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Lol, the study lasted for a month. They extrapolated energy requirements based on weight loss, so of course when the low carb groups lost their 5lbs of excess water weight, it showed up as having a net positive effect on energy balance. The study also wasn't protein-controlled. Flawed, useless, and pushing Dr. Ludwig's agenda.
From my understanding on the study, they used indirect calorimetry to establish REE, so the methods are legitimate. First they had all the subjects lose weight on a normal cal restriction diet until they lost 12.5% of BW. Then they put them on isocaloric diets of either the low-carb/low-fat/low-GI diets. Then they found that while on the low-carb diet (using a randomized crossover design, so the study lasted over three months) that patients had the highest REE/TEE on the low-carb diet. So the results seem solid...
But I still have a bad taste in my mouth because despite the fact that physical activity did not differ between any group, and while REE/TEE were different, there was no difference in weight loss while on the different isocaloric diets. Also, they used a DEXA scanner to assess body fat percentage in the run-in weight loss stage, but didn't use it for the isocaloric stage. Why? Why would they use the DEXA, which costs money and time, on the phase of the experiment that they weren't even testing, and then not use DEXA during the phase they were testing, especially when they found REE/TEE values to be different with no difference in actual weight lost? To me, it screams out that they omitted results on body fat percentage data because it wasn't favorable. They poured so much money into this study, I know they had the funding to pay for more DEXA scans (for 27 patients it would only cost them an additional ~$700 to run a DEXA after each trial diet, which is a drop in the hat compared to how much everything else costs).
I think this study actually just took a weakness in indirect calorimetry methods and used it to their advantage. REE measurements look at O2/CO2 and sometimes urea nitrogen waste. For the O2/CO2 REE measurements, the method is inherently biased towards estimating a higher REE when you have a lower RQ output. RQ is always lower on high-fat diets because of the increase in fat oxidation, which lowers the CO2 output. Here is the formula:
REE = [VO2 (3.941) + VCO2 (1.11)] 1440 min/day
What do you think will happen to REE when VCO2 drops and VO2 raises? You guessed it, REE will be significantly higher because the coefficient for VO2 is over triple that of VCO2.