Have you done the same for every study that points to calories in/calories out? In fact, there aren't many such studies actually. Somehow this was given the benefit of being the null hypothesis, which is an underserved benefit in my opinion and many others including Taubes. One of the other things he does in GCBC is go through the anthropological evidence as well. We know quite well that our ancestors ate a very high fat/low carv diet because they mainly ate the organ meat. I don't think that is actually in dispute. Its also part of the foundation of the whole paleo/primal movement.

At the end of the day, Taubes might be wrong about some or all of what he thinks. But the reason why he is generally well liked on HN, a community of very smart, very analytical people, is because Taubes is highly analytical and highly rigorous in his approach. This isn't some woo-woo magic stuff. I've never met a more methodically and rigorously researched book than GCBC. I can't review every study he cites because that would take 5 years at least.