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Why doesn't the rate of photosynthesis increase with increasing light energy (frequency)?
Why doesn't the rate of photosynthesis increase with increasing light energy (frequency)? I know that green light is not absorbed by chlorophyll, yet I am confused as to why this certain "frequency" is not absorbed. Intuitively, it makes sense that increasing frequency would make the rate faster.

I don't think this question is sufficiently different from other well-answered questions about the wavelengths of light used by plants for photosynthesis: (1) What types of light can't a plant photosynthesize in?, (2) Does the light color spectrum and frequency matter for photosynthesis?

To understand why the wavelength doesn't change the rate of photosynthis you have to look at the chemical processes. I won't name the molecules and all the stuff but I'll try to paraphrase it in generic terms.
Photosynthesis means that in the end a carbohydrate has been assembled where you had only water and carbon dioxide when you started. The assembly of carbohydrates can be broken down in very clear steps. The power needed for this assembly comes in well defined quantities. These quantities are fixed by the amount of energy needed to activate a certain center (in fact two different ones) inside the chlorophyll. It is clear, that any surplus energy doesn't change the modification of the molecule (electron transport), because when the needed energy is delivered, the reaction takes place. The surplus energy is lost and dissipates in different ways (photons, phonons etc.), because there is no other place where it can foster a reaction.
The other fact related is: Light also comes in portions and not as a continuum. Single light quantums accidentally hit the centers where they can deliver the energy for a single reaction. So the energy from a light quantum can start the reaction if it contains enough energy but only one. Neither it can't be spread over more reaction centres nor can the surplus energy transferred as "change" to another reaction. Even if possible, the arrival of the surplus energy of photon A used in reaction 1 must be rather synchronous to the arrival of photon B at reaction 2. This is very unlikely.
That's why lamp manufacturers declare the usable power of their grow lights with μmol/s and not in Watts or lumens. Only the number of photons counts. More energetic photons (having a shorter wavelength) can't start more than one reaction per photon.

There are 2 frequencies/wavelengths absorbed and used by green chlorophyll  ( forgot the numbers). To increase photosynthesis rate you need to increase the amount of light ( lumens) at those frequencies. Not provide different frequencies .

side note: It is unlucky to use lumens in this context. Because depending on wavelength there's a very different power and also a very different photon count for one lumen. I recommend referring to the particle flux (μmol/s) when talking about light for photosynthesis.


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Why don't sodium Voltage Gated Channels open during Repolarization?
During Depolarization the Sodium VGC open when they receive the Threshold Stimulus. But when Repolarization occurs there comes a point when the cell interior has exactly the the same potential that it had during Depolarization i.e.,60mV but the Sodium VGC remain closed. Am I getting something wrong? If no, please explain.

Voltage-gated sodium channels have three basic states that represent different conformations of the protein: closed, open, and inactivated.
When a voltage-gated sodium channel is open at depolarized voltage, there is space for part of the channel to shift into a position that blocks the pore. When this happens, it gets stuck blocking the flow of sodium, and it requires a negative membrane potential to remove the block. We call this the "inactivated" state, and this model is called the ball and chain model of sodium channel inactivation.
The inactivation gating process is also referred to as the "h-gate", because h is the variable representing the gating in the classic Hodgkin-Huxley model.
Wikipedia currently has a useful table on the sodium channel page showing the different states that a sodium channel goes through during different phases of an action potential.

source: Stack Exchange

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

sort: votes


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Do beavers' tails hurt from being dragged?
I understand that when beavers walk on land, they drag their tails behind them on the ground. Their tails look quite large and rather heavy, and the ground is often rough - does dragging the tail not cause abrasions and pain for the beaver?

No, it does not, otherwise beavers wouldn't walk with their tails dragging. Here is a picture of the bottom of a beaver's tail:

Found here
and here is a closeup (probably of the top, but they're very similar):

Royalty-free stock photo from Dreamstime
As you can see, the skin looks almost like reptilian scales. It is likely highly-keratinized and is quite thick, as you can see below. Innervation is probably net very close to the surface, like callouses we develop on our hands and feet, so it doesn't hurt to be dragged over sharp surfaces like rocks or thorns. Here is a cross-section of the thick part of the tail close to the body:

Source: Cannundrum blog

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


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Lower optimum temperature of plant Catalase
Most resources give an optimum temperature of 35° C for Catalase. after performing the AP Catalase enzyme lab in school, using blended potatoes, our results gave a greater reaction rate at a room temperature of 25° C. we hypothesized that this is due to the fact that potatoes cannot regulate body temperature, so catalase works better at room temperature. The only source we could find that backed up its claim was an excerpt from a Pearson textbook: Here

Do plants have a lower optimum temperature like the textbook suggests, or was something wrong in our experiment?

(75 students, half did potatoes, half did liver)

There are two points you need to do here. 1. Tell us clearly what the results were for catalase from the two sources. You do not do this and therefore I cannot see what you are trying to explain. Please rewrite it. 2. Find whether your results contradict published results. Although the generalization in Pearson is reasonable, it need not apply to all enzymes. There is no reason why an enzyme in an organism that metabolizes at ambient temperature might have greater activity at a higher temperature that it never encounters. I can’t see this being selected against.


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Can we see the cell cycle of the cells administered using IVIS-like device?
My question;

Can we measure the cell cycle of the administered cells from outside the body, while the recipient is still alive ?　Preferably, by using a device such as IVIS that can read fluorescent labelling in the body non-invasively.

In this paper, cells incorporating a reporter called Fucci are transplanted into mice in which a skin-flap window was created. The mice were observed in CLSM while alive through the skin-flap window. As a result, the cells were individually imaged at very high resolution.

Fucci-explessing cells change colour as the cell cycle progresses, so the researchers were able to visualise which stage of the cell cycle each transplanted cell was in.
However, this method is invasive. So we need a simpler method. The required resolution should  give what proportion of cells are in which stage of the cell cycle.　We don't need the single cell resolution.


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When does the Cas9 nuclease stop?
If I understand correctly, the steps of gene editing with CRISPR-Cas9 are roughly as follows

Cas9 nuclease and guide RNA form a complex.
Cas9+guide RNA complex scans genomic DNA and recognizes the sequences homologous to the guide RNA
Induces a double strand break in DNA upstream of the PAM sequence (only breaks when the homologous sequence of the guide RNA is in the vicinity of the PAM).
Genetic modification using the mechanism of DNA repair (NHEJ, HDR) after double-strand break.

If so, in the gene editing with CRISPR-Cas9 , gene editing is likely to continue as long as the Cas9 does not lose its activity, am I right?
My question

When does the Cas lose its activity?
What was the logic of the experiment that identified the timing? / If the matter itself is unexplored, what kind of experiments could be done to find out the timing when the Cas lose its activity?

As this movie shows, if the gene editing occurs successfully, it will indeed introduce a mutation in the target gene.
However, even if it does,-this is just my guess from here on out- it is likely to remain complementary to the target gene, at least upstream of the guide RNA. However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation. So, even if one successful gene edit is completed, I think it's possible that gene editing could happen again in the same location. Moreover, even if the targeted site is successfully edited, there is still the possibility of subsequent off-target editing elsewhere. That's why I think the tools exist to stop CAS.

A guide RNA binds to the target gene that has been bitten by CAS. The strand opposite the strand to which the guide RNA was bound has just been cleaved.
Quoted from this video.
An idea for an experiment to detect when CAS goes quiet
If a single cell colony was created from a gene-edited population and there was genetic variation in the cells born from that colony, then I think that would mean that there would have been Cas9 activity even after the single cell colony was started in culture. Is this idea correct? Could there be a smarter experiment?

Once the cut is made and DNA of interest is inserted will the guide RNA have the same template to bind to?

@ Roni Saiba   Thanks for your comment. Is your answer that the target gene in the template after editing is no longer able to bind to the guide RNA　by mutation occurred on the template side?
But even if mutation does occur, can the guide RNAs still bind to the target gene? The ability to bind may be weakened, but it may still be possible to bind.　Otherwise, there would be no such thing as "Cas that can be deactivated by light" or "a peptide to stop Cas9".

Perhaps the more Chunked downed question might be to create an assay to compare "which method of stopping is more certain to stop the CAS".　If I look for a paper on the means to stop CAS, perhaps I will find the answer to this question. Because such experiments would be necessary to clarify whether peptides or the light (Written in Japanese) can really stop CAS.

the deactivation mechanisms may also have been placed to stop off target activity after the job at the primary site is done. But I am in pure speculation territory now. I'll add an answer if I find enough material with references to convince myself of the mechanism.

@ Roni Saiba Thank you for your help. Maybe the extent of the subsequent CAS rampage may vary depending on what part of the target gene the mutation enters. If I understand it correctly, the way the mutation occurs is a matter of probability. So I think this variation in probability should be taken into account in order to "identify when the CAS will become docile."

Regarding the loss of Cas9 activity, you are already touching on the answer in your question. Cas9 as a nuclease/enzyme is always active, and will continue to cleave double-stranded DNA as long as there are complementary target sites and guide RNAs to guide it there. If the target site is not mutated or completely removed after cleavage, Cas9 can indeed cleave the same site again.

However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation.

I'm not sure if I misunderstand the point you are trying to make here, but the introduction of mutations is usually enough to prevent recurrent cleavage of the same site (although studies of off-target effects clearly show that this is not always the case):
Both Streptococcus pyogenes and Staphylococcus aureus Cas9 cleave their target sites between positions -3 and -4, counting from the end of the 20-nt guide sequence (see attached figure below). The double-stranded break can then be repaired either via non-homologous end joining (NHEJ), or via template-driven homologous recombination (HR).

In the former case (NHEJ), double-stranded breaks are sometimes repaired with small errors. These errors usually accumulate near the break site (read about NHEJ to understand why), and such mutations will typically destroy the gRNA recognition site. Note, however, that not all (in fact, very few) NHEJ repair events will result in the introduction of mutations, and "perfectly repaired" breaks both can and will be re-cleaved by Cas9. But since repeated cleavage is lethal to the cell, there is a selective advantage for mutations that prevent re-cleavage of a target site. Also note that the introduction of mutations (and thereby gene editing) via NHEJ is a random process, with no direct control by the researcher.
In the latter case (HR), the DNA template used for repairing the double-stranded break can typically be chosen by the researcher. It can for example be a chemically synthesized DNA fragment or PCR product with at least some sequence homology to regions flanking the cleavage site. But since there is no specific sequence requirement for the region in between the homology regions, this interspacing region can be designed such that it partly or completely replaces the original recognition and/or PAM sequence (violet region in figure below).

Thank you for your answer. I have confused two independent issues; "CAS's own activity" and "Once altered, can other target-genes be altered twice"? I understood the latter one, thanks to your answer. But, I think the first one is still not clear; for example, how many times does it take for a cell to divide to make the CAS docile? How can we measure the 'activity of CAS itself' at a given point in time?

When you write CAS (in capital letters), are you referring to Cas9?

It's not clear to me what you're after with your first question. In what setting do you expect Cas9 to lose activity? Are Cas9 and gRNAs expressed or introduced into the cell via transfection/transformation? Like I tried to point out above, Cas9 itself doesn't lose its activity, and loss of DNA cleavage activity therefore boils down to knowing how long Cas9 and/or gRNAs exist inside the cell, i.e., their "lifetime" or half-life. Bacterial proteins are often very stable in eukaryotic cells and are not actively degraded, but I'm not sure if this is also the case for Cas9.

Sorry the CAS means the Cas9.

To be exact, certainly that depends on how we get Cas9 into the cell . If the Cas9+gRNA complex itself is introduced into the cell, the problem is how long does it takes for all Cas9 to lose its activity from the point of introduction them into the cell. Perhaps it would be more reasonable to use a half-life, as it is difficult to say "the time until everything loses its activity". If you are using a vector expressing Cas9, then all Cas9 will not lose their activity until the last born Cas9 loses its activity.

More important thing is my second of question. It is important to know what experiments are needed to determine "when Cas9 loses its activity" in a given system.　In other words, there are several assays of Cas9 or its analogues (henceforth collectively referred to as CAS) that have been engineered to artificially stop its activity, but how do they prove that CAS has indeed lost its activity?

I see. I will leave it to someone else to properly respond your question, but this sounds like an in vitro rather than an in vivo assay. See for example one of the very first papers by Doudna and Charpentier. A similar assay could be used to demonstrate inhibition of enzymatic activity.

@gaspanic Can you give me a reference of the 'Bacterial proteins are often very stable in eukaryotic cells and are not actively degraded'. It will be helpful for designing future assays.

@RoniSaiba sorry, this is more based on personal experience and communication, so I should probably correct myself by saying sometimes rather than often. But there are techniques for regulating the half-life of proteins via degrons, take a look at the N-end rule for example.

@gaspanic Thank you.


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Is there a survey on whether people have gained or lost weight as a consequence of lockdown?
I am not sure if this is the right forum for asking such a question. Moderators can of course close it if it isn't and please migrate it to relevant site.
Is there a survey/study that statistically checks whether people have gained or lost weight as a consequence of lockdown?
Of course, it would be a complicated as there would be a need for number of controls such as age, usual changes in lifestyle of subjects (independent of lockdown), etc.

Weight is not usually something surveyed. The female part of the population will not answer, half of the men don't know nor care and a good proportion of the rest will answer with a wrong number. Weight is something you really need to measure. I expect that what you are after will come out of controlled studies that measure weight routinely and need to account for the confounding effect of the pandemic.

Thanks for your comment. I have edited the question accordingly.


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Why do earthworms have so little colour?
Earthworms (or at least the ones that I have seen) tend to be pinkish, but with the front dorsal region being a camoflagued brown. Why is this the case, rather than the entire body or back being pigmented. I couldn't find any reference to the reasons behind earthworm colouration

Here is a picture from the wikipedia page on earthworms, showing the concentrated pigmentation

If they spend most of their time under the ground where nothing can see them, then what use is pigmentation?

@jamesqf But when it is raining they move to the surface where they are visible. And rains are not that rare. And besides that, why pink, of course?

@rus9384: Re "rains are not that rare", that depends on where you live, but even in a rainy place, the time spent above ground (and during the day) is a very small fraction of an earthworm's life, thus any color selection pressure would be small. (Besides, a lot of dirt IS more-or-less earthworm color :-))  As for pink, flesh is generally pinkish, especially if your blood contains hemoglobin, as that of earthworms does: https://en.wikipedia.org/wiki/Earthworm#Circulatory_system

@jamesqf But why would the pigment of an earthworm be so concentrated on the back, rather than more spread out?

@Ichthys King: Is it?  I am no expert on earthworms, beyond those I run across while gardening &c, but they seem fairly uniformly colored to me.

@jamesqf I have definitely seen earthworms with completely brown backs and pale pink bellies and rear-ends

The reason appears to be the light cells of Hess, which are light-sensitive cells distributed over the back of earthworms, being more concentrated towards the head

This doesn't seem to answer the question which is "Why?" i.e. for what (adaptive) reason. The light cells of Hess are not a reason so much as a small part of a mechanism.

When creatures live in caves and darkness, they have negative selection against skin color, so they develop albinism.
Here's a quote:
Epidermis pigmentation normally protects organisms from the harmful effects of UV irradiation, reduces the extent of predation through camouflage and mimicry, and facilitates sexual reproduction by mediating colorful behavioral displays (Protas and Patel 2008).
Healthy soil has easily 100-200 worms per square meter of soil, (as many as 1000 even), and we only see 1% of that, so it suggests they spend nearly all the time underground.
When it rains they migrate some distance.


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Is there any evidence for sperm parameters being connected to fitness of the offspring produced by that sperm?
In most (if not all) sexually procreating species the amount of offsprings a male can produce is limited not by the amount of sperm he can produce, but by the amount of eggs his sperm can fertilize (with rare individual exceptions).
Because of that the optimal strategy would be to fertilize eggs with the best sperm.
Therefore it is reasonable to assume that there would be adaptations making sperm with deficient genes less likely to fertilize an egg.
But is there any evidence of this happening? E.g. would fertilizing eggs with less motile sperm (potentially with IVF) produce a less genetically fit offspring or result in a miscarriage?

The only way that natural selection can act on genes is when they're expressed, there's no mechanism for reading and assessing the "quality" of a gene in a sperm. Obviously the genes that effect the quality of the sperm will be selected for/against.

Well, it could be that genes which would make a "lower quality" offspring also would make a "lower quality" sperm. How is an interesting question, but genes should be seen as a part of the whole system (genome) rather than indepedent individual entities.


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Why there are two types of medium (YPGlu and YPGal) in the *K. lactis* Protein Expression Kit?
I am planning to use the K. lactis Protein Expression Kit from NEB for the expression of certain protein. I am not experienced with working with yeast. I started by reading the manual for this kit and I am a bit confused with the fact that there are two types of medium: YPGlucose and YPGalactose. Do I understand correctly that YPGlucose medium should be used for cell propagation while YPGalactose should be used for protein expression and if so, why is that?

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, it isn't reasonable to expect users of this site to find and read this manual for you! At a minimum you should make sure you've read all the entire material and then provide quotes and links for the relevant sections that you are having trouble with. ——— The answer is probably in there (in particular pay attention to the promoter on the expression vector that drives expression of the transgene). Thanks!

NEB also has very good customer support, you can always call or email them to get in contact with the people that actually design and produce the kits.


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Is there a way to derive Bazett's formula to correct QT interval in ECG?
As we know that QT interval in ECG is a function of heart rate (HR) and to comment on the pathology associated with altered QT interval, we must neutralise the effect of HR. For this Bazett's formula is broadly accepted, i.e. $QT_c=\dfrac{QT}{\sqrt{RR}}$.
Is it purely based on experimental data? Or, there is some mathematical logic behind it?
Here, $QT_c$ = correcred QT interval; $QT$ = measured in original ECG; $RR$ = RR interval.

Would anyone like to share their personal insight into this question?


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Why is half dose of Oxford's vaccine of covid more effective than full dose?
I recently read in a newspaper that the half dose of the Oxford's vaccine is 90% effective while the full dose is only 62% effective.
Why is this the case ?

The true answer is nobody knows yet - even the developers of the vaccine have admitted they don't know the true reason yet. It may be the case that it is a statistical artifact of a reduced sample size in the group which was given the half dose. Either way, we need to wait at least until the paper is out until proper judgement can be made.

These explanations in nature magazine are very, very vague: https://www.nature.com/articles/d41586-020-03326-w If it's not an artefact of statistics, they say it could be because the larger dose caused the body to attack the associated adenovirus complex on which the vaccine is delivered into the body and blunt the immune reaction to the covid-19 complex,

There are also very recent news articles about manufacturing errors causing the wrong dosage, e.g. https://www.bloomberg.com/news/articles/2020-11-26/astra-faces-more-vaccine-questions-after-manufacturing-error  So perhaps the vials marked "half dose" were really full doses?  So the "answer" is that nobody knows yet.


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Quantitative Physiology Textbooks Recommendations?
I am currently completing a 2nd year (UK) Mamamilian Physiology Module and a Neuroscience Module. However, my degree is also 40% Maths and Statistics. So in order to learn the content better, I am thinking I may be more suited to a quantitative first explanation before the qualitative description.
I am asking here as I don't want the biology to be glossed over as I am being assessed by Physiology Professors not my Statistics Professor

Has your professor suggested any book as a part of the course?

@RoniSaiba yes the Pocock and Richards Textbooks and points us to research papers in the slides


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Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software
I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have written a code for the backbone alone (i.e) to construct cartesian coordinates of each atom in backbone from the respective internal coordinates(without side chains). However I got to know that this can be done in a software (maybe in PyMol or VMD). I am completely a beginner in this field of biochemistry/bioinformatics/biophysics. Does it really possible to do this in software like PYMOL/VMD? I'll be very happy if I can do this in python itself. I want to generate cartesian coordinate of a given tetrapeptide for all possible Ramachandran angles (within the allowed region)

Do you have the structure of the tetrapeptide provided or you want to run a simulation and get all the possible dihedral angles (they are not called Ramachandran angles)?.

No, I have just bond angles, bond lengths (standard values). Now for a given set of dihedral angles (Ramachandran angles) for tetrapeptide I need to generate the cartesian coordinates. I need to simulate the structure. I don't want the minimum energy structure. I just want to get the structure of tetrapeptide for a given set of internal coordinates ). @RoniSaiba

VMD by itself can't generate MD trajectories. You will need some other software like NAMD or the like to do so. However, once you have a trajectory, you can write a script (in Tcl) for VMD which will give you the cartesian coordinates of the atoms in a txt file which you can then process in python, R etc. Here is a Tutorial on how to use NAMD and VMD to get the job done. You will have to first make a .PDB of your tetrapeptide. You can use Avogadro to do that.

Is it a biology or bioinformatics STACK forum question ??? It could be also a chemistry one if talking about molecular dinamics ?? A penny for your thoughts

Have a look at Biopython
There are specific questions about the specific internal coordinates on Bioinformatics forum i.e. :
https://bioinformatics.stackexchange.com/questions/18849/help-using-biopythons-ic-chain-functionality-for-getting-protein-3d-coordinates
or
https://bioinformatics.stackexchange.com/questions/19570/read-pdb-file-extract-dihedral-angles-modify-dihedral-angles-reconstruct-cart/19597#comment28645_19597


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Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is it really not necessary for any simulations while predicting the 3D structure of proteins? For instance, if we have a protein chain of N amino acid sequence, there will be 2N dihedral angles. Of which we need to specify only the 2N-2 (apart from the first and the last amino acid dihedral angles) dihedral angles. Why the two angles are ignored? Let's assume all the bond angles and bond lengths are provided for the entire chain.
I have seen this statement in the following ppt, slide number -9, titled representation of internal coordinates, under bullet point 3.
https://www.cs.umb.edu/~nurith/cs612/Manipulation.pdf

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, we expect you to do research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). What's different about the bonding of the terminal residues? See also this sites criteria for "homework", which can apply to questions even if they are not assigned as homework. Thanks!

Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one incident segment rather than two.


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Is there any evolutionary reason why male traits appear in the heterogametic sex and female traits in the homogametic sex?
If you define male as the heterogametic sex, and female as the homogametic sex, then my question sounds like a tautology. But, what I'm trying to get at is why is it that the traits we associate with "males" (e.g. having an unlimited amount of possible offspring, greater average height, etc) appear in the heterogametic sex, and why traits that we associate with "females" (e.g. having a limited amount of possible offspring, shorter average height, etc) appear in the homogametic sex. Or, is it simply by chance that the homogametic sex became the female sex and the heterogametic sex the opposite?
As far as I understand it, heterogametic chromones allow for a greater chance of mutations being displayed, so I wonder whether there is something advantageous about this occurring in the male sex rather than the female sex. Perhaps it is because males are more "expendable" since they can have an unlimited number of offspring? Is this line of reasoning accurate, and are there any alternative explanations that go deeper than this?

The title question,

Is there any evolutionary reason why male traits appear in the heterogametic sex and female traits in the homogametic sex?,

suggests that male always is the heterogametic sex, but this is not true.  ("Male" is usually defined as the sex with the small, mobile gametes, i.e. sperm, as contrasted with the large, nutritive gametes, i.e. ova.) There are many species where females are the heterogametic sex, such as birds, most snakes, some fish, crustaceans, and insects.[a] These species use the "ZW" sex-determination system, which is essentially the inverse of the more familiar "XY" system.[a]  Other species don't have a heterogametic sex, but rather use lack of one chromosome as the determiner ("XO", "ZO"), and yet others use lack of one half of all chromosomes as the determiner ("haplodiploidy"). Others don't distinguish sexes by chromosomes, but use environmental stimuli.[b]
All this variety in forms of sex determination suggests that there are not substantial evolutionary advantages to having the heterogametic sex be the male.
[a] "ZW sex-determination system", Wikipedia.
[b] "Sex-determination system", Wikipedia.

+1 OP's whole question is based on a false premise. Mammal-centrism strikes again.


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How is the recipient's probability of survival calculated in Hamilton's Rule?
This is Question 99 from the 2012 USABO Semifinals Exam:

Assuming that "snonting" is an altruistic behavior that is maintained due to kin
selection, consider the following situation:

A reproductive male, X, lives with his mate near his parents. His other
siblings are all females and no longer live nearby. Based on your observations,
you know that X is likely to produce 12 MORE offspring during his life. His
parents, however, are older and will only produce 3 more offspring during
their lives. One day, a situation arises where X’s parents have a 50% chance of
death. However, if X snonts, his parents will survive with 100% probability.
Given this information, use Hamilton's rule to predict the maximum probability
of death that X can incur in this situation in order for snonting to be favored.

I calculated the answer based on Hamilton's Rule (r⋅B>C), where r = 0.5, B = (1-0.5)⋅3, and C = x⋅12. Solving for x, I arrived at an answer of 6.25% probability of death for individual X. However, the answer listed on the test is 12.5%, which I assume is arrived at by giving the recipient a probability of survival of 1, instead of an increased probability of survival of 0.5. I am wondering which interpretation of Hamilton's rule is more accurate, or if I have misinterpreted the question.
Thanks!


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How does glucose uptake happen in the various tissues of the body?
I know that the GLUT4 transporter allows for insulin-dependent uptake of glucose in skeletal muscle, liver and adipocytes. I also know that GLUT2 transporters are present in the liver and allow it to absorb glucose in the absence of insulin, and GLUT1/GLUT3 allow glucose to cross the blood-brain barrier and enter neurons.
However in my research I could not find the mechanism for glucose uptake in the remaining tissues of the body (Ex. epithelial tissue, connective tissue). Are there other types of transporters for glucose in these tissues? Surely these other cells also need glucose to survive.

As far as I am aware, all tissues have glucose transporters, but there are many different types with varying tissue distribution. A short review in Biophysical Reviews (2016) by Navale and Paranjapei is freely available and provides a summary with links to original papers.
In short, there are two types of glucose transporter, those involving sodium symport (SGLTs) and those operating by facilitative diffusion (GLUTs). The review lists six SGLTs and mentions thirteen GLUTs, belonging to three different structural classes.
The tissues specifically mentioned in relation to one or more of these transporters include:
For SGLTs — small intestinal cells, proximal tubule of nephron, intestine, testes, uterus, lung, brain, thyroid, kidney, liver, uterus, pancreas.
For GLUTs — pancreatic beta cells, liver, kidney, brain, heart, skeletal muscle, adipose tissue, small intestine, testes, placenta.
I reproduce below a table from Chapter 6, Insulin and Sugars, in Gerald Litwack
Human Biochemistry (2018). The chapter is available if you belong to an institution with a subscription to Springer publications.


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How do organelles divide?
I'm sure by the nature of this question you will come to know my amateurish knowledge in biology. During mitosis, they simply state that the organelles just replicate...while we are provided somewhat detailed information regarding the division of the cell. How do the nucleus and the other organelles divide? Mitochondria used to be prokaryotes apparently so do they divide by binary fission? while we're on that what exactly are the organelles composed of? There is a spike in protein production during interphase...so how do the organelles even go about dividing?

Well, the nucleus does not divide per se. Remember, the nuclear membrane dissolves during mitosis. It starts reforming after metaphase. Here is a review detailing the process and the mechanisms which are known. By extension, the Endoplasmic reticulum gets portioned as it is derived from the nuclear membrane.
Organelles also rely on the cytoskeleton and associated motor proteins for distribution between the daughters. A debated aspect in this regard is whether the organelles are distributed at random or is there an active process that ensures similar distribution between the daughters.
Finally, on to mitochondria. Till this point we have assumed symmetric cell division i.e. both daughters get almost equal amounts of maternal material. But in stem cell divisions, the non-stem daughter is smaller in size. Interestingly, this paper shows that the stem like daughter gets younger mitochondria (less damaged mitochondrial DNA).
As you can see, it is impossible to cover all the organelles in a single answer. And we are not even considering physiological differences between different cell types. Cheers!


text:
How many hairs per sq. cm. (or inch) do hamsters have on average?
How many hairs per square centimeter (or inch) do common pet hamsters (Mesocricetus auratus or Phodopus sungorus) have on average?
I thought this would be easy to find by googling, but the best I've been able to find is this 1986 article, which isn't very clear in answering the question.

According to Paul et al. (2007), shaved fur patches of male Siberian and Syrian hamsters had a mass of about 12 mg/cm2 dorsally and 3 mg/cm2  ventrally.
This search give me the page.

Fig 1 from Paul et al. (2007) compares mass of fur growth across time for 2 groups exposed to differing lengths of daylight (long, LD, and short, SD) to examine winter fur adaptation.

Paul, M.J., George, N.T., Zucker, I. and Butler, M.P., 2007. Photoperiodic and hormonal influences on fur density and regrowth in two hamster species. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology, 293(6), pp.R2363-R2369.

Thank you, but it looks like the results are in mass of hair per cm^2. It would help if I had data for what was the mass of 1 hair (or 1,000 hairs), but unfortunately, I don't have such data.

@Enivid calculating the mass of a single hair is less time consuming than counting all the hairs, and it's certainly something you could try yourself to add such info to this post. Any secondary or post-secondary school will have a balance that I'm sure they'd let you use. I'd recommend a digital model


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Why doesn't the concentration of one ion affect the concentration gradient of another ion across a plasma membrane?
In the initial stages, some ion channels across the plasma membrane open to allow for ions to flow down their concentration gradient into or out of the cell. I understand that each ion's overall electrical potential across the membrane would affect the other ions', thus affecting their transport across the membrane. However, I don't understand why the concentration of ions aren't taken as an overall concentration because surely, if we are looking at diffusion of ions caused by Brownian motion, then all molecules on either side of the membrane would affect the other molecules on that respective side of the membrane?

Why do you think this about Brownian motion?

Because Brownian motion affects the random movement of the ions?

But, what aspect of Brownian motion makes you think the concentration of one ion affects the concentration of another?

Brownian motion is the random, uncontrolled movement of particles in a fluid as they constantly collide with other molecules (Mitchell and Kogure, 2006). Therefore, wouldn't the ions collide with one another and if there is a greater concentration of one ion outside a cell, it would increase the number of ions that can collide with the other ions, hence increasing the frequency of collisions, affecting the overall ion concentration gradient (is this a scientific term)?

No, it would not. I do not understand how you are going from frequency of collisions to a concentration gradient. In any case, the equations that are important are pretty well understood (Nernst, Goldman/GHK) - maybe best to start from those and try to understand what they say rather than speculation?

So is the point here that the concentrations of each ion only affect each other to the extent of their electrical potentials because the main thing that affects whether they can pass through the plasma membrane is the permeability of the leak channels/voltage-gated channels (in the case of diffusion).

Yes, that would be the main point evidenced by those equations.


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Do fish depend on plants for survival?
As far as I know, all land life depends on plants for survival. Plants convert sunlight to energy using photosynthesis, herbivores consume plants, and carnivores consume herbivores. All the energy is coming through the sun and being gradually processed by this food chain. If plants were removed from the system, all animals would eventually die as they would run out of energy.
Do fish and other water creatures also depend on plant life in the same way?

It might be useful to clarify what you mean by 'plant life'. Wikipedia lists four different definitions of the word 'plant': https://en.wikipedia.org/wiki/Plant#Current_definitions_of_Plantae

 Short answer
All marine life needs energy to survive and reproduce. "Heterotrophic" organisms get their energy from eating other organisms and digesting the molecules of their tissues for driving cellular respiration/function. Ultimately, though, entire ecosystems and food webs are dependent on the non-biotic energy (e.g., sunlight) captured by "autotrophs" (aka "primary producers") and stored in the molecules of their bodies.
Plants make up only a portion of the autotrophs present in the oceans. Photosynthesis by phytoplankton accounts for the majority of Net Primary Production (total energy stored by autotrophs minus energy used by autotrophs to live) in our oceans. Chemosynthesis of bacteria and archaea in the ocean depths account for a small degree of NPP, too.
Heterotrophic organisms eat the autotrophs, and higher trophic heterotrophs eat lower trophic-level organisms. Dead matter (still containing energy-rich molecules such as sugars and fats) drift to lower ocean depths to provide organisms farther from the photosynthetic surface regions with most of their energy. At all trophic levels, energy is used to drive cellular work or lost as heat; as such, less and less energy is available at higher trophic levels and therefore necessitates eating more and more food.

 Illustration by Tim Gunther. Source: National Geographic
SUMMARY: all marine organisms are dependent on primary producers, most primary producers are photosynthetic, plants are responsible for a significant (though minority) amount of productivity in oceans, and phytoplankton account for the majority of energy capture in our oceans.
 Long answer
The Basics
All biological systems on earth require energy and matter for survival. Primary producers are the organisms that acquire energy from non-biological sources to make them available to the rest of the biotic component of the ecosystem (i.e., their associated food web; sometimes visualized as an energy pyramid).

Most commonly, primary producers (or autotrophs) acquire energy from the sun, and therefore are referred to as photoautotrophs. Other organisms, however, acquire energy from non-solar sources (e.g., thermal vents and cold seeps at the ocean bottom), and are termed chemoautotrophs.

Radiosynthesis might also be a thing...

If all other organisms in an ecosystem depend on these primary producers as an energy source, it's important to try to quantify how much energy the autotrophs are converting from non-biotic sources and storing in their cells. We can quantify this in terms of productivity:

Gross primary productivity (GPP) is a measure of the conversion rate of the above non-biotic energy sources (typically solar) into stored chemical energy (typically in sugar molecules) by the autotrophs.

Net primary productivity (NPP) is essentially GPP minus energy used by the autotroph to survive (i.e., respiration).

Read here for more information about energy flow basics.
Primary Producers in Oceans
Although photosynthetic plants are the best known primary producers, they are not the only autotrophs on earth. In fact, the large portion of ocean productivity is a result of phytoplankton, a diverse collection of photosynthetic protists and cyanobacteria.

 Image source: NASA, originally from Sally Bensusen, NASA EOS Project Science Office
The photosynthetic activity of plants and phytoplankton provide the majority of NPP for the entire ocean, but they are both limited in where they are located.
Sunlight is limited by water depth, reaching depths of less than 300 m.

 Image source: NASA
Since sunlight-availability dictates NPP to such a large extent, we can divide the ocean into vertical zones based on light availability. Only the top 200 m, referred to as the euphotic zone, has enough sunlight available for photosynthesis.

 Image source: NOAA
Both of these photosynthetic organisms are also limited by nutrient availability.

For example, phytoplankton are most abundant in upwelling zones where sinking nutrients are brought back up to the ocean's surface. These occur both in the open ocean and along coastlines.

Plants, which absorb nutrients through root systems, are further limited by the availability of substrate within the euphotic zone. In other words, they need somewhere to "anchor" down. As such, plants are only found along continental shelfs or other shallow benthic or sedimentary regions within the euphotic zone. In other words, we would say plants are limited to coastal or littoral zones.

Although the majority of production in oceans is a result of euphotic photosynthesizers, very small amounts of production are the result of chemosynthesis at thermal vents and cold seeps in deeper ocean depths. the chemoautotrophs here are all bacteria or archaea.
NPP of our Oceans
So far we discussed the importance of net primary production (NPP), the autotrophs responsible for the ocean's NPP, and the limitations of where such autotrophs can live. The question still remains: to what degree do the oceans rely on these variable sources of NPP?
According to Fox et al. (2020), "Assessments of marine primary production...are made difficult by the extreme plasticity in phytoplankton physiology". However, certain broad trends are apparent.
Well, given that both plants and phytoplankton can exist in coastal/littoral zones, these zones (especially those associated with estuaries bringing in additional resources from freshwater systems), tend to have the greatest NPP per unit area of anywhere in the world.
However, since the pelagic, or open-water, portions of the euphotic zone make up such a large percentage of the earth's surface (~70%), this so-called epipelagic zone accounts for more NPP per year than any other biome or life zone globally just due to the immense area/volume for phytoplankton to live and photosynthesize.

Although phytoplankton make up <1% of the earth’s photosynthetic biomass, Field et al. (1998) estimated such phytoplankton are responsible for almost half the world's annual NPP.

George Kling (University of Michigan) provides 2 simple graphics demonstrating these two points on a course website of his here. I've copied lower quality images here for reference:

 Modified from figures 4-5 of George Kling (University of Michigan) course page
Since only autotrophs can convert non-biologic forms of energy into chemical stored energy that heterotrophs such as fish and other water creatures can consume, all non-photosynthesizing organisms throughout the ocean's depths rely on the consumption of these autotrophs (or lower trophic-level heterotrophs) for energy. In fact, according to sigman and Hain (2012), usage of the energy captured but autotrophs and utilized by higher-trophic heterotrophs is so robust that all but <1% of the energy initially captured ever reaches the ocean floor as fallen debris/wastes/decomposing "snow".
As mentioned previously, a minor degree of chemosynthesis along the ocean floor exists, but such chemosynthesis adds minimal NPP to those zones. I could not quickly find a source that quantified the degree to which NPP of these deep zones comes from chemosynthesis (though see McNichol et al. (2018) for a fairly recent publication discussing and examining this topic). However, such chemosynthesis can only occur at thermal vents or cold seeps and therefore are quite limited in their spatial scope. Suffice it to say, that a very limited amount of NPP come from such chemosynthesis and the degree to which chemosynthesis adds to the NPP is spatially variable based on the presence/prevalence of inorganic energy sources such as thermal vents and cold seeps.

Further reading:
Chapter 17 "the Flux of Energy through ecosystems" in Begon, Townsend, and Harper. 2006. Ecology: From individuals to ecosystems. Blackwell Publishing, Malden, MA, USA.
Sigman, D. M. & Hain, M. P. (2012) The Biological Productivity of the Ocean. Nature Education Knowledge 3(10):21 [see here]

Citations:
Field, C. B., Behrenfeld, M. J., Randerson, J. T., and Falkowski, P. G. (1998). Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240. doi: 10.1126/science.281.5374.237
 Fox, J., Behrenfeld, M.J., Haëntjens, N., Chase, A., Kramer, S.J., Boss, E., Karp-Boss, L., Fisher, N.L., Penta, W.B., Westberry, T.K. and Halsey, K.H., 2020. Phytoplankton Growth and Productivity in the Western North Atlantic: Observations of Regional Variability From the NAAMES Field Campaigns. Frontiers in Marine Science.
 McNichol, J., Stryhanyuk, H., Sylva, S.P., Thomas, F., Musat, N., Seewald, J.S. and Sievert, S.M., 2018. Primary productivity below the seafloor at deep-sea hot springs. Proceedings of the National Academy of Sciences, 115(26), pp.6756-6761.
 Sigman, D. M. & Hain, M. P. (2012) The Biological Productivity of the Ocean. Nature Education Knowledge 3(10):21 [see here]

Great answer. Followup questions: I understand that unlike land plants, phytoplankton can move around. Does it do so strategically, like an animal? Does it run away from predators and such?

@Ram most phytoplankton are non-motile, and simply move along with the ocean currents. I suppose dinoflagellates can move minor distances with the use of their flagella, but they are so small that I'm not aware of any intentional mass movement of phytoplankton worth noting. See here and here for more info.

@Ram although phytoplankton don't generally move strategically, the heterotrophic  zooplankton that feed on them do: https://www.nature.com/scitable/blog/saltwater-science/what_makes_plankton_migrate/

They're heterotrophic though, so they still maintain the rule of "a creature that does photosynthesis can't move"

Yes, photosynthesis provides nearly all of the ocean's biomass and energy. The best is to study oceanic food chains and webs.

It looks like there aren't enough plants in the ocean because they don't form huge reserves of foliage and branches... 10% of land plant mass dies and is replaced every year, and 100% of oceanic plants die and are replaced every week:
"Biologists set out to estimate the total biomass of phytoplankton and calculated that less than one billion tonnes of the single-celled microorganisms were alive in the ocean at any one time. There were 45 billion tonnes of new phytoplankton each year, 45 times more than their own mass at any given time. The phytoplankton would therefore have had to reproduce themselves entirely, on average, 45 times a year, or roughly once a week. In contrast, the world's land plants have a total biomass of 500 billion tonnes, much of it wood. The same calculations showed that the world's land plants reproduce themselves entirely once every ten years.
https://www.nature.com/articles/483S17a
Every step of the marine energy pyramid has about 10% efficiency, so the shrimps and zooplankton take about 10% of the phytoplankton energy, then small fish 1%, and big fish 0.1% of the plant energy.
For every 500,000 units of radiant energy that hit the ocean surface, 2% is converted to phytoplankton at the base of the trophic pyramid, and the 500,000 units are necessary for every 10 units that a tuna consumes. https://oceantracks.org/sites/oceansofdata.org/files/energytransfer.png
https://en.wikipedia.org/wiki/Marine_food_web
In biology, we typically study coccolithophores and phytoplankton to learn the marine food web.
Areal map of sea chlorophyll in Mg/m2.

@theforestecologist I've found a quantitative estimate of the biomass of phytoplankton in the oceans, it's 1 billion tonnes of phytoplankton at any one time versus 500 billion for terrestrial plants including their wood. https://www.nature.com/articles/483S17a

@theforestecologist The researchers said that the average kg of oceanic vegetation survives 7-8 days, and the average kg of terrestrial vegetation survives about 10 years. The photosynthetic activity of all the lands and all the seas are about the same, a bit higher for terrestrial vegetation.


text:
Is it possible to determine the initial population given the final one?
It is possible to determine the initial population of, say, bacteria given a measure at a later time?
Let's say I use the logistic growth model
$$\dot N (t) = rN(t)\left(1 - \frac{N(t)}{K}\right)$$
and let's assume I know $K$. Let's imagine I have a mouse and I inject it with a dose of Shiga-toxin producing Escherichia coli (STEC). After 24 hours, the mouse dies, and I measure STEC with qPCR, obtaining a value of 20 million cells.
Can I calculate how many bacteria were in the initial shot, $N_0$?
And how many parameters do I need to know? For instance, let's say the mouse simply died some times after the injection. Can I know $N_0$ even if the absence of the time parameter?
How do I calculate $K$?
Is the logistic equation valid for live models? I understand it is good for chemostats, but is it valid for a mouse. Of course, a mouse can also reach saturation, since if $K$ is reached, the mouse dies, as in the example. Or is it a better description for bacterial growth in animals?
Thank you

can you link any study which shows quantification of bacterial numbers using qPCR. I just want to see how it is done.

The second here https://pubmed.ncbi.nlm.nih.gov/?term=bacterial+load+by+qpcr&ac=no&user_filter=Review&schema=none&size=100 explains also how to make the standard curve for the quantification...

For the logistic equation,
$$\frac{\mathrm{d}N(t)}{\mathrm{d}t} = rN(t)\left(\frac{K - N(t)}{K}\right)$$ the solution that allows you to calculate population population size at any time is:
$$N(t) = \frac{N(0)Ke^{rt}}{K - N(0) + N(0)e^{rt}}.$$ Looking at this equation algebraically with a set of knowns—$K$, $t$, and $N(t)$—and a set of unknowns—$r$ and $N(0)$—we see with this one equation that we have two unknowns, which are the intrinsic rate of growth and initial population size. So, the short answer is there is insufficient information to know the initial population size without additionally knowing the intrinsic rate of growth.
Hopefully this makes intuitive sense as well. If we know what the population size is, we just don't know how fast it arrived at that value. The intrinsic rate of growth could be small with a large initial population size on one extreme of the intrinsic rate of growth could be large with a small initial population size.
Calculating $K$ is problematic since $K$ is a maximum value. Better would be to use the original Verhuslt logistic equation, where the parameter $\alpha$ represents the decrease in population growth rate as a function of individuals added to the population:
$$\frac{\mathrm{d}N(t)}{\mathrm{d}t} = rN(t) - \alpha N(t)^2.$$
Note here that is the same if equation if $K = r/\alpha$. In the $K$ equation, $K$ is conflated as both a maximum and an equilibrium, which is never the case in real populations or any extension of the logistic model (e.g., including harvest or species interactions).
There are many single-species models of growth. The equation is valid, depending on what's done with it. The logistic equation is a generalized model that is elegant in the sense that is simple and has relative high qualitative explanatory value. But if you are looking to forecast population dynamics or look at bacterial populations among populations of mice, then there are many different and preferred approaches that are more mechanistic, predictive, and realistic. HTH.


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Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?
The C-terminal domain (CTD) of human RNA polymerase II has 52 repeats of a similar heptapeptide sequence.
Will the RNA modification proteins only bind to some repeats at specific locations on this (e.g. the 1st repeat/the 10th repeat/the last repeat, etc), or will they bind randomly to any of the repeats?
If they bind to specific repeats, how can this specificity achieved?
If they bind to any of the repeats, then it would seem to me that several molecules of an RNA modification protein could be bound to a single RNA polymerase II CTD. Does this happen?

Part 2 last question. Lock and key is not the only mechanism for ligand recognition/binding. Induced fit models don't require fixed structures. In fact, the CTD is disordered. Also, please create separate questions for let's say protein binding, and then another for specificity. As it stands now, few would dare to undertake the monolithic task of answering this question.

What research of your own have you done to try to answer this question?

I've edited your question to clarify it a little etc. If I have changed your meaning, please say so and edit it accordingly.

@David Wikipedia

The entry in the Wikipedia article on RNA pol is just a couple of paras, and the references cited are all over ten years old. This tends to be the problem with Wikipedia — all entries are by individuals and after the first burst of enthusiasm people pass to other things and there is no incentive to maintain them. It's difficult if you haven't got access to a university library, but one needs to try harder for more recent review articles.

In attempting to answer questions about protein structure, the first port of call (which one might expect the questioner to have also visited) is the Protein Data Bank — the global repository of such structures. There one can search for RNA Polymerase II CTD, look for complexes with other proteins, find recent publications in which they are reported, and consult them to find the state of knowledge of a topic.
Knowing nothing of the protein in question, I adopted this approach, and after looking at a few proteins and a few papers the following points seemed to emerge.

The CTD has a series of 7-amino acid (heptad) repeats — in mammals 21 of these are consensus(YSPTSPS), and 31 non-consensus (K7, rather than S7).
Further heterogeneity is afforded by phosphorylation (especially) and also glycosylation and proline isomerization, together with modification of the lysine of the non-consensus repeats.
It is thought that different post-transcriptional modifications are responsible for differential activation of 5′-capping or 3′-processing enzyme activities.
The CTD is disordered (unresolved) in the crystal structure of RNA Polymerase II, indicating that in the protein itself it does not adopt a fixed structure.
There are no structures of the CTD complexed to proteins it activates, so the question cannot be answered definitively.
There are structures of proteins complexed to short peptides (10- to 19-mers) based on the repeating sequence. These suggest that the structure of CTD in the complexes may be a spiral bound by specific interactions in a groove. The spiral formation may involve hydrogen-bonded β-turn motifs. A deduced structure from one such study with a 10mer is shown, together with indications of specific protein–protein interactions.

(Phosphorylated 10mer based on CTD complexed to the conserved CTD-interacting domain of mRNA processing factors RPRD1 and 2 — Adapted from Ni et al., Nature Structural and Molecular Biology (2014) 21, 686–695)
Concluding Remarks
The question contains two invalid assumptions — that proteins that interact with the CTD should interact with a single repeat, and that repeat should have a compact structure. Nevertheless, the functionality of the repeats and whether there are multiple interactions are valid questions. It appears from discussion in the paper by Ni et al. that the interacting unit is a 24-mer that binds to a dimer of the interacting protein (CID), and they propose that for phosphatases (and I presume protein kinases)15 molecules interact with the CTD at once.
What the situation is with 5′-capping or 3′-processing enzymes is another matter. There will only be one mRNA emerging from the RNA polymerase, so multiple binding would appear to make no sense. How much of the CTD is needed as rope to attach the processing enzyme soap? Does the soap slide along the rope? One would hope that eventually such questions would be answerable by molecular visualization techniques (see e.g. this BioRxiv preprint).

The question is asking about "repeat specificity" (i.e, will the binding of a specific protein on the CTD only happen on some specific repeat, or randoms on any repeat), not the specificity of the binding to a repeat. I'm not sure whether you get this?

@jw_ David mentions that the structure of CTD complexed with its binding partners are not known (yet). In absence of this data the only way you can check specificity is by painstakingly deleting 51 repeats, while ensuring you maintain a similar conformation with the filler sequence you have entered. As you can see it is an extremely complicated thing to achieve. As such, I think this question is not likely to get a definite answer in the near future.

@RoniSaiba I just realize that every result in biology come from real experiments (tons of work)

@jw_ I live in a different time zone from you and posted without "wrapping my answer up", which I now have done. I believe it addresses your question.


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How come only a handful of animals can do photosynthesis?
As far as I understand, all the energy that living beings rely on comes from the sun. It's processed by plants in photosynthesis. These plants are consumed by herbivores, which in turn are consumed by carnivores. Energy trickles down that way, with photosynthesis being the crucial basis for all the other layers.
A couple of days ago I was wondering, how come animals don't do photosynthesis? This story talks about a few exotic animals that can do photosynthesis, but they seem to be an edge case.
It seems like there's a rule of thumb: Iff a creature can do photosynthesis, it can't move. Why is this so? Wouldn't it be beneficial for a herbivore-like mammal to be able to create sugars directly from sunlight? They wouldn't have to graze at all, just find water and sunlight. It's possible they'd have an easier time avoiding predators and expanding into more territory.
Can you think of a good reason why such creatures never became mainstream?

This paper will be of help: https://academic.oup.com/jxb/article/59/5/1069/537020

It is all about energy.
It is estimated to take 5000 square meters of plants to feed the average person in the developed world, while the same source gives the lowest possible for a human under ideal conditions at 700 square meters.  In comparison, the average person covers less than 1 square meter.  While there is a lot of waste (animals are able to eat only a few percent of the energy the plant produces), the total energy available from photosynthesis is still orders of magnitude smaller than daily requirements for a typical animal.
Even in the case of the slug you linked (which you would expect would need about as little energy as possible for a mobile animal), it seems they obtain little or none of their actual energy from photosynthesis.
Hence you see photosynthesis restricted to life that has extraordinarily low energy requirements, which typically means being stationary (or moving very, very slowly as in the case some plants).  As soon as you adapt to a mobile, higher energy niche, you need access to a lot more energy than photosynthesis can provide.

I don’t think that completely answers the question though. Yes, photosynthesis alone is definitely not enough to sustain any animal with a non-trivial energy requirement, but what’s stopping animals from evolving photosynthesis anyway? Wouldn’t it be advantageous to have photosynthesis as a complement to energy from food? Besides, assuming photosynthesis in animals would also be chlorophyll-based, wouldn’t that give animals better camouflage in places like rain forests?

@Kal Nothing is stopping animals from using photosynthesis (some do), but even in the case of the low energy slug, the amount of energy they can get from photosynthesis is so small it cannot complement food intake (see link).

The amount of energy coming from the Sun is limited (about 750 W/m^2, perpendicular to the incoming light).  It takes a comparatively large amount of energy to move around, so a photosynthetic animal wouldn't be able to move much or very often.  (And in fact the known examples don't.)

The key issue isn't the lack of incident solar energy, but the inefficiency of photosynthesis. The average human power output is only about 100W, but photosynthesis can only harness about 5% of the Sun's power, so it's still not enough.

@Nuclear Hoagie: I thought the inefficiency was a given.  But note that even with much more efficient PV cells (over 20% for the commodity sort you'd put on your roof), electric motors, and nothing used for unrelated metabolic functions, it still requires wheels & very efficient aerodynamics to move things with solar power.


text:
How does RNA polymerase II CTD bind to the RNA modification proteins if the tail is flexible?
The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more "rigid" structure (i.e. fold into a structure that has less rotation freedom inside a repeat)? If not, then how can the proteins bind some repeat with high specificity? (you can't make lock and key with soft material)

Please clarify. First provide a source for your statement, even if it is a textbook. Is “flexible” really the right  word, or do you mean it has no fixed structure in a crystal of that protein alone. Second, what do you mean by secondary structure? The repeat is only seven amino acids — why would you think it would be alpha-helix or beta-sheet, and why do you think this is a requirement for protein–protein interaction. Your question seems to me to make a series of assumptions, the dubiety of which you don’t appear to realize.


text:
Is this a bed bug? Found this on the pillow as I was putting my daughter to sleep
My husband found this small (~4mm long) insect on a pillow while putting my daughter to sleep in our New Jersey (USA) suburb home.
We checked our daughter's and our own mattress as well as the rug, but we found no mark or other bugs. No one has recorded any bites.
We had bedbugs years ago in another home in another city, but have not seen evidence previously in this home. We moved in about 2 months ago at the end of September. We have not travelled recently due to Covid.
We are petrified and will call someone first thing in the morning but need to know

Unfortunately, yes it looks like you've got a bedbug. See the linked post for more details. Good luck!!

Can it be the only one or does it mean my house is infested? We have no other sign and we checked thoroughly as we had an issues at another place years ago

you need to update ([edit]) your post with additional information for anyone to provide additional accurate information. Please provide the dimensions of your specimen (and a clearer photo would be ideal), your location (city, state/province, country), more information about the building you found the insect in (is this your home?, how long have you owned/rented it?, are you in a multi-home unit?, are you urban or rural?), and information about recent travel or having new materials come into the home (e.g., suitcases, clothes, bedding, etc.). thanks.

Size is important, by the way, because bed bugs must feed prior to every molt. So if your specimen is large enough to be classified as an adult, it would indicate this specific specimen has taken a blood meal multiple times. If you truly have found no evidence of bed bug bites and have found an adult, it suggests it hitched a ride into your home. However, this isn't full-proof, since some people have minimal reaction to bed bug bites so such blood meals may have in fact gone unnoticed. So please update with more info. also, see my linked post for additional useful links for what to do...

As is suggested by my comment above, it is possible to have a single individual hitch a ride into your home. However, a single bedbug could also lay up to 100+ eggs per month with initial broods of eggs hatching in 6-10 days. So even if only one came in, more could be present. Your situation is not clear. Again, the more info you provide, the better chance we can provide you detailed and accurate feedback. (If nothing else, be prepared to provide this information and more to an exterminator in the AM). Update the post if you'd like more feedback; otherwise I wish you good luck!!

We did not travel (covid ...) But we had contractlr

The size (4mm) is similar to a late-stage nymph (~4.5mm), but is likely too small to be an adult (5-9 mm). (see here for size ranges). Only adult females can lay eggs (see here and here for sexing tips). Their small (~1/10") white eggs are laid in clusters in mattresses, furniture, or in cracks in the wall, baseboard, or floorboards. (See here for more egg info).


text:
When the leaf length ranges are given in a plant species' description, what do the numbers in parentheses represent?
Referring to a plant species, a paper I am reading (see citation below) says: "Blades are 4–5(6) mm long and (0.5)1–1.5 mm broad."
I understand the numbers 4-5 and 1-1.5 would be the ranges, but what do the numbers 6 and 0.5 in the parentheses represent?
Domínguez, Y., Valdés, C. M. P., & de Miranda, V. F. O. (2012). New features of Cuban endemic Pinguicula filifolia (Lentibulariaceae) and considerations on its habitat and ecology. Flora-Morphology, Distribution, Functional Ecology of Plants, 207(11), 838-841.

Anytime you see this being used in terms of a range...

the numbers outside the parentheses represent the normal or expected range, and

the numbers inside the parentheses represent atypical extensions beyond the normal range that are uncommon but possible and recorded.

Radford, Ahles, and Bell's 1968 flora, Manual of the Vascular Flora of the Carolinas confirms this in its preface (page vii):

In instances where most measurements for a character fall within one part of the total range of variation, the more infrequent or extreme size range is given in parenthesis as an extra measurement: e.g., "leaves 4-8 (16) cm wide", not "leaves 4-16 cm wide."

So, in your example, you can interpret the first range as follows:

Blades are typically 4-5 mm long (but sometimes 6 mm long) and typically 1-1.5 mm broad (though sometimes only 0.5 mm broad).

 Radford, A.E., Ahles, H.E. and Bell, C.R., 1968. Manual of the vascular flora of the Carolinas. Univ of North Carolina Press.


text:
Does Topiramate work by supplanting Pyridoxal phosphate in enzymes?
I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the activated form of vitamin B6).

A significant similarity is that both have an "offshoot chain" (Topiramate's sulfamate taking the place of PLP's phosphate) where PLP's phosphate is what binds it to enzymes in the first place, and both have a more electronegative element in the middle of what would otherwise be a six-carbon ring, apparently important in the typical PLP enzyme reaction.

I have been wondering if Topiramate supplants PLP in the enzyme glutamate decarboxylase, changing the reaction into a deamination. This would deplete glutamate, causing the pill's migraine relief, and the deamination could even cause Topiramate hyperammonemia.
If it does the same or similar to serine hydroxymethyltransferase, which is also PLP dependent, it could cause glycine deficiency, thus collagen deficiency - and this would even explain Topiramate hair loss.
When you look at it this way, it's frankly hard to imagine the mechanism of action is anything different. Have I stumbled upon it? Or has this been suggested already?

After reading the comments I have 3 reminders: 1) Be NICE, 2) Comments aren't for answers or extended discussion, 3) Voting to close shouldn't be used if you simply dislike a post or think it has a simple answer, especially when the OP shows research effort. Downvoting is more appropriate. @MarchHo I think your VTC comment could be converted to an answer

Comments are not for extended discussion; the remaining un-deleted comments of this conversation have been moved to chat.


text:
Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?
I read on https://doi.org/10.1038/d41586-020-03348-4:

Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (CASP 11)?

A guess is that the tests given in the competition are of bigger proteins or the organisers have more of a pool to select challenging ones from because of the process getting cheaper in dollar terms. These proteins may be harder to model because of there being more pairwise force interactions between residues, so the average (y axis) will decrease for more difficult to model proteins unless better modelling can compensate for this.

I’m voting to close this question because it is about the historical details of computational challenge rather than a biological problem itself. As such it is, in my opinion, off-topic here, but is probably on-topic for SE Bioinformatics.


text:
How to calculate the occurrence of a stretch of nucleotides in a genome?
I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites:
a = (g/2)^G+C × ((1-g)/2)^A+T,

where:
a = probability
g = G+C content of the target genome
C+G = number of G and C in the stretch
A+T = number of A and T in the stretch.

An example was given for the mitochondrial genome and the restriction site for EcoRI (GAATTC). I calculated, based on the example:
a = (0.44/2)^2 × (1-0.44)^4 = 0.0005

given that the length m of the mitochndrial genome is 16 000 bp, the number of occurrences is:
n = am = 0.0005 × 16 000 = 4.92 (against 4.80 reported in the paper).

I then tried to calculate the occurrence of a primer based targeting E. coli: GTGTCCATTTATACGGACATCCATG.
The GC content of E. coli is 50.8%, thus:
a = (0.58/2)^11 × (0.42)^14 = 1.22×10^-6 * 3.24×10^-10 = 3.95×10^-16

and the number of occurrences is:
n = 3.95×10^-16 × 16*10^6 = 6.32×10-9

Looks to me, that the primer should not occur at all in the E. coli genome.
Are the formula and its application correct? Also, I don't like the fact that one needs to know the CG content beforehand (although, one can assume 50% content) and an exponent at the 11th power; is there an alternative formula?
Thank you.

Strictly speaking the question is from the realm of probability theory. If the probability of a nucleotide $X$ in the genome is $p_X$ ($\sum_x p_X=1$), then the probability to encounter a particular sequence, where nucleotide $X$ occurs $n_X$ times, is
$$
\prod_X p_X^{n_X} = p_A^{n_A}p_C^{n_C}p_G^{n_G}p_T^{n_T}.
$$
The formula given in the question is a particular case for $p_C=p_G=g/2$, $p_A=p_T=(1-g)/2$,
$$
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
which is obviously always the case for DNA, where the numbers of Cs and Gs (or As and Ts) are always the same, but the more general formula could serve for RNA or proteins.
What one should keep in mind is that the formula above is for a sequence with a particular order of the nucleotides! If the order is immaterial, and only the content of the sequence matters, the formula has to be multiplied by a binomial factor, which is effectively summing over all the possible arrangements of the nucleotides. Thus, for the case of DNA we obtain
$$
{n_A + n_C + n_G + n_T \choose n_C + n_G}
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
You can check yourself that the difference due to the binomial factor is striking!

Thank you. Would you have a reference paper for this formula?

@Gigiux I can't give a reference for specific use in biology. Generally this is known as the binomial distribution: https://en.wikipedia.org/wiki/Binomial_distribution

Are the formula and its application correct?

Your formula is correct, and Vadim gives a good discussion of the underlying theory.  However, concerning your application...

Looks to me, that the primer should not occur at all in the E. coli genome.

This is the point of primers -- because of their length, they are unlikely to occur at random in a given DNA sequence.  So, starting with a known DNA sequence, you can create a primer that matches that sequence and have good confidence that you are not getting off-target priming, which may give you false-positive amplification in PCR.  This is precisely what the authors do in your linked paper.1  Using the known sequences for Rfb and SLT-1 genes in E. coli O157:H7, the authors make primers for the specific detection of those genes in drinking water, and, by extension, the presence of the organism that harbors those genes.

Bonetta S, Borelli E, Bonetta S, Conio O, Palumbo F, Carraro E. Development of a PCR protocol for the detection of Escherichia coli O157:H7 and Salmonella spp. in surface water. Environ Monit Assess. 2011 Jun;177(1-4):493-503.

I tried to calculate the values given your binomial formula. The number of EcoRI sites in E. coli should be:
a = (0.44/2)^1 * (0.44/2)^1 * ((1-.44)/2)^2 * (0.56/2)^2 =
= 0.22^2 * 0.28^2 = 0.0484 * 0.0784
= 0.0038
which is ten times the value given in the paper.

The expected number of restriction sites is:
n = 0.0038 * 1.6*10^7 = 60 712.96.
This is hundredfold more than the expected value of 645 reported by this paper (https://mmbr.asm.org/content/mmbr/62/3/985.full.pdf). In the paper, they calculated the number of expected 6-mer in a genome as long as that of E. coli (1113) but they did nor provide the calculation.

As for the primer, the probability of findig it in the E. coli genome is:
a = 0.25^5 * 0.25^6 * 0.25^8 * 0.25^6 =
= 8.810^-16
n = 8.810^-16 * 1.610^7 =
= 1.410^-08.
Again, there should be -- as acvill pointed out -- unique.

I did not understand how the binomial factor is defined. It should be:
B = n! / x! (n-x)!
where n is the number of trials and x the number of success. Thus it should look something like:
B  = 16 000! / (6!15 994!)
B' = 1.610^7! / (25!1.610^7!)
which are very big numbers. I understood this calculation was an easy one. Where am I getting it wrong? Thank you


text:
What did (domestic) cats evolve from?
I have received this question during a recent discussion about pet birds and cats. We know that birds evolved from the dinosaurs before the mass extinction that happened about 66 million years ago.
However, I could not find such clear information about the most prolific creature on the Internet.
This article suggests Felis attica (reclassified to Pristifelis attica) as an ancestor which seems to have lived about 12 million years ago.
I am interested in filling the gap between the mass extinction and Felis attica to have an answer for my question, but I cannot find an article diving even further in cats history.
Question: What did (domestic) cats evolve from?

I think you need to be a bit more specific: are you asking what cats in general (that is, the group felines like lions, tigers, jaguars &c) evolved from, which would be akin to "birds evolved from theropod dinosaurs", or are you asking which wild felines the domestic cats evolved from?  Which would be like asking which bird species my pet canary evolved from...

@jamesqf I am interested in a rather deep ancestry of domestic cats. This would be the first option from your comment.

Not an true answer to your question, but this Ologies episode with Dr. Mikel Delgado does a great job of explaining when cats came into our lives and how/if they were domesticated.
https://www.alieward.com/ologies/felinology

The carnivora can be seen in this phylogeny tree which comprises most of today's mammals. They suggest that rodents, elephants, monkeys, dogs and sea mammals all diverged from about 30 million years before the asteroid, until 5 million years after. The placentals and marsupials had a common ancestor previous to 100 million years ago.
Image from genomic study:

Previous to the Felix clade we have Feliforma, which includes mongooses and hyenas.
Image from wiki Feliformia:

There's a tree here
The last common ancestor of cats and dogs was about 40-55 million years ago. Feliforma family tree.
If you want to see previous to that, there are some basal carnivora, where the Feliforma are at the end of the tree.

Please reference where you've taken images from.

Ok, added reference. It's from wiki and the resizing is wrong. thanks.

Domestic cats ancestor was likely Felis silvestris or Felis lybica
Now this is actually just our best guess, little on the way of fossil evidence has been found but based on genetics Felis silvestris is the closes genetic match to the domesticated cat. However questions have arisen due to the risk of interbreeding, so it is possible Felis lybica may be it and Felis silvestris may only be a closely related sister group.
The big problem, Felis silvestris and Felis lybica form what is known as a species complex. That is a a collection of populations that may or may not be separate species. They are so closely related and physically similar that it  is difficult to be sure they even are separate species. There is a lot of debate over which population leads to the domesticated cat and evidence is tentative at best. Both species readily crossbreed with domesticated cats so a form answer may never be possible.
Source
Source 2


text:
Why did ants and meliponine bees lose their sting? What's the evolutionary advantage in it?
We know Aculeata is the Hymenoptera’s lineage where the ovipositor evolved into a venomous sting. However, most ants have lost this sting, as well as meliponine and some other bees.
Kerr & Lello (1962) say that “there are at least thirteen ways in which stingless [meliponine] bees protect themselves, making stings obsolete”. Since this subject is being researched for more than 50 years, we hope that some advances have been made in the understanding of this specific evolutionary change.
What's the evolutionary advantage for these groups to lose this apparently awesome defense system?

Does https://biology.stackexchange.com/q/35532/27148 help answer your question?

@BryanKrause It does raise interesting hypothesis, but I'm hoping a specific study may exist on the subject I've brought. For instance, counting how many times the sting was lost within Aculeata, proposing specific hypothesis about why the sting wasn't any longer required in each clade, etc. Within meliponines, some species have painful bites, but others don't. How do the latter compensate for that apparent lack of defense abilities?

It's not typically possible to do anything but speculate and tell just-so stories in these cases, which is why we have that canonical answer.

@BryanKrause It's not always a matter of simply just-so stories. There may be specific structures, behaviors, hormones, etc, that have evolved in such groups that provide a more plausible explanation for them.

I voted to close for Hwk (how far did you get with your own research?) because the post Bryan mentions answers the question you are asking sufficiently. If there is something you have found that specifically contradicts or expands on that answer, I'd include it here.

@James I asked a question about evolution of Hymenoptera, not a general question about evolution. Kerr & Lello (1962) say (in the abstract) that "there are at least thirteen ways in which stingless bees protect themselves, making stings obsolete". However, Western science is not open to the public, and this site, which could be an option to that, is full of perfectionists like you trying to close perfectly valid questions. C'mon!

@Rodrigo Maybe this is an XY problem? You are asking about why ants and some bees have lost their stings, but if what you actually want to know is what alternatives these stingless insects have to protect themselves why not ask that question instead, citing Kerr & Lello?

@BryanKrause Even if we know about other defense mechanisms, it would still be interesting to know the evolutionary costs and benefits of each -- this could explain the change. So I think the way I asked is more direct.

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

@MattDMo That's the first comment here, for which the answer is No.

Many ants do have functional stingers. see the fire ant.

@John I know, the text of the question says "some ants". And fire ants don't have a sting, as far as I know, Ponerinae ants and some other subfamilies do.

@Rodrigo fire ants do have a venomous string, https://thekidshouldseethis.com/post/sting-prey-raft-the-successful-behaviors-of-red-imported-fire-ants

@John Indeed, sorry. I thought that, like most Myrmicinae, they didn't.


text:
Binding BSA to silver surface via large difference in isoelectric points of the two materials
I would like to bind BSA to a silver surface so that I can utilize plasmonic sensing to detect the BSA. There seems to be two methods of doing this: 1) to rely on electrostatic forces or 2) to form a covalent bond. The former seems to be the easier route, especially for someone like me who does not have a background in chemistry/biology.
So I found a paper (https://doi.org/10.1016/0021-9797(91)90121-N), which has been cited 54 times, that determined a silver (oxide) surface has an isoelectric point (iP) of ~10 pH. So this should mean that it has a positive charge when a neutral pH solution covers the surface. In other literature BSA has been shown to have an iP of pH 4-5, so it should become negatively charged in a neutral pH solution. So the BSA should bond to the silver surface in a neutral solution, correct?
The reason I ask is two-fold. First, I found a more recent paper (https://doi.org/10.1021/am400909g) that has a conflicting value for the iP of a silver film (~3 pH). Second, I found a paper (https://doi.org/10.1016/j.vibspec.2003.09.003) were the authors adsorbed BSA onto silver films, but with the intermediate step of applying 2-mercaptoethanesulphonate to the silver surface. Why the need for this if the silver should attract the BSA electrostatically?
In addition, if BSA bonding to silver were to work in this way, am I correct in thinking that a neutral solvent such as phosphate buffered saline would hinder the electrostatic bonding process because the positive and negative ions from the salt solution would bond to the respectively charged molecules and neutralize the charge?

Concerning the apparent discrepancy between your first and second citations, the difference in values is addressed by the authors in the more recent work:

Perusal of the literature yields few IEP values for silver metal. Chau and Porter reported an IEP of 10.4 for an evaporated silver film as determined by contact angle titration.(6) The method employed in their investigation used only neutral and basic liquids, and the maximum contact angle achieved on the silver films was ∼35°, in contrast to the maximum we observe of 52° at pH 3.2 (Figure 1d). This dichotomy may be indicative of the amphoteric behavior of the native oxide at the surface.

Concerning your third citation where the authors bound BSA to silver via a 2-mercaptoethanesulphonate linkage monolayer, the authors give their reasoning in the abstract:

The direct adsorption of proteins on metal surfaces usually leads to loss of their enzymatic activity

So, to answer one of your questions

Why the need for this if the silver should attract the BSA electrostatically?

BSA here is a proxy for other proteins.  The purpose of the research was to examine how the structure of the linkage monolayer changed in response to protein adsorption, not how BSA specifically binds a silver substrate.

Oh I see now. So although both papers claim to have an oxide layer on their silver, paper #2 is claiming that Chau and porter did not use a sufficient number of pH solutions over the whole range, and therefore did not have enough data points to extract the iP value (Fig 1 of paper #2). But that value of 10 has been cited after paper #2 was published. Maybe I should just choose a different metal such as copper.
What exactly is loss of enzymatic activity?

"Loss of enzymatic activity" means that the adsorption of an enzyme to the substrate leads to changes in conformation that reduce or eliminate enzyme function.

Ok. So I think if I am only interested in binding BSA to silver for the sake of sensing BSA, then loss of enzymatic activity should be irrelevant.

Probably, but I'd suggest editing your question to better address what it is you are actually trying to accomplish. By your comment, this question smells of an XY problem.

I wanted to have reassurance before I possibly wasted money buying the products.