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How did the human brain evolve?
A common question posed is, "how did the eye evolve?", because the eye is so complex.  However, this has been answered rather clearly and there are several examples around the world of animals in which the eye has evolved independently.
The human brain, however, only seems to have evolved once in the history of life on Earth - a brain which is capable of advanced speech, predicting the future given information on the past, producing art, imagining advanced abstract concepts such as algebra, creating advanced tools, etc.
How, then, could the human brain have evolved?  What stimulus was there for progressive Homo individuals to have brains that were slightly more advanced than the previous one's?  I've heard Richard Dawkins summarize it as "big brains are sexy", but that's a comment made in hindsight (and not even shared by all members of the human species today!)  At the time, why would a human female choose a male with a slightly larger brain, so slightly larger that the increased intelligence probably wouldn't be noticeable?  Or why would such an individual have an evolutionary advantage?

You should't confuse "big" with functional. Brain size is a side-effect.

Strongly suggested reading: The Accidental Mind by David J Linden

Hi Jez & a belated welcome to the Biology part of SO! This is a well written & well-received question. I think that it falls in the same trap as the eye question. Either the answer to the question "how did the human brain evolve" is "little by little and over large time scales", or as @nico points out, easily fills a book (or 20000 related research articles). The current answers here focus on a small part of a complete answer or lack detail for a complete answer. I do not think stack exchange will produce a wholly satisfying answer to this interesting question :(

New work suggests a prominent role for genes in the SRGAP2 family, as explained here. Data suggest a mechanism where incomplete duplication - most likely at SRGAP2C - created a novel gene function some 2–3 mya, which is a time corresponding to the transition from Australopithecus to Homo and the beginning of neocortex expansion. Further, in the mouse neocortex, Srgap2 promotes spine maturation and limits spine density, supporting sustained radial migration and leading to the emergence of human-specific features.

Very interesting, and if one gene duplication did indeed result in our brains suddenly getting more sophisticated, it would mean that Dawkins is dead wrong - there really would be one mother who didn't have "high intelligence capability" and a child that did suddenly have "high intelligence capability".  I can see how that's easier to explain evolutionarily than brains very slowly increasing in size.

@Jez, I don't think this means Dawkins was "dead wrong". Just because one gene mutation sets a species on a new evolutionary trajectory, it doesn't mean anything changes overnight. Note that while this mutation produced human-like features in rodents, the rodents didn't get any smarter. The mutation may have allowed human brains to develop, but it certainly didn't cause the jump you're talking about.

You made a few statements in the beginning of your question, I'm just going to focus on the last paragraph (which seems like your question).
When people try to understand evolution, a common fallacy is to assume you're looking at a linear progression, in this case that each surviving child is slightly more intelligent than his parents. This is confusing in part because it's at odds with day to day observation: dumb people have smart kids, tall people have short kids, etc.
It may help to visualize a it as a cloud rather than a line, with the really incompetent people being constantly clipped off the low end and the really competent being, as Richard Dawkins puts it, "sexy". Slowly, genes which tend to land people in the "really dumb" side are weeded out, genes that sometimes produced above-average intelligence are propagated. You can't think about evolution without considering the entire population.

OK, so I ask you the same question I did Preece; if this is such an obvious selection mechanism, why is it so extremely rare in evolution (only ever happened in humans)?  The next-most intelligent animals, chimps, can barely learn simple sign language, and they're on the same twig of the tree of life as us!

no one said it's an obvious selection mechanism. Having a large brain is expensive, for one thing, our brains consume about 20% of our energy, and run exclusively on glucose. In addition, human birth is far more excruciating than most mammals because babies have such huge heads. Our bodies are, in many ways, in a very awkward evolutionary state because the benefits of a big brain have only recently come to fruition.

why would such an individual have an evolutionary advantage?

First thing to keep in mind, is that natural selection will seize upon even very slight advantages and evolve them until the point where evolving them is no longer viable. So, to you a slight increase in intelligence might be unnoticeable, but in a naturally selecting system it would be very noticeable. Don't mix up sexual selection (where the preference of one sex shapes the selection of genes) with natural selection (where fitness to the environment shapes the selection of genes). Sexual selection may or may not have helped shape brain evolution, I can't produce evidence that it did.
But the increased fitness that slight gains in intelligence convey are easier to create evolutionary anecdotes about. It's simplistic to speak of just "intelligence" as evolving. Many different nervous structures evolved through out the animal kingdom, each with a function that directly increased fitness. I get the feeling that you're specifically talking about the evolution of the neocortex, because you reference human intelligence.
So, what I guess you're really asking is what evolutionary advantage does the neocortex convey? The answer isn't that hard, once you understand a little about the neocortex. It is an organ that simply models the external and internal world as perceived by your sensory organs. By external world, I mean modeling things like vision, hearing, touch, etc... By internal world, I mean modeling the actions you can perform, the plans you make, and so on. Increasing the size of the neocortex is essentially increasing the possible complexity of these models. Not only can you find more subtle and complex patterns out there, you can develop increasingly subtle plans and ruses too.
Watching documentary footage of tribal hunters provides a really stark look at just how useful the neocortex is. It frames our intelligence in terms of a situation similar to one we evolved in. It's not hard to imagine why the growth has been explosive. Outsmarting other animals is a great niche that in our evolutionary history was virtually unexploited.

But if it is so easy to see the advantage of our large neocortex, why is it so extremely rare (has never evolved outside of humans)?  Why wouldn't it also be beneficial enough in some other species to evolve to the same extent?

You're imagining that the human brain is unique in some way. It really isn't, we have the exact same structures as almost every mammal, from rodents to apes to dogs and cats. The main difference is that out neocortex is larger. Asking why the neocortex has only evolved in humans is like asking why white fur has only evolved in polar bears. Every mammal has hair, it's not "rare", it's just slightly different in different species. Also, consider that it's possible that intellectual gains are exponential to linear increases in cortical size.


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What is this marmot-like animal (Tigray, Ethiopia)?
I was searching what are the animals I frequently saw in the north of Ethiopia. I took some bad quality pictures.
For me it looked like a large squirrel, local people called it a rat, and on the internet I find rock hyraxes are quite frequent in the region, but they appear not to have a long tail like the animals I saw, and they don't have the white lateral line

It's definitely not a rock hyrax, it looks a lot like a ground squirrel.

This looks like some sort of ground squirrel. Especially in the second picture, the posture is  very characteristic of squirrels in general. The tail also looks very squirrel-like to my eyes. My best guess, without better pictures, is the Striped Ground Squirrel (Xerus erythropus).
See the images at:
http://www.flickriver.com/photos/8834404@N02/2902284598/
http://www.flickriver.com/photos/kpzaremba/5094580855/

The Wikipedia picture isn't particularly good, but searching for Xerus erythropus on Google Images gives some results that look a whole lot like your squirrel.

source: Stack Exchange

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sort: votes


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Would a spinal injury decrease human height?
A woman I know has been losing height at a rate of few cm a year following a severe spinal injury. How is this possible? What kind of injury could cause such progressive loss of height? Could this be a genetic defect? Are there any disorders that cause this type of shrinking?
In case it could be relevant, her brothers are very tall.

i asked this question as well on fitness.stackexchange.com and on http://skeptics.stackexchange.com, they think here is a better place, so they downvoted my question, i hope you don't downvote me too, I just want to know what's wrong with this woman before she dies, that's all. I searched all around the web for disorders, couldn't find any! i just want an explanation

please see http://www.healthboards.com/boards/bone-disorders/609860-shrinking-young-age.html

I dont have a definite answer for this but this is what I speculate: spinal injury can cause paralysis which leads to atrophy (wasting away) of skeletal muscles. This may be the cause of the observed reduction in height.

atrophy happens because of prolonged disuse

Her height is that of a small bottle of cola? You expect us to believe you know a human being who is ~20cm tall?

@terdon i'm talking about this bottle

That bottle has a height of 18 cm, are you saying you know someone who is less than 20cm tall? I am sorry if this is a failure to communicate but it sounds like your question is a joke. The shortest person in the world had a height of 50.8cm, more than twice what you describe. It would take a hell of a lot more than a spinal injury to shrink someone to that size, and I really doubt that the human body would continue to function. If this is just an exaggeration, please remove it from your question.

@terdon lets not argue about the height, you wont believe me and we'll not get any answer, my question is "is there any disorder (or spinal injury) that would cause you to keep shrinking for the rest of your life?" we know that the brain tells the body to grow, would a shock or something make the brain tell your body to shrink instead of growing? i don't care about her height, i care about the problem she has

Fair enough, and I'm sorry, I thought this was a joke. If you don't mind I will edit your question to remove the bottle reference so others don't make the same assumption.

@terdon that's fine, i also made a mistake by mentioning that

@Fischer.. did you consider muscular atrophy as a possibility.. i dont know if bone atrophy is also triggered by continuous disuse..

As @WYSIWYG pointed, muscular atrophy is the main cause for height decrease.
A spine injury leads to neural impairment and paresis / paralysis. This affects directly muscular trophism. It also limits physical activity, this being another favoring factor for muscular atrophy and overweight issues [1]. Association of bone degenerative processes (osteoporosis, osteopathy, osteolysis) is also a factor and it is dangerous because it promotes spinal cord injuries if vertebral height reduction amount is notable [2].
Focusing on muscular atrophy, here is how it can decrease height: by increasing vertebral column curvatures mostly on the upper region with articulating vertebrae. The vertebral column tends to gain a spring-like, spiral shape, associating accentuated cervical lordosis, accentuated thoracic  kyphosis and thoracic scoliosis.

Image source: Scoliosis Treatment Alternatives. Chiropractic for Scoliosis Treatment Review (2014). Accessed 21.07.2014
While reading the comments to the question I found something interesting:

we know that the brain tells the body to grow, would a shock or something make the brain tell your body to shrink instead of growing?

Yes, the brain (hypotalamus) initiates a neuroendocrine response that leads to growth hormone secretion. The secretion is about 700 micrograms/day in a young adolescent, while in a healthy adult it is about 400 micrograms/day [3]. The deficiency in an adult person leads to a tendency of fat mass increase and a relative decrease in muscle mass and, in many instances, decreased energy and quality of life [4]. The brain can't "tell your body to shrink", but the lack of "communication" between the brain and organs leads to less to absolutely no use of that organ, thus inducing atrophy. The lack of both external and internal stimuli leads to atrophy (in general) [5].

References:

Gupta N, White KT, Sandford PR. Body mass index in spinal cord injury -- a retrospective study. Spinal Cord. 2006 Feb;44(2):92-4. doi: 10.1038/sj.sc.3101790. PubMed PMID: 16030513.
Ji L, Dang XQ, Lan BS, Wang KZ, Huang YJ, Wen B, Duan HH, Ren F. Study on the safe range of shortening of the spinal cord in canine models. Spinal Cord. 2013 Feb;51(2):134-8. doi: 10.1038/sc.2012.99. PubMed PMID: 22945745.
Wikipedia contributors, "Growth hormone," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Growth_hormone&oldid=616959802 (accessed July 21, 2014).
Molitch ME, Clemmons DR, Malozowski S, Merriam GR, Shalet SM, Vance ML, Stephens PA. Evaluation and treatment of adult growth hormone deficiency: an Endocrine Society Clinical Practice Guideline. J. Clin. Endocrinol. Metab. 2006 May;91(5):1621-34. doi: 10.1210/jc.2005-2227. PubMed PMID: 16636129.
Wikipedia contributors, "Atrophy," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Atrophy&oldid=611770442 (accessed July 21, 2014).

This answer is just wow!!

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How do animals with fur get enough sunlight to produce vitamin-D?
How is vitamin D synthesized in animals with fur; how do the cells get enough sunlight? If vitamin-D cannot be synthesized because of limited sunlight reaching the skin, do these animals have to obtain the vitamin from the diet or are there any alternate mechanisms of synthesis?


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What does common viruses found in the body weigh?
On NPR public radio news it was said that if the bacteria that is natural that assist in body function or just present in your body was put it into a ball it would weigh more or less 7 ounces (approximately 200 grams). I tried to find the exact quote but am still looking for it and will revise when I find it.
Can viruses assist in body function as in extending life in any way?
Can a body be 100% free of viruses of not how much would the total virus weigh if put in a ball?

It seems like after your edit you now have a bunch of questions rather than one.

Our analysis also updates the widely-cited 10:1 ratio, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and their total mass is about 0.2 kg. (0.4 pounds) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991899/

Possible duplicate of https://biology.stackexchange.com/q/74887/3340

Viruses, in general, are obligately pathogenic i.e. they don't usually co-exist (as commensals or symbionts) with our body cells. Their mechanism of survival involves usurping of the host cell machinery to produce their own proteins and genetic material. However, as pointed out in the comments, there are some viruses such as the GBV-C which can infect the host but seldom cause any disease. Moreover, this virus has been shown to have a positive effect on the innate immune response and inhibitory effect on HIV [1].
(Also, have a look at: Do beneficial viruses exist? If so, what examples are there?)
In our genome, here are some remnants of viruses that had infected our ancestors long back in past. A prominent example is that of retrotransposons. Retrotransposons are DNA sequences that constitute a significant part of our genome and they are structurally similar to the genome of retroviruses (like HIV). Retrotransposons had been considered junk DNA in the past but recent studies have shown that they do play some important roles in our body. For example, L1 retrotransposons cause somatic diversity (genetic diversity at the cellular level) of neurons and may possibly contribute to increasing the plasticity of our brain[2,3]. Retrotransposons can also regulate gene expression[4].
Other than that, there may be infectious viruses that are present in the body but are dormant. These may become active later (when the conditions are conducive) and cause the disease in that individual or spread to another person.
You can perhaps calculate the weight of these viral remnants (retrotransposons). It won't provide any great insight to anyone. You just have to calculate the percentage of genome these DNA sequences occupy and multiply it with molecular weight of the genomic DNA and total number of cells in the body. I'll leave that exercise to you.

Viruses are not obligately pathogenic. There are a number of free viruses (i.e., viruses that are not retrotransposons) that are beneficial. GBV-C, for example.

There are also many many viruses that do not appear to be associated with any disease, but have not been demonstrated to be beneficial. There is much still to be learned about the human virome.

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Bacteria surviving a β-lactam antibiotic
What changes can occur in the cell wall of a bacteria for it to survive a β-lactam antibiotic?
I think that because a bacteria possesses peptidoglycan in its cell wall, they are β-lactam sensitive, hence the only way it could survive a β-lactam treatment would be the presence of a resistance gene caused by a mutation.
I can't think of another way.
Any ideas?

There can be infinite possibilities actually. One can even say that the bacteria can evolve to make the cell wall made of a different material. This question is broad. Please add details to narrow down the question or else it will be closed.

There's no need to add more details, this question is the basis of a question I got from a General Microbiology exam a few years ago, now I'm studying for my exam. Moreover, the only detail was given in the exame was that the bacteria had peptidoglycan in its cell wall, and it survived a β-lactam treatment, then what changes may have occur in its cell wall?

This question formulated as it is, shows that I've thinked of it, I've developed my own theory. Moreover, I've read a lot the Brock's book and still I don't know the full answer to this question. I've seen lots of questions don't showing even a little bit of own work, and still with positive reviews. I see absolutely no reason for this question to be closed.

Just because it was asked in an exam doesn't make it a precise question. The possibility of a resistance gene, as you mentioned in your answer is one of the obvious reasons and I am pretty sure the examiner wants this only. However, as I said, there can be several reasons. Penicillin-binding proteins can lose their affinity to penicillin or cell wall composition itself might change such that penicillin has no effect. Bacteria can also express efflux pumps to remove ampicillin or simply the bacteria may remain as protoplast and survive the treatment.

I am not saying that this is a bad question. Just saying that there can be a lot of possibilities and hence the examiner who asked this question should have asked a better question. One way to make the question precise is to ask what are the documented mechanisms which let the bacteria survive the antibiotic treatment. Then we can at least not think of the myriad of theoretical possibilities.

@WYSIWYG, thanks. Your second comment it more like an answer. Then one answer could be saying some possibilities, and say that these are not all. That is all I wanted. New ideas.

Although changes in the bacterial cell wall are theoretically possible, I don't think this is really feasible since you need to change a lot of biosynthesis pathways and their enzymes in very short time.

What kind of Beta-lactam treatment? When using ampicillin resistant plasmids, I often skip the SOC media incubation and just plate the cells. They usually stay alive long enough to make the lactamase and then begin to grow on the media. It's also feasible that if the dose were insufficient the bacteria in question could "coast" until the antibiotic concentration was low enough to no longer matter, beta-lactams aren't exactly the most stable molecules around.


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Statistically, why is the number of mutated genes in eggs treated with chemical mutagenesis one?
Excerpted from the Guide to Research Techniques in Neuroscience [1]:

In chemical mutagenesis, a scientist applies a mutagenizing chemical, such as ethyl methane sulfonate (EMS) or N-ethyl-N-nitrosourea (ENU), to thousands of eggs/larvae, which statistically creates lines of ani- mals with mutations in a single gene in the genome.

My hypothesis is that the discrete probability distribution of the number of mutated genes can be approximated by a normal distribution with mean=1, thus it is said statistically the number of mutated genes is one. But how can the scientists know which organism or cells contains only one mutated gene, or for that matter one mutated gene that is caused only by chemical mutagenesis?

[1] Carter, Matt, and Jennifer C. Shieh. Guide to Research Techniques in Neuroscience. Academic Press, 2015. ISBN: 978-0-12-374849-2

The expected number of mutation would not follow normal distribution (ND) as you speculated because a ND would have negative values too as it ranges from $(-\infty,\infty)$, as Remi has also pointed out. In many cases a ND can be approximated because the variance would be so less that you can practically find no negative values. However, it is a wrong assumption to consider all biological statistics as ND by default. Please see this post. Basically, ND approximations can be made on multiple measurements that follow the central limit theorem. Now, in your case of a ND centered at 1, I'll tell you how that is impossible. You can have 2 and more than 2 mutations but you cannot have less than 0 mutations. The distribution is not symmetric and is skewed towards right. You also cannot have fractional mutations and therefore the distribution has to be discrete and not continuous.
Mutagenesis itself can be modelled as a Poisson process. For more information on this please see this post. So the probability of $k$ mutations in a time window, $t$, can be represented by the following equation:
$$P(n=k)=\frac{(\lambda t)^ke^{-\lambda t}}{k!}$$
Where $\lambda$ is the rate of mutagenesis.
The mean number of mutations (and also the variance for a Poisson distribution) would be $\lambda t$.
Now, the rate of mutagenesis would be proportional to the concentration of the mutagen. I speculate that the relationship between them would follow a saturation kinetics (like Michaelis-Menten) but at lower concentrations it would be essentially linear.
Moreover, the rate of mutagenesis would also depend on the cell type.
Therefore, standardization is required and labs working in this area for a long time develop standardized protocols (with specific mutagen concentrations and treatment times) which would let them avoid multiple mutations. Even then, they have to screen a lot of individuals to filter out the non-mutants.
Basically, there is no magic number.

What I think the text is saying
The text you quote is a little unclear (note that it is not a peer-reviewed article given the language used). I would think based on the quotation that the treatment is chosen so that the expected number of mutations is 1.

But how can the scientists know which organism or cells contains only one mutated gene?

You assume they are screening through the lines to find out those who contain a single mutation. This is not what the quoted text is claiming. The quoted text only states that the treatment create mutations at a rate of 1 per genome.
If they would have to screen through the lines to select those that have had one single mutation somewhere, then sequencing would be the only solution.
Note on Stats
The number of mutated genes after treatment is probably Poisson distributed, not normally distributed. A normal distribution is a continuous probability distribution anyway and is bounded between $-\infty$ and $+\infty$, while a negative number of mutations makes no sense.
Note on the design of the post
You should link to you source directly. It will be easier for those willing to answer

Not just because of the continuous nature, there cannot be a normal distribution with mean at 1 because there cannot be negative values for this whatsoever whereas there can be more than 2 mutations (which will skew the shape). You are right about Poisson distribution as we have discussed in your other post.

With the forward genetic screen approach you would treat the organism with your mutagen, and cross them to produce mutants. With forward genetics, you're using a phenotype to map out a gene. You isolate the mutants based on phenotype, and perform a complementation test to determine if the mutation was on the same gene or different genes. This was classically done with Drosophila.

By the classical genetics approach, a researcher would then locate (map) the gene on its chromosome by crossbreeding with individuals that carry other unusual traits and collecting statistics on how frequently the two traits are inherited together. Classical geneticists would have used phenotypic traits to map the new mutant alleles. Eventually the hope is that such screens would reach a large enough scale that most or all newly generated mutations would represent a second hit of a locus, essentially saturating the genome with mutations. This type of saturation mutagenesis within classical experiments was used to define sets of genes that were a bare minimum for the appearance of specific phenotypes. However, such initial screens were either incomplete as they were missing redundant loci and epigenetic effects, and such screens were difficult to undertake for certain phenotypes that lack directly measurable phenotypes. Additionally a classical genetics approach takes significantly longer.

Source: Wikipedia
The reason that I posted this answer is due to the context of chemical mutagenesis, provided on 335 of your source:

Chemical mutagenesis The use of chemical agents, such as EMS or ENU, to mutagenize
  hundreds or thousands of eggs/larvae for the purpose of performing a forward
  genetic screen.


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Disease-causing allele frequency and modern medicine
I was thinking about what the impact modern medicine might have on human evolution based on a couple assumptions.
If we assume that:

modern medicine has massively cushioned the selection pressure against people with inborn errors of metabolism, weak immune systems, disabilities, and genetic defects more broadly.
that these people, due to modern medicine, are able to live past reproductive age.
and that these people (broadly speaking) go on to produce offspring at the same or marginally lower rate as those without these defects.

could we expect to see these defect-causing alleles increasing in frequency in the now and more so in the future? or maybe at some point, given the constant improvements in modern medicine, these alleles essentially become fixed in subpopulations or maybe even the global population?

Can you please provide a reliable source for the massive cushioning modern medicine has provided these individuals? Thanks.

I can't find any study, but surely its reasonable to assume it. And I don't think there will even be studies in this topic for the near future anyways, given that there is no benefit from researching this. But that doesn't mean its perfectly resonable. for instance,  as a higher percentage of people who would've died from infection are kept alive at least up until reproductive age.

Your three down votes and close votes would argue against your certainty. This site requires you show your attempts to answer your own questions. If you hover over the DVD’s button, one reason is “shows no effort”.

It's worth considering that other factors such as sanitation and a plentiful and reliable food supply play by far the most major part in decreased mortality, then other confounding factors such as pollution and increasingly sedentary lifestyles make it even more tricky to identify what effect medicine has.

@anongoodnurse https://biology.stackexchange.com/questions/64424/where-do-birds-and-squirrels-go-to-die and https://biology.stackexchange.com/questions/89886/do-air-purifiers-work-against-bacteria-and-viruses both did not cite anything. and maybe because it was phrased in anecdotal way. But my question is abstracted from anecdote, I HAVE a genetic defect and without modern medicine I'd die before reproductive age, no doubt about it. Besides, I never claimed that my assumptions were true, what I said was IF these assumptions WERE true, could we expect to see such alleles increasing in frequency

@JiminyCricket surely, in some contexts we can, take the sickle cell hypothesis, if my hypothesis is true, then we'd expect to see that west african populations with good access to antimalarial drugs, vaccines, and bed nets have gradually lower frequencies of sickle cell carriage or disease. Also, food supply generally doesn't affect the relative frequency of alleles, it increases population count but doesn't make those with genetic defects more likely to propogate (unless the defect impacts diet, e.g. the ability to fast)

@anongoodnurse I can't cite any direct evidence, but I will list you diseases that without modern medicine and scientific knowledge would've cut short peoples lifespan to before reproductive age or affected their reproducetive abilty. Phenylketonuria, Cystinuria, Glycogen storage diseases, Lysosomal storage disease, Leukemias, Type 1 diabetes, Asthma, neurofibromatosis, Fibrodysplasia ossificans progressiva, porphyrias, hemophilia, IgG deficiency, Haemochromatosis, and so on.  and this exludes infections, so my point stands. It's reasonable.

This question is strongly associated with the pseudoscience of eugenics, and specifically the idea of "dysgenics", supposing that modern interventions "weaken" the gene pool. I don't suggest this is your intention, I merely point out the connection. For more information I'd google "medicine dysgenics", which brings up scholarship such as this. Trivially... sure, there is probably some effect. Substantially, it's not clear that this has much effect at all.

I believe @MaximilianPress has put it best. I also think you do not give credit to those with inborn errors of metabolism; most would not likely choose to procreate knowing that they are passing a fatal gene to their offspring. Anyone can claim anything on the internet. Did you know that I can fly? It’s an autosomal dominant mutation, obviously, because all of my children are good flyers as well. And the sun has no effect on our wings.

Finally, speaking as a physician, of the more than 1000 IEMs, only a metaphorical handful (not a massive cushion) can be treated with the individual reaching adulthood able to reproduce (for a variety of reasons). Some IEMs aren’t diagnosed until mid to late adulthood, so are probably common enough. Frame of reference is everything. Someone with a treatable IEM might win a Nobel prize someday for something that changes the world for the better. You never know.

@MaximilianPress I understand that that was always a possiblity because how easy it is to misinterpret what I'm trying to ask. But thank you, anyways for at least providing a use term, and an attempted answer, albeit without a source.

@anongoodnurse you bring up a good point, that people who are daignosed with genetic defects, IEM's, and disabilities might not choose to procreate. So the selection pressure is definitely not mitigated for alleles that cause those conditions. But I think there's definitely a grey area where negative selection is mitigated for those with alleles that cause mild to moderate disease that doesn't warrant genetic tests, which would also apply to polygenic traits like weaker immune systems, and certain mental disorders, for instance, but probably not to flying, though, sorry.

I’m so confused about what exactly it is that you’re asking… However, if you believe with any degree of certainty that medicine has massively cushioned the death rate from IEMs, why do you have difficulty believing that my offspring and I can fly? They’re about equally true…

@anongoodnurse I think you have missed my point. first of all, I'm not referring to IEM's across the board, nor am I referring to IEM's alone, I am saying modern medicine has massively cushioned negative selection pressure for CERTAIN ALLELES causing CERTAIN DISEASES. and therefore, WITH THE ASSUMPTIONS i have made, we should expect an increase in the frequency of such alleles. This is basic population genetics; removing or mitigating a selection pressure will cause alleles selected against to increase in frequency.

@anongoodnurse and who said I have difficulty believing you can fly, the traits practically fixed where I'm from ;) ,but you seem to have difficulty merely entertaining my position, perhaps its your ideology. Here's an example I'll try to explain, where I'm from Williams syndrome is underdiagnosed, and so what happens is only the resulting complication (usually cardiovascular) of Williams syndrome is treated, without the diagnosis of Williams syndrome being given. These treatments will prolong the life of the patient to at least reproductive age and so the alleles should increase in frequency.

Yes, in principle, but it could take a very long time. Consider phenylketonuria, which is a severe genetic disease that is completely preventable by excluding phenylalanine from one's diet. Suppose that PKU is now completely neutral due to our ability to screen for PKU alleles and counsel carriers appropriately (not to avoid reproducing, which would induce selection against PKU, but to make sure that their children are tested and put on an appropriate diet).
How long will it take PKU to fix due to genetic drift?
From here, the time to fixation
$$
E(T) = -4N_e [p \ln p + (1-p) \ln (1-p)] \textrm{ generations}
$$
where $N_e$ is the effective population size and $p$ is the starting frequency (this counts fixation at either 0% or 100% but should be a lower bound for fixation at 100%).
The highest frequency of PKU in any population in the world is around 70% (Gundarova et al. 2018); starting from here, the fixation time would be $0.63 N_e$ generations. Even in a very small population (e.g. $N_e = 200$), this will take hundreds of generations/thousands of years ...
The time scale might be much shorter if there were positive selection, i.e. some selective advantage to carrying the allele that also/formerly caused disease. This is known, or speculated, to be the case for many deleterious recessive alleles (sickle-cell, thalassemia, cystic fibrosis ...). However, in many of these cases the selective advantage is against infectious diseases such as malaria whose effects have also been mitigated by modern medicine ...

Gundorova, Polina, Rena A. Zinchenko, Irina A. Kuznetsova, Elena A. Bliznetz, Anna A. Stepanova, and Aleksander V. Polyakov. “Molecular-Genetic Causes for the High Frequency of Phenylketonuria in the Population from the North Caucasus.” PLoS ONE 13, no. 8 (August 1, 2018): e0201489. https://doi.org/10.1371/journal.pone.0201489.

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


text:
Can SARS-COV2 strain competition be modelled by inter-species lotka volterra equations?
Currently studying infectious diseases epidemiology and never studied ecology. But I was wondering if the interspecies Lotka Volterra equations could model and explain strain dominance.
r = could be the effective reproductive number of the virus;
x = prevalence of people currently infected with a certain strain;
alpha = formally is the inhibitive effect of species one on species two; Here I think they'd be equal to each other. if a strain infects someone, he or she cannot be infected by the other competing strain.
Finally K, which is in the ecological context, the carrying capacity defined as the maximum number of individuals of that species the ecosystem is able to accommodate, where the number of births is equal to that of deaths so for this case it may be defined as the prevalence of the strain where the number of infected individuals remain at an equilibrium i.e. every infected person infects, on average, one other person so the effective reproductive number = 1.
So for instance Omicron and Delta in the UK.
where it took omicron only one month to supplant delta as the dominant strain.

https://www.frontiersin.org/articles/10.3389/fmicb.2020.572487/full

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In addition, note that "if a strain infects someone, he or she cannot be infected by the other competing strain" is unlikely to be true — one of the ways that viruses change occurs when different viruses infect the same cell. If you have evidence that this can't happen for coronaviruses, please add that to your question.

@tyersome its more parsimonious to assume that active infection with a particular strain will constrain another strain from establishing infection when exposed, given that the innate immune response is heightened making the respiratory tract inhospitable. And besides as far as we know human coronaviruses do not undergo antigenic drift. So what i really meant was once a person is infected and becomes symptomatic, they will not be able to be infected with the competing strain until the person becomes susceptible to the competing strain again (because of cross protection)

From everything I’ve read about SARS-CoV-2, it absolutely has experienced antigenic drift throughout the pandemic. Of course, the sensitivity of an existing immune response (or priming due to vaccine or a prior infection) to that drift is still an area of research. That said, the degree of vaccine escape by omicron (along with the many mutations relative to past variants) implies some amount of antigenic drift.

@Greenstick sorry I meant to say antigenic SHIFT not drift. Because tyersome was implying that coinfection of the same cell could produce genetically distinct strains, which is the definitely the case with flu but not so with human coronaviruses.

FWIW, coronaviruses can recombine too, just not in the same way as influenza.

Presumably by "interspecies Lotka-Volterra equations" you mean the L-V competition equations (the predator-prey version is much better known).
Let's start with a two-strain epidemiological model without coinfection, i.e. a host can only be infected by one strain at a time:
$$
\begin{split}
S' & = S (-\beta_1 I_1 + \beta_2 I_2) \\
I_1' & = \beta_1 S I_1 - \gamma_1 I_1 \\
I_2' & = \beta_2 S I_2 - \gamma_2 I_2 \\
R' & = \gamma_1 I_1 + \gamma_2 I_2
\end{split}
$$
This doesn't look like the L-V competition equations, which reach some sort of competitive equilibrium, because there is no renewal of the "resource" (in this case, susceptible people); the epidemic runs its course and dies out. However, we could allow waning immunity and make an SIRS model so that the recovered people eventually become susceptible again:
$$
\begin{split}
S' & = S (-\beta_1 I_1 + \beta_2 I_2) + \phi R \\
R' & = \gamma_1 I_1 + \gamma_2 I_2 - \phi R
\end{split}
$$
(the $I$ equations stay the same). This is getting closer, but still doesn't quite match the LV equations. We have to take one more step (which is actually away from the direction of a realistic COVID-19 model) and allow recovering people to become susceptible immediately (i.e. no immunity, as in a disease like gonorrhea), so that we get:
$$
\begin{split}
S' & = S (-\beta_1 I_1 + \beta_2 I_2) + \gamma_1 I1 + \gamma_2 I_2 \\
I_1' & = \beta_1 S I_1 - \gamma_1 I_1 \\
I_2' & = \beta_2 S I_2 - \gamma_2 I_2 \\
\end{split}
$$
This is an "SIS" model. In the SIS and SIRS models the population size is constant, so in particular for the SIS model we can write $S = N -  I_1 - I_2$ and drop the redundant $S$ equation so we get
$$
\begin{split}
I_1' & = \beta_1 (N - I_1 - I_2) I_1 - \gamma_1 I_1 \\
I_2' & = \beta_2 (N - I_1 - I_2) I_2 - \gamma_2 I_2 \\
\end{split}
$$
which we can rearrange to
$$
I_1' = (\beta_1 N - \gamma_1) I_1  - \beta_1 I_1^2 - \beta_1 I_1 I_2
$$
and a symmetric equation (exchanging $_1$ and $_2$ subscripts) for $I_2$. We can rewrite this as
$$
I_1' = (\beta_1N-\gamma_1) I_1 \left( 1 - \frac{I_1 + I_2}{N-\gamma_1/\beta_1}\right)
$$
Comparing this with  (one particular parameterization of) the L-V competition equations,
$$
N_1' = r_1 \left( 1 - \frac{N_1 + \alpha_{21} N_2}{K_1} \right)
$$
We see that these are equivalent with $r_1 \equiv \beta_1 N - \gamma_1$, $K_1 = N-\gamma_1/\beta_1$, $\alpha_{21} = 1$.
A few general comments:

a lot of your guesses are right. For this case the two strains are equivalent (each occupies one unit of "resource", i.e. one susceptible host), so $\alpha_{12} = \alpha_{21} = 1$.
the r in the L-V equations is a growth rate (i.e. rate of exponential increase when rare), not a growth multiplier per generation ($R$ or ${\cal R}$), so it's $\beta N - \gamma$ (with units of 1/time) rather than $\beta N/\gamma$ (unitless)
The carrying capacity is indeed the number of hosts infected by $I_1$ at a monoculture equilibrium, i.e. $N ( 1- 1/{\cal R}_{0,1})$
in order to have a usefully realistic model of COVID-19 competition, you would probably need some of the following:

go back to a short time scale and forget about the detailed equivalence with the L-V model
allow for imperfect cross-immunity, i.e. one of omicron's big advantages is that it appears to be able to reinfect people who have recovered from delta while the converse seems less likely (although that is much less well known)

the assumption of no co-infection seems like a reasonable simplification, given that the prevalence (fraction of the population infected) is low relative to the population size even at the peak of a COVID-19 spike (i.e., a small percentage of the population has an active infection)

Wow, thank you! I wonder if there is an established field devoted to modelling infectious diseases epidemiology as ecological phenomena, I am defnintely interested to dig deeper! Thank you again for the answer!

There are very close connections between ecological and epidemiological modeling. For example, Robert May https://en.wikipedia.org/wiki/Robert_May,_Baron_May_of_Oxford was both a theoretical ecologist and an  eminent epidemiological modeler. One other example: Martcheva, Maia, Benjamin M Bolker, and Robert D Holt. “Vaccine-Induced Pathogen Strain Replacement: What Are the Mechanisms?” Journal of the Royal Society Interface 5, no. 18 (January 6, 2008): 3–13. https://doi.org/10.1098/rsif.2007.0236.

I'm wondering now why strictly adhering to the L-V model would not result in a useful/realistic COVID-19 model for predicting strain competition. Is it because of practical factors such as vaccination and lockdowns (and other interventions) or is it inherent to the model itself?

The most unrealistic aspect is that it assumes there is no natural immunity after recovery.


text:
Why is the thyroid gland in the neck?
The neck seems like an odd place for it. All other neck anatomy must interface between the head and abdomen (trachea, esophagus, circulation, spine etc).
Surprisingly I have not been able to find any explanation for the thyroid’s location.

Why does the neck "seem a vulnerable place"? If you get a neck injury, the thyroid is the least of your worries. Especially in fish (the thyroid evolved early in vertebrate evolution).

You’re right. I removed that part.

I don't understand the downvotes, I think it is a valid question. Maybe people cannot face that they have no idea. :D

Almost certainly not the pituitary proximity hypothesis. Simple counter-examples include the adrenal gland (ACTH-cortisol axis), liver (GH-IGF1 axis) and  the gonads (LH/FSH axis).

Tib is referring to the theory that the the thyroid must be close to the pituitary to respond to TSH stimulation. I have since removed that theory from my original question.

@Doug I don't think so. We are talking about hormones and to be regulated by hormones you don't have to be close to the source, they travel with the blood. Maybe this way it can answer in 1 min instead of 5 mins, but I don't think that makes a real difference. Maybe you would freeze to death easier if it were be lower, but that is just a guess. I think the real answer is something totally different and we should read more about the evolution of this organ.


text:
Preventing paracetamol overdose
Paracetamol overdose is one of the most common drug toxicities. It may be treated by intravenous N-acetylcysteine which replaces the glutathione that is used up in paracetamol metabolism to prevent the harmful effects of NAQBI.
Why can glutathione, NAC nor an inhibitor of the alternate cytochrome metabolism be added to paracetamol to prevent the possibility of acute liver failure? I imagine there is a reason as this is too obvious a solution.

I cannot recall the sources, but I remember that a) glutathione is not well absorbed as a supplement and b) N-acetycystein has some possible side-effects that are too harmful to give it regularly together with paracetamol. Maybe checking the wikipedia article of glutathione might give some of the sources for this, but I think parts of it I got from the german version.

As skymninge correctly states N-acetycysteine has some side effects. Most serious of which is anaphylaxis. I should think giving a medication to huge amounts of people that can cause anaphylaxis would cause more deaths than it would help prevent due to paracetomol overdose.

I assume you mean "why can't glutathione, NAC .. be added"
From lef.org

There is one problem. The FDA prohibits combining existing drugs and
  dietary supplements unless a New Drug Application is filed, tens of
  millions of dollars of clinical studies are performed, and the FDA
  agrees to allow the combination to be sold. The whole process can cost
  upwards of $100 million and take a decade to complete.

It's sad that would would be very likely an effective solution for the deaths and liver damage is not available or made more widely known.
Only about 10% of acetaminophen is metabolised through the glutathione conjugation pathway via NAQBI (the other 90% is direct sulfation and glucuronidation of acetaminophen). Many people take NAC supplements regularly (I used to).  While high does can have some side effects, a typical supplement level dose of a few hundred milligrams daily are well tolerated.


text:
Cranial Nerve Decussation
I want to get my head round this once and for all so if you guys could help me would really appreciate it! I understand lesions to the optic nerve. It is the other nerves that I find difficult.
So far this is my understanding, please correct me if I'm wrong. The cranial nerves do not decussate generally with exceptions being CN2, CN4, CN7 and CN12. That means if a lesion affects Cranial Nerve 1, 5, 8, 9 and 11 or the respective nucleus there is either sensation loss or atrophy of the muscle (dependent on what the nerve does) of the ipsilateral side. For example in a lesion affecting CN6, the eye cannot look out in the side of the lesion.
In the case of CN4, I'm not too sure what happens but I imagine if there is damage to the nucleus the opposite side is affected (meaning superior oblique in the contralateral side will not work). If the nerve is affected, it is typically the ipsilateral side. The same I imagine is true for CN12.
In CN7, the forehead is bilaterally innervated so if the upper motor neurone is affected eyebrows can be raised but the lower side of the face is affected ipsilaterally. In a lower motor neurone lesion, there is complete loss of one side of the face ipsilaterally.
Am I correct?

As you mentioned, the resulting impairment depends on the level of the injury: nuclear, fascicular, central / peripheral. So, you should differentiate lesions inside the brain tissue (which can be at nucleus, at any location of a tract, before crossing or after, and outside. From this, the first thing we should explain is the normal anatomy.  From normal anatomy we can understand the pathology.
One interesting fact you probably wanted to know is that Optic Nerve it not a real nerve in a classic definition, because it begins outside the brain as grouping axons of RGCs (retinal ganglion cells) and after leaving the eye becomes a “nerve”. From this, you can understand its damage better, because the damage to the visual fields depends on the level of insult.
IV nerve is the only cranial nerve that completely crossed (decussated). Thus, the lesion before the crossing/decussation (you were right mentioning the nucleus, but we extend the “region” until the decussation) will cause palsy and consequent atrophy contralaterally to the lesion. After the decussation the palsy and atrophy will be ipsilateral.
Considering cranial nerve XII we should speak about nuclear-infranuclear and supranuclear damage and with this notion supranuclear damage will cause contralateral transient tongue paresis. Nuclear-infranuclear damage will cause more permanent palsy, which is mostly bilateral because the nuclei are close to each other.
Considering VII pair, nuclear-intranuclear damage (“peripheral”) will cause ipsilateral hemifacial palsy including the brow and eyelid, while supranuclear (“central”) lesion will cause contralateral facial palsy with brow/eyelid sparing.

I just wanted to add, regarding CN VII.
CN VII receives stimulation via the facial nucleus from both the ipsilateral and the contralateral corticobulbar tracts. The upper muscles of facial expression (particularly around the eyes) receive stimulation from both the ipsilateral and the contralateral corticobulbar tracts. The lower portion of the face is innervated only from the contralateral corticobulbar tract. So in case of a stroke which wipes out an entire track (either left or right), there will be total loss of the lower muscles of facial expression, however there will be some sparing of the upper muscles because of the ipsilateral pathway redundancy.

Classically, only the CN.IV "decussates" (at the superior medullary velum) but some cranial nerve nuclei are on the contralateral side, so a lesion to the upper moto neurone or to cranial nerve nucleus of some cranial nerves will cause a contralateral deficits.
This is seen in cranial nerves VII & XII
Lesions at the lower motor neuron of cranial nerves will always cause an ipsilateral deficit.
As Daniel has pointed out, the upper motor neurons (corticobulbar tracts) that serve the facial nerve  (CN.VII) send fibres to synapse with both ipsilateral and contralateral lower motor neuron of the facial nerve, hence, the redundancy. This redundancy unfortunately does not involve the facial nerve that supplies the lower face (from the lower lip downwards).
If there is a lesion to the upper motor neurone that supplies the facial nerve on one side, there will be a contralateral paralysis of only the lower lip but not of the upper face because of the redundant supply to the upper face by the upper motor neurone on that side of the face.
A lesion to the lower motor neuron of the facial nerve as in Bell's Palsy will result in an ipsilateral paralysis of both the upper face and lower lip.

thanks for your contribution... though if you could add some external sources for validation it would be greatly appreciated. This is mostly for individuals to read further who do not have a good background in the question/answer.


text:
How does protein denaturation work?
I was wondering how protein denaturation works.

Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation irreversible in most cases if only non-covalent bonds are involved?
Is it possible to denature protein by rapid changes in electromagnetic field or pressure? (The articles I have read so far mention only stress factors like sudden pH, osmolarity, temperature changes...)
How can I protect a protein against denaturation? e.g. in PCR we use a heat resistant DNA polymerase, so certain amino acid sequences might protect against heat denaturation, but I need reassurance about this.

I investigated the topic too, so here is my answer.
To understand thermodinamic stability of water solved globulins or membrane proteins (all of them proteins hereafter) we have to understand protein folding. Proteins have a 3d structure (composed by their primary, secondary and tertiary structures). The structure of the proteins is constantly changing between the folded and unfolded states. The folded state has a lower free energy while the unfolded state has a higher. Between them there is a free energy barrier which determines the speed of the folding on a specific temperature.
Changing structural on environmental factors can affect these free energies and can shift the equilibrium to the unfolded state. The unfolded protein can suffer irreversible changes (aggregation, disulphide exchange, proteolysis, irreversible subunit dissociation, chemical degradation, etc...), so the denaturation of the protein can be reversible or irreversible.
Note that this is a very simplistic view, I think there are different degrees of unfoldedness, and so different things can happen when the protein is in one of these. For instance by a low degree of unfoldedness misfolding can happen which results a stable, but inactive folded state without coagulation (this can be more or less reversible). By a higher degree of unfoldedness coagulation can happen.
Folding mostly depends on one simple rule: all of the hydrogen bonds have to be satisfied, because a non-satisfied hydrogen bond has a very high energetic cost. The proteins have polar surfaces, which form hydrogen bonds with the water, and one or more apolar center, which have inner hydrogen bonds as backbones. Burial of an unpaired polar amino-acid (e.g. non-satisfied hydrogen bond) is very destabilizing and so it is non-existent in natural working proteins. Other factors, like salt bridges, aromatic-aromatic interactions, disulphide bonds, etc... can affect the stability as well, but hydrogen bonds and hydrophobic interactions are the major factors. The weights of these two major factors is most likely protein dependent (a study suggested 75% and 25%, while another 40% and 60%).
The backbone hydrogen bonds are usually most stable around room temperature, so the lowest free energy and the maximum stability is around 20°C by most proteins and both heating and cooling lowers the stability and can lead to denaturation. High temperatures (>80°C) can cause covalent degradation, and so irreversible denaturation. Pressure has similar effect on the hydrogen bonds and the stability as cold denaturation.
The osmolyte cosolvents like urea or TMAO contribute differently to the free energy of the folded and unfolded states and so shift the equilibrium between them. for example urea can cause denaturation, while TMAO protects the protein from denaturation. I think it is evident that changing pH and saltiness has strong effect on the charges of the amino acid side chains, and so the hydrogen bonds and the stability.
Both ultrasound and pulsed electric field (PEF) can cause denaturation. The effect seems strongly depending on the parameters of ultrasound/PEF and the type of the protein. Interesting that PEF can increase the enzyme activity too. It is hard to find studies about the denaturation mechanisms by these methods.
If we want to increase the protein stability, the method we choose can depend on what we want to protect the protein from. One or more methods from the following list can help to increase the stability:

increase of compactness and better packing (minimalization of surface/volume ratio)
increase of electrostatic interactions (formation of additional ion pairs, e.g. more glutamic acid)
additional hydrogen bonds
additional disulphide bridges
increasing hydrophobic interactions (greater proportion of buried hydrophobic residues)
change protein microenvironment (use osmolytes, change pH, saltiness)
glycosylate the protein surface
decrease chain length
change surface amino-acids (the effect can be completely unpredictable, but there are surface residue patterns with known effect on stability; add more ionisable amino acids to the surface; bury hydrophobic residues; etc...)
protein fixation can change the stability as well

References:

Thermodynamic stability of a protein that unfolds and refolds rapidly,
  reversibly, cooperatively, and with a simple, two-state mechanism. The
  easiest proteins in which to study folding and stability are those
  that exhibit this sort of rapid reversibility. Both experimental
  design and also theoretical treatment of data are simplified by
  reversible systems. Thus, it is no surprise that most of the
  literature reports about stability discuss this type of reversible
  system. The stability of the protein is simply the difference in Gibbs
  free energy, dG, between the folded and the unfolded states. The only
  factors affecting stability are the relative free energies of the
  folded (Gf) and the unfolded (Gu) states. The larger and more positive
  Gu, the more stable is the protein to denaturation.
If a protein unfolds reversibly it may be fully unfolded and inactive
  at high temperatures, but once it cools to room temperature, it will
  refold and fully recover activity. In the case of irreversible or
  slowly unfolding proteins, it is kinetic stability or the rate of
  unfolding that is important. A protein that is kinetically stable will
  unfold more slowly than a kinetically unstable protein. In a
  kinetically stable protein, a large free energy barrier to unfolding
  is required and the factors affecting stability are the relative free
  energies of the folded (Gf) and the transition state (Gts) for the
  first committed step on the unfolding pathway. Irreversible loss of
  protein folded structure is represented by: F <-> U -> I, where I is
  inactive due to aggregation, disulphide exchange, proteolysis,
  irreversible subunit dissociation, chemical degradation, etc...

1996 - The Source of Stability in Proteins
2009 - Charge–charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
2006 - Why Are Proteins Charged? Networks of Charge–Charge Interactions in Proteins Measured by Charge Ladders and Capillary Electrophoresis

Evidence from proteins and peptides supports the conclusion that
  intrapeptide hydrogen bonds stabilize the folded form of proteins.
  Paradoxically, evidence from small molecules supports the opposite
  conclusion, that intrapeptide hydrogen bonds are less favorable than
  peptide–water hydrogen bonds. A related issue—often lost in this
  debate about comparing peptide–peptide to peptide– water hydrogen
  bonds—involves the energetic cost of an unsatisfied hydrogen bond.
  Here, experiment and theory agree that breaking a hydrogen bond costs
  between 5 and 6 kcal/mol. Accordingly, the likelihood of finding an
  unsatisfied hydrogen bond in a protein is insignificant. This
  realization establishes a powerful rule for evaluating protein
  conformations.
In their description of the alpha-helix, Pauling et al. (1951)
  asserted that the energy of the peptide N–H• • •O=C hydrogen bond was
  of order -8 kcal/mol, and that “such instability would result from the
  failure to form these bonds that we may be confident of their
  presence.” Pauling’s earlier estimate of the total protein hydrogen
  bond energy was -5 kcal/mol (Mirsky and Pauling 1936). From solution
  studies of urea dimers, Schellman estimated that an intrapeptide
  hydrogen bond would be enthalpically favored over a peptide–water
  hydrogen bond by ~1.5 kcal/mol (Schellman 1955). These and similar
  early studies led to the conclusion that the peptide hydrogen bond is
  a significant factor in stabilizing protein conformations.
This view was to change dramatically following a famous review by
  Kauzmann (1959), who invoked the thermodynamics of small model
  compounds to argue that stabilization of the folded state of a protein
  is due almost exclusively to the hydrophobic effect. Soon after
  Kauzmann’s proposal, Klotz and Franzen (1962) determined that the
  enthalpy of the interamide hydrogen bond of N-methyl acetamide in
  water was zero, and concluded that “the intrinsic stability of
  interpeptide hydrogen bonds in aqueous solution is small.” Similarly,
  hydrogen bonding involving another small molecule,
  epsilon-caprolactam, in dilute solution was shown to be negligible
  (Susi and Ard 1969). Kauzmann’s proposal, bolstered by these later
  studies, led to the widely held view that the hydrophobic effect makes
  the major energetic contribution to protein stability, with hydrogen
  bonds contributing little, or perhaps even opposing, the folding
  process. See Baldwin (2003) for a recent discussion of these issues.
Protein hydrogen bonds are ubiquitous, directional, and largely local,
  partitioning the polypeptide chain into alpha- and 3_10-helices,
  beta-sheet, and beta-turns. Together, these hydrogen-bonded backbone
  structures account for at least 75% of the conformation, on average,
  with remaining residues participating in both additional
  intramolecular hydrogen bonding and hydrogen bonding to water.
  Unsatisfied backbone polar groups are energetically expensive, to the
  degree that they almost never occur.
Force measurements between surfaces functionalized with lipids having
  hydrogen bonding headgroups (NTA, A, T, and MeT lipids) lead to a
  reproducible value of the energy of a single hydrogen bond in pure
  water: ~0.5 kcal/mol. It shows that it is energetically more favorable
  for the headgroups to make hydrogen bonds with each other than to make
  hydrogen bonds with water molecules. This is coherent with past
  studies made on proteins stability, which showed that intramolecular
  hydrogen bonds in a folded protein are energetically more favorable
  than bonds with water molecules in an unfolded protein with an average
  stabilization of ~1 kcal/mol per intramolecular hydrogen bond.

1996 - Forces contributing to the conformational stability of proteins.
2005 - Do all backbone polar groups in proteins form hydrogen bonds?
2011 - Backbone-Driven Collapse in Unfolded Protein Chains
2006 - Hydrophobic collapse in (in silico) protein folding
2002 - Thermodynamic Consequences of Burial of Polar and Non-polar Amino Acid Residues in the Protein Interior
2003 - Thermodynamics of Heat Activation of Single Capsaicin Ion Channels VR1
2003 - Temperature Range of Thermodynamic Stability for the Native State of Reversible Two-State Proteins
2009 - Protein Cold Denaturation as Seen From the Solvent
2010 - Construction of Peptoids with All Trans-Amide Backbones and Peptoid Reverse Turns via the Tactical Incorporation of N-Aryl Side Chains Capable of Hydrogen Bonding
2002 - Energy of Hydrogen Bonds Probed by the Adhesion of Functionalized Lipid Layers
2012 - How, when and why proteins collapse: the relation to folding
2011 - Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation
2011 - Membrane protein folding: how important are hydrogen bonds?

The main determinant of cold denaturation tendency is likely the
  stability decrease of backbone hydrogen bonds at low temperatures,
  which in turn is affected by the packing manner of the hydrophobic
  core cluster
Using a newly developed pressure cell, we have now mapped pressure-
  and temperature-dependent changes of 31 hydrogen bonds in ubiquitin by
  measuring HBCs with very high precision. Short-range hydrogen bonds
  are only moderately perturbed, but many hydrogen bonds with large
  sequence separations (high contact order) show greater changes. In
  contrast, other high-contact-order hydrogen bonds remain virtually
  unaffected.
We study the stability of globular proteins as a function of
  temperature and pressure through NPT simulations of a coarse-grained
  model. We reproduce the elliptical stability of proteins and highlight
  a unifying microscopic mechanism for pressure and cold denaturations.
  The mechanism involves the solvation of nonpolar residues with a thin
  layer of water. These solvated states have lower volume and lower
  hydrogen-bond energy compared to other conformations of nonpolar
  solutes. Hence, these solvated states are favorable at high pressure
  and low temperature, and they facilitate protein unfolding under these
  thermodynamical conditions.
We further find that it is the changes in hydrophobic hydration with
  decreasing temperature that drive cold unfolding and that the overall
  process is enthalpically driven, whereas heat denaturation is
  entropically driven.
As a consequence of a weaker penetration upon pressurizing, it was
  found that the pressure-denatured state was partially unfolded
  compared with the heat-denatured state. The mechanism of pressure
  denaturation was related to the disruption of the hydrogen-bond
  network of water onto a set of clusters characterized by strengthened
  O – H interactions, inducing a hardening of protein dynamics. The
  mechanism is opposite to that observed upon heating, i.e., the
  softening of the hydrogen bond network of water inducing a softer
  protein dynamics.
We can conclude that the main driving force of protein denaturation at
  high pressures is the decrease of the hydrophobic effect as a
  consequence of the changes in water structure, without contradicting
  any of the current theories on the hydrophobic effect.
For the pressure denaturation the weakening of the hydrophobic
  interaction between the bulky side chains is found to be crucial at
  lower temperatures, leading to an apparent destabilization of the
  folded backbone structure at elevated pressures.

2013 - Molecular dynamics simulation indicating cold denaturation of beta-hairpins.
2012 - Cold-Induced Changes in the Protein Ubiquitin
2008 - Microscopic Mechanism for Cold Denaturation
2009 - Hydrophobicity at low temperatures and cold denaturation of a protein
2012 Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network
2012 - Unifying Microscopic Mechanism for Pressure and Cold Denaturations of Proteins
2012 - Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation
2011 - Molecular mechanisms of the anomalous thermal aggregation of green fluorescent protein
2011 - Analysis of the Mechanism of Lysozyme Pressure Denaturation from Raman Spectroscopy Investigations, and Comparison with Thermal Denaturation
2008 - Cold- and Pressure-Induced Dissociation of Protein Aggregates and Amyloid Fibrils
2009 - The Behavior of the Hydrophobic Effect under Pressure and Protein Denaturation
2004 - Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study

It is found that the energetics involving backbone hydrogen bonding
  controls these shifts in protein stability almost entirely, with
  osmolyte cosolvents simply dialing between solvent-backbone versus
  backbone-backbone hydrogen bonds, as a function of solvent quality.

2008 - Structure and Energetics of the Hydrogen-Bonded Backbone in Protein Folding
2008 - Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group
2011 - Backbone and Side-Chain Contributions in Protein Denaturation by Urea
2009 - On the mechanism of SDS-induced protein denaturation
1995 - Hydrogen Bonds and the pH dependence of Ovomucoid Third Domain Stability
2004 - Effects of Chaotropic and Kosmotropic Cosolvents on the Pressure-Induced Unfolding and Denaturation of Proteins:? An FT-IR Study on Staphylococcal Nuclease
2002 - The hydration structure of guanidinium and thiocyanate ions: Implications for protein stability in aqueous solution

Overall, the sonication process had little effect on the structure of
  proteins in WPC solutions which is critical to preserving functional
  properties during the ultrasonic processing of whey protein based
  dairy products.
The data presented here suggest that among proteins of fibrinolytic
  systems, the fibrinogen is one of the most sensitive proteins to the
  action of ultrasound. It has been shown in vitro that ultrasound
  induced fibrinogen aggregates formation, characterized by the loss of
  clotting ability and a greater rate of plasminolysis than native
  fibrinogen in different model systems and under different mode of
  ultrasound treatment.

2011 - Effects of ultrasound on the thermal and structural characteristics of proteins in reconstituted whey protein concentrate
2011 - Effects of low frequency ultrasound on some properties of fibrinogen and its plasminolysis

The results obtained with the different experimental protocols
  indicate, however, that the conformational equilibrium of GrpE is
  insensitive to electromagnetic fields in the tested range of frequency
  and field strength.
Effects of pulsed electric fields (PEF) treatment (0–547 µs and 0–40
  kV/cm) on physicochemical properties of soybean protein isolates (SPI)
  were studied. Solubility, surface free sulfhydryls (SHF) and
  hydrophobicity of SPI dispersions (20 mg/ml) increased with the
  increment of the PEF strength and treatment time at constant pulse
  width 2 µs, pulse frequency 500 pulse per second (pps) and sample flow
  rate (1 ml/s). When the PEF strength and treatment time were above 30
  kV/cm and 288 µs, solubility, surface SHF, and hydrophobicity of SPI
  decreased due to denaturation and aggregation of SPI by hydrophobic
  interactions and disulfide bonds. Size-exclusion chromatography and
  laser light scattering analyses demonstrated further that stronger PEF
  treatment-induced dissociation, denaturation and reaggregation of SPI.
  Circular dichroism analysis showed that PEF treatment did not produce
  significant secondary structure changes of SPI.
A compact and low cost bench-top, pulsed electric field treatment
  system was designed and developed. The unit consisted of a
  high-voltage pulse generator (? 30 kV) and a treatment chamber with ?
  148 ml capacity. Over the set-up voltage range of 4–26 kV, 30 pulses
  (with instant charge reversal) were applied to eight different enzyme
  solutions using a 0.3-cm electrode distance, a 13–87 kV/cm field,
  0.5-Hz pulse frequency, 2-µs pulse width and 20 °C process temperature. For some enzymes, activities were reduced after the pulse
  treatments: lipase, glucose oxidase and heat-stable ?-amylase
  exhibited a vast reduction of 70–85%; peroxidase and polyphenol
  oxidase showed a moderate 30–40% reduction whereas alkaline
  phosphatase only displayed a slight 5% reduction under the conditions
  employed. On the other hand, the enzyme activities of lysozyme and
  pepsin were increased under a certain range of voltages. Electric
  pulse profile (instant charge reversal) played a very important role
  in reducing the activities of various enzymes.
Effects of high-voltage pulsed electric field (PEF) on native or
  thermal denatured enzyme activities were studied. When PEF was applied
  to various native enzymes, 105–120% of initial enzyme activities were
  observed after PEF treatment. It was suggested that an activation of
  enzyme would be possible by PEF treatment. We attempted a refolding of
  thermal denatured enzyme by using PEF. When PEF was applied to
  denatured peroxidase, enzyme refolding was accelerated in PEF and 60%
  of initial activity was observed after 12 kV/cm and 30 s of PEF
  treatment although spontaneous refolding of this enzyme resulted in
  40% of initial activity. On the other hand, when PEF was applied to
  thermal denatured lactate dehydrogenase (LDH), further PEF-induced
  inactivation was observed. It was suggested that the influence of PEF
  is dependent on the type of enzyme.

2014 - Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability
2007 - Effects of pulsed electric fields on physicochemical properties of soybean protein isolates
1997 - Effects of high field electric pulses on the activity of selected enzymes
2007 - Influence of pulsed electric field on various enzyme activities

In halophiles, protein stability and function are maintained by
  increased ion binding and glutamic acid content, both allowing the
  protein inventory to compete for water at high salt. Acidophiles and
  alkalophiles show neutral intracellular pH; proteins facing the
  outside extremes of pH possess anomalously high contents in ionizable
  amino acids.
These facts suggest that globular proteins should be maximally stable
  around room temperature. Twenty-six of these are unique, and 20 of the
  26 are maximally stable around room temperature irrespective of their
  structural properties, the melting temperature, or the living
  temperatures of their source organisms. Their average temperature of
  maximal stability is 293 ± 8 K (20 ± 8 °C).   The average energetic
  contribution of the individual amino acids toward protein stability
  decreases with an increase in protein size.
Analysed in terms of their effect on the protein structure, the ways
  in which thermophilic organisms obtain relative stabilization of their
  proteins can be classified as follows:

increase of compactness and better packing
increase of electrostatic interactions
additional hydrogen bonds
additional disulphide bridges
increasing hydrophobic interactions
protein microenvironment
glycosylation

The rational modification of protein stability is an important goal of
  protein design. Protein surface electrostatic interactions are not
  evolutionarily optimized for stability and are an attractive target
  for the rational redesign of proteins. We show that surface charge
  mutants can exert stabilizing effects in distinct and unanticipated
  ways, including ones that are not predicted by existing methods, even
  when only solvent-exposed sites are targeted. Individual mutation of
  three solvent-exposed lysines in the villin headpiece subdomain
  significantly stabilizes the protein, but the mechanism of
  stabilization is very different in each case. One mutation
  destabilizes native-state electrostatic interactions but has a larger
  destabilizing effect on the denatured state, a second removes the
  desolvation penalty paid by the charged residue, whereas the third
  introduces unanticipated native-state interactions but does not alter
  electrostatics. Our results show that even seemingly intuitive
  mutations can exert their effects through unforeseen and complex
  interactions.
These results suggest that surface charge-charge interactions are
  important for protein stability and that rational optimization of
  charge-charge interactions on the protein surface can be a viable
  strategy for enhancing protein stability.
We have discovered a novel property of single-walled carbon nanotubes
  (SWNTs)their ability to stabilize proteins at elevated temperatures
  and in organic solvents to a greater extent than conventional flat
  supports. Experimental results and theoretical analysis reveal that
  the stabilization results from the curvature of SWNTs, which
  suppresses unfavorable protein-protein lateral interactions. Our
  results also indicate that the phenomenon is not unique to SWNTs but
  could be extended to other nanomaterials. The protein-nanotube
  conjugates represent a new generation of active and stable catalytic
  materials with potential use in biosensors, diagnostics, and bioactive
  films and other hybrid materials that integrate biotic and abiotic
  components.
The main chain to side chain salt bridge between the N-terminus and
  Glu 14 was, however, found to stabilize PFRD-XC4 by 1.5 kcal mol-1.
  The entropic cost of making a surface salt bridge involving the
  protein's backbone is reduced, since the backbone has already been
  immobilized upon protein folding.

2000 - Stability and stabilization of globular proteins in solution
2002 - Maximal Stabilities of Reversible Two-State Proteins
2014 - Enzyme Thermostabilization: the State of the Art
2012 - Rational modification of protein stability by targeting surface sites leads to complicated results
2012 - Disulfide Bonding in Protein Biophysics
2011 - Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins – A Combined Molecular Dynamics and NMR study
2011 - Contribution of Hydrophobic Interactions to Protein Stability
1997 - Protein thermal stability, hydrogen bonds, and ion pairs
2005 - Thermal stability of proteins.
2004 - Protein structure, stability and solubility in water and other solvents.
2000 - Rational Modification of Protein Stability by the Mutation of Charged Surface Residues
2006 - Protein Stability and Surface Electrostatics:? A Charged Relationship
2003 - Contribution of Surface Salt Bridges to Protein Stability: Guidelines for Protein Engineering
2000 - Influence of Sucrose on the Thermal Denaturation, Gelation, and Emulsion Stabilization of Whey Proteins
2006 - Increasing Protein Stability through Control of the Nanoscale Environment
2000 - Contribution of Surface Salt Bridges to Protein Stability
2003 - Elastic coupling of integral membrane protein stability to lipid bilayer forces

This is an impressive list of references, but how many of these are available to the general public outside an university?

@Chris I think about 5-10% (bigger libraries usually have access to scientific articles as well). I too don't have access to the full text, just the abstracts in most of the articles, but it is usually enough to add one or more important sentences to my post. It is pretty hard to collect the information this way (as you can see I used around 30 references for a single page). Reading books is not enough either if you want to be up to date... :S

Longest Biology.SE answer! Good job!

@TanMath Actually 5/10 is mine answer from your list. Does not matter. I just like using long quotes and lots of references.

Really the question how does protein folding work?  But let me answer your questions...
1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself.  Denaturation is only reversible in relatively few cases in fact.  A few proteins, usually very small ones can be nursed back into a native folded state from an unfolded one, and then only a percentage of the sample will reattain the folded state.
2) Sure.  In fact pressure changes the hydrogen bonded structure of the water and also therefore the thermodynamics of protein structure and has been used to study protein folding. Generally the electomagnetic field does not affect the state of the protein fold.  I cite the fact that many many proteins have been studied via nuclear magnetic resonance, in which the proteins have been inserted into some of the most powerful magnets that can fit into a reasonably sized room.   That is not to say that the protein function might not be affected by such a field.  I'm sure by the time the field is large enough to ionize water or the peptide change you would see something... so you can always push things too the breaking point.
3) Many proteins from thermophilic organisms are more resistant to denaturation and companies actually engineer proteins to be resistant to all sorts of outrageous conditions and still be folded and functional.  Laundry detergent is full of crystallized enzymes that will sit happily in detergent for a long time.  I don't even know if these products have a shelf life.
Overall proteins are vulnerable to denaturation for a good reason- the cell degrades them when it doesn't need their function and can recycle them for their component amino acids. If they were all this robust the cell would starve to death quickly.  If there is a biological role to a protein that is denatured and then refolds itself it is only for extremely rare situations.  Proteins for the most part don't fall apart once they are folded and if they do, they are done.
Some possible exceptions: some antibiotic peptides which fold into pores that kill their targets and the amyloid plaque which takes on a different fold when in the brain which is associated with - but may not cause - Alzheimer's.

Some RNAse enzymes are capable of renaturing, makes it annoying to get rid of them.

"Very few proteins have disulfide bonds or really any covalent bond stabilizing the amino acid chain " - can you add some reference about this? e.g. insuline, egg yolk proteins, gluten, hair proteins contain disulfide bonds. I guess every protein with multiple cys can and maybe does have that, so I don't think it is rare. This part of question was about: do primary bonds form by denaturation or not? If not, then why is it irreversible? I don't think you can explain that only with secondary structural changes. e.g. by egg yolk it becomes white, so I guess there is protein aggregation involved.

"Generally the electomagnetic field does not affect the state of the protein fold. " I hardly believe that, afaik based on the pH amino acids can have negative or positive charges, so the EM field can pull one end of the protein chain and repel the other end, but I think most of the proteins are not affected, because there is an even distribution of +/- charged amino acids along the chain. But that's just my theory. I can accept this part of your answer.

"companies actually engineer proteins to be resistant to all sorts of outrageous conditions" - That part of the question was about how to engineer such proteins in theory. I suspected, that the technology already exists.

added references. i misunderstood what you meant by electromagnetic field.  the specific arrangement of charges can be quite important to a protein... usually this is seen as direct couloumbic repulsion or complementarity.  most of the long range electrical fields from protein charges affect how proteins interact with each other.  a harder question to answer definitively.

i could go on about protein engineering. heres an example refrerence http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242557/

+1, I think this is a good answer, but it was too basic for me. Btw. I hate to accept my own answer. :S

Are you taking in an in vitro context for preventing protein denaturation after protein isolation from for example E. coli or are you more worried about proteins in the context of the whole cell?
I'm no expert in the protein folding/conformation studies but from laboratory based prospective if you want to achieve denaturation for experimental purposes, you treat your samples with SDS and high heat (~ 100 oC for 10 min) to eliminate H-bonds and to get rid of disulphide bonds, you use a reducing agent such as beta-ME or DTT, which is commonly found in molecules such as Ab or cell surface receptors such as EGFR so obviously for western-blot experiments which you need your disulphide bridges to be preserved you do not use reducing agents but you still heat your samples and treat with SDS to get rid of the hydrogen bonds and linearalise your protein.
Based on this study, which used BSA and β-lactoglobulin, denaturation caused by high pressure is similar to that caused by the cleavage of hydrogen bonds with urea or guanidine hydrochloride so, yes, rapid changes in environmental conditions can have denaturing effects similar to chemical based agents.
If you are trying to prevent protein denaturation in a whole cell, then you need to treat them with cryo-preservation media containing usually 10% DMSO such as this. If you are working just with proteins alone, the best method is to work with your samples freshly prepared (lysed etc) and when isolating your proteins for future used, snap freeze them in liquid nitrogen and store at -80 oC. If your proteins are attached to beads such as GST-tagged proteins, then store your beads in a buffer congaing glycerol and put at -20 oC. I use 50% glycerol (v/v) and it works well for me! If however this response does not answer your particular question or concern, please edit and elaborate on what exactly you are worried about in your line of work and I shall modify my response accordingly. Hope this helped in some way!

Thanks you answer it was interesting. +1 I am not worried about anything, I just want to learn more about the details of how denaturation works. I want to refresh my memory about bioengineering, I skipped the last 3 years, since I learned software engineering. Instead of relearning the whole stuff I thought it would be better to ask more detailed questions about one or more topics... I meant in vitro proteins, for example egg white, etc..., and it was a theoretical question, but it was good to see some laboratory practices again. Just be careful with mercaptoethanol, it can cause cancer! :-)


text:
Is there a known glucosepane cross-link breaker?
I read the following on wikipedia:

There is, however, no agent known that can break down the most common
  AGE, glucosepane, which appears 10 to 1,000 times more common in human
  tissue than any other cross-linking AGE.

(AGEs are related to oxidative stress, aging and chronic diseases.)
I was wondering maybe the article is out of date, and there is a glucosepane cross-link breaker available. Do you know anything of that, or a current research which aims to find that?

Unfortunately at this time, there are no known glucosepane breakers which can feasibly be used in a living organism.  There is a small (very small) amount of research being done on the topic by Yale university in cooperation with the SENS foundation, but the focus is extremely early stage - nothing more than synthesis and detection of artifical glucosepane and precursors.
It is a rather frustrating situation, as there are very good arguments indicating glucosepane as an almost universal 'bad thing that should be fixed', and the molecule itself isn't particularly complicated.  It seems that this would be a low effort/high reward research area.

Welcome to Bio SE and thanks for your interesting answer! Could you add some resources (web links, or preferably citations to articles) to this answer?

I accepted the answer, because I have found nothing after a few days of search either. You should add references to your answer especially about the research on Yale university you mentioned.

You may want to look at Chebulic Acid as a potential inhibitor of AGE cross linking AND a breaker of AGE cross-linking.
Review this article:  http://biofoundations.org/?p=1004

Thanks, it is interesting! :-) It is hard to find anything relevant, but according to this it is unlikely that CA breaks glucosepane. https://www.quora.com/Can-triphala-chebulic-acid-break-glucosepane-crosslinks-Can-it-increase-lifespan Ofc. there is still hope, I think we need more experiments.

The problem is the glucosepane bond is very strong, hence the molecules which would break this bond need be necessarily toxic and damaging to other molecules in the body.  Glucosepane breakers already exist, but they are too toxic, and perhaps all will necessarily be that way.  All hope is not lost however.  Other very effective medical drugs (like clot breaking agents) are extremely toxic although life saving if applied in a local fashion via angiography under controlled conditions.  My hunch is that the same will need to be done for the known glucosepane breakers.  Glucosepane is extracellular, so the problem is really to avoid liver and renal toxicity.  Animal studies should concentrate on delivering known glucosepane breakers under special conditions of renal, liver, and cardiovascular and respiratory support and though hyper-hydration, hypothermia, ECMO, dialysis, metabolic blocking agents, etc, to limit systemic toxicities.  It won't be easy, but it could be well worth the effort if such single shot therapies could be developed which might then have long lasting effects as glucosepane would take many years to decades to build up again.

I came across this new research from Yale University:

We are currently in the process of evaluating the enzyme’s mechanisms of action and identifying other metabolites generated. This is the first demonstration that glucosepane can be broken down enzymatically.

http://diabetes.diabetesjournals.org/content/67/Supplement_1/1229-P

The link is broken. Probably just server malfunction and they will restore later.


text:
How to find a Cancer PPI network data
I need a Protein Protein Interactions network of Cancer (any type - just I want a PPI of any type cancer), I search and see DIP PPI and ....
How to specify that is  Cancer PPI and how to get a PPI of Cancer ?

What Cancer? What species? Please [edit] your question and make it more specific.

I assume that your are looking for human data. Take a look at these papers:
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
From the abstract:

Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network). The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%). We illustrate the interface related affinity properties of two cancer-related hub proteins: Erbb3, a multi interface, and Raf1, a single interface hub. The results reveal that affinity of interactions of the multi-interface hub tends to be higher than that of the single-interface hub. These findings might be important in obtaining new targets in cancer as well as finding the details of specific binding regions of putative cancer drug candidates.

Tools for protein-protein interaction network analysis in cancer research
From the abstract:

As cancer is a complex disease, the representation of a malignant cell as a protein-protein interaction network (PPIN) and its subsequent analysis can provide insight into the behaviour of cancer cells and lead to the discovery of new biomarkers. The aim of this review is to help life-science researchers without previous computer programming skills to extract meaningful biological information from such networks, taking advantage of easyto-use, public bioinformatics tools. It is structured in four parts: the first section describes the pipeline of consecutive steps from network construction to biological hypothesis generation. The second part provides a repository of public, user-friendly tools for network construction, visualisation and analysis. Two different and complementary approaches of network analysis are presented: the topological approach studies the network as a whole by means of structural graph theory, whereas the global approach divides the PPIN into sub-graphs, or modules. In section three, some concepts and tools regarding heterogeneous molecular data integration through a PPIN are described. Finally, the fourth part is an example of how to extract meaningful biological information from a colorectal cancer PPIN using some of the described tools.

Thanks, I looking for Cancer Data of Human or ... ! These are use Cancer data ?

Can you please expand your answer beyond dropping in some links? Some text about what is written in the articles would be great. Links tend to disappear sometimes which would make this answer useless.

@Digicom yes they focus on cancer data. Please take a look at http://www.doc.ic.ac.uk/~natasha/course/docs/cytoscapeTutorial.pdf to see a practical example of PPINs. Just follow the steps in the tasks and try to answer the questions. It will give you hands-on approach with what I suppose you are looking for.

@asalic Thank you. I will perform your tutorial and read your article.

@Chris All right, now the links won't disappear, unless DOI.org does. I cited the abstract from the papers, so any reader can now have an idea about the texts.

@Digicom You're welcome. Good luck and have fun.