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We tend to count calories in foods via combustion of their components then adding the average caloric content of each gram of fat (9kcal/g), protein (4), alcohol (7), and non-fiber carbohydrate (4) in the average serving size of that food. Keep in mind that US food calories on labels are equivalent to a kilocalorie.

Last I checked, combustion was not one of the stages of digestion in the human digestive tract. I'm not a nutrition researcher, but it's always seemed intuitive to me that different compounds behave differently in a complex, gradual chemical system even if they behave similarly in a simple, rapid high-energy reaction. This is already acknowledged in the fact that dietary fiber is known to be mostly excreted and so isn't counted along with other carbohydrates.

This story is much about a small change by proportion changing several aspects of how digestion works in a mammalian digestive tract, including how efficiently the energy is taken up from other parts of the diet. Now in vitro is not in vivo and cattle aren't humans. But I think we're still far from settled on all calories being the same, and more evidence is building for the opposite conclusion. There are even multiple cases of fecal transplants leading to weight gain or weight loss, with the recipient's digestion suddenly resembling that of the donor causing body weight changes.

https://www.scientificamerican.com/article/how-do-food-manuf...

https://clinicaltrials.gov/ct2/show/NCT03789461



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