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Why beautiful people are more intelligent (pdf):

(1) Men who are more intelligent are more likely to attain higher status than men who are less intelligent.
(2) Higher-status men are more likely to mate with more beautiful women than lower-status men.
(3) Intelligence is heritable.
(4) Beauty is heritable. If all four assumptions are empirically true, then the conclusion that beautiful people are more intelligent is logically true, making it a proven theorem.

Given the available empirical evidence, we feel confident to conclude that people have the perception that beautiful people are more intelligent because they indeed are more intelligent.