There are several reasons why calories- in and calories- burned equations are too simple for the complexity of animal physiology. For one thing, the calories in protein are handled differently from those in fat or in carbohydrates. Another reason is that our metabolism adapts to our nutritional intake as best it is able to.
Other than hibernating animals, few animals are adapted to handle the sort of abundance that humans have remarkably produced with brains capable of entirely changing the planet's surface and modifying nutritional sources for its own purposes. Humans are nutritional outliers, and it is not "natural." In a sense, humans are not natural animals because of the extent to which they remake nature for their convenience.
One example: What Does It Mean to Be Fat-Adapted?
It means you have trained your body to adapt to a plentiful flow of fresh carbs and sugars (sugar is carbs and vice-versa) so it takes the burden off using fat as a fuel. Intake trains the body that way. Thus what we term the "False Hunger" of overweight people. Human physiology will never adapt to modern abundance of food because fatness tends to kill or disable people after child-bearing years.
Among other reasons, Fat Adaptation is one of the reasons heavy people feel more hunger and end up consuming food more avidly and in higher volume than trim people. In fact, overweight people have zero dietary energy requirements and minimal nutritional requirements despite subjective hunger.
