Ishaan comments on Critiquing Gary Taubes, Part 2: Atkins Redux - Less Wrong
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Gastric bypass patients are an example of a population where there is reason to think that the stable weight loss is due mostly to fewer total calories, and they do seem to experience positive effects.
Liposuction, on the other hand, does not seem to share this positive health profile. (Of course, the "fat loss" in liposuction is very location specific)