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SilasBarta comments on Cryptanalysis as Epistemology? (paging cryptonerds) - Less Wrong
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I just remembered EY's post that alien message, and I don't think I'm making too dissimilar an argument: In EY's story, the aliens aren't as smart as humans, so we can infer the patterns in their messages, predict new ones, and inject new code.
As aliens were to those humans, so is nature to us.