Two comments. First, your point about counterfactuals is very valid. Hofstadter wrote an essay about how we tend to automatically only consider certain counterfactuals, when an infinite variety are theoretically possible. There are many ways that the world might be changed so that Joe one-boxes. A crack in the earth might open and swallow one box, allowing Joe to take only the other. Someone might have offered Joe a billion dollars to take one box. Joe might aim to take two but suffer a neurological spasm which caused him to grasp only one box and then leave. And so on. Counterfactuals are a weak and uncertain tool.
My second point is with regard to determinism. What if the word in general, and Joe in particular, is nondeterministic? What if QM is true but the MWI is not, or some other form of nondeterminism prevails? Ideally, you should not base your analysis on the assumption of determinism.
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Readers of Less Wrong may be interested in this New Scientist article by Noel Sharkey, titled Why AI is a dangerous dream, in which he attacks Kurzweil's and Moravec's "fairy tale" predictions and questions whether intelligence is computational ("[the mind] could be a physical system that cannot be recreated by a computer").
[edit] I thought this would go without saying, but I suspect the downvotes speak otherwise, so: I strongly disagree with the content of this article. I still consider it interesting because it is useful to be aware of differing and potentially popular perspectives on these subjects (and Sharkey is something of a "populist" scientist). I think the opinions it espouses are staggeringly ill-conceived, however.
"[the mind] could be a physical system that cannot be recreated by a computer"
Let me quote an argument in favor of this, despite the apparently near universal consensus here that it is wrong.
There is a school of thought that says, OK, let's suppose the mind is a computation, but it is an unsolved problem in philosophy how to determine whether a given physical system implements a given computation. In fact there is even an argument that a clock implements every computation, and it has yet to be conclusively refuted.
If the connection between physical systems and computation is intrinsically uncertain, then we can never say with certainty that two physical systems implement the same computation. In particular, we can never know that a given computer program implements the same computation as a given brain.
Therefore we cannot, in principle, recreate a mind on a computer; at least, not reliably. We can guess that it seems pretty close, but we can never know.
If LessWrongers have solved the problem of determining what counts as instantiating a computation, I'd like to hear more.