It's great to spend 5 years of life getting a PhD reading millions of papers and doing actual research and then have people on the internet tell you it's all wrong because they read some website.
The Athlete A/Athlete B example is actually a great question. If we assume that both athlete A and B had some training experience and had added some lean tissue to their frames, then if conducted perfectly Athlete B would detrain slightly and lose muscle tissue even if he is eating maintenance because he has dropped resistance training. In this case he will lose lean tissue and his maintenance calories will either no longer be 3k or he will have to drastically increase his exercise (essentially become a marathoner). If he continues to up his training to make up for the loss of metabolically active tissue then he will actually lose lean tissue but not add fat as time continues. Eventually athlete B will be lighter but with the same amount of fat as he started with because he has exercised exactly enough to make up for his relatively large energy intake compared to his body size.
This is certainly a flaw in the calories-in-calories-out model. It does not take into account the loss of lean tissue that will occur from detraining (for example you will lose muscle and bone in outer space even if you eat well above maintenance). The model is also flawed when macros are extreme. For example if someone eats under maintenance but consumes no protein at all, they simply won't rebuild lean tissue and will actually store excess energy (carbs and fats) as fat even though they are technically under their energy expenditure for the day. Additionally, if someone gorges on protein only and severely restricts fat and carbs they will not store as much fat as would be expected because of the metabolic overhead to convert protein to fat is expensive.
The calories-in-calories-out model certainly seems to be poorest at predicting results for extreme situations. Still, for normal situations, ie. You are not beginning or ceasing a new resistance training program, you are not protein deficient nor severely restricting fat and carbs, you are not on steroids or in puberty, you are not in outer-space, you have not developed diabetes, etc, THE MODEL WORKS PRETTY DAMN WELL. Especially on the overweight.
The benchmark study:
http://www.nejm.org/doi/full/10.1056/NEJMoa0804748This is a study of over 800 overweight patients on calorie restriction.
Result: Reduced-calorie diets result in clinically meaningful weight loss regardless of which macronutrients they emphasize. A study which attempts to show that calories-in != calories out.
http://www.ajcn.org/content/79/5/899S.full?ijkey=f3919ec7617632925bb12e0ffb8deeb08a678686CONCLUSION
We conclude that a calorie is a calorie. From a purely thermodynamic point of view, this is clear because the human body or, indeed, any living organism cannot create or destroy energy but can only convert energy from one form to another. In comparing energy balance between dietary treatments, however, it must be remembered that the units of dietary energy are metabolizable energy and not gross energy. This is perhaps unfortunate because metabolizable energy is much more difficult to determine than is gross energy, because the Atwater factors used in calculating metabolizable energy are not exact. As such, our food tables are not perfect, and small errors are associated with their use.
In addition, we concede that the substitution of one macronutrient for another has been shown in some studies to have a statistically significant effect on the expenditure half of the energy balance equation. This has been observed most often for high-protein diets. Evidence indicates, however, that the difference in energy expenditure is small and can potentially account for less than one-third of the differences in weight loss that have been reported between high-protein or low-carbohydrate diets and high-carbohydrate or low-fat diets. As such, a calorie is a calorie. Further research is needed to identify the mechanisms that result in greater weight loss with one diet than with another. Couple anecdotes:
Twinkie diet professor:
http://www.cnn.com/2010/HEALTH/11/08/twinkie.diet.professor/index.htmlCrazy fasting lady:
Fat beginning;
http://www.youtube.com/watch?v=bY9_Qviei7g&feature=list_related&playnext=1&list=SP52CFD735D7B5734E1 year later (still crazy, much healthier) :
http://www.youtube.com/watch?v=YFbvOAbhcT8&feature=relmfu Anyway, this debate REALLY has been put to rest. In normal cases, if you want to lose weight you simply have to eat less. Different macronutrient ratios will make some differences and you certainly don't want to be protein deficient, but the bottom line is EAT LESS ENERGY (metabolism-wise) and calories are a pretty good approximation of that energy.