Everyone processes foods differently and calories are based on burning food in a machine and measuring heat etc This machine (not the human body) is called a bomb calorimeter.

http://www.oxygenbombcalorimeter.com/pdfs/literature/Measuring-Calories-in-Food.pdf

Counting calories makes as little sense to me as determining muscle mass by weighing one's self and taking off 50% for bones, fat, water etc

"(′bäm kal·ə′rim·əd·ər)

(engineering) A calorimeter designed with a strong-walled container constructed of a corrosion-resistant alloy, called the bomb, immersed in about 2.5 liters of water in a metal container; the sample, usually an organic compound, is ignited by electricity, and the heat generated is measured."

"A thick-walled container for measuring the energy content of food. The food is placed in a bomb calorimeter filled with oxygen. An electric spark ignites the food which is completely burned in the oxygen-rich atmosphere. The heat liberated from the burning food changes the temperature of water surrounding the chamber. Measurements of the temperature changes are used to calculate the energy content of the food"
http://www.answers.com/topic/bomb-calorimeter-engineering

burnable energy burned with heat and oxygen is not quite exactly how the body processes food or derives energy from it - also everyone "burns" food differently (never mind none "burn" like this machine does.