army1987 comments on Dark Arts of Rationality - Less Wrong
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The model I'm familiar with is that muscular soreness comes from microscopic trauma to the muscle fibers being exercised, and that the same trauma ultimately leads to increased strength (as muscles adapt to prevent it). That's clearly a simplified model, though: for example, later exercise can help ease soreness (though it hurts more to start with), while the opposite would be true if it was a pure function of trauma.
With my sketchy evopsych hat on, I might speculate that it helps prevent possible damage from overexertion, but that people in the EEA would rapidly habituate to their normal (albeit very high by our standards) levels of activity. Now that we're relatively very sedentary, such a signal, at least at its ancestral levels of sensitivity, might end up being counterproductive from a health perspective.
From the “reliably”, “repeatedly” and “systematically” in FeepingCreature's comment, I guessed they weren't talking about a previously sedentary person just starting to exercise. (I think I was going to clarify I was mainly talking about the middle and long term, but forgot to.) I do expect it to be normal for my muscles to hurt when I've just started exercising after weeks of inactivity.