text:
How does imatinib recognize the constitutively active Abl-BCR even though it binds to the inactive conformation?
In chronic myelogenous leukemia (CML) ABL-BCR is constitutively active (always on) and it can be inhibited by imatinib and dasatinib. A study says that imatinib binds to the inactivated state of the (Abl) enzyme while dasatinib binds to the activated state of the (Abl) enzyme (i.e. can recognize multiple states of the enzyme).
from the study I concluded that Abl is studied as a model for Abl-Bcr fusion protein but What I don't get is :
How can Abl-Bcr be constitutively active and can be recognized in multiple states (activated and inactivated)?
Thanks

Can you please add links to these studies you cite?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513788/

Should your question maybe be: How does imatinib recognize the constitutively active Abl-BCR even though it binds to the inactive conformation?

Briefly: According to the paper you are linking, Abl-BCR is not "recognized" by the drugs in the active or the inactive state but rather it assumes a conformation that is similar to the active or inactive state of Abl once the drug binds. Simply put: the paper does not study what conformation Abl was in before the drugs bind, they rather discuss the conformation after the binding of the drugs.
Just to provide some background: Abl is activated by fusion to BCR because the regulatory part of Abl gets damaged such that the tyrosine kinase is constituously active. This damage is in the regulatory part of Abl and not in the nucleotide binding pocket (the part where the drugs bind and the part that strongly changes conformation between the active and inactive states).
Both imatinib and dasatinib (like other kinase inhibitors) are competitive inhibitors that bind to the ATP binding pocket. This means that both drugs occupy the ATP binding site, preventing ATP from binding and the ABL protein from executing its kinase activity no matter whether it is in the active or inactive state.
The difference is that imatinib binds to (and blocks) the pocket where normally the phosphate groups of ATP bind, forcing Abl (and Abl-BCR) into a conformation that is similar to the inactive state. The drug can still bind to the active state but upon binding, Abl changes its conformation and then looks similar to the inactive state.
Dasatinib on the other hand binds to (and blocks) the part where normally the base of ATP binds. This part does not strongly change its conformation between active and inactive state and thus dasatinib should be able to bind to both active and inactive conformation. However note that the ability of dasatinib to bind to either conformation is simply a hypothesis they state in the paper and is not substantiated by data (in fact they themselves say that the data indicates that dasatinib binds stronger to the active conformation).
Note no matter which conformation the protein has (active or inactive) it cannot perform its function as soon as any of the competitive inhibitors binds because the inhibitors block the ATP binding site and without ATP, Abl cannot phosphorylate anything because ATP is the source of the phosphate group which Abl would normally transfer to its target.
Some more background on how Abl works: Abl is a tyrosine kinase which means that it transfers a phosphate group from ATP to a tyrosine residue to its target protein. Also: Abl has some regulatory parts that control whether it performs its tyrosine kinase activity. In the inactive state it will not do anything even in the presence of ATP and its target protein. In the active state, it still needs ATP and its target protein to perform its kinase activity.

but don't you see that "recognize multiple states" means it was inactive or active before binding  ?

I adapted my answer to try to be more clear as to why it is completely irrelevant for the function of the drugs whether Abl was in the active or the inactive conformation before the drug binds.

I'm convinced with your explanation, concluding that: ATP binding site can occur in the active and inactive conformation while the enzyme is still activated by means of absence of it's regulatory part which has different binding site from that of ATP.

My score prevent me from upvoting :D

You're welcome, thank you for your valuable information.


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What was the precursor of testosterone?
Testosterone evolved about 500 million years ago (says 8fact.com). What was the precursor of testosterone (if any)? If possible, what caused the 'precursor' to evolve?

This question is very vague and I am unsure if you are really familiar with how sex hormones work. Why would testosterone prioritse sex per se? What have you already learned about the functions of testosterone in the (presumably human) organism? What hypotheses do you have based on that knowledge? Please clarify by editing your question.

Testosterone drives sex drive and has a role in starting puberty and producing sperm. How could that not encourage sex?

Organisms that do not produce testosterone do also produce sperm. Testosterone is definitely not needed for sexual reproduction at all. For me this question does not make sense.

Yes, but that is not my point. It still has a role in sex, does it not?

Just because you do not understand my question doesn't mean you should downvote it. I have put a lot of effort into editing, which by the way got rid of the question you didn't understand.

If you ask a precise and understandable question I will remove the downvote for sure. As is, I do not see any informative discussion coming out of a question as vague as this (no reference for the fact, what do you mean by precursor?, how could one - even theoretically - know what this precursor was? this is not how evolution works, the reason for evolution of a more than 500 MY old precursor is more a matter of opinion than fact, the relationship between the function of testosterone in the human body and sexual reproduction, ....) which in my view qualifies for a downvote.

If you do not know the answer, don't answer. It's that simple. No one forced you to answer so don't pull out that excuse. The word precursor is the analogue of ancestor, and only part of my question is (possibly) opinion based so there is no reason to dismiss it. Testosterone plays a major part in the sexual development of human males such as driving libido (sex drive), starting puberty and producing sperm. Just tell me how that is not related to sex. Answer my questions before you continue adding more to your argument.

Please add a citation that people can actually read. Your link simply redirects to what appears to be an advertisement for an app called Cookie, which I do not intend on even looking at, let alone downloading. There are plenty of web sites out there.

It says right on the page now linked in your question that testosterone developed from estrogen. So what's your question?

Someone else added that on and I did not know that existed so that know makes my question obsolete.

Welcome to Biology.SE
The question suggests that you have important lack of knowledge in Biology (which is fine). It will be impossible to explain everything in a post. I therefore just provide a short answer and redirect you to some source of knowledge that will be necessary to read for you to really be able to understand the basis of molecular biology and evolutionary biology.
Short Answer

Testosterone cannot 'evolve' per se because it is a hormone, right?

Testosterone is a chemical that is synthesize by our body. This synthesis is regulated by proteins which are coded in our DNA. The sequences in our DNA that code for proteins is called a gene (quickly speaking).
So, a mutation in a gene (or in a regulatory sequence) can impact the synthesis of testosterone and therefore be under selective pressures.

Was it to prioritise sex and in turn pass on your genes?

I don't understand what you mean by "prioritise sex". But yes, those individuals making efficient synthesis of testosterone and good use of this signalling molecule had/have a higher fitness.

Did the evolution of testosterone happen because of sexual reproduction?

Testosterone is directly used for sexual dimorphism, so in this sense it evolved in its current form because genders exist. However, the evolution of hormone synthesis (and related biochemical pathways) do not require sexual reproduction (asexual reproduction being the alternative).
Source of Information
I will recommend free online resources.
You should start with a basic understanding of the cell machinery. Make sure to really understand what DNA, RNA, proteins are and their relationship. I recommend Khan Academy > Biology. It is a long series of video, so I particularly recommend series on the so-called (and poorly called) central dogma.
Then you might want to have a look at Understanding Evolution (by UC Berkeley), which is a very introductory course on evolutionary biology.

I know about translation and transcription but I do not think you get what I am saying. Firstly, you did not answer my main question 'how did testosterone come to be?' and secondly, how exactly does my question demonstrate a lack of knowledge?

Maybe I misunderstood indeed. I thought you had an important lack of knowledge and you seemed to not understand the relationship between DNA and the synthesis of a hormone. Can you please further what you mean by "how did testosterone come to be?". For the moment this question is very unclear to me. Are you interested in the precursor of the current form of testosterone?

Yes, that is what I am essentially looking for the precursor of testosterone. Plus, I edited my question to make it short and concise.

I would advice that you edit the post to specifically say something like "Testosterone evolved about 500 millions years ago (citation). What was the precursor of testosterone (if any)?". For the moment, the expression "How did testosterone come to be?" is still unclear IMO.

I have edited the post now, thank you for your contribution and help. I sincerely appreciate it.

Thanks for the edit. Can you please add the link to 8fact?

Let us continue this discussion in chat.

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How to calculate apparent diffusion coefficient (ADC) with example?
Can someone give an example calculation for the apparent diffusion coefficient (ADC)?
There appears to be multiple ways that this can be calculated, e.g. as discussed here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166577/

Do you like R ? if so, look at this package "dcemriS4"  and its example http://www.inside-r.org/packages/cran/dcemriS4/docs/adc.lm
install.packages("dcemriS4")
install.packages("minpack.lm")
library(dcemriS4)
library(dcemriS4)

S0 <- 10
b <- c(0, 50, 400, 800)  # units?
D <- 0.7e-3              # mm^2 / sec (normal white matter)

## Signal intensities based on the (simplified) Bloch-Torry equation
dwi <- function(S0, b, D) {
  S0 * exp(-b*D)
}

set.seed(1234) # this is just to make the example reproducible
signal <- array(dwi(S0, b, D) + rnorm(length(b), sd=0.15),
                c(rep(1,3), length(b)))
ADC <- ADC.fast(signal, b, array(TRUE, rep(1,3)))
unlist(ADC) # text output
par(mfrow=c(1,1)) # graphical output
plot(b, signal, xlab="b-value", ylab="Signal intensity")
lines(seq(0,800,10), dwi(S0, seq(0,800,10), D), lwd=2, col=1)
lines(seq(0,800,10), dwi(ADC$S0, seq(0,800,10), ADC$D), lwd=2, col=2)
legend("topright", c("True","Estimated"), lwd=2, col=1:2)

Here you can see an example of the steps used for mir http://rsl.stanford.edu/moseley/tensorcalc/tensorcalc/Steps/ADCmaps/adc.html
here is to understand the math behind of its calculation
http://www.ajronline.org/doi/full/10.2214/AJR.12.9231
if you don't like R but you like Matlab, here you can use this code to calculate it in Matlab http://www.mathworks.com/matlabcentral/fileexchange/21130-dti-and-fiber-tracking/content/DTI.m one of the output is ADC for mir data

I think you should explain the principle behind the calculation rather than posting a code. The code is of little value in this site and if the OP is actually interested in coding then this is not the site for such questions. I guess that is not the case here.

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Are antibiotic-resistant bacteria necessarily less virulent than their original strain?
In the absence of antibiotic treatment, is there a reduction in the average severity of disease caused by resistant strains of pathogenic bacteria compared to wild-type ones?
I would assume that bacteria that have adapted to be able to withstand antibiotics would have to allocate extra resources in order to counter the antibiotics, making them perhaps less growth-efficient than the "original" (non-resistant) strain.

This question is rather vague and unclear, and cannot be succinctly answered in its present state. There are a very large number of pathogenic bacteria (let alone other microbes), a large number of antibiotics, and a multiplicity of routes to antibiotic resistance. Please [edit] your post to focus on a single strain of bacteria and preferentially a single type of antibiotic. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much.

I've edited it slightly to narrow the scope; I think it is answerable now (and I'll have a go at answering it if I have time later). It's arguably a duplicate of this, though: http://biology.stackexchange.com/questions/14350/can-antibiotic-resistant-bacteria-compete-with-normal-one-in-an-antibiotic-free?rq=1


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What are extracellular matrix pathways?
I was reading a research paper dealing with acute myeloid leukemia and the term "extracellular matrix pathway" came up. What does it mean? I found literature on extracellular matrix, but I'm not sure what the "pathway" indicates.

Can you add a link to the paper? This might help.

@Goldname read this one, http://joe.endocrinology-journals.org/content/209/2/139.full

Sorry, I can't link it because the paper is not available online yet

Can you at least [edit] your question and add a paragraph or two of context?


text:
Insect making continuous sound in summers
In deciduous to tropical-deciduous forests and residential places with such vegetation I have found this insect to make continuous sounds all through the day (even in nights sometimes) during the summers. Average summer temperature > 30 C around noon and ~ 28-29 around nights with high humidity.
I want to know what is the reason they make this sound ?
Recently, I found several of them dead near light poles etc..., and some sit very close to windows of air-conditioned rooms. I think they want some cool environment.

These are Cicadas, of the superfamily Cicadoidea of the order Hemiptera.
These sounds are made by the males to attract mates. There are a lot of species, each making there own specific sound to attract the right mate. However, to the human ear, these sounds don't sound different. Cicadas are also able to produce other sounds, in distress or during courtship and mating, but the continuous sound during night and day is to attract mates.

As a resident of Costa Rica, especially one who's seen plenty of these, I can confirm.

Two minor points – most cicadas (there are exceptions) don't sing at night (other than dusk) unless conditions are unusually hot and humid along with an unusual light source such as a full moon.  Nighttime sounds tend to be crickets, katydids, and frogs.  Also, most species-specific cicada songs can be recognized by the human ear with a little practice/attention.

These are definitely cicadas and mating is the primary reason for their long calls. As for the reason you've found many dead or dying cicadas, their lifecycle is primarily spent underground where they feed on tree roots. They will emerge and transform into their adult form which enables them to make their calls and mate, and many species die shortly after mating, having fulfilled their evolutionary function of reproduction. Some species spend up to 10+ years underground before emerging to mate for only a short week or so.


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What percentage of a Neanderthal's DNA could be in a Denisovan?
My questions arose from an online course video at 3:11-19
The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70% Neanderthal's DNA, there was found mixing between Denisovans and an even earlier mysterious species.
The followings are my questions:

Did he mean that most of Neanderthals were prone to inbreeding? Why?
I'm not sure if that was exectly what he meant by 70% Neanderthal's DNA could exist in a Denisovan. If that were true, why not just called it Neanderthal if only 30% is not Neanderthal?

You should be very careful trying to conclude something from what is known about Neandertal genetics.
To answer question 1: NO! This is probably not what he meant. To date, we have only two high-quality full genomes of archaich humans, one being the (Neandertal from Denisova cave, called Altai Neandertal (Prüfer et al., 2014)) and one being the (Denisovan from Denisova cave (Meyer et. al., 2012)). From this sample (which is exactly one Neandertal) you cannot draw conclusion for the whole population. It seems, however, that this Neandertal individual from the Altai Mountains was indeed inbreed (high runs of homozygosity in the genome) - it does, however, not even tell us in what way her parents were related. Prüfer et al. (2014) write

We conclude that the parents of this Neandertal individual were either half-siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson.

You cannot say more. You also cannot say if this was due to preference in mate choice, or caused by the fact that this group was very isolated, or  that this population had an extreme small effective population size (note that it is debated whether the last two effects are actually equivalent).
To make a long story short: based on the available data it is not wise to draw general conlcusions about Neandertal mating behaviour. Altai is the only example where direct inbreeding could be shown, all other genetic data from Neandertals suggest that genetic diversity was just low.
To answer question 2: I do not really know what this means, 70% Neandertal DNA in Densiovans. I can just generally tell you something about Densiovan-Neandertal differences. The Densiovan might be the only (at least mammal) species that was defined based on genetic information alone. Alle that was found were a few teeth and a pinky bone. People thought this was another Neandertal. After sequencing the DNA from that bones to high coverage (vaguely, a measure of qualtiy), one found that the DNA falls both outside the variation of modern humans - showing that this was not a Homo sapiens, but interestingly it also clearly falls outside the variation of known Neandertal sequences - showing that this was not a Neandertal. It also became clear that Densiovans are more closely related to Neandertals than to modern humans (you might now ask yourself how this is possible with just one genome. In fact, there are more genetic data availabe: low coverage genomes, exome sequences, mtDNA and all of them show the same thing: Neandertals and Densiovans are different but more closely related to each other than to modern humans). Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans).
Long story short: There seem to have been admixture events between Denisovans and Neandertals but I do not know how to relate this to the 70%. Prüfer et al. (2014) detected about 0.5% contribution from Neandertals in Denisovans.
One last comment about this mysterious species (nobody says it but most people think of Homo erectus): again, Prüfer et al. (2014) found some interesting patterns of derived allele sharing between present-day Africans, Denisovans and Neandertals (this should be equal for African-Denisovan and African-Neandertal comparisons, but present-day Africans share about 7% more derived alleles with Neandertals than with Densiovans - even 13-16% in alleles fixed in present-day Africans). This is either ancient population structure (however, with very deep lineages) or, as suggested in the paper, due to gene flow from a (genetically) unknown archaic hominin into Denisovans.
I hope this clears things up a bit. Feel free to ask in the comment and I will edit the post as it might be a bit unstructured.

Can you explain about what you mentioned --"Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans)"--     As what you said ,It seems both species have rather low genetic diversity, but with whom we are comparing ?  Does that mean there is a mistake in the video ,which mentioned -- the Denisovans were very diverse--?And also being against the quote from the link you give --several gene flow events occurred among Neanderthals, Denisovans and early modern humans--?

I compare genetic diversity between 'relevant' species that have a comparable evolutionary history and are closely related, i.e great apes: chimpanzees have about 3-4 times more genetic diversity than present-day modern humans (and other apes even more). I have not seen the whole video, so I am careful calling it a mistake. In the Meyer (2012) paper cited above you will find evidence that the genetic diversity in Denisovans was by far lower than that in present-day modern humans. And yes, there seem to have been multiple gene flow events.

Thanks for your reply ,but I still not understand :Why couldn't  "multiple gene flow events" relate to "high genetic  diversity'' ? Aren't they equivalent ?  To quote-- present-day Africans share about 7% more derived alleles with Neanderthals than with Densiovans--(I conclusively say that it means we are more relative to Neanderthals than Denisovans ) and-- It also became clear that Densiovans are more closely related to Neanderthals than to modern humans --Can I say that Neanderthals were tend to interbreed so their genetic diversity were higher than both modern humans and Denisovans?

You are mixing up some concepts there. 1. Gene flow does not automatically cause genetic diversity. If you have gene flow between hypothetical identical populations, the diversity stays constant. Neandertals and Denisovans were closely related - gene flow obviously did not lead to excess diversity in any of them as both populations lacked high levels of diversity. 2. The 7% shared derived alleles do not mean that Neandertals and humans are more closely related than humans and Denisovans - they just share some haplotypes. In fact, humans are equally related to Neandertals and Denisovans.

(continue) 3. You cannot say that Neandertals tend to interbreed (see my answer. The high quality genome available just happens to come from an inbreed individual. You will find inbred individuals in almost any population, also in present-day modern humans. You must not generalise this to the whole population.) 4. Inbreeding does not cause  genetic diversity. In contrast, inbreeding decreases genetic diversity as closely related individuals share alleles by descent so you will have a lot of homozygous sites in inbreed individuals (homzygosity is proxy for genetic diversity).


text:
What is the actual storage form of energy in muscles? ATP or Glycogen?
I was asked this question in my latest exam. I think the answer is Glycogen because ATP doesn't store energy for a long time so it isn't the ACTUAL storage of energy. Some classmates argue that in muscles there are other substances, not only glycogen, that are used to produce ATP. In the process of contraction ATP is required so, they say, the question needs the answer to be ATP. Could someone please clarify this discrepancy?

This is a typical MCQ which in order to answer you have to have been at somebody’s lectures or be able to read his mind. The antithesis of education! Cells don’t store energy like car batteries.
Glycogen in muscle is a store of carbohydrate. It can be used to generate ATP if it is broken down to glucose and the glucose glycolysed. I wouldn’t have chosen this as an answer.
The concentration of free ATP in the muscle cell is not sufficient for it to act as store of a high group-transfer potential compound (which is presumably what the question means by energy). This is definitely not the right answer.
However if creatine phosphate (a.k.a. phosphocreatine) was a choice on your MCQ, that was probably the answer expected as it is used in muscle as a storage molecule which can be rapidly converted by creatine kinase creatine and ATP.
PS
As you say in your comment that the only choices were ATP or glycogen, then glycogen is what is expected.

OK, David, but I didn't have creatine phosphate as a choice I had ( Glucose - Glycogen - ATP) , and you have jus told me that the latters are wrong and I don't think that glucose is the correct answer, but the question really confuses me. You said that Glycogen is broken down to generate ATP, why wouldn't you chose it as an answer then?

Because It's a two-step process to get ATP from glycogen. However if there's no creatine phosphate choice I imagine that's the expected answer. My point is you should be able to understand and describe a process. For example, if I asked you to describe what happens when muscle glycogen is exhausted (no MCQ), would you be able to?

I would be able to describe what happens, but the MCQ confused me, so anyway thank you, David.

You're welcome Asmaa, and don't mind me. I detest MCQs, but fortunately don't have either to answer MCQs or (any more) to set them. However you have no choice but to play the system. Just try to see the big picture as well.

If you are only given glycogen and ATP as choices, then glycogen is the correct answer. The reason for this is, that muscle cells need ATP also for other very important processes (such as keeping the membrane potential stable and preventing cramps). Thus, while ATP is the actual fuel that powers myosin to create the muscle force, the cell needs to keep the ATP concentration constant in order to avoid negative impacts on other metabolic processes. Therefore glycogen is the actual energy storage.
However glycogen is not the only energy storage used in muscles. The muscle actually uses a quite clever energy management system:
During the first 2-7 seconds it uses phosphocreatine (or creatine phosphate) to quickly replace used ATP (as mentioned in the answer by David). This means a 100m Sprint can be almost completely performed using this energy storage system.
For the next ~30 min (but can be up to several hours for well trained endurance athletes), the muscle relies mainly on energy stored as glycogen. The glycogen is broken down into glucose and the glucose is then converted into glucose-6-phosphate and then ATP during glycolysis. Glycolysis creates ATP much faster than oxygen respiration. However, a side-effect of this is that glycolysis generates lactic acid which is further broken down by oxygen respiration, and in the liver. Overtraining can cause lactic acid accumulation whcih can acidify the muscle and cause lactic acidose
There is much more energy stored in glycogen than in phosphocreatine which also makes this the more likely answer to your question.
Finally, after glycogen stores are depleted, the muscle needs to reduce its energy output and rely on external energy provided by the liver and by fat reserves of the body. This is the reason why some trainers claim that you need to exercise for more than 30 min to start burning fat and thus to reduce weight but this is wrong because the glycogen stores in the muscles are also restored using energy from body fat (which means that the best and only way to loose weight is to burn more energy than you consume either by increasing exercise or reducing food intake or both).

ATP is the end result of breaking apart glycogen. This isn't a trick question, it's in every textbook that glycogen is a primary store of "will soon become ATP" materials, like glucose.
The keyword here is "primary," as there are other ways of getting and storing ATP... that is, putting oxygen and glucose into the cells, and then there is always glycolysis, which doesn't use oxygen (makes lactic acid which is why muscles burn during weight training, because there was no more oxygen for cellular respiration).
But glycogen breaks down fast, and holds thousands of calories, hundreds in the muscles alone, so it is the primary store of ATP.

What is the storage form of ATP?
Answer: Creatinine phosphate

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text:
Beta Sheets vs Alpha Helix - Strength
Is there a hard and fast rule of which one is stronger than the other, or does it depend on their context in a protein?

The mechanical stability of a protein (I am assuming by strength you mean mechanical stability) depends greatly on the general context and there is no clear connection between alpha helix or beta-sheet content and stability. For example fibroin, one of the main components of spider silk and one of the strongest proteins known, consists mainly of beta sheets while keratin another very stable structural protein (the stuff hair and fingernails are made of) consists of four alpha helices alternating with three beta turns is believed to get most of its strength from hydrophobic interactions within its alpha helices. Also, actin and myosin muscle fibers consist mainly of alpha helices. The list goes on and on with no clear pattern which secondary structure forms more stable proteins.


text:
Examples of biological turing machines
Are there any examples of biological Turing machines? And what can they do?

Take a look at: https://www.quora.com/Is-DNA-a-Turing-machine or http://www.nature.com/nrg/journal/v13/n7/full/nrg3197.html.

Welcome to BiologySE and thanks for your question! It always helps by adding references and some background information so that others can understand what you're asking - and it will strengthen your question.

Are you asking for "natural" Turing machines or artificially created ones?

Hm interesting question. I think natural Turing machines would be way more interesting. But both are interesting.

There have been several Turing machines constructed using DNA computing. One of these machines has been used to solve the boolean satisfiability problem, another was used to solve the bounded post correspondence problem, both NP-hard combinatorial problems which are difficult for conventional computers to solve.
Also, a DNA computer was constructed that plays the optimal strategy in tic-tac-toe.
DNA computers store information in DNA sequences and perform calculations by DNA baseparing and other molecular biology strategies. In principle, DNA stores Information much denser than any modern hard drive and uses orders of magnitude less energy per calculation than a conventional computer ($10^{-22}$ vs $10^{-10} \frac{J}{operation}$) however, so far i/o is slow and calculations are comparatively error prone, limiting the practical use of DNA computing.
Also, a recent article has demonstrated that molecular motors can perform basic addition and solve the NP-complete subset sum problem by exploring nanolithographically fabricated networks. This could also, in principle, be used to construct a turing machine.

Thx, that's about artificial ones. What about Turing machines in nature?

Well, the brain most likely fulfills the criteria for a turing machine on some level. Also, there is this very nice answer to the question "is DNA a turing machine" on quora. That details how protein biosynthesis could be viewed as (almost) a turing machine. Finally, transposons fulfil many of the criteria of a turing machine. However, none of these examples are turing complete, except maybe for the brain but there it is not well understood how.

Thx very interesting.


text:
Do animals' facial expressions have similar meanings to humans'?
In the following pictures, the dog seems to be smiling to the camera. People staring at these picture also tend to feel comfortable and relaxed, presumably because they think it's very happy playing with the swing.
However, my question is, is the dog really happy, or we are just (incorrectly) interpreting the dog's facial expression according to our experience used to read humans' facial expression?

Not a scientific article but a pretty good answer: http://www.smbc-comics.com/?id=3172

I have no reference, so this is not an answer, but when I was a veterinary student I was told that the dog smile as illustrated above is seen only in dogs, and is only used to humans.  It is apparently true that dogs can discriminate smiling humans from a blank face, so the leap is not completely ridiculous.

I would say no, facial expressions in humans do not generally relate to facial expressions in other animals. Even though there are some cases (as described in the comments an previous answers) that refer to domesticated animals, I do not know of any convincing evidence that the facial expressions of humans are faithfully interpreted, or even mimicked, by other animals - at least outside the group of great apes. Further, the cases arguing that (domesticated) animals can do it are often anecdotal (I am not saying wrong!). Taking an evolutionary perspective, I would not even expect it to be happening (or rather by very close relatives only, i.e. other great apes) because facial expressions as behavioural signals are part of communication and therefore often rather species-specific.
But not only that ... there is emerging evidence that facial expressions are not even interpreted uniformly in all human populations: in this article by Crivelli et al. (2016) in Front. Psychol. the authors argue to include anthropological data to cognitive studies. According to their findings, not including a human evolutionary perspective might result in strong biases. They strengthen their point by giving an example of differential interpretation of facial expressions in a Melanesian society which is described in more biological terms in PNAS [Crivelli et al. (2016)]. What they found is that adolescents of this society interpret a facial expression (gasping face) that in other societies conveys fear as a threatening and angry expression.
Generalising this means that if there is divergence in signaling by facial expressions even among human populations, I would consider it unlikely that there is a general homologous system of facial expressions among mammals. There might, however, be a trend in domesticated animals to understand human expressions and adapt behaviour according to them. It still is an extraordinary claim to infer from this that they can actually mimic these expressions, and I have not yet seen convincing evidence for that.

Our cousins in the primate world share the same base facial expressions as we do, happy, sad, disgust, etc; it would make sense that other mammals are capable of facially displaying emotional registers.
However, canines can't pass the mirror test for self awareness, but chimps can. However however, it is known that dogs' oxytocin level rises when they stare into our eyes (similar for female human into her baby's eyes). Thus, if the dog is experiencing elevated feel good neurotransmitters, then a smiling face would appear to make sense.
The question is, have you seen dogs smiling in abused situations?
My other thought on this is that the smile could just be a pavlovian manifestation: you become happy shen the dog smiles, so the dog smiles more--the dog has an association of you being happy to something good happening to it, so it wants to make you happy more.
Sorry I don't have a definite answer for you, but afaik the neuroscience / psychology of dogs keeps expanding in complexity, so I would say that yes, the dog is happy.

Beautifully written answer. Please do add some links and/or sources to back up what you wrote.

This post requires references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted. Please see this meta discussion for more.

Thanks for the kind words :) most of my post came from stuff I remembered from my psychology classes at university. I would have to hunt down my old textbooks, but to anyone interested you can pick up an introductory / survey psych textbook for a penny on Amazon; check out the chapters on neurotransmitters and emotion. The dog and primate example are pretty common.
I'll have to keep in mind to get sources prior before answering further. It was kind of a spur of the moment thing ^-^ glad that it was intriguing to you!

Get to know dogs' facial expressions and you will find that there are comparable facial expressions of a canine with that of humans.


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What is this insect found commonly in coastal India?
I have lived in two cities on the western coast of India and I have seen quite a few of these insects(?) in both places.

It basically has an outer cocoon of sorts, which looks a lot like dirty lint. The actual insect is a small wormlike creature at the top of the cocoon. It almost always tries to keep climbing up walls and when it dies, it remains stuck to the wall from its topmost point. The overall length of it, including the linty cocoon is about half a centimeter.
Can someone tell me what these are and if I need to actively avoid them or prevent their appearance in my closet?

Also http://biology.stackexchange.com/questions/47912/identify-this-cocoon-worm#comment83618_47912 ... and also http://biology.stackexchange.com/questions/1808/small-worm-living-in-some-kind-of-cocoon-what-are-these-animals

Related: Identifying a creature that appears to be a worm wrapped in a cocoon, What is this black and white worm in a white case?,  Help in identifying an unknown arthropod, What insect is this? (India), Identify this smooth-cocoon worm from Southern India, Small worm living in some kind of cocoon......

Related:  What is this animal that hides in dustlike structure?, What in the world is this critter?, What is this hard shelled insect in my house?, What is this insect found commonly in coastal India?, Insect identification - pantry moth vs clothes moth


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Hybridization of an Indo-Aryan ethnic group and a Tibeto-Burmese ethnic group
The state in which I reside houses these two distinct ethnic groups.
Physical Traits of the Indo-Aryan group
Height:Medium
Eyes:does not posses epicanthic fold
Nasal bones:is not flat and broad
skin color:significant minority has fair complexion
faces:round shaped and small,but not flat.
body hair:abundant
cheekbones: not protruding
Thus the appear  as a south Asian version Caucasoid.
Physical Traits of the Tibeto-Burmese group
Height:Medium
Eyes:possess epicanthic fold
Nasal bones:is  flat and broad
skin color:significant minority has dark complexion
faces:round shaped and small,but flat.
body hair: not abundant
cheekbones:protruding
Thus the appear  as a south Asian version of Mongoloid.
Since the Indo-Aryan group has migrated recently,there is unavailability significant hybridized population.And I am interested in knowing how the offspring of inter-ethnic mating would physically look like.
But I have failed to apply laws of genetics here as I do not know which are dominant traits?
So,my question is What would be the physical traits of a 1st generation hybrid offspring  according to law of genetics?

You are looking at multi different traits of which at least a few are multigenic in their occurance. This is not like breading beans and simple (even Mendel had quite some amount of luck...).

Which of these traits are multigenic?

Eye and skin color for example.

They are most likely all multigenic, but many may segregate together, leading to the appearance of a monogenic trait. Given enough time, though, they will all blend together.


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Why Crocodiles don't eat Hippos?
I have been following documentaries about crocodiles and amazingly, crocodiles and hippos apparently seem to live happily in the same pond together without attacking each other.
Why is it so? Like no matter how strong hippo is, its soft skin is no match to the brutal jaws of a crocodile?

Can a crocodile's jaws actually bite into something the size of a hippo?

Skin
First, you are being misled by your wrong assumption that hippos have soft skin. Hippos have a 5 cm thick skin! For fun, here is a picture of a hippo skin.

They are big and pretty fast
An adult hippo weighs on average 1.5 and 1.3 tons for males and females respectively (with a record at 4.5 tons) and can run up to 30 km/h on land and up to 8 km/h in water (according to wikipedia > hippopotamus).

They have an aggressive nature
Hippos are aggressive animals (esp. males). Hippos kill about 500 people a year (against 1000 for crocodiles) according to this BBC article (but estimates seem to vary quite a bit from source to source).

They have serious teeth
Hippos have a big mouth with very long teeth. Lower canines are 50cm (19.7 inches) long (see wikipedia citing Estes 1991)!

Hippos live in herd
As suggested by @ChinmayKanchi in the comments, because hippos live in a herd, a crocodile that attacks a hippopotamus might have to deal with more than one enemy.
Videos
You can find here a video fight between a crocodile and a hippopotamus (thanks to @TahlaIrfan) and here is a video of a lion waking up a hippo. You will easily find other videos on YouTube.

@Remi.b Can you please cite the reference about the speed and weight? Thanks.

My reference is simply wikipedia (wiki does not give further reference).

@Remi.B First video link no longer works -- could you find an alternative source? 2nd video link is great :).

They don't look like prey animals. This is one of the most impressive skulls to stand beside of any living animal:

The skin weighs about 270 kilos for an adult hippo of 1.5 tons, ranging from 12 to 35mm thick.

on page 3 https://physoc.onlinelibrary.wiley.com/doi/pdf/10.1113/expphysiol.1964.sp001695

Hyenas are really badass. I saw a video last week when they killed even a hippo.

The skin look more than 35 mm thick in your last picture...

I know, I was puzzled by that so I checked an anatomy document which states 12-35 cm epidermis so presumably it's fat, on the hyperlink.

As Remi.b explained above, the average hippo is just too big and dangerous for the average croc to handle. That said, there were cases that very large crocodiles (such as the infamous Gustave) attacked and ate juvenile hippos (or very old or sick hippos). But usually the two practice a mutual "respect and awe" relationship with tense tolerance to each other, which may turn into a brutal fight if one of the sides gets too close to the other.

Could you add references to backup your answer?

For Gustave: https://en.wikipedia.org/wiki/Gustave_(crocodile), see also Google


text:
Do disaccharidases require a cofactor or coenzyme to function?
I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly appreciated.

Most enzymes (especially ones catalyzing simply reactions like this) do not require cofactors or co-enzymes.

It seems that beta-glucosidases do not require co-factors but some alpha-glucosidases are co-factor dependent.
Some bacterial alpha-glucosidases (GH4 family) require NAD+ to function (Hall et al., 2009). Thermotoga maritama alpha-glucosidase (GH4 family) requires Mn2+, in addition to NAD+ to function (Lodge et al., 2003). Ferroplasma acidophilum alpha-glucosidase seems to contain iron but its role as a co-factor is not known (Ferrer et al., 2005).
For more information on alpha-glucosidases see BRENDA.

+1 I missed that (although there is a crystal structure with NAD+ that I couldn't find when I was writing It's here. Wierd thing is that apparently the NAD isn't being used as an oxidizing cofactor as it is  reported to be unchanged in the reaction.

Apparently not for lactase and β-galactosidase, as one might expect for this sort of hydrolytic reaction. There are also Wikipedia entries for maltase, sucrase and trehalase with references you can follow up to check yourself.


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Why is the manchineel tree so poisonous?
The machineel tree is incredibly toxic to humans. What advantage could Hippomane mancinella have for being so poisonous? It's name even apparently translates to “little apple that makes horses mad”.
Is it an incidental toxin, or an evolutionary hangover from a previous predator, or is it still actively predated by a species with high immunity?
I ask because this seems somewhat paradoxical; the tree has fruit, yet is toxic to animals.

I found an answer at http://www.atlasobscura.com/articles/whatever-you-do-do-not-eat-touch-or-even-inhale-the-air-around-the-manchineel-tree.

I answered a catch-all version of this: http://biology.stackexchange.com/questions/36977/how-did-zootoxins-evolve/36979#36979 The same applies to trees.

I've made some drastic edits to the post to make it answerable (it was a bit rambly)! Feel free to roll back; I may have changed the question in some way unwittingly. Also, your linked article doesn't answer the question you asked. It unverifiably says iguanas have been seen eating it in one continent, and that nobody knows why it's toxic to humans.

The sap is full of Phorbols. Phorbol esters are so carcinogenic, labs use them to cause cancer in animal models.

@James The question you linked is asking about animal venom, which may not be completely relevant to this question.

@MarchHo I can't image plants would be exempt. They absolutely could get stuck in an arms race in order to not to be predated upon. Perhaps iguanas which don't seem to be affected are eating the seeds which should be dispersed by the fruit decaying. The plants that are more toxic become more prolific at dispersal et cetera. Of course, my argument is moot without a bona fide example! I never meant to imply this is a duplicate question, but an answer may touch on similar elements.

The article I linked gives a theory about the evolutionary reason that probably wasn't proven but doesn't give a biological reason.

According to http://www.atlasobscura.com/articles/whatever-you-do-do-not-eat-touch-or-even-inhale-the-air-around-the-manchineel-tree, it evolved to be poisonous to discourage animals from digging into it. Here's one possible way that could have happened. It was once only a tiny speck more poisonous than other trees by random fluctuations in toxicity. By natural selection, animals evolved to prefer it less. They were more likely to dislike the taste of the more poisonous manchineel trees, which in turn caused it to evolve to be more poisonous. Maybe it was such an advantage to get more energy by eating some of it that some species evolved to be more resistant to the poison so that they could eat some of it. That caused the manchineel tree to evolve to be even more poisonous to discourage animals from eating it. It was an evolutionary disadvantage for the apples to be poisonous. That was just an accidental result of the rest of the tree being so poisonous. Indeed, they did evolve to be much less poisonous than the sap for that reason. Animals evolved to dislike the taste of the apples because they're poisonous. The less poisonous ones were more likely to get eaten and have their seeds spread. Since they couldn't evolve to be nonpoisonous, they instead evolved to taste like there's nothing wrong with them so that they could get eaten. Since iguanas did evolve to be immune to the poison apples, there wasn't much of an advantage in them evolving to be even less poisonous.


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How to recognise the type of allele by pedigree analysis diagrams?

It was said that this interference pattern is due to dominant allele. I fail to see that.
In general how to recognise the type of allele by pedigree analysis diagrams?

This question is a bit broad. You have to understand a lot of concepts to figure out the nature of the allele. I'll just point out some basics:

If an allele is dominant it should affect both males and females equally (not X-linked)
If one of the parents shows the trait (while other does not) then at least one offspring should show the trait (basic Mendelian segregation)
If both parents show the trait and one of the offspring does not then it means that the parents are heterozygous and the allele is dominant.


text:
Density of Receptors of a mammal
I know it's a very open question. It's for a paper.
So as a reference I'm looking maybe for the average density of insulin receptors per cell of a human tissue. I want to compare it to the density of MC1R (around 1000 per cell) and it says that's a low amount.

Depends on the type of tissue.

i'd appreciate any receptor of any tissue

It would depend on the type of tissue. But if you are interested in any tissue, then have a look at this BioNumbers entry. It says that there are 100000 insulin receptors per cell in rat adipose tissue. Divide it by the surface area of the cell and you'll get the density. Cell dimensions can also be found in BioNumbers


text:
What exactly are genes, DNA and chromosomes. How do they relate to each other and what is their function?
So I am new to biology and I have been reading, and searching the web, but I couldn't understand the whole framework of a cell. So as I understood:
A DNA, is a double chain of Nucleotides (A,T,G,C and a sugar) and a phosphate residue. Some parts of a DNA code a gene and some do not, exons and introns accordingly. As I understand it these the sequences of exons hold genes and the whole sequence is called genome. Now I read in the book Introduction to Computational Molecular Biology by J. C. Setubal and J. Meidanis. that I cite Each cell of an organism has a few very long DNA molecules. Each such molecule is called a chromosome. So each X shaped thing called a chromosome holds one DNA molecule?
Or is each "hand" of the chromosome one complete double helix of DNA so we have 23 pairs of such chromosomes? or is it that each we 23 pairs Xs?
Shouldn't we have just one uniquely identifiable DNA sequence? I am asking this, because I have also read that each chromosome encodes a different part of one's genome. Does this mean we have several DNA sequences?
This is really bothering me, since I can't figure out the correct structure of a cell.
EDIT:
Now if each chromosome contains a pair of DNA helices. We have 46 chromosomes so overall within the cell there are 92 DNA sequences? All of which are the same? Or are they different? If they are different how do they code for different aspects of one's genome?

Your understanding of DNA is correct. DNA is a heteropolymer of monomers called nucleotides and each nucleotide is made up of a sugar (deoxyribose), phosphate and a "base" (A, T, G, C).
As you already know, DNA is organized as a double helix with the Watson-Crick pairing rules.
A chromosome contains a single DNA double helix. Many organisms have multiple chromosomes which are very different in their DNA sequence. In diploid cells (such as the somatic cells in humans), each chromosome has two copies. The two copies are almost identical and are called "homologous chromosomes". As you know each parent contributes to one of the homologous chromosomes.
During eukaryotic cell division, each chromosome is duplicated. The duplicates (or sister chromatids), are joined at a region which is called the centromere. Centromere is an attachment point for spindle fibres that pull the sister chromatids apart.
Each chromosome has multiple genes. A gene is a region of DNA that is transcribed i.e. it can give rise to an RNA (which can either be a mRNA that in turn codes for proteins or a non-coding RNA). There are other regions of DNA that are not transcribed and these are generally referred to as intergenic regions. In many eukaryotic genes some parts of the transcribed RNAs are removed as a result of splicing. The retained parts are called exons and the removed parts are called introns.
Some organelles like mitochondria and chloroplasts also have a unique genome within themselves. A genome is the entire set of chromosomes including the homologous chromosomes and the organellar chromosomes.
However, when talking about a reference genome, which is just a bioinformatic information and not an actual genome, we just have one sequence for each unique chromosome (for example, in humans, chromosomes 1-22, X-chromosome, Y-chromosome and the mitochondrial DNA). A reference genome is used as a basal set and in a population genomics study, differences from the references are highlighted instead of presenting the entire sequences.

Picture source: https://cnx.org/contents/9TxHOD3O@4/The-Nucleus-and-DNA-Replicatio  Note that paired chromosomes (X shape) are found only during replication. Usually the chromosome is like a single thread. Chromatin is the name of the assembly (for e.g., we don't say chromatin-21).

Bottomline: We have 46 chromosomes then it means we technically have 92 DNA sequences. However you should consider the double helix as one entity (or a metamolecule) because the strands always stay together. For more details you should read a book. Genes by Benjamin Lewin and Molecular Biology of the Gene by James Watson et al. are good books on this topic.

By saying "Many organisms have multiple chromosomes which are very different in their DNA sequence." You mean that each of my 22 (3) chromosomes has a different DNA helix? Or did you mean that different species have different helices? I'm assuming the former (well obviously the latter is also true) given what you wrote about reference genome, but I am still under the impression that all organism should have just one DNA sequence.
I am sorry, my English isn't very good.

@VahagnTumanyan Yes each chromosome has a different DNA helix. Different species have different number and composition of chromosomes and within each species the chromosomes will have different sequence.

I'd suggest adding some images to illustrate this answer - it's the sort of problem some people will understand better with pictures.

@arboviral Done

@WYSIWYG and now upvoted! :)


text:
How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight?
I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-mercaptoethanol, and two bands with lower MW (27–30 kDa) when 2-mercaptoethanol is omitted.
How can these results be explained? What is the easiest and lowest cost method to separate closely related proteins (if that’s what these are, and not just subunits of a single protein)?

I have made edits to try and make this question more readable. Please check my edits to ensure I have not changed your intended meaning.

What do you mean by "purified protein"? Are you asking if your protein is actually purified, or are you confident that it is pure and want to know how to handle next steps?

2-mercaptoethanol (2ME) reduces the disulphide bonds in proteins. If disulphide bonds are connecting two polypeptide chains ("intermolecular") then 2ME would cause them to separate and therefore instead of a higher molecular weight (MW) band you would get one or more lower MW bands.
However, if there are disulphide bonds in the same polypeptide chain, they may cause the chain to fold up. This results in the polypeptide chain to effectively have a smaller hydrodynamic radius compared to the fully denatured chain. In such cases reducing the disulphide bonds using 2ME would cause the band to shift to a higher MW.

What is the easiest and lowest cost method to separate closely related proteins

This is a different question altogether and there are several techniques depending on how "dissimilar" or "similar" the closely related proteins are. 2D PAGE (with isoelectric focussing) is one technique that can offer higher resolution compared to a normal SDS-PAGE. There are many other chromatographic methods.

@R.Rasoulpour iayork's comment is under the question. Anyway, if you think this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered.

this is the right answer


text:
ssDNA library amplification
Assume we are given approx. 80,000 dsDNA fragments of 40 bps length each.
I would like to amplify of each of the 80,000 fragments just one particular strand, such that I obtain amplified 80,000 ssDNA fragments of just 40 bps.
Also beforehand if could be helpful to amplify the 80,000 dsDNA fragments, so where the amplified fragments stay double-stranded.
If you could help me for both amplification steps, particularly the first one, I would be very delighted!
Many thanks in advance!

It is not possible (without any additional upstream steps). For example, how would you define which of the strand should be amplified?

Well I think of extending the fragment by say 10 bps upstream and downstream for each fragment, which is identical for all. Then I could selectively amplify a particular strand via the primers that match to the 10 bps each.

How would you add this 10bp sequence; by ligation?


text:
Transfer of electrophoresis bands to MS
I have a lab question that is confusing me. Just to be clear this is a homework question but I've done some extensive research and can't find what seems to be a "good" answer.
The question is this:
List the steps in order that need to be taken between gel electrophoresis band excision and MS?
The only things I can think of are cleaning the salts out of the sample if salting out was used and removing any detergents that were used like SDS. The question seems to imply that there is a specific order or steps required leading me to think there is something I am missing. Any thoughts appreciated.

There are plenty of protocols available on line for Protein identification  by LC-MS from gel bands. Just google for it, also try searching for in-gel digestion.

You have to remove the salts, remove the dye, digest the protein, extract the digested peptides from the gel etc.
For details, see this protocol.


text:
How does UV light damage the DNA when the chromosomes are deep inside the cell?
When UV light falls on the skin it has to go through the cell membrane and the nuclear membrane to reach the chromosomes. So it looks like that the DNA is protected but it probably isn't. Won't membranes be damaged first and the so that the cell dies before the DNA is affected and is replicating wrongly (if it is damaged too)? Or is DNA just really much more vulnerable than cell membrane?

UV Rays kill the cells by damaging the DNA. UV lights do not disrupt the cell membrane. If a cell is exposed to UV light, it creates THYMINE dimers (bond). Thymine dimers are the actual disruption in the kinks of DNA. UV exposure to skin is proportional to the cell damage.
P53 is a gene product which takes care of fixing cell damage. However it has a tolerance. If the damage is less, P53 sends damage repair machinery. If it's non-fixable, then P53 directs the cell to programmed death.
More UV exposure, more thymine dimers causing more cells to die (cell death). If the damage is not extensive, then that may cause cancerous cells (Result of cell damage).

It sounds like it is better to get a lot of uv rays than a bit to much....

Please cite your sources

When UV light is on your skin it has to go through the cell membrane
  and to the membrane of the core. So it looks like that the DNA is
  protected.

I don't understand what you mean by membrane of the core (perhaps nuclear membrane) but yes there is cell membrane and other cytosolic components. You should, however note that not all cells are spherical; some cells like skin cells are flat and along the thickness axis the DNA is much "less buried".
However, UV light does get attenuated by different cellular components. Melanin (which gives the skin a tan), for instance, absorbs UV and protects the DNA.
In spite of all this UV can reach the DNA. Furthermore, DNA (basically the bases) can absorb UV because of the nature of their chemical structure. After absorbing UV they reach an excited state and can become reactive. Reactions such as pyrimidine dimerization happens because of UV absorption. Note that this kind of an effect is elicited only by high energy UV (200–300 nm) (Durbeej and Eriksson, 2002; Svobodová et al., 2012).
Low energy UV (UVA) does not damage the DNA directly but can do that indirectly by generating free radicals. These free radicals are generated when other cellular components absorb UV and become reactive. Lipids are also affected by UVA and UVB; lipid peroxidation happens in the presence of UV and these peroxides are a source of free radicals (Morliere et al., 1995). So, the membrane is indeed "damaged".
It is also interesting to note that UVA is the most available to the skin cells because UVC and UVB are filtered to a great extent by the ozone layer and also scattered/absorbed by skin components (What is the relationship between UV wavelength and penetration depth into human skin?).
To summarize, DNA is more vulnerable to certain UV ranges but the damage frequently happens indirectly by other free radicals generated in the cytosol.

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


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Book recommendation: Modern Synthetic theory
I'm a zoology minor. I wish to study modern synthetic theory (evolution) is there a good book available online for reading?
The book should cover a basic idea about what the elements of modern synthetic theory are and briefly what are the conclusions of the theory.
Feel free to suggest edits.

Please add details outlined in the tag-wiki for book-recommendation..

@WYSIWYG Is it okay ? I don't have much to write.

There is no modern book of evolutionary biology that is not about the modern synthesis. So what you are looking for is just an introductory book to evolutionary biology.
I think the 2 most common introductory textbook to evolutionary biology are:

"Evolution: Making Sense of Life" by Carl Zimmer
"Evolution" by Futuyma

Note by the way that one can find recommendation on population genetics (subfield of evolution) here.


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Are the subordinate genes of a repressed operon really "turned off"?
Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says:

In addition to being physically close in the genome, these genes are regulated such that they are all turned on or off together. ... The ability to turn ... genes on or off as a group therefore provides an efficient way to quickly adapt to environmental changes. ... mutations affecting the promoter can prevent all of the operon's genes from being expressed, ...

The thing that confuses me is that I've also heard genetics aren't all or nothing, that genes can only be "down regulated" or "up regulated", not truly turned on and off.
Obviously, differing amounts of moderate levels of whatever effector is modulating the repressor could lead to different levels of downstream expression. But, what about situations where nothing is inactivating the repressors? Will the regulated genes be (for all intents and purposes) be turned off? Additionally (and relatedly), is it even a realistic scenario for an operator to always (or almost always) be bound to by such a repressor?

There are several mechanisms by which the expression of a gene can be completely turned off. Certain network architectures can ensure foolproof repression (for e.g. by using multiple repressors parallely or additional epigenetic silencing mechanisms). Bistable switches can also ensure robustness of expression in a way that small fluctuations in the transcription factor levels do not lead to expression of the gene. Sometimes the activator molecules need to co-operatively activate the expression. In such conditions the activation graph is sigmoidal with respect to activator concentration. All these mechanisms can prevent leaky expression.
Some genes do have a basal expression but it is not necessary for all cases. However, basal expression is absolutely necessary for proper functioning of the lac operon (see this post).
Having said this, there is always some non-zero probability of expression of a gene when it is actually turned off. This probability may be very low but it would not be zero. This small accidental expression may or may not have any significant downstream effects.


text:
What animals have a blood-brain barrier?
I am curious about how old the BBB is, in terms of evolution. Is it present in all vertebrates? or just mammals? or what?

It appears it is all vertebrates.
"All vertebrates started out with a glial blood-brain barrier 4–500 million years ago"

All extant vertebrates have a blood-brain barrier (BBB), a specialized layer of cells that controls molecular traffic between blood and brain, and contributes to the regulation (homeostasis) of the brain microenvironment. ... The barrier is formed by vascular endothelial cells in most groups, but by perivascular glial cells (astrocytes) in elasmobranch fish (sharks, skates, and rays). It has been unclear which is the ancestral form, ... we conclude that the ancestral vertebrate had a glial BBB. This means that an endothelial barrier would have arisen independently several times during evolution, and implies that an endothelial barrier gave strong selective advantage.

So, all vertebrates have one; in some fish, it is composed of glial cells rather than endothelial cells.
However, insects do have something similar:
"Evolutionary conservation of vertebrate blood-brain barrier chemoprotective mechanisms in Drosophila"

Insects also possess protective neural barriers, but they differ anatomically from vertebrates (Figure 1). Drosophila melanogaster (Dm) has an open circulatory system that is separated from the CNS by a thin layer of glially-derived epithelial cells (Treherne JE, 1972; Carlson et al., 2000; Stork et al., 2008), making the Dm humoral/CNS interface topologically much simpler than the vertebrate BBB. However on a cellular level, the vertebrate and insect BBBs share many common features.


text:
Constantly wiggling moth pupa - will it emerge soon?
Today I found a moth pupa in the soil in my garden in western Sweden. It's about 15 mm long.
I have found similar ones before, but this one is wiggling a lot more, even after I put it down and put a bit of dirt over it. It's been moving for more than an hour now, but less now than in the beginning.

I was hoping to see it emerge, but if it will take more than a day or so, I will probably put it back. So, what I'm wondering is if this wiggling is any indication of how soon it will emerge. Or if there are other ways to tell.
Update: an hour later it has stopped moving. Maybe it was just very disturbed by my presence. I'm keeping it in a jar with soil and a stick for climbing up on, and I'll decide what to do with it tomorrow.
Update: 12 hours later and it seems very still. But I'm letting the question remain since I really want to know if there are any signs to look for.
Final update: After 16 days it had turned almost black, and was still very active when handled.

And after 17 days this moth came out:

I posted the same question on tumblr and got an answer:

It depends on the species. This one looks like a Noctuid. I’d give it
  two weeks to a month or so. You may be able to see its wings showing
  through the darkening pupal case when the time draws near! Just make
  sure you give it somewhere to climb up and expand its wings when it
  ecloses.

After keeping it until the moth emerged, I now know that wiggliness is not an indication of maturity, but turning dark is.


text:
Do ants have a "stay away" signal?
Last night I discovered many ants entering my house through a window with an imperfect seal. I placed a poison ant bait on the window sill and within seconds they were feasting on it. This morning I noticed there were still many ants near the bait, but they were all bypassing it as if they were somehow warned to stay away. Do they have such a signal? If so, how would they know the bait is a problem? If not, what could cause them to be so interested last night and not interested at all today? (I can see that there is still plenty of food inside.)
Update: after a little bit more research, I decided that ants do not have a "stay away" signal, and that the only explanation for ignoring the bait would be a stronger scent trail leading somewhere else. Last night when I opened the window I found the jackpot. There was some sort of sticky substance all over the bottom of the window, and hundreds of ants celebrating the find. My conclusion is this was much more attractive than the bait, even though it was merely an inch away from their path.

It is a long time since I set in a Computer Sci (AI) talk about this….  This explains it a bit.

Once ants have eaten they return to the nest.
On the way back to the nest they put down a scent.
This scent fades with time.
Most ants follow the scent.
(A few ants walk randomly to find new food, or a new faster way to the current food.)

So if the agents eating your poison bait do not make it back to the nest, there is no scent trail leading to the poison for more ants to follow.     But the ants that went round the bait to find other food, did make it back to the next, so setup a new sent trail.
If a poison kills the ants quickly, the customer is likely to see dead ants and therefore buys more of the poison.   However a poison that kills the ants slowly, so the ants don’t die until they get back to the next, is likely to get more of them, as there is now a strong sent tail to the poison.

interesting answer... makes sense - are there any available references that you could cite to back up the answer? It would improve its strength. Thanks for your efforts!

@VanceLAlbaugh, sorry nothing better then what anyone can find with google themselves.   But I have shown that a "keep away" signal is not needed to enable ant to "keep away" from something that kills them quickly.

I'm pretty sure the ant bait I used takes 1-2 days to kill the ant, so there should be enough time for them to get back to the nest. However, your implying that there was a stronger scent to a different food source turned out to be correct.

Yes, ants communicate with members of their colony by releasing specific chemicals and pheromones to indicate danger. The ants that entered your house and ate the poison must have released a "danger" chemical, thereby warning the rest of the colony. I suggest sticky traps for capturing the remaining ants.
Here is an interesting article on the matter.

Sorry, I'm not convinced. The article you referenced talks about a scent that only living ants have, which fades out about 40 minutes after death. Once the living scent is gone the ants know to remove them from the colony. It doesn't speak of a danger scent. I believe some ants do have a "danger" scent, however my understanding is that it's the opposite of "stay away". I believe it means "come here and fight, something is attacking us". So if the "danger scent" was released, I would expect more ants to appear (and perhaps frantically take the bait?), not avoid the bait altogether.


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Hydrophobic elution times in ionic exchange columns
What would the order of elution be of say Gly, Val, Leu?
My argument is that hydrophobic residues will try and get away from the resin and the more hydrophobic the residue is the faster it will elute. This seems to run contrary to the steric argument however, where larger residues would take longer to elute. Which argument is right?

What kind of column are you using?

Does it matter? Since all the pI's are the same?


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Why was the study of "Concordance of Monozygotic and Dizygotic twins for traits" designed in this way?
I am confused by the twin study 'Concordance of Monozygotic and Dizygotic twins for traits.' My questions arose from 3:17-4:17 of the video
And this is the related data I  have referred
I have the following questions:
1 Is the dizygotic twins also separated in different families? If true, didn't the DZ group lack the Control Variables of 'same environment 'or'identical genes'? Or should we make the '50% identical genes' as control variables?
2 why do we need Dizygotic-Twin groups in the experiment, if we need to find the environmental influences why not just find a pair of unrelated individuals and set them at a same family (environment)? Alternatively, is it necessary to compare the monozygotic groups with dizygotic groups instead of any others that aren't dizygotic twins?

It's unclear what your questions are and you should avoid asking so many questions at once, and questions should be able to stand alone (we should not need to watch the (bad) video).

Thanks for your suggestion,I have isolated my questions .

I established the other question   Hope you can check it out.

My interpretation of the first question is why do traits determined by the environment appear to be equally similar among monozygotic and dizygotic twins in these twin studies. The studies he is talking about look at twins that are separated and adopted in to different families. These different families provide a different environment for either twin, and with enough samples, you can compare similarity between dizygotic and identical twins. So imagine you measure the trait of interest (height) in all individuals, and find that identical twins more closely resemble each other than dizygotic twins do. This would indicate that height is somewhat genetically determined - the more genetically similar pairs were more phenotypically similar.
Why use mono- and dizygotic twins individuals to test environmental effects? Comparing mono- and dizygotic twins is a good experimental design - it removes the effects of being a twin (nutritional environment in the womb may differ if you use monozygotic twins vs single born siblings), effects of year and season of birth, effects of womb environment among the two single born individuals, and in one group you have zero genetic variance, while both groups should have the same amount of environmental variance. Read here about heritability, he gets the explanation wrong in the video, heritability is not a measure of how genetic something is, it is how much of the phenotypic variation ($V_P$) is explained by additive genetic variation ($V_A$).
$$h^2 = V_A/V_P$$

Thanks for your answer ,but I still have some questions about the first part of your answers. If there is a TRAIT determined by environment ,  both the identical twin group and fraternal twin group have 100 samples in each of two families.  After the research , in identical  or fraternal group , it is found that both families have 30 of 100 samples that have TRAIT,so 30% people have same trait in the  group.My question is why the difference of both  environments can cause that 30% same TRAIT, and also equally similar to those in the other group.

If the trait was genetic then the trait would be more common in the group that is more genetically similar (the identical twins), but if the trait is entirely environmental (and assuming both groups experience the same environmental variation - requires large unbiased sampling effort) then there is no reason for either group to differ in the frequency of the trait.

For example; if trait is caused by exposure to chemical-A and 30% of people are exposed to chemical-A then both groups should have a trait frequency of 0.3 (or 30%). However, if trait is determined by genetics, then identical twins are identical for trait, i.e. if one has trait, the other in the pair also has trait, while in the non-identical twins the presence of trait in one twin is not as informative about the other in the pair (the second twin may have trait, but not necessarily)


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Why is nitrogen isotopic labelling required for protein NMR?
Why is labelling required for Nitrogen (by 15N) for studying structure of a protein using NMR?

It is not strictly required. Isotope labelling is required when the usual isotope does not have a magnetic spin (for example 12C). 14N has a spin of 1 and exhibits 3 spin states: -1, 0 and 1. The isotope, 15N has a 1/2 spin. As noted in this book, analytical methods exist for both nitrogen isotopes.
However, 15N is preferred for NMR studies because the chemical shifts produced by 14N can be too broad to be detected by high resolution NMR spectrometer.
From wikipedia:

Nitrogen-15 is frequently used in nuclear magnetic resonance spectroscopy (NMR), because unlike the more abundant nitrogen-14, that has an integer nuclear spin and thus a quadrupole moment, 15N has a fractional nuclear spin of one-half, which offers advantages for NMR like narrower line width.

From http://chem.ch.huji.ac.il/nmr/techniques/1d/row2/n.html:

The 1D 14Nitrogen NMR experiment is much less sensitive than Proton (1H) but has a much larger chemical shift range. Its signals are broadened by quadrupolar interactions. The larger the molecule and the more asymmetric the nitrogen's environment, the broader the signal. Hence, the small and highly symmetric aqueous ammonium ion gives a very sharp line (fig. 3), less than one Hertz wide. Liquid ammonia, being less symmetric, is 16 Hz wide (on a 400 MHz spectrometer at room temperature). Urea is larger and asymmetric so the line-width is approximately 1 KHz. Molecules that are significantly larger than urea yield signals too broad to be observed with a high-resolution NMR spectrometer. However, the nitrogen chemical shift range is wide and so may be readily used for distinguishing nitrogen species for very small molecules.


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How does stimulus reach neural threshold?
I understand that when the stimulus into a neuron is greater than the threshold it triggers the action potential. Do all the contributing stimulus have to occur at the same time, or can they occur over time?
If neurons A and B connect to C, and C needs both A & B to activate to reach the threshold; can A fire first, then B - or do they both need to fire simultaneously?
If they can contribute towards the threshold over time then is there a decay that eventually returns the neuron to resting potential?

There is temporal summation of the stimuli. This is modeled in the Hodgkin and Huxley model .
To imagine the whole process, you should know that in the dendrites of the neuron, electric impulses are propagating passively ( the strength of the stimuli is decreasing over distance and time), in the axon the electric impulse is active ( in the form of action potential(AP) ).
Let me explain your second question with the help of mathematics:
Let's assume that T is the threshold value.
Func(x, t) is a function of the stimuli, where the depolarizing effect is decreasing with time and distance:
Func(A, t) > Func(A, t+1)
So after your assumption:
Func(A, 0) + Func(B, 0) = T
If we don't take into account temporal summation, in other words, if we are looking at only just one phase of the time, and A and B stimuli are not simultaneous, and in t=0, then there will be no AP.
Func(A, t1) + Func(B, t2) < T , where t1 != t2
But with temporal summation we can add previous stimuli into the equation. For example:
From the previous asyncronous stimuli, we got our two decreasing depolarizing factors, and over time we got one more stimulus from A, then with temporal summation they CAN produce an AP.
Func(A, t1) + Func(B, t2) + Func(A, 0) >= T,
if Func(A, t1) + Func(B, t2) >= Func(B, 0)
So after a depolarizing effect, the neuron enters into a hyperpolarized state and most of the sodium channels are inactive. This is called the refractory period. This is when, even A and B is applied simultaneously there will be no AP. And after the membrane potential gets back to his resting potential, then the whole process (including the temporospatial summation) starts from the beginning.


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Computing Percent Identity between DNA / Amino Acid Sequence
What are some tools where I can input a pair of DNA sequences (or alternatively a pair of Amino Acid Sequences) and compute a percent similarity identity metric between them?
Is BLAST the right algorithm for this or something else?
The context is that a certain patent protects all sequences at least 90% or more identity to a given sequence. I wanted to test some candidate sequences and verify the percent identity metric.
Below I post a patent-snippet where they actually define their identity metric.

tBLASTn, BLASTx and tBLASTx can be used.
It is clearly illustrated here.
If you have just two sequences you need not do a search against the database. You can simply align them using Smith-Waterman or Needleman-Wunsch algorithms, as David mentioned. However, you still need to translate your DNA to protein before doing the alignment. Again, as pointed out by David, with protein alignments you do usually not use identity. Scoring matrices like PAM or BLOSUM are used to calculate similarity.

If you want to compare two specific sequences that you already have, then BLAST itself is not the program you need. BLAST is a program that uses heuristics for rapid searching of a large database for sequences similar to a query sequence. Each of the highest scoring sequences obtained is ‘finished’ for presentation by running an implementation of quite different older and slower dynamic-programming algorithm, which is non-heuristic.
There is an option at the BLAST implementation at NCBI for just comparing two sequences, but this seems strange as one may as well just use the dynamic-programming alignment algorithm. Furthermore the output is not what you want as it scores a local alignment, whereas what your patent specifies is a global alignment (see below).
So for pairwise comparison of two sequences one normally uses a program that implements the Smith and Waterman dynamic programming algorithm for local alignment (only the regions of best similarity are compared) or the Needleman and Wunsch algorithm for global alignment (the whole of both sequences are compared). From your patent specification you clearly want a global alignment and a value for percentage identity.
You can find free web implementations of both of them at the EBI website (among other places) where the program ‘Needle’ performs the global alignment you require. Alternatively, there is an implementation of the Needleman and Wunsch algorithm at NBCI, tucked misleadingly into the BLAST suite.
I do see one theoretical problem with these programs in relation to the patent, although this may not matter in practice. The patent says that “The optimal alignment is the alignment in which the percentage identity is the highest possible”. But these programs try to find the ‘best’ alignment not on the basis of the highest identity score, but on the basis of the highest similarity score. This is done by using one of a number of emperical scoring matrices that encompass the likelihood of particular amino acid substitutions. For example a match between similar amino acids (e.g. Glu/Asp) may give a score of 4, compared with a perfect match score of 5. Moreover, a perfect match for an amino acid like Trp scores much higher than one for Gly. (More info on this and these terms can be found in the  Wikipedia Sequence Alignment entry or in the BLAST Glossary.)
Now you would expect that the ‘best’ sequence alignment obtained by optimizing for similarity in this way would also give the best identity score. This is quite likely for sequences of 90% identity or higher, but there is no reason it should necessarily be the case. In theory to get the highest identity score you should use a scoring matrix in which all perfect matches scored the same, and all mismatches zero. This is possible using an implementation of Needleman and Wunsch that allows you to use your own comparison matrix, e.g. this online EMBOSS-Explorer implementation. The problem is what score to give the perfect match (the average of match scores?), as this has to fit with the scoring penalties for mismatches. Or perhaps you should drop the mismatch penalty altogether, as you are only interested in the highest identity.
My advice would be to go for the Needleman and Wunsch algorithm, accept the defaults, and check you get the same score with different implementations. If your lawyers want anything more, I can offer a consultancy ;-).

BLAST does implement Smith-Watermann. The OP would still need to "translate" the DNA to compare it with the protein sequence.

@curious_cat if you have just two sequences then you can directly use Smith-Waterman or Needleman-Wunsch depending on what you really intend to do. With protein sequence you don't usually work with "identity"; you use scoring matrices like PAM or BLOSUM. In any case, the DNA has to be translated to protein in order to be compared with the other protein sequence.

@David The lawyers apparently tried to think this through. See the edit  in my answer. I post a snippet from the patent. It tries to address the question about how to score gaps. Now the question is how to get a score that matches this lawery-definition. Will BLAST out-of-the-box work to give a score matching their definition? They do recommend BLAST.

@curious_cat —Aaah. You mean identity. It seems counter-intuitive in plain English to talk about 90% identity, but that's the tech usage to distinguish it from "similarity" where you use a matrix of scores for different amino acid combinations. I'll do a test of my own and report back.

@David Thank you very much. I started a related thread here: http://biology.stackexchange.com/questions/48294/needleman-algorithm-for-optimal-alignment-of-two-amino-acid-sequences Would love your comments on that if you can!

@David Thanks. I've deleted a bunch of my comments too. I've kept a few that I thought added some relevant info.


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Amount of variation between a canonical gene sequence in various samples
Suppose there is a GeneBank DNA sequence listed that produces a specific enzyme in a specific species of plant. e.g. A terpene Synthase.
Now if someone samples various trees of the same species would one expect to get the exact same sequence each time? Or is a certain amount of variation expected from tree to tree?
The drift behind my question is: Obviously not all tress of the same species are exactly identical in phenotype. So are the causative factors seen in sequence variations of various enzymes etc.? Or can we expect the various samples to have exactly identical amino acid / DNA sequences for particular genes / enzymes.
e.g.  e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?

It may or may not vary much. Unless you have additional information, it would be hard to tell. Try looking at conservation across different species. That may give some clue.

Is there a correlation between conservation across different species & within species variation?

Can't say for sure and I have not come across any study like that but conservation across different species can indicate that variation in the sequence may probably reduce fitness and same may apply for "within species".

Thanks @WYSIWYG I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too.

@curious_cat: I just stumbled across this: http://www.sciencedirect.com/science/article/pii/S2213596014001238. There it was found some conserved genes between humans and fruit flies in which there is substantial sequence variation within the respective species.

Your question is quite vague so I can only give you a vague answer saying what I would expect given only the information of your question.
The vagueness mainly comes from the huge amount of functional sequences in the genome, particularly also in enzyme-coding genes, each being more or less conserved. You say

I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too.

I would say that there is no feasible way of studying this question. You will find different selective constraints on every single enzyme and breaking this down to DNA this means that every single locus can be target of different selective pressures. And even if you figured out how to answer that question comprehensively for a given species (which probably will not happen), generalising it to every single species in every ecological niche, with every possible population history and so on is close to impossible. That is why one studies sequence diversity/conservation in model organisms and mostly on a per-gene basis.
In general, without knowing any background of a species and enzyme, I would however expect two things when looking at molecular variation between individuals of that species. These are merely based on general evolutionary principles and the nature of the genetic code. Keep in mind that these are trends, meaning that many genes will match these expectations but some definitely will not due to lineage-specific evolution.
First, I would expect generally high levels of amino acid conservation (but not always identity) especially in functional enzymes of core pathways. However, this depends on the function of the gene product. If the gene is a target of balancing selection, which maintains genetic variation within a population, there can also be considerable amino acid variation.
Second, there will generally be higher levels of DNA variation because of mutations with little or no fitness effect (synonymous variation or intronic variation which tends to have lower selective pressure).
To relate this to your last question: even though I would always expect a general amount of variation, even in the amino acid sequence of core enzymes, this variation will probably not be the main reason why you see different phenotypes. Phenotypic plasticity - the differential response of a given genotype to a given environment - is often stronger in plants than in animals as plants are stationary organisms. This plasticity will probably be the main cause of striking phenotypic differences between individuals.

Sorry about the vagueness. Can you comment on what parts I have left ambiguous so I can improve my question?  e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?

I did not mean your question was hard to understand. The vagueness comes from that there is no information on the species and the species' population history. This strongly affects the expectations of variation within a species. My answer are just some vague pointers what to think about. I will later think about if I have something more to add. :)

Thanks! I added some info. about the enzyme as well as the species so maybe that helps you formulate a more concrete answer?

To expand more: I know that there are homologous enzymes across species e.g. The enzyme or gene coding for (say) Squalene from its precursor will look similar with some regions changed. And BLAST etc. identifies this. What I am wondering here is within the same species but in different samples, how much variation is there typically in the sequence of the same enzyme.

@curious_cat: I added some further comments on the problem. In my view this is not really a biological problem but rather a philosophical one.

Interesting. I'm still not sure about your point. e.g. It should be a question entirely amenable to empirical study. Say, I take 100 random samples from one species & plot the variation in (say) 10 enzymes of interest I have one number. We do it for more species & now we have some picture. I'm not saying we will get one single number for a within species variation but it could be that mostly the similarity is 99%+. Or just 80-85%. But right now we just have no clue.


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Why People have skin color between fair and dark?
According to Mendel's laws traits do not show any blending. So according to his laws people only with fair or dark skin should exist. Do the alleles in this case blend? And why?

There are several traits that do not follow the simplistic Mendelian rules. With skin colour, the trait is actually polygenic (and also quantitative).

Mendel also fudged his data. Traits blend all the time.

this question has been well addressed here: http://biology.stackexchange.com/questions/34565/skin-color-explanation
( so I guess it might be marked as duplicate ).

Mendel's laws were very basic to aid in the comprehension of genetics.  You think of Mendel's genes as an +- pair where + is dominant and - is recessive, making our +- gene produce offspring with the + trait but still being a carrier of the - trait.
However, when it comes skin colour, eye colour, hair colour, height, tendency to muscle growth, and a thousand other things, the gene is more like a series of ++-++-+++-, + is more recessive than -, but some of + will still show up over -.
In short, the colour of a person's skin is not a simple +- gene of dark and fair; everyone carries a certain amount of pigment genes and certain number of non-pigment genes.  The amount that one carries of each of the genes will determine his skin colour and his/her ability to pass on the dark/light characteristic.

To give a basic idea about the dimensions: if I remember correctly, from genome-wide association studies, height is currently known to be influenced by approx. 500 genes - that is 2-3% of all approx. 20000 protein-coding genes. However, studying these loci explain only about 20% of the variation seen in the phenotype height.

A minor suggestion: Instead of X and Y use some other symbols. X and Y can be confused for chromosomes.

Good point, @WYSIWYG .  Hadn't thought of that.


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Why do mints make your mouth feel cold?
Why do mints make your mouth feel cold?  And specifically, why does your mouth feel so cold if you eat a few mints and then drink a glass of cold water afterwards?

Hmm.. duplicate of http://chemistry.stackexchange.com/q/558/170, but different stack!

Duplicate of http://biology.stackexchange.com/q/31648/3340

Personally, I think @Daniel's dupe marking is more accurate.  I would have been hard pressed to find the post on biology as it refers specifically to oil on the outside of the skin.  Granted, they have the same answer, but how was I to know?

Whatever accurate or not, for me at least, all such link-up helps me a vast lot assemble the pieces to the whole picture.

Does menthol get easily evaporated at room-temperature? then the latent heat loss due to evaporation, may be a cause , though partly

The feeling of cold from mints is caused by menthol. Menthol affects the TRPM8 receptor on skin and also in the mouth. TRPM8 is also a general cold receptor: so if you are in contact with menthol the receptor reacts just like when you are exposed to cold (Bautista et al., 2007).
The receptor is strongly activated at temperatures below 26 degrees Celsius (Bautista et al., 2007). Drinking water is usually colder than that. So if you ate mints and drink cold water afterwards, the receptor response is even stronger.

And it's very refreshing!

So if I eat mints and drink water that's warmer than 26C, nothing much should happen?

Do menthal and Capsaicin cancel out?

@David Richerby: Menthol would still trigger the receptor which creates a cold sensation independent from other influences.

@JDiugosz: I would not except cancelling out as only the mechanism is comparable: Capsaicin activates a different receptor (TRPV1). I do not really know what effect the combination actually has in terms of cold/heat sensation  - I will try this out later and report. ;)

@AlexDeLarge That would probably be a very weird sensation.

@AlexDeLarge "Today, I am going to eat a breath mint dipped in hot sauce... FOR SCIENCE!"

I can only say one thing: Yuck.

@JDiugosz: It does not seem to cancel out - you actually keep both the hot/pungent sensation and have a cooling effect (I ate a tomato curry spiced with Bhut jolokia and had a Fisherman's Friend afterwards). In fact, e.g. Turkish cuisine uses both spicing with mint and pul biber, probably exploiting these sensory antagonistic effects..

@DavidRicherby, he said it was strongly activated at temperatures below 26 degrees Celsius.  That probably means that it is activated, just less strongly, above that temperature.

@AlexDeLarge You have good taste not only for mint candy and sauces, you have good taste for humor. Btw, we have separate heat receptors and cold receptors. so it is no strange to get hot and cold feeling at the same time.

As well mint lozenges are not only cold. they are very sligh-t-ly pungent ('hot'). Aren't they?

a related- good article http://www.scholarpedia.org/article/Thermal_touch