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gwern comments on Rationality Quotes September 2011 - Less Wrong
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I have many times heard fans say this. Not once have any produced any evidence. Can you do so?
The only evidence I have is that it's so obviously the way the story should be. That's good enough for me. It does not matter precisely what fallen demiurge corrupted the parable away from its original perfection.
ETA: Just to clarify, I mean that as far as I'm concerned, brains used as computing substrate is the real story, even if it never crossed the Wachowskis' minds. Just like some people say there was never a sequel (although personally I didn't have a problem with it).
And like any urban legend, that is why this explanation spreads so easily.
Is not the alternative plot as faulted as the original plot, insofar as if the brainy computing substrate is used for something other than to run the originial software (humans) there is are no need to actually simulate a matrix?
Not only that, but I'm pretty sure building an interface that'd let you run arbitrary software on a human brain would be at least as hard and resource-intensive as building an artificial brain. We reach the useful limits of this kind of speculation pretty quickly, though; the films aren't supposed to be hard sci-fi.
You just need to stipulate that the brain can't stay healthy enough to do that without running a person.
But I'm not much interested in retconning a parable into hard science.