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Khoth comments on Two-boxing, smoking and chewing gum in Medical Newcomb problems - Less Wrong
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There is a difference - with the gene case, there is a causal pathway via brain chemistry or whatnot from the gene to the decision. In the original Newcomb problem, omega's prediction does not cause the decision.
Even in the original Newcomb's problem there is presumably some causal pathway from your brain to your decision. Otherwise Omega wouldn't have a way to predict what you are going to do. And there is no difference here between "your brain" and the "gene" in the two versions.
In neither case does Omega cause your decision, your brain causes it in both cases.