Taubes is a quack, pure and simple. Most of the studies he cites that I'm familiar with use self reported food intake. Any study that uses self reported food intake should be entirely disregarded for physiological purposes (perhaps useful for studying psychology).

You can get razor sharp lean on a diet with lots of carbs in it and you can get nice and fat on a ketogenic diet.

No controlled calorie study supports the idea that carbs, fats or proteins have any particular metabolic advantage over the minor differences in their thermic effects of feeding (TEF) (essentially energy required to digest).