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The thing that people don't understand, when they point out that this is just evolution on a faster timescale, is that the potential intolerances occur on a faster scale too. Evolution is a dance between both populations, the eater and the eaten.
Say a strain of tomatoes develops naturally in the wild with a gene mutation. There's a chance, perhaps even a good chance, that some portion of the human/animal population is not going to tolerate that new gene sequence as well--is not going to be able to digest it as easily, is going to be more likely to be allergic to it, happens to cause a greater incidence of heart disease, whatever. But since that strain took 20 years to occur, and would take another 100-200 to spread widely across the land, those incompatible individuals are weeded out just as slowly. This is why tomatoes are generally good for us--not because they're magically good for us, but because the people for whom they were not good died. Conversely, if too many animals/people are intolerant of the new gene sequence, then the tomato dies out instead of spreading because no one is eating it, and ejecting the seeds wide and far through their fecal matter.
Immediately change the gene sequence of a huge portion of the food supply, and you've skipped that dance. Maybe most of the population can't tolerate it, in a subtle but insidious way--say, I don't know, they're allergic to it. Did you know that peanuts were one of the first widely-spread GMO foods?
And hey, maybe that's better in the long run. Maybe we make our species stronger faster by sickening and brutally weeding people out faster. But you can't just speed up one half of evolution without speeding up the other.
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