Eugine_Nier comments on Vegetarianism - Less Wrong Discussion
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There was a lot of discussion of nutrition a while ago. The general conclusion is that the literature is too confused to assign any one hypothesis high probability, but was leaning toward Atkins-style low-carb high-protein diets.
The conclusion I remember was learning towards low glycemic load diets, which includes low-carb diets but also includes pretty much anything that cuts down on processed sugar and flour. Notably also includes the leading diet among medical practitioners, the "eat your fruits and vegetables and cut down on the sweets" diet.