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Blueberry 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.
The universe being a simulation does not entail that the administrators of such a simulation are capricious. And that we have demonstrated the existence of a large number of natural regularities suggests they are not.