Myth No. 5 was “‘Calories in, calories out’ is the most important factor for long-term weight gain.” In other words, the number of calories you intake minus the number of calories that are expended equals the number of calories that are stored in the body most likely as fat. Is this a myth?
The article mentions “research does not suggest that eating more will cause sustained weight gain that results in becoming overweight or obese. “Rather, it’s the types of foods we eat that may be the long-term drivers” of those conditions, said Dr. Dariush Mozaffarian, a professor of nutrition and medicine at the Friedman School of Nutrition Science and Policy at Tufts University.”
However if we take a step back, we should first clarify that our concern is with calories and not the total mass of food. So a smaller amount of high calorie junk food can be worse (has more calories) than a greater volume of low calorie food such as fruits and vegetables.
Second, according to first law of thermodynamics (Figure 1), calories in minus calories out does in fact equal stored calories. There must be energy conservation, and so if you consume more calories then you expend, then the extra calories will be stored as chemical energy most likely store in the form of fat, although if you are working out then the calories can be stored as protein.
Of course the devil is in the details, and the tricky part about caloric bookkeeping is how second order effects can influence the balance. For example, not all calories are fully absorbed by the body; some may pass through the digestive system and then be excreted. On the other hand, other foodstuffs may be absorbed quickly in the intestines and then efficiently converted into fat versus being processed more slowly or even diverted to some other energy store such as protein. The second order effects do not change the basic equation, but can affect how many calories get in and out, and the nature of the stored calories (fat versus protein).
It is certainly true that not all food is created equal with caloric density being one important property that varies dramatically among different food products. A small amount of junk food may be less filling and tastier, then a larger amount of fruits and vegetables that contain the same number of calories. As a result, one may be tempted to consume far more calories in the form of junk food.
But ultimately a calorie is a calorie, and detailed accounting of calories can be performed with the caveats mentioned above. Namely there are a number of considerations that help to explain why the mass of food may not correspond in a one-to-one fashion to the number of calories being converted into stored calories (i.e. fat). The simplest being that some foods possess higher caloric density.
Fundamentally, the first law of thermodynamics is a statement about energy conservation which includes calorie counting. This law is not a myth and most likely represents the most important factor in obesity.
Figure 1. "First Law of Thermodynamics says that energy cannot be created or destroyed, instead it changes from one form to another" (link).

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