I am not sure I am convinced by this argument, for the following reasons:
If you think of calorie content / thermodynamics as an upper bound on how much energy can be extracted from the food, you have to make an argument for what happens to the unused energy. Even if you are in a biochemical state where not all the energy is used, there is still energy floating around in your body in the form of carbohydrates, fat and protein. I can think of three possible mechanisms for what happens to this extra energy, and I am not convinced by any of them:
(1) Calories are excreted unused in their original form. However, I don’t think this happens to a meaningful extent
(2) If there is excess fat, nutrients are broken down to molecular constituents in a less efficient mechanism of cellular metabolism, ie, producing less ATP. This is a little more plausible than 1, but I think it would be evolutionary maladaptive to reduce the fuel efficiency of your engine unless it was absolutely necessary. Note that there are cases when the body does reduce the fuel efficiency (such as anaerobic metabolism), but I can’t see how this applies here
(3) (Added): If there is excess fat, the body begins to run processes that are not strictly necessary, thus using more fuel. However, I am not sure what these processes would be, or why they would be triggered by fat and not carbohydrates.
I find it plausible that increasing fat intake will help you lose weight due to regulatory pathways such as insulin, but I think this pathway operates almost exclusively through changes in appetite. I fail to see any arguments why we cannot use thermodynamics (calorie input/output) as a very good approximation of predicted weight change.
EDIT: This comment is being downvoted. I am happy to delete it if it doesn’t add to the discussion, but it would help me immensely if someone could explain why my reasoning is wrong...
EDIT2: I am not sure if I misunderstand the karma system, but I don’t think you are supposed to downvote someone for disagreeing with their conclusions. It is possible that I am wrong in my conclusions, but I don’t think this in itself is reason for downvoting.
If you disagree with my arguments, you can dissect them in the comments. Reasonable arguments with incorrect conclusions are still valuable in a discussion, and if you show why they are wrong, you will not only help me update my priors, but also help reveal a flaw in how non-trolls come to their beliefs. Hiding the comment prevents this. I don’t see any reason for downvoting, and I think the downvoters need to ask themselves if they are downvoting due to mood affiliation / cognitive bias.
The OP’s assertion is true. Stratifying on certain variables can introduce bias.
Consider that you have a cohort of initially healthy men, and you are trying to quantify the causal relationship between an exposure (eg eating hamburgers) and an outcome (eg death). You have also measured a third variable, which is angina pectoris (cardiovascular disease).
Assume that the true underlying causal structure, which you are unaware of, is that hamburgers cause cardiovascular disease, which subsequently causes death.
Now look at what happens if you stratify on cardiovascular disease: In the strata consisting of men who don’t have cardiovascular disease, you will find no cases of death. This will lead you to conclude that in men who don’t have cardiovascular disease, eating hamburgers does not cause death. This is false, as eating hamburgers will cause them to develop cardiovascular disease and then die.
What you have done in this situation, is stratify on a mediator, thereby “blocking” the pathway running through it. There are also many other situations in which adjusting for a variable introduces bias, but it gets more complicated from here.
For further information on this I suggest reading an upcoming book called “Causal Inference”, by James Robins and Miguel Hernan, who taught me this material. The first ten chapters are available for free online at http://www.hsph.harvard.edu/faculty/miguel-hernan/files/hernanrobins_v1.10.9.pdf .