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David_Allen comments on The conscious tape - Less Wrong
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The idea is that everything in the universe is a computation run by the universe. So yes, option 2 certainly.
But functionalism describes a philosophy where the mind is formed by levels of abstraction. The substrate that performs the computation for any particular level is not important. This is option 1.
So option 1 and 2 are not incompatible. They are context specific perspectives.