Fascinating that the core study the article focuses on is using strictly male subjects. I thought this had been a controversial approach[1] for quite some time now - yet they still claim the study's main goal is "doing it right."
It is controlling for variables. They are trying to determine the role of macronutrients on food partitioning and, ultimately, weight. One can argue they should have used all women instead, but I think the challenge there is women have a more varied hormonal environment due to menstruation[1], which, again, adds a variable. As I understand it, fat partitioning appears capable of change during menstruation.
Of course, then we run into a problem that the results may not apply to women. Nutrition science sucks.
[1]: http://well.blogs.nytimes.com/2010/06/30/phys-ed-what-exerci...