Why calories in doesn't equal calories out

Michael Eads in an interview on 4 Hour Work Week tells us why calories in doesn't equal calories out:

The energy balance equation states that the change in weight equals calories in minus calories out.

Δ Wt = kcal in - kcal out

Many people think that the items on the right side of that equation are independent variables. In other words, if kcal in decreases weight will be lost because kcal out stays the same. But it doesn’t work that way because those terms aren’t independent variables - they are dependent variables. If kcal in goes down, often kcal out goes down as well to compensate. If people increase kcal out by exercising, they end up increasing kcal in because they eat more. It’s called working up an appetite. And since exercise doesn’t burn a whole lot more calories than simply sitting on one’s butt, it doesn’t take a lot of food to compensate. This effect is called adaptive thermogenesis. (Here is a full text article that goes into depth regarding the mechanisms involved.)