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MichaelVassar comments on The Sword of Good - Less Wrong
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You won't be able to evaluate their thoughts exactly, but there's a LOT that you should be able to tell about what a person is thinking if you can perfectly record all of their physiological reactions and every pattern of neural activation with perfect resolution, even with today's knowledge. Kock and Crick even found grandmother neurons, more or less.
I'd still expect it to be hard to tell the difference someone between thinking about or wanting to kill someone/take over the world and someone actually intending to. But I can imagine at least being able to reliably detect lies with that kind of information, so I'll defer to your knowledge of the subject.