Duality Is One
The fundamental mistake is pretending that there is a nature and nurture duality. There is no physical and emotional; there simply is.
The interplay between neurons, the beginnings of Chinese Room language learning, the loving gaze of a mother - all these interact in a dialectic that leaves the other affected.
Pretending that the two are separate is a fallacy - and one that creates a large amount of confusion and misunderstood interpretation of data. This is not to say that the techniques that work on either are wrong, just that they're inseperable.
Is this a bad thing? I don't think so; as with so many other things, the problems arise when the interplay is ignored. Pretending that things are "just" one or the other, though, is going to cause problems whether its done on a personal level or a societal level.