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Tim_Tyler comments on Fundamental Doubts - Less Wrong
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Harvesting human body heat for energy might be stupid and inefficient way to use stored food - but I don't think it would violate the second law of thermodynamics. Maybe you are thinking that the flesh of the dead was the only source of food? That would indeed be even more silly - but the movie doesn't make that claim.
Fundamentally, the problem is that you need to get the energy somewhere. Currently, we get it indirectly from sunlight. In a world with no ability to obtain sunlight (as the justification of the Matrix goes), the second law means that barring geothermal (which doesn't require humans as a go-between), the total usable energy will decrease to zero.
It's like recycling. Can you ever expect to get better materials, or more materials than you started with without putting anything else in? (Including energy)