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An article at gnolls.org claims that there is no such thing as a calorie to our body, and our stomachs aren't steam engines and therefore the concept of calories and our way of measuring them is unhelpful.

The concept of the “calorie”, as applied to nutrition, is an oversimplification so extreme as to be untrue in practice.

Another article at The Healthy Omnivore claims that CICO (calories in, calories out) is a myth, because of biochemical individuality. Quoting the article:

  • Genetics: What is your ancestry? Are you from a cold climate or warm climate? How does your body handle starchy carbohydrates? How does your body handle fatty proteins? How do you do with the sun? Etc. Etc. Etc. Secondly, physiologically, how have we handled our environment and time.
  • Sleep (Are you allowing your body to recover?)
  • Toxins (Tobacco, Alcohol, Sugar, Artificial Sweeteners)
  • Food Sensitivities (Gluten, Soy, Dairy, etc.)
  • Medications (Over The Counter, Prescription)
  • Stress (Chronic and Acute)
  • Quality of Health (Recent Illnesses, Immune System Health, Degenerative Disease, etc.)
  • Hormonal Health (Insulin, Cortisol, Glucagon, Leptin, etc.)
  • Age (Menopause, Andropause, Accelerated Aging)
  • Past Caloric Restriction History (Dieting, Bulimia, Anorexia, etc.)

Common sense would tell me that all the above factors do play a role, but that this role has limits.

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    That gnolls article is carefully calibrated to contain just enough gibberish to make my eyes start to glaze over and ignore the details, but not quite enough to dismiss it out of hand. The claim they attempt to refute is that dietary calories are largely fungible, and thus the total count is the most important metric. Arguing that the energy is going to different destinations is not a refutation of that claim. – Oddthinking Mar 24 '13 at 12:09
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    The headline question is different from the content here. Physics tells us if energy in is greater than energy out then something is being stored (i.e. fat and other tissues) so is this question really about terminology and semantics? – Rory Alsop Mar 24 '13 at 12:56
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    There are several conflicting claims here and as Alsop points out the headline does not match the body of the question. Is it "useful"? Yes, it is used by researchers, physicians, food labels, and people who eat food. Is it "true"? A meaningless question. Do other factors play a role? Of course. – denten Mar 25 '13 at 1:31
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    Is it useful for what? Marketing food? Weight loss? Overall health? – Flimzy Mar 25 '13 at 5:08
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    CICO is the only way dieting can possibly work: your body must expend more energy than it absorbs in order to become leaner. What all the factors above do is modify what is meant by in and out or where in and out take place. – Kaz Dragon Mar 26 '13 at 15:37
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In summary:

  • X calories from equal meals can have significantly different fattening effect on different individuals, even when we burn the same amount of calories by exercise, because our basal metabolic rates can differ by as much as 140%.
  • X calories from different meals consumed by the same individual can also have different fattening effect, because the thermic effect of various macronutrients can differ by as much as 30%.
  • The "calories in, calories out" principle still stands in the sense that you won't gain weight if you consume only as many calories as you burn them by BMR + exercise. If two individuals consume the same amount of calories, the one with low BMR will need to exercise more to burn them than the one with high BMR. So, a calorie is always a calorie, only that some people can burn them "easier" by having higher BMR.
  • The calories on the nutrition facts labels quite accurately tell us how much usable energy we get with food.

What do calories on the nutrition labels mean?

The calories on the nutrition facts labels tell you how much metabolizable energy the food contains:

Bomb calorimetry directly measures the heat of combustion of a food and thus gives values for gross energy (23), whereas stated food values are metabolizable energy estimations (ie, gross energy corrected for assumed obligatory energy losses before energy is available to the body). (American Dietetic Association)

Calories not available to the body are mainly in undigested nutrients, like dietary fiber, lost in stool.

The metabolizable energy can be used for:

  • Maintaining physiological functions
  • Physical activity
  • Heat production

When are calories fattening?

When your calorie intake exceeds the calories lost by your basal metabolism, physical activity and produced heat.

1) Differences in basal metabolic rate (BMR)

The BMR between individuals can vary greatly, for example, from 1,027 to 2,499 kcal/day (4,301-10,4555 kJ/d), which is a 140% difference, as measured in one study in 150 adults (AJCN, 2005). The main contributor to BMR was lean body mass (all the mass, except fat), so a short thin woman will have much lower BMR than a tall muscular man.

2) Calories burnt by physical activity

They are charts that estimate how many calories you burn by a certain type of exercise available. According to Harvard Medical School, a 70 kg (155 lbs) man in 30 minutes burns:

  • 167 kcal by walking 4 mph
  • 220 kcal by swimming
  • 300 kcal by running 5 mph
  • 450 kcal by bicycling 16-19 mph
  • etc.

3) Thermic effect of food (diet induced thermogenesis)

Different macronutrients have different thermic effects, which refers to the loss of consumed energy due to increased metabolism triggered by food (Nutrition and Metabolism, 2004):

  • protein: 15-30%
  • alcohol: 10-30%
  • carbohydrates: 5-10%
  • fat: 0-3%
  • a mixed diet: 10%

This means that a calorie from proteins and alcohol and large meals should be a bit less fattening than a calorie from carbohydrates and fats and small meals:

In conclusion, it is evident that overfeeding on carbohydrate and/or fat results in body composition alterations that are different than overfeeding on protein. It is commonly believed that 3,500 kcal is equivalent to 0.45 kg (1 pound) of fat and that changing energy balance in accordance with this will produce predictable changes in body weight. However, the overfeeding literature to date does not support this assertion. Dietary protein appears to have a protective effect against fat gain during times of energy surplus, especially when combined with resistance training (International Journal of Exercise Science, 2017).

In conclusion, the main determinants of diet-induced thermogenesis are the energy content and the protein-and alcohol fraction of the diet. Protein plays a key role in body weight regulation through satiety related to diet-induced thermogenesis. (Nutrition & Metabolism, 2004)

The following review focuses mainly on various percents of fat and carbohydrates: "Calories in, calories out” and macronutrient intake: the hope, hype, and science of calories (American Journal of Physiology, 2017):

Weight gain or loss is not primarily determined by varying proportions of CHO and fat in the diet, but instead by the number of calories ingested. Changes in EE, which metabolic pathways are used and other considerations are quite modest when compared with caloric intake. Until high-quality, metabolic ward primary data become available indicating otherwise, a calorie is still a calorie. (CHO = carbohydrates, EE = energy expenditure)

In general, the review suggests that by far the most important factor contributing to weight gain is the total calorie intake and that food composition is less important.

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