I've been doing a lot of nutrition reading yesterday (on pub med & peer reviewed articles - not Bubba's Get Muscled Now Blogs) and this is what I've found.

Protein apparently takes more calories to just digest than carbs or fat. So the thermogenic affect of eating protein is greater than for any other food source.

One article took two groups of women, kept their calorie expenditure the same but fed one group a high protein, low carb low fat diet & the other group a high carb, low protein, low fat diet. The high protein group lost more weight and retained more muscle than the low protein group all other things being equal..

None of these studies were sponsored by Atkins or other high protein gurus.

A problem with protein is that it can cause your body to become more acid. In an attempt to correct that balance, your body will release substances that are base, i.e., calcium from your bones. Vegetables & fruit, however, are base. So, if you combine those with your meats (think salad with cooked chicken breasts or cottage cheese with fruit) the two will balance out. Disclaimer - I did not see as many believable articles on this theory, but have heard for years that high protein diets make your bones brittle. In any case, the two food combinations are certainly healthy, add good carbs to your diet and if you keep the fat content down, will probably aid in weight loss.