I'm just stating what I have been told and believe it since it was people in the fitness community that are highly regarded and much more knowledgable than I.
Edit: Spelling.
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.
This is a fundamental law of thermodynamics.
As far as it goes, it is a useless statement anyway. The point of calories in/calories out rhetoric is not about the physics; it's about how animals regulate their weight. You could make the same case that body temperature is about heat in/heat out but that would be missing the point of how humans regulate body temperature. The criticism of calories in/calories out is in this vein. Do you think you control your body temperature by consciously monitoring heat transfer? Then what makes you thinks complex animals control their body weight and composition by consciously controlling their calorie usage and intake?
I didn't find him to be misrepresenting studies, and I didn't find research that disproved the claims I found implausible. I was underwhelemed by the rigor of a few of the studies he cited, but he was either citing them as historical curiosities or alongside other, more rigorous notes.
I regularly pull sources for the science I read and Taubes fared far better than usual.