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Why do mutations not take place in mRNA of higher eukaryotes?
Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations

Do you have a reason to believe mutations do not occur in mRNA?

If mRNA gets mutated then it would make malformed proteins which in best case might get degraded or in worst case hamper with cellular metabolism or even lead to cancer if cell cycle regulatory protein coding mRNA were to be mutated.

The premise of the questions suggests that mutations cannot take place in the mRNAs of higher eukaryotes.
To answer your question I think it is important to consider two viewpoints:
First, from a theoretical point of view, since DNA and RNA are as you pointed out composed of nucleic acids, they both can be mutated if enough energy is provided (UV light, chemicals, etc) which invalidates the premise of the questions.
Now, from a practical point of view, as you mentioned most mRNAs molecules have a short half life typically in the minute to day range whereas DNA molecules exist during the whole existence of the organism.
While it can occurs that mRNAs are mutated people are not interested to study this aspect for the following reasons:
You pointed out in the comment section, a mutation in a mRNA molecule might lead to translated malformed protein which can easily be degraded. It will be only one mRNA transcript from thousands transcripts. With a short half life, the mRNA an proteins will be degraded which will not have a long standing impact of the cell/organism. As such it will be very difficult to observe a phenotype which will affect the whole host.
Thus RNAs mutations have only transient effects which will not affect the host in the long term. RNAs molecules are not more protected than DNA molecules just that they are short lived so the host is protected from the effects of RNA mutations.
Hope this helps!

Additionally DNA is inherently more stable due to the removal of the hydroxyl group from the C2 carbon on the ribose making it less reactive. This could be pointed to as an example of the limiting factor in the inherent complexity of any organism that uses RNA instead of DNA for long term data storage. That would be a discussion for another thread though.

Your answer is more of a comment as it does not really address the main issue of the question.

Your supposition is incorrect. RNA does accumulate "mutations" because the RNA polymerase also makes errors. The misincorporation rate of bacterial RNA polymerase is ~10–5 per nucleotide (Traverse & Ochman, 2016). Compared to that, DNA polymerase has much higher fidelity and has misincorporation of ~10–10 per nucleotide per generation (Zhu et al., 2014).
As pointed out in the other answer, RNA mutational effects are short-lived as RNAs are short-lived. However, RNA mutations can contribute to phenotypic heterogeneity which can, in some cases, be beneficial to the organism (Ackermann, 2015).

There is nothing special about higher eukaryotes as replication and transcription process is quite similar across different domains of life. Viruses are special, however. They rely on higher mutation rate for faster adaptation.

Mutations do occur in mRNA. This can occur during transcription, when RNA polymerase incorporates a non-cognate nucleotide into the nascent RNA strand (this may be because the DNA forms a short lived tautomer from quantum tunnelling, or because ). Alternatively, just like DNA bases, RNA bases are inherently unstable due to things like deamination events, but RNA is also capable of base catalyzed hydrolysis. To say that mutations are not interesting in RNA is also wrong as RNA editing is something that may be used to treat numerous diseases. RNA editing is transient, which is useful for treating diseases caused by temporary changes in cell state and modifying disease-related signal transduction through editing serine, threonine and tyrosine residues to affect phosphorylation sites. mRNA mutations are also important in understanding the affects of splicing on phenotypes and I'm sure there are more reasons, but these are just off the top of my head.
For more information about RNA editing see: DOI: 10.1126/science.aaq0180, a really cool potential of CRISPR


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What is the difference between transpiration and evapotranspiration?
According to my point of view transpiration and evapotranspiration are different things, but i am confused about this topic. After great effort, I found a major difference between it.
Transpiration: The loss of water in the form of vapour from plants surface is called transpiration.
Evapotranspiration: The loss of water from any surface in the form of vapour is called evapotranspiration. Such as water surface, soil and any body surface.
By educationspot
Is it correct? Please explain.

Essentially, evapotranspiration is the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere.

Here are some links to articles about transpiration: https://biolympiads.com/plant-anatomy-and-physiology/

source: Stack Exchange

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

sort: votes


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DNA like marine animal or egg
What is the name of the marine egg or living being that is transparent like a jelly fish or a Venus girdle, with a shape like a DNA or better like a chain of infinites, long as half of a hand and large as half of a hand nail?

Imagine a DNA-like strand but with no internal "sticks", white-ish, 10 cm long and 2 cm wide

Alternatively, how do I narrow my research in order to find the name of what I saw underwater?
The image seems too simplified but I just saw something like that, pretty simple, essential and little.

Is there a way to upload an image here? I used a paste bin but in case I can upload it. ( link to pastebin: https://pasteboard.co/Iv4fT7W.png )

@AMDP You can [edit] your post and copy the image into the question editor or use the image uploader. See How to upload an image to a post?

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


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Europe: big fly with black/yellow striped body: I'm guessing a horse fly?
This one made a summer night visit to the room and tried to escape by banging against the ceiling. What is it? I found nothing which corresponds, though "horse fly" might be a close match.

Location: Central Europe, Luxembourg
Locality: Where the suburb morphs into the not-yet-conquered countryside
Time: Late August, Nighttime
Weather: Quite warm (~27°C). Dry.

Here is an MP4 of the beast: https://i.imgur.com/F5yqMQ8.mp4
It is about 2 cm (0.8 inch) large. Relatively plump, keels over and likes to clean itself a lot.

Large head, large eyes, a bit hairy, two black stripes

Once it falls on its back it wallows a bit, there is clearly a probabilistic algorithm to get itself out of the predicament:

@BryanKrause Thanks Bryan. I have added some info. And a link to an MP4

Its not a horsefly (Tabanidae), but rather, a flower fly (Syrphidae). I don't know what species.

At first, because of the size and shape, I thought that it was a horsefly, but no horsefly looks like that (at least not in Luxembourg). It turns out that it was a hoverfly, just as Karl Kjer said. The species is Volucella zonaria, or the hornet mimic hoverfly. This hoverfly lives in most of Europe (including Luxembourg) and is 15-25 mm in length, consistent with your 20 mm estimate.
In this image you can see the same coloration and abdominal markings as your insect.

The markings in your photo are very difficult to see but are there.

Wikipedia page
original image source

Thanks. I had forgotten about that question. Good id.


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Does Cholestyramine (CSM) raise Tyramine levels?
This is a layman's question.
Will ingesting Cholestyramine (CSM, the resin, in powdered form to be specific) raise tyramine levels?
I am asking because Cholestyramine clearly has "tyramine" in its name, so i don't understand the chemistry behind all this and/or how this interacts with the body.
Thank you.

I'm not sure why "tyramine" is in the name "cholestyramine", but the molecular structure of tyramine is not present as part of the molecular structure of cholestyramine. Specifically, in tyramine the amino group is on the beta-carbon from the ring, and in cholestyramine the ammonium group is on the alpha-carbon (note the different number of points between the ring and the nitrogen in the line structures provided). I find it highly doubtful any reasonable metabolic reactions by the body could generate tyramine from cholestyramine.
Cholestyramine molecular structure
Tyramine molecular structure


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If number of children born were spread more evenly among all parents, would our species' genetics have more variability?
Instead of some parents having lots of kids, if the number of kids were spread more evenly to parents having few kids and people who have no children, would it introduce more genetic variability in our species in general?

Well the obvious answer is of course yes of course it would. That is the essence of natural selection. Variability leads to different phenotypes and selection for and the amplification of beneficial traits. Evolution. Except if there is no selection (everyone has the same amount of kids) no traits are amplified so everything in a large population is static. Until you introduce mutations and that increases variability. Eventually each individual would have such a large degree of variation from the next that I would assume speciation would be a very imminent result of any form of seperation or selection, which is against your original premise.

This is a good answer, and the only thing I would add is that the question does not mention whether all children have an equal chance to grow up and reproduce.  Given that accidents and illnesses might not be entirely random and might have genetic dependencies, natural selection would still be free to operate in a society where fecundity was evenly spread.

To answer this question we need to recourse to the concept of "effective population size" ($N_e$). This is the number of individuals which actually counts in maintaining a population and generally does not coincide with the number of living individuals (the census size $N$). $N_e$ was defined by Sewall Wright as "the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration".
In an idealized population with constant size, the chance of generating offspring is the same for all individuals, in such a way that the distribution of the number of offspring per individual is Poisson. In this situation $N_e = N$. In real populations, of course, the number of individuals of the two sexes that actually reproduce may be highly unbalanced, there is a large variation in fertility of different pairs, the number of individuals fluctuates from one generation to another, etc. All these factors lead to deviations such that $N_e < N$ (in most cases $N_e \ll N$).
The effect of variation in progeny size on $N_e$ is modeled by the equation $$N_e = \frac{4N - 2}{V + 2},$$ where $N$ is the total number of individuals (half males half females), and $V$ is the variance in progeny size per mating pair. It may be noted that if $V = 2$, which is the Poisson variance of a population with constant size, $N_e \approx N$ for reasonably large $N$, whereas $N_e$ decreases as $V$ increases.
Therefore, the answer to the question is yes, genetic variability is maintained at a higher level if the number of children is distributed more evenly among pairs.
An interesting point to note is that if the variance in progeny size is less than Poisson, we find $N_e$ > $N$, a result that may appear surprising (if $V = 0$, $N_e \approx 2N$). This suggests a strategy to maximize the effective size of captive populations of species at risk; by sampling a male and a female born from different pairs to mate for sustaining the population, the genetic variability transmitted to the offspring is maximal and the inbreeding is minimized.


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What are the methods for detecting anagenetic versus cladogenetic change?
I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.

This is thorny, but also depends on exactly what you're asking. What sort of evolutionary changes/traits are you interested in?

Additionally, are you interested in studying anagenetic change within the context of phylogenetic inference, or within the context of trait evolution along an inferred phylogeny?

I'm interested in the evolution of a multistate trait along an inferred phylogeny. I want to know if there is any reason to think that the trait changes are associated with cladogenesis (i.e., took place around the time of cladogenetic events).

If you're interesting in connecting traits to rates of speciation and extinction, then this paper might offer some leads. I'm not sure about how one would go about it for a particular node or set of nodes, but perhaps methods based on stochastic mapping could be helpful?

Thank you! That article was very helpful.


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What is the basis of the endocochlear potential?
I am learning about the endocochlear potential. According to different sources, the ionic composition of perilymph is about as follows (in mM): 150 Na+, 4-5 K+, 1.2 Ca2+, 1 Mg2+, 120 Cl−, and 20 HCO3−; and that of endolymph is 1 Na+, 157 K+, 0.02 Ca2+, 0.01 Mg2+, 132 Cl−, and 30 HCO3−.
This means (in a naive attempt to quantify ionic charges) that the sum of charges in perilymph is 150+4.5+2*1.2+2*1-120-20 = +18,9.
And in endolymph it is: 1 + 157 + 2*0.02 + 2*0.01 - 132 - 30 = -3,94.
From these numbers, it seems like perilymph contains more positive charges than endolymph. How is it possible that the potential of endolymph is highly positive (80-90 mV) compared to perilymph? Shouldn't it be the other way around?
I have searched the forum and the internet for answers, but my question seems so basic (or based on a very fundamental misunderstanding) that I can't find anything of help. The only explanation I keep seeing is that the high potassium concentration accounts for the potential. However, isn't that outweighed electrically by the excess of negative ions in contrast to the perilymph?

Not an idiot or stupid at all, please don't describe yourself that way - in fact since it is not true I will edit it out of your question :) You have a very common misconception for people studying this material, which is not realizing that the positive and negative concentration inside and out is effectively equal (you just don't have the full list). See if this previous answer: https://biology.stackexchange.com/questions/79619/why-is-the-resting-membrane-potential-of-excitable-tissue-not-affected-by-the-ex/79623#79623 helps out. If not, I can tailor a fresh answer here.

Hello Bryan!
Thank you so much for your nice reply! Unfortunately, I still don't quite understand it. As a matter of fact, I think I may be even more confused, and I'm not sure if I can put into words what exactly why. I will give it a try. First, if the charge concentrations are the same on both sides, shouldn’t the measurable voltage be zero? A potential of 90mV designates that an electric (not chemical) potential is actually measurable across a membrane, doesn’t it? Why is that if the electric net is the same of both sides?

My simplified understanding of electrochemical potentials used to be like this: if there is a concentration gradient across a membrane (for example of KCl), which is only permeable for K+ (but not Cl-), K+ will stream to the side of lower [KCl] to reach equal distribution. However, as no equal amount of negative charges follow (!), the charge concentrations will be different on either side and due to repulsion/attraction, an equilibrium between ‘chemical driving force’ and ‘electric driving force’ will be reached at some point.

If the charge concentrations remain basically the same on both sides, as you just said, how does the electric component exist at all?
Thank you!!

I am going to add follow-up question 3: in my example, the endolymph has a positive electric potential compared to the perilymph. If this does NOT imply more positive charges on the endolymph side, what does it mean at all?
If I misunderstood and you are saying that such a difference is there, but small; wouldn't that mean that the most important ions (in the original post) are not listed? Because the (even if slightly) more positive side can't have a more negative net charge, right? I think I am not getting this at all.

I think you're actually very close. I'll try to write up an answer in the next 24hr or so. This system is a bit more complicated than other membrane potentials because there is actually a third compartment involved, and the endolymph/perilymph do not share a permeable membrane.

Thank you a 1000 times in advance. I'm looking forward to your answer!

In the meantime check out: https://www.pnas.org/content/105/5/1751 and see if it helps at all.

About biological electrical potentials generally
Biological potentials on the order of tens of millivolts depend on very very few ions moving (about 1/100,000 of the potassium concentration, for example, for a typical neuronal potential).
Therefore, the sum of positive and negative charges in any compartment is always almost zero (to several decimal places and beyond measurement; if you say a ). Electrical forces are very powerful, and
Some previous answers that are related:
https://biology.stackexchange.com/a/57066/27148
https://biology.stackexchange.com/a/77925/27148
https://biology.stackexchange.com/a/81571/27148
The endocochlear potential in particular - this is really cool
Everything I said above basically can be summarized in a quick statement: you can't figure out potentials just by measuring ion concentrations and summing them up. If you counted all the ions (including charged proteins, etc), you'd get ~0 in any biological solution. Instead, you have to think about where the concentration gradients are and how particular ions are moving. Let's tackle the endocochlear potential... Hibino et al 2010 has an excellent diagram, adapted from their previous 2008 paper:

Let's walk through the key features here, focusing on panel (b). First, the general structure: there are three extracellular spaces, which are all electrically isolated from each other. Between these extracellular spaces, there are two layers of cells where all the business happens.
Between the perilymph and intrastria space, there are a collection of cell types all connected via gap junctions. We can treat them sort of like one big cell, I'll call it the syncytium. A sodium-potassium ATPase uses energy to pump potassium into the syncytium and sodium out (upper left of [b]). Additionally, because there is now low sodium in the syncytium, more potassium enters through NKCC channels, which are symporters that move 1 sodium, 1 potassium, and 2 chloride ions together.
Potassium  would accumulate in the syncytium, except there are Kir4.1 channels permeable to potassium on the other side of these cells, open to the intrastria space. So, potassium flows down its concentration gradient into the intrastria space. This also creates an electrical potential and makes the intrastria space very positively charged (shown as +90mV on the diagram; the syncytium would similarly get a negative charge from the flowing potassium, but that isn't shown).
Normally, not many ions would actually flow to create this potential (on the order of the 1/100,000 I mentioned above) and everything would stop there. However, there are another set of pumps and channels in the marginal cells. The marginal cells also pump potassium in, via the sodium-potassium ATPase and NKCC channels, keeping potassium concentrations in the intrastria space low, such that potassium continues to flow down its concentration gradient from the syncytium.
The marginal cells also have potassium channels on their opposite face, and these are open to the endolymph. The high concentration of potassium ions in the marginal cells and the positive charge in the intrastria space gives the necessary drive to push the concentration of potassium in the endolymph high.
Ultimately, there is a full circuit of potassium because potassium is flowing into hair cells from the endolymph, and then back out to the perilymph. The sodium-potassium pumps use energy in the form of ATP to maintain the imbalance between perilymph and endolymph.

Hibino, H., Nin, F., Tsuzuki, C., & Kurachi, Y. (2010). How is the highly positive endocochlear potential formed? The specific architecture of the stria vascularis and the roles of the ion-transport apparatus. Pflügers Archiv-European Journal of Physiology, 459(4), 521-533.
Nin, F., Hibino, H., Doi, K., Suzuki, T., Hisa, Y., & Kurachi, Y. (2008). The endocochlear potential depends on two K+ diffusion potentials and an electrical barrier in the stria vascularis of the inner ear. Proceedings of the National Academy of Sciences, 105(5), 1751-1756.

Hello Bryan, thank you so much for your explanation. I think I got a better idea now. There are just two things I'm still confused about.

You say that the sum of all charges is 0 in any biological context. Why do electrodes on either side of the membrane measure +90mV then? There must be more + ions that - ions on the more positive side for that to happen, or do I misunderstand the entire concept of voltage? 2) The K+ flowing into the intrastria space cause a positive potential. That made sense to me until I read they are effectively removed. Shouldn't the potential leave with them?

To clarify, I do understand the flow directions and the dependences on concentration gradients. It is the voltage measurements that throw me off. I don't understand how an electric potential is reconcilable with the same net charges on both sides, and why the voltage between syncytium and intrastrial space would still be positive after the positive ions moved on already.

@Jimmy Check out the first other answer I linked, I have a couple back of envelope calculations for how many ions are responsible for a biological potential. It works out to be something like 1/100,000. So although the concentration of positive to negative ions is equal out to at least 3-4 digits (well beyond any ability to measure actual concentration) it's that tiny little bit that makes the difference.

For the intrastrial space, potassium is getting pumped out but other ions are moving too between the marginal cells. Probably the better way to think about the +90mV is that if the space is less than +90mV, more potassium would flow from the syncytium and the potential would rise. +90mV is the voltage at which the net flow from syncytium to intrastrial equals the net flow from intrastrial to marginal. (same for the endocochlear potential itself)


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Can anyone identify this spider

This is in Wroclaw, Poland.
I'll be here a few months and I've noticed that they come in large groups in the evening. They are everywhere outside, but I haven't seen any inside.
They seem to live in colonies because when you see one, there are 50 others next to it, all sizes (age I guess), but always the same type.
The large ones have body about 1-1.2 cm long but the colonies have some significantly smaller with them, like 1/4 of the size.

It's clearly an orbweaver, judging by the typical head-down position in a vertical web.  The scalloped pattern on the abdomen reminds me of one of the Lariniodes species, but I'm not familiar enough with European spiders to be confident of an identification beyond that.  I would assume that there are bright lights, and possibly a pond nearby, given that you mention a lot of them close together.

yes, they gather close to the city's river and are always seen where there are floodlights, at night; can't see any during the day

Most of the night-hunting orbweavers hide near the web during the day (so they don't get eaten), although late in the season, as they get larger, and closer to laying eggs, some may stay in the web during the day.  These are not normally found in clusters, but where there is enough food, they can cram together in surprisingly large numbers.  There is a sewage treatment plant near my home that recently was documented to be something out of a horror movie - masses of webs of orbweavers and thousands of spiders filling the higher levels of a giant open building over the settling tanks..


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Species Distribution Modeling: Mammal river species
When working with mammal river species, what parameters would you use to study them  (I have max and min temperature, average rain, slope and obstacles in the river)
Something like type of riparian forest?
Is there any good example of species distribution modelling of mammal river species?
Thanks, Héctor.

I think it will depend on what aspect of the species you are looking at. For example, if you want to model distribution to study predator-prey interaction, you might want to get information related to predator presence, geographical aspects (e.g. for helping camouflage) etc. In contrast if you want to study distribution for the purpose of migratory behavior, you can consider reproductive age, time and other ecological aspects etc. Their weight will depend of your goal.

I just tried "species distribution model river otter" (picking the first river-dwelling mammal I could think of) on Google Scholar and got quite a few hits ...

Mainly the aim is to know which is the  most negative parameter that is affecting it. Problem is that it is really associated to the river,  much more than the otter, depending its diet on athropods... (No data of arthropods), ¿Anything abiotic that could affect?(snow didn't affect...)

can you tell us what species you're interested in? voles? manatees?  river dolphins ... ????

Yes,  it's Galemys Pyrenaicus ( Pyrenean desman)  related to  moles


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Does the arrangement of amino acids in a protein matter for nutrition?
Let's say there are two diets, consisting of entirely different proteins. If you split up all of the proteins from one day of each diet, you'll get the same set of amino acids and the same count of each. Assume everything else about the diets is the same.
Would these diets have the same effect on the protein composition in your body? Different polypeptides, but overall the monomers are identical. Does your body break down proteins entirely, or will it reuse some chains of amino acids?

I'm thinking this question would be better suited to the Biology exchange, but it's not clear to me what "same effect on your nutrition" means and I'm guessing the folks in Biology will have the same problem. Can you clarify that aspect of your question?

I changed "the effect on nutrition" into "the effect on the protein composition in your body" to make it clear what you are asking. During digestion, proteins are not necessarily broken down into individual amino acids but, to some extent, also into di- and tripeptides or even larger peptides that can be absorbed. This question would better suit in Biology SE or maybe Chemistry SE - they discuss about biochemistry there a lot.

Arrangement of amino acids determines the protein structure which in turn can determine how easy it is to digest the protein. I cannot think of an example right now; never really checked if two entirely different proteins have identical composition. However, it is not really surprising. In chemistry, it is known that different isomers have vastly different physical properties.
So if the two proteins have different digestibility then they will have different nutritive values.
Regarding, protein digestion and nutrition. New proteins are built from individual amino acids and not pre-formed oligomers. Read about translation. So at some point the ingested protein has to be completely broken down into amino acids.

It's your last sentence that's crucial. It is known that some, even large peptides, can be absorbed, so it's not necessary for a protein to be digested into a single amino acid in the intestine in order to be absorbed into the bloodstream. You are suggesting that all body proteins can be created only from individual amino acids, so any dietary peptides/proteins may need to be broken down at some later point...Translation is about single amino acids, but can some pre-formed (dietary) peptides find the way into body proteins...This would answer a lot of related questions...

@Jan "can some pre-formed (dietary) peptides find the way into body proteins".. Not in my knowledge.


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What are the negative consequences of a narrowed biodiversity to the planet?
In this question about the fires in the Amazon rainforest, a user responds with

It [the Amazon] is still a part of nature and burning it can narrow
  the diversity of both plants and animals, which can have consequences
  on the whole planet.

What are the negative consequences of a narrowed biodiversity to the planet?

Welcome to Biology.SE! We encourage you to do some research on your own and share what you have learned when asking questions here. In particular, this is an enormous question and there are many resources available with answers at everything from the elementary to the research level — e.g. google scholar ——— Please also take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

From an ecological sense, cycles of living beings are intertwined. Breaking cycles affects life being able to live, reproduce, and die in a manageable way. Insects, animals, and plants help feed each other and help them reproduce. Fewer insects are less of a food source for animals and can't pollinate plants as much. Reduced animal populations are less of a food source for scavenger insects and don't feed plants through manure or decay after death. Fewer plants means less food and protection of insects and animals from predators. Predators overload on newly-available prey and their populations crash. It all intertwines.
From an environmental sense, the results of a narrowed biodiversity include putting more carbon into the atmosphere. In addition to warming the planet and the ocean, the ocean acts a carbon sink, acidifying in the process. This damages existing sea life that can only live within a certain pH and temperature range without sickening or dying. Some fish are trying to migrate and are dying off, due to lack of food where they are headed.
From a medical sense, burning down forests is stupidity. There are drugs that are naturally found in their rare plants, which have been developed into medications that save lives, e.g. Paclitaxel or Taxol. Only 1% of remaining rainforests have been explored for these plants and their compounds and we're stupidly burning them up. Nature has evolved many useful remedies, but we'll never know about the ones we destroyed, and that means more sickness and death.
For people obsessed with money, that medical sense translates just as well into pharmaceutical products and the resulting loss of jobs and profits.
All of these factors are linked together, hand-in-hand.

I appreciate the effort, but there are aspects of this answer I'm not thrilled with.  It mixes together loss of population density (paragraph 1: "fewer insects ... fewer plants ... fewer animals ..."), changes in the biogeochemical cycle (paragraph 2: warming and ocean acidification),  and changes in biodiversity.  Only the paragraph on bioprospecting is actually directly connected to biodiversity.


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Are tumor-associated antigens unique to cancerous cells?
Are tumor-associated antigens found only on the membrane of cancerous cells or just over-expressed on the membrane of carcinogenic cells?
In other words, are these antigens also found on healthy cells?

Welcome to Biology.SE! We encourage you to do some research on your own and ask questions  informed by what you have already learned. In particular, your question assumes that all cancer antigens are the same, which reading the brief wikipedia article on tumor antigens reveals to not be true.  ——— Please also take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

@tyersome I already know that cancer antigens aren't all the same but I want to know if these antigens can be found also on healthy cells or at least in some rare cases?

I'll answer a slightly different interpretation of the question, which is whether the proteins (epitopes, actually) that are presented by cancer cells are neoantigens (varieties of proteins that only occur in the cancer cell due to mutations) vs 'wild type' antigens that can be found in other non-cancerous cells, but are over-expressed (or improperly expressed) in the cancer cell.
For melanoma, some of the potentially most useful immune-system targets are 'normal' proteins that are over expressed in cancer cells and rarely expressed in non-cancer cells.  These include cancer testis antigens, which are proteins normally mainly expressed in germ line cells, but are accidentally expressed on cancer cells and lead to these cells being targeted by t-cells.  See (for instance) the paper Cancer testis antigen and immunotherapy, ImmunoTargets and therapy (2013), pp. 11-19.  For non-small cell lung cancer, Analysis of GAGE, NY-ESO-1 and SP17 cancer/testis antigen expression in early stage non-small cell lung carcinoma.

your answer is amazingly clear and useful

Carcinogenic tumor associated antigens correspond to any peptide chain (antigen) which triggers an immune response from the host. This means that they can be found anywhere inside, at the membrane, and outside of the cell: inside the cell (intracellular), at the cellular membrane and exposed to the extracellular environment, or even secreted.
Depending on the oncogene, they can be also eventually be over-expressed (anywhere there are supposed to be, including the membrane of cells).

It would be worth to mention that there is a major difference between antigens recognized by antibodies and peptide antigens presented by MHC-I, since especially in the tumor context small mutations make the latter ones more likely to be significantly different from endogenous non-immunogenic peptides/antigens

Good point Nicolai, thank you for your feedback, I'm going to edit my answer to include these points too.

Your answer would also be improved by recognizing that antigens are not necessarily proteins/peptides — for example, they will often be carbohydrates.


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How could be the concentration of airborne pathogens in a specific indoor space be measured?
I wonder if it is possible to measure the concentration of airborne pathogens in a specific indoor space in order to extract a percentage value. This value would be helpful to determine specific infection control strategies that would decrease this percentage and improve the indoor air quality.

I have no idea how practical it would be for your intended application, but people do estimate airborne concentrations of fungi and bacteria by sampling aerosols (i.e., filtering a volume of area to extract dust etc. that can carry the target organisms) and then using quantitative PCR with primers targeted at generic fungal or bacterial DNA sequences to estimate concentrations of particular classes of organisms.
Luhung, Irvan, Yan Wu, Chun Kiat Ng, Dana Miller, Bin Cao, and Victor Wei-Chung Chang. “Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis.” PLoS ONE 10, no. 11 (November 30, 2015). https://doi.org/10.1371/journal.pone.0141158.

Thank you for your reply, I want to monitor the concentration of airborne pathogens in order to test alternatives of infection control strategies within the built environment and state how these modifications affect the concentration of airborne pathogens. I have searched for several methods such as using tracer gases, using electron capture detectors, or using biosensors, however, I need something which is more practically available and could detect the concentration precisely.

unfortunately, I can't help any more; my answer pretty much says what I know about this topic - I'm an ecologist, not an environmental DNA person. Sounds hard. Hope this points you in a useful direction.


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Farsightedness and the eye
When a farsighted person looks at a distant object and sees it clearly, what is the state of their eye lens? Is it relaxed?
Rationale:
It is something we read about in class that is confusing.I know a person with 20/20 vision would have a relaxed lens when looking at a distant object. I think a farsighted person would have a relaxed lens when looking at far objects since they can see distant objects, but since they have trouble seeing close objects the lens would not be relaxed when looking at close objects. Those that are nearsighted would have a relaxed lens when looking at close objects, but not when looking at distant objects. So, a relaxed lens just means the eye does not need to strain when looking at something?

Is this a homework question? Please show us what have you researched so far regarding this. Maybe something from optics chapter?

related: https://biology.stackexchange.com/questions/30504/what-is-the-difference-between-myopia-and-hyperopia?rq=1 - does that answer your question?


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What is the native structure of amyloid-beta protein under physiological conditions?
The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?

What research have you done yourself to answer this question?  There are many sources of information on this topic if you search the Internet. Tell us what you have found and why it doesn’t answer your question. See the Help on asking questions.


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Pharmacokinetics and cell-membrane permeability of Adenosine triphosphate disodium hydrate
【My Question】
(1) Please tell me the pharmacokinetics of this ATP (or Adenosine triphosphate disodium hydrate) when it is administered orally or intravenously. In particular, Does this material has permeability to the Blood-Brain Barrier?
(2) When human cells (for example, fibroblast, MSC,…,) are cultured in a medium supplemented with this material, how much ATP is taken into the cells. (Please tell me about the cell-membrane permeability of this material.)
The known effects of Adenosine triphosphate disodium hydrate are as described below.
【Effects of this medicine】
This medicine increases the blood flow by its vasodilatory effect and activates the metabolism of the body to improves the functions of the organs.
It is usually used to improve symptoms accompanied by aftereffects from head injury; to treat heart failure or chronic gastritis associated with dysfunction of the digestive tract, Meniere's disease, dizziness based on inner ear disorder; to stabilize the accommodative function in accommodative asthenopia.
【References】
http://www.rad-ar.or.jp/siori/english/kekka.cgi?n=1808#
P.S.
P.S. I'm not very good at English, so I'm sorry if I have some impolite or unclear expressions. I welcome any corrections and English review. (You can edit my question and description to improve them)


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"Straight" or "linear" helix
If an alpha helix is discontinued for a short while and then continues in a different direction, I prefer to call in "kinked". If the helix is simply uniformly following one direction, I prefer to call it "straight", but I have been corrected, and been told that it is called "linear". Which is right?
Thank you!

Welcome to SE Biology. Please read the Tour and the Help on asking questions. There you will see that you should demonstrate that you have tried to research a question yourself before asking, especially apposite in this case as this sort of terminology is merely a question of convention. In fact there is no right or wrong, just clarity of expression.

OK, let me put you out of your misery. You have a basic misconception. The first image is not of an alpha-helix, but two. It could be a helix-turn-helix. And so the terms straight and linear are superfluous. Anyway, I’d avoid “straight” for the lower one, unless you wish to consider changing “kinked” to…

Okay.. Thanks, but I guess my question is unclear. Yes - it is two helices, it it is not really the helix the is kinked, that is true. It is the conformation I want to describe, a "kinked conformation" vs a "straight conformation" of a protein segment.

Read about protein secondary structure to learn how it is described. You are trying to reinvent the wheel and getting it square.


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Could we have endless pleasure?
Are there any studies that point out that we could have a device in the future  or drug that could give us endless amount of pleasure by stimulating or blocking processes in the brain or nerve system?
Drugs and alcohol end up saturating receptors in the brain. Is it known inside out how this mechanism of rewards / saturation / abstinence work in the brain and how it relates to consciousness?
It is well known that you cannot have the same amount of pleasure by repeating the same action over and over again but is it truly known how that works? Would it be possible to reset the receptors in the brain to accomplish this?

Biological receptors will saturate after some time. So my guess is it will not be possible (unless some mutant). However, at the end it will become philosophical question about what do you call "pleasure". After experiencing constant "pleasure", you might feel it as normal.

@Dexter are there any serious studies getting into detail? Would it be possible to desaturate the receptors or to block the pain signals sent from the body? Are there any theoretical potential possibilities?

I have little knowledge of neurobiology but I can point out to some similar results in the cell biology. There are constitutively activated GPCRs which always keep signal ON. So theoretically it is possible but concept of "pain" or "pleasure" is multidimentional and their mechanism is complex and not as simple as activation and deactivation. There are some medical conditions where person do not feel any physical pain.

Welcome to Biology.SE! We encourage you to do some research on your own and ask questions informed by what you have already learned. ——— Please also take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

Of course.
There is a famous set of experiments (Milner & Olds) in biology that basically started modern behavioral research in which a wire was inserted in to a rats brain allowing for direct electrical stimulation of the pleasure center. as long as the current continued the rats experienced extremely high levels of pleasure. To the point they were unwilling to engage in any voluntary behavior, including seeking food and water, even when right next to them if it would interrupt the pleasure. You could keep stimulating the pleasure center until the rats died of thirst.

As long as the experiment is legit and there were no flaws in it this is valid answer. Deep Brain Stimulation could potentially create a "miracle drug".

What we call pleasure is effectively the way that we have evolved brains that learn to do what promotes survival and reproduction. Animals get pleasure when we do things that contribute to our survival and reproduction, like eating certain foods or mating; this makes animals (including humans) tend to repeat the behaviors that led to those rewards (of course, just because something is pleasurable doesn't mean it evolved to be that way for the same reasons as other attributes).
We already have ways to "create" pleasure: to do so, you activate the brain receptors artificially that normally are used to inform the rest of the brain that you just did something "good": heroin works great. So do amphetamines, cocaine, MDMA, etc: drugs of abuse. That's why they are drugs of abuse: they hijack the brain's reward system to make taking the drug pleasurable and therefore encourage future behavior to achieve that pleasure.
In animal models, we can also be more direct and use electrical stimulation in the brain to do the same thing: stimulate in the medial forebrain bundle and animals will learn to do whatever led to the stimulation (German & Bowden 1974), even to the point that the reward is saturated (Waraczynski et al 1987) and to the exclusion of other normally pleasurable activities: for example, water-deprived rats will lever-press instead of drinking water (Morgan & Mogenson 1966).
There might be usefulness of these approaches in treating certain types of depression, but otherwise "endless pleasure" seems to not be all that pleasurable due to adaptation and because pleasurable stimulation is relative.
Summary
We can already artificially stimulate the areas of the brain involved in "pleasure"; the result is not great in the long term.

German, D. C., & Bowden, D. M. (1974). Catecholamine systems as the neural substrate for intracranial self-stimulation: A hypothesis. Brain research, 73(3), 381-419.
Morgan, C. W., & Mogenson, G. J. (1966). Preference of water-deprived rats for stimulation of the lateral hypothalamus rather than water. Psychonomic Science, 6(7), 337-338.
Waraczynski, M., Stellar, J. R., & Gallistel, C. R. (1987). Reward saturation in medial forebrain bundle self-stimulation. Physiology & behavior, 41(6), 585-593.

With drugs and alcohol receptors get saturated. The pleasure is temporary not permanent.

@PbxMan Right. Pleasure is "change in reward level"; so, to get more pleasure you have to get more reward. Drugs and electrical stimulation can go all the way to the brain's maximum representation of reward. At that point, there can be no change in reward, so, effectively, no pleasure. Waraczynski is an example.

I think that if you have endless pleasure (with marijuana for example I've read this here) you will not know you have pleasure so it won't exist anymore because you do not know the difference. So could be but you do not realize so is it still pleasure then? Maybe this answer is more philosophical then scientific.

Funny I was told that in the philosophy SE. https://philosophy.stackexchange.com/questions/65609/authors-on-consciousness-and-its-relation-with-suffering What makes you not have the same amount of pleasure with the same thing over and over again? Is that known from a neuroscientific point of view or it is all theoretical

@PbxMan My answer already touches on that, but in general, if you have more questions you should ask them as individual, researched questions, and not ask more questions in comments. You've already edited your answer to include a lot more than it originally did.

@BryanKrause it's just the same question. I added a bit to clarify that it's not a simple question. I'm expecting somebody to post a couple of links saying "if we could do X.... yes or not"."or we don't know how conspicuousness works  yet..." If you feel there is a better formula to ask what i mean please let me know. I'll close the post.


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What makes synaptic vesicle release probabilistic?
The fusion of synaptic vesicles (SVs) with the plasma membrane of the active zone (AZ) upon arrival of an action potential (AP) at the presynaptic compartment is a tightly regulated probabilistic process crucial for information transfer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773589). In a typical forebrain synapse, only ~15% of APs arriving at the presynaptic terminal cause fusion of a synaptic vesicle.
My question is, what factors make this process probabilistic? What happens at the molecular/cellular level that an action potential can lead to the fusion of synaptic vesicles one time and not another time? Is it due to some differences between different synaptic vesicles, how the vesicles are positioned inside the synapse, variations in the synapse's environment, differences between action potentials, etc?

From the source you provided, the answers seem to be outlined well from the authors' sentence that states:

The Pr [release probability] of SVs [synaptic vesicles] at the AZ [active zone] is set by a complex interplay of different presynaptic properties including the availability of release-ready SVs, the location of the SVs relative to the voltage-gated calcium channels (VGCCs) at the AZ, the magnitude of calcium influx upon arrival of the AP, the buffering of calcium ions as well as the identity and sensitivity of the calcium sensor. These properties are not only interconnected, but can also be regulated dynamically to match the requirements of activity patterns mediated by the synapse.

Below, I use an analogy to provide a framework for understanding how these factors come together to mediate Pr as a whole, but you can read a scientific review on that here:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059705/.  However, the actual molecular/proteinaceous machinery that underlie these phenomena are pretty well explained in your source (particularly in the sections "SV Proteins Regulating Pr" and "Recruitment of Calcium Channels to the AZ").
To use an analogy, think about the presynatpic terminal as the 100 meter dash at the Olympics.  The track only has so much space, so not everyone can run the race at the same time.  That's why there are multiple heats of the race.  The first point from the authors is availability of release-ready SVs, which your source discusses as part of the readily releasable pool (RRP) of vesicles.  Think of those SVs as the runners in a heat, lined up in the start position waiting for the gun to go off.  Their equipment is ready (starting blocks set, shoes tied, proper uniform and tag on, etc.). They're all in position, awaiting the signal, and they will take off as soon as they get that signal.  Therefore, the more SVs you have in that position with equipment/molecular machinery prepared to "go" in response to a signal, the more likely you are to have SV release.  The second point is location of the SVs relative to VGCCs.  In our example, this would be equivalent to having a lane closer to the person shooting the start pistol.  The closer a runner is to that, the more likely they are to hear the pistol go off and start the race.  Conversely if the person with the start pistol is at the finish line, it's possible less runners will hear it go off and miss their cue to start running. Since SVs require calcium to undergo membrane fusion and release their contents into the extracellular space, the closer these vesicles are to calcium channels the more likely they are to get that necessary substance for fusion/release. Third, the magnitude of calcium influx upon arrival of the AP, which we can think of as the volume of the start pistol.  If the start pistol is loud (a high volume of calcium comes into the cell), it's more likely the runners will hear the shot go off and start running (SVs will fuse to the membrane).  However, a very quiet start pistol (low influx of calcium) is less likely to be heard by the runners (less likely to bind SV proteins important for fusion). Lastly, they list buffering of calcium ions as well as the identity of the calcium sensor.  What's important to remember about the process of SV fusion is that it requires free calcium that can bind to the necessary vesicle proteins, so any other proteins (calmodulin, calbindin, the list goes on forever) that bind free calcium and make it unavailable to the vesicle will decrease the likelihood of successful vesicle fusion and neurotransmitter release.  This would be like someone giving the runners ear plugs before the race, which dampens the sound of the start pistol and decreases the likelihood of runners hearing their cue to start.  Again, there are nuances not covered in this analogy, but I'd recommend going through your source again with this framework in mind to pick up where those nuances come in.


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Optimal Growing Conditions concerning CO2 level (ppm) for aquatic plants
I know this is rather specific but I would like to know what level of CO2 concentration in the water is optimal for the highest possible plant growth rate.
I did an experiment where the growth rate increased with higher CO2 levels in the water of the plants. The highest ppm were 60 but I don't know if higher levels would keep increasing plant growth or decline due to high acidity of the water.
The specific plant if this helps would be limnophila sessiliflora
Any information on this would be much appreciated.
Jonas

have you tried Google Scholar yet ... ? it looks like some plants also use HCO3- ... https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.1981.tb03198.x


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What is the name of this little plant?

It was found in Malaysia in my school compound.

Looks like something in the mint family.  Does it have an odor?

May be Scoparia dulcis but I am not sure at all. Do you find a dense hairy structure on its corolla?


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What percentage of Americans have Native Indian ancestry?
What percentage of americans have native indian ancestry?
I tried to find the answer online and it's difficult to search for.

Probably unknowable unless you find genetic markers, and do genetic studies on a statistically significant fraction of the population.  And of course you have sub-populations with greater or lesser percentages.

I found some averages from 23andme on sciencemag. It doesn't state the figures for all americans, although it says that 8 percent of white americans have some native american ancestry, afro-americans have on average 0.8%, and latino have 18% native american ancestry.


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Does body absorb nutrients less efficiently if we ingest the same amount at the same time, opposed to spreading over a larger period?
I would like to understand if ingesting a certain amount of nutrients will result in different absorption from my body, depending on whether I ingest that amount spread over time or everything at once.
For example, considering all the food I eat in one day: does my body absorb the same amount of fat and protein if I eat that same amount of food all at once, compared with eating it spread by different meals?
Similarly, could it be possible that my body absorbs less fat if I eat 4 hamburgers at the same time, compared with eating them spread along the day?

LARGE MEALS AND ABSORPTION
When consumed in usual amounts, the percent of absorbed macronutrients (carbohydrates, proteins, fats, alcohol) should not differ significantly when coming from one large or several small meals.
As an example of the composition of a single large meal, let's imagine something that fits into Acceptable Macronutrient Distribution Ranges (AMDR) in a 2,000 calorie diet: 250 g of carbohydrates, 70 g of proteins and 80 g of fats.
Most carbohydrates are digested into glucose and fructose. Glucose, when absorbed as the only carbohydrate (ingested as glucose or starch), can be absorbed at the rate 60 g/min, but the addition of fructose can increase the absorption of both together to as high as 126 g/min. When fructose is absorbed as the only carbohydrate or in the excess of glucose, it's absorption limit from one meal can be as low as 5 g or as high as 50+ grams. Certain sugar alcohols (see Table 4) (sorbitol, isomalt..) can trigger diarrhea when consumed in amounts greater than ~20 g/meal.
Virtually all ingested protein is absorbed by healthy humans (Surgery Journal). The rate of absorption depends on a type of protein: about 10 g of whey protein and 3 g of egg protein can be absorbed in one hour (JISSN).
At least 60 grams of fat consumed at once can be normally absorbed, concluding from a study in which they investigated the relationship between the amount of fat consumed and atherosclerosis.
In conclusion, the amount of macronutrients (except fructose and sugar alcohols) consumed with a single meal does not seem to significantly affect the percent of macronutrients absorbed, but it prolongs the time in which they are absorbed.
LARGE MEALS AND DIET INDUCED THERMOGENESIS
After eating one large meal, more of the consumed calories will be lost as heat than after eating several small meals:

Consuming the same meal as a single bolus eating event compared to
  multiple small meals or snacks was associated with a significantly
  higher DIT [diet induced thermogenesis]. (Nutrients, 2016)
TEF [thermic effect of food] was measured by indirect calorimetry
  for three hours following each meal and was found to increase
  systematically, in a nonlinear fashion, as meal size was increased.
  (Metabolism, 1984)


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Can UV radiation be safe for the skin?
It is well known that UV radiation can damage the DNA and generally harm our skin.
We also know that UV radiation helps on the production of melanin and Vitamin D.
From what I could find, the DNA absorption spectrum goes to almost zero for wavelengths higher than 300 nm. This seems to suggest that we would be safe to use UV radiation between 300 and 340 nm in our skin (as long as the power or exposure is not too high/long to make burns), for therapeutic purposes such as the stimulation of Vitamin D production.
Is this assumption correct? Are there any evidences that we could use this UV wavelength range safely?

Remember that UV can damage DNA indirectly by creating ROS.

You're talking about long-wave UV, or UV-A radiation. In the 80s, experts claimed that this was a safe wavelength. Protection against UV-A was not part of sunscreen in the early days. Consequently, UV-A was (and still is) used in tanning beds due to its perceived safety over UV-B. However, a lot of research has been done since.
UV-A is well understood now to also be unsafe in unreasonable amounts. Currently, UV-A protection is a typical feature of sunscreen and tanning beds are still not a healthy alternative to moderate, healthy doses of sun. Here is a recent review covering some of the aspects comparing different UV range effects on skin. I really suggest you put a search engine to good use here; it makes little sense for us to expound on the literature when it is so clear and easily available.
In summary,

UVA certainly contributes to the development of skin cancer.
UVA penetrates deeper into the skin than UV-B (which is largely responsible for 'burning' of the topmost layer of skin, without directly affecting the deeper layers). For this reason, UV-B is associated primarily with burning and UV-A is primarily associated with aging and aging diseases like cancer.
It is important to note that 95% of UV light in every day life is UV-A, because it does not vary seasonally and can penetrate clouds and windows. Therefore, in spite of the fact that short wavelengths carry more energy per photon, the ratios of UV-A and UV-B exposure are far from equal.

These are only a few of the explanations as to why we observe an incidence of aging and skin damage and disease upon UV-A exposure.

Great answer. Thank you. Your literature suggestions have shown that, despite many evidences that UV-A and UV-B being harmful, some authors seem to point out that "moderate" exposure brings many benefits (not only Vitamin D). Apparently, it's not clear yet what "moderate exposure" is, or if there is such win-win scenario regarding UV exposure. Interesting stuff...

Just to add a nice reference, following my comment, for those who might be interested: https://onlinelibrary.wiley.com/doi/epdf/10.1111/bjd.17992/

So, no benefits to being out in the sun then...

There are (at least) two sides to this story. One is direct DNA damage being caused by UV-B light which happens to have photons with just the right amount of energy to interact with thymine. This has been known, and assumed not just during the 80s, but until the late 2000s to be The One major thing that causes cancer, or trouble in general (there's papers from ~2008 claiming that).
Meanwhile, it is known that UV-A can excite an electron in a chromophore (i.e. some more or less random unspecified molecule, or part of it) in a way which turns out being less desirable than one would wish.
Photons exciting electrons isn't something particularly new or stunning (think photosynthesis or our ability to see), it happens all the time, almost every time a photon hits something. But some molecules react more favorably, and some... don't.
For example, melanin happens to be our "sun protector" molecule because it has the property that it almost instantly drops its excitement into heat, which is quite harmless.
Other "random" molecules do not necessarily have such favorable properties and may either form radicals or stay excited for a long time until they finally bump into something and interact with it in some way, giving off that energy in some unspecified, haphazard manner. When that happens, well, things happen, whatever they may be. The damage, finally, doesn't even have to be at the exact location where the sun was shining.


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Cannot identify this insect
Can anyone please help identify this insect. It seems to be some sort of caterpillar but I'm stumped.

Location is in Suffolk, United Kingdom
Length is around 1cm, width is perhaps 4 or 5mm.

Image opens a video clip on YouTube.

Is there a way to embed the video into the question?

There are a number of larvae that glue detritus to their backs. I'm not sure what this one is.

Welcome to Biology.SE! For identification questions please edit your post to: 1) include the location (e.g. country and region — the more specific the better), and 2) an estimate of the size of the creature. The location and size can be essential clues for identification. ——— If possible a clear, closeup photo would also be helpful. ——— Please also take the time to take the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

That appears to a "bag worm", which is as you surmised a caterpillar.
This suggest that it is from the family Psychidae, but I won't even try to guess at the species.  However, if you see any adults you may be able to identify them using this website.
An example image of an North American species:

Thank you. After viewing some videos of this bag worm / case worm moth, it seems to appear, and also move in the same manner. Case closed!


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Are there any evolutionary reasons for the different tree shapes? If so, What are they?
So we know there are a thousand types of trees with different shapes.
We have Columnar shaped trees:

Pyramidal or Conical shaped trees:

Weeping shaped trees:

And we also have Round, Vased, Open-Shaped, and Umbrella shaped trees. So im not really into botany so forgive me if I butchered some phrases. But I got into a conversation about evolution at school and we switched the conversation to plants this time.
We got into the photosynthesizing cycles of leaves, Like of course we know green is the leftover color from the light spectrum, Orange and yellow colors means the plant is utilizing Carotenoids as it ages, And Anthocyanins for pink to red leaves to protect it from intense sunlight.
But we got into the topic of the different tree shapes. Since plants are living things and goes through the same process of natural selection, Is there any evolutionary reasons for their different shapes? What made some trees that way and how do they fare differently from one another?

I'm VTC as this is too broad, but, as usual, yes, there was evolutionary pressure for trees as well as every living thing, and think "niche" (hot/dry/windy vs wet/warm/sunny vs wet/cold/shade vs every other climate.. We have spread trees out of their niches for ornamental purposes, but environmental pressure is everything.

Trees have to balance several different things , how fast they can grow, how much sun they can get, how much water they loose, how much wind they have to withstand, herbivores, etc. On top of that they have internal differences like different vascular systems. Given all these different forces and how much they vary from place ot place it is no wonder shapes vary.

You might want to look into L-systems and how simple rules (impemented at the genetic level) can cause differences in shape.  And if the shape survives, it persists & evolves.  See https://en.wikipedia.org/wiki/The_Algorithmic_Beauty_of_Plants

I disagree with close-voters -- I don't think this needs to be closed as too broad.Some comment can certainly be made about tree shapes and relating them to sun availability, wind-protection, temperature-regulation, etc.


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Comparative evolutionary study: is amino acid or nucleotide comparison more useful?
I am a high school student and am currently learning about evolutionary relationship study in biology.
My teacher said that a comparative study of amino acid sequences is more useful than a comparative study of nucleotide sequences, because the genetic code is degenerate in nature — several codons may code for the same amino acid.
However, I just do not understand the logic.
Since several codons may code for the same amino acid, I (as a math person) consider the conversion of a nucleotide sequence to an amino acid sequence as a non-injective function, and thus is information-losing.
(Analogy: consider the function $f(x)=x^2$. Imagine that you have a number, and you plug it into $f(x)$ to get $1$ as the output. You would never know if the original number is $1$ or $-1$.)
Therefore I arrive at the exact opposite conclusion. Is my conclusion correct or not, and why?

I have corrected your misuse of Genetic Code leaving only the single correct instance of use (and tidied your question a little). I have explained this in the first part of my answer and given some more references.

I have provided you with a well documented answer. (Your teacher is right in most circumstances.) Please read it and let me know if there is anything you don't follow in the biology. We (or at lest I) cannot help you with the maths, so consider my suggestion that you — as a mathematician — find the flaw in your logic, and perhaps let us know when you have done so. This is a real-world example of the dangers of simplistic application of mathematical logic, so it worth your attention.

@David I think I need more time to understand as it is a bit complicated to me. Please be patient.

No hurry.  In fact it might be better to ask the question on a Maths site. One difficulty for you will be lack of familiarity with the sequence comparison algorithms. Because these algorithms compare sequences on a letter-by-letter basis, when they compare DNA they are not using the information of the genetic code, which would involve comparison in groups of three. There must be other examples where mathematical transformations driven by external considerations produce a more useful form of data.

Each has its own utility, depending on the time-frame you are looking at. For evolutionary studies, you need variation, but not so much variation that one substitution at the same position overwrites a previous substitution. So if you are looking at deep splits, over hundreds of millions of years, it may be that amino acids are more reliable. But you are correct in that since they are functionally more important than silent substitutions (nucleotide changes that don't change the amino acid), it is possible to have amino acids converge on the same state, independently. Nucleotides do this too. Both require statistical models (maximum likelihood) that accommodate the possibility of multiple changes at the same site. If you are looking at recent evolutionary splits, there may not be enough (or any) amino acid changes to compare, so in this case, nucleotides would be better. You would not measure continental drift with a stopwatch, or a 100-meter dash with radiometric dating.

The Answer
It is correct that the product of the conceptual translation of a nucleotide sequence into an amino acid sequence results in the loss of certain information present in the former. An obvious example is that the amino acid sequences of the same protein in two individuals may be identical, but there may be silent mutations in the DNA, and these can be useful in tracing ancestry. The one part of Crick’s Central Dogma about which there can be no argument is that you cannot go from protein to DNA because the information for the nucleotide sequence is not present in the protein, with or without the genetic code.
However…
An amino acid sequence contains information that is not present in the gene from which it originates, if we just consider the sequence as mathematical sequence of symbols. And, with 20 letters instead of 4, this new information has a different (and greater) complexity. The mistake is an unspoken assumption that the information of the genetic code is inherent in the nucleotide sequence. It is not. Yes, if we have the information of the genetic code, then the nucleotide sequence also has the information of the amino acid sequence, but that is not the practical question at issue.
So (addressing the poster) in the majority of practical instances your school teacher is correct. I am not a mathematician, so I cannot be sure what is the flaw of your argument. Perhaps it is the fact that only a subsection of the information can be used in the sequence comparison, perhaps the fact that you are talking three symbols from a set of four in your non-injective function to produce one symbol from a set of 20, or perhaps it is the biology. That’s something for you to work out. But if your conclusions are wrong (which they are) there must be a flaw in your logic)
The Question at Issue
The practical question at issue is:

Which is more suitable for determining the evolutionary relatedness of
  two organisms — a pairwise comparison of the amino acid sequences of a functionally
  similar protein (e.g. cytochrome c) or of the nucleotide sequences of the corresponding gene?

The general answer is:

It depends on the relatedness of the organisms, but, except for very
  close kinship (e.g. humans and neanderthals) or certain specialized
  problems, the answer is likely to be the amino acid sequences.

How can this be?

In relationship to the evolutionary distance between organisms, it
  is necessary to consider the different rates at which nucleotides and
  amino acids mutate, and the constraints on what mutations are likely
  to occur. If the rate of mutation is too fast there will be a time
  difference after which it will be difficult or impossible to
  calculate their evolutionary divergence accurately and ultimately even
  to detect any relationship between them.

Nucleotides mutate more rapidly than amino acids, and in practice comparison of nucleotide sequences is less useful than comparison of amino acid sequences for longer timespans.

Because of the degeneracy of the genetic code (the fact that an amino acid can be encoded by more than one triplet of nucleotides) it is possible for one or even two nucleotides to mutate without affecting the amino acid sequence. (And the similarity between sequences is computed from a letter-by-letter comparison.)
Statistics is not my forté, but in a general sense, because there are only four bases, 25% identity between two nucleotide sequences would be expected to occur by chance, whereas two amino acid sequences that are 25% identical would be statistically significantly similar because there are 20 amino acids. (Only 5% identity would arise by chance.)

There is a further aspect of divergence of amino acid sequence that is useful for evolutionary comparison, and this is that the nature of the mutation of amino acids is far more constrained than that of nucleotides. Admittedly purine-to-purine or pyrimidine-to-pyrimidine mutations are more frequent than purine/pyrimidine mutations, but amino acid mutations are often constrained by the role the amino acid plays in a protein. However one can construct empirical matrices of the likelihood of different amino acid mutations to obtain a more subtle and accurate estimate of relatedness.
What this means in practice is that instead of having to use a scoring system for comparisons of amino acid sequences that is either 1 for identity or 0 for non-identity, one can use a scoring system that gives ‘half marks’ (as it were) for structural/functional similarity. Thus, two amino acid sequences having 5% identity in pairwise comparison could be shown to be related because  of an overall higher ‘similarity’ score.
Appendix 1: Sequence Comparison
It is important to realize that however much information resides in nucleotide or amino acid sequences, only the information that is actually used in the practical methods of determining evolutionary differences is relevant. These methods involve computer programs that compare sequences according to mathematical algorithms to answer the question of how similar two (or more) sequences are. So, regardless of the fact that the amino acid sequence is generally computed from the gene sequence, the question is “should I imput nucleotide or amino acid sequences into the program to get the best comparison?”. It is in this context that the remarks above about rate of change and likelihood of interconversions should be taken.
To quote from an article by one of the pioneers in sequence comparison, W. R. Pearson:

“Protein (and translated-DNA) similarity searches are much more sensitive than DNA:DNA searches. DNA:DNA alignments have between 5–10-fold shorter evolutionary look-back time than protein:protein or translated DNA:protein alignments. DNA:DNA alignments rarely detect homology after more than 200–400 million years of divergence; protein:protein alignments routinely detect homology in sequences that last shared a common ancestor more than 2.5 billion years ago (e.g. humans to bacteria). Moreover, DNA:DNA alignment statistics are less accurate than protein:protein statistics; while protein:protein alignments with expectation values < 0.001 can reliably be used to infer homology, DNA:DNA expecation values < 10−6 often occur by chance, and 10−10 is a more widely accepted threshold for homology based on DNA:DNA searches.”

There are Wikipedia articles about sequence alignment, and about the use of BLOSUM and PAM matrices. The section on sequence alignment in Berg et al. online — which involves amino acid, rather than nucleotide sequences — may also be of interest.
Appendix 2: Terminology and Definitions
As the term, Genetic Code, was misused in the unedited version of the question — and is widely misused in the press — I thought that a glossary of terms might be helpful
DNA (from which the genome and its constituent genes are constructed) are linear polymers of 4 nucleotides. The order of these is called the nucleotide sequence, or, because the only the purine or pyrimidine base varies between nucleotides, the base sequence.
Proteins are linear polymers of 20* amino acids. The order of these is called the amino acid sequence.
The Genetic Code is a cipher — and can be represented as a table showing the correspondence between 64 triplets of three nucleotides and the 20 amino acids and three stop signals when these nucleotides are part of the translatable part of a gene. The genetic code is highly — but not absolutely — conserved between organisms (and differs for proteins encoded by mitochondrial DNA).
In NO circumstances can the word Genetic Code be used as a synonym of Genome, although this is abused by even the scientific press, and is difficult for computer programmers to come to terms with, working as they do in a field where the noun ‘code’ is used for the product of encoding instructions.
*The genetic code has a certain plasticity and two additional amino acids can be encoded by termination codons in certain circumstances.

In your referenced answer you say, "An amino acid sequence contains information that is not present in the gene from which it originates, if we just consider the sequence as mathematical sequence of symbols. And, with 20 letters instead of 4, this new information has a different (and greater) complexity. The mistake is an unspoken assumption that the information of the genetic code is inherent in the nucleotide sequence." Please explain this in more detail. Having a larger alphabet does not imply greater complexity nor that proteins contain information not written into them by DNA.

@S.McGrew — I think it speaks for itself. The poster is concerned with a theoretical informational problem (of his own making). I explain how he has forgotten the additional information required if one performs the conceptual translation of a nucleotide sequence into amino acids. The practical explanation of why protein sequences are used for evolutionary comparisons over periods longer than a particular time is different. It is just that the same number of mutations produce smaller changes in proteins than DNA. For comparison within a species or between closely-related species DNA is better.

You seem to be stating that a protein (encoded by DNA) contains more information than the DNA that encodes it.  Ts certainly not self-evident and, according to my understanding, incorrect.

@S.McGrew — No. I am saying that a string (in computer terminology) composed of the four characters ATGC has less mathematical complexity than a string containing the 20 different letters of the alphabet minus B, J, O and Z. Although it is possible to derive the latter from the former this does not violate the second law of thermodynamics (as applied to information) because 1. The knowledge of which One of the six reading frames to select has to be invoked (I don’t think I mentioned this) 2. A hash table (a description of the Genetic Code in programming terms) has to be used.

The "structure" of a protein encoded by DNA is of course different from the "structure" of the DNA  encoding it,  but the Kolmogorov  complexity pf the two is identical.  There is no new information in the protein, unless you are asserting that mutations occur spontaneously in proteins and are then inheritable.

@S.McGrew — Again, I am saying nothing about mutations and real proteins. Perhaps mathematical is not the right word. The poster talked about gain and loss of information. In his terms I demonstrate in a qualitative sense how the conceptual translation of 64 codons into 20 amino acids might result in a net gain, rather than a net loss, in information. Karl Kjer deals with the broader real world problem.

Sorry to be obnoxious, but IMHO you stated, but did not demonstrate,  any net gain.  A code consisting of 4 characters in four-character words does not inherently contain more or less information than a 20- character code consisting of words of arbitrary length.  Measures of complexity are well understood in information theory, and contradict the statement.

This has turned into a conversation and illustrates well the purpose of the StackExchange model. I haven't even looked at my answer again properly. I don't do chat on principle, but I have had an idea for another approach for addressing this question and will either extend my answer or add a new one in the next few days. It's an old question, so it has to take its turn.


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Who invented dN/dS?
I am writing a paper, and I want to refer to the original paper that coined the term dN/dS (or Ka/Ks for that matter). I have found early works on dN and dS (like Miyata and Yasunaga 1980), but cannot find the first paper that used the ratio dN/dS. Does anyone know which paper is the best to cite dN/dS?
Edit: dN is the rate of non-synonymous substitutions per non-synonymous sites; dS is the rate of synonymous substitutions per synonymous sites. dN/dS is simply the ratio between dN and dS.
Reference: Miyata, T., & Yasunaga, T. (1980). Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. Journal of Molecular Evolution, 16(1), 23–36. https://doi.org/10.1007/BF01732067

I would suggest that you write the full names of the variables (dN, dS) it might help to better understand the context of the question and get more answers

In the paper you cite, we see KA and KS defined by the authors.

The direct comparison between a pair of known
  nucleotide sequences in coding regions permits us to evaluate both the nucleotide differences
  per site caused by nucleotide substitutions leading to amino acid changes,
  KA, and those leading to synonymous changes, KS, simultaneously.

The same year, Motoo Kimura published A Simple Method for Estimating Evolutionary Rates of Base Substitutions Through Comparative Studies of Nucleotide Sequences, in which he derives similar terms k'(nuc)S and k(nuc)A.

Writing k'(nuc)S rather than kS' to emphasize
  that this refers to the rate per nucleotide site, we get, using Eq. 14, the following
  formula.
$k'_{(nuc)S} = -\frac{1}{4T} log_e (1 - 2P - Q)$
The corresponding formula for amino acid-altering substitutions may be obtained by
$k_{(nuc)A} = \frac{K"}{2T}$

The reason why neither paper cites the other is because they appeared in the same edition of Journal of Molecular Evolution.  Based on the extensive cross-citation between these authors, as well as some co-authorships, it's likely that the development of the KA and KS metrics was simultaneous, if not collaborative.


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How does chromosome doubling occur?
Sterile hybrid with genome AB undergoes doubling of chromosome set to form fertile tetraploid with genome AABB.
But since A and B is not homologous, synapsis cannot occur at prophase I, so there is no meiosis.
So how does the chromosomes double? If through non-disjunction in mitosis, where did it occur? Did it occur in one cell only or all of the cells in the organism?
Did non-disjunction occurs at gonad to produce AABB cell, then it undergo meiosis to form AB gametes, and then self fertilise with AB gamete to form AABB offspring?

Kindly elaborate in which step of this entire process you are indicating non-disjunction? it seems simply a DNA replication can cause chromosome doubling or polyploidy. .

@AlwaysConfused  DNA replication occurs only at meiosis or mitosis right? So in this case, it occurs in mitosis?


text:
What is this insect (Germany)?

It was hovering and in between it was very fast and hard to photograph. I'm not even sure if it is an insect? Photographed in Germany.

It's hard to tell from your photo, but you should check whether Macroglossum stellatarum (German: Taubenschwänzchen/ English: hummingbird hawk-moth) looks similar to what you've seen.
This moth is living in Germany (and other regions) and due to it's way of flying (hovering and audible humming) it's sometimes confused with a hummingbird.

Seems to be right. I tried hard to make a good photo but it was too fast and I never got it into the seeker fast enough...

@mike I've seen it once and fully understand that it's hard to take a proper picture :)


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What is the current thinking on the typicality (or otherwise) of fossils as representatives of their species?
Since fossil records represent a tiny percentage of species populations, how do paleontologists determine how typical those specimens are?
Is there any research or analysis to determine how the distribution of fossil specimens within a species corresponds to the distribution of specimens of the species population as a whole?

Your title seems a bit iffy, but your question seems to be of palaeontology rather than biology.

Welcome to Biology.SE! The typos/automiscorrections in your title make it very difficult to understand what you are asking! In addition, as i think @David was suggesting, this might be better suited to the earth sciences site. ——— You may also wish to go through the help pages starting with [Ask] questions effectively on this site. Thanks!

Ugh... sorry about the title typo. I've corrected that. Regarding the appropriate site - both this site and the Earth Sciences one have a palaeontology tag (and this site has 50% more questions with that tag, so it's hard to know which is the more appropriate site. However, this question is much more aligned with biological processes than physical one, so (absent any other information), this feels like the right place.

Tags do not justify posts. To learn what is on topic here read the Tour and the Help. The representative nature or otherwise of fossil specimens is not biology in terms of this list.

I disagree with David, I think it is completely on topic for exactly the reasons described: this is about the biological side of paleontology (though David is also correct that tags do not determine topicality).


text:
Identification of this bug or insect
I found this bug dead in my house in Mississauga, ON, Canada.
I didn't have a ruler around so a regular toothpick was used to show the size.
I'm thinking it's a pill bug but I want to make sure.

Yes, that is a pillbug, or "roly-poly", Subphylum, Crustacea, class Malacostraca, family Armadillidiidae.  https://en.wikipedia.org/wiki/Armadillidiidae


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Do conservation oriented genetic database exist?
Are there any projects for the creation of the international genetic database of all endangered species, so we, at least, have a chance to clone them in the future if our current conservational efforts fail?

Welcome to Biology.SE! I assume you meant conservation rather than conversation? Please take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

First, it isn't entirely clear to me why you would want such a database.  Essentially all sequences are available in one (typically all) of the big databases.
For example if I search the NCBI database for "extinct" I get this.  There will be many more sequences for species that are "only" endangered.
Second, having a genome sequence isn't sufficient for "de-extinction" of a species.  The reasons for this are beyond the scope of this question, but can be explored starting from this section of the wikipedia article.
You will likely also find this discussion to be of interest.


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What do we mean by MHC molecule diversity? Does each human have a variety of MHC molecule isoforms?
I'm going to try and explain what I think I know
From what I understand, MHC/HLA molecules present peptides to T cells. To be able to present peptides from a wide variety of pathogens, they need to have diversity in their peptide binding domains.
My lecture handout tell me that MHC diversity comes due to polygeny and polymorphism.
Polygeny refers to there being 3/6 (handout says 3, textbook says 6) MHC class I loci leading to 3/6 class I isotypes, and 3/5 MHC class II loci leading to 3/5 class II isotypes.
Polymorphism refers to multiple alleles of each gene, meaning a variety of allotypes produced from each gene.
These processes lead to the generation of a wide variety of isoforms of MHC proteins in the human population.
The textbook also states that there is no rearrangement or structural change of the genes encoding the MHC proteins.
So I get that in the population, there is huge diversity of MHC molecules. But in each human, since there is no rearrangement of genes as in the case of antibodies to generate antibody diversity, is there therefore only one type of MHC protein being encoded? So by MHC diversity, we are not referring to diversity in each human, rather in the entire population? And if so, how do our MHC molecules become capable of binding to any antigen from any pathogen?
Please could someone clarify for me if I've misunderstood something, and also if my above explanation is factually correct, with the appropriate use of terminology?

You're right that both polygeny and polymorphism contribute to the diversity of a given gene in the population correctly described what they mean individually.
However, you missed that the polygeny of MHC means that the human genome has 3 different loci/genes (called MHC-I A,B & C) in the haploid genome, meaning that any given human as actually 6 copies of the gene (i.e. 3 copies from each parent). All of these copies perform the same function of presenting peptides to CD8+ cells, but will have slightly different binding preferences for the peptides that they load. This is where the MHC diversity in a single human comes from.
Additionally each of the 3 MHC-I loci/isoforms is polymorphic, meaning that for each of them multiple alleles/variants exist in the human population. Since the number of these variants is pretty big (hundreds to thousands), most humans have different alleles on their paternal & maternal chromosomes and end up with 6 unique MHC-I genes.

Ah yes, okay. So is the diversity produced from just those 6 genes enough to allow peptides from potentially any pathogen to be recognised and bound, and then presented to T cells? And does that mean the variation in MHC alleles between individuals produces only a very small difference in phenotype? I.e. are there large or only small differences in the types of antigen/peptide that each individual's MHC molecules can recognise? I just can't get my head around how such a few number of MHC molecule isoforms can bind such a wide variety of peptides

@Alex Yes, individual diversity just comes from having 6 different MHC-I genes. Generally they all bind broadly ~8-12aa pepdites with a few additional requirements, but still a big variety. Discussing the specificities, differences etc of peptide binding between the different subtypes & alleles is outside of the scope of this question/comment though - I'd recommend you read up about that in a proper textbook.


text:
Book recommendation on experimental mycology
I am looking for any book that elaborates experimental methods to study multiple  aspects of experimental study about fungi including culturing, induction of sporulation and other reproductive structure, fungal hormones/signaling molecules, biochemical characterisation, biosafety while working with fungi, fungal chromosome and DNA isolation, etc.


text:
Why are human wastes yellow?
Except for the feces, which is more brownish, all the human wastes (urine, earwax, snivel, phlegm, and rheum) are usually yellowish. Why is that?
I heard that urine is yellow due to bilirubin(?). What about others?

its interesting that many of the biological materials are more or less yellowish, may it be blood plasma or tree wood or curdled milk; but i cant see any significance for it. Seem to be coincidence. Or Maybe electronic structures of the molecules be a reason?

It is because of the pigment stercobiline which is present in human faeces

If your phlegm &c are yellow, you probably have a respiratory infection.


text:
Any idea what plant is this?

I was asked by my biology teacher to find out it’s name but it seems like a pretty common plant to me so I have no idea how to start. Any idea what type of plant it is?
It was found in Malaysia in my school compound

If you know where and when this was found, this could be helpful extra information to add to your question.

can you kindly add the image of inflorescence, flower and fruit of this plant? close-up if possible. Dissecting a flower helps greatly.  also add a photograph of the whole plant, twigs and trunk.

I have no idea how to start

You probably need an "identification key", or some kind of guide, that will help you identify the plant based on a series of questions or identification criteria.
To be able to use such keys or guides, you will need to familiarize yourself with technical vocabulary used in plant description. Some idea of the kind of ecosystem where the plant lives in would likely help too.
If the plant seems common, you will maybe find it on listings of common plants for your area.

This branch of the plant look very similar to the Indian Curry Leaf plant -Murraya koenigii.
It is used as a spice, garnish and also as a taste enhancer in Indian cuisine. It grows in almost every Indian household in their gardens or kitchen for fresh use.

It could be some thing else too, I am a little bit unsure because the edges of the leaves look rough but in Indian Curry Plant, The leaf edges are smooth, Here are some pictures...

I hope this helps in guessing the species,
Best Wishes!

Leaf margins, as you say, do not match. Your answer also lacks citations and does not rectify why this Indian plant would be in Malaysia. Please avoid simply guessing and only answer if you can provide adequate support. Thanks

The Leaf Edges look rough, I agree to that but that could be due to the drying of the leaves for storage, also the Curry tree as it is called, is also found in Malayasia, as the growing conditions required for the plant as same for both the regions (India and Malayasia). Please avoid simply commenting by looking into the answer superficially.

but that's exactly my point. Your answer needs to be complete and stand on its own. The points I made in my previous comment are serious concerns when determining the validity of your ID. Such concerns should be met with cited support if you'd like to receive positive voting response here. Please see [help] and here and here for further guidance. Thanks!