Asklemmy

"Calories" is actually two different things. The first thing is a unit of energy. In this sense, calories are very much interchangeable. Wood has calories, which is why we use it for fire. However, if you tried eating wood, you would mostly just be increasing the caloric value of your poop. This is not inherent to wood; if you were a termite and tried eating wood, you would actually get nutritionally relevant calories from it.

For nutritional purposes, we generally use some variant of the Atwater system. The core idea was to measure the caloric value of food, as well as the caloric value of the subjects feces and urine. This gives you a better estimate of how many nutritionally relevant calories there are.

Nowadays, we have standard values various core food components (e.g various fats, proteins, etc). By breaking down a food into its components, we can apply the standard conversion for each component and add up the results to get a value for the food as a whole.

This process is actually pretty bad. The digestibility of individual components does not perfectly predict the digestibility of a whole food. The measure of individual components is not perfect. The actual digestibility of some foods can vary significantly between people.

As a practical matter, "counting calories", really just means eating less in a way that roughly measures food by effective energy content. It turns out that an accurate accounting of calories just isn't super important or useful for this. There is even bigger variance in the "calories out" department (including the annoying tendency of bodies to become more energy efficient when less energy is available). Further, all of the errors in calorie counting tend to be consistent. If you reduce calories by reducing the quantity of food you eat, you are reducing actual metabolized calories, even in the exact measurement is wrong.

It is a little more complicated if you reduce calories by changing the composition of the food you eat, but broadly speaking lower reported calories are actually lower effective calories there as well. Further, if you are adjusting the composition of your food specifically enough for this to be a problem, then you are well past the point where you should be caring about other nutritional factors.