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What timing! I just picked up the second GitS movie by chance browsing a local store. Since you deem the series so highly, I'll have to take a stab at renting it after all.
As for that missing CPU, I would think that it would be a virtual CPU. What ever interface is made to allow the human mind to access the "machine" language I'd wager would emulate both the BIOS and CPU.
Think of it like the artificial limbs that are emerging, some say that they can transmit hot or cold sensations. I remember reading an article (in popular mechanics perhaps?) that one even goes as far as to detect varying degrees of pressure, kinda like the sense of touch but with out actually being able to feel. You know you are touching something, but is it a rock or your mates tender arm.
I'll try to find that article again. Chances are I probably tossed it though.
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