As a former physique nut, I have been on countless diets, my favorite being the low/no carb diet. I can tell you that I was able to maintain and even gain some weight on an atkins type diet, I had to cut back before I saw significant weight loss. That said, man can I pound down the food...
It really is an energy in/energy out equation, what the diets do is modify either or both sides of the equation. For me, low carb diets curb my appetite, thus I eat less and lose weight.
If you have a certain amount of fat, then your body will respond differently physiologically to a certain food intake, or to a certain exercise, than someone else.
And one other thing about Atkins -- some people like to use Eskimos as an example of how people can eat high-fat, high-protein all the time without cardiovascular consequences (I think Taubes mentioned a study with a couple of people living on an Eskimo-type diet without getting scurvy, and which tracked their blood lipid profiles as well). One thing I have wondered is whether anyone as controlled for
a) ambient temperature (while at the MN State Fair I saw a presentation by some Arctic or Antarctic explorers who explained that they have to eat 5,000 calories A DAY to stay alive or they would freeze to death: the only way to get those calories in a form compact enough to bring along is to eat a pound or more of butter every day. They had a contest to see who could eat a stick of butter the fastest...)
b) race, somewhat correlated with the above, as Negros seem to be more associated with equatorial climes than polar; and also because their higher melanin content makes it harder for them to synthesize vitamin D with exposure to sunlight, whereas there is not enough direct sunlight for much of the year in higher latitudes. And vitamin D is being found to be important in a gazillion cellular processes, why not look to see if it is involved in metabolism as well?
Cheers!