I think thermodynamics is perfectly applicable to metabolism; we may not have a full enough understanding of the complexities of metabolism to see it in full effect, but it certainly governs the process. It's when we simplify metabolism with comparison to internal-combustion engines and concentrate only on the "thermo" and forget about the "dynamics" that we get into trouble, assuming that metabolic processes are the same regardless of the fuel source and ignoring or oversimplifying the other, often variable, conditions governing the performance of the system.

In this case, Barbara Rolls of Pennsylvania State University (is she a scientist, researcher, student, janitor, or what?) tries to cast doubt upon the efficacy of a low-carb plan by suggesting that it could work only if it violates the laws of thermodynamics or produces some "miraculous metabolic effects", ignoring the widely accepted premise (as pointed out by LisaN above) that metabolizing fat is less efficient than metabolizing other fuel sources. If a scientist observes a process that appears to violates the laws of thermodynamics, she should know enough to redo her observations, reconsider her understanding of the system, or revisit her conclusions. From this, I conclude either that she does not have a background in science, or that she don't REALLY think the laws of physics have been violated, but rather, she has a dogmatic aversion to the premise.