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People uploading their consciousnesses into a computer is also one of those cases of "it might as well be magic." Our current understanding of the human brain is pretty limited. Even coming up with a way to get an accurate picture of the wiring, let alone copying it, is something that still eludes neuroscientists. I have a feeling that even if they were to crack that particular nut, it would be incredibly difficult to translate all those neural pathways and connections into the binary language of computers. At the very least I would be incredibly surprised if the file size for a person's brain came out to anything less than hundreds (if not thousands) of zettabytes of data.
Want to defeat a bunch of cyborgs? The easiest way might be to simply cut off their supply of electricity. Without it they won't have any way to power their machine bits...and don't get me started on issues associated with waste heat dissipation. Another classic example of not thinking things through is your average cyborg with prosthetic arms picking up a car and throwing it. Maybe it looks cool, but in real life it would result in dislocated shoulders and/or a crushed spine. Deus Ex: Human Revolution does address this sort of thing to some degree by having the main character's superhuman abilities toned down along with bionic reinforcing across the shoulders and back. Then again, if you're playing Shadowrun, who cares? In a setting filled with elves, dwarfs, orcs, trolls, dragons and magic, why worry about realism at all? Well...it depends on what kind of story the author is trying to tell. Oftentimes the appeal of cyberpunk is its closeness to the world we currently live in. Bigotry, corruption, and exploitation are common thematic elements of the subgenre. They're also the kind of thing that resonates with many because it rings true. Before it was called cyberpunk the term "tech noir" got passed around a lot as a descriptor. While I won't got into the definition of noir, I will say it gained a lot of popularity by "telling it like it is." In the case of cyberpunk I think its strength lies in "telling it like it will be."
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