The difference is murder: Seriously!
Surely a system that could read the signals in the brain with the exactitude necessary to recreate those signals in another system would have to be so invasive as to destroy the original tissue.
But is it murder? You find yourself in the machine. You have lots of sensors hooked up to you, you have plenty of interesting reading material on your harddrive, and you have the ability to explore places you could never have gone before. You're happy as a clam. (A digitized computerized clam, but a clam nonetheless.) Are you dead? I wouldn't think so: You have the same drives and emotions as before the transfer. So where's the murder?
And what's running on the machine? The same program that was running in wetware is now running in hardware. Just because you port a video game from PC to Mac doesn't mean that the program itself must be fundamentally different. So now that you've ported from wetware to hardware, aren't you still you? The same program on a different machine?
Sounds like a soul, to me. And like a program. And I'm not sure there's a difference.
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