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What is the Edward O. Wilson fuss about?
I have just read this article on E. O. Wilson and I don't understand what the difference is between what he is arguing and "standard" natural selection.
I read "the extended phenotype" some years ago and from what I vaguely remember that argued that everything about selection comes down to genes: they are the units of what is inherited and drive everything else (and their reach can be quite surprising).  At first glance that seems inconsistent with the article, since it mentions "group selection".  But when you read the details it includes things like

Group selection begins when a colony of creatures develops a behaviour
  that gives it a competitive advantage over other groups. Initially,
  this could be down to a random genetic mutation.

which sounds like it's gene-based too (and examples seem to come from ants and the like which I thought were closely genetically-related across a colony too...).
So what is the fuss about?  And how will it be resolved?
Maybe the difference is easier to explain in terms of some difference between mathematical models?  If so, that's fine (I hope - it might make more sense than jargon in a field I am unfamiliar with ;o).
[Is this too "general public" for this site?  Apologies if so.]

After reading the article, the fuss is about this:
In currently accepted theory Eusociality or "kin selection" explains altruistic behavior (the sacrifice of yourself or resources you control for the betterment of something else besides you) by relating the act to the amount of genetic information passed on.
The relevant equation is Hamilton's rule:
                                                                $rB > C$
C is the cost to the actor (the person giving up resources). B is the number of others involved, and r is the relationship value to the actor in terms of genetic similarity.
So if you and two full-siblings (who each share on-average 50% of your genome) and a bus comes straight at the group, and you have the capability to push them out of the way while dying yourself, kin selection suggests you shouldn't because the genetic cost is equivalent. You eliminate yourself from the gene pool, and save the equivalent of yourself for future generations (2 x 1/2 = 1).
However, if you and three siblings were in the situation, then it's evolutionarily advantageous to be altruistic. You would die (a cost of 1), but you would save the equivalent of 1.5x your genome (3 x 1/2 = 1.5) to pass on to future generations.
Thus, communal and social behaviors like those of ants basically boil down to: Everybody is so closely related that spending resources to help your kin is essentially spending resources to ensure the majority of your genome survives (which is the big point of evolution, after all).
Wilson's argument, what I can glean from the small brief of the study and the article, is that you don't need the relatedness equation to explain altruistic behavior in social situations (basically the row is he's saying the currently accepted theory is wrong). All you need to start with is a genetic mutation somewhere along the line that causes the offspring to stick close to home. Once you have a few generations that don't leave the nest, you start to develop social behavior that results in altruism because you've gone from selfish individuals to a group setting.
The article and Wilson don't give any more insight other than altruism apparently develops spontaneously from the formation of groups. Simply being social is the explanation for why some individuals will give resources to others to ensure the success of the others.
Whether or not Wilson is correct isn't really discussed. He openly admits to needing a lot of research, some of which is being performed.

Hamilton's rule... :)  I feel that the fundamental argument for individual selection is as much ideological as it is scientific.  There are quite a few edge cases which both sides explain away I feel.  To me the big question is how does this explain human social behavior, which is the brass ring, still ungrabbed by biology.

I started reading David Sloan Wilson's work on group selection a decade ago and am surprised that the field still has such a reluctance to move on.

@Abe - The duty of scientists is only to move on if better information is presented. I'm not familiar with D. S. Wilson's work, but the current textbooks feature Hamilton's Rule. If Wilson's work provides a better explanation, it will eventually get accepted. :-)

So what is the fuss about?

The fuss isn’t so much about biology as it is about the circumstances of the argument. in particular, I gather that there are two complaints people have with E. O. Wilson’s (and his collaborators’) arguments:

The Wilsonians pretend that kin selection (inclusive fitness) is just a quaint, outdated theory which is trivially dismantled because its mathematics don’t work, while in reality it represents the view of most people in the of field evolutionary biology, and has for years. Regardless of its actual scientific value, it certainly isn’t outdated – it’s the majority view among experts.
Proponents of kin selection feel that the Wilsonians misrepresent their views by citing and attacking outdated knowledge rather than the state of the art, thus creating a straw man argument. In the same vein, they argue that since Wilsonians obviously don’t know the state of the art, they cannot contribute meaningfully to the debate.

In addition, proponents of kin selection argue that group selection theory simply doesn’t hold up in theory1. I find those arguments highly compelling. At the same time, I’m not an expert and the Wilsonians argue that kin selection is equally flawed so I won’t weigh in on the debate.

1 The article is not written by an expert in the field but it has been endorsed by experts as a lucid explanation of the matter.

How is the fact that group selection does not hold in theory reconcile with observations / experimental tests? Is there another explanation for inherited religious, social, or political groups?

@Abe I’m not an expert but as far as I know none of those actually requires group selection. Many phenomena are simply explainable by kin selection. And while we don’t have comprehensive explanations for large-scale phenomena such as religion etc., you can construct potential explanations without invoking group selection. Indeed, just because there’s interaction within and between groups involved doesn’t mean that evolutionary selection happens on the level of groups, just like genetic selection doesn’t happen on the level of individuals, it happens on the level of alleles.

It is maybe of note that E O Wilson is first and foremost an entomologist and has developed many of his ideas to explain the evolution of ants and bees first.


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Literature that demonstrates organisms have a competitive advantage in numbers
I'm studying two bird populations that are competing against each other for a resource: Population A and Population B.
Population A is present in much higher numbers than Population B, and as a consequence, I think that Population A has a competitive advantage over Population B.
I'm looking for literature that demonstrates that when one population is present in higher numbers than the other population, the population present in higher numbers has a competitive advantage. Can anyone point me in the direction of literature that demonstrates this?

This is not necessarily true. Take for example elephants and aphids that both feed on the same plants (competition for the same resource). It is not necessarily the case that relative quantities are linked directly to competitive advantage.

I don't see your logic that the more abundant species need to have a competitive advantage (I assume that populations A & B are referring to different species), at least without more information. There is often a negative relationship between body size and population density, and there are many other things that are affecting population abundances. Why are you assuming that competitive advantage is the key factor? Are they directly competing for the same resource? What type of resource are you referring to?

I have found these papers:
http://www.sciencedirect.com/science/article/pii/S0169534713002322
http://www.sciencedirect.com/science/article/pii/S0040580912001360
http://www.ncbi.nlm.nih.gov/pubmed/19416834
http://www.ncbi.nlm.nih.gov/pubmed/21930936
The last two argue that larger groups have better "problem solving" capability, and this is a clear advantage in competition.

Can you please expand your answer beyond just dropping links? This is not helpful, even if the articles might be...

He asked for papers and I gave him links to pertinent scientific publications... However, the main point is that in a larger community there is higher chance of finding solutions to problems. In case of birds, bigger is the swarm and easier will be to solve issues. This in general gives a reasonable advantage. So if two groups of the same species (or very close) are in competition the bigger group have greater chance to prevail.

Chris - answer is helpful because I asked for papers

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Hibernation, Metabolism and Aging
People are beginning to seriously research space travel applications of therapeutic hypothermia, specifically for reducing metabolism and stress on humans traveling to Mars.
It seems that as you decrease the temperature, the metabolism decreases. My question is regarding the relationship between ageing and metabolism. Do we have any data that answers the question if lowered metabolism also lowers the rate of ageing?
I'm wondering if these hypothetical astronauts going to Mars are actually losing 6 months of their lifespan in an unconscious state, or is their ageing rate being lowered as well? And by how much?
For the sake of simplicity, let's ignore the effects of radiation on ageing during the travel.

Therapeutic hypothermia certainly is an extremely useful short-term treatment for hypoxic and ischaemic injury to tissues (caused by loss of blood flow and/or oxygen) and is part of the protocol for treating people in intensive care who have had out of hospital cardiac or respiratory arrest as well as being used during heart surgery in cardiopulmonary bypass. In addition there is currently research into treating people who have just had heart attacks and strokes, both conditions where there is acute loss of blood flow due to a clot.
However, there is little evidence as regards use of chronic (long term) hypothermia to prevent aging. While severe hypothermia does suppress cellular respiration and slow down metabolism and bodily function, it also often causes other abnormalities such as:

Disturbances in cardiac conduction that can lead to cardiac arrest
Markedly reduced blood flow to skin and limbs which can lead to tissue death in fingers, toes, etc.
Clotting dysfunction (haemorrhage if there is any injury)
Pulmonary oedema - fluid in the lungs causing inability to oxygenate and/or ventilate the blood
Increase in infections

There is, however, quite a lot more evidence in regards to slowing down cell ageing from oxidative stress using diet energy restriction and this has been replicated in rodents.
In other words, there really isn't any good evidence at this stage in regards to long term hypothermia, but currently, given the high risks of cardiac dysfunction and death, without invasive monitoring and intervention (such as in an ICU) it is not feasible.

Interesting. But your last paragraph suggests that invasive monitoring and intervention could perhaps help to achieve long term hypothermia? can you give a little bit more detail on what you are thinking?

At a minimum you'd need a way to feed the person and dispose of waste- without introducing infection (a major risk of catheters and long term intravenous lines), as well as pacing wires or a defibrillator. You would also probably need a way to monitor blood test results and treat any problems with peripheral circulation and lung problems. Certainly too complex to be automated.

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Can all mammals swim?
When I checked it seemed trivial to answer: yes, all mammals can swim. But research on the internet provided different information. I found:

people and primates cannot swim, but can be taught how to swim
giraffes can't swim
someone claimed elephants can't swim, but this video ad shows the reverse
porcupines nor rhinos can't swim
at least some bats can swim, but according to this source there's insufficient data.

Of each hit, I found other hits that claimed the reverse, sometimes with proof. Common sense tells me all mammals can swim, but is this true?

There are over 5,000 species of named, extant mammals. So to show that all can (or cannot) swim would be a monumental task.

@Kevin: fair enough. Yet, to prove that all mammals can swim may require research on each of the species, but to prove the opposite only requires proof that one species really can't swim.

Well, what is your definition of swimming? That needs to be cleared before getting any further.

@CHM: the way I see it, moving through the water without drowning and without walking on the bottom of the river/lake.

possible duplicate of Why can all animals swim in water without learning to swim but humans cannot?

@dustin I am in a dilemma about which one to close. I VTCed the other one.

I'm votin this to be left open as the other one has already been flagged as duplicate and voted for closing on that one.

@WYSIWYG this is is more general where the other is more specific which is why I think this one should be closed as opposed to the other one.

@poka.nandor close votes can be retracted. Click close again and you will see the option. Also, just because one has been voted on doesn't mean we have to leave it if it doesn't make sense.

@dustin - I know clos votes can be retracted, I just try keep my voting consequent. As WYSIWYG, I too have dillema. I'll read both questions for a few more times and revise my decision if needed.

Plenty of primates swim, the Japanese macaque is famous for it.

With respect to the giraffe claim, this article seems relevant:
D. M. Henderson, D. Naish, Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis, J Theoretical Biology 265 (2010) 151-159.
It cites several non-"random person on the internet" claims that giraffes cannot swim:

It is generally thought that giraffes cannot swim, but relevant
  observations are few. Shortridge (1934) and Goodwin (1954) state that
  giraffes were poor waders and unable to swim. Crandall (1964)
  discussed a case where a captive giraffe escaped from a carrying
  crate, ran to the end of a jetty, and fell into the water. The animal
  reportedly sank without making any attempt to swim. MacClintock (1973,
  p. 54) stated ‘Giraffes cannot swim. Rivers are barriers they do not
  cross’. Wood (1982, p. 20) noted that ‘Because of its extraordinarily
  anatomical shape the giraffe is one of the very few mammals that
  cannot swim – even in an emergency! Deep rivers are an impassable
  barrier to them, and they will avoid large expanses of water like the
  plague’.

They then go on to show that a model giraffe could plausibly swim, writing: "For practical and ethical reasons we are unable to use live giraffes..."
They conclude:

In summary, the results and speculations of this study show that it is
  not impossible that a giraffe could propel itself in water, but in
  terms of energy efficiency relative to that of the horse, it would
  appear that the costs of aquatic locomotion might be too high. It is
  reasonable to expect that giraffes would be hesitant to enter water
  knowing that they would be at a decided disadvantage compared to being
  on solid ground.

+1 Interesting, nice find! I just found out that hippos can't swim either, because they're too dense and would sink. They "walk" across the bottom.

I feel like the answer by Kin invalidates the part of the quoted claim that says "Rivers are barriers they do not cross", perhaps deep rivers yes but there is video showing them at least attempting to cross a river.  Not that this is evidence of them swimming, because it looks like they're just walking.

I have found videos of porcupines, armadillos, anteaters.. all swimming.
The porcupine seemed to have no trouble at all.
As for apes - quite well it seems. http://newswatch.nationalgeographic.com/2013/08/20/new-surprising-video-shows-apes-swimming/
Rhinos:
www.youtube.com/watch?v=DbqF4AA0Z8U
The water looks deeper than it's head at times, for sure. But whether it is actually swimming or can just/almost reach the bottom is unclear.
Giraffes:  http://www.arkive.org/giraffe/giraffa-camelopardalis/video-ti06.html
It seems to me that if these animals couldn't manage at all in the water, that they wouldn't likely do so, from an evolutionary standpoint.
I'm sure not all manage terribly well, but the videos seem to show that they managed at least.
Pretty cool.  :)

The video of the giraffes shows that they don't swim, as the moment that they consider it too deep, they instantly return to shore. And indeed, the rhino walks across the bottom of the riverbed.

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Why do plants have green leaves and not red?
I know plants are green due to chlorophyll.
Surely it would be more beneficial for plants to be red than green as by being green they reflect green light and do not absorb it even though green light has more energy than red light.
Is there no alternative to chlorophyll? Or is it something else?

I find it even more puzzling why plants don't absorb all of the visible spectrum altogether (resulting in the leaves being black).

@CrazyJugglerDrummer - I thought about it but didn't want to get the chlorophyll response without people reading =P

It is even more strange becouse green algae evolved in water. And red light is absorbed by water. Rhodophyta (red algae) are red due to phycoerythrin but it seems that red color is advantageous for them only in sea depths.

@AdamZalcman: There's probably no organic substance with this absorption spectrum, and adding further pigments to cover the entire VIS spectrum might not pay off.

@MartaCz-C: I think that's because of the solar spectrum, and as you said water absorbs red light stronger so at deep sea levels red light becomes more and more unusable and can the red-absorbing pigments can then be dropped in favour of green absorbers

Surely it would be more beneficial: not if the red pigment is less efficient in converting light to energy...

I would like to point to a dissuasion that took place at John Baez's google+ on the subject https://plus.google.com/117663015413546257905/posts/emyoML3CrvY It contains relevant links along with references to actual  articles devoted to the question. This is a nice point to begin further investigation.

If anybody is interested in a short video on the topic (~6.5 min), watch Physics Girl's video: Why aren't plants black? disclaimer: This is not my video, but I think it is very well researched and informative.

I know it's been a couple of years, but I just added a new answer to this question that focuses on the early evolution of plants. Hope this helps!!

The real answer is that they do not. The majority of plants have green leaves, not all of them. It's just they don't need to evolve towards having leaves of other colors, the same way as human don't need to evolve to get rid of nails, hair and coccyx. There are even black plants.

According to a new model of photosynthesis plants are green to reduce noise: https://www.quantamagazine.org/why-are-plants-green-to-reduce-the-noise-in-photosynthesis-20200730/

Surely it would be even more beneficial for plants to be black instead of red or green, from an energy absorption point of view. And Solar cells are indeed pretty dark.
But, as Rory indicated, higher energy photons will only produce heat. This is because the chemical reactions powered by photosynthesis require only a certain amount of energy, and any excessive amount delivered by higher-energy photons cannot be simply used for another reaction1 but will yield heat. I don't know how much trouble that actually causes, but there is another point:
As explained, what determines the efficiency of solar energy conversion is not the energy per photon, but the amount of photons available. So you should take a look at the sunlight spectrum:

The Irradiance is an energy density, however we are interested in photon density, so you have to divide this curve by the energy per photon, which means multiply it by λ/(hc) (that is higher wavelengths need more photons to achieve the same Irradiance). If you compare that curve integrated over the high energy photons (say, λ < 580 nm) to the integration over the the low energy ones, you'll notice that despite the atmospheric losses (the red curve is what is left of the sunlight at sea level) there are a lot more "red" photons than "green" ones, so making leaves red would waste a lot of potentially converted energy2.
Of course, this is still no explanation why leaves are not simply black — absorbing all light is surely even more effective, no? I don't know enough about organic chemistry, but my guess would be that there are no organic substances with such a broad absorption spectrum and adding another kind of pigment might not pay off.3
1) Theoretically that is possible, but it's a highly non-linear process and thus too unlikely to be of real use (in plant medium at least)
2) Since water absorbs red light stronger than green and blue light deep sea plants are indeed better off being red, as Marta Cz-C mentioned.
3  And other alternatives, like the semiconductors used in Solar cells, are rather unlikely to be encountered in plants...
Additional reading, proposed by Dave Jarvis:

http://pcp.oxfordjournals.org/content/50/4/684.full
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691134/
http://www.life.illinois.edu/govindjee/photosynBook/Chapter11.pdf
https://www.heliospectra.com/sites/default/files/general/What%20light%20do%20plants%20need_5.pdf

I would also add the fact that blue light reaches earth surface greately scattered due to Rayleigh scattering, so the absolute amount of energy carried blue light is comparable (or even less) than that of other parts of the visible spectrum.

@AlexanderGalkin: True, but that should already be included in the red curve (together with atmospheric absorption): for blue you can see a stronger deviation from sunlight (yellow curve) than for red/IR (Unfortunately I don't have the dataset but it would be better visible for the photon density)

If leaves were black, they would get too hot.

@David only if the absorbed energy weren't used efficiently, which would, as you suggest, be a reason for leaves to be not black. You could also have green but inefficient and therefore hot leaves, but evolution would have gotten rid of these already

@TobiasKienzler green leaves stay cool via transpiration, not because they efficiently use solar radiation.

Also don't forget - evolution only produces something which is good enough - not optimal. If green turned out to be good enough, then there would be impetus to develop black leaves.

I'd note as well that there are other photosynthesizers that utilise the energies that plants do not - so-called purple bacteria - and these may predate green photosynthesizers. It's plausible that the "green gap" originally evolved as a means to exploit light not exploited by competing organisms.

I think it is as S.Albano says: In normal conditions, plants collect more photons than they can process by the photosynthetic chemistry. Excess energy creates singlet oxygen, which is highly toxic. Plants are getting rid of the excess energy with help of carotenoids in xanthophyll cycle. I think that chlorophyll is preferred because it also has largely structural role. (Special pair in the reaction center, photosynthetic antennae, etc.)

Worth noting that leaves are white in infrared. Only we can't see this with a naked eye.

@sanmai That's a rather confusing statement, what do you mean by "white in infrared"? Reflective?

@TobiasKienzler yes, they don't absorb infrared because there isn't enough energy in it to start photosynthesis, and moreover you don't want to overheat; hence reflection

This still does not explain why they are green and not say yellow or purple.

You say that "deep sea plants are indeed better off being red", however according to Wikipedia there are no deep sea plants.
"Natural light does not penetrate the deep ocean, with the exception of the upper parts of the mesopelagic. Since photosynthesis is not possible, plants cannot live in this zone. Although some light penetrates the mesopelagic zone, it is insufficient for photosynthesis". - Wikipedia

The high energy photon thing is a RESULT of them being green, not the cause. With a different pigment instead of chlorophyll they could absorb it just fine.

I believe it is because of a trade off between absorbing a wide range of photons and not absorbing too much heat.  Certainly this is a reason why leaves are not black - the enzymes in photosynthesis as it stands would be denatured by the excess heat that would be gained.
This may go some of the way towards explaining why green is reflected rather than red as you suggested - reflecting away a higher energy colour reduces the amount of thermal energy gained by the leaves.

I think the solar spectrum is also quite relevant.

It is more to do with the specific photon energy level (see Tobias) than the thermal heat  supplied per se. Heat is probably not a concern for temperate/arctic plants which are also green.

Heat is the least of a plant's problems. That is why we can breed black tulips without self-cooking petals. ;)

There is quite a fun article here which discusses the colours of hypothetical plants on planets around other stars.
Stars are classified by their spectral type which is dictated by their surface temperatures. The Sun's is relatively hot, and it's spectral energy distribution peaks in the green region of the spectrum. However the majority of stars in the Galaxy are K and M type stars which emit mainly in the red and infrared.
This is relevant to this discussion since any photosynthesis on these worlds would have to adapt to these wavelengths of light in order to proceed. On planets around cool stars plant life (or its equivalent) might well be black!
OK, this is not entirely pie in the sky astrobiologist rubbish. It is actually quite relevant to the search for biosignatures and life on other planets. In order to model the reflectance spectrum of planets we observe (i.e. the light reflected from the primary star) we need to try and take into account any potential vegetation.
For example, if we take a reflectance spectrum of the Earth, we see a characteristic peak in the red "the red edge" which is due to surface plant life.
NASA also has a short page on this here.

nice links, though I doubt black plants are likely to happen anywhere since that would most likely need too many different pigments

OK, maybe not completely black but very dark. There are various terrestrial plants which have very dark leaves (e.g. Oxalis triangularis). Admittedly, many are cultivars but this does demonstrate that there are some dark pigments available (I suppose anthocyanins?)

good point. Maybe in most cases absorbing green was just the first thing that happened (by evolution) and it was sufficient, but I'm just speculating...

I know this question was asked and answered a number of years ago (with many great answers), but I couldn't help but notice that no one had approached this from an evolutionary perspective (like the answer to this question)...
 Short Answer
Pigments appear as whatever color is not absorbed (i.e., they appear as whichever wavelength(s) of light they reflect).
Blue light was the most available wavelength of light for early plants growing underwater, which likely led to the initial development/evolution of chlorophyll-mediated photosytems still seen in modern plants. Blue light is the most available, most high-energy light that continues to reach plants, and therefore plants have no reason not to continue taking advantage of this abundant high energy light for photosynthesis.
Different pigments absorb different wavelengths of light, so plants would ideally incorporate pigments that can absorb the most available light. This is the case as both chlorophyll a and b absorb primarily blue light. Absorption of red light likely evolved once plants moved on land due to its increased abundance (as compared to under water) and its higher efficiency in photosynthesis.

 Long Answer
 Early Plants Develop Modern Photo-system
It turns out, just like the variability in transmittance of different wavelengths of light through the atmosphere, certain wavelengths of light are more capable of penetrating deeper depths of water. Blue light typically travels to deeper depths than all other visible wavelengths of light. Therefore, the earliest plants would have evolved to concentrate on absorbing this part of the EM spectrum.

However, you'll notice that green light penetrates relatively deeply as well.  The current understanding is that the earliest photosynthetic organisms were aquatic archaea, and (based on modern examples of these ancient organisms) these archaea used bacteriorhopsin to absorb most of the green light.

Early plants grew below these purple bacteriorhopsin-producing bacteria and had to use whatever light they could get. As a result, the chlorophyll system developed in plants to use the light available to them. In other words, based on the deeper penetrative ability of blue/green light and the loss of the availability of green light to pelagic bacteria above, plants evolved a photosystem to absorb primarily in the blue spectrum because that was the light most available to them.

Different pigments absorb different wavelengths of light, so plants would ideally incorporate pigments that can absorb the most available light. This is the case as both chlorophyll a and b absorb primarily blue light.

Here's two example graphs (from here and here) showing the absorption spectrum of typical plant pigments:

 So Why Are Plants Green?
As you can guess from the above paragraphs, since early under water plants received so little green light, they evolved with a chlorophyll-mediated photo-system that did not have the physical properties to absorb green light. As a result, plants reflect light at these wavelengths and appear green.
 But Why Are Plants Not Red?...
Reason to ask this question:
This would seem to be equally plausible given the above information. Since red light penetrates water incredibly poorly and is largely unavailable at lower depths, it would seem that early plants would not develop a means for absorbing it and therefore would also reflect red light.

In fact, [relatively] closely related red algae did evolve a red-reflecting pigment. These algae evolved a photo-system that also includes the pigment phycoerythrin to help absorb available blue light. This pigment did not evolve to absorb the low levels of available red light, and so therefore this pigment reflects it and makes these organisms appear red.

Interestingly, according to here, cyanobacteria that also contain this pigment can readily change it's influence on the organism's observed color:

The ratio of phycocyanin and phycoerythrin can be environmentally altered. Cyanobacteria which are raised in green light typically develop more phycoerythrin and become red. The same Cyanobacteria grown in red light become bluish-green. This reciprocal color change has been named 'chromatic adaptation’.

Further, (although it's still under debate) according to work by Moreira et al (2000) (and corroborated by numerous other researchers) plants and red algae likely have a shared photosynthetic phylogeny:

three groups of organisms originated from the primary photosynthetic endosymbiosis between a cyanobacterium and a eukaryotic host: green plants (green algae + land plants), red algae and glaucophytes (for example, Cyanophora).

So what gives?
Answer:
The simple answer of why plants aren't red is because chlorophyll absorbs red light.
This leads us to ask: Did chlorophyll in plants always absorb red light (preventing plants from appearing red) or did this characteristic appear later?

If the former was true, then plants don't appear red simply because of the physical characteristics that the chlorophyll pigments evolved to have.

As far as I know, we don't have a clear answer to that question.

(others please comment if you know of any resources discussing this).

However, regardless of when red light absorption evolved, plants nevertheless evolved to absorb red light very efficiently.

A number of sources (e.g., Mae et al. 2000, Brins et al. 2000, and here) as well as numerous other answers to this question,  suggest that the most efficient photosynthesis occurs under red light. In other words, red light results in the highest "photosynthetic efficiency."

This NIH page suggests the reason behind this:

Chlorophyll a also absorbs light at discrete wavelengths shorter than 680 nm (see Figure 16-37b). Such absorption raises the molecule into one of several higher excited states, which decay within 10−12 seconds (1 picosecond, ps) to the first excited state P*, with loss of the extra energy as heat. Photochemical charge separation occurs only from the first excited state of the reaction-center chlorophyll a, P*. This means that the quantum yield — the amount of photosynthesis per absorbed photon — is the same for all wavelengths of visible light shorter than 680 nm.

Note, however, that other sources suggest blue light is better than red. For example, see Muneer et al, (2014).

Biomass and photosynthetic parameters increased with an increasing light intensity under blue LED illumination and decreased when illuminated with red and green LEDs with decreased light intensity

 Why Did Plants Remain Green?
So why have plants not evolved to use green light after moving/evolving on land? As discussed here, plants are terribly inefficient and can't use all of the light available to them. As a result, there is likely no competitive advantage to evolve a drastically different photosystem (i.e., involving green-absorbing pigments).
So earth's plants continue to absorb blue and red light and reflect the green. Because green light so abundantly reaches the Earth, green light remains the most strongly reflected pigment on plants, and plants continue to appear green.

(However, note that other organisms such as birds and insects likely see plants very differently because their eyes can distinguish colors differently and they see more of the strongly reflected UV light that ours cannot).

Citations
 Moreira, D., Le Guyader, H. and Philippe, H., 2000. The origin of red algae and the evolution of chloroplasts. Nature, 405(6782), pp.69-72.
 Muneer, S., Kim, E.J., Park, J.S. and Lee, J.H., 2014. Influence of green, red and blue light emitting diodes on multiprotein complex proteins and photosynthetic activity under different light intensities in lettuce leaves (Lactuca sativa L.). International journal of molecular sciences, 15(3), pp.4657-4670.

This answer needs more love, it is the only one that actually explains why plants are green and not say yellow or pink.

what a brilliant answer!!!!!!

There are two factors at play here. First is the balance between how much energy a plant can collect and how much it can use. It is not a problem of too much heat, but too many electrons. If it were a question of heat, a number of flowers selected for their black pigmentation would have their petals cooked off. ;)
If a plant does not have enough water, is too cold, is too hot, collects too much light, or has some other condition that prevents the electron transport chain from functioning properly, the electrons pile up in a process called photoinhibition.
These electrons are then transferred to molecules that they should not be transferred to, creating free radicals, wreaking havok within the plant's cells. Fortunately, plants produce other compounds that prevent some of the damage by absorbing and passing around the electrons like hot potatos. These antioxidants are also beneficial to us when we eat them.
This explains why plants collect the amount of light energy they do, but does not explain why they are green, and not grey or dark red. Surely there are other pigments that would be able to generate electrons for the electron transport chain.
The answer to that is the same as why ATP is used as the main energy transport molecule in organisms rather than GTP or something else.
Chlorophyll a and b were just the first things that came about that fulfilled the requirement. Certainly some other pigment could have collected the energy, but that region of parameter space never needed to be explored.

I think you are right, that the bottleneck is not in collecting the photons, but in processing them without creating too much singlet oxygen. One of important factors might be that chlorophyll plays also a big structural role: It is not only a collector of light, but also allows separation of charge in the special pair of the reaction center and constitutes many pigment-protein complexes structurally.

The biologist John Berman has offered the opinion that evolution is not an engineering process, and so it is often subject to various limitations that an engineer or other designer is not. Even if black leaves were better, evolution's limitations can prevent species from climbing to the absolute highest peak on the fitness landscape. Berman wrote that achieving pigments that work better than chlorophyll could be very difficult. In fact, all higher plants (embryophytes) are thought to have evolved from a common ancestor that is a sort of green alga – with the idea being that chlorophyll has evolved only once. (reference)
Plants and other photosynthetic organisms are largely filled with pigment-protein complexes that they produce to absorb sunlight. The part of the photosynthesis yield that they invest in this, therefore, has to be in proportion. The pigment in the lowest layer has to receive enough light to recoup its energy costs, which cannot happen if a black upper layer absorbs all the light. A black system can therefore only be optimal if it does not cost anything (reference).
Red and yellow light is longer wavelength, lower energy light, while the blue light is higher energy. It seems strange that plants would harvest the lower energy red light instead of the higher energy green light, unless you consider that, like all life, plants first evolved in the ocean. Seawater quickly absorbs the high-energy blue and green light, so that only the lower energy, longer wavelength red light can penetrate into the ocean. Since early plants and still most plant-life today, lived in the ocean, optimizing their pigments to absorb the reds and yellows that were present in ocean water was most effective. While the ability to capture the highest energy blue light was retained, the inability to harvest green light appears to be a consequence of the need to be able to absorb the lower energy of red light (reference).
Some more speculations on the subject: (reference)

Water absorbs red light far more than blue light! That's why everything looks blueish below a certain depth. This explains why phytoplankton always hovers on the top layers of the ocean. And it's perhaps an explanation why chlorophyll has a second absorption peak in the blue region.

There are several parts to my answer.
First, evolution has selected the current system(s) over countless generations through natural selection.  Natural selection depends on differences (major or minor) in the efficiency of various solutions (fitness) in the light (ho ho!) of the current environment.  Here's where the solar energy spectrum is important as well as local environmental variables such as light absorption by water etc. as pointed out by another responder. After all that, what you have is what you have and that turns out to be (in the case of typical green plants), chlorophylls A and B and the "light" and "dark" reactions.
Second, how does this lead to green plants that appear green?  Absorption of light is something that occurs at the atomic and molecular level and usually involves the energy state of particular electrons.  The electrons in certain molecules are capable of moving from one energy level to another without leaving the atom or molecule.  When energy of a certain level strikes the molecule, that energy is absorbed and one or more electrons move to a higher energy level in the molecule (conservation of energy).  Those electrons with higher energy usually return to the "ground state" by emitting or transferring that energy.  One way the energy can be emitted is as light in a process called fluorescence.  The second law of thermodynamics (which makes it impossible to have perpetual motion machines) leads to the emission of light of lower energy and longer wavelength.  (n.b. wavelength (lambda) is inversely proportional to energy; long wavelength red light has less energy per photon than does short wavelength violet (ROYGBIV as seen in your ordinary rainbow)).
Anyway, chlorophylls A and B are complex organic molecules (C, H, O, N with a splash of Mg++) with a ring structure.  You will find that a lot of organic molecules that absorb light (and fluoresce as well) have a ring structure in which electrons "resonate" by moving around the ring with ease.  It is the resonance of the electrons that determine the absorption spectrum of a given molecule (among other things).  Consult Wikipedia article on chlorophyll for the absorption spectrum of the two chlorophylls.  You will note that they absorb best at short wavelengths (blue, indigo, violet) as well as at the long wavelengths (red, orange, yellow) but not in the green.  Since they don't absorb the green wavelengths, this is what is left over and this is what your eye perceives as the color of the leaf.
Finally, what happens to the energy from the solar spectrum that has been temporarily absorbed by the electrons of chlorophyll?  Since its not part of the original question, I'll keep this short (apologies to plant physiologists out there).  In the "light dependent reaction", the energetic electrons get transferred through a number of intermediate molecules to eventually "split" water into Oxygen and Hydrogen and generate energy-rich molecules of ATP and NADPH. The ATP and NADPH then are used to power the "light independent reaction" which takes CO2 and combines it with other molecules to create glucose.  Note that this is how you get glucose (at least eventually in some form, vegan or not) to eat and oxygen to breath.
Take a look at what happens when you artificially uncouple the chlorophylls from the transfer system that leads to glucose synthesis.  http://en.wikipedia.org/wiki/Chlorophyll_fluorescence  Notice the color of the fluorescence under UV light!
Alternatives?  Look at photosynthetic bacteria.

Small addition to the conversation: plants reflect green yes, but chlorophyll (a and b) does not (it is mostly transparent to it).
The organic material (walls of cells, etc.) around the chlorophyll behave as reflectors and scatterers of the non-absorbed green light, and that's what we see.
https://www.tandfonline.com/doi/full/10.1080/00219266.2020.1858930
In general there are 3 types of interactions of a photon with matter:

reflection (and scattering elastic or not)
absorption (inelastic process)
transmission (no energetically-lossy-interaction)

(My reply targets better the OP formulation of this duplicate question)

Tobias Keinzler does a good job of explaining why black plants would not work, this is an explanation of why plants are green and not some other color.
Color of foliage is based on whatever the color is of bacteria (or archaea) that get incorporated to become chloroplasts. Or more specifically the color of their light absorbing pigments. there is a huge range in nature for color in photosynthetic organisms, plants are green becasue chlorophyll is green, it could have just as easily been red or purple. http://www.ucmp.berkeley.edu/glossary/gloss3/pigments.html
There is decent evidence that chloroplast ancestors absorb the  margins of the visible spectrum becasue halobacterium absorb the major constituents, becasue the chlorophyll users did not compete with them directly instead absorbing the leftover light.  It was only later when they got incorporated into larger cells that they came to dominate and eventually giving rise to plants.
Plants are not green becasue green is better, plants are green becasue that is the first efficient photosynthetic pigment to evolve that did not compete with the dominate photosynthesizer.


text:
Human evolution: Where *exactly* did the first human come from, whose parents were not?
Layman here. So I have never really quite understood this facet of human evolution, (or any other for that matter), in that, I understand the evolutionary process, but I get lost on the 'border' cases.
For example, we, as humans, evolved from monkeys, (to use the colloquial term, I am not a biologist by any measure).
My question is, doesn't this mean that at some, discrete point, there had to have been a human, whose parents were not? If that is true, how does that work, in the sense that we now have species1 giving birth to species2.
If not, then how exactly does this border case work? The only other alternative I see, is that the borders are 'fuzzy', but then that necessarily means that the definition of a species is itself fuzzy, which I understand is not the case.
Thanks!

Take a bucket of blue-dyed water and start slowly pouring yellow-dyed water into it. Is there a discrete point at which it becomes green?

@RussellBorogove Interesting - please see my comment/question to Konrad on this matter though.

My two cents in addition to all these wonderful answers: The spectrum of phenotypical/genetic/epigenetic variation is always there, until natural selection hits the continuum and breaks it in to pieces (species) by destroying "unfit" elements in this continuum.
I may be dead wrong though, I'm no expert on evolution (aside from causing evolution to Pens/strep resistant bacteria in my incubator, that is. :) )

For a review of the definition of species (with application to human) have a look at How could humans have interbred with Neanderthals if we're a different species?.

Actually, your last paragraph is more the case than not.
There are currently three common definitions for delineating discrete species:
1) Phenotypically different from related species (looks or acts differently).
2) Produces viable offspring in the wild.
3) Some % of genetic difference.
There are strengths to all three:
1) Very easy to ascertain and measure.
2) Most common conception of a species.
3) Genes control the first two, so genetic divergence gets to the heart of the matter.
There are also weaknesses to all three:
1) Is notorious for mis-labeling and missing species.
2) Some species which can mate and produce fertile offspring under enclosed conditions do not do so in the wild (Tigers and Lions, for instance).
3) The amount of divergence has, thus far, been completely arbitrary. If there is a certain % or patterns of mutation required in the genome, science hasn't yet discovered it.
The fuzzy definition of species, combined in the not-exactly-intuitive generational-type thinking required for understanding evolution, and the answer to your question is (at least to the best of my understanding) the following:
Yes, at some point one of our ancestors gave birth to the first Homo sapien that was somehow genetically different from its parents. However, the magnitude of the difference is probably not as great as you might think.
We've already observed our closest evolutionary cousins, the Bonobos, making basic tools through flint napping: http://www.newscientist.com/article/dn22197-bonobo-genius-makes-stone-tools-like-early-humans-did.html
It's also possible that disputes between male chimpanzees are mediated by an older female: http://www.cpradr.org/Resources/ALLCPRArticles/tabid/265/ID/121/Primates-and-Me-Web.aspx
And that both Chimpanzees and Capuchin monkeys can be taught the concept of currency (which, somewhat comedically, they then used for prostitution): http://www.nytimes.com/2005/06/05/magazine/05FREAK.html?ei=5090&en=af2d9755a2c32ba8&ex=1275624000&partner=rssuserland&emc=rss&adxnnlx=1118160068-1EGJuan4FJH1LooxHYd5/g&pagewanted=all
Then there's the everlasting impact of Koko, the Silverback Gorilla who was taught - and perfectly capable of replying in - sign language: http://en.wikipedia.org/wiki/Koko_%28gorilla%29
The idea that humans jumped onto the scene with unforeseen amounts of intelligence and capability probably isn't what happened. Obviously we are capable of constructing and using the most advanced tools on the planet, but this is after several thousand generations of innovation. The very first human might have been more intelligent (or at least had the capacity to be), but otherwise probably fit in pretty well with its parents and other relatives since the vast majority of what we learn comes from our parents and personal experience.
Then over time the number of individuals with the capacity for higher modes of thinking increased as a result of the genetic inheritance of whatever mutation created the first human. The first human, to put it simply, was successfully able to pass on their mutation which gave them our unique traits, and their offspring were also successful - until you have an entire population of humans living amongst each other. Eventually our innovative capacity lead, step by step, to our dominant position on the planet.
Even now humans are yet evolving. Lactose tolerance (the ability to consume dairy products after childhood) is a very new trait among humans (and unprecedented among all mammals) only a few hundred generations old (roughly 10,000 years) that evolved twice in separate populations of humans (North Africa and Northern Europe). Our jaws are getting progressively smaller (which is why some people have to remove their wisdom teeth to maintain a straight smile - and some people don't have wisdom teeth at all), some muscles are disappearing (the Palmaris Longus is one example - it's present in about 80% of humans), and other subtle changes are occurring.
Just don't make the mistake of equating "evolved" with "superior." Evolution is dictated by the ever-changing demands of the environments we find ourselves in, and what's beneficial today isn't guaranteed to be beneficial forever.

Thank you, but let me understand you. You are saying that yes, there had to be a discrete point in history, where the first homo-sapien, was literally, born to parents who were not homo-sapiens? 1) What species were those pre-homo-sapien parents? 2) Was there just one instance of this first-homo-sapien being born? A figurative 'Adam'? Or were there multiple first-homo-sapiens being born at around the same time to different parents throughout the tribes/groups etc? 3) If (2) is true, why/how the sudden convergence of many homo-sapiens being born at the same time?

Are you also saying that even though those first-homo-sapien(s) were in face human and their parents were not, they most likely didnt act that different from their parents? In that, they had the capacity for everything we take humans for granted today, but this capacity was never used? 5) Silly question but I have to know, if they were humans and their parents were not, how did they look relative to their parents? If their parents were not human, but the offspring was... wouldnt their parents be hairy apes and the offspring not so hairy humans? Not being facetious, serious question! :-)

Don't want to be pedantic but Homo Sapiens is singular, no need to take off the s when talking about one (also because that is not the way plurals work in Latin). On a separate note, you may want to have a look at the Wikipedia pages for Mithochondrial Eve and Y-chromosomal Adam

It's hard to know for sure. It doesn't help early humans interbred with other close cousins, like Denisovans. The species prior to Homo sapiens (thanks Nico) may have only existed for a very short time and may not have left any records. 2) Probably, as genetic mutations are passed linearly from parent to child. However, the mutations could occur twice, though it is unlikely. As Nico points out, we have, indeed, found a "Mitochondrial Eve". 3) They weren't born all at once. The population most likely gained numbers steadily over generations. Humans generally follow exponential growth.

They probably acted like their parents because that's all they knew how to do. The capacity for creative problem solving probably came in handy, which is why they lived long enough to reproduce. However, it was probably later humans which really got the ball rolling is what I meant. 5) Probably pretty close, again. You're assuming, however, the parents were more ape-like than human-like, which wasn't the case. You would probably mistake them for humans if they were alive today! While apes are our closest living cousins, there's still MILLIONS of years of divergence. Lots of time for change!

@MCM As a guy constantly looking for more sound evidence I was very excited at first when you brought up another ancestor with signs of tool-making: "bonobos". In context, you were mentioning just prior to that about the homo sapien being different from its parents, and I thought perhaps I was going to find that Bonobos was a new addition to our fossil record. It was a bummer to find that you referenced a modern life-form and called it our ancestor instead. That's a non-sequitor. Please refrain from making incorrect logical links like this because it's hurting support for evolution. :(

@Jim - I didn't call them our ancestors. I called them our 'closest evolutionary cousins' as the species we evolved from are now extinct (although they did use tools as well - but we've known that for some time).

Bonobos are no closer to us than other chimpanzees

It's a mistake to say "humans" were born from "non-humans" and then  compound the mistake to say lots of "humans" all appeared in one generation. This is biology ala Marvel Comics. Much better to go with the spectrum analogies.

@NickKeighley - Humans were born from non-humans, but I specifically addressed why saying that is an issue in the first half. We call ourselves human, but defining a single "species" is extremely difficult on on a small scale. Yes, the spectrum is a better analogy that has more upvotes. :) Also, I didn't say that lots of humans appeared in one generation. I said the advantageous traits were passed on through many generations. Thanks, though. :)

words are discrete terms used to solidify an unending spectrum of meaning. like colors, blue, red, green, where does one stop and the other begin. you should understand that all words you use have different limits in the range of things they describe in different languages. that is why i feel this is an amator question.

Another big problem with definition 2 and 3, they don;t work on fossils.

but I get lost on the 'border' cases.

Not surprisingly, since there are no borders, and this is probably the greatest misunderstanding: Evolution is gradual. It’s not generally possible to say where a complex feature (or a species) starts and another one ends. We could in theory say, for individual mutations on the genetic level, in which generation they first occurred, or when they became fixed in the population. But we cannot infer from these atomic changes where our ancestors started becoming humans. So the whole concept of “first human” is not biologically meaningful.
The best analogy remains a gradient between two colours. Going from the left, where does blue end and red start?

By the way, you spotted this very well by yourself:

[if there is no first human] then that necessarily means that the definition of a species is itself fuzzy

Exactly, that’s the case. For more details on definitions of species, refer to MCM’s answer. But it’s indeed crucial to note that the definition of species (or any other biological classification) is an ever-changing approximation which tries to fit a definitive yes/no answer onto a gradually changing scale.

Hmm, interesting... but then let me pose the question in a different way... what distance between any two colors on this scale, when mated together, cannot give an offspring that can then reproduce?...Do you see what I am asking? What is this minimal distance? Perhaps this is then the true measure of 'specieness'.

There's no hard-line rule for that either. There are a large number of genetic and developmental factors that influence reproductive viability. You can have two closely related "species" that actually can interbreed successfully one in a thousand times. You can also have two members of a single species population that can't successfully interbreed. How many species are represented by a lion, a tiger, and a fertile female liger? (http://en.wikipedia.org/wiki/Liger)

@Mohammad Excellent question. Unfortunately, Russel’s answer is spot-on. For instance, some species of dogs cannot inter-breed simply because of size differences, not due to other genetic incompatibility. Some species of crickets could inter-breed but aren’t sexually attracted to each other due to different mating calls. Some species, such as the Larus gulls (technically, all one species) can both inter-breed with a third, but not with each other.

@KonradRudolph Perhaps I have phrased it badly - let me rephrase, de-emphasizing reproducibility - What is the minimal delta of distance between colors we might chose, so as to maximize delta, with the constraint of producing a viable/compatible 'all around healthy' resulting offspring? What is the distance at which the resulting offspring might still result in qualities of some respectibility, VS where this respectibility completely breaks down in some coarse optimality space? (Let us just use humans in this gedankenesperiment).

@KonradRudolph For example, if I was to take a human, and mate it with the first proto-mammal - I do not think that I would get anything worthy out of it. (Red on blue). In contrast, what if I mated a modern human with one from 1000 years ago? 5000 years ago? 50,000 years ago? 250k? Where does it start to break down?

@Mohammad I had understood the question but the answer remains that 1. we do not know, and 2. it varies. Concerning your specific example, it’s not even known whether humans and chimpanzees (not ancestors, but closely related species) could produce viable offsprings. Many biologists are convinced that they could, even though their chromosome numbers are different. Of course, this is an impossible, because unethical, experiment. Mating modern humans with 250kya ancestors would almost certainly work.

There are points where speciation is final and abrupt though, aren't there?  I'm thinking of large chromosomal rearrangements and fusions.

@shigeta I’m uncertain – a single individual with a mutation does not a species make. That said, speciation can be fairly abrupt simply because (separated) subpopulations have to respond to sudden changes in environment.

I was just remembering that Mules (products of donkey and horse matings) are viable while both parents have different chromosome counts, so there has to be some forgiveness there.

There are cases of abrupt speciation, I think, when chromosomes are duplicated in a hybrid that would otherwise not be able to reproduce sexually. The duplication restores the ability to form viable gametes (the chromosomes can now form pairs during meiosis: http://en.wikipedia.org/wiki/Meiosis#Prophase_I). This is documented in plants, where vegetative reproduction allows survival of a sterile hybrid population until chromosome duplication occurs.

There are, of course, plenty of examples where different species in a genus can interbreed and produce fertile offspring.  The most familiar is probably the dog genus: dogs, wolves, coyotes, and other species all interbreed: https://en.wikipedia.org/wiki/Canid_hybrid

Ernst Mayr, distinguished elder statesman of twentieth-century
  evolution, has blamed the delusion of discontinuity — under its
  philosophical name of Essentialism — as the main reason why
  evolutionary understanding came so late in human history. Plato, whose
  philosophy can be seen as the inspiration for Essentialism, believed
  that actual things are imperfect versions of an ideal archetype of
  their kind. Hanging somewhere in ideal space is an essential, perfect
  rabbit, which bears the same relation to a real rabbit as a
  mathematician’s perfect circle bears to a circle drawn in the dust. To
  this day many people are deeply imbued with the idea that sheep are
  sheep and goats are goats, and no species can ever give rise to
  another because to do so they’d have to change their ‘essence’.
  There is no such thing as essence.

The barrier would not come suddenly. There would never be a generation
  in which it made sense to say of an individual that he is Homo sapiens
  but his parents are Homo erectus. You can think of it as a paradox if
  you like, but there is no reason to think that any child was ever a
  member of a different species from its parents, even though the daisy
  chain of parents and children stretches back from humans to fish and
  beyond. Actually it isn’t paradoxical to anybody but a
  dyed-in-the-wool essentialist. It is no more paradoxical than the
  statement that there is never a moment when a growing child ceases to
  be short and becomes tall. Or a kettle ceases to be cold and becomes
  hot. The legal mind may find it necessary to impose a barrier
  between childhood and majority — the stroke of midnight on the
  eighteenth birthday, or whenever it is. But anyone can see that it is
  a (necessary for some purposes) fiction. If only more people could see
  that the same applies to when, say, a developing embryo becomes
  ‘human’.

The Ancestor’s Tale Richard Dawkins,

This is quite fantastic! If only because images convey so easily what is so hard to convey in words! Thanks for this, it is clearer now. I will say however, that a legitimate aspect of confusion comes from the use of 'species' as a term. We cannot be told that there exist giraffes and men, and that we are of different species, only to then simultaneously be told that there is no border defining this difference of species we were originally informed about to begin with.

Hi @apoz - this answer is considered useful by the community but still needs to consist of more than direct quotes.

I'd just like to expand on Konrad and MCM's answers. If I understand you correctly, your main question is "what were the 1st human's parents". You cannot really get an answer to that because the question itself is wrong.
The idea that evolution moves in discrete bounds, that is that speciation occurs suddenly, from one generation to the next (also known as Lamarckian evolution) has been abandoned years ago. That is simply not how evolution works (our modern knowledge of epigenetics notwithstanding). The color analogy given by Konrad is indeed a good one.
So, there was never an individual 'proto human'. This is also the case for all other species. What you do get, usually, is that a change in a species' environment (e.g. temperature, atmospheric pH, the introduction of a new predator etc) causes a particular mutation, or set of mutations, to become advantageous.
One has to remember that a genome (an organism's genetic material, their DNA) is not stable. It is in fact extremely dynamic and constantly undergoing mutational changes. Most of these mutations are neutral, they do not affect the organism in any way. However, when an external change such as I mentioned before occurs, some of these mutations may become advantageous.
Imagine a random mutation that causes an individual of a species to be more resistant to cold. If this occurs at the beginning of an ice age, that individual is more likely to reproduce, passing the mutation to its offspring. Over time, since the mutation-carriers are likelier to survive and reproduce, this mutation will spread across the population and become "fixed".
At some point these changes accumulate past a certain indefinable point and we call a speciation event. This does not occur at the individual but at the species level. A good analogy here is the sorites paradox. How many stones does it take to make a pile?
So, to sum up, humans did not evolve from monkeys. Humans and monkeys at some point shared a common ancestor. Then, over a long time period, successive changes caused the two species to diverge. That is not the same thing. The linear concept of evolution that has one species morphing into the next is one of the greatest misrepresentations of a scientific concept ever perpetrated by the media and inflicted upon the unsuspecting public.

"[H]umans did not evolve from monkeys" - I strongly dislike this claim. There is no doubt in my mind that the common ancestor of humans and currently extant monkeys would be classified as a monkey so I think a more correct statement would be "humans did not evolve from any current living species of monkey".

@jackaidley The point is that the hypothetical ancestor does not exist. Whether it would have been classified as a monkey or not is moot. Humans did not evolve from the animals we know today as monkeys. In any case, it is the construction that really bothers me. Species do not really evolve from one another. They evolve. The "from" implies a sense of linear progress that is simply wrong as explained by the various answers on this page.

The hypothetical ancestor most certainly does exist. It's just not extant. Your point about "from" is a good one, but yet I don't see any sensible way to discuss the evolutionary history of species without without using it or a similar construct.

@JackAidley I just tend to avoid using a preposition to get around it. And no, it does not exist. It has existed, but it does not exist today. Both exist (in the present tense) and extant mean that something is in existence at the moment.

There seems little point arguing over the exact meaning of the words exist and extant, so I'll merely note my disagreement and leave it at that. As to the rest, how then do you convey the evolutionary history which is concisely described as "humans evolve from monkeys"?

Agreed, this is not the place for linguistic disagreements. I convey the history by saying that monkeys and humans share a common ancestor. Otherwise, you are implying that humans have somehow evolved from the monkeys we see today.

That's okay in the case where both are extant (although I think it misses the point that the common ancestor would have been classified as a monkey), but what if you want to convey evolution from a group now extinct?

let us continue this discussion in chat

There are a lot of good answers here, but let me try to streamline things a bit: @Konrad's analogy to the color spectrum is spot on - where does red begin in that spectrum? This is essentially your question - where in the continuum of generations does the Homo sapiens species begin?
Just like our definition of color is imprecise (we usually can identify bright red and deep blue, but we cannot be sure about the shades in between), our definition of species is imprecise. We can identify a modern human and we could identify a far ancestor as such, but if we were presented with somebody from an intermediate generation, we could not confidently say if they are Homo sapiens or not.
We could, arbitrarily, point to a particular individual and say it was the first human, but it would not have any scientific meaning.

Lucas, thanks for your answer. Yes, I am trying to figure out, where the biological scientific community draws a discrete like in the sand and says anything less than this is not human, anything more is human. (I understand that it can be somewhat arbitrary, but surely there is an agreed upon threshold, if only so that not everyone makes their own arbitrary thresholds in the literature?). And what exactly do you call them? Humanish? 64%human? 12%human? How does it work in the literature?

@Mohammad, I don't think this issue comes up for humans that often - after all our nearest species relative that is not extinct, is easy to tell apart from human, except maybe in a dark room :). As far as classifying prehistoric "missing links", giving them a percentage of "humanness" does not make any sense, since that would imply that we could accurately describe what a 100% human was and relate it to them. I suppose, if we suddenly discovered a remote populated island, whose inhabitants cannot reproduce with the rest of humanity, we might need to deal with that issue :)

Lucas, in other words, the actual physical lack of evidence from swaths of the spectrum (by virtue of extinction) has nicely delineated in a clear way what is a human, and what is not, and hasn't forced the issue onto the biological community. Fair enough, I suppose I can reluctantly accept that. :-)

@Mohammad, yes, I think you make a good point. To use the color analogy again, if all we could see was blue, red and purple, we could point to purple and say "this is not red".

The border is fuzzy.

but then that necessarily means that the definition of a species is itself fuzzy, which I understand is not the case.

The concept of species, applied at one moment (or brief period) in time, is (fairly) well-defined. It breaks down if you try to apply it over a stretch of millenia.
The most commonly used definition of species is "a population whose members are capable of interbreeding with each other". (This was Ernst Mayr's definition.) So, take a group of humans and a group of chimpanzees. Humans can make babies with humans, and chimpanzees can make babies with chimpanzees. A human and a chimpanzee can't make a baby, even if they try. There's no fuzziness or ambiguity here. They're separate species.
Yet we share a common ancestor. So some of our ancestors could mate with some of their ancestors. And the transition from that state of affairs to this one was fuzzy.
(The sort of thing that might have happened is this. Once upon a time there was a population of chimp-ish creatures. Then, some of them ended up on the other side of a canyon and stayed there. Gradually, whether through genetic drift or local adaptation to slightly different conditions, they became sexually incompatible. This might have started off as simply behavioural - even if they met, they wouldn't find each other sexy - but eventually became more of a genomic, biochemical incompatibility, such that even if they did try to mate, either (earlier on) the baby would be sterile or (later on) nothing would come of it.)

Actually, there are indeed fuzzy cases where this species concept isn't perfect, even when applied contemporarily. A fun one is this picture. There's a horseshoe-shaped mountain range, with salamanders that live on it. Salamanders in the green bit can't mate with salamanders in the purple bit. But they can mate with salamanders in the yellow bit; and yellow can mate with red; and red can mate with magenta; and magenta can mate with purple. So are all these salamanders a "population capable of interbreeding", or not? And how many species are they?
(There's a fun chapter about these salamanders in Richard Dawkins' The Ancestor's Tale, making the point about fuzziness.)

While the definition of species certainly is fuzzy, the process of species generation is easily defined: migration of a population part leads to two geographically isolated gene pools which do not communicate genetic information. Both pools will, through genetic drift (mutations/inserts/deletions), develop away from each other to the point that, if they were to meet again, they could no longer produce offspring with each other. Voilà, a new species.

The process of species generation, speciation,  is most certainly not easily defined. It is still the subject of many a PhD thesis. The definition you offer is only relevant to sexual species. Most species on the planet do not have sexual reproduction. Also, many of those that do can interbreed with other species. Quite a few examples of this have already been mentioned in previous answers.

Just one point: if species can interbreed with species, contrary to definitions of the speciation process, then it is plausible to hypothesize they weren't species to begin with.


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What is "theae folium"?
I wanted to buy black tea at a pharmacy and the pharmacist told me that russian tea is actually black tea so I bought it instead.It's made out of theae folium leaves and for some reason I can't find anything about that plant on the internet and I know that black tea is made out of camelia sinensis leaves, not theae folium.Can anyone tell me what is this plant and is it really russian tea (i found somewhere that russian tea is made from a different plant) and what is this "Russian" tea good for?

Judging by this image in wikipedia, I would say Theae folium is another name (probably a name in another language) for Camellia sinensis

It's Latin for "Tea leaf".

@CactusWoman, the answer is "tea leaf". Camellia sinensis is a flower and here  is just an example of tea. there are others theae folium, not related to this flower.

Camellia sinensis is the botanical name for the plant whose leaves are used for the beverage commonly known as tea in English (green tea, black tea, etc.).  The plant of course has a flower in the normal course of its growth (as well as leaves, seeds, roots, etc.)

If the labelling is correct, this should be Camellia sinensis, the plant that produces black tea, green tea, etc. (although not many things that are commonly referred to or marketed as herbal teas).
Thea is the original genus name given by Linnaeus to the species we now call Camellia sinensis.
There's an old pharmacy tradition of specialized latin terminology for plant medicines. These will indicate the plant and also often the plant part. In this tradition, plants are often indicated with different terminology than modern scientific names. Here's a 19th century pharmacy textbook (Parrish and Weigand) explaining why:

And here's the same source discussing the naming of plants parts (as CactusWoman mentions, in this case folium = leaf):

You still see this terminology around in some places (some European texts and occasionally translations of Traditional Chinese Medicine preparations), but it definitely has an 'old-fashioned' feel from the perspective of a botanist.

Parrish and Weigand 1884 A Treatise on Pharmacy

http://farm2.static.flickr.com/1434/5114191089_e95dd1f1c9.jpg is where I first encountered this form of antiquated nomenclature (in traditional Chinese medicine)


text:
Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?
I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm high, just enough to fit the slide and a small amount of buffer. As far as I know such thing is not commercially available, so before I make it I want to make sure that it's going to work. The main issue is the cost of the electrode (has to be platinum wire). I don't want to spent that much money just to realize that it doesn't work.
My question is: is a 3cm electrode in a 60-70cm3 enough? Basically, are there any physical restrictions on the size and the position of the electrodes and the shape of the chamber?
Since I am a biologist and my knowledge in physics are quite limited, I would greatly appreciate any information about this.

These instructions for building an electrophoresis chamber don't comment on the minimum length of wire, but on the other hand they suggest using something called Monel Seizing Wire (Ni/Cu alloy - £8.95 for 10 m in the UK) or 20-gauge copper wire, so if you follow their advice you probably don't need to worry about cost.
I imagine that alloy electrodes won't last as long, but they would be cheap to replace - in fact you would be looking for opportunities to use up all of your excess wire!

I had already read these instructions and made a bigger electrophoresis chamber using copper wire. The main issue is that copper reacts with the running buffer and makes it blue. Because of this, I'll have to change the running buffer every time (not a big deal) and change the wire quite often. That's the reason why I wanted to use platinum, everything else wears out. One the other hand, I don't mind replacing it every now and then but I'm worried about the effects on the electrophoresis.


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What did we learn with Nazi human experimentation?
Was there actually any useful knowledge gained from the Nazi experiments on human test subjects? Wikipedia cites freezing and phosphine gas reactions, but I would like to know other potential results from the Nazis.
At a first glance, it looks like the problem is that, in addition to the obvious ethical issues, there was also a lack if scientific rigor. Is this true or can some results actually be of some use?

Can you add links to the relevant wikipedia articles, or other references you have looked at. This makes it easier for others to fill in.

Basically nothing.  The Nazis did unfathomably terrible things of little value, and they did it poorly.
This* is a fascinating, albeit long, read.  It goes through some of the ethics of the data, but first lists some more of the "experiments" the Nazis performed.  To add to your list: high-altitude, sea water potability, tuberculosis, poisoning, artificial insemination, and numerous woundings.  They also did terrible things to twins.  Aside from being torturous and cruel, the "experiments" rarely if ever used anesthetics and were usually designed to kill the prisoner.
The article goes on to list a few case studies where some of the Nazi works came up and could have been considered, but were repeatedly shot down.  It then details a number of reasons why the "experiments" were worthless.  In particular,

"[I]t is doubtful that physiological responses of the tortured and maimed victims represented the responses of the people for whom the experiments were meant to benefit."
Nazi "researchers" were racists who were looking to validate their own beliefs.  No good science comes from that.
The results weren't ever actually published.
The "data" are inconsistent.

The article moves into ethical arguments and hypotheticals, but ends up saying theoretically some of it could be considered, or that "Absolute censorship of the Nazi data does not seem proper, especially when the secrets of saving lives may lie solely in its contents."  It's a complicated scenario where that would arise.

Editing a few years later to add this discussion from the NY Review of Books.  It's a little removed in tone, and is over-generous as regards the intent of the Nazi torturers, but makes the interesting point that one good thing to come out of the experience was the first codified guidelines for human experimentation:

As part of the judgment, the court issued the celebrated Nuremberg Code in 1947—the first, shortest, and in many ways most uncompromising of the major ethical codes and regulations for the conduct of medical research on humans. Although the code had no legal authority in any country, it had great influence on ideas about human experimentation, and subsequent international codes and legislation.

In particular, the concept of "informed consent" is directly traceable to the Nuremberg Code:

The first provision of the Nuremberg Code is unqualified: “The voluntary consent of the human subject is absolutely essential.” No exceptions are permitted... Furthermore, the code is clear that consent must be given by subjects who are fully informed.

*I should note that the article is from a Jewish law website, so some may discount that as not a perfectly neutral source.  Which is silly.

This is an interesting question and one that really has two parts: the factual and the ethical. I remember discussing this topic in my 'ethics training' classes in graduate school (where I admit that I may have acted as an ass simply to demonstrate that our ethics training was unfailable).
The factual: "Are there any valuable findings published by the Nazis?" Actually, yes. There is a classic anatomical atlas by Eduard Pernkopf, 'Pernkopf Anatomy,' that was quite probably put together using the bodies of political prisoners as subjects. However, it may be that this is the only text that has real value, but it's enough to get us to the second question.
The ethical: "Should we persist in using information assembled under unethical conditions? Doesn't this provide an incentive to these practices - or at least not condemn them sufficiently?" Here my assly behavior was meant to send a message of, 'all morals/ethics are relative. And why should we not benefit from all sources possible? I would deny funding for unethical methods, but I would still read the paper. (obviously this part of my answer is just opinion and really shouldn't be printed here, but I think the question demands that it be considered)


text:
Amount of Heterozygosity
How many loci in the human genome are heterozygous? How about other species?
EDIT:
I was wondering, considering for example the whole world population, how many of the human genes actually have two or more different alleles, or, vice versa, which genes everybody shares because there are no different versions of them. Since this seems not to be clear, I don't consider a mutation in a single individual an allele, maybe take 1% occurrence amongst all individuals as a start? I'm no biologist though...
By loci I mean whatever you think makes sense. Again, I don't mean single bases, preferably something like the classic idea of a gene. But I'm happy for whatever you can tell me.

Please elaborate on you question. Do you consider heterozygosity as the presence of two contrasting alleles in a diploid individual or the presence of two different alleles for a trait in the species genome?

in diploid organism, theoretically every locus can be heterozygous.

Please don't add words just to make your post long enough to get past the quality filter - if the site isn't accepting your question it's usually an indicator that you're not including enough information.

I was wondering, considering for example the whole world population, how many of the human genes actually have two or more different alleles, or, vice versa, which genes everybody shares because there are no different versions of them. Since this seems not to be clear, I don't consider a mutation in a single individium an allele, maybe take 1% occurence amongst all individuals as a start? I'm no biologist though...

If you want an actual number, well, it depends (of course).  First off, what is your definition of loci?  That term is broad, and can be construed to mean everything from large, megabase-length genes to every individual base.
That being said, it turns out there are some serious runs of homozygosity (ROH, meaning long regions of the genome that are homozygous) in human populations.  This of course will vary widely from population to population, and amongst outbred individuals.  This paper has some AMAZING figures that are worth checking out but are a little more involved.  Here is a table from this paper which is likewise quite excellent; also, check out figure 3.

EDIT
Your new/edited question is actually very difficult to answer.  For an extreme example, look at the Human leukocyte antigen; some have hundreds or thousands of alleles, but if you were homozygous for each it would be bad (disease susceptibility) but you'd be fine otherwise.
Again, it depends on what you consider an allele or locus.  Most studies look at single base changes (SNPs) because they are 1. easy and 2. useful.  It turns out that there are a lot of these single changes.  The Human HapMap project is hard at work on this and recently published a data set with 3.1 million of these SNPs, among 270 individuals from different populations, roughly one every kilobase.  In a similar vein, the 1000 genomes project recently published an enormous catalog of variation from almost 1,110 individuals in 14 populations.  Both projects focused on major variants.
The best answer I can give you from these studies is that, within a given population, any two DNA strands are around 80% identical, of which around 0.5% is by direct relation (table 5.  Those numbers vary hugely between populations, with Yoruba Nigerians being the most diverse, followed by Utah Whites and then Han Chinese and Tokyo Japanese.  This is just an average across the entire genome, as purported functional differences are comparably rare, with over 85% of protein-altering changes being very rare (<0.5% frequency).
In summary, almost every single site we know of has more than one version somewhere.  Most traits are very complex and are affected by many genes, so even similar appearances can come from very different genetics.  Individuals tend to be highly heterozygous, even if populations on a whole have limited heterozygosity.  A single pair of siblings mating can produce massive defects, showing just how necessary our heterozygosity is.  We each have dozens of large, lethal mutations (deletions, mostly) that don't usually matter thanks to heterozygosity.

Thanks for your answer. I'm no biologist though, and I have no idea what these papers are talking about, or what a run of homozygosity is, or how to find an answer to my question from your data. Would you mind reading my edited question, and elaborate a little bit? I'm wondering how many of the human genes are so important that having a different version than everybody else is fatal; roughly speaking, how much of what we are is actually our parents and how much is merely human

@Bananach I tried to match that a little better, it's a complex question.  My summary at the end tries to be a short answer for you.

Thanks again. My interest comes from statements like "The genome of humans and chimpanzees is to 98% the same" and what they actually mean.

@Bananach: Perhaps you should have a look at this question: Do apes and humans share 99% of DNA or 99% of genes? What is the difference?. If that isn't adequate, you might ask another question getting at the issue.

actually this just raises more questions. like, what do you mean by sharing a locus? what do you do if one bases is deleted in humans? (then all the following bases differ in direct comparison with the chimp bases). do you allow the same genes to be on different loci in the different species? how do you compare the different frequencies of alleles on one locus? (maybe humans have 99% allele A and 1% allele B and chimps the other way round. does it still count as the same?) summing it all up, a percentage just doesn't seem to make sense to me at all

and by 'you' I don't mean you, but the general biologist who compares DNA :)

@Bananach You're absolutely right, percentage really doesn't make sense.  It's convenient and popular in the press, but alignments are more complex than a simple fraction.  To your point, I saw a fantastic presentation once trying to show that what separated humans from chimps wasn't mutations but deletions.

Ok, thanks. I think this is what made me dislike biology in school. The more you learn about a thing the less you understand it :)

The number of possible genotypes from only a few loci is great, and can be calculated using the formula
k(k+1)/2
where k is the number of alleles at a particular locus.
The parameter k also represents the expected number of homozygous genotypes, and k[(k-1)/2] represents the expected number of heterozygous genotypes. The observed heterozygosity can be compared to the expected heterozygosity, and the deviations between these values can indicate important population dynamics.


text:
How to calculate extent of Sequence similarity
I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity.
I have a Problem Statement: we have a sensor (its like a magnetic compass and has a dial with twelve equal zones- 30 degrees each) that every second outputs where its pointing. The typical random output of the sensor may look like (for example):

30 30 30 30 30 30 120 120 120 120 120 120 60 60 60 60 60 60 330 330 330 330 30 30 30 30 210 210 210 210 210 60 60 60 60 60 60 60 60 60 60 60 60 60 ……… etc.

We wanted to see if we can calculate a measure of similarity of two 4-minute sequence samples taken at different times during the day. (It would be great if we could state something like - the sequences are similar and there is a 1 in million (say) chance that we may be wrong.)

very interesting ... the standard methods all work on linear values, and not angles. Is the pattern "30 60 90" similar to "120 150 180"? (I.e. do you only care about relative movement, or also about the actual direction?)

It seems OP asked the question and never returned...

The first thing that comes on my mind is to use cross-correlation (CCF).
Essentially you compare one trace with variously shifted version of the other to see if there is a correlation between them.
For example (I am using R but you should be able to adapt this to your software of choice, I have added comments), say A and B are very similar, but shifted of a certain amount in the x axis (10 units in the example) and C is extremely different
# Set the random seed to get a reproducible example
set.seed(12345)
# Number of points per trace
n <- 1000
# All of the possible sensor values
values <- seq(0, 330, 30)
# Sample with replacement to get 100 random values
A <- sample(values, n, replace=TRUE)
# Let B = A shifted by 10 positions and then change one value every 5
B <- c(A[-1:-10], A[1:10])
B[seq(0, n, 5)] <- sample(values, n/5, replace=TRUE)
# C is a completely different trace
C <- sample(values, n, replace=TRUE)
# Plot the traces (I'm offsetting B and C just for visual clarity)
plot(A, t="l", col="red", lwd=2, ylim=c(0, 1200))
points(B + 360, t="l", col="green", lwd=2)
points(C + 720, t="l", col="blue", lwd=2)

# Now calculate the CCF
c.AB <- ccf(A,B, 100)
c.BC <- ccf(B,C, 100)
c.AC <- ccf(A,C, 100)

# Superimpose the CCF plots
plot(c.AB$lag, c.AB$acf, t="o", col="green", ylim=c(-0.5,1), ylab="CCF", xlab="Lag")
points(c.BC$lag, c.BC$acf, t="o", col="red")
points(c.AC$lag, c.AC$acf, t="o", col="blue")
abline(v=10, col="grey", lty=3)
legend("topleft", c("A-B", "B-C", "A-C"), col=c("green", "red", "blue"), lty=1, lwd=2, pch=20)

The CCF graphs look like this:

This graphs means that there is a strong positive correlation (max correlation = 1, here you have 0.8) between A and B and that they are shifted of 10 units. You can see this because the peak is at lag=10, corresponding to the gray dashed line, so the maximum correlation is when you shift trace B by 10 units.
B and C and A and C are instead uncorrelated.

I tend to agree that bioinformatics has no special general help for matching sequences of numbers.  Most of the specialized algorithms in bioinformatics are string oriented.
If distance metrics, Fourier or wavelet decomposition don't work, you might want to look for motifs in your sequence, then you might try a motif dictionary similar to an alignment algorithm.  They are like NGram algorithms, but then they extend out.

Build dictionary of all sequences of numbers from your reference sequence: say of 5 or 7 length.
Identify identical or better yet linear combinations of those dictionary entries and then expand the comparison by one index in either direction to get the maximal length of comparable identity/similarity.
List all your 'hits' by a score - a length and distance based metric.

is this the sort of thing you were looking for?

Well. You perhaps need not use the bioinformatic algorithms of string matching. These algorithms were primarily developed because of the extensive search space.
In your problem you just need to compare two recording experiments and you should use mathematical metrics for it. You have a 60x4 i.e 240 dimensional random variable. Moreover this variable is not discrete, it is continuous. For similarity measurements you have to use statistical tests or otherwise define a cutoff either on each element of the vector or the total magnitude defined by any norm.

You can try dynamic time warping, or string kernel as a measure of similarity. However, similarity is highly context-dependent, and you may have to invent your own notion of similarity. First you need to ask yourself what do you consider similar. This is a hard problem, and borrowing arbitrary solutions from different fields may not be the best idea.


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Whole genome amino acid composition tool?
I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.
I've looked in MeSH terms database but I'm a bit lost when I search for "Genetic Code" and Software.
I'm looking for an output like this one:

Please clarify a little. What is "genetic code usage"? Do you mean the code that a species uses or are you thinking of codon biases? What are you trying to do with MESH? How do you get aa composition at the genome level? You mean the usage ratio of aas in the whole proteome? Please [edit] your post and include the actual scientific question you are trying to answer.

Just to amplify the comment from  @terdon - do you mean the amino acid composition of the proteome (i.e. taking into account protein abundance) or do you mean that simply calculated from the translation of all open reading frames?

In response to the comments, I edited my question and added my ideal output.

check this.
You can get the tables for multiple genomes and then apply your statistics. You can use a script to automate the download

@Masi could you clarify how you would like the answer to be improved? Perhaps edit the question to define a specific statistical calculation you would like to see?

More practical examples and more comparison to other existing tools. I have seen some in different laboratories and would like to have different views why to use some tools. This is a huge topic and I cannot see that my answer can answer this question.

I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript.
You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be installed by default with your Perl distribution. Finally, the script expects to be run from a Unix/Linux operating system.
Example run
 ensembl_get_codon_count.pl human > human.csv

Example output
Gene Name   Gene ID      Transcript ID  Ala_GCC Ala_GCC_% Ala_GCA Ala_GCA_% Ala_GCG Ala_GCG_% Ala_GCT Ala_GCT_%
CRLF2   ENSG00000205755 ENST00000400841    6       40        6      40         0       0         3       20

In the example above, the transcript ENST00000400841 of the human CRLF2 gene, contains a total of 15 Alanine residues, 6 of which are coded for by the GCC codon (40%), 6 by the GCA codon (40%) and 3 by the GCT codon (20%). The GCG codon is not used (0%).
This is a cut version of the output, the actual output lines are much longer since they include all codons and there will be one line per protein coding transcript.
This script should at least get you started since it will provide you with the raw data needed to perform your statistical analyses. If you use it in published work, I would appreciate it if you could let me know (my email is included in the script) and perhaps mention me in the acknowledgements :).


text:
What would classify those findings of the University of Sheffield experiment as aliens?
It's in the news that some experiment was able to capture some alien specimens during a meteor shower:
http://www.ibtimes.com/aliens-are-here-scientists-say-they-have-proof-alien-life-there-should-be-plenty-skepticism-1408322
Despite all the skepticism that has already been said about this finding, what would be a proof that such specimem came from outer space? Is there any established protocol to assure that some form of life didn't come from Earth?

I can migrate it, but this could be a good skeptical question given the claims being made.

I wouldn't say that there is an established protocol - claims of alien life are not commonly testable or even legitimate - but if something were discovered and deemed "alive," a fairly good sign it was alien would be if its genetic makeup were based on something other than DNA or RNA.  That would be a dead giveaway the organism had side-stepped every known organism on Earth and while that doesn't prove alien-ness, it would certainly hint strongly of a non-Terran genesis.  There are arguments for and against carbon/CHNOPS-based life but that is nowhere near as definitive.
Also, there's another really good technique.  I don't like to resort to ad hominem attacks, but ideally the discovery should be by someone who has not already made verifiable false claims on the same topic.

Isotopic ratios could theoretically be useful, in particular carbon or oxygen (a la the Allende meteorite), but there are so many ways to get different numbers that an alien origin hypothesis would rank pretty low.  It could be informative but it certainly isn't a magical "push button, get number" scenario.  Wonky ratios have already been observed many times for definitely Earth-bound life.