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Is there already discovered non-carbon form of life?
I have heard of some rumors going around about a living organism based on non-carbon. Is Has research been done with real form of life based on non-carbon? Or carbon-based life is only type of life what humans know of?
Carbon chauvinism

See http://www.thewestheimerinstitute.org/pubs/Is%20there%20a%20common%20chemical%20model%20for%20life%20in%20the%20universe%3F.pdf

See http://biology.stackexchange.com/questions/3652/what-elements-are-a-possible-basis-for-life

I think the question can be phrased better than "rumors going around" - I don't think "rumor mill" is quite in line with this site's vision. Can you be more specific about who is the source of these claims, and what exactly they said? Otherwise, the question is unanswerable.

In a word, no.  There are some good chemical reasons to expect all life to be carbon-based.
Of course, it is no longer a silly fantasy to imagine an artificial intelligence that might qualify as life.  (Still FAAAARRRR in the future, though, if ever.)

Thank you. Is there any proof of unpossibility of existence the non-carbon life, e.g. phosphorus-based or boron-based? Or this is hypothesis, similar to those where talked "The Earth based on 3 elephants, 3 elephants based on turtle, etc..."

@perpetuity You have asked a very concrete question about findings so far, but your comment is about possible future findings. I think you should ask that as a separate question.

Carbon is much more abundant than silicon or phosphorus, while being more reactive at room temp and forms gases and liquids at cooler temperatures than silicon compounds. A silicon based organism would probably only be possible on a really hot planet where the silicates are more reactive and more flexible, but still unlikely. I don't know what solvents would be acceptable at those temperatures and the silicon equivalent to CO2 is SiO2, which is solid, not a gas, so probably shouldn't expect an oxygen based metabolism.


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Why do organisms excrete nitrogenous wastes?
Organisms excrete nitrogenous wastes in the form of urea, uric acid or ammonia. But isn’t that a bit of a waste? There is a shortage of biologically available nitrogen in the ecosystem, and plants convert nitrogen in ammonia and nitrates into amino acids. Why do organisms then deaminate these amino acids and then excrete them?
It seems to me that it would make much more sense to store the nitrogen for further use. I understand that ammonia is toxic, but surely it could be stored in some specialized structure.

Some amino acids are essential, that is, they cannot be synthesized.  For all the others, however, you need building blocks.  Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination.  Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate).  The body has thus produced some amino acids and metabolized others for energy,  but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.
To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em.  I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full.  You could ask the same question for any substance we might eventually want.

Preamble: The problem with questions on evolution
Obviously, evolutionary biology is a reputable discipline, but unfortunately there are two types of questions on evolution that are posted on this site that I believe are often of dubious value and can lead to dangerously unscientific habits of mind.
The first is questions of the type “Why did such and such evolve this way?”. The problem with this type of question is that there is generally no way of proving a hypothesis because it makes no predictions — the end product of the evolution is known. There is sometimes an anatomical or biochemical paper-trail to support arguments, and I have presented one such in an answer to another question. However many answers to this type of question are pie-in-the-sky or circular reasoning.
The second type — typified by this one — asks “Why has such and such not evolved, it would obviously be advantageous?” The posters of such questions tend not to ask themselves why, because if they did they would realize that the answer is likely to be either:

“It would be too difficult, costly or would have disadvantageous
  consequences”

or

“The assumption that it would convey a selective advantage (and
  that is what evolution is about) is incorrect.”

The accepted answer to this question addresses the former explanations. Although this is an old question at the time of my answering it, I am doing so partly because a similar question came up recently, but also because I feel it would be generally useful exercise to consider the second explanation — to emphasize the need to question the assumptions of those who think that they know better than Nature.
A story my mother told me
The story is apocryphal, but it is true my mother related it to me. It concerns two youths who had applied for a general office job. (This was not quite Dickensian, but not so much later.) In order to chose between them they were each given a parcel to unwrap. The first youth carefully untied the string, took off the paper wrapping, neatly folded it, and placed the parcel, the string and the wrapping paper on the table. The second youth ripped off the wrapping and stuffed it into the waste paper basket and placed the parcel on the table. Who do you think got the job? In the era in which the question was posed, most people (including myself) assumed that the youth who had saved the string and paper for reuse would get the job, rather than the youth who wasted them. However (in the story) it was the latter who got the job — the manager was interested in speed and efficiency, not in economy in office stationary. And the moral is that if you make the wrong assumptions (that avoiding waste was paramount) you will come to the wrong conclusion. So it is with “wasting nitrogen”.
Is the assumption in the question valid  for human metabolism?
Although the original question had plants in mind, like @Amory I shall consider it from the perspective of a single species, Homo sapiens. The argument in the question is, in effect:

“There is a shortage of biologically available nitrogen in the
  ecosystem, so why do organisms deaminate amino acids and excrete them
  rather than store the nitrogen for future use.”

The first logical flaw is equating the shortage (limitation?) of nitrogen in the ecosystem with a shortage in any individual species. Let us, however, consider a modified argument:

“Nitrogen is a necessary component of proteins and nucleic acids, the
  synthesis of which is necessary for life. If this were stored in good
  times it could help survival when dietary protein became unavailable.”

This seems more reasonable. But one first needs to ask whether there is actually no storage of nitrogen. In effect there is in the form of structural protein, which is broken down in starvation. This is relevant, as considering this phenomenon allows one to address the real question:

“Would (further) storage of nitrogen in some more dedicated molecular
  form provide a selective advantage by enhancing survival during
  periods of starvation?”

This is the office boy question, but whereas we had no way of knowing what was most important in the office — speed or frugality — here we have information from which to draw a conclusion. In prolonged starvation protein is broken down to amino acids. Why? To utilize the carbon backbone of glucogenic amino acids to provide glucose for the brain when all other substrates for gluconeogenesis have been exhausted. This is key to survival. What happens to the nitrogen? It is partly used as ammonia to buffer the acid produced from some of the ketone bodies produced from ketogenic amino acids and the rest is excreted as urea. It is certainly not used to make protein or nucleic acid, which would entail using precious carbon constituents. Thus, it is clear that energy requirements, and particularly the generation of glucose are the limiting factors in survival during starvation — not nitrogen. The conclusion, therefore, is that there is no point in storing nitrogen in times of plenty: what needs to be stored is carbohydrate/fat.
One might raise the existence of Kwashiorkor, a disease of protein malnutrition. However this is a relatively rate disease, and it affects only children: it is not the normal situation in starvation. Clearly the demands for protein and nucleic acid synthesis are much greater in growth than adulthood.
Coda: Another counter-intuitive evolutionary development in nitrogen metabolism
The fallacy of “wouldn’t it be better to evolve…” is evident if one considers another aspect of nitrogen metabolism — our lack of the apparently useful facility to make all the amino acids, resulting in a dependency of man on certain so-called ‘essential’ amino acids. Here the situation is not one of failing to evolve a facility, but actually loosing it — simpler organisms from which we have evolved had it. The inescapable conclusion is that such a facility can never have been sufficiently advantageous to result in an evolutionary disadvantage for those who had lost it. Presumably we have evolved in a way that allows us (or a sufficient number of us) to survive in our particular ecological niche, not to be supermen.

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Puffball mushroom species ID?
Found this mushroom today. It's a kind of puffball mushroom and I think pestle puffball but I hope someone can confirm that/point me to other likely species.
It was in Central Eastern Sweden (Uppsala) in a pine and birch forest. Autumn has been quite dry so the season may be a bit delayed. They were in bunches of 2-5 mushrooms, they are about 1-4cm across the ball and the stem is quite fat plus about 1-3cm long. They are white through the middle.

As an addition - we ate it, none of us are dead at present. It tasted quite good.

Gutsy on eating it.  Did it have a sour, bitter, or nutty flavor by any chance?

My first thought is Lycoperdon perlatum.  I don't suppose you took any photos as you cut it up to eat it?

@AtlLED It was eaten based on the conclusion it was either l perlatun or the pestle puffball, both of which are edible, I couldn't find anything poisonous that looked similar. Flavor was a little nutty. Are these perhaps a little too small to be pestle puffballs?

Strange mushrooms which I am seeing it for the first time ! Would it be 'Lycoperdon echinatum' ? I think genus 'Lycoperdon' will give some answer to this.

I've been reading on it a bit, and from descriptions of the way the spikes/warts came off the surface I'd agree that it is L.perlatum.

@AtlLED No pictures were taken of the inside, it was just plain white.

Given what you've said in the comments, and how much more common they are, I'm going with my first gut reaction of Lycoperdon perlatum.  The big give away for me was that you said there was a good taste.  L. Perlatum has a rich nutty flavor (my wife grows them), but Handkea excipuliformis (pestle puffballs) don't have much taste if any.  They are seriously notably bland.  H. excipuliformis can take on the flavor of what ever you cook them with, so if you cooked in a nut oil or with nuts, then you would have given the flavor that way.
Not that I support taste as a primary means of id...  In this case most of the puffballs are edible so you were in a low risk situation.  I just don't want to start a wave of fungus ID's that include taste info!

A taste based field guide to fungi, perfect for adrenaline junkies interested in foraging!

@GriffinEvo The business model is easy.  We give away the guide, and charge a "killing" for the anti-toxins.

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Yellow/Orange Fungus on Oak Tree
What is the fungus pictured below? The photo was taken October 6, 2013 near San Antonio, TX.
I have Googled it and my results suggest Laetiporus root rot (Laetiporus sulfureus).
According to this website the presence of this fungus indicates the tree should be removed.
Is there any chance that this is something else? I would hate to remove such a beautiful oak tree.

Please mention when and where the picture was taken. Also ask around you neighborhood in case anyone is missing a brain, just in case ;).

Any chance we can get a closer shot of the section attached to the tree?  Regarding felling the tree, is it at risk of hitting a tree should it come down? From the photo it looks like it's pretty open.  You can also anchor trees with cables so that should they fall, it would be away from structures.

@losthorse please [edit] your question to add exra information rather than put it in the comments where it is easily overlooked.

@AtlLED - Unfortunately, I have already removed the fungus. It does not seem to be at risk of hitting another tree should it fall, but I would have to take a closer look to be sure.

@losthorse Well if it's not in danger of hitting anything, there is very little reason to fell it.  If nature wants to bring it down, it will.  More to the point, I question Laetiporus sulfureus id.  You normally see much clearer shelving with that, or at least all the ones I ate growing up did.  Do you live in the Rockies?

@AtlLED - thanks for the input and perspective... the tree is in south central Texas.

@losthorse If you took down the fungus, can you give us any more details on it?  Was it hard, slimy, smelly, or brittle?  Did it have gills/fins on the back towards the tree.  Does the tree show any of the other signs of heart rot?

I can't say for sure but it looks like a species of the Laetiporus mushrooms. Please refer to its wikipedia page for the full info.
edit: I did not read your question fully and now I see that you reached the same conclusion. Just ignore my answer. As to the second part of your question asking if it could be anything else, that is quite hard to visually determine as there are many look alikes in the mushroom kingdom. Read this for some imposters.

authors: حمدي عبد الباسط


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Is telomere shortening consistant over consecutive cell divisions from zygote to a differentiated cell?
Considering the complexity of embryogenesis, a temporal referance would be helpful to coordinate the developmental sequences during embryogenesis and fetal development which is to be completed within the gestation period. Can telomere shortening if consistant be used as a reference by every cell to do what it is destined to do at particular time frame? This is without considering the influence of telomerase etc.
This is also without prejudice to the role of DNA directed molecular signalling.
To repeat the question is telomere shortening consistant over consecutive cell divisions from zygote to a differentiated cell? If so can it function as temporal control of embryogenesis?

It is not consistent, and so cannot function as a temporal or generational signal. Not because the telomere shortening is unpredictable, but because of telomerase activity in the embryo.
If it did, gamete production in specialized tissues like the ovaries or testes would have shorter telomeres than the zygote they originated from. Each generation would have shorter telomeres than their parents. They would be genetically 'older', which can't go on forever.
Development is incredibly complicated and mediated by a large number of genes. Try homeobox genes for developmental layout.


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What if $rB=C$ in Hamilton's rule?
Hamilton's rule states that if $rB>C$ then a gene giving altruistic behaviour will increase in frequency in the population. What would happen if $rB=C$? Will an individual perform the altruistic act?

Why has this been downvoted?

@Biogirl How have you tried to analyse the problem? Also, I rephrased your Q to better fit with a standard way of stating Hamilton's rule.

Could you edit your title so it doesn't have dollar signs in it please.

I agree with @Amory in the sense that Hamilton's rule is not a rule that applies to each specific individual and explain their behavior (or other traits). The Hamilton's rule describe the direction (and not the dynamic) of how a social traits evolve. A social trait is any trait which does not only affect the fitness of its carrier but also affect the fitness of other individuals in the population. Theoretically, all (or almost) traits are actually somehow social traits.
$RB>C$ is a simplistic way of looking at Hamilton's rule which might bring you to some confusion. This formula makes more sense to me by replacing $B$ by $\frac{dw(x,y,z)}{dx}$ and $C$ by $\frac{dw(x,y,z)}{dy}$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual drawn from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again). In the particular case where there is no population structure $y$ equals $z$. $\frac{dw(...)}{dx}$ describes the partial derivative of the fitness function according to the variable $x$.
Therefore the Hamilton's rule can be rewritten as:
$$R\cdot\frac{dw(x,y,z)}{dx}>\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$.
Altruistic behavior evolves if (but not "if and only if") this rule is respected. Hope this reformulation of Hamilton's rule helps a bit understanding it.
In the special case where $R\cdot\frac{dw(x,y,z)}{dx}=\frac{dw(x,y,z)}{dy}$ then, the trait of interest is not selected (neither counter selected). Therefore the trait will evolve under genetic drift alone. While the allele frequencies are modified by drift, the Hamilton's rule might (or might not) differ from the equality and then the trait would not be neutral anymore.

I loved your answer !

"Hamilton's rule states that if rB>C then a gene giving altruistic
  behaviour will increase in frequency in the population."

To start here are some examples of how Hamilton's Rule works...
In a population of four individuals a pair of adults mate. A first unrelated male (r=0) is genetically coded to help raise their offspring by an allele (selfless) at the "sociality" gene. A second male, also with r=0, has a different allele (selfish) at the same locus which makes him not help with offspring care. The pair raises 4 offspring if they go it alone, and 10 if another male helps. By helping, a male sacrifices his ability to mate so produces no offspring. Going it on his own he would produce 4 offspring.
By helping, when r=0, a male passes on no copies of his genes to the next generation (fitness = 0, no offspring in the next generation have genes that are identical by descent [ibd] to his), by being selfish he passes on 4ibd copies of half of his genes (fitness = 2 = 4*0.5). Thus the male carrying the selfish allele should do better and genes promoting social behavior should not evolve in the population because 0*(10)<2 (by helping he sacrifices the fitness score of 2, this is the cost).
Now with related males, say the father's brothers. This time the males will on average be related to the offspring of the pair with a relatedness coefficient of r=0.25. With the same results of helping and selfish behavior, genes for social behavior should evolve because 0.25*10>2, the selfless male has more IBD genes in the population than the selfish male. The next generation would have many individuals in it with the selfless allele.
Hamilton's rule is used to estimate whether "selfless" type alleles will spread through a population, to do so there must be some sort of relatedness within a group otherwise r=0 so rB will never be greater than C. In populations where relatives stay together there is more chance that altruistic behavior will affect a relative, when relatives can't/don't disperse away from each other much then genes promoting altruism should evolve. In more fluid societies they should not be as common.
Hamilton's rule is not definitive though. The closer that rB and C are to each other, the weaker selection will be at driving out alleles which reduce fitness, that is because the gain of having the correct allele is so marginal. For example, if r=0.5, B=100, and C=49, then selfless alleles are 2% fitter than selfish alleles. In comparison, if we keep r=0.5 and B=100, but change C to 40, then the rB>C still holds and selfless alleles have more strongly favorable selection (they are 25% fitter) so will spread more rapidly. If C=0 the behavior is likely to evolve because r=0 is unlikely in a population (even if you only include polymorphic loci).

"What would happen if rB=C? Will an individual perform the altruistic
  act?"

Whether animals can use Hamilton's rule to decide behaviors plastically is different application of the equation in Hamilton's rule. It is a similar concept, but evolution does not happen with the individual; the genetic makeup of an individual will not change as a result of selection. However, ignoring the definition of how Hamilton's rule is used you could use the same equation to estimate likely behavioral outcomes when an individual is given a choice. Here is an example where an individual is given the option to give or keep food and can judge relatedness, it is a very simplified model.
Example: A locus has two alleles G and g. Individuals can then be GG, Gg, and gg and each genotype has an easily discernible unique trait. Thus when a GG individual meets a GG individual it knows it is perfectly related, r=1. For Gg r=0.5, and gg r=0. When the individuals meet our focal individual (GG) has the option to either provide something for the other one or not provide (let's say give it some food).
For our GG individual the cost of providing the food to the other is the energy it took to find the food, say 50 calories. The benefit to the recipient is the energy within the food, lets say 120 calories. Thus we can say, GG should give the food to the other individual if the other is GG (because 1*120 > 50) or Gg (0.5*120 > 50) but not when it is gg (0*120 < 50). If we reduce the value of the food to 80 calories it becomes that GG should not help Gg (0.5*80 < 120).
There are a few limitations to consider...
Firstly, how well can an individual quantify relatedness? Just using Wrights Coefficient of Relatedness we would come out with roughly accurate measures on average. But there is variability due to mutations and the second law of Mendelian inheritance; independent assortment.
Secondly, how well can an individual judge benefit of its actions? The effect on the recipient is likely to be complex, it could have serious knock-on effects such as increased fitness later in life, longer lifespan, the action might reduce predation risk for the recipient that day etc..
Thirdly and similarly, how well can the provider judge the cost it incurs? If it is giving away food, it does not know if and when it will actually find it's next food item, foraging might cause it to be predated upon, and it might lose out on a mating opportunity if a receptive mate comes by while it is foraging etc..
When rB truly equals C (unlikely due to the complex nature of r, B and C) or is approximately equal, then the individual will be less likely to make the correct choice. When it is obvious that the cost is large and benefit is small it is more likely to make the correct decision. This is analogous to the ability of selection to drive out the incorrect allele as outlined above.
This is a rewrite of a previous answer made after some thinking and I think it provides a much better answer than the previous incarnation which I have deleted

Thanks for such a wonderful answer ! Actually, this question arose because there was this question : If an individual with an alternative of rearing its own 1 offspring or rearing its cousin's offspring,what is the minimum no. of offspring its cousin should have ? I know that 1own off. = 4 cousin off. So should the minimum no of offspring be 5 or is 4 an apt answer ?

@biogirl Well I guess you could always say that an individual might choose to help regardless of the benefit due to its lack of ability to differentiate, but that would be a risky idea! I'd suggest explaining 3-5 offspring. Such that at 5, given the individual can distinguish relatedness, costs and benefits quite accurately, that it would be altruistic. At 3 it should behave selfishly. And at 4 it theoretically could choose either strategy with no adverse effects. As long as you show your working (0.254=1, 0.253<1, and 0.25*5>1) and explain those three you should nail it on the head.

As far as I understand it, Hamilton's "rule" isn't really meant to apply individually, it's meant as a way of thinking about kin selection and altruism that can be reduced to individual cases.  The reality is that B and C can rarely, if ever, be easily measured or determined.  If the two sides were equal then who knows?  You'd have to observe it.  Presumably it would split 50-50.  Or maybe laziness takes over.  Or maybe some species are inherently altruistic.  That being said, exact equality is a near-impossible occurrence in the wild, and B and C are movable targets, so you'd have to measure it, which is, as stated, very, very difficult.


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The probability of indirect human fertilization (follow-up)
This question is a follow-up to
this one.
I've been wondering how small that probability is. As we all know, "safe" sex, that is (correctly) using a condom and all that, isn't perfectly safe. So, in order to put this question into perspective, I'd like to know which one (safe sex or indirect insemination) has the greater chance to lead to impregnation. In other words, can you explain the probability of this scenario in terms a layman like me can understand?
Thanks in advance!

This question appears to be off-topic because it is about sexual products and not biology.

I'm sorry if it comes off that way but the comparison to condom use is used as an attempt to put the other question into perspective, as I already mentioned.

Safer sex techniques are more risky.  Perfect condom use is associated with around a 2% pregnancy rate within a year.  According to that, even sterilization has a 0.1% (male) or 0.5% (female) rate.  Combining techniques is, of course, safer.  "Indirect," as you proposed in the other question, will border on an infinitesimally small chance, as answered there.

Not impossible though, see my answer here :).

@terdon Still the best news story ever.  I remember everyone freaking out when they read that.


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Why do most mammals have long snouts?
It seems like most mammals, e.g. dogs, have long snouts. My pet dog's snout would seem to me like an evolutionary disadvantage, since her canine teeth are way out at the end of her jaw, which acts as a force-reducing lever. I suppose the lever does increase the jaws' range of motion and possibly allow the jaw to snap shut more quickly. For an herbivore such as a horse, I don't see any advantage to the long snout. It doesn't need to snap its jaws shut rapidly, and it doesn't need to wrap its mouth around anything very large.
Is there a mechanical reason for the long snout, or is the evolutionary advantage due to some other factor such making the nose have enough surface area to give a sensitive sense of smell?

Obviously there is an evolutionary advantage for those animals which has a long snout/muzzle. That is why they are still around.
For carnivores the canine is the most important tooth and it is positioned strategically at the front corners of the jaw. Canines are meant to pierce and is essential for holding on to the prey and preventing from escaping. They are also essential for tearing flesh.
Lower jaw or the mandible is a class 3 lever. The lesser mechanical advantage is compensated by the extremely powerful muscles. Since the muscles are closer to the joint or fulcrum the movement produced by the muscles are amplified at the outer end of the jaw allowing for wider opening of the mouth. Since the canines are sharp and long there is enough force to pierce.
Herbivores like cattle and sheep have no canines (horses do have canines). The longer snout/muzzle may help in grazing as it would help in reaching the ground along with longer necks. The longer snout/muzzle means more space for the premolars and molars which can be more in number or larger fro grinding the food.
Crocodiles which are not mammals also have long snouts.
In short the longer snout/muzzle in different animals developed due to evolutionary advantage based mainly on diet.

This seems plausible, but is there any evidence to back it up? Does this account make any testable predictions? Does it explain anything about the exceptional animals that don't have long snouts?

When asking why a particular group of organisms, such as mammals, has a particular feature, such as a long snout, you must be careful about the hypothesized reasons.  While the other answers here propose various adaptive reasons, they do not actually explain the presence of the long snout in the majority of mammals.
Instead, you have to look at the evolutionary history of mammals and vertebrates. Modern mammals have long snouts because they inherited the trait from their earliest mammalian ancestors, such as Morganocodon. In turn Morganucodon and other early mammals had long snouts inherited from their synapsid ("reptilian") ancestors like the sphenacodontid (see the first phylogenetic tree below). Why did the synapsids have long snouts, then?  Because the earliest tetrapods like Ichthyostega had snouts. Before that, the lobe-finned fishes like Eustenopteron and Panderichthys had the elongated snouts (see the second phylogenetic tree below).

Of course, the mammalian snouts were modified through natural selection to take on various shapes and sizes (or become greatly reduced) for various (presumably) adaptive reasons, as suggested by the other answers.
An analogous question is why do all mammals have four appendages (arms and legs)? They inherited the four appendages from their common tetrapod ancestor, which in turn inherited the appendages from their ancestral lobe-finned fishes. The appendages are later modified by natural selection. That same reasoning applies to this question about mammalian snouts.
When using phylogenetic trees to study the adaptive changes of particular traits (such as snouts), a researcher can first use comparative techniques like phylogenetically independent contrasts to tease out the effects of inheritance due to common ancestry. See for example Felsenstein, J. (1985) and the many, many papers that cite this one.

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.

Credits
Eusthenopteron to Pederpes phylogeny modified from Maija Karala, Wikimedia Commons (CC-BY-SA-3.0).
sphenacodontid by dmitrchel, Wikimedia Commons (public domain).
Morganucodon by Michael B.H., Wikimedia Commons (CC-BY-SA-3.0).
Ichthyostega by ArthurWeasley, Wikimedia Commons (CC-BY-2.5)
Tiktaalik by Nobu Tamura, Wikimedia Commons (CC-BY-2.5).

An analogous question is why do all mammals have four appendages This doesn't seem analogous to me at all. There are obvious reasons why the tetrapod body plan should be highly conserved, and therefore it makes sense to look for its origin very far back in time. But snout length is not highly conserved. E.g., dogs and humans have a common ancestor on a time scale much shorter than the one you're talking about.

@BenCrowell Snout length is conserved, reflecting evolutionary history. This mammal phylogeny shows that most mammals have a snout. Human faces began to flatten during hominid evolution. Our closest relatives (chimps) have snouts as adults but flat faces as juveniles (scroll down to photo). Adult humans retain a flat face, which is probably paedomorphic, likely due to genetic changes during development.

You say "snout" but you might more specifically mean "muzzle" if you're focusing on the teeth aspect.  Ram Manohar M hypothesizes some good reasons that make sense but for some other examples of snouts, here's a fun link that describes a few uses:

Tapir: "nose and upper lip form a trunk he uses to grip, handy for grabbing and cleaning branches and plucking fruit."
Aardvark: "finds all his food through his sense of smell, so his long nose leads the way in his quest for dinner."
Proboscis monkey: "The large nose amplifies the male monkey's mating calls, gaining the female's attention and potentially intimidating the competition."
And of course the Elephant.

You are right. I did consider them but the question obviously did not imply those. There are pretty short snouted/muzzled animals with acute sense of smell.

I have corrected the answer by replacing snout with snout/muzzle. there is some overlap in dictionary meanings.

I'm not a scientist, so this is my best guess:
Since humans are an uncommon exception among mammals for lacking snouts, we should find the benefits of a snout by looking at other ways that humans are unique among animals, enabling us to not have snouts.
I think the answer is the opposable thumb; animals need snouts because it does for them what thumbs do for humans.
For most animals, their mouths are all they have to manipulate their environments — it's what they use to lift, carry, or break objects, as well as hunt and fight. Humans have thumbs, as well the ability to use tools, to do all these things.
A snout provides more surface area for biting or carrying, better dexterity to grasp between bones, rocks or other obstacles, a larger mandible for powerful jaw muscles to attach to. It also places the mouth in front the eyes rather than below them, which should make it easier for an animal to see what it's about to pick up with its mouth. I think that all these things would suggest that an animal with a shorter snout is at a disadvantage.
Another explanation for snouts that I've seen is that hairy animals cool off through their mouths rather than through their skin, and a snout gives them a larger mouth and more surface area to do so.

It would be great if you added some references to your response.

Long snouts may have an advantage in long noses. A longer nostril could give more room for olfactory neurons and allow for a more sensitive sense of smell. Animals would rely on smell to find prey or avoid predators, so better smell would give better advantage. The only predators I can think of off the top of my head that would have short snouts would be big cats, but lions and tigers have more prominent snouts than house cats.


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Distinguishing between mitotic metaphase and metaphase II of meiosis
I'm sorry if this seems like a silly question, but I was brushing up on some cell cycle dynamics and realized that everyone was talking about the differences between metaphase I and II, and since metaphase II was so different from metaphase I (random orientation, tetrad, etc...) the distinguishing of the two didn't seem difficult.
However, I also always hear that metaphase II is similar to mitotic metaphase. In fact, I can't really figure out what the observable difference would be, though I'm certain this must be possible?
How exactly is metaphase II of meiosis different from metaphase of mitosis? I'm sorry if this seems like a silly question, but I haven't been able to figure it out.

I assume you want a differentiating element other than counting the number of chromosomes(i.e. assuming we do not know the haploid chromosome number of the cell)?

@SatwikPasani That is indeed correct.

I'm inclined to agree with @SatwikPasani.  I think you really can only know the difference by knowing what comes before and after (context clues).  If you are observing at the mRNA level, then there are some signaling differences, but the appearance down a scope would be quite similar.


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Will a garter snake eat unusual prey if made to smell like something normal?
I have noticed that my garter snake only eats after it has smelled it's prey to make sure it is a slug, and it doesn't matter whether it's moving or not. If I were to coat, say, a caterpillar with slug slime, would my snake try eating it?

Probably, try it and let us know.

He's not hungry right now I tried feeding him a slug but he barely noticed it. I'll try tomorrow and let you know the results.

Not sure about garter snakes, but this is a common technique to get "difficult" snakes to eat. Back when the Madras Crocodile Bank used to keep king cobras (which exclusively eat other snakes), they would coat rats with a concoction consisting of the shed skin of other snakes (usually Indian rat snakes) to get the king cobras used to the new prey.

He still isn't eating anything. I fed him a lot though, so he's probably just still full.

@Skyhawk Did the caterpillar coated with slug slime trick work?

Yes, changing the scent has been accepted by most snake breeders as a method to feed stubborn snakes (reference). For example, if your snake prefers chicken, and wont accept mice, rub a chick on a pre-killed mouse and this may trick it into eating the mouse (reference).  With regard to garter snakes, the diet may change based on its habitat, its age and even being kept in captivity can change its diet. This article should provide you information with feeding your garter snake if it is stubborn (reference).


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What are the benefits of elucidating the three-dimensional structure of a protein?
I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we potentially learn from the structure in terms of biological significance?
Are there examples of drugs, or treatments that have only been made possible because of a known crystal structure?
Generally speaking, why do people spend so much money on synchrotrons, laboratories, robots and so on, for a protein structure?

Out of curiosity, what is the protein/what does it do?  If you don't mind me asking...

Protein structures, which can be obtained from protein crystals or from concentrated solutions of pure protein via NMR, are arguably the primary source of knowledge that we have about how genes perform their function on the molecular level.
RCSB.org is the protein structure repository in the US. They write up a story on an important protein structure monthly - its a great way to pick up some fascinating stories.
The precise atomic positions from a protein structure are indispensible for several reasons.  Since biological processes are all fundamentally chemical ones.  The specific positions of the atoms reveal how proteins, nucleotides, lipids, drugs and other biological molecules specifically interact.
Examples:

Protein structures broke the ground in biological inheritance (Watson / Crick / Franklin's DNA structure)
Protein structures of lysozyme and proteases were the first to show exactly how proteins bind their substrates and enzymatically catalyze chemical reactions.
Protein structure of hemoglobin in both oxy- and deoxy- forms (i.e. with and without oxygen bound). showed that proteins change their spatial arrangement to modulate their function.

This list goes on to more recent breakthroughs in how signals and molecules interact with the cell through the membrane.  There is literally no topic in cellular biology which has not substantially benefitted from having a protein structure revealed.
The advantages of working with protein crystals are that they can be larger proteins and certain kinds of difference experiments an be more easily performed when a protein crystal is obtained.  For instance if you have a crystal of a 100 kDa (~900 amino acid) protein, you can often find the binding pocket of the enzyme without a tremendous amount of work.
The disadvantage of working with protein crystals, as you probably know well is that getting crystals is often a quixotic effort soaking up months or years, often with little or no results.  Pretty demoralizing until you hit the target.
If you're astounded to think that proteins, which are often hundreds or thousands of times larger than a salt or mineral you usually find in crystals...you are dead on.  The crystals are often very tiny - a decent sized crystal measures about a millimeter on one side, but often are only a fraction of that size.  That's why protein crystals often are taken to synchrotrons, linear accellerators or other free electron X-ray sources which are millions (?) of times more intense than a dental x-ray. I would guess that most protein crystal structures are obtained using special beamlines created especially for biological crystallography.
That sort of tells you the funding priority science is willing to put into x-ray protein crystal structures.  Simply the idea that protein crystals might be easier to grow in microgravity (along with the low weight of the experiment) justified over a decade of protein crystal growth experiments on the shuttle and ISS.
Interesting note: The Guardian (which is based in the UK where crystallography, protein or otherwise started out) has posted a short video outlining highlights of crystallography's contributions over the past 100 years.  If you watch assiduously you will see protein crystallography cropping up with a litany of nobel prizes.
New thoughts:
There are signs that crystal structures are coming to an end.  Using an electron micrograph to simply take a picture of many thousands of individual proteins laying about can be digitally averaged to create low resolution structures they are gradually becoming higher resolution and are a lot less work than preparing and making a protein crystal - and it works well on larger proteins and protein complexes!

Having studied a little geology, I immediately thought of X-ray diffraction, but I could see how X-rays might be more problematic for proteins. Wikipedia's NMR crystallography article might be worth linking.

The method to stabilize the crystals since the early 90s has been to freeze the crystals with a stream of nitrogen at about liquid N2 temperatures.  Since then, its been a lot easier to get good diffraction data.  The hard part is still getting crystals in many cases tho.

I always wondered this myself, but the structure of a protein  can end up being quite important for a number of reasons.  Most relate to the fact that protein function often depends on specific domains, and while a protein may have multiple functional domains it is important for all domains to be properly aligned and constructed in three-dimensional space.  Misfolded proteins often have negative phenotypes, so being able to visualize the improperly folded areas can be enlightening.  Perhaps more commonly, these techniques can be used to validate an artificially produced protein before approving it for therapy.
Additionally, while we can know the sequence of amino acids in a protein very easily we don't necessarily know which ones are useful.  A region oriented toward the outside of a protein may partake in a biological function.  If a specific protein domain is imbedded inside the center of the protein, it is not very available for function, either by the protein or for other targets such as antibodies.  For example, one of the big projects in HIV research now is to get very good and very fine structure of viral proteins on the envelope of the virus; knowing which regions are readily accessible would make for potential good drug/cell/antibody targets.
Finally, the structure itself can give some insight as to function.  Proteins may not have homology by amino acid sequence, but similarly-structured proteins can have similar functions.  People smarter than me can recognize those features and can learn quite a bit about a protein just from its shape.

Here's a fun little anecdote I conveniently just came upon.  It's a quote from Your Inner Fish by Neil Shubin (© 2008) about two researchers, Linda Buck and Richard Axel, who in 1991 discovered a family of genes that allow us to smell.

Experiments showed that odor receptors have a characteristic structure with a number of molecular loops that help them convey information across a cell.  This was a big clue, because Buck and Axel could then search the genome of a mouse for every gene that makes this structure.

Expanding on something Amory said:
They are very beneficial in drug discovery. This is because it is absolutely essential that you have a structure to do any sort of molecular dynamic simulation. In the early phases of drug discovery it is cheap and easy to do these types of experiments on a computer, rather than setting up an assay for different potential therapeutics. You just take the crystal stucture of the protein, and a structure of your compound, and a program will simulate how they will interact with each other. From this you can see if the compound is able to enter the active site of the protein, the orientation it would be in, etc. Using a supercomputer you can do this with hundreds of compounds in a matter of hours. Molecular dynamics has other useful purposes, drug discovery is just one example.

Why study protein structure?

“What is the secret of life?’ I asked. ‘I forget,’ said
Sandra. ‘Protein,’ the bartender declared. ‘They found something
out about protein.‘ ‘Yeah,’ said Sandra, ‘that’s it.”

[Kurt Vonnegut, Cat’s Cradle]
Proteins are essential molecules in living organisms serving a range of intriguing different functions. Determining their individual structures is essential to understand how they perform these functions. So, quite simply, we study them out of scientific curiosity.
Proteins and medical science
As implied above, the basic reason most scientists study proteins is scientific curiosity, and an answer to the question in the title could be “a greater understanding of life”. But of course, it goes without saying that they realize that the resulting understanding provides the intellectual framework for much of modern medicine, and many proteins are chosen for study because of their physiological or pathological relevence. However, only a small part of the medical application of our knowledge of proteins is on drug design, and this generally does not involve the scientists who determine proteins structures but the pharmaceutical companies that have the resources and expertise for the long and expensive process of drug development.
Proteins and Drug Design
Nevertheless, drug design is frequently given as an example when explaining the medical relevence of research to the general public, so I think it is quite reasonable for the poster to ask:

“Are there examples of drugs, or treatments that have only been made
possible because of a known crystal structure?”

As this part of the question has not been addressed in any of the answers I present some examples below. It will be evident that the drugs listed have only been licensed over the last 20 years, whereas the first protein structure (myoglobin) was determined in 1958.

Drug
Target Protein
Organism/Disease
Year approved
Drug Company

Zanamivir/Relenza
neuroamidase
influenza
1999 (FDA)
Glaxo

Imatinib/Glivac
bcr-abl kinase
leukaemia
2001 (FDA)
Novartis

Aliskiren/Tekturna*
renin
hypertension
2007 (FDA)
Novartis

Raltegravir/Isentress
integrase
HIV
2009 (EU)
Merck

Vemurafenib/Zelboraf
B-Raf kinase
melanoma
2011 (FDA)
Plexxikon/Roche

Avibactam
β-lactamase
resistant bacteria
2015 (FDA)
Actavis/AstraZenica

Erdafitinib/Balversa
FGFR
various cancers
2019 (FDA)
Janssen

SPR720
DNA gyrase
M.tuberculosis
2020 (clinical trial)
Spero Therapeutics

*Marketing terminated 2012 due to contraindications
References
These examples are taken from the following reviews, in which details of their discovery and other examples may be found:
Nero et al. (2018) Protein structure and computational drug discovery
Maveyraud and Mourey (2020) Protein X-ray Crystallography and Drug Discovery
Staker et al. (2015) Recent contributions of structure-based drug design to the development of antibacterial compounds

As for generating a table in posts - instructions are available from the edit bar.

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


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Is there an optimal composition and length for protein linkers in FRET?
I'm designing a protein that I'd like to use in FRET reporting.  General idea on the shape is:
FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2.  I would like to know what AA are best for the linker, or does it matter?  I have heard SSG is a good choice, but when I started a lit review I become unconvinced.  If it doesn't matter, I may try and put more convenient restriction sites there.
Is there a good way to theoretically determine optimal length?  I realize that may change depending on which FRET protein pair is chosen.  The cleavage sites are between 15-18 AA long.  Unfortunately, I don't think I can give any more detail than that on the cleavage sites.
Response to answer:
So far there have been no FRET systems or tests published with the cleavage sites I want to study.  In fact, I haven't even heard of anyone else trying.  If I'm forced into a positive FRET probe, which I'm worried that I am, does anyone have any FRET pairings that don't interfere with Texas-Red on the spectrum?  My first choices were Venus and Cerulean, but if I have to make a positive probe then I don't think they are a good choice.

I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind:

Length of linker. The length of the linker (including any cleavage sites), follows an concave optimization curve. A linker too long (> 18 amino acids) or too short (< 5 amino acids) and the FRET signal rapidly diminishes. When considering a FRET reporter in which no cleavage site is introduced, I've seen reporter an optimal linker length of 7-8 amino acids. When including a cleavage site, I've seen optimal liker lengths reporter of 18 amino acids. TO my knowledge, there is no theoretical way to predict the FRET efficiency based on linker sequence, and from scientists I've talked to, they conduct a trial-and-error approach using purified protein products to screen for an optimal length if it appears necessary to do so.
Type of FRET reporter. Cleavable FRET reporters fall into two classes. Positive reporters, in which signal appears after cleavage, must use longer linkers to separate fluorophores enough to reduce the FRET phenomenon. Negative reporter, in which FRET signal is lost after cleavage, must necessarily employ both short cleavage sites and linkers, to maximize the FRET phenomenon prior to cleavage. Since you mention the cleavage site itself is 15-18 AA, I would certainly expect very little FRET when uncleaved, assuming that the linker and cleavage site are unstructured, as the distance between the two fluorophores is quite large for the FRET phenomenon. Alternatively, intramolecular FRET reporters are usually designed as positive FRET controls, using short linkers to maximize the FRET phenomenon. When tagging two proteins seperately for FRET, short linkers are also chosen, relying on some external interaction to bring them together, however, this requires a lot of optimization of linker length for both fluorophores for maximum efficiency.
Choice of linker amino acids. This part here is somewhat subjective. The choice I often see in the literature are the tiny and small amino acids (especially Ser, Ala and Gly). The choice of these is mostly because they will likely have the least interaction among the linker structure and adjoining proteins and will be the most flexible. The linker should be chosen to avoid use of putative sites for modification (e.g., phosphorylation, glycosylation), rigid geometry (Pro, or bulky aromatics) and excessive charged amino acids.

I should note that I have found no comprehensive review of these three parameters for FRET construct design, and I have gleaned them from the literature. In my opinion, linker length is more critical to optimize than its amino acid sequence, provided that the linker does not lend itself to stable/rigid geometry and modification.
I would also suggest seeing if FRET constructs have been made using your cleavage site of interest already, and perhaps use the same linking sequences. From this, you could construct a slightly shorter and longer construct to see if one is more optimal over the other.

+1 This was my impression as well.  I am trying a series of cleavage sites which range from 15-18AA.  I think that means that I will have to design a positive probe (and I was originally planning on negative).

Keep in mind that if you are designing a positive probe, you'll need a way to make sure the proteins will interact, otherwise there will still be no FRET occurring.

Yeah, this is my concern.  That's why I'd rather make a negative probe, but the length seems like to much.  I may end up trying a split protein reporter instead.

We could talk offline about probe strategies if you are willing to share a bit more detail of your project.


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Synthetic construct with multiple ORFs not expressing
I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation by different cis-elements (2-3 different cis-elements can be studied simultaneously).
The construct is like this:
SmaI-RES1-CMV-RES1’-GFP-MCS1-SV40PA-Linker-RES2-CMV-RES2’-RFP-MCS2-SV40PA-Linker-RES3-CMV-RES3’- YFP-MCS3-SV40PA-ΔLinker-SmaI

where:
RES1 = KpnI [GGTACC]
RES1’= SalI [GTCGAC]
MCS1 = EcoRI+BamHI [GAATTCTGGATCC]
RES2 = ClaI [ATCGAT]
RES2’= NheI [GCTAGC]
MCS2 = SpeI+HindIII [ACTAGTAAGCTT]
RES3 = XbaI [TCTAGA]
RES3’= PvuI [CGATCG]
MCS3 = NotI+SacI[GCGGCCGCGAGCTC]
Kozak consensus sequence = GCCACCATGG
Linker (100bp) = AATTCTGGATCCTGCAGCTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCGAATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGC

GFP, RFP and YFP are fast turnover variants with MODC pest sequence. I took the sequences for these proteins from Evrogen website. I took the Sv40 polyA signal sequence from one of their vectors in order to avoid any event of incompatibility. Kozak sequence was also taken from those vectors only. The total size it ~4.8kb. For CMV promoter I took the standard sequence used in most vectors.
With this vector I could clone any post-transcriptional regulatory sequence between stop codon and SV40PA, and could change promoters as well.
With the CMV promoter and no 3'UTRs I see a very faint expression of GFP, but could not see any RFP expression. I used pMaxGFP and dsRed as a control for filter sensitivity.
I transfected the plasmid in Hela and Neuro2a and at various concentrations (1-5μg) using lipofectamine. The controls express well (transfected 1μg each) but I see very faint GFP expression and dont see any RFP expression.
I checked the sequencing QC report given by the company and there were no indels or other mismatches. I am clueless about why the construct fails to express.
Is the linker a problem; is 100bp not sufficient ?

Did the company synthesize the sequence as above or did they codon optimize it for a species?  You can really mess up folding if you're not careful with translation gradients.  Also where did you put the Kozak sequence?  I couldn't tell from the question.  Need to make sure we have everything in the right order, gene start-stop, etc.

i just gave them the sequence.. it is codon-optimized for mammalian expression. Kozak sequence was obtained from the ORF source i.e Evrogen vector.. Kozak sequence is overlapping with the start codon and I just took the entire sequence from start of kozak sequence to stop codon

I have used an GFP+RLuc plasmid before that had linker just shy of 100BP, so I don't think that's the issue.  Have you done any westerns or northerns to see if you're getting some kind of read-through?

no.. I dont have the antibody or the primers/probes yet.. I have also tried electroporation.. no great difference.. I'll try it once more and see.. Point of using GFP was to have a direct readthrough

GFP antibodies are not too hard to run across.  I might try and see what your base level of expression is.  Otherwise the only way I know to go above CMV in expression is to use T7.  And then you have to worry about your T7 source.

I m not sure if it is a weak expression because of the promoter.. CMV promoters are quite common and give high expression.. I wonder if this is the case with CMV, how will I use other promoters like Tet-On and UAS... i guess their efficiency is less than CMV

let us continue this discussion in chat

@AtlLED: would you summarize the points that you mentioned in an answer.. it might be useful for others too..

I'm afraid there's not much of answer but back to the bench with you! (That's why it's called re-search).
There are several factors that could be playing a role here.  You could have transcriptional or translational read through.   You should check your sequence and the cells you are going into to make sure you aren't getting Amber (UAG) suppression.
Before you do anything, you should check your DNA of all your groups.  Run it uncut on a gel and make sure the majority of the DNA is super coil.  The next easiest thing to check is translation problems.  Get an GFP antibody, possibly a few that recognize different epitopes, and see if your GFP is coming out the right size.  It may not be processed correctly or folded correctly.
You can run into problems by optimizing the sequence.  First, synonymous mutations can cause folding variants (1).  Second, you might be causing a hair pen or other disadvantageous secondary or tertiary structure.  If you can't detect any problems in your Western, you might consider doing a Northern to trouble shoot the transcription.
If you rule everything else out, and you are just getting poor expression, then the only way I know to boost over CMV is to use T7.  The problem with T7 is always going to be what use for a source.  If you can use BSR/T7 cells and you can get your hands on them, they work great.  Otherwise you're looking at a T7 plasmid or MVA-T7 as common sources.  The plasmids never lead to a great deal of expression in anyone's hands I've ever known.  MVA-T7 works, but to say that it confounds things would be the under statement of the year.

Re-search That's perfect.

Can't take credit for that one.  Heard it back in the 90's from an advisor, and I'd bet he didn't come up with it ether.

It never had the time or resources to modify the vector and eventually gave up this project. I am accepting this answer as it summarizes all issues and would be useful for others who seek to work on synthetic biology.


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Why would the Camargue horses have a white coat while the foal have a dark coat?
The current issue of the magazine Lonely Planet India(Oct 2013) presents a photo of Camargue Horses which are white coated and mentions that they are born with dark hair. A search shows that the foal are either black, grey or brown coated and gradually turn white around the Third/fourth year.
What could be the possible advantage of that kind of difference between the young and the adult?

I will have to do more research into the Camargue, but many animals have pigment changes over time just because they haven't developed the melanocytes to have adult coloration.  It simply isn't advantageous to spend energy on coloration when you're growing bone. And sometimes the melanocytes are hormonally stimulated. A possible behavioral selection could be something like "foals are not seen as mate competition until their color changes," and thus avoid competitive behavior of say a large alpha male.

Our own hair will also turn gray (indeed, yours seems to be on its way, if you don't mind me saying so) but there need not be an advantage to that; if it doesn't affect our ability to have successful children it probably doesn't matter much to evolution or selection.  When it comes to animals that interact with humans, though, many traits are selected for, even those without an advantage, in fact often we select for disadvantageous traits (if they were advantageous, we might not need to select for them in the first place).
As this 2008 paper from Nature Genetics goes into, the "graying with age [phenotype] is an autosomal dominant trait" overwhelmingly caused by "a 4.6-kb duplication in intron 6 of STX17 (syntaxin-17) that constitutes a cis-acting regulatory mutation".  To answer your question, though:

The Gray horse provides a notable example of how humans have cherry-picked mutations with favorable phenotypic effects in domestic animals... The prestige of riding a white horse has thus led to selection of the Gray-causing mutation by humans; this mutation is by far the most common cause of white color in horse.

This phenotype is actually often detrimental, as white/gray horses can have eye problems and higher rates of skin cancer; Camargue's are particularly susceptible to melanomas, present in around 70% of horses by age 15.  There does seem to be some benefit, though, as the second paper I linked suggests these horses are subject to fewer fly attacks.
EDIT: I seem to have been unclear and you seem to have misunderstood my answer.  Let me break it down:

Camargue horses are gray.
Gray color is a simple mendelian autosomal dominant phenotype caused by a loss of pigment in adulthood.
Gray color is generally bad but sometimes good; either way, it's probably not a huge detriment.
Camargue horses are homozygous for gray color.
Humans have in the past selected for gray color in horses in general.

That is an example of why something negative or pointless might persist, as would a dominant inheritance pattern that is fixed in a population: negative traits that are only weakly deleterious have a non-negligible chance of fixation.  Asking what the advantage is is somewhat of a moot question because every single Camargue horse has the trait; asking what caused a seemingly-negative phenotype to become fixed is a good question, but likely an unanswerable one as it occurred long ago.
As a side note, how long a breed has been in an area does not simply imply breed purity.  Here's a quote from the International Museum of the Horse:

Through the centuries many armies have passed by the Camargue, including the Greeks, Romans and Arabs. The horses brought with these armies influenced the Camargue over time. It has even been suggested that the Camargue has had some influence on the early breeds in Spain as armies took them back home.

Your answer is not acceptable. 1. The Camargue Horses are neither 'cherry-picked' or cross bred. Read these quoted lines from Wikipedia "The Camargue horse is an ancient breed of horse indigenous to the Camargue area in southern France. Its origins remain relatively unknown, although it is generally considered one of the oldest breeds of horses in the world".

You are suggesting that the hair of the horse ages before the horse even before it reaches puberty?  There has to be a better explanation. It looks like you have cherrypicked the answers. Is it possible to get an answer from someone with some insight in this site?

@RamManoharM I expanded my answer, but I don't know where you find reason to accuse me of "cherry-picking" or find a mention of puberty.  I simply mentioned our own hair color as an example of seemingly-drastic changes that need not be selected for.

@RamManoharM  2 might not be to far off.  It's almost certainly related to the KIT gene (CD117, dealing with the SCF).  Early coloration being caused by in utero influences on the cells, but the later lack of coloration is cause by the failure of melanocyte migration.


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Fusion of neuron with a S phase cell
There was some experiment in which a S phase cell was fused with other cell and the other cell also began to replicate DNA. Would the same happen if fused with nerve cell ? Why or why not?

fusing cells is not feasible in all cases (it also causes polyploidy).. cells are immortalized by using oncogenes..

you can also look at this post

Just an addition to the WYSIWYG's answer: phenomenon of neuronal de-differentiation under the influence of oncogenes was shown.

This specific experiment has not been done. Fusing cells is difficult and it also leads to polyploidy. Cells are immortalized by overexpressing oncogenes (or viral replication genes); for example HEK293 cell line was established by transforming embryonic kidney cells with adenovirus.
Now transforming a neuron would immortalize it but would also make it lose its function; for a cell like neuron, replication would compromise its activity for e.g. loss of established synapses. As mentioned in the comments by har-wradim, it was shown that transforming neurons with oncogenes leads to their de-differentiation. Another experiment of transforming neurons gave a contrasting result. Feddersen et al transformed purkinje cells in mice by expressing SV40 viral t-antigen from a purkinje-cell specific promoter and surprisingly it lead to degeneration of cerebellar tissue. Also have a look at this article.


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Why is weight gain a symptom of Cushing's Syndrome?
Cushing's syndrome results from increased levels of cortisol in the body.
Cortisol as I understand it however, promotes the breakdown of glycogen and amino-acids in the process of gluconeogenesis, to increase blood sugar - opposing the action of insulin.
Why then does Cushing's syndrome lead to weight gain rather than weight loss?

Cortisol causes lipolysis, however, metabolism is slowed and free fatty acids are not actually metabolized they're just redistributed -such as in Cushing's disease.

Cortisol is released when body goes through stress situations like while working out in gym, physiological activities outdoor etc. As you have already mentioned about what Cortisol does, it accumulates in the body after the stress situation and then with the intake of food and other nutrients it replaces the consumed carbohydrate and fat in the body i.e. a kind refueling. So this is how Cortisol maintains the body weight normally if our body gets enough exercise or has proper metabolism.
Whereas in Cushing' syndrome which comes usually by taking glucocorticoid drugs, or diseases that result in excess cortisol, adrenocorticotropic hormone (ACTH), or CRH levels. In this case Cortisol content will be more than the normal level which in turn requires more carbohydrate. So cortisol metabolizes the food and reefuels the body even when there is no requirement within the body. So because of excessive cortisol content body simply gets excessive fat accumulated in various parts which mainly results in obesity.
One more explanation from High level of Cortisol effects:
Chronically high levels of cortisol plays a big role in the development of obesity.

Cortisol helps the body handle stress; so, when stress goes up,
  cortisol also goes up. Cortisol stimulates fat and carbohydrate
  metabolism during stressful situations. This leads to increased blood
  sugar levels required for fast energy. In turn, this stimulates
  insulin release which can lead to an increase in appetite.

Adrenaline increases alertness and metabolism by helping fat cells release
  energy. When the immediate stress is over, the adrenaline levels
  return to normal. But, cortisol lingers to help bring the body back
  into balance after stress. One of the ways it gets things back to
  balance is by increasing appetite to replace the carbohydrate and fat
  used for the flight or fight response.

The problem is that in today's society, stress-causing situations do
  not really require the body to use up a lot of energy. So, cortisol
  ends up causing the body to refuel after stress even when it doesn't
  really need to refuel. This excess fuel or glucose is converted into
  fat resulting in increased storage of fat.

"So cortisol metabolizes the food and reefuels the body even when there is no requirement within the body. So because of excessive cortisol content body simply gets excessive fat accumulated in various parts which mainly results in obesity." doesn't really make sense to me, if it metabolises the food, it should lead to weight loss.  Also your answer is mostly about stress, but I'm interested in cushing's syndrome.

In Cushing's syndrome when the cortisol level goes up, it makes body to consume more food which in turn leads to fat build up. This is unnecessary fat which body gets when it does not need it. I gave stress as an example but higher level of cortisol was the main highlight which results in fat.

why does cortisol make you consume more food?

How different hormones are interrelated and What is the potential link between stress, cortisol, and appetite?

I read this somewhere. In Cushing's syndrome the excessive cortisol disables metabolism of proteins and fats rather than increasing it ( I don't know the reason). Hence, fat gets accumulated, mainly in the abdominal region resulting in weight gain

Can you please add some references?

http://www.3fatchicks.com/how-cushings-syndrome-can-contribute-to-weight-gain/


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Natural selection and the Galapagos Islands
Woodpeckers found on the South American mainland are able to peck insects from the bark of trees. Would the woodpecker finch have been able to survive if woodpeckers had found their way to the Galapagos Islands where this finch is found?

Dunno, depends on who eats more. Perhaps both would have diversified into different species or one of the two would have gone extinct, or both or whatever. We have no way of knowing what would have happened.

While this is an interesting question, I think it's too hypothetical for the SO format of questions and answers.  Invasive species can and do happen, even without human intervention, but it would be entirely speculative to try and model how a habitat invasion would play out here.


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The real definition of carbohydrates
Carbohydrates are often defined as compounds with only C, H, and O and the H and usually the O atoms are in a 2:1 ratio.
Exceptions like deoxyribose exist, but why is it recognized as a carbohydrate?
What distinguishes a carbohydrate from other compounds?

The definition of carbohydrates as compounds containing $C$, $H$ and $O$ usually with the empirical formula ${C_m(H_2O)_n}$, is outdated.
More rigorous and a accurate definition would be Polyhydroxy Aldehydes and Ketones composed of Carbon, Hydrogen and Oxygen. Moreover, the nomenclature including Mono-, Di-, Oligo- and Poly- "Saccharide" is preferred over the now obsolete and too-general term "carbohydrate", since the etymological origin of the word "carbohydrate" is from the greek words Carbo- for carbon and hydor- for water which indicates that the carbohydrates are "hydrates" of carbon and have the empirical formula ${C_m(H_2O)_n}$, which is not always true. Instead "saccharide" is derived from the greek word for "sugar" and hence is much more accurate as it does not limit the definition to any empirical formula.
Apart from the polyhydroxy aldehyde or ketone characteristic of carbohydrate, they have a marked structural and functional variation from other biomolecules. This includes the absence of $S$ (as in proteins), $P$ and $N$ (as in proteins and nucleic acids), presence of Glycosidic bond (as compared to peptide bond in proteins, phosphodiester bond in nucleic acid, and ester linkages in fats or glycerides) and much greater structural uniformity as compared to other biomolecules.However, these characteristics are not absolute as is evident from the fact that several monosaccharide derivatives do contain $S$ or $N$ atoms. Actually, the entire group of amino-sugars (Hexosamines etc.) are usually classified under carbohydrates since they are primarily monosaccharide derivatives obtained through enzymatic amination.
These characteristics distinguish this class of compounds without having to assign a empirical formula to it.
ADDENDUM
Adding the clause compounds which can, on simple hydrolysis yield polyhydroxy aldehyde or ketones in the definition helps involve certain non-reducing sugars like Sucrose.

Nice summary, but haven't you gone a bit far with the "absence of..." section? What, for example, would you classify N-acetyl glucosamine as? Or isopropylthio D galactoside? These are derivatives of saccharides containg N and S respectively, and it makes no sense to not classify them, broadly speaking, with their parent molecules.

@AlanBoyd The absence is not absolute and I forgot to mention that(corrected). However, the compounds you mention are referred to as monosaccharide-derivatives and not monosaccharides as such. These derivatives, usually cannot be classified into one of the traditional groupings which are not defined by strict structural criteria. Broadly speaking they are carbohydrates (i.e. monosaccharides) but while distinguishing, omitting a few exceptions might help us grasp the uniqueness of each group and I guess is what the asker meant with "What distinguishes a..?".

@SatwikPasani That's exactly what I meant. Thank you for this rather slick summary - very clever to limit the composition with C, H and O.

@TomD The addendum tries to resolve this problem.


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Can you detect if a mutation is spontaneous or induced?
Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic agent)?

Since mutations arise as a result of, speaking broadly, a chemical reaction or process my instinct is to say that I don't see how you could ever rule out that a mutation happened spontaneously.

I edited question to clarify.

In the future, please make question titles a full sentence, that starts with a capital letter.

Here's a quick answer; hopefully someone will give a more complete one.  But meanwhile you've got something.
Some genotoxic agents have predictable results.  For example, they cause Gs to substitute for Cs, or they cause mutations at specific spots on the genome.  So if you had a bunch of mutations in a single cell (or collection of related cells) that matched the modus operandus of a known genotoxic agent, then it would be reasonable to conclude that the mutations were induced.  But not all genotoxic agents are like that.  And if you only have 1 or 2 mutations, that's not enough to prove they were induced.  Also, of course, it depends on your sample size and your controls.

The above answer is mostly right. In the lab one can show that induced mutations are caused by exposure, compared to unexposed controls (e.g. in bacteria). The induced mutations will have a frequency, position, and type which can be typified. As a group, theyc ompris a "spectrum" of mutations. In a real case problem, such as humans exposed to diesel exhaust, the number of mutations and their trype are usually going to be too few to have a"spectrum". Naturally occurring (a serious misnomer in its own right) could also occur in those same positions and types. The usual language is that the observed mutations are consistent with an exposure, but does not prove the exposure caused them.


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Genetically speaking, are dogs exactly similar to humans and chimps both?
Richard Dawkins mentions in his book The Greatest Show on Earth that dogs are exactly similar to both humans and chimps. Supposing that a cell contains the genetic similarity between 2 species, he says

The human/dog cell should have an identical resemblance score to the chimpanzee/dog cell because humans and chimpanzees have exactly the same degree of relation to dogs. It should be identical, too, to the monkey/dog cell and the lemur/dog cell. This is because humans, chimpanzees, monkeys and lemurs are all connected to the dog via their common ancestor, an early primate (which probably looked a bit like a lemur)

He later says that this will be found within "statistical margins of error".
Because the common ancestor of both chimps and humans was more similar to chimps than to humans, it stands to reason that chimps will be more genetically similar to the common ancestor than humans. Therefore (not a direct therefore), dogs and humans can't be exactly similar as dogs and chimpanzees are, even theoretically. Humans and apes are even more dissimilar. Therefore ape/dog cell will not be exactly same value as the human/dog cell.
Please explain where I am wrong.

Is this premise of your argument correct? - "the common ancestor of both chimps and humans was more similar to chimps than to humans". Since chimps and humans have been evolving for the same amount of time since they diverged, why do you think that chimps are closer to that ancestor than are humans?

I agree a lot with what Alan said.  If I have time I will come back later with a full answer.  At the moment you should read up on genetic distance, which is what we are talking about here.  I doubt if you were to actually calculate it, they would be identical, but you have to go back far enough in mammalian history to a shared ancestor of dogs and humans/chimps. The assertion is that the most recent shared ancestor between all three was the same species.

Physical similarity doesn't guarantee genetic similarity, I understand, but it seems a little intuitive that some genes from a common ancestor pass unchanged in a descendant A that had a similar environment, while changing in another B, that had a different environments, thus making it possible that A will be more genetically similar to its ancestor than B.

maybe you could expand the dawkins quote?  it doesn't really make sense to me.  chimps are much more closely related to us than dogs by most measures.

expanded the Dawkins quote

@AtlLED I accept that it might not be so, but will dogs and chimps have 'exactly' the same degree of relation as dogs and humans? Can we even make such sweeping statements? I think the variation would be noteworthy, and the statement misrepresents the topic.

@Daud even that idea is questionable we don't know what the common ancestor of chimps and humans looks like, some even hypothesize it was an upright animal based chimp knee structure. Also humans ARE apes, human are not dissimilar to apes.

Dawkins is overgeneralizing.  Genetic distance is a fairly new field, and a heated topic, since your answer depends upon which genes you are comparing.  If you picked ONLY strongly-conserved genes for your genetic distance comparison, then you'd find that humans, bonobos, dogs, mice, mosquitos, shrimp, and bakers' yeast are all equally distant (and that the distance is small).  But if you pick ONLY very weakly-conserved genes for your genetic distance comparison, you can get crazy results -- humans are more closely related to yeast than to horses, for example.  (Creationists have had a heyday making fun of some early genetic distance studies that, in retrospect, had poorly-chosen genes.)  So biologists doing genetic distance comparisons try to pick genes that are common to many species, and that have some drift to them, but not so much that the answers are obviously goofy.  Another problem that has arisen is that sometimes an entire gene in several species appears to have been obtained from a very dissimilar species, in a different phylum or kingdom even.  (Current theory is that this is the work of viruses.)  The "tree of life" paradigm might need to be changed to the "web of life."  Needless to say, there's still a lot of argument about which (and how many) genes to pick for genetic distance studies.

Yes and no.  Yes their DNA, like every living thing’s DNA, is made of the same building blocks of A’s, T’s, G’s, and C’s.  But their DNA isn’t exactly alike.   All those A’s, T’s, G’s, and C’s are put together in different orders for dogs and people. You have to understand that 4% with chimps is a difference of actually 35 million single nucleotide differences and ∼90 Mb of insertions and deletions. With a dog only 25% matches up perfectly with a human. I think what he was saying was that all living matter has a common ancestor. From fruit fly to human being according to macro evolution we all came from the same ancestor.
http://genetics.thetech.org/ask-a-geneticist/dog-vs-human-dna
http://genome.cshlp.org/content/15/12/1746.long


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Negative value on linear gene expression in microarrays
I am starting to use microarrays and maybe this is a dumb question:
Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?
And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or flooring (converting negative values to zeros)?
Thanks

I'm not personally familiar with Illumina arrays, but I can give some notes here.  This link is a paper which describes the array quality controls specifically. This presentation describes the calculation of the intensities in bioconductor.
The answer is yes: you will find negative numbers sometimes.  They should be rare.  The Intensities numbers from a scanner which essentially takes an image of the bead fluorescence on the glass slide and tries to subtract a background signal.
The background is the typical level of signal you see on a bead with no sample DNA bound to it.  You will get some pixels lighting up a bit even there.
In expression microarrays, this is not a perfect system as each bead has a different nucleotide sequence on it.  Each bead has a specific DNA sequence has non-specific binding which is pretty much unique on the slide.  That is to say, the oligomer on the bead might bind strongly to DNA from your sample which is not its reverse complement to varying degrees.
I think what happened is that there will be a handful of cases you can find a bead which has less fluorescence than the background controls on the slide.  It's possible that the probe has a design flaw but I would generally assume that the negative number means that there is no detectable target cDNA in the sample for that oligo.
I probably wouldn't convert the number to a zero, but you could probably justify it to yourself in some cases.  Most difference experiments are the logarithm of the ratio so zero is not a great number in those cases.
@Luke 's comments are well said.
I think that negative values can still represent signal because of the variance of sequence-dependent effects for the purposes of scaling, and difference experiments.  But I'd tend to think of them as zero signal in any case.  There are probably genes which express at or below detection threshold all the time, which is not zero information, so the number has some value.

This is pretty spot on. The "intensity" values you end up getting are relative values to the background levels. These tend to be normalized to an arbitrary value - "100" could be the arbitrary threshold for background, above which you see a reliable signal. A probe with very low intensity could therefore be below 0.

do you have any suggestions about what to do with a negative intensity @Luke ? I tend to ignore things with such low values, but it can make a difference in comparing 2 small amplitude measurements i guess.  (i'd still tend to ignore them in that case!)

Anything below the background threshold is by definition an unreliable signal (i.e. detection P-value > 0.05). The 2 options for dealing with this is either to set values below the background threshold to "missing", or to leave them in but be aware that below the background threshold the values are no longer meaningful (you might do this if, for instance, 60% of your sample were below background for this probe, but the rest were above - this is still meaningful because it means that 60% of your sample express less than the 40%, so you do not want to set them as missing, as this may be relevant


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Phenoptosis, behavior evolved for good of species?
I was reading this and felt like the argument is being made that organisms die for the good of species. Isn't this nonsense?
This especially bugged me:

"'Age-induced, soft, or slow phenoptosis'" is the slow deterioration and death of an organism due to accumulated stresses over long periods of time. In short, it has been proposed that aging, heart disease, cancer, and other age related ailments are means of phenoptosis. "'Death caused by aging clears the population of ancestors and frees space for progeny carrying new useful traits.'"

Per the selfish nature of genes, it might be okay if it was only your offspring you are dying for, but even that only when you know you can't reproduce further. And the above argument says that old age death is exactly that.

two other wikipedia links one might want to read: http://en.wikipedia.org/wiki/Evolution_of_ageing
http://en.wikipedia.org/wiki/Senescence#Theories_of_aging

I guess, programmed death for the purpose of freeing space to new individuals can be explained by: 1) kin selection (Given that aged individuals are damaged by various stress and has a lower per year number of offspring than new individuals, it might be beneficial to die if the expected relatedness to the new offspring is high enough compare to the ratio of offspring the old and the young can raise (RB>C)).
Or by 2) lineage selection: lineages (species) that dies early (so that it frees space for new individuals) have a lower extinction rate (or speciation rate).

But I think that when thinking about senescence, it is important that you know about Haldane's (and some others) work. Their hypotheses make much more sense to me than the hypothesis that individuals die to free space to others.

I don't really have an opinion on whether or not this is the main or even a reason for the evolution of senescence and death, but it is certainly not nonsense.
Death can indeed be good for a species. Diversity is always good and the death of the elders allows phenotypes that have been selected for more recently to take hold in the gene pool. If the young need to compete with the old, this will make it harder for them to grow and reproduce. In situations with a limited food supply, having to support old individuals who can no longer forage/hunt for themselves will be a strain on the species/society/pod or whatever it is we are looking at.
Therefore, genotypes that encourage the death of elders who are past the age of reproduction could be selected for. This does not contravene the selfish gene hypothesis at all, these individuals have already reproduced, the selfish gene no longer 'cares' about them. The main idea of the selfish gene hypothesis is that the genes themselves 'want' to be passed on, not that the genes 'want' to save themselves. Once their host has reproduced, they loose interest so to speak.
The selfish gene theory is just a conceptual tool, it should not be taken literally. It does not suggest that genes are actually selfish or in charge of their own evolution in any way. It is just a useful approach to take when studying evolution and was instrumental in our understanding that the gene (the nucleotide actually) and not the individual is the smallest unit of selection.
Anyway, in the strictest sense, the statement in your question is absolutely compatible with the selfish gene hypothesis. If you can no longer pass your genes along, you are useless and just a drain on the species, why should you keep living?


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What are artifacts in microbiology?
What kind of objects can be qualified as artifacts? How do we distinguish such objects?

Can you give a little context?  Where did you read or hear about it?

During a microbiology lecture, though I can't recall right now what exactly was called artifact during that lecture.

Could you perhaps mean as seen in a microscope?

I believe what you are asking about-  artifacts in biology - generally means characteristics or behavior of living things which are not advantages to reproduction.  Does that sound right?   If so lmk and I can write a response.

An artifact in biology usually refers to experimental error or other spurious results. In the context of microbiology, you will get artifacts if, for example,  you sneeze on the plate you are growing a colony on.
The term is generally used for any result that is not actually true but stems from bad analysis or experimental procedures. Take, for example, this definition from biology-online.com:

Something artificial, a distortion that does not reflect normal anatomy or pathology, not usually found in the body. For example: in radiology, the appearance on an x-ray of a surgical metal clip that obscures the clear view of an anatomical structure.

This is a very good question! There are many factors there so the list would be very long. There are many kinds of artifacts too, some related to processes and the other on technical devices. Some of the processes we do not know or we have not defined those rigorously mathematically. It depends on the methods used to get the final list. You need to specify exactly the research tool(s) and narrow the scope still to be able to define exactly some artifacts.


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Lizards are sometimes called cold-blooded because they depend on their surrounding temperatures to keep them warm.
Predict how the composition of the cell membrane of a lizard might change from winter to summer. Justify predictions.
Can someone please help me figure this out. Does it have to do with fluidity?

I didn't really get your question. Is it: "Cell membrane composition (or other properties of the membranes) depends on temperature. Why is it so?"

Be sure to tag homework questions with the homework tag.  It also helps if you let us know what level class you are taking.  To your question, look up how cell walls in general help maintain homeostasis.  Edit your question with what you find, and feel free to answer your own question if you figure it out.  Give it a little more effort and come back to us with what you found.

Just going to follow up on your thought here.
The fluidity of the cell membrane does vary with composition.  Off the top of my head there are four main components of the animal cell membrane:
1) proteins.  membrane proteins are responsible for the import and export of nutrients, waste, information etc from the cell, so lets assume that this needs to be fairly constant part of the composition while the seasons change.
2) cholesterol and similar compounds.  These are flat an inflexible compounds which will tend to lower the fluidity of the membrane.
3) unsaturated fatty acids and lipids.  These are long carbon chained compounds with some double bonds in them.  Because the double bonds cause the chains to be less mobile, but they don't pack well as they are not as flexible, so tend to make the membrane a bit more fluid.  Think about how butter (mostly saturated fats) is solid at room temperature while olive oil (monounsaturated oil) is liquid.
4) saturated fatty acids and lipids.  These are completely mobile carbon chains.  Without any double bonds, these tend to be the more flexible and can create a more tightly packed membrane, resulting in a stiffer membraine.
You can imagine for the cell to maintain the same flexibility at the lower winter temperatures (4) and (2) would tend to decrease and (3) might tend to decrease.
Does this make sense?


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Genotoxic agent and their metabolic pathway
What are the mechanics (set of biochemical reactions) allowing a given genotoxic agent

to modify the mutation rate at a given spot?
to induce only a given type of mutation (from Gs to Cs for example)?
some other consequence of the kind that you think is worth talking about!

I am not necessarily seeking for a very detailed explanation of the biochemical pathway but rather some kind of understanding of how such things are possible (not evolutionary speaking but in terms of physiology and cytology).
This question comes in reaction to this post.

Here is a somehow related question I asked a month ago and which is still unanswered. It might interest you. http://biology.stackexchange.com/questions/10011/how-can-a-mutation-influence-the-recombination-rate-of-a-specific-sequence

In terms of DNA mutations, it's usually just pure chemistry.  The mutagens article gives a brief rundown of some of the usual suspects, but to pick a few of the ones I'm familiar with:

UV light can cause pyrimidine dimers, which clearly is a dimerization of Cytosines or Thymines, which can cause replication issues.
Deaminases, which remove amine groups, is probably the coolest example.  Deamination can occur naturally, turning Cytosine into Uracil, but is often done deliberately as part of bisulfite sequencing to determine methylation status.
Alkylation can occur, in particular of Guanine, which can lead to a preference in binding for Thymine; subsequent replication will result in an Guanine to Adenine conversion.

Similarly, there are many base analogs that will fill in for a given nitrogenous base.  These analogs often prefer to bind to an "incorrect" base as above (and in the figure below with 5-bromouracil) which will lead to specific errors.

On a more intentional basis, biotechnological tools such as zinc finger nucleases, TALENs, and the (oh-so-sexy) CRISPR system can be used to specifically alter genome sequences of choice.  ZFNs are in particular being used as a gene therapy tool for just that reason.
Otherwise, viruses (and transposons) that insert into the genome can cause specific mutations or errors if they do so non-randomly.  Figuring that out, though, can be tricky; most oncoviruses cause mutations through specific genes that allow uncontrolled growth and tumorigenesis, not in a site-directed manner.  There is, however, a growing hypothesis that certain retroviruses which tend not to cause cancer, in particular HIV, may be inserting into sites with certain characterizations, such as chromatin level.  That is far from known, though.
If you're looking for random causes, that's easy.  Anything that disrupts DNA repair mechanisms such as p53 or Rb will do that.  For chemicals, intercalators such as ethidium bromide and thalidomide insert in between DNA bases and prevent proper DNA repair.


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Why do different bacteria have different shapes?
Why do different bacteria have different shapes? Is it only related to their function?

Due to multiple evolutionary forces acting over long periods of time (along with chance events, heterogeneous environments etc)? I really don't see this as a constructive question. You could just as well replace with "Why do birds have different colours?" or "Why do fish have different sizes?"

@fileunderwater: I see it as a very interesting biological question. I would rather compare it to "why do birds have differently shaped beaks?"

@nico I see that question as too broad as well - too many possible answers and reasonable mechanisms to be answerable in less than a book.

Reasons for Bacteria with different shapes as given in Wikipedia/Bacteria:

The wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the
  ability of bacteria to acquire nutrients, attach to surfaces, swim
  through liquids and escape predators.

There is an article based on research by Kevin D. Young Bacterial morphology: Why have different shapes? which highlights 3 main points which defines the shape of Bacteria:

Nutrient uptake: Cell shape, in and of itself, affects nutrient acquisition and argues that other nutritional situations may create conditions that favor one bacterial shape over another.
Motility: Motility imposes a heavy selective pressure on cell shape. Fast cells are better off as rods with a certain length-to-width ratio, chemotactic cells must adopt shape ratios in line with their environments, and cells that forage near surfaces or navigate viscous environments may do best if they are slightly curved or spiral.
Predation: In their struggle against being eaten, bacteria have adopted morphological defenses that may have produced the wealth of shapes we now observe.

These factors play a role in shaping bacteria. Further he explains what in general gives the shape to bacteria:

Bacterial morphology is affected by a combination of selective pressures - access to nutrients, cell division, attachment/dispersal, predation and motility (among others). Among these different factors, our understanding of the relationship between motility and cell shape is most complete; for example, highly motile bacteria are usually rods with a specific (optimal) shape and size, and movement through viscous fluids seems to a favor spiral shape. But since multiple selective forces are always in play, there is at the moment no way to predict cell shape based on the environment or vice versa.

Shape Matters: Why bacteria care how they look - This article highlights Kevin's work explaining why shapes matter for bacteria and they take it seriously for survival.
So adaptations to various environments could be possible but depending upon the environment we can not predict the shape of bacteria because some other factor might have played major role in giving shape to it. But the above mentioned 3 main factors gives some explanation.

As for how certain bacteria achieve their shapes, the cell wall plays an important role. Almost all bacteria have a cell wall made of a substance called peptidoglycan, a mesh of peptides and saccharides that provides rigidity and strength to the bacteria. This wall is produced through a complex series of steps that starts inside the cell, where the peptide and sugar units are attached to a lipid to make a compound called Lipid II. However, Lipid II must be flipped to the outer layer of the cell membrane to deliver the peptides and sugars to the growing cell wall. The proteins responsible for flipping the Lipid II are believed to be FtsW, RodA, and SpoVE. FtsW is considered the main enzyme for most cell growth. RodA is found in rod shaped bacteria and is considered necessary for cell elongation. SpoVE is used to build the thick cell walls of bacterial spores. By controlling how Lipid II is delivered to the growing cell wall, these proteins play a role in controlling cell shape.
References:

Structural similarity among Escherichia coli FtsW and RodA proteins
and Bacillus subtilis SpoVE protein, which function in cell division,
cell elongation, and spore formation, respectively.
Specificity of the transport of Lipid II by FtsW in Escherichia coli