ChristianKl comments on Autism, or early isolation? - Less Wrong
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Alternative hypothesis 2
(At this point I should point out that I like your hypothesis, I just think it is not necessarily single-cause)
Satoshi Kanazawa's charmingly simple theory that general intelligence tends to suppress and displace most of your instincts. This means being smart pretty much automatically means being bad at a lot of things. The way I interpret it is that attention is a finite resource and you either pay attention to your analytical engine or your instincts or share it, but you cannot give full 100% attention to both. So if the analytical engine demands your attention the insticts shut up/down.
I have observed intelligent people being bad at the following instinctive things (not all of them, not in all of these):
There are smart people with bad social skills and there are dumb people with bad social skills.
Intelligence helps http://cogsci.stackexchange.com/a/9807/625
It also helps with all the other things you listed.