Does high protein explain the low-carb "metabolic advantage"?

In 2012, David Ludwig's group published a paper that caused quite a stir in the diet-nutrition world (1). They reported that under strict metabolic ward conditions, weight-reduced people have a higher calorie expenditure when eating a very low carbohydrate diet (10% CHO) than when eating a high-carbohydrate diet (60% CHO)*.

In other words, the group eating the low-carb diet burned more calories just sitting around, and the effect was substantial-- about 250 Calories per day. This is basically the equivalent of an hour of moderate-intensity exercise per day, as Dr. Ludwig noted in interviews (2). The observation is consistent with the claims of certain low-carbohydrate diet advocates that this dietary pattern confers a "metabolic advantage", allowing people to lose weight without cutting calorie intake-- although the study didn't actually show differences in body fatness.

In Dr. Ludwig's study, calorie intake was the same for all groups. However, the study had an important catch that many people missed: the low-carbohydrate group ate 50 percent more protein than the other two groups (30% of calories vs. 20% of calories). We know that protein can influence calorie expenditure, but can it account for such a large difference between groups?

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