Ben_Jones comments on Reductionism - Less Wrong
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"However, reductionism is incapable of explaining the real world."
Is that the argument against Reductionism? That there are things it can't, as yet, explain? That's the same position the Intelligent Design people put forward. Your post is a big fat Semantic Stop Sign.
No, we don't understand protein folding yet. Precedent suggests that one day, we probably will, and it probably won't be down to some mystical emergent phenomenon. It'll be complicated, subtle, amazing, and fully explicable within the realms of reductionist science.