"A calorie is a calorie" violates the second law of thermodynamics
Richard D. Feinman and Eugene J. Fine
Nutrition Journal 2004, 3: 9
A widely held belief in both the popular and technical literature--that "a calorie is a calorie"--is analyzed and found to be without foundation on purely thermodynamic grounds. More precisely, the content of the belief--that, for given purposes (e.g. losing weight), it does not matter where your calories come from as along as they amount to the same magnitude (i.e. technically, an isocaloric diet)--is shown to be authorized only by the first law of thermodynamics and not by the second law of thermodynamics.
The first law of thermodynamics asserts that neither matter nor energy may be created nor destroyed; they can only be converted from one form to another. The second law of thermodynamics qualifies the first law by asserting that the conversions of matter and energy from one form to another is not unlimited. Over time, as matter and energy is qualitatively degraded by frictional and diffusive insults, their capacity to participate in further conversions at any constant, finite rate of conversion is ultimately extinguished. Only infinitesimal rates of conversion (unattainable in the real universe) can assure the indefinite conversion of matter and energy from one form to another.
In effect, the second law tells us that there are qualitative differences in the matter and energy participating in conversions such that initial and final states and conversion rates and pathways differ. Because of such qualitative differences, it cannot be maintained, on purely thermodynamic grounds, that a calorie is a calorie. Indeed, lipids (fats), carbohydrates, and proteins have different thermic effects (i.e. the heat generated by food processing in the body) at 2-3% for lipids; 6-8% for carbohydrates; and 25-30% for proteins. This means that that, as a source of pure calories, fats are the most efficient and proteins the least efficient. (Hence, the preference of polar bears for seal blubber over seal meat as they store fat for winter.)
Accordingly, given alternative isocaloric diets but with differences in calorie deriving from lipids, carbohydrates, or proteins, if it is desired to lose weight, then those diets with the lowest fat content and the highest protein content are to be preferred on purely second law-thermodynamic grounds. If other factors, such as food satiation (which determines frequency of eating), homeostatic mechanisms (which maintain metabolic balance, over time), and total health concerns are taken into consideration, however, then the choice of diet becomes more complicated (i.e. context specific).