The calorie in/out thing is not entirely true. The human body definitely digests some calories more efficiently than others, and our scientific understanding of how that happens is very poor. For example it was only recently discovered that humans are very poor at converting sugars back into fats, and we rely heavily on dietary fats for fat storage. There's also all sorts of conflicting studies about whether humans can create new fat cells.
A major issue is that many of our dietary models were created using rats. Rat metabolism is nothing like human metabolism. Rats are true omnivores and ruminates. Humans are generally very poor at breaking down anything complex. We rely entirely on meat and cash crops, which we've engineered to have relatively simple and easily broken down nutrients.
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