That doesn't mean that "more calories in than calories out" is wrong... it means that "calories out" is FAR more complex than people give it credit for. We don't even know all the variables yet. Taubs' writings do bring to light some of our unknowns. We keep finding more variables for the equation, but that doesn't mean the equation is wrong... just incomplete.
Not to mention that if the "more calories in than calories out" people aren't measuring the calories in their excrement or (in the case of diabetics) the amount of glucose in their urine, then they aren't getting the complete picture anyway regardless of what gets stored where. They would also have to factor in how many calories are burned to process each type of food.
As you say, it appears to be more complex than just watching how much you take in.
