Yeah, I was trying not to pull you ahead. But dealing with the big picture is more my style.

Taubes certainly does say things that seem to suggest that, but what it would even mean for that to be true?

I think he says it pretty directly actually. Good Calories, Bad Calories:

When Rony discussed positive energy balance, he compared the situation with what happens in growing children. “The caloric balance is known to be positive in growing children,” he observed. But children do not grow because they eat voraciously; rather, they eat voraciously because they are growing. They require the excess calories to satisfy the requirements of growth; the result is positive energy balance. The growth is induced by hormones and, in particular, by growth hormone. This is the same path of cause and effect that would be taken by anyone who is driven to put on fat by a metabolic or hormonal disorder. The disorder will cause the excess growth—horizontal, in effect, rather than vertical. For every calorie stored as fat or lean tissue, the body will require that an extra calorie either be consumed or conserved. As a result, anyone driven to put on fat by such a metabolic or hormonal defect would be driven to excessive eating, physical inactivity, or some combination. Hunger and indolence would be side effects of such a hormonal defect, merely facilitating the drive to fatten. They would not be the fundamental cause. “Positive caloric balance may be regarded as the cause of fatness,” Rony explained, “when fatness is artificially produced in a normal person or animal by forced excessive feeding or forced rest, or both. But obesity ordinarily develops spontaneously; some intrinsic abnormality seems to induce the body to establish positive caloric balance leading to fat accumulation. Positive caloric balance would be, then, a result rather than a cause of the condition.”

Why We Get Fat includes more like the above, but the copy I have with me doesn't allow for easy copy and pasting. But that's the story basically. Yes, people who are fat are going to necessarily have had a positive caloric-intake balance from when they were not fat. But that doesn't mean that the causal node to intervene on is a) how much a person eats or b)how much they exercise. Taubes's claim is that the fat composition of your body is determined by your hormones, insulin in particular which is secreted based on your blood-sugar levels. Your body then overeats -- or avoids burning calories-- to compensate.

Illustrative of this effect are a wide variety of lab animal experiments that induce obesity by manipulating the animal's endocrine system while controlling food intake.

Why don't we start there. What do you find incoherent about that?