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SilasBarta comments on Parapsychology: the control group for science - Less Wrong
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Yes, but then we would have to give up on the scientific method anyway, because the laws of physics would be whatever the adminstrators of the Matrix felt like changing them to.
What Jack said -- you can still notice regularities in the Matrix even if it's sometimes capriciously tampered with. That is, these overlords do not automatically make our universe a high-entropy white noise bath.
I discussed some of the implications of a simulated universe and the implications of the 2nd law of thermodynamics on it here.