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Organisms excrete nitrogenous wastes in the form of urea, uric acid or ammonia. But isn’t that a bit of a waste? There is a shortage of biologically available nitrogen in the ecosystem, and plants convert nitrogen in ammonia and nitrates into amino acids. Why do organisms then deaminate these amino acids and then excrete them?

It seems to me that it would make much more sense to store the nitrogen for further use. I understand that ammonia is toxic, but surely it could be stored in some specialized structure.

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Some amino acids are essential, that is, they cannot be synthesized. For all the others, however, you need building blocks. Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination. Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate). The body has thus produced some amino acids and metabolized others for energy, but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.

To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em. I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full. You could ask the same question for any substance we might eventually want.

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Preamble: The problem with questions on evolution

Obviously, evolutionary biology is a reputable discipline, but unfortunately there are two types of questions on evolution that are posted on this site that I believe are often of dubious value and can lead to dangerously unscientific habits of mind.

The first is questions of the type “Why did such and such evolve this way?”. The problem with this type of question is that there is generally no way of proving a hypothesis because it makes no predictions — the end product of the evolution is known. There is sometimes an anatomical or biochemical paper-trail to support arguments, and I have presented one such in an answer to another question. However many answers to this type of question are pie-in-the-sky or circular reasoning.

The second type — typified by this one — asks “Why has such and such not evolved, it would obviously be advantageous?” The posters of such questions tend not to ask themselves why, because if they did they would realize that the answer is likely to be either:

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

or

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

The accepted answer to this question addresses the former explanations. Although this is an old question at the time of my answering it, I am doing so partly because a similar question came up recently, but also because I feel it would be generally useful exercise to consider the second explanation — to emphasize the need to question the assumptions of those who think that they know better than Nature.

A story my mother told me

The story is apocryphal, but it is true my mother related it to me. It concerns two youths who had applied for a general office job. (This was not quite Dickensian, but not so much later.) In order to chose between them they were each given a parcel to unwrap. The first youth carefully untied the string, took off the paper wrapping, neatly folded it, and placed the parcel, the string and the wrapping paper on the table. The second youth ripped off the wrapping and stuffed it into the waste paper basket and placed the parcel on the table. Who do you think got the job? In the era in which the question was posed, most people (including myself) assumed that the youth who had saved the string and paper for reuse would get the job, rather than the youth who wasted them. However (in the story) it was the latter who got the job — the manager was interested in speed and efficiency, not in economy in office stationary. And the moral is that if you make the wrong assumptions (that avoiding waste was paramount) you will come to the wrong conclusion. So it is with “wasting nitrogen”.

Is the assumption in the question valid for human metabolism?

Although the original question had plants in mind, like @Amory I shall consider it from the perspective of a single species, Homo sapiens. The argument in the question is, in effect:

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

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

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

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

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

This is the office boy question, but whereas we had no way of knowing what was most important in the office — speed or frugality — here we have information from which to draw a conclusion. In prolonged starvation protein is broken down to amino acids. Why? To utilize the carbon backbone of glucogenic amino acids to provide glucose for the brain when all other substrates for gluconeogenesis have been exhausted. This is key to survival. What happens to the nitrogen? It is partly used as ammonia to buffer the acid produced from some of the ketone bodies produced from ketogenic amino acids and the rest is excreted as urea. It is certainly not used to make protein or nucleic acid, which would entail using precious carbon constituents. Thus, it is clear that energy requirements, and particularly the generation of glucose are the limiting factors in survival during starvation — not nitrogen. The conclusion, therefore, is that there is no point in storing nitrogen in times of plenty: what needs to be stored is carbohydrate/fat.

One might raise the existence of Kwashiorkor, a disease of protein malnutrition. However this is a relatively rate disease, and it affects only children: it is not the normal situation in starvation. Clearly the demands for protein and nucleic acid synthesis are much greater in growth than adulthood.

Coda: Another counter-intuitive evolutionary development in nitrogen metabolism

The fallacy of “wouldn’t it be better to evolve…” is evident if one considers another aspect of nitrogen metabolism — our lack of the apparently useful facility to make all the amino acids, resulting in a dependency of man on certain so-called ‘essential’ amino acids. Here the situation is not one of failing to evolve a facility, but actually loosing it — simpler organisms from which we have evolved had it. The inescapable conclusion is that such a facility can never have been sufficiently advantageous to result in an evolutionary disadvantage for those who had lost it. Presumably we have evolved in a way that allows us (or a sufficient number of us) to survive in our particular ecological niche, not to be supermen.

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