Rafe_Furst comments on Reductionism - Less Wrong
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It's not that reductionism is wrong, but rather that it's only part of the story. Additional understanding can be gleaned through a bottom-up, emergent explanation which is orthogonal to the top-down reductionist explanation of the same system.
It is important to take seriously the reality of higher level models (maps). Or alternatively to admit that they are just as unreal, but also just as important to understanding, as the lower level models. As Aaron Boyden points out, it is not a foregone conclusion that there is a most basic level.