"Simple physics requires that to lose weight, we must burn more calories than we ingest"
THAT fallacy is how the author leads the reader in to HIS strawman argument, that somehow Taubes is unaware of, or disregards, the laws of thermodynamics.
1) Ingesting calories is not relevant, digesting is.
2) We don't "burn" any calories whatsoever. We use various components of food as raw materials for various biological processes. One conceptual example: when you ingest some sort of protein, your body might break it down in to amino acid chains and then repair a muscle fiber using those raw materials.
Talking about the human body as if it is a closed system that burns food is just silly. We're accidentally taking our metaphors as literal. Yes, if we literally burned all the calories we ingest, the thermodynamics argument would be correct. However, that just a metaphor, don't mistake the map for the territory.