Earlier quoted context omitted.
> This is not a meme but basic physics. The issue is: How are we defining calories IN? Consider the extreme example of having a parasitic worm living in your digestive system. Is IN == [food passing mouth] or is IN == [food not being ingested by worm(s)]? Now consider "normal" digestive flora. How are we defining IN here?
All of that doesn't matter. Calories in just serves as a reference point for you to see how much you are actually eating. Then you can make changes to calories in, and see results on the scale. Sure everyone is at different efficiencies, that doesn't matter though. You are basically putting in less gas in the tank; that's going to make a hybrid and a gas hog both go for less miles than what a full tank would do.
1. Having a hole in your gas tank (parasite(s) e.g. a tapeworm)
2. Having a modification to your fuel tank to convert ethanol into octane (non-parasitic digestive microorganisms a.k.a. "gut flora")