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That paper is defining a calorie as the chemical make up of a particular macronutrient. Which is wrong. A calorie is a unit of measure of energy.

Plus, if something violated a law of thermodynamics, that law would have changed. And it hasn't.

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I probably should have added more comment, but the point is the "Calorie is a calorie" argument as applied to diet was pretty thoroughly debunked over decade ago. Calorie counting is a poor predictor of weight, while source of calories is a much stronger predictor. However, plenty of other people have commenting with more detailed explanations as to why, so I won't go on.

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