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From an evolutionary standpoint, legumes, milk, and grains are "artificial" food, at least for humans. Agriculture is a recent thing. Would you also endorse the Paleolithic diet movement?
(I do actually endorse the paleolithic diet as probably optimal at the moment and I agree with your central point - I just want to point out that even unprocessed modern diets are already rather unnatural.)
Although agriculture is only about 10,000 years old, humans have been gathering and eating wild grains for 30,000.
Which is an order of magnitude less than the 200,000 years that we've been anatomically modern - although who is to say that they didn't gather wild grains back then, too.
Of course, even 10,000 years is more than enough time for evolution to change us.