RichardKennaway comments on Rationality Quotes September 2011 - Less Wrong
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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?
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.