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mattnewport comments on Dealing with the high quantity of scientific error in medicine - Less Wrong
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You're missing the other side of the story. Humans evolved to obtain their nutritional needs from those foods that were available in the EEA and this effect is probably more significant than the selection pressure in the other direction (on fruits to be nutritionally beneficial to animals that eat them). Humans are adapted to a diet that includes things that were available to them during the long pre-agricultural evolutionary period.
OK. So reading between the lines somewhat and pushing the argument further, would it similarly/analogously/generally be the case that eating nearly any part of an evolutionarily 'old', highly evolved autotroph would usually be healthy, because they have learned how to make things that are useful for living things to have? (That is, ignoring the part of the argument possibly implying that we might have evolved a dependency upon apples in particular, because that seemed unlikely to me. Though I could be convinced because know it is the case to some degree for oranges and scurvy, for example.)
I would guess this is not true in general since many things do not want to be eaten and so evolve various defense mechanisms. In turn the organisms that eat them may develop counter-measures that enable them to safely digest their meal despite the defense mechanisms but this will depend on the complex evolutionary history of both organisms. Ruminants are adapted to a quite different diet than humans for example.