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The way I understand the story is that you have a scan of the relevant physical structure of the brain, plus the knowledge of how to simulate every component precisely enough. You may not know how different parts interact with each other, but that doesn't prevent correct functioning.

Just like you can have somebody assemble a complex device by just putting together pieces and following instructions. You could for instance assemble a working analog TV without understanding how it works. It's enough to have the required parts, and a wiring plan. Once you have a working device then you can poke at it and try and figure out what different parts of it do.



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