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How do high concentrations of carbon dioxide suffocate fish?
How do high concentrations of carbon dioxide suffocate fish?
It is common knowledge in fishkeeping that high concentrations of carbon dioxide are harmful to and can even kill fish. I am trying to understand why.
One explanation is that carbon dioxide displaces oxygen in water. However, this doesn't have much scientific basis, as different gases that don't react with each other do not affect each other’s solubility.
Another factor is that carbon dioxide reduces the pH of water by producing carbonic acid, but to y knowledge fish seem generally able to tolerate wide ranges of pH according to many studies done on the topic.
So there must be another reason that carbon dioxide suffocates fish.

I've found several studies indicating that hypercapnia induces hyperventilation in fish. Hyperventilation is bad in mammals, so I wonder if this is the pathway for harm to fish in hypercapnic conditions.

Elevated CO2 levels in aquatic environments pose significant threats to fish physiology and behavior. Fish are particularly vulnerable to increased CO2 due to their small PCO2 gradient between body fluids and the environment (Ishimatsu et al., 2005). High CO2 concentrations impair vital functions such as respiration, circulation, and metabolism, potentially reducing growth rates and population sizes (Ishimatsu et al., 2005). Moreover, elevated CO2 levels compromise the olfactory system of marine fish, reducing their ability to detect odors and respond to sensory cues (Porteus et al., 2018). This impairment is linked to suppressed transcription of genes involved in synaptic strength and cell excitability in the olfactory system (Porteus et al., 2018). The underlying mechanism of behavioral disruptions is associated with alterations in ion gradients across the GABAA receptor, which is responsible for inhibitory input in neural circuits (Heuer et al., 2019). These physiological changes ultimately increase mortality and affect fish survival in high-CO2 environments (Amador, 2018).

Thanks, the Ishimatsu paper seems to be very promising in its description of the mechanism by which CO2 causes harm to fish. I'm having trouble finding the Amador paper - can you share the title of it?

I think I found it. "Sea bass (can't) smell trouble under elevated CO2"

First author and year are not a sufficient citation, please update to include enough information to identify the source.

Could it be that high CO2 levels would reduce the O2 binding by the hemoglobin in the gills? leading to asphyxia?

@heracho Yes, the Ishimatsu paper "Physiological effects on fishes in a high-CO2 world" mentions the Bohr and Root effects which reduces the ability of O2 to bind to hemoglobin. In the scenarios tested, the fish could satisfy oxygen demands when not moving. Some fish exhibited a significant decrease in ability to consume oxygen, while other more hardy ones did just fine.


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Can one use DSSP (secondary structure assignment) for short peptides of size 6, 10 and 18?
I have large number of PDB files of peptides of size 6, 10 and 18. I wanted to cluster the peptide structure based on the secondary structure. I used DSSP in mdtraj module in python to assign DSSP code to backbone residues of each peptide sequence of various sizes of various pdb files. My question is whether it is reliable to use DSSP for peptides?

Surely visual inspection will tell you. The PDB provides a viewer.  Alpha-helix prediction would be low hanging fruit.

It predicts incorrectly for some of them. That is why I am doubtful

Well in a way you know the answer then. But as I remember, DSSP assigns a conformation description to individual residues based on dihedral angle. That is not quite the same as predicting secondary structure for an extended region of a chain. Have you checked the original paper, and can you add an example of incorrect assignment?

They use electrostatic interaction between backbone $C-O ---  H-N$ and compare whether the value is less than some cut off value. I guess this creates the problem

Use an ab initio tool like https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

you certainly can run DSSP as you did but the algorithm is designed for full length proteins but it will work on these short structures too.

At the moment your answer is just an assertion, lacking detail or supporting citation. It could be made into something more valuable by explaining the algorithm and what aspects of it cause it to fail with short peptides.

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There are plants and animal genera with the same Latin name. What are the scopes of uniqueness?
The genus Leptochilus occurs as a genus of wasps, and of a genus of ferns.
What are the parts of the phylogenetic tree where uniqueness is required, and how many of them are they?
(Where can I read about this, without reading all the individual standards?)
Ref: https://www.inaturalist.org/observations/154939850

Does this answer your question? What instances are there in which two species share the same binomial name?

Thank you! Yet no. If the person who asks is correct, an alternative formulation of my question is: What kingdoms exist with respect to nomenclature?
Obviously plants and animals, but what about fungi - different from animals as witnessed by Asterina gibbosa, but are they among the plants? What about diaphoretickes? Bacteria? Viruses? I only find special articles, no overview.
Ah, and I assume that uniqueness is already at genus level, not binomial. (Both is interesting of course.)

@Falko https://en.wikipedia.org/wiki/Kingdom_(biology)

Ups. Diaphoretickes contains plants of course. I intended to mention Stramenopiles.

@BryanKrause Yes, so we have n kingdoms, where n = 2 ... 8 :-)

@Falko there are few instances where a systematist might confuse an animal with a plant etc., so uniqueness should only need to extend to kingdom.

Here https://biology.stackexchange.com/a/73452/63850 Karl Kjer mentions, that animals, plants, and bacteria have their own independent nomenclatural codes. This seems to settle it. (I'm still reading though.)

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Saturated Mutagenesis Screening
I am hoping to mutate the active site of the enzyme I am researching that has 5 residues in proximity with the substrate. I am wondering how many colonies I'll have to assess to theoretically sample all the possible mutant combinations?
I am guessing that just screening the number of possible combinations will not be very successful because I am likely to sample a particular mutant more than once?
I have been looking at 'NNK Saturated Mutagenesis' which uses the redundancy in the genetic code to be able to create all residue encodings where N = A/G/C/T and K = G/T, while limiting the number of repeated residues from synonymous codons.
Are there any other ways of performing this sort of mutagenesis with better codon compression?

It depends a bit how you are generating the mutations and the residue combinations and what your goals are. e.g. do you expect the genotypes for each mutant position to be independent? Do you want to sample every amino acid at every position, and then do combinatorics of the $20^5$ combinations across the 5 positions? That's a lot of combinations to sample (3.2 million)! Why not a greedy approach, wherein you saturate mutations at each residue independently, and then construct combinations based on whether substitutions have an effect/seem interesting?

@David 'Synthetic biology is a field of science that involves redesigning organisms for useful purposes by engineering them to have new abilities' - genome.gov,  I am looking to re-engineer my enzyme for new purposes

An enzyme is not an organism.

@MaximilianPress It is a lot of combinations but I feel it is neccessary given the dependency of residues within the small space of an active site. I am not sure you would get the theoretical global fitness optima with a greedy approach but I think this is an interesting idea for maybe tackling even larger libraries

@MaximilianPress Greedy definitely isn't effective for some of the related problems like RBS and promoter engineering, and I won't expect it would be effective for active site engineering.  One might reduce the space by considering AA permutations rather than NA, but I'm not sure if there's a good mutagenesis protocol for that.

@David An enzyme is not an organism, but if you want to give a new chemistry-related function to an organism, a typical starting point is to select enzymes to add to the organism to implement the desired function. Often, because you're transferring the enzyme from its native context to a new context, you need to engineer it, e.g., with techniques such as the one being asked about.

@jakebeal Tags are meant to indicate what the question is actually about, not what it might lead to. They are meant to help people find questions in their sphere of interest. On the basis of your argument you could add "cancer research", "covid", "evolution" and anything you thought an engineered protein might be useful for. But it would not be useful to people interested in these fields. It is not always easy to find the best tag — there is no tag for mutagenesis here, so in the list of relevant tags I have put in my edit I have put mutations. It doesn't need to be perfect, just not wrong.

@David I appreciate the careful explanation of your reasoning, which is much more constructive than your now-deleted comment that led me to my prior interpretation of your reasoning. I particularly think the "protein-engineering" tag is useful. In my own thinking about taxonomy, I would tend to consider that a subset of the "synthetic-biology" tag, but can see how others with different backgrounds could evaluate their relationship differently.

This sort of method is indeed quite useful and frequently used in synthetic biology: I've used a similar approach before to generate 5' insulators for promoters.
Calculating the exact theoretical likelihood of what you want, so far as I understand, is a complex combinatoric equation that I wasn't able to get a nice closed form on with a few minutes of work. For your purposes, however, I expect that a reasonable estimate will do as well, and that can be made much more easily by modeling the population of each combination as an independent series of biased coin flips, i.e., a binomial distribution.
Consider a situation with $n$ potential combinations that you attempt to cover with $k$ random mutants. If we focus on a particular combination, we can see that each random mutant has a $\frac{1}{n}$ chance of hitting that combination. The whole set of mutants is thus a series of $k$ biased coin flips, with a probability $p_0 = (1-\frac{1}{n})^k$ of getting no mutants that hit that combination. This means that the probability $p_c$ that the combination is covered is $p_c = 1-p_0$, expanding to: $$p_c = 1-(1-\frac{1}{n})^k$$
With a large number of potential combinations and a large number of mutants, we can make a reasonable approximate by treating each combination as independent. In this case, the probability that all combinations are covered is the product of the probabilities that each combination is covered independently. They aren't actually independent: each combination that gets covered slightly detracts from the ability of other combinations to be covered. An estimate using an independence assumption is thus an overestimate of the actual likelihood, and the higher that $k$ is the closer the estimate should be to the exact probability. In short:
$$p_{all} < (1-(1-\frac{1}{n})^k)^n$$
This smells like the sort of equation there ought to be a nice identity for, but I don't know the identity, so I'll just give a couple of examples of calculating with it:

NNK = 32 combinations, 50 mutants (n=32, k=50): $p_{all}$ < 0.07%
NNK = 32 combinations, 100 mutants (n=32, k=100): $p_{all}$ < 25.5%
NNK = 32 combinations, 200 mutants (n=32, k=200): $p_{all}$ < 94.6%

As you can see there's a sharp transition as the coverage count increases.
Important caveat: the theoretical value may not give you what you want. In the paper I linked above, we used two degenerate primers with 18 N bases to inject 36bp of random material, which means we had $4.7x10^{21}$ possible combinations and should never have seen a repeat --- except that sequencing showed that we did indeed get several repeats out of only a few hundred colonies. Thus, biases in the biology may lead your statistics to be skewed from what the theory suggests.

CyberDope was first written at MIT, then again at Kairos, then again by me (privately) in Mathematica.  The program gives the best "dopes" for a target set of amino acids.  You will need someone who has Mathematica to view this program in ".nb" format and to run it.  I would further suggest they upgrade the program into Mathematica version 12.  I just now uploaded a copy to the Wolfram cloud (public):
CyberDope
The original publcation is:
Arkin and Youvan
Twenty years ago, the work was at this stage:
https://www.researchgate.net/publication/228715857_Directed_evolution_and_solid_phase_enzyme_screening
If you just want to "eye-ball" a good dope, look at this figure, circle the amino acid residues you want, and then look at the three nucleotide axes:

(That's from Wikipedia's Genetic Code article)

@David - Please have another look.

@jakebeal - I was not on this forum when you posted.

@Youyan I'm having a hard time understanding how this answers the original question. It looks like relevant software, but I don't see how one gets from this to a number of random mutants.

@jakebeal I saw you had mentioned NNK mutagenesis, which will increase in complexity with 32^n, where ^ is exponent and n is the number of amino acids you are simultaneously changing in the protein.  For a given n, CyberDope can help you reduce the base of 32 to a lower number.  That effects the number of mutants which you will have to screen if you select a good target set of amino acids.  Lets say you want to try the aromatic residues at a site. Looking at the cube (no program), U(UAG)(UG) gives you F,Y,W with a nucleotide complexity of 6.  NU(GT) is hydrophobic, NA(GT) is hydrophilic.

@JEJS Sorry I got OP confused with users who had answered.

Thank you for the interesting reference. As a matter of process, however, if you want to respond to an answer, the recommended way to do so on StackExchange is via a comment on that answer, rather than another answer that may not be addressing the question.

The OP is dealing with combinatorial complexity, too.  So they might want to look at this figure if they are mutagenizing at the second position of the codon.  Again, from Wikipedia (Genetic Code)


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Can you help identify this tree from my garden?
The picture is an evergreen tree.
I have seen very similar trees in Northern Italy. I would appreciate any help.

Welcome to Biology.SE! Do you have any idea if this tree is native (have you seen very similar trees around) or do you think the seed / tuber have been imported from elsewhere and planted here?

The tree in the picture is growing in dublin, Ireland. Most likely imported ad I have never seen them here before (not an expert) but I have seen what look the same in northern Italy

It's a Juniper, genus Juniperus.
If will feel prickly, and if you run your hand along the branch from the out to the inside it will feel very prickly. If you run your hand in to out, it will be marginally less so, but still uncomfortable,
Crushing the leaves in your fingers will release a sharp, tangy, not unpleasant smell.
Juniper Juniperus communis is native to some parts of in England, Scotland and Wales, and north and west of Ireland, and in fact most of the temperate forest regions https://en.wikipedia.org/wiki/Juniperus_communis#/media/File:Juniperus_communis_range_map.png
The berries are used to flavour gin.
However there are many other species of Juniperus that are often planted as ornamental trees, so it could well be one of these. https://en.wikipedia.org/wiki/Juniper
Best way for a positive ID is take a small bit with you to a large garden centre, or arboretum, and head to the juniper section and compare the look, feel and smell of the specimens.

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What kind of insect is this? (seen in Goma, Democratic Republic of the Congo)
We recently (in November) saw this insect in Goma, DRC.
I would appreciate help identifying it.

Common name is "Giant Water bug". These are hemipterans, in the family Belostomatidae. Images can be found here: https://bugguide.net/node/view/12796

Also, it's best practice to add another image of your species to confirm that you are talking about the same species. -1

Except for distinctively marked species, with insects, species identification often requires expert microscopic examination. Photo ID to species is generally impossible.

While I would absolutely agree with the other comments that you should elaborate and provide photos to allow your answer to be assessed, I'd certainly agree with this. I'd also explain in your answer that 'giant water bug' is the common name for the entire family, and therefore that while identification to species level may be impossible from the information provided, it's still correct to identify it as a giant water bug.

This answer still requires some elaboration to gain my upvote (and presumably upvotes from others as well).

@Bryan Krause. You must be into vertebrates. This is as close as you can get with photos of insects.

Tell us why you think that family, give information in your answer rather than a link, etc etc. I never asked you to give a specific species. Your answer as is does not meet the standards of the site.

I guess it might have something to do with the way this completely unique and unmistakable family looks. I did not take DNA samples from it, but I am as confident of my identification as I would be in calling a giraffe a mammal.

Karl, you've established yourself as an insect expert here, and your point about species-level IDing is understood and respected by many of us who frequent ID posts. However, I agree with @Bryan that your post (& others) could be improved by providing more detail (e.g., clues you used, characteristics (and sources/keys) the OP could use to ID to species, life histories, etc.) and/or a photo (even if it clearly states that it's just an example species from the genus/family). This post would qualify as a comment if the link died, but could serve as a great teaching aid with a bit more detail! :)


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What is the name of this bird?
Does anyone know the name of the bird in the pictures? It was found in the south of Spain in the month of June. (it is certainly neither a house sparrow nor a swallow nor a robin). Thanks for the help!

It could be female "Common blackbird" (Turdus merula)

Yes, it is may be a female, but it is surely not a "Common blackbird".

what is its size? otherwise tell compared with other known birds.

Sorry I don't have its exact size. It looks like a house sparrow, but it is a little smaller than a house sparrow. Its head is also smaller than the head of a house sparrow.

Is it possible that it was a species escaped from captivity?

Sorry I don't know. Maybe.

I asked if it would be escaped because by the colors it looks like a Chestnut Sparrow but it does not live in Europe but in Africa (Kenya, Tanzania and around). Otherwise it could be another sparrow family (the shape of the beak looks it is the Passeridae family) but difficult to say like this.

Couldn't it be a juvenile of some well known species ?

http://www.king5.com/story/news/local/pets-and-animals/2015/04/05/little-brown-bird-sings-happy-easter-song/25335167/

Yes it could also be a juvenile but I do not know too much about variation of colors for these birds; it could also be so old that it just get dry and loose its original colors.

Thats a difficult one but my gut feeling is a 'bunting' and maybe a Rock Bunting juv ? - the bill is definitely bunting-like and there does seem to be a black and white eye stripe going on . There arent that many buntings in the south of Spain especially with a very warm brown colouring

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Can any one ID my tortoise?
I have got a pet tortoise and I was wondering if any one could identify it. I think it's a male around 2 years old.
I'm not quite sure, it is quite small, very shy and goes very fast.
He likes carrots, pears, apples and tomatoes.
At the bottom of his shell there's sum light orange color.
Basically light line of orange on each side but only on the bottom of his shell.
If this helps at his last owner house he was bitten by a dog and his shell was repaired by a local farmer with fibreglass.

For getting more accurate answer I would add some more details like if you found the tortoise in the nature or if you got from another way. Telling which country you're living would also add better match if you found it in the nature. For me it looks like a Hermann's tortoise but as I am not specialist, it could be another one from the Testudo family (or even another if yours is not coming from Europe).

Normally for determining the gender, i think it's the length of the tail which differs. I would add one more picture with the tail fully out. The end of the tail can also detarmine the family / genus of the tortoise.

Another point about size: it is quite small is very subjective and as they grow very slowly, the specimen you shows does not look so small. If you can just put how many Centimeter (or Inch) it is (ideally length, width and high) it would also help other people to have a better estimate.


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Can Anyone Identify This Bug
I am looking for someone to identify this bug:

I'd like to have a closer image, but at first glance, it looks like some sort of weevil

Can you tell us where you found the insect?

This is definitely some species of grain weevil. If you can provide more about it's size, location, where you found it (e.g., what type of food), and whether or not you've seen it fly, then someone should be able to give you an exact ID.

It is an ormányosbogár species. :D
Curculionidae in Latin. I don't know the exact species, but it is common here in Hungary.
It is something like Mecinus janthinus, but it seems like shorter. Probably Mecinus pyraster or another Mecinus species.

Figure 1 - Mecinus janthinus - source

I think it is Sitophilus granarius aka. wheat weevil, but it is hard to decide because of the poor quality photo...

Figure 2 - Sitophilus granarius - wheat weevil - source

The second one looks better, it fits the ratio of the original image better, your first image has a thorax that looks too short.

@user137 Yepp, I think too that it is the second one.

Note that Curculionidae is a very species-rich family though (e.g. 780 species in Germany, >500 in Sweden, ~60000 known worldwide). Without size, location and a better picture I don't think this can be determined to species.

@fileunderwater I agree, better photo needed, or DNA sample :-)

This is definitely Sitophilus granarius [wheat weevil].It is a common pest in India, as it mostly attacks wheat grains stored in sacks.When we buy plain grains of wheat from shops we can see these pests inside and there may be plenty of them drilling the wheat and leave the empty crest of wheat behind.

You should provide evidence with your answer - it's part of writing a good answer, see the help pages.


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Do you know what plant it is?
I saw this plant when I was on my trip to the Ukraine.
I wonder if those berries are edible.

I noticed you asked the answer writer how they knew what it was. Check out my post over on The Great Outdoors StackExchange (Plant identification methods) to get an idea of how to best go about IDing unknown plants using primarily the internet!  (And it just so happens that my post is also in reference to a Phytolacca plant!!!) 0.o

It is of Phytolacca genus plant which could be toxic for mammals, DO NOT eat as is - it should be cooked properly to be usable/edible (the older, the more toxic leaves are).
Phytolacca acinosa:

Thanks a lot! Is there some sort of plant dictionary which can help identify plant species? Or did you just know what it was?

@TeikoAbe It is easily traceable - you should learn what Inflorescence is - https://en.wikipedia.org/wiki/Inflorescence and what Venation is - https://en.wikipedia.org/wiki/Leaf#Venation_.28arrangement_of_the_veins.29, from there it is very simple to know any specific plant.


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If I sent a bag of rice to the bottom of the ocean and brought it back, could I eat it?
Suppose I filled an oceangoing container with rice and sunk it to the bottom of the ocean… say, a kilometer or so, then brought it back up.
Would it be edible?
Would it retain nutrients?
Do these things depend on how long it's been down there (at very low temperatures, mind you).
Asking for myself because, you know, I think ocean-bottom rice would be tasty.
Thanks!
Edit (after Doctor Whom's answer): I guess I should have mentioned that wrapping it in plastic is an option.  The pressure is what I was most interested in but I did a really poor job conveying that.

How much time do you plan to keep it there? Is it cooked or just plain uncooked rice

...asking for a friend.

Uncooked rice, certainly.

Depends on the container.  The bottom of the ocean has three main properties that would affect the rice:

Water
Salt and floating materials
Pressure - at the bottom of the Mariana Trench, the pressure is 1000x that standard atmospheric pressure at sea level.

Rice is absorbent.  Depending on the container, if it is permeable to water, then both seawater and pressure will affect the rice.
Rice + Water = soggy rice with a different texture than cooked rice.
Rice + Brine in Seawater = soggy rice that absorbed salt and fine particulate materials from the surrounding water.  (Cooking this would probably taste just like using seawater to cook rice.)
Rice + Intense pressure = the water, salt, and other materials would be absorbed on its way down more quickly due to the increased pressure, and any air within the grains would be replaced with water as the grain is compressed.
I do not believe it would work at all like a pressure cooker does due to the cold temperature; I am fairly certain that it would be only the grainy soggy rice - cooked rice is different from dry rice because of changes to the starches by the heat when cooking (and obviously the absorption of water).  The rice itself is a starch, so the carbohydrates would not likely respond differently to the pressure in the absence of heat.
I am curious if anyone might come up with anything on the chemistry of carbohydrates under pressure at near-freezing temperatures - whether any chemical bonds may be altered (like deformation of the beta-1-4 glycosidic linkage).  That's beyond my level of chemistry/physics knowledge.
But the duration of the journey would likely result in mush by the time it came up.  There are not many nutrients to white rice in the first place, other than the carbohydrates, so the nutrient change would be what it gains in the brine.
If I am missing something, please point it out.  But I believe this is the extent of the effects on the rice.
However:
If your rice were in a sealed container capable of withstanding the pressure without collapse or leaking, I am fairly certain that the rice would arrive back to the surface completely unchanged.  Humans are able to go down to the sea bottom in specially designed vehicles.

Thanks for your thorough reply!  I guess I should have said that watertight sealing is possible if it helps (which it certainly seems it would, by your answer), so the part I was really interested in was this: If your rice were in a sealed container capable of withstanding the pressure without collapse or leaking, I am fairly certain that the rice would arrive back to the surface completely unchanged. -- thanks, that's what I wanted to know!

Humans who scuba dive deep or are exposed to significantly higher pressures than sea level have some issues of gases esp. nitrogen that dissolve in the blood due to pressure; upon rising can exit as gas and cause all sorts of problems including air emboli - the phenomenon (not just emboli) is called "the bends" and can be serious, which is why we rise slowly when depressurizing.  But in a sealed can, there's not really much of a change in pressure if any.  http://deepseaadventures.com/photos/opportunities05/DualDeepWorker.pdf


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Many black people I've met have bigger lips than white people, why?
I noticed that many black-ish people I've met have bigger lips than the white-ish people I've met. However, not all black-ish people have big lips.
Is there any explanations in terms of natural selection, geographic localisation, common ancestors, or something else that could explain why a subset of dark skin people have bigger lips on average than pale skin people?
Edit: This question is different from the other one because the answer talks about the nose and its function (air temperature) linked to the environmental factors. I don't see how this applies to lips.

Regard this one as a comment

I prefer to cite some text form this website instead of providing the link only (as it could be removed).

In general, this pattern can be observed across the planet with the
  size of lips and nose decreasing as we move away from the equator
  towards the poles. So what could the reason be?
For someone living in hot climatic conditions, cooling down the body
  is critical for their survival. Our body has many cooling mechanisms
  and one of them is simply disseminating heat when it comes in contact
  with colder air (simple thermodynamics). This however requires larger
  surface area so that more heat can be disseminated.
Given that a significant portion of breathing also happens through the
  mouth (especially when exposed to heat), lips are pretty much like the
  gateway for colder air being inhaled and exhaled. So, the larger the
  lips, the more heat that can be disseminated. Thus, people living in
  hotter climatic conditions gradually evolved to have bigger lips.
The opposite is true for people in colder climates. They get a
  survival advantage if they are able to retain as much heat as possible
  and so they gradually evolved to have smaller lips thus limiting the
  amount of heat that can escape when cold air brushes past their lips
  while inhaling and exhaling.

Notably, there was no scientific source provided for this claim, however intuitively this could make sense.

(This is an extended comment rather than an answer.)
One important thing to note is that depending on where you live, the "black-ish people you've met" may not be at all representative of black people worldwide. For example, if you live in the Western Hemisphere, then the large majority of the black people who live in your country are probably descended from Africans who lived in the so-called "Slave Coast of West Africa", which roughly comprised the modern-day nations between Sierra Leone and Nigeria. For example, here is a photograph of a present-day resident of Ghana (where many descendants of modern-day black inhabitants of the Western Hemisphere lived), and here is a photograph of a present-day resident of Eritrea. They look very different.


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Distribution of the number of clover leaves
Being no expert at all in this field I am just interested in emprical studies of the frequency $f(n)$ of clover plants with a given number $n$ of leaves.
I would suspect naively from general considerations that the frequency follows an exponential distribution.
Any hints are greatly appreciated.

Roughly: You find around 1/10000 four leaves clover. If you want to get into the details, know that each observation isn't independent from the other (as two "clover" are sometimes the same individual sharing the same genetics) and the time of the observation (summer or spring) may change this rate (more four leaves in summer). I advise you to search this website to find good and referenced answers to your questions. If it is not what you were looking for, edit your answer to give  what you understood from other questions and what you are still looking for.

@ Untitpoi Thank you for your comment. I would appreciate if you could be a little more specific which website I should search for what? Neither during the formulation of my question nor in the margin section of related stuff something relvant has popped up.

did you check that answer : https://biology.stackexchange.com/questions/57860/are-four-leaf-clovers-mutations-developmental-errors-or-something-more-complic the Tashiro et al. 2010 reference seems to be a good empirical study on four leaves clover!

I have found a study [1] of 2017 (http://www.sharetheluck.ch/single-post/How-rare-are-four-leaf-clovers-really) which answers a great part my question, and I'd like to show those results together with some additional evaluation.
They have counted 5.7 million clovers and found the following numbers compared to 3-leaflet clover:
4-leaflet clover    1 in 5,076
5-leaflet clover    1 in 24,390
6-leaflet clover    1 in 312,500
For the 4-leaflet clover they have corrected appreciably the common figure of 1 in 10,000 (see e.g. the comment of Untitpoi here).
A logartihmic plot of these relative frequencies shows interesting features
(i) a fairly regular exponential decay of the frequency in the range n=4,5,6
(ii)    a significant "exception" from this rule is the "normal" clover with n=3

How can these observations be explained?
It would also be interesting to extend the study to n>6, and maybe also to the range of "deficient" clover which posesses only one or two leaflets. The latter are most probably very rare so that the complete log-plot would resemble an inverted letter V.
The question of 2-leaflet clover was raised here [2] https://www.quora.com/What-are-the-chances-of-me-finding-a-two-leafed-clover. But no quantitative answer was given.
References
[1] http://www.sharetheluck.ch/single-post/How-rare-are-four-leaf-clovers-really
[2] https://www.quora.com/What-are-the-chances-of-me-finding-a-two-leafed-clover
[3] https://en.wikipedia.org/wiki/Four-leaf_clover#cite_note-auto-6
A comprehensive reference which I have only partially explored up to now

Thank you, Dr. Hintze, for citing our work (http://www.sharetheluck.ch/single-post/How-rare-are-four-leaf-clovers-really). We were frustrated about the lack of a reliable source for the '1 in 10'000' estimation of the prevalence of 4-leaf clovers (it is most likely a circular reference that was once started simply by guessing), so we started our own research (complementing the philantropic side of our project www.sharetheluck.ch). This let us come up with the below-mentioned numbers.
We do keep record of clovers with 7 and 8 leaflets, but we believe that the numbers are too small (yet) to be of significance.
Substantially higher numbers of leaflets have beeen obeserved only after inbreeding, to our knowledge.

@ U Sperling Could you provide the numbers for 7 and 8 even though they are not reliable enough? I'd like to put them into my graph and see if the rule continues approximately.


text:
Need help identifying this plant
I found this guy growing in my compost, but have no clue, what it could be.
Any expert here who want to take a guess?

What is your location?  And when was the photo taken?  You are almost certainly looking at something in the genus Persicaria and the family Polygnonaceae.  The clue is the ochrea, which is the papery sheath wrapping around the stem at the base of the leaves.

@BryanHanson This was taken in Hamburg, Germany a few hours ago

Alright someone familiar with European species in this genus will have to answer.  US species I am familiar with would not bloom until late summer.


text:
What determines the nucleotides incorporated into RNA by polynucleotide phosphorylase?
Polynucleotide phosphorylase, in addition to its role as an exonuclease, is also involved in the post-transcriptional addition of nucleotides to RNA in a template-independent manner:

“Polynucleotide phosphorylase not only synthesizes long, highly heteropolymeric tails in vivo, but also accounts for all of the
observed residual polyadenylylation in poly(A) polymerase”

My question is:
What determines which nucleotides are incorporated as the process is template-independent?
I have not been able to find any information about this. Is it purely chance?

There would seem to be two possibilities:

The enzyme has differential specificity for different substrate NDPs.

or

The deciding factor is the relative concentrations of the different NDPs in the cell.

Although the structure of the enzyme has been determined there do not appear to be any studies that would distinguish between these possibilities. This is perhaps because most recent attention has focussed on the exonuclease activity of the enzyme.


text:
Peptide fragment software in mass spectrometry
I am trying to study peptide fragmentation in mass spectrometry.
My goal is to find software with which I can retrieve the molecular structure of the peptide and see the a,b,c fragments.
I found these two online tools.
Pep draw & Fragment Ion Calculator. Ι entered a short sequence and I retrieved the m/z values for the a.b.c and x.y.z values in a table.
Is there any software /online tool that I will add a peptide sequence and automatically generate the chemical structure? I want this image generated but for my peptide sequence instead of the side chains.

By "generate automatically the chemical structure" do you mean the 3-d structure of the fragment peptide? If you google "predicting 3d structure of peptides from sequence" you'll find references to a bunch of software that attempts to do this, the PEP-Fold server for example. Of course as the fragment gets larger the problem gets harder, and you end up needing Alpha-Fold.

@CharlesE.Grant I just edited my post. Maybe now is more clear what I am searching for.


text:
Do identical twins have the same metabolism rate at birth?
Will monozygotic twins defecate at the same time if fed at the same time during the first weeks of life?
They should have the same genetics (and epigenetics) since they are monozygotic and the same environment since they live in the same house and they are just born.
I looked if metabolism (assuming it is correlated to defecating) is a genetic trait. I found this review about basal metabolism of infants but it stated that the methods aren't good and not comparable.
If there is no information for humans, what about other mammals?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, questions should be clear and narrowly scoped (i.e. answerable in a few paragraphs rather than needing an entire book). To be clear you need to say what you mean by "metabolism". I would say that most humans have the same metabolism since with rare exceptions we all possess the same suite of metabolic enzymes. However, that has nothing to do with intestinal transit times, so you must mean something else. ...

...  ——— Note that we also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

At the first year of my biology teacher program in university,a professor wrote on board "x=/x"(x isn't identical to/same as x) to indicate the difference of individuals no matter how much they look the same. Monozygotic twins have identical DNA and hereditary characters, but the bodies that are formed under the guidance of the DNA aren't identical.

@Harun could you elaborate? In plantsI learned that somatic clones are assumed to be identical in any aspect since the rate of rando mutations, transposone jumpings etc. is relativley small and causes no significant difference at the start

Do identical twins have the exact same gut flora? Does exposure to the same environment produce the same gut flora? Is there an element of randomness in there?

yes, genetic trait. thank you. I guess they will have. I learnt that most of the microbiome of a child comes from his mother and the rest from the (same in this case) environment. There will be randomness but will it be significant?

@Hachiloni How exactly does a baby's gut flora come from the mother?

@RodrigodeAzevedo - Partially & Hachiloni, yes it would be significant. Microbiota greatly influence metabolism.

I like admire your interest.
Organisms in development rely not only on their genetic make-up but also: their environment and epigenetics (no matter how early in development).
In addition to variables other than the ones stated...
In reality if we were to test this - the twins wont eat at the same speed, expend the same amount of energy, stay the same temperature, eat the same amount, or drink the same amount as each other.
With so many extraneous variables, it leads one to believe that it is very unlikely identical humans or other organisms would defecate at the same time.
I can direct you toward some (no-pay wall) literature on the Nature/Nurture debate or Twin studies.

thank you for the answer. As far as I know identical twins should have the same epigenetics and environment initially, that's why we do this kind of experiments on them. I understand from your answer that this is a too difficult to answer question. I would dig into the literature you posted.

Epigenetic patterns are similar, but not the same between identical twins. Well environment is not even true, they may not always be together and so it is again, similar but not the same. It would take small amounts of carcinogens to dramatically alter results. I am sorry this isn't the answer you like. But it is the best answer available.

I meant a too difficult to answer scientificly as there are many uncontrolable variables. Not that you answer wasn't a good fit for my question. Apologies if I wasn't clear

Not too difficult to answer scientifically. Even if we tried as stated above in my answer - it is highly unlikely. Does that not answer your question? It does. But it's not the answer you wan? You cannot get SE members to solve arguments for you.

They should have the same genetics (and epigenetics) since they are
monozygotic and the same environment since they live in the same house
and they are just born.

https://childrenswi.org/medical-care/fetal-concerns-center/conditions/infant-complications/twin-to-twin-transfusion-syndrome

If untreated, the survival rate for TTTS twins is approximately 10 to
15 percent.

So in your scientific opinion, that whole website and condition is just pure garbage, and the parents and doctors are making it all up, right?
Because of course twins always have the exact same metabolism?
Do you have the scientific integrity to admit your conclusion here?

I think I mentioned I'm not a animal biologist but a plant scientist so I don't know all the possible syndromes. Obviously this condition will make identical twins non-identical and therefore they are excluded from my question.
Your comment seems agressive. And, from the comments and answers I got this sites seems too agressive and oversensitive to be a good place to ask questions


text:
Does the ribosome have protein kinase activity?
The ribosome synthesizes proteins by translating the mRNA. The nascent peptide needs to go through the nascent polypeptide exit tunnel in the large ribosomal sub-unit before it reaches the cytosol where it becomes exposed to possibe modification.
Is there a ribosomal protein capable of phosphorylating the amino acids of nascent polypeptides before they exit the ribosome?

No — there is no ribosomal protein with protein kinase activity.
It is difficult to provide conclusive evidence for a negative statement, but the two objective points I can make in support of my view are:

All eukaryotic (and prokaryotic) ribosomal proteins have been sequenced in a wide range of organisms. None shares the characteristic motifs of protein kinases.

There are hundreds of different protein kinases in eukaryotic cells, and these show a wide range of specificities towards different proteins. Many proteins are not phosphorylated at all. Hence, it is difficult to imagine what purpose a ribosomal protein with protein kinase activity could serve.

However…
The protein RACK1 (Receptor for Activated C-Kinase 1) is closely associated with the small subunit of many eukaryotic ribosomes, even though it is not designated a ribosomal protein under the standard Sx numbering system. The substrates of the activated C-kinase for which it is the receptor are not the proteins being synthesized on the ribosomes, but apparently cellular proteins involved in signalling pathways.


text:
How is it thought that phosphine is synthesized by living organisms on Earth?
The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York Times:

But scientists have yet to explain how Earth microbes make it.
“There’s not a lot of understanding of where it’s coming from, how it forms, things like that,” said Matthew Pasek, a geoscientist at the University of South Florida in Tampa. “We’ve seen it associated with where microbes are at, but we have not seen a microbe do it, which is a subtle difference, but an important one.”

What are the current hypotheses about how phosphine is formed?

I haven't had a chance to read the full Nature Astronomy paper, but I would assume that the authors cover at least some of this in there.

@MattDMo — Not really. One of the co-authors of the paper is also an co-author of the paper I quote in my own answer, and her work is referenced. But the problem would seem to be that the conditions in which phosphine appears to be produced biologically on Earth, are very different from those in Venetian clouds.

The number of researches of venusian phosphine will promptly go up to the thousands, measuring and detecting all the other biological signatures which can exist on venus astronomically and in the lab, and there will be some high-profile critics of the study. A lot more evidence will be coming in soon, for the moment it's a bit murky.

I have made some presentational changes to your question, given that what was "today" is now yesterday and tomorrow... I also thought it fairest to describe the Nature Astronomy paper using its exact tile, gave the formula of phosphine, and added the astrobiology tag. Hope that's OK.

The background to phosphine production on Earth can be found in a review entitled “Natural Products Containing ‘Rare’ Organophosphorus Functional Groups” by Petkowski et al. in Molecules 24, 866 (2019). The four authors are also co-authors of the Nature Astronomy paper. They state (my emphasis):

The detailed biosynthetic pathway for microbial phosphine production
is currently unknown. For detailed discussion of the biological
production in the environment, its biochemistry, and atmospheric
chemistry see three recent papers by Bains, Sousa-Silva and colleagues
[482,494,495].

These three papers are from the authors, one of which I followed up:

Bains,W.; Petkowski,J.J.; Sousa-Silva,C.; Seager,S. New environmental model for thermodynamic ecology of biological phosphine production. Sci. Total Environ. 2019, 658, 521–536.

The abstract to this includes (my emphasis):

In this paper we show through thermodynamic calculations that, in
specific environments, the combined action of phosphate reducing and
phosphite disproportionating bacteria can produce phosphine.
Phosphate-reducing bacteria can capture energy from the reduction of
phosphate to phosphite through coupling phosphate reduction to NADH
oxidation. Our hypothesis describes how the phosphate chemistry in an
environmental niche is coupled to phosphite generation in ground
water, which in turn is coupled to the phosphine production in water
and atmosphere, driven by a specific microbial ecology.

The paper itself is not of the ‘author-pays’ type, so you may need institutional access to read it. There is a graphical summary provided, however, which summarizes the hypothesis:

The paper consists of detailed thermodynamic arguments for the scheme suggested at the particular temperature, pH and anaerobic environment of marshes and swamps. Under these conditions, the authors postulate that the purpose of posphine production is to gain energy†. The analogy would be with the production of NADH as in anaerobic glycolysis to gain energy, but needing to be reoxidized to NAD+ to allow this to continue. The reduction of phosphate to do this would be analogous to the reduction of pyruvate to lactate or to ethanol. Like ethanol, phosphine would be a by-product of no value to the organism.
However the possible role envisaged for phosphine production in Venusian clouds is different. In the Supplementary Information for the Nature Astrobiology paper, there is the following:

Initial modelling based on terrestrial biochemistry suggests that biochemical reduction of phosphate to phosphine is thermodynamically feasible under Venus cloud conditions. Biological phosphine production on Venus is likely to be energy requiring. However, life can make substantial energy investment into compounds that provide important biological functionality. There are many potential useful biological functions including signaling, defense, or metal capture for which phosphine has useful properties, so endergonic biosynthesis cannot be ruled out.

The suggestion here is that phosphine is a useful product, synthesized at an energetic cost.
The only biochemical connection between the two would be that if, as appears likely, life on Earth can produce phosphine (by biochemical pathways that remain to be discovered), then these same biochemical processes would be candidates for phosphine production by life on Venus if the authors are correct in arguing that (at least known) non-biological candidates have been excluded. The question does not ask for opinions on the latter, nor would I presume to present those that I hold.

† The thermodynamic approach involves calculation of Gibbs Free Energy changes (ΔG) for reactions. Often on this site discussing standard biochemistry we (or at least I) talk in terms of standard free energies — ΔG˚ (or ΔG˚′ for normal cellular conditions). However the actual value of ΔG for a reaction is influenced by temperature and the concentration of reactants (which will include hydrogen ions), so that the ΔG calculated for terrestrial marshes and the like is likely to differ from that in Venusian clouds.

The paper also appears to be on arXiv  https://arxiv.org/abs/2009.06593

@usernumber — That is a preprint of the Nature Astronomy paper, the final version of which is freely available, I believe. However, clearly some people have known about it for a while.

It looks like a good read of Bains's related work would be of interest to the OP.  Trivalent Phosphorus and Phosphines as Components of Biochemistry in Anoxic Environments is another that looks worthwhile (though I come to this from the physics side).  According to the Nature Astronomy paper (Greaves et al) Bains has another paper on the way, but that's more on the Venusian side.

I guess the reasonable follow-on question would be whether the process described there could feasibly operate in the sulfuric clouds of Venus.

@T.E.D. The atmosphere in Venus is mostly carbon dioxide. Only a trace amount of sulfur is found. Also, hydrogen was theorized  to have present in relatively short supply in the Venusian atmosphere but most of them is lost to space with the remainder(trace)  being bound up in sulfuric acid and hydrogen sulfide. Also, the Vesuvian clouds composing of sulfuric acid are formed in the upper atmosphere. Even if it rains, it evaporates around 25 km above the surface and thus not affecting the microbes present in the ground. But research is still going about the feasibility of this cycle on Venus.

@T.E.D. I'm sure that's discussed in Bains's new 103-page preprint

Detection and role of phoshine in phosphorus cycle was first discussed in 19881. They examined phosphorus cycle in open-air sewage treatment plants where they discovered a gas releasing from sediments of 1-2 meter deep water which was found to be phosphine. They calculated that 5 g of phosphine was released from 2000 m3 of sewage. They also further proposed that:

Under laboratory conditions, it was also demonstrated that phosphine
is released by bacterial reduction from a medium containing
inorganic phosphorus. The phosphorus content of the medium decreases
by nearly one half.

This bacterial reduction of phosphine was further explained in a 2000 paper2(Also see ref. 3):

A microbial basis for bioreductive generation of phosphine is
proposed, which could account at least in part for the presence of
this toxic gas in natural anaerobic environments and in sewage and
landfill gases. Phosphine generation under anaerobic growth conditions
was dependent upon both the culture inoculum source (animal faeces)
and enrichment culture conditions. Phosphine was detected in headspace
gases from mixed cultures under conditions promoting fermentative
growth of mixed acid and butyric acid bacteria, either in the presence
or absence of methane generation. Monoseptic cultures of certain mixed
acid fermentors (Escherichia coli, Salmonella gallinarum, and
Salmonella arizonae) and solvent fermentors (Clostridium sporogenes,
Clostridium acetobutyricum and Clostridium cochliarium) also generated
phosphine. Generation of phosphine by these
bacteria could explain the apparent correlation between methanogenesis and the formation of phosphine in nature.

But this phosphine reduction was found to be thermodynamically unfavorable and hence a proper biochemical reduction pathway has not been identified4:

Thermodynamic considerations indicate that it is very improbable that
the reduction of phosphate to phosphine is endergonic. Therefore the
generation of phosphine cannot be compared with sulphidogenesis and
methanogenesis. There seems to be a link between the existence of
highly reactive gaseous phosphorus compounds and increased levels of
metal corrosion. The reactive compounds could be formed by
micro-organisms or they are liberated from phosphorus-containing
impurities in the iron by the action of bacterial metabolites. The
biochemical pathways responsible for the production of gaseous
phosphorus compounds have not been characterized yet.

But then in a 2014 paper, a possible redox reduction method has been proposed5:

No other common reducing agent can produce phosphine at the
concentration at which it is observed in nature, as reduction from
phosphate is energetically unfeasible unless phosphite or
hypophosphite are present in the environment (important members in
phosphorus cycle). Phosphite and hypophosphite generate phosphine and
phosphate from disproportionation reactions:
$$\ce{4H2PO3^− + H+ -> PH3 + 3H2PO4−}$$
$$\ce{2H2PO2− + H+ -> PH3 + H2PO4−}$$
Phosphine production is primarily dependent on the concentration of
phosphite and hypophosphite, but is also dependent on pH, temperature,
and total dissolved P concentration. If the majority of the reduced P
occurs as hypophosphite, then more PH3 should be expected
than if the reduced P occurs as phosphite.

Conclusion: Phosphine should be/is considered to be an integral member in phosphorus biochemical cycle as it is found to be formed from the reduction of phosphites/hypophophosphites (important members in PBC). About 10% of the phosphorus produced in the atmosphere from PBC is PH3. Direct production of phosphine gas occurs in some specialized, local conditions like deep-marine environment where PH3 concentration was found to be 0.01 ng/m3 - 100 ng/m3.
PBC is itself an important process for sustaining life on Earth. It synthesize life-sustaining molecules important for the biosphere. Since, it is found in Venus, we can hypothesize anaerobic life on Venus although it hasn't been confirmed yet. In future, we might see life on Venus.
References

Dévai, I., Felföldy, L., Wittner, I. et al. Detection of phosphine: new aspects of the phosphorus cycle in the hydrosphere. Nature 333, 343–345 (1988). https://doi.org/10.1038/333343a0
Jenkins, R & Morris, T & Craig, P & Ritchie, A.W & Ostah, N. (2000). Phosphine generation by mixed- and monoseptic-cultures of anaerobic bacteria. The Science of the total environment. 250. 73-81. 10.1016/S0048-9697(00)00368-5.
Liu Z, Jia S, Wang B, Zhang T, Liu S. Preliminary investigation on the role of microorganisms in the production of phosphine. J Environ Sci (China). 2008 ;20(7):885-890. doi:10.1016/s1001-0742(08)62142-7
Biological formation of volatile phosphorus compounds
Joris Roels, Willy Verstraete, Bioresource Technology, Volume 79, Issue 3, September 2001, Pages 243-250, DOI: 10.1016/S0960-8524(01)00032-3
Phosphorus redox biogeochemistry, Matthew A. Pasek, Jacqueline M. Sampson, Zachary Atlas, Proceedings of the National Academy of Sciences, Oct 2014, 111 (43) 15468-15473; DOI: 10.1073/pnas.1408134111

"Conclusion: Phosphorus biochemical cycle is an important cycle for sustaining life on Earth." I don't wish to be critical of another answer, but I cannot see how this statement can be concluded from the (excellently presented) information you present. You make no mention of a cycle or explain the fate of the phosphine. Even if it is reoxidized to phosphate, you do not state how much it contributes to overall phosphate availability. Phosphorus is a necessary component of living things, but I doubt that it depends on a phosphate/phosphine cycle.

@David Thank you for the feedback. I tweaked my answer a little bit.


text:
Understanding beat annotations of arrhythmia ECG dataset
I'm trying to understand the rhythm changes in the MIT BIH dataset.
In annotations, there are 2 main types. Beat annotations and rhythm annotations.
Rhythm annotations (aux_notes field) contains rhythm changes. After each rhythm change point, there are empty strings till the next rhythm change.
Does that means all beats after the rhythm change are in the same rhythm till the next rhythm change?
For an example, take a look at the below wave with annotations (202 record of MIT BIH dataset from 21:19 to 21:49).

In the above diagram does the beats between '(N' and '(AFIB' are all normal rhythm beats? and does the beats after '(AFIB' are atrial fibrillation rhythm beats?
Here,

'(N' means a Normal rhythm annotation
'(AFIB' means an atrial fibrillation rhythm annotation

Postscript
You can reproduce the above diagram via this online tool. Parameters are,
Choose input window

Database = MIT-BIH arrhythmia database (mitdb)
Record = 202

View/edit window

Go to = 00:21:19
Window duration = 30 seconds


text:
Square-cubed law and health
Does the square-cubed law lead to possible health detriments for taller people?
I'm not sure what the optimum height is for humans (e.g. due to their cross-sectional bone density constraints), but given the square-cubed law at some greater height wouldn't a human begin to experience health detriments, whether small or large? For example, lets say that the optimum height is 175cm for a male (I don't know what the actual optimum height), wouldn't each marginal increase in height add excessive pressures to the body?
Or is there any sort of allometric plasticity that humans possess to take into account the physical pressures of being taller, making a range of height being optimal?
Any thoughts, opinions, papers on this would be much appreciated.

Can you please clarify why the question is phrased as specific to humans? Would you expect that smaller is always better in all species?

Well it can be applied to any species, but I phrased it specifically to humans because I was curious of any evidence for health implications in the biomedical field.
I should have given moire detail to my question, I'm sorry! I wouldn't expect that smaller is always better in all species, since it would be costly for a species to have a cross-sectional bone density higher than it needs to support its small relative mass determined by its size. I don't know what the optimum height would be to match bone density in humans, but I was hoping that the 150/180cm example got across the question.

here is a paper linking body size and longevity, but it is not something that can easily be applied to humanity as a whole. http://manoa.hawaii.edu/news/article.php?aId=6515

The question is unclear. However, think about it this way: imagine an extreme case, a human who is 2.5 meters tall. I imagine there would be multiple health issues involved, many which would be 'physical' in nature. In fact, this is the case with people with gigantism. Joints would be under strains they were not 'designed for', cardiovascular issues would present too. Things are not linear, which is the crux of the square-cubed law. A heart of diameter of 20cm grows less rapidly than the appendages and circulatory volume of a super lanky person. It would be a simple plumbing/pumping issue.
There are other corollaries: lung surface area increases much more slowly than its volume. This is why lungs have different structures, and indeed, why lungs look as crumpled as they are. A balloon-shaped lung would not do for any large animal.
Also, taller people have a significantly shorter life expectancy. There are very many easily-accessible resources upon querying the Google machine.


text:
Are there any theories using thermodynamics/statistical mechanics or information theory principles to modelling in ecology?
So far, I've only known one: the MaxEnt theory. It uses the maximum information entropy developed by information theorist, which in turn inspired by the thermodynamics from physics, to predict the number of organism in an area. This theory is developed by John Harte.
You can read about this theory in Quanta Magazine.
I also know the book Towards the Thermodynamics Theory for Ecological Systems, written by Jørgensen and Svirezhev.
I find it hard to find another theory similar with the two theories above. Do you know any theories using the thermodynamics or information principles to modelling in ecology?
I have opened a reddit discussion about this.

I'm still not quite sure what you are looking for. Do you want to know about additional theories in ecology that are similar to Harte's MaxEnt? Or are you more broadly interested in the application of thermodynamic principles in other fields?

First question should be prioritize, but the second one is interesting to know too

You might wanna have a look at this paper: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12152/abstract

@Hav0k thanks for the paper. I know what I'm looking for now: theories in ecology that use thermodynamic or information principles to modelling

John Harte's work on applying the mathematical theory of maximum entropy to ecology is certainly one of the better known examples of the application of this area of mathematics to science, in part because he literally wrote the textbook: Maximum Entropy and Ecology: A Theory of Abundance, Distribution, and Energetics (Oxford Series in Ecology and Evolution)
To be clear, maximum entropy (also known as MaxEnt in some of the literature, though most/all researchers use the longer form in publications) is a mathematical tool stemming from the fields of probability theory, statistics, and information theory.  Its use is classically most often seen in thermodynamics, statistical thermodynamics, physics, and information theory, primarily because these were the areas in which E.T. Jaynes was working when he posited the idea. Wikipedia has links to his two seminal papers.But because of it's mathematical form, it can be applied in a multitude of areas, typically where one can utilize probabilistic methods.
If you're looking for additional areas of application, simply google the phrase "applied maximum entropy" and you'll find a wealth of areas including: econometrics, natural language processing, nuclear medicine, queuing systems, mass spectrometry, image processing, machine learning, and many others.
For ecology related work, a cross search on maximum entropy and "genetics", "evolution", "species", and similar words will provide a wealth of papers like "A maximum entropy approach to species distribution modeling".
Given the generic nature of your question, I might suggest that you'll find E.T. Jaynes' paper "On the Rationale of Maximum-Entropy Methods" (IEEE, 1982) useful.
Those generally interested in the broader applications of information theoretic methods to biology will likely appreciate some of the work that came out of last year's NIMBioS Workshop on Information and Entropy in Biological Systems (which Harte both attended and presented at), the BIRS Workshop Biological and Bio-Inspired Information Theory, and the 2014 CECAM Entropy in Biomolecular Systems. The NIMBios Workshop was organized by John Baez, a physicist, who has worked with MaxEnt methods and explored them on his blog "Azimuth".
Those with a more sophisticated mathematical background (including measure theory, functional analysis, etc.) may appreciate Henryk Gzyl's text The Method of Maximum Entropy (World Scientific: Series on Advances in Mathematics for Applied Sciences, Vol 29, 1995).
-- Additional thoughts after the question was edited --
First for those who don't have the background, I highly recommend reading the two seminal papers on information theory and statistical mechanics by ET Jaynes and the standard text on information theory Elements of Information Theory by Thomas M. Cover and Joy A. Thomas.
In addition to the information theoretic related areas, you might want to take a look at the discipline of complexity theory, which has primarily grown out of the Santa Fe Institute over the past several decades and which includes information theory as part of its disciplines. If you're unfamiliar with the broader topic, Melanie Mitchell has an excellent overview with her book Complexity: A Guided Tour. Also related to complexity is the area of cellular automata which one could view as a very base model of more complex ecological systems. Here, perhaps Stephen Wolfram's A New Kind of Science or Cellular Automata and Complexity will be enlightening. The broader theories coming out of these primarily mathematical areas may be useful to you.
In particular, given the types of models in ecosystems, I might suggest taking a look at some of the mathematical modeling going on at the intersection of complexity and economics. For a relatively simple introduction to this area, one could look at the relatively introductory text Complexity and the Economy by W. Brian Arthur which is very interesting. The economy is essentially a very specific type of ecology dealing with human beings, assets, and the monetary system.
Another area which I've seen a lot of literature over the last few years is applicable to the ideas of resiliency and complexity in cities, for assisting in designing more robust city planning. This really isn't that far from the naturally evolving systems being looked at in ecology settings.
For those looking for researchers in the area of complexity, I have a list of many who are on twitter in a variety of sub-areas. In addition to individuals, it also includes a number of institutes and related organizations as well.
I'd also suggest, that for the broadest theoretical setting, one could actually start with the topic known as "Big History" which takes the broadest approach of looking at history and the evolution of the cosmos over 13.7 billion years since the big bang. This conceptualization includes ideas like evolution, complexity, and emergence on the biggest scales, a set of theories that could be similarly applied to ecologies both large and small. For this viewpoint, I would suggest two works by David Christian including Maps of Time: An Introduction to Big History and Big History: The Big Bang, Life on Earth, and the Rise of Humanity.
In essence, with many of these topics and viewpoints, one is treating individual animals or even entire species as elementary particles and then using the mathematical models of statistical thermodynamics to tease out specific types of data or trends. As layers of overlapping "particles" interact with each other, they cause emergent types properties, and then these resultant emergent properties combine to create further layers of emergent properties, none of which might have been necessarily deduced from the initial conditions. Within Big History, these types of emergence go from the big bang and basic particles in the early universe to the ultimate evolution of humankind by way of a variety of stages.

Chapter 10 in Harte's book discuss about the connections between his theory and other theories. Thanks for the link

I have rethought my question and slightly edited it. Glad if you come back and see.

Many of the papers and texts mentioned above will have a wealth of additional references listed in their bibliographies sections.
They're not necessarily ecology-specific, but I've been collecting literature at intersection of information theory & biology/molecular biology.  Textbooks that may be applicable: https://www.goodreads.com/review/list/3250760-chris-aldrich?order=a&shelf=itbio&sort=position. Similarly journal articles in a shared Mendeley group at: https://www.mendeley.com/groups/2545131/itbio-information-theory-microbiology-evolution-and-complexity/.

Thank you so much. I find the NIMBioS link is extremely useful

An alternative way to understand this issue has been ultimately named (in its more recent publications) as Organic Biophysics of Ecosystems. Some of their publications (several of them are available either on ResearchGate or on https://interdisciplinaryscience.es/publications) are (If you are interested, I would advise reading the articles in the exact reverse order of time to that shown below).
This approach uses equations whose mathematical structure is simpler than other models in this field, and which are equivalent in structure to those equations used by conventional physics.
Rodríguez, R.A., Riera, R., Herrera, A.M., Duncan, J.M., Vanni, M.J., Delgado, J.D., González, M.J. 2019. Degrees of freedom: Definitions and their minimum and most meaningful combination for the modelling of ecosystem dynamics with the help of physical principles. Ecological Modelling 392: 226−235.
Rodríguez, R.A., Duncan. J.M., Delgado, J.D., Vanni, M.J., Riera, R., González, M.J. 2018. Additional empirical evidence on the intrinsic trend to stationarity in the long run and the nested relationship between abiotic, biotic and anthropogenic factors starting from the organic biophysics of ecosystems (OBEC). Ecological Modelling 383: 23-30.
Riera, R., Rodríguez, R.A. Herrera, A.M., Delgado, J.D., Fath, B.D. 2018. Endorheic currents in ecology: an example of the effects from scientific specialization and interdisciplinary isolation. Interdisciplinary Science Reviews 43(2): 175-191.
Rodríguez, R.A., Riera, R., Delgado, J.D. 2017d. Ecology: Science or philately? An interdisciplinary analysis of sustainability by exploring if it is possible to get more and more information by reducing collateral environmental damages. Science of the Total Environment 596/597: 43−52.
Rodríguez, R.A., Duncan, J.M., Vanni , M.J., Melkikh , A.V., Delgado, J.D., Riera, R., Herrera, A.M., Camarena Luhrs , T., Quirós , A., Fernández Palacios, J.M., Miranda, J.V., Perdomo , M.E., Fernández Rodríguez, M.J., Jiménez Rodríguez , A., Otto, R., Escudero, C.G., Navarro Cerrillo , R.M., González , M.J. 2017c. Exploring the analytical consequences of ecological subjects unwittingly neglected by the mainstream of evolutionary thought. Ecological Modelling 355: 70-83.
Rodríguez, R.A., Duncan, J.M., Delgado, J.D., Vanni, M.J., Riera, R., Herrera, A.M., González, M.J. 2017b Assessment of ecosystem trophodynamic power: A model based on the power equation for an oscillating string. Ecological Modelling 362: 80-86.
Rodríguez, R.A., Duncan, J.M., Riera, R., Delgado, J.D., Quirós, A., Vanni, M.J., Camarena, T., Miranda, J.V., Perdomo, M.A., Herrera, A.M., González, M.J. 2017a. Thermostatistical distribution of a trophic energy proxy: Extension for modelling energy pyramids at the inter taxocene scale and under non stationary conditions. Ecological Modelling 361: 113−121.
Rodríguez, R.A., Herrera, A.M., Duncan, J.M., Riera, R., Quirós, A., Perdomo, M.E., Jiménez-Rodríguez, A., Fernández-Palacios, J.M., Vanni, M.J., Otto, R., Escudero, C.G., Camarena, T., Navarro-Cerrillo, R.M., Delgado, J.D., González, M.J. 2016c. Response to comments on “Uncertainty principle in niche assessment: A solution to the dilemma redundancy vs. competitive exclusion, and some analytical consequences”. Ecological Modelling 341: 1‒4.
Rodríguez, R.A., Herrera, A.M., Quirós, A., Fernández-Rodríguez, M.J., Delgado, J.D., Jiménez-Rodríguez, A., Fernández-Palacios, J.M., Otto, R., Escudero, C.G., Camarena Luhrs, T., Miranda, J.V., Navarro-Cerrillo, R.M., Perdomo, M.E., Riera, R. 2016b. Exploring the spontaneous contribution of Claude E. Shannon to eco-evolutionary theory. Ecological Modelling 327: 57–64.
Rodríguez, R.A., Herrera, A.M., Santander, J., Miranda, J.V., Perdomo, M.E., Quirós, A., Riera, R., Fath, B.D. 2016a. From a stationary to a non-stationary ecological state equation: adding a tool for ecological monitoring. Ecological Modelling 320: 44–51.
Rodríguez, R.A., Herrera, A.M., Riera, R., Escudero C.G., Delgado, J.D. 2015b. Empirical clues about the fulfillment of quantum principles in ecology: potential meaning and theoretical challenges. Ecological Modelling 301: 90–97.
Rodríguez, R.A., Herrera, A.M., Riera, R., Delgado, J.D., Quirós, A., Perdomo, M.E. Santander, J., Miranda, J.V., Fernández-Rodríguez, M.J., Jiménez-Rodríguez, A., Fernández-Palacios, J.M., Otto, R., Escudero, C.G., Navarro-Cerrillo, R.M. 2015a. Thermostatistical distribution of a trophic energy proxy with analytical consequences for evolutionary ecology, species coexistence and the maximum entropy formalism. Ecological Modelling 296: 24–35.
Rodríguez, R.A., Delgado, J.D., Herrera, A.M., Riera, R., Navarro, R.M., Melián, C., Dieguez, L., Quirós, A. 2013b. Effects of two traits of the ecological state equation on our current understanding of species coexistence and ecosystem services. Ecological Modelling 265: 1–13.
Rodríguez, R.A., Herrera, A.M., Delgado, J.D., Otto, R., Quirós, A., Santander, J., Miranda, J.V., Fernández, M., Jiménez-Rodríguez, A., Riera, R., Navarro, R.M., Perdomo, M.E., Fernández-Palacios, J.M., Escudero, C.G., Arévalo, J.R., Diéguez, L. 2013a. Biomass-dispersal trade-off and the functional meaning of species diversity. Ecological Modelling 261/262: 8–18.
Rodríguez, R.A., Herrera, A.M., Otto, R., Delgado, J.D., Fernández-Palacios, J.M., Arévalo, J.R. 2012. Ecological state equation. Ecological Modelling 224: 18–24.

it's a little weird to respond with just a long list of your own papers. Not that I discourage people with specific expertise from participating, but using expertise to break down a complex topic into a simple and direct answer is preferred.

"Some of their publications (...) are" -- Are what?

Hey Ricardo, thanks for the answer and for bringing your expertise to Bio.SE!  However, if you don't expand this answer to at least explicitly demonstrate/summarize how any of these papers answer or are are related to the OP's question, then this post will continue receiving negative votes and may even be marked as "spam" (only to promote your work). Please expand your answer so that the OP or future users actually receive an answer without having to leave this webpage. Your citations should remain as a source of additional details, but you need to expand your answer to avoid deletion. Thx!


text:
The use of proteins in memory creation
I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some articles which say, and I quote the article just linked

Memories are made by messenger RNA (mRNA) that encode β-actin protein.

Now, correct me if I'm wrong but proteins of any sort have mass. So, why following this rule of proteins being used to create the memory does our brain not grow in mass with each memory we create/ encode. And also, if our memories are encoded using proteins, why can neurodegenerative  (E.g. Alzheimer's) cannot be cured by artificial proteins in the same way we use insulin. I quote again,

memories were merely out of reach

full article
Surely this means that, it is possible to, by using artificial proteins or possibly electrical stimuli we could recover memories. Or have I wandered off on a wrong track here? Am I correct? Or are my concepts of memory slightly wrong?

Read about synapses; you'll be clear ..

I think its important to mention that the particulars of memory storage in the brain are still being worked out.  I think what we do know about it is that memory storage depends a lot on the physical configuration of the neurons in the brain.  They move about and make new connections as they process information (and probably also when they are not processing information!).  Different regions of the brain store short vs long term memory and different sorts of memories.  They neurons themselves have a lot of internal cell physiology that can change as well - there are many different neuroreceptors that constitute the synaptic junctions.
All these things may not be a comprehensive list.  But at the basis of all these processes, the cell expresses new proteins in mRNA and these proteins are doing all this work.  beta-actin and histone de-acetylase, as mentioned in your link, are responsible for the cell rearranging itself in the cell shape and in terms of its internal transport processes and in the nucleus respectively.
I'm pretty sure that exactly what is happening here is not really well understood.  monitoring the interior of the cell is difficult.  The work where histone deacetylase is inhibited is a fresh new thought, showing that the arrangement of the chromosomes in the nucleus is involved in hiding memories.  Its still the equivalent to getting a stopped watch to start again by shaking it - there are parts there that fell into place and started ticking again, but we don't really know what the parts are doing in any detail yet.
This hints that if you were to disrupt the cells in some ways you might be able to free up memory, but its a long way from guaranteeing that any given approach will work.  I'd be surprised even if Dr Tsai's cell treatment worked even 70% of the time in her experiment.  Hypnosis or a focused meditation session might still be just as effective.  I think that its a bit too much to expect that Alzheimer's memories are completely preserved and recoverable.  In some cases probably, but categorical statements rarely hold in bioscience.
Like a lot of neuroscience, this work is suggestive, but still just progress towards a clearer understanding of these processes.


text:
What are some useful physical information of a protein?
Beside energy and heat, I don't know any useful physical information of a protein. Can you help me list some of it. Somethings like Fourier-transform infrared spectroscopy to provide protein structure aren't what I'm looking for.

What about the sequence and the 3D-structure? This is important information...

Please clarify what kind of information you are looking for.

Somethings like energy, heat, entropy, which are physical measurable things. The structure is a good point, I don't know what the sequence information are.

sounds like you mean 'typical means of monitoring the folding of a protein' or something like that?  such a question would work...

Something like that. I need some new conceptions to research deeper.

I'll make a list, by wavelength then 'others'.  This is only the most common techniques list.  i'd be here all week if I tried to get all the applications.  Scientists are crafty and are always coming up with stuff.
Electro magnetic protein derived measurements:

NMR spectroscopy (radio) - can detect the structural variations in
the individual amino acids allowing a protein structure with the
dynamics of the peptide chain to be modeled.
IR spectroscopy - can
look at bond-bond vibrations.  Mostly used to observe for non-peptide
moities and cofactors of the protein like heme in hemoglobin for
instance.
RAMAN spectroscopy - also an IR spectroscopy, but which
can look for dynamic qualities of the interatomic vibrations.  Like
IR this is used with cofactors usually and not the protein, which
looks very much the same over most of a peptide.
UV/visible spectroscopy - on the low end, examine the behavior or concentration of chromophores associated with the protein.  used for kinetics - study of enzymes in the act of catalysis.  On the high end can also be used for things like watching photon-energy transduction in photosynthetic systems and things like this. The peptide itself has no Visible absorption, but the colored molecules are often used as a probe to watch the peptide in action - like folding.
FRET is a technique that can measure how far apart two colored labels are - two separate points of a protein are labelled and a distance measurement obtained.
UV circular dichroism.  the aromatic side chains of Phe, Trp, Tyr, His etc absorb in the UV and are directly observed to follow folding some times.  Circular dichroism looks for differences in the absorption of right and left circularly polarized light and can show secondary structure.
X-ray.  Scattering of proteins in solution can measure the so called 'radius of gyration' which profiles the overall shape of the protein.  X-ray scattering off of 2D and 3D crystals can reveal the molecular protein structure.

Others:

Calorimetry.  By tracking the heat capacity/heat given off/taken in by a protein, its folding state, binding and other structural characteristics of a protein sample can be measured.
Mass Spectroscopy - generally this just measures whether a protein is present, by fragmenting it and measuring the mass of the fragments.  useful for mixtures of many proteins (like a living cell).
Peptide sequencing - like Mass Spec, but often used when there is just one protein in a pure sample.

There's lots more - just depends on where you want to cut off the list.  Hopefully this is a good start.

All the information about a protein, biochemical or functional is encoded in its structure, which are primary (Amino Acid (AA) sequence), secondary (alpha helix or beta pleated sheet), tertiary (overall 3D structure of a single peptide) and quaternary (overall 3D-structure of a protein composed of multiple peptides which are attached together through various different bonds) structures (http://en.wikipedia.org/wiki/Protein_structure).
Obviously, the key determinants for all these structures is the AA sequence of a protein, since that determines the biochemical property of a protein as well as its function (e.g. enzymatic residues and active sites, functional domains, motifs, whether it is post-translationally modified or not by phosphorylation and whether that causes its activation or inactivation through conformational changes or its interaction with other proteins etc).


text:
Why do flipped cockroaches sometimes lose their heads?
Sometimes I see in my house there are flipped cockroaches whose lose their heads. I used to have a cat, but there is no pet in my house anymore so I think it's only ants can be involved in this. But if so, the headless cockroach should be preyed already. Is there any explanation for this?

In all likelihood, it is your cat who crunches the cockroach's head once it catches it and/or finishes playing with it.
Ants do eat bugs but they are usually not so selective that they'll carry off the head alone. With more manageable insects, they carry the whole thing off; otherwise they take it apart and carry it away in pieces if they're interested in it as a food source.
If you watch a cat with a mouse, chipmunk, bird, large insect, etc, they often seek to kill the animal with a throat or nape bite if they are done 'playing' with it. I've found headless prayer mantises and other large insects in my garage many times, and have seen my cats beheading them.
The techniques that cats use to kill prey vary with prey size

I found a clip in YouTube showing a cat eats a chipmunk's head. Does it swallow the cockroaches' heads or just beheading them? Why they bother to kill them when they don't even eat them?

Sometimes they eat the insect's head, sometimes they don't. They have instincts that are unrelated to hunger. For example, dogs love to chase moving objects. That's great when it's a frisbee, but not so great when it's a child. Cats have this instinct as well.

Today I found a headless cockroach in my house again, even though my cat has gone. Do you have any explanation for this?

@Ooker - Nope. none. What do other cockroaches eat?

I don't know. Maybe food trash?

Maybe dead cockroach heads...?


text:
How is the Energy Systems Language used in ecology?
Is the Energy Systems Language useful in systems ecology? It is developed by Howard T. Odum, "the father of system ecology", to make analogies between ecological systems and electronic circuits. But how far this analogy remains correct? What important results have been found from it? Is it widely used by ecologists in other subfields? If yes, then why isn't it applied to other fields?

Related: What are the branches of system ecology?

Energy systems language is definitely still used in systems ecology, ecosystems ecology, and ecological engineering. It can be used in other aspects of ecology depending on the approach of the ecologist, some ecologists appreciate it more than others. For a broad snapshot of how science is currently building upon Odum's 1983 Intro to Systems Ecology, check out a Google Scholar search for the latest papers citing that text by Odum.
In my experience with it, energy systems language and energy flow diagrams introduced by Odum are used as helpful conceptual tools: understanding and organizing complex systems qualitatively and then potentially quantitatively; putting useful constraints and guidelines on brainstorming the effects of adjustments to complex systems; etc. This can be done in a teaching context, helping students understand systems and bridging the fields of engineering and ecology. It can also be done in a high-level professional context, sorting out the intricacies and potential solutions of very complex environmental problems.
I find that energy systems language is used most wherever the study of complexity and ecology intersect. This is especially true in the study of ecological complex adaptive systems and in studying agro-ecology. Even in those cases it depends on the ecologist in question: those with more of an engineering background tend to appreciate Odum's framework, whereas those without an engineering background may rely on other frameworks.

Can you list some other frameworks? What are the differences between them?

@Ooker Outline of ecology lists various ones, especially Landscape Ecology under "Level of Complexity" and all those under "By technique used for investigation" and "By environmental approach". Those all offer distinct ways of exploring ecology, and the same ecological phenomenon could be explored quite differently using those different approaches & frameworks (systems ecology being one of them). The eco-involved interdiscplinary fields will often have frameworks from the discipline(s) they combine with ecology, e.g. accounting in eco-econ.