Most of the comments so far are missing the point. The paper points out that the energy available from food, for doing work, creating fat, or any other process,

Most of the comments so far are missing the point. The paper points out that the energy available from food, for doing work, creating fat, or any other process, is not, and can not be, equal to the energy content of the food: it is reduced by thermogenesis. Because the reaction pathways are different for different types of food, a calorie of protein does not provide the same usable amount of energy as a calorie of lipid, for example. A greater portion of the protein calorie goes to waste heat. However, from their Figure 2, you can see that the effect of even large changes in dietary composition have a small effect on the energy available from food. You can drastically reduce your carbohydrate consumption, while maintaining your 2000 calorie intake, and that amounts to only about a 100 calorie reduction in available energy. The conclusion: to a reasonable degree of accuracy it really is CICO. To lose weight, eat fewer calories.