There are also dozens of studies showing exactly the opposite (I've googled up just two):
http://www.nejm.org/doi/full/10.1056/NEJMoa022207,
http://www.nejm.org/doi/full/10.1056/NEJMoa022637. It's pretty safe to assume that currently science is not overly conclusive about this subject.
From the point of biochemistry that claim doesn't make much sense either, as calories measured in the food (which is done by measuring the heat when you burn it) are not the same calories that you end up having as ATPs in your blood stream. No digestion is 100% efficient and it's much more complex process than just the simple oxidation. Different foods and food combinations and different gut bacterias in each human create hundreds of variables in how efficient the conversion process is. We have variable food quality, variable food combinations interacting chemically, variable gut bacteria and digestion chemistry, variable metabolism for each person. Our body is a chemistry lab and making stuff repeatable and simple in the lab is usually very hard. Digestion itself also uses energy itself and how much depends on the type of the food. It also matters how often do you eat, eating all your calories all at once and than starving for the rest of the week is definitely not the same as having a balanced calorie intake. Presuming that it's all simple "just sum it all up from standardized tables" is overly simplistic look on a highly complicated chemical process that has many bio-feedbacks involved and is far from being a constant. Which of course doesn't mean that it's not a good enough simplification for the purpose of keeping the dieting simple enough for people who are not interested in the biochemistry, but that is just the same kind of approximation that all other technics do: "Follow these rules and you'll probably lose some weight".