Solvent comments on On accepting an argument if you have limited computational power. - Less Wrong
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One approach is to apply the scientific method: every model must have testable predictions. For the case of Pascal's mugging, you can ask the mugger to demonstrate their "magic powers from outside the Matrix" in a benign but convincing way ("Please show me a Turing machine that simulates an amoeba"). If they refuse or are unable to, you move on.
Well, that sometimes makes it more awkward to design the thought experiment. See the Least Convenient Possible World.