I don't think anyone disputes the laws of thermodynamics, just how the body processes different macronutrients in the presence of certain levels of hormones. By changing those hormones, you change the balance of the total energy equation. For example, I know someone with crohns disease, and her body just doesn't metabolize nutrients the same way mine does. I burn a donut more efficiently than she does. In this case it isn't about hormones, but about inflammation, but it's generally the same concept just on a more apparent scale.