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I agree that isocaloric nutrition, as you call it, is at best a rough reflection of what is actually occuring within the human body.
Glad we could agree on something.
Isocaloric nutrition is just the best available means of influencing and controlling body composition.
You're certainly entitled to this opinion.
Isocaloric nutrition mah be proven to be akin to ptolemiac astronomy in that it is able to lead to fairly reliable predictions, but is not even a remotely accurate representation of reality and underlying mechanisms.
This was my main concern. The portrayal of an accuracy that doesn't exist. Even if you believe said underlying mechanisms of a system aren't important (which has been clearly demonstrated), it doesn't mean that a broad generalization is suddenly attributable to accuracy. That's just plain not good procedure.