I actually did see this study when it came out (or at least I read the news article on it, this is my first time seeing the origional). Honestly I thought it was poorly constructed in that it was testing diets that, even according to the theories of the people promoting low carb and low glycemic index diets, are equivalent.
For example, in a low carb 'Atkin's' type diet, the theory that Dr. Atkins proposed was (basically) that patients underwent a dramatically faster weight loss, with a much greater percentage of their weight loss from fat as opposed to muscle, when patients consisently ate a VERY low carb diet (less than 80g/day digestible carbohydrate at a maximum, most people stick to around 50g/day). The theory here is that the body retools it's metabolism in response to the low carbohydrate system, both running your nervous system on ketoacids (ketoacid metabolism lacks the 100% efficiency of glucose --> more calories lost), while a high ratio of glucagon & CCK compared to insulin, after a meal, promotes satiety and a greater ratio of lipolysis to gluconeogenesis (insulin being the major anti-ketogenic hormone in the body). However, even according to Atkin's own theory, if you're over that 'ceeling' of digestible carbs your body maintains its normal metabolism, normal insulin:glucagon ratios after meals, and normal weight loss for a given calorie intake. In other words for a given calorie intake a 600 carb diet = a 200 carb diet, but NOT a 60 carb diet. At least according to Atkin's theory.
Now, it's reasonable to dispute the Atkins theory, and to do research disputing it. However it is not reasonable to test the theory using, instead of a true low carb diet, a diet that is 'rich in whole grains, fruits, and vegetibles' but has a greater percentage of fat and protien. According to the study
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Diets consisting of 'similar foods' are meeting the current guidelines for cardiovascular health (low fat, at least several hundred carbs/day) are necessarily not what people mean when they're talking about a low carb diet. Basically this study is disproving claims about a diet no one has claimed is effective. Just my opinion, and no I don't have any stock in Atkins.