I wonder why an apple should be healthy. Wouldn't any animal be satisfied with a fruit that just had calories? Enough, in any case, to come back for more and scatter the seeds? Why should an apple -- or anything 'natural' -- be so especially healthy for humans?
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.)
In a recent article, John Ioannidis describes a very high proportion of medical research as wrong.
Part of the problem is that surprising results get more interest, and surprising results are more likely to be wrong. (I'm not dead certain of this-- if the baseline beliefs are highly likely to be wrong, surprising beliefs become somewhat less likely to be wrong.) Replication is boring. Failure to replicate a bright shiny surprising belief is boring. A tremendous amount isn't checked, and that's before you start considering that a lot of medical research is funded by companies that want to sell something.
Ioannidis' corollaries:
The culture at LW shows a lot of reliance on small inferential psychological studies-- for example that doing a good deed leads to worse behavior later. Please watch out for that.
A smidgen of good news: Failure to Replicate, a website about failures to replicate psychological findings. I think this could be very valuable, and if you agree, please boost the signal by posting it elsewhere.
From Failure to Replicate's author-- A problem with metastudies:
The people I've read who gave advice based on Ioannidis article strongly recommended eating paleo. I don't think this is awful advice in the sense that a number of people seem to actually feel better following it, and I haven't heard of disasters resulting from eating paleo. However, I don't know that it's a general solution to the problems of living with a medical system which does necessary work some of the time, but also is wildly inaccurate and sometimes destructive.
The following advice is has a pure base of anecdote, but at least I've heard a lot of them from people with ongoing medical problems. (Double meaning intended.)
Before you use prescription drugs and/or medical procedures, make sure there's something wrong with you. Keep an eye out for side effects and the results of combined medicines. Check for evidence that whatever you're thinking about doing actually helps. Be careful with statins-- they can cause reversible memory problems and permanent muscle weakness. Choose a doctor who listens to you.
Forum about self-experimentation-- note: even Seth Roberts is apt to oversell his results as applying to everyone.
Link about the failure to replicate site found here.