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I don't think it's that simple. Our bodies are not simple warehouses or bank vaults but complex chemical factories. What we eat dynamically influences how our bodies process and store what is eaten.

Well, yes, and since the body is a complex chemical factory, it has to act within the confines of biochemistry and its own limitations on what it can do in light of its storage capacities for the macronutrients when it's faced with unusually large amounts of any one macronutrient. I have described this above in the relative shifting of substrate oxidation based on intake.

However, on the matter of overall energy basis, it is as simple as more kcals taken in than expended = weight gain; fewer kcals taken in than expended = weight loss. Certain other factors, such as one's level and type of physical activity (combined with the types of substrates), will determine whether or how much of one's weight gain or weight loss is in fat mass or fat free mass. For instance, if you go on a moderately severe energy restriction and reduce your physical activity to that of a sedate lifestyle, you'll lose a lot more fat free mass (muscle mass) than someone who maintains a higher level of physical activity. Both will lose weight, but it's the one who keeps physically active that will lose a larger percentage of that weight as fat.

That said, though, if you use 2500kcal of energy throughout a day, this means that you've got to absorb at least 2500kcal of energy (regardless of the blend of macronutrients) to stay in energy balance. If your intake is less than expenditure, your body must take that from somewhere; it cannot create more energy than it takes in in the form of food. If, over a period of time, you are in energy deficit, that total amount of deficit has to be supplied not from the outside world via food but from body stores: glycogen (about 3 days worth max), lean body mass (mostly your skeletal muscles and organs--they aren't considered storage forms, though they can be catabolized to provide amino acids for protein synthesis and energy use in either the glycolytic or ketolytic pathways), and fat. As body stores are used, your weight decreases accordingly. If you maintain an energy deficit of 150 kcals per day over 100 days, you'll have used up 15,000 kcals of energy--it will have to have come from your body's internal resources. If you keep up your level of physical activity, a large portion of that deficit will have been made up through fat oxidation.

In the same way, if you absorb more energy than you expend, those absorbed macronutrients have to be disposed of in some way. They can be stored to various degrees of efficiency (glucose: limited; protein: none, unless you build more skeletal muscle, which takes a lot of work; fat: virtually no effort at all). However, once the capacity of glycogen stores is reached, and once the body has shifted substrate usage as far as it can toward glucose oxidation and away from fat oxidation, if you're still in excess energy balance, the excess will be stored as fat.* There is no place else for the excess energy to go. You can't eat anything that will dissolve it or make it disappear (though you can surgically remove it, but this still has metabolic consequences). You can't exhale it. You can't pee it away. Once the nutrients are absorbed, there is no other way short of storage or energy expenditure to take dispose of them.

And your body won't stop absorbing nutrients, because your survival under austere conditions depends on being able to take in as great a quantity of macronutrients as easily as possible. Aside from the luxury of living in a diversified economy with little necessity of physical activity for survival and an almost endless food supply, one is never entirely sure where his next meal is coming from. The body is adapted or designed (take your pick) to absorb and store huge quantities of energy (mostly as fat) against the days when there is little or nothing.

This is just the default state of being for surviving in a world of scarcity. When this physiology is put into the context of an inexhaustible supply of food, into a world of wealth, it's absolutely unremarkable that widespread obesity should occur. When it's put into this context along with historically low levels of physical activity (people around the turn of the 20th century expended much, much greater amounts of energy per day than at present), it's completely unremarkable that diseases related to physical inactivity should codistribute with diseases related to and perhaps exacerbated by obesity.

The bottom line is that if you expend more energy than you take in through nutrients, the difference will be taken from the substance of your body--your body's mass will be reduced. If you expend less energy than you take in through nutrients, the difference will be added to the substance of your body--your body's mass will be increased.

*A small portion of human body fat comes from de novo lipogenesis, the major portion from dietary fat--when fat cells reach capacity, more fat cells are made from fat stem cells. Once made, they can be filled and depleted of fat, but they won't die; they will, however, when depleted, send out hormonal messages saying, "Hey, we're getting empty; you're in danger of starvation. You better start eating." It's better to keep from increasing one's number of fat cells to begin with than to try to keep them empty.

That said, though, if you use 2500kcal of energy throughout a day, this means that you've got to absorb at least 2500kcal of energy (regardless of the blend of macronutrients) to stay in energy balance. If your intake is less than expenditure . . .

Determining total caloric intake is fairly straightforward. It's the expenditure side of the equation that gets complicated. That's where the Atkins diet makes fresh new sense to me. It makes sense that some foods would require an expenditure of more calories to digest and process than other foods. It makes sense that some foods would trip the saity chemical signal at a lower caloric level than other foods. Conversely, it makes sense that some foods would condition the body to crave more of the same food--a bad thing if the food has a high caloric value and you're trying to lose weight. It makes sense that some foods would wreak havoc with insulin levels or interfere with liver function, impacting the fat storage process. It makes sense that some foods would cause the body to retain water excess to bodily needs. It makes sense that some foods would cause a person to feel more inclined to sleep or rest and less inclined to physical actvity.

I have come to the conclusion through monitoring by own body's responses to foods (as measured by weight gain and loss, frequency and type of food cravings, perceived sense of energy and vigor, cholesterol and triglyceride levels etc) that a diet filled with starches and heavily processed foods filled with sugar causes me to gain weight and feel less healthy. Conversely, a diet built around meat, fat, and simple vegetables tends to bring me back to my ideal weight very quickly and make me feel more energetic and healthy. It also dramatically reduces my triglyceride and "bad" cholesterol levels and blood pressure (currently 100/65).

That's only my personal experience--not a scientific study.