The Calorie Myth by Jonathan Bailor once again proves that TA's "calories in/calories out" is such an over simplification that it shouldn't be taken seriously. Of course it is true that the only way one is going to lose weight is to be in a caloric deficit but TA neglects the intermediate step that not all calories going in have the the same effect on the body once they are "in". Eating 500 calories of pure sugar will have a much different effect on the body, including weight loss or weight gain, than consuming, say, 500 calories of whey protein.
Getting half your calories from drinking beer will have a much different effect on your body than if those calories came from, say, oat meal. Even if protein and fat caloric intake are the same.