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In my textbook "Harper's illustrated biochemistry" chapter 27 it is written that

The existence of nutritional requirements suggests that dependence on an external source of a specific nutrient can be of greater survival value than ability to biosynthesize it. Why?

Because if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of negative survival value, because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.

I could not understand the part that I have emboldened.

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    $\begingroup$ Seems like a simple word substitution error in editing, and it should read ATP and nutrients are required to replicate the DNA even if that DNA is not expressed. That doesn't fix the argument, but maybe makes it easier to follow. $\endgroup$
    – hobbs
    Mar 25 at 19:17

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It’s a very dubious argument in my opinion.

Whenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.

I‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.

The more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.

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    $\begingroup$ I totally agree, it's a spurious argument easily disproved by things like loss of ability to synthesize vitamin C - only found in anthropoid apes, guinea pigs, some bats, some birds and teleost fish. If it were about energy it would be much more widespread among frugivorous species. $\endgroup$
    – bob1
    Mar 22 at 23:32
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    $\begingroup$ Good answer. Yes, the argument exaggerates the power of natural selection on things that don't matter any more. There is essentially no selection for or against junk DNA, for instance. The loss of unimportant abilities (like synthesizing vitamin C) is accounted for by genetic drift: "genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious." $\endgroup$
    – Wastrel
    Mar 23 at 14:58
  • $\begingroup$ The argument also strongly implies that evolution is a smart, thinking process. When it's far more likely that the ability was just lost because it didn't matter enough (because those nutrients were available in the diets) $\endgroup$
    – Hobbamok
    Mar 25 at 13:01
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The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.

If you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.

Even if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.

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I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to turn off the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.

However, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take thousands of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.

Also consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a defective gene, not due to a lost gene.

It's more of a case of "use it or lose it": a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.

Still, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.

What is additionally required is a bottleneck in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.

Then the founder effect in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.

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The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential.

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