You might be interested in Aaronson's proposed theory for why it might be physically impossible to copy a human brain. He outlined it in "The Ghost in the Quantum Turing Machine": http://arxiv.org/abs/1306.0159

In that essay he discusses a falsifiable theory of the brain that, if true, would mean brain states are un-copyable. So Yudkowsky's counter-argument may be a little too strong: it is indeed consistent with modern physics for brain simulation to be impossible.