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Originally Posted by psyang
However, science has to define the system it operates in, and the scientific method, by definition, relies solely on empirical evidence. If there is anything beyond the physical, the scientific method will by definition exclude it.
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I'm not sure this is quite right. Science would not exclude something beyond the physical if there was evidence that something beyond the physical exists. I'm not sure if this is a contradiction in terms... I think I'd have to consult a cosmologist. But I'm pretty sure it isn't. Empirical evidence can obviously suggest the presence of other things that can't presently (or in some cases ever) be empirically measured by us, which is how black holes were posited. There are more extreme examples.
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I guess the question is what you consider free thought. If a neuron can generate free thought, and so Bob at 1:53 today chose chocolate ice cream instead of vanilla, could a parallel universe that mimics ours in every way allow Bob to choose vanilla instead? If so, why? What is the difference? If there is no difference, then the scientific method can't hold.
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I'm not sure this is true either. All evidence to date is that the answer to your question is now: in a parallel universe that mimics ours in every way, Bob will choose chocolate every time. However, this doesn't preclude the possibility of some as-yet undetermined factor that would change that conclusion. Maybe that's the same as what you're saying and I'm just misunderstanding.