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army1987 comments on Solved Problems Repository - Less Wrong
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So long as your diet isn't nearly that lopsided, IME (YMMV) the calories-in calories-out is a more decent first-order approximation than many people realize. See also The Hacker's Diet. Second-order effects exist, but they're second-order effects.
That's basically the point.
Places way too much focus on losing weight. See parent; losing weight by losing muscle mass isn't desirable.
Your claim here hinges on the presumption that CI and CO are the only first-order effects, which is almost certainly false. Age, body fat proportion, maximal oxygen uptake, etc., are plausible candidates that I've seen in mathematical weight models.
In my experience, these tend to be taken into effect when calculating the "calories out" part of the equation. By what mechanism were you thinking that these mattered, that's not "calories out"?