While you're certainly right that from a thermodynamic sense it is definitely a case of energy in vs energy out, you're presenting it in very simplistic terms a

While you're certainly right that from a thermodynamic sense it is definitely a case of energy in vs energy out, you're presenting it in very simplistic terms and I think you're missing the point of the article. There's all sorts of poorly understood processes happening in our body that affect the amount of energy stored as fat. That "1 lb / 3500 calories" figure you quoted isn't an absolute law, but more like a rule of thumb. What we don't fully understand is to what extent things like gut bacteria, environmental toxins, sleep cycle etc alter that figure. The body's a hugely complex system. The recent study explicitly says that people on the same diets today are fatter than they were 40 years ago. Assuming their finding is true, that means that either metabolisms are slower or the rate at which bodies gain fat from excess calories is higher than it used to be. We as a society have been filling the world with all sorts of never-seen-before chemicals which our bodies and the huge interdependent ecosystem we live in are unable to deal with. We've spent the last 60 years pumping our livestock full of drugs to make them bigger and live longer. It's not outwith the sphere of possibility that one or a combination of these contribute to changes in the way humans store fat.