first.
Undoubtedly, it's my own opinion, may carry some shortcomings generally.

Welcome to Biology.SE! Answers on this site are expected to be based on facts (not opinion or speculation) and consequently are much more likely to receive a favorable response if they include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion, and therefore is inappropriate for this site. ——— Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site and then [edit] or delete your answer accordingly. Thanks!

well your point of view is really different and original, though I am a little skeptical about it, it really relates to the paraphrase written in the same book on the next page relating to Partial regulator


text:
Can a person be infected with Polio even after vaccination in childhood?
We know that a person develops antibodies by active immunisation after the administration of vaccines (either in dead form / live attenuated form). Is there any chance of developing the same disease in immuno compromised persons after reaching adulthood?

Short answer: Yes.
Slightly longer answer:
Recall how a vaccine works - it introduces an antigen to the body, which provokes the body to produce antibodies towards that antigen.
Antibodies, simply explained, call upon the remainder of the immune system to fight off a potential infection of foreign body. If there is no immune system to mobilize, the infection would most likely run its course. However, the immune system would have to be sufficiently weakened in order to not be able to fight the infection.

While I don't know about polio specifically, some diseases do require "booster shots" as the initial immunity can be "forgotten" by the immune system*.  For instance, it's recommended to get a tetanus booster shot every 10 years or so.  But with other diseases, immunity apparently lasts for life.  https://en.wikipedia.org/wiki/Booster_dose
*This is different than getting annual flu vaccines.  In this case, it's the virus that tends to mutate, so that previous vaccines are no longer effective.


text:
Why males are more prone to cardiovascular diseases such as heart attacks than females?
I often see more people of males undergoing treatment for heart disease. It is often said that female reproductive hormone (oestrogen) has some cardio-protective action by preventing constriction of coronary arteries. Can any one explain this?

Can you please provide some reference to support the statement? Your observations can be biased and the sample size may be too small to make such claims.

A potential cause is the different distributions of body fat in males and females.
Men typically store their fat in their midsections and women store it in their hips/legs.
Ectopic fat, a type that puts people at a greater risk of cardiovascular disease, is stored more in the midsection of people.
Therefore, men are more likely to get cardiovascular diseases.
https://press.rsna.org/timssnet/media/pressreleases/14_pr_target.cfm?ID=1983


text:
Is every flower on a plant unique?
I've noticed on my dahlia plants that sometimes there's a flower which looks completely different then the rest . Either color or structural.  I dig these bulbs up each fall and keep inside to replant.  So my question is are these simply mutations, or caused by environmental factors or? I would assume the dna should be identical to the mother plant ? Thanks

Since the eggs in the flower are produced by meiosis they are all uniquely different.The products of fertilization are also unique combinations of DNA.

Dahlia cultivars are known to undergo somatic mutations, e.g. mutations that occur during growth that can lead to different flowers. See for example this old paper.
So it would be very possible that your bulbs yield somatic mutations that crop up as you regrow them each year. This could be the case even if your bulb has not undergone the mutation, because the mutation possibly is occurring in the meristem of the plant as it makes new shoots or inflorescences from the bulb.
Other possibilities would include epigenetic changes which do not actually modify DNA but can possibly lead to modifications of the expression of genes. These can occur due to changes in environment, but they are a bit more difficult to demonstrate as such.