Why Calorie Counting Fails: The Metabolic Science Behind Weight Gain and Loss

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Introduction

Traditional nutrition guidelines emphasize calorie counting as the key to weight management. The concept of “calories in, calories out” (CICO) suggests that weight gain or loss is dictated solely by energy balance. However, real-world observations reveal that two individuals consuming drastically different caloric-content diets can experience opposite and unexpected, quite counterintuitive, metabolic effects: one may lose weight while consuming 3,000 kcal of animal-based food, while another gain weight on just 800 kcal of a mixed Standard American Diet (SAD) or a plant-based diet.

The stark contrast in metabolic outcomes highlights the fundamental flaws of the calorie model and underscores the importance of macronutrient composition, hormonal regulation, and metabolic flexibility. In this article, we’ll explore the physiological and biochemical mechanisms driving these differences.

I am writing this article because I see so many exercise gurus and strength training experts (even in my family!) push Calorie-Counting (known as CICO) as a way to encourage their clients to lose weight, but it rarely ever works and makes people very frustrated. In fact, reducing the Calories one eats may easily backfire and make them gain weight!

In this article I disentangle a very complicated subject into small bits of information you can understand.

Why 3,000 kcal of Carnivore Diet Leads to Weight Loss but 800 kcal SAD or plant-based Diet Lead to Weight Gain

1. Thermic Effect of Food (TEF)

The energy required for digestion, absorption, and metabolism varies significantly among macronutrients:

  • Protein: 20-30% of its calories are burned through digestion.
  • Carbohydrates: 5-10% are used up in processing.
  • Fat: 0-3% is expended in digestion.
  • Fiber: Near zero; it is a waste product that increases fecal energy loss.

Total kcal lost by the processing of the food on a carnivore diet, exclusively made up of animal products, is 20-33% of the total Calories. In a mixed meal that also contains carbs, the protein amount is reduced and is replaced by carbs, so the total loss is significantly reduced. A person consuming 3,000 kcal of an animal-based diet (high protein, high fat, zero plant carbs) will naturally burn off 600-900 kcal purely from TEF, drastically reducing net energy intake without caloric restriction (see also here).

2. Hormonal Response: Insulin vs. Glucagon Dominance

The carnivore diet’s macronutrient profile keeps insulin low (used only for protein synthesis) and glucagon high, leading to:

  • Increased fat oxidation (fat breakdown)
  • Ketogenesis (energy derived from ketones)
  • Muscle preservation via amino acid recycling

By contrast, the SAD and many plant-based diets are high in refined carbohydrates, which lead to chronic insulin elevation, inhibiting fat breakdown and promoting fat storage (lipogenesis) even in a caloric deficit (see here). 

3. Mitochondrial Efficiency & Uncoupling Proteins (UCPs)

Mitochondria generate energy efficiently or inefficiently based on what we eat:

  • Animal-based diets upregulate uncoupling proteins (UCPs), leading to increased heat production and energy wasting rather than storage (see also).
  • High-carb diets suppress UCP expression, making mitochondria more efficient at storing energy as fat and leads to reduced heat production.

This means that on a high-fat carnivore diet, more energy is dissipated as heat, while on a SAD or plant-based diet, energy is conserved and stored as fat.

4. Increased Fat Oxidation & Metabolic Flexibility

The carnivore diet promotes fat oxidation and ketone production, allowing a seamless transition between stored fat and dietary fat for energy. The SAD and plant-based eating, however, maintain glucose dependency, making it difficult to mobilize stored fat.

Why 800 kcal of SAD Can Lead to Weight Gain

1. Insulin Resistance & Lipogenesis

Even at low caloric intake, a high-carb diet triggers excessive insulin secretion, which, as noted before:

  • Inhibits lipolysis (fat breakdown)
  • Increases fat storage in adipose tissue
  • Promotes hunger and overeating via leptin resistance (see here and here)

This explains why a person eating 800 kcal of a carb-heavy diet can continue to gain weight despite severe caloric restriction, while being very uncomfortably hungry most of the time. This is why long-term calorie-reductions don’t work.

2. Adaptive Thermogenesis & Starvation Response

On a low-protein, high-carb, calorie-restricted diet, the body responds by:

  • Lowering metabolic rate to conserve energy (disproportionate reduction in metabolic rate).
  • Breaking down muscle for protein needs (needed because protein intake is insufficient for protein synthesis).
  • Slowing down fat oxidation, favoring storage over burning.

Thus, a person consuming 800 kcal on a SAD or plant-based diet may experience muscle loss and increased fat storage, leading to overall weight gain, the exact opposite of what is desired, whereas a person eating a high calorie diet high in protein and fat may lose weight by retaining high metabolic speed (see here)—quite counterintuitively.

Physics & Metabolism Chemistry

From a biochemical standpoint:

  • Protein-rich diets lead to greater energy loss through digestion and heat energy expenditures.
  • Carbohydrates trigger fat storage via insulin, making weight gain independent of caloric intake.
  • Ketogenic states favor exothermic reactions (heat loss), while glucose-dependent metabolism is optimized for energy conservation.

Summary of Mechanisms

Eating carnivore (CD) vs Standard American Diet (SAD) or plant-based:

Factor3,000 kcal CD (weight loss)800 kcal SAD (weight gain)
Thermic effect of food (TEF)High (protein: 25-30% TEF)Low (Carbs: 6-8% TEF)
Insulin & GlucagonLow insulin, high glucagon → Fat oxidationHigh insulin, low glucagon → Fat storage
Mitochondrial EfficiencyInefficient (UCP upregulation) → More heat lossEfficient → More fat storage
Metabolic FlexibilityHigh (burns both fat & ketones)Low (relies on glucose)
Adaptive ThermogenesisIncreased (burns more energy)Suppressed (slows metabolism)
Muscle vs. Fat LossPreserves muscle, burns fatLoses muscle, stores fat

Conclusion

The CICO model fails because it ignores the complex biochemical and hormonal responses that dictate energy storage and expenditure.

  • A high-protein, high-fat diet like carnivore increases energy expenditure, preserves lean mass, and prevents insulin-driven fat storage.
  • A low-calorie, high-carb, mixed SAD or plant-based diets lead to hormonal dysregulation, metabolic slowdown, and increased fat accumulation.

This explains why someone can eat 3,000 kcal of animal-based food and lose weight, while another person eats 800 kcal of SAD and gains weight.

Understanding these mechanisms is critical in shifting the conversation away from calorie counting toward metabolic optimization.

Additional Reading:

Thermic effect of feeding carbohydrate, fat, protein and mixed meal in lean and obese subjects

Effect of composition of mixed meals–low- versus high-carbohydrate content–on insulin, glucagon, and somatostatin release in healthy humans and in patients with NIDDM

Thermic effect of a meal and appetite in adults: an individual participant data meta-analysis of meal-test trials

Alterations in Glucagon Levels and the Glucagon-to-Insulin Ratio in Response to High Dietary Fat or Protein Intake in Healthy Lean Adult Twins

Comments are welcome, as always, and are moderated for appropriateness,

Angela

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About Angela A Stanton, Ph.D.

Angela A Stanton, PhD, is a Neuroeconomist focusing on chronic pain--migraine in particular--physiology, electrolyte homeostasis, nutrition, and genetics. She lives in Southern California. Her current research is focused on migraine cause, prevention, and treatment without the use of medicine. As a forever migraineur from childhood, her discovery was helped by experimenting on herself. She found the cause of migraine to be at the ionic level, associated with disruption of the electrolyte homeostasis, resulting from genetic variations of all voltage dependent channels, gates, and pumps (chanelopathy) that modulate electrolyte mineral density and voltage in the brain. In addition, insulin and glucose transporters, and several other variants, such as MTHFR variants of B vitamin methylation process and many others are different in the case of a migraineur from the general population. Migraineurs are glucose sensitive (carbohydrate intolerant) and should avoid eating carbs as much as possible. She is working on her hypothesis that migraine is a metabolic disease. As a result of the success of the first edition of her book and her helping over 5000 migraineurs successfully prevent their migraines world wide, all ages and both genders, and all types of migraines, she published the 2nd (extended) edition of her migraine book "Fighting The Migraine Epidemic: Complete Guide: How To Treat & Prevent Migraines Without Medications". The 2nd edition is the “holy grail” of migraine cause, development, and prevention, incorporating all there is to know. It includes a long section for medical and research professionals. The book is full of academic citations (over 800) to authenticate the statements she makes to make it easy to follow up by those interested and to spark further research interest. It is a "Complete Guide", published on September 29, 2017. Dr. Stanton received her BSc at UCLA in Mathematics, MBA at UCR, MS in Management Science and Engineering at Stanford University, PhD in Economics with dissertation in neuroscience (culminating in Neuroeconomics) at Claremont Graduate University, fMRI certification at Harvard University Medical School at the Martinos Center for Neuroimaging for experimenting with neurotransmitters on human volunteers, certification in LCHF/ketogenic diet from NN (Nutrition Network), certification in physiology (UPEN via Coursea), Nutrition (Harvard Shool of Public Health) and functional medicine studies. Dr. Stanton is an avid sports fan, currently power weight lifting and kickboxing. For relaxation (yeah.. about a half minute each day), she paints and photographs and loves to spend time with her family of husband of 45 years, 2 sons and their wives, and 2 granddaughters. Follow her on Twitter at: @MigraineBook, LinkedIn at https://www.linkedin.com/in/angelaastantonphd/ and facebook at https://www.facebook.com/DrAngelaAStanton/
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