TheOtherDave comments on Were atoms real? - Less Wrong
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Very small children understand "real" to be "what's inside" -- what's hidden, essential. Sometimes literally inside: ask toddlers "If you took a dog, and gave it the bones and insides of a cat, would it still be a dog?" they say "no," but "If you took a dog and made it look like a cat on the outside, would it still be a dog?" they say "yes." (I'm getting this from Paul Bloom's "How Pleasure Works.") Young children are essentialist about gender as well -- they assume more differences between the sexes than actually exist, not fewer.
What psychological evidence I've seen suggests that we're in some way wired to see categories as real. "Natural kinds." To think that there's a real difference "out there" between dog and not-dog, not just a useful bookkeeping convention. I'm inclined to believe that Anna's reasoning about "atoms are real" and Eliezer's reasoning about categories actually make more sense than essentialism -- but I suspect that this kind of question-dissolving is not the standard, evolution-provided brain pathway.
If the subject interests you, I recommend reading Women, Fire, and Dangerous Things. It's somewhat slow going, but the author lays out a detailed story about the process of category formation in humans (that is, why we create the categories that we do) that does wonders for clarifying the issues involved.
I have no idea whether the specific story he tells is right or not, but sometimes it's useful to just have an example of what such a story might look like.
thanks!