Science is amazing when it explains very cool ideas . It is also very interesting (if a bit frustrating) when the scientific inquiry process is ongoing and open to debate. Weight gain is one such area that is of great concern and large amount of study but some issues are still unclear. I have discussed this before. I think that calories in compared to calories consumed is a good first approximation. I believe it makes sense that the efficiency of our bodies at capturing the calories and turning them into weight gain could be affected by things other than the total calories in. It might be the type of calories or it might be other factors (bacteria or chemical present)…
A widely reported study  that came out in January in The American Journal of Clinical Nutrition (AJCN) would seem to dispute this finding: it confirms the belief in the energy balance model, and has been cited as proof by many researchers working in the field. I asked an author of the study, Dr. George Bray, professor of medicine at Louisiana State University, about the myriad of additives and industrial ingredients in our food that were not accounted for in this study. “It doesn’t make any difference,” he said in a telephone interview. “Calories count. If you can show me that it doesn’t work, I’d love to see it. Or anybody else who says it doesn’t — there ain’t no data the other way around.”
It seems to me that it certainly makes sense to reduce calories if you need to lose weight. And it sure seems the strongest evidence is for calories being the most important factor.
I also believe exercise is good, for overall health. It also seems more and more evidence is being found about how difficult it is to lose weight which reinforces the importance of preventing the weight gain in the first place.
Related: Healthy Diet, Healthy Living, Healthy Weight  – Study Shows Weight Loss From Calorie Reduction Not Low Fat or Low Carb  – Study Finds Obesity as Teen as Deadly as Smoking  – Eat food. Not too much. Mostly plants.  – Obesity Epidemic Kind of Explained