...and possibly move the goal posts, while we're at it. One thing at a time. Discussing the prevalence of these other mechanisms in the population makes little sense if we do not agree that they exist.
Do you agree that there is evidence for other mechanisms aside existing apart from solely "calories in vs. calories out"? Is the sacred cow unassailable?
Yes, I agree there is some evidence. Does that evidence explain the phenomena we are interested in?
As always, it comes down to not the facts we agree on, but the significance of those facts. As an example, the paper in Nature shows a difference of less than one Calorie per gram (of stool) difference between the types of intestinal flora. Does this support or disconfirm the hypothesis? Would it explain a 25% difference in fat over 10 weeks?
But in the larger picture, it doesn't matter if gut bacteria are offering up a significantly higher amount of calories (from the same food) or if the bacteria are influencing fat storage after absorption - all we want to know is if there's a difference in weight gain.
I thought I was helping by not dipping into the nuances, but simply granting them provisionally to see where the "best case" gets us. Does it get us where we want to go on the obesity trend question or not?
Secondly, do alternate hypothesis have to force us to abandon calories in/calories out, or do they merely modify the curve a bit?
The reason these questions are important is because the calories in/calories out model does not depend on how efficiently I handle calories - that's already considered when we say weight loss/gain is relative and subject to individual variation. It is not a model that requires one specific number of calories for every individual - it's titrated. However, if external, acute (as opposed to chronic, which is already captured) processes overwhelm the calories in/calories out model, then that's pretty significant.
I think it would be a straw man to suppose that environmental changes can't/don't affect calorie usage. I can think of a few easy cases - I lose a couple arms. I have less tissue to support and therefore can use more calories to make fat. Or I move to a warmer climate and don't have to burn as many calories keeping my body temperature up. Neither of those would abrogate the calories in/calories out model, because they end up being chronic considerations. But so too, they don't fundamentally challenge the "eat less, move more" idea.