Why “Calories In, Calories Out” Misses the Point: Rethinking Energy Balance Through Biology

We’ve all heard it before: “Weight loss is simple — just eat fewer calories than you burn.” The idea sounds straightforward, almost mathematical. And in a way, it is. Energy balance — calories in versus calories out — is just basic arithmetic. But biology isn’t math. Your body isn’t a bomb calorimeter that counts every calorie precisely and then decides what to do with it. It’s a dynamic, adaptive, hormonally regulated system.

In this blog, I’ll dive into the physiology behind fat gain and loss, debunking the myth that calories alone dictate outcomes and highlighting why neuroendocrine signals—hormones like insulin, leptin, and ghrelin—are the real drivers of weight regulation.

What Exactly Is a Calorie?

Before we can question the usefulness of calorie counting, we need to understand what a calorie actually is — and where the concept came from.

A calorie is a unit of energy borrowed from physics, not biology. Technically, one calorie is the amount of heat required to raise the temperature of one gram of water by one degree Celsius. In nutrition, we actually use kilocalories (kcal) — enough heat to raise one kilogram of water by one degree. So when a food label says “200 calories,” it’s really referring to 200 kilocalories.

What a “Calorie” Actually Means

• In physics, 1 calorie (small “c”) is the amount of heat needed to raise 1 gram of water by 1°C.

• In nutrition, when we say “200 calories”, we actually mean 200 kilocalories (kcal). One “food calorie” = 1 kcal = 1,000 physics calories.

So when you see “200 calories” on a label, that’s shorthand for 200 kilocalories, which equals 200,000 physics calories.

Historically, scientists measured this by literally burning food in a bomb calorimeter — a sealed chamber where the food sample is combusted, and the heat released warms a known quantity of water. The temperature change revealed how much energy the food contained.

In the late 1800s and early 1900s, American chemist Wilbur Olin Atwater adapted this approach for human nutrition. He measured the energy content of macronutrients (fat, protein, carbohydrate, alcohol) and created the system still used today:

• 9 kcal per gram of fat

• 4 kcal per gram of protein (technically ~5.6 kcal/g gross, but adjusted for nitrogen losses)

• 4 kcal per gram of carbohydrate

• 7 kcal per gram of alcohol

This Atwater system was a breakthrough for the time, giving a way to compare foods on a single “energy” scale. But it was always an approximation, never a precise measurement for every individual.

Here’s the key point: your body is not a bomb calorimeter. You don’t burn food into ash and capture every last bit of heat. You digest it, absorb a portion of it, lose some in stool, urine, or breath, and then — depending on your hormonal state — either burn the energy, store it as fat, or dissipate it as heat.

So while calories tell us how much potential energy a food contains, they tell us nothing about how your body will respond to that food. Two foods with identical calorie counts can have dramatically different effects on hunger, hormones, and fat storage.

While each food provides the same energy on paper (200 calories), their effects on hormones, satiety, metabolism, and long-term health are vastly different. Calories are a unit of energy, but metabolism cares more about the quality and context of those calories than the number alone. Here are some examples of foods, which provide 200 calories, however have a completely different metabolic outcome.

Technically, all of these foods provide “calories.” But lumping them together as if they’re the same misses the bigger picture. It’s a bit like saying water and petrol are both liquids. True—but you wouldn’t drink petrol, and you certainly wouldn’t put water in your car.

In the same way, 200 calories from soda, almonds, or chicken may be equal in energy on paper, but their effects on your body—blood sugar, hormones, satiety, and long-term health—are worlds apart.

Why the Body Doesn’t Count Calories

Now that we know what a calorie is — a unit of heat measured in a lab — here’s the key point: your body doesn’t count them.

The human body doesn’t have a “calorie sensor.” Your stomach can’t tell if you just ate 500 calories of steak or 500 calories of soda. What it does sense are:

• Stretch – how much volume you ate (through stretch receptors in the stomach wall).

• Nutrients – presence of amino acids, glucose, fatty acids (via specialised gut sensors) etc.

• Hormones – chemical messengers released in response to food, like insulin, GLP-1, PYY, ghrelin, and CCK.

These signals go to the brain — specifically the hypothalamus — which integrates them and decides what happens next:

• Should you feel hungry or satisfied?

• Should your metabolism speed up or slow down?

• Should you store energy as fat or burn it?

'Calories' themselves play no direct role in these decisions. They’re just a bookkeeping number we humans invented. This explains why two diets with the exact same calorie count can have radically different effects on weight, hunger, and fat storage. A high-protein, high-fibre meal triggers satiety hormones, keeps insulin low, and encourages fat burning — whereas a highly processed, high-sugar meal spikes insulin, drives fat storage, and often leaves you hungrier sooner.

In other words, your brain “understands” hormones, not calories. And hormones are what ultimately control energy in (how much you eat) and energy out (how much you burn).

Image Credit: Harvard Health

Thermodynamics and the Problem with “Calories In, Calories Out”

One of the most common arguments for calorie counting goes like this:“Energy cannot be created or destroyed. If you eat more than you burn, you’ll gain weight. If you eat less than you burn, you’ll lose weight. It’s a law of physics!”

It sounds compelling — but let’s slow down and examine whether this “thermodynamic truth” really applies to the way human biology works.

The First Law of Thermodynamics

The first law of thermodynamics states that energy cannot be created or destroyed, only transformed from one form to another. This is absolutely true in a closed system, like a bomb calorimeter, where every input and output is measured.

But the human body is an open system, constantly exchanging both energy and matter with its environment:

• We absorb oxygen and nutrients.

• We expel carbon dioxide, heat, water, and waste products.

• We can even lose energy through ketones in breath or urine.

So while the total energy is conserved in the universe, what we really care about is how that energy is partitioned inside the body — and that is not dictated by physics alone, but by biology. That means “calories in” and “calories out” are not fixed numbers you can measure once and rely on forever. Let’s break this down.

“Calories In” — Not Everything You Eat is Absorbed

• Gut absorption varies. High-fibre diets can cause 5–10% of calories to pass out in stool, whereas highly processed diets (low fibre) are almost fully absorbed.

• Protein absorption isn’t perfect. Depending on the source (plant vs. animal), 5–15% may be lost.

• Fat absorption can drop if intake is very high or if there are gut issues (e.g., bile acid malabsorption).

• Thermic Effect of Food (TEF). Protein requires up to 20% of its calories just to be digested and metabolised — effectively reducing “net calories in.”

So the number on the food label isn’t necessarily the number that makes it into your bloodstream.

“Calories Out” — Not Everything You Burn is Predictable

• Basal Metabolic Rate (BMR) can fluctuate by hundreds of calories depending on sleep, thyroid hormones, stress, or illness.

• Non-Exercise Activity Thermogenesis (NEAT) — all the fidgeting, standing, pacing you do subconsciously — can vary by 500+ kcal/day between people.

• Adaptive Thermogenesis — when you cut calories, your body defends itself by slowing metabolism 10–30%, lowering thyroid hormones, and making you tired so you move less.

• Energy losses through ketones (on low-carb diets), heat (brown fat activation), and even sweat/urine are usually unmeasured but can account for 5–10% of energy.

Even in a lab, measuring energy expenditure precisely requires expensive tools like metabolic chambers or doubly labelled water. And what you burn in a lab isn’t necessarily what you burn in real life.

Here’s why outcomes diverge:

IF (low insulin)

– Glycogen depletion occurs.

– Lipolysis (fat breakdown) activated.

– Fat oxidation increases.

– Greater share of CO₂ exhaled comes from fat stores.

– Possible extra calorie loss via metabolic inefficiencies (gluconeogenesis, ketone excretion).

High insulin / grazing

– Glycogen rarely depleted.

– Fat oxidation suppressed.

– Dietary energy preferentially stored.

– Less reliance on fat stores → less fat loss at same calorie level.

Same 2000 kcal, different metabolic “routing.”

The bottom line

• The first law is always true — energy is conserved.

• But biology is about routing, not just totals.

• Hormones, feeding pattern, food type, and metabolic context decide:

  • How much of “energy in” is absorbed,

  • How much is excreted/wasted,

  • How much is stored vs oxidised,

  • Whether “energy out” is fat or glycogen.

So CICO is a framework, not an explanation. Saying “just eat less, move more” is like telling a failing business: “just spend less than you earn.” Technically true, but it ignores all the structural reasons why that’s not happening.

The Takeaway

Yes, energy balance exists — over the very long term, your weight reflects whether more energy was stored or burned. But you cannot directly control it with precision. Both sides of the equation are constantly shifting in response to hormones, food quality, stress, and your environment.

This is why “just eat less and move more” sounds good in theory but fails so often in practice. You’re not a passive bucket where calories simply pile up or drain out. You’re an adaptive organism whose physiology is actively defending weight, sometimes even in ways that seem to “break” the math.

Why “Calories In” Aren’t Fully Counted by the Body

One of the big problems with calorie counting is that it assumes every calorie on the label is fully absorbed and available for energy. But in reality, a significant portion of what you eat never even makes it past your gut into circulation — and what does get absorbed is handled differently depending on the nutrient type.

Here’s a breakdown:

Factor	Fibre	Protein	Fat
What Happens in the Gut	Partially fermented by gut bacteria into short-chain fatty acids (SCFAs); remainder passes out in stool. Gas production (H₂, CH₄) also represents lost energy.	Mostly digested, but 5–15% escapes absorption (especially plant protein). Nitrogen must be converted to urea and excreted, costing energy.	Generally well absorbed (>95%), though absorption drops with very high intakes or bile acid insufficiency.
% of Calories Absorbed	~50–70% (varies by fibre type). High-fibre diets can lose 5–10% of total daily calories in stool.	~80–90% metabolizable energy (from gross 5.6 kcal/g → 4 kcal/g).	~90–98%
Implications for Calorie Counting	Food labels overstate usable energy from high-fibre diets. Two equal-calorie diets (one high-fibre, one low-fibre) can have very different net energy intake.	Labels assume 4 kcal/g, but net usable energy is lower due to thermic effect (10–20% burned just to process).	Fat counts are more accurate, but small unabsorbed amounts and type of fat can still influence net calories.
Role in Energy	SCFAs can be used for energy but are also key signalling molecules for gut and metabolic health.	Primarily used for building/repair — only burned for energy in starvation or with very high intake.	Some fats (like omega-3s) are prioritised for cell membranes, hormones, and brain health before being burned for fuel.

It’s worth noting that the gross energy of protein is closer to 5.6 kcal per gram when measured in a bomb calorimeter. But the body spends energy converting amino acids into usable forms and excreting nitrogen as urea, leaving only about 4 kcal per gram of metabolizable energy — the number we use in nutrition.

And there’s another twist: protein has a high thermic effect (10–20% of its calories burned just to digest and metabolise it). This is counted as part of your “calories out,” not subtracted from the 4 kcal figure, which means the net usable energy is even lower in practice. This is one reason high-protein diets can boost metabolism and aid fat loss without deliberate calorie cutting.

Example: Whole-Food Meal vs. “Net Usable Energy”

Let’s take a balanced, nutrient-dense meal:

Meal:

• 150 g grilled salmon (protein + fat)

• 150 g roasted sweet potato (carbs + fibre)

• 1 cup broccoli (fibre, micronutrients)

• 1 tbsp extra-virgin olive oil (healthy fat)

Macronutrient Breakdown (Approx.):

• Protein: 40 g → 160 kcal

• Fat: 25 g → 225 kcal

• Carbohydrate: 25 g (6 g fibre) → 100 kcalTotal “Calories In”: ~485 kcal

Step 1: Adjust for Absorption & Gut Loss

• Fibre: 6 g x 4 kcal/g = 24 kcal listed on paper — but only ~50–70% is fermented and absorbed as SCFAs → ~12–17 kcal actually available.

• Protein: 85–95% absorption = ~34–38 g makes it into circulation → ~135–150 kcal available.

• Fat: 95–98% absorbed = ~214–220 kcal available.

Adjusted Total (Post-Gut): ~465 kcal (20 kcal already lost in stool/gas).

Step 2: Subtract Thermic Effect of Food (TEF)

• Protein TEF: 10–20% burned during digestion = ~15–30 kcal lost.

• Carb TEF: 5–10% = ~4–7 kcal lost.

• Fat TEF: 0–3% = ~2–6 kcal lost.

TEF Total: ~25–40 kcal lost as heat.

Net Usable Energy

Final “Net Energy”: ~425–440 kcal

That’s 10–15% lower than the number on the food label — despite this being a very clean, whole-food meal.

Why This Matters

If we miscount by 10–15% per meal, that adds up to a huge margin of error over a day or week. And that’s without accounting for:

• Differences in individual gut microbiomes (some people absorb more/less).

• Variations in protein source (plant protein often has lower bioavailability).

• Hormonal state (e.g., thyroid, insulin) that changes how much energy is stored or burned.

This is why “just hit your calorie target” is oversimplified — we don’t even have a precise measure of what that target really means inside the body.

The Bottom Line

If we can’t even say with confidence how much of the energy in fibre, protein, or fat is actually absorbed, we’re already starting calorie counting with a margin of error.

And even when these macronutrients are absorbed, they aren’t all destined to be burned for fuel — some are used for structural roles, signalling, and repair. This means that “calories in” is just an estimate, not a precise number you can use as a control knob.

Why “Calories Out” Can’t Be Precisely Measured Either

Even if we knew exactly how many calories we absorbed (we don’t), we’d still have to know how many we burned. But “calories out” isn’t a single fixed number — it’s a constantly shifting total made up of multiple components.

Factor / Component	Basal Metabolic Rate (BMR)	Non-Exercise Activity Thermogenesis (NEAT)	Thermic Effect of Food (TEF)	Planned Exercise (PA)	Adaptive Thermogenesis (Metabolic Adaptation)	Heat & Non-shivering Thermogenesis	Ketone & Other Chemical Losses
What it is	Energy used to keep basic life processes going at rest (organs, circulation, respiration, cellular maintenance).	All spontaneous daily movement not classified as exercise (fidgeting, posture, walking errands).	Energy used to digest, absorb and metabolise food.	Energy used during intentional exercise (gym, running, weights).	The body’s down- or up-regulation of metabolic rate in response to calorie change or environment.	Heat produced by brown fat, shivering, or other thermogenic responses; includes heat lost to environment.	Energy lost as ketones (breath/urine) and small chemical/urea losses in urine/sweat.
Typical size (example)	~1800–2500 kcal/day for many adults (varies by size, sex, age).	Can vary by 0–800+ kcal/day between individuals; typical inter-individual spread ~200–600 kcal/day.	Protein 10–20% of protein kcal; carbs 5–10%; fat 0–3% — overall TEF typically 5–15% of intake.	0–1000+ kcal/day depending on training volume and intensity.	Can reduce TDEE by 10–30% during prolonged calorie restriction; can increase modestly with overfeeding or cold exposure.	Variable; maybe 0–200+ kcal/day depending on cold exposure, brown fat activity, and protein intake.	In ketosis, ketone loss may account for ~5–10% of fat-derived energy; urine/chemical losses ~1–2%.
Main drivers of variability	Body composition (lean mass), thyroid status, sex, age, genetics.	Job type, fidgeting tendency, commute, sleepiness/fatigue, illness, environment.	Macronutrient mix (protein high TEF), meal size, processing.	Exercise type, duration, intensity, fitness level, compensatory movement changes.	Magnitude of calorie deficit/surplus, hormonal state (thyroid, leptin), illness, sleep.	Ambient temperature, cold exposure, sympathetic activation.	Diet (low carb/ketosis), metabolic state, kidney/liver function.
Measurement difficulty	Lab: indirect calorimetry. Estimation equations (Mifflin-St Jeor) often ±10–30% for individuals.	Extremely hard to measure outside lab; wearable step counts are a rough proxy but miss posture and small movements.	Can be estimated from macros, but individual TEF varies; labels don’t include it.	Wearables and MET estimates are imprecise; doubly labelled water best but not practical.	Practically invisible without lab methods (doubly labelled water, metabolic chamber).	Measured in research settings; not available to lay users.	Usually ignored in mainstream calorie calculators.
Practical implication for calorie counting	A person using a generic BMR estimate may be off by hundreds of kcal/day.	Two people with same BMR+exercise could differ by several hundred kcal/day purely from NEAT.

The Takeaway

Even the best formulas for “calories out” (like Mifflin-St Jeor or Harris-Benedict) are just statistical averages — they can be off by 10–30% for any given individual. And because your body adapts dynamically, the number is never fixed.

So just like “calories in,” “calories out” is a moving target — and one you can’t directly measure without expensive lab tools (and even then, it changes outside the lab).

The Problem with the “Just Cut 500 Calories” Approach

A common rebuttal to the idea that calories can’t be precisely measured goes something like this: “Okay, maybe it’s not exact. But you don’t need perfection. Just cut 500 calories per day, wait a week or two, and keep adjusting downward until you see results.”

It sounds simple — but here’s why this approach is flawed.

1. Metabolic Adaptation Undermines the Deficit

When you reduce calories, your body senses an energy shortfall and adapts to defend its weight:

• Basal Metabolic Rate (BMR) drops — sometimes by 10–30%, meaning you burn fewer calories even at rest.

• NEAT (spontaneous activity) declines — you fidget less, sit more, unconsciously conserve energy.

• Hormones shift:

  • Thyroid hormone (T3) decreases, slowing metabolism.

  • Leptin falls, making you hungrier.

  • Ghrelin rises, increasing cravings.

This means your carefully planned 500 kcal deficit may shrink to 200 kcal — or vanish entirely — within weeks. So you keep cutting more, but the body keeps adapting, leading to frustration and often rebound weight gain.

2. Muscle Loss Lowers Long-Term Energy Burn

Continuous calorie reduction without a focus on protein and resistance training causes loss of lean body mass. Less muscle means a permanently lower metabolic rate — making future fat loss harder and weight regain more likely.

3. Hunger and Compliance Become the Limiting Factor

As you continue to cut, hunger hormones rise and cravings intensify. This isn’t about weak willpower — it’s biology pushing you to restore energy balance. This is why so many people can “white-knuckle” through calorie restriction for a few weeks, only to binge and regain weight later.

4. The “Numbers Game” Ignores Food Quality

Blindly reducing calories doesn’t address the hormonal environment that controls fat storage. For example:

• A 1500 kcal diet of ultra-processed food may keep insulin high and block fat burning.

• A 1500 kcal diet of whole foods with adequate protein may keep insulin low, preserve muscle, and promote fat loss.

Same calorie target — very different outcome.

Practical Example

Here’s a short, concrete worked example that shows how a planned 500 kcal/day cut can progressively evaporate because of real physiological adaptation. I’ll show the numbers week by week, then explain the practical implications.

Scenario (baseline)

Baseline estimated energy use (typical example):

BMR = 1,600 kcal/day

NEAT = 400 kcal/day

Planned exercise = 300 kcal/day

TEF = 200 kcal/day

Total daily energy expenditure (TDEE) = 1,600 + 400 + 300 + 200 = 2,500 kcal/day

Planned intake = 2,000 kcal/day → initial planned deficit = 2,000 − 2,500 = −500 kcal/day (a 500 kcal deficit).

How adaptation can shrink that deficit (worked example)

We keep intake constant at 2,000 kcal/day and model reasonable physiological changes over six weeks: small drops in BMR, larger drops in NEAT, and a modest fall in TEF as the body adapts to lower intake and reduced activity. Exercise is held constant here to isolate the hidden shifts.

Week	BMR (kcal)	NEAT (kcal)	TEF (kcal)	TDEE (kcal)	Daily deficit = intake − TDEE (kcal)
0	1,600	400	200	2,500	−500
1	1,550	340	197	2,387	−387
2	1,520	300	194	2,314	−314
3	1,500	270	191	2,261	−261
4	1,490	250	190	2,230	−230
5	1,480	230	184	2,194	−194
6	1,450	200	180	2,130	−130

Numbers above are illustrative but intentionally conservative and realistic: over six weeks the example assumes cumulative BMR reduction ≈150 kcal/day, cumulative NEAT reduction ≈200 kcal/day and TEF reduction ≈20 kcal/day. The result: the initial 500 kcal/day deficit falls to about 130 kcal/day by week 6 — a 74% reduction in the planned deficit.

What those numbers mean in practice

If you expect 500 kcal/day to produce rapid weight loss, this example shows why results often slow or stop: the body defends itself. The planned deficit didn’t vanish because of measurement error alone — physiology actively reduced expenditure.

A few practical consequences:

• Slower-than-expected weight loss. A 500 kcal/day initial deficit might produce a brisk start, then a long tail of much smaller deficit where weight loss plateaus.

• Pressure to cut further. People often respond by cutting calories more, which provokes further metabolic adaptation and increases the risk of muscle loss, fatigability and excessive hunger.

• Increased hunger and cravings. Hormonal changes (lower leptin, higher ghrelin) make the reduced intake harder to sustain. That’s why adherence often fails, and weight is regained.

• Hidden behavioural changes. Lower NEAT is partly unconscious (less fidgeting, slower walking, poorer posture), so simply “adding more exercise” often does not restore the planned deficit fully because NEAT and BMR keep shifting.

Why “just keep cutting until it works” is a fragile strategy

• The “knob moves as you turn it” — the body lowers expenditure as you lower intake, so you chase an ever-diminishing return.

• Repeated, deep calorie cuts raise the risk of losing lean mass unless protein and resistance training are prioritised. That makes long-term metabolic rate lower and future attempts harder.

• It ignores hormonal drivers of appetite and partitioning (insulin, leptin, ghrelin, thyroid), and ignores food quality — which determines satiety, TEF and how much energy is actually absorbed.

A more robust alternative

Rather than continually shrinking calories, a better approach is to change the hormonal and behavioural levers that let the body regulate itself with less resistance: prioritise protein and fibre, favour whole foods over ultra-processed foods, preserve muscle with resistance training, and optimise sleep and stress. Those actions reduce appetite, raise TEF and NEAT (or at least prevent large falls), and protect BMR — meaning the practical deficit you create is larger and more sustainable without constant micro-cuts.

Bottom Line

The “just cut and adjust” strategy assumes that calories are a reliable control knob. In reality, the knob moves as you turn it — because the body adapts, hormones change, and hunger kicks in.

Rather than chasing smaller and smaller numbers, it’s more effective to improve food quality, satiety, and hormonal balance — which lets your body naturally reduce intake and increase fat burning without constant micromanagement.

Conclusion: Why CICO Fails and What We Should Focus on Instead

We’ve now seen why “calories in, calories out” is an oversimplified and often misleading way to approach fat loss:

• Calories are a measurement, not a signal. Your body doesn’t count calories — it senses nutrients, hormones, and energy status, and adjusts metabolism accordingly.

• “Calories in” aren’t precise. Fibre passes out in stool, protein has lower net energy after urea losses and thermic effect, and individual gut absorption varies dramatically. The label number is a rough guess, not an exact input.

• “Calories out” constantly shifts. BMR, NEAT, TEF, and thermogenesis are not fixed — they adapt in response to diet, stress, sleep, temperature, and hormones. The 500 kcal deficit you planned on paper can shrink or disappear in a matter of weeks.

• Food quality drives outcomes more than calorie totals. Two diets with the same calories can produce opposite results depending on how they affect insulin, leptin, ghrelin, satiety, and fat partitioning.

This doesn’t mean thermodynamics is wrong — energy is still conserved. But focusing on calorie math as a “control knob” ignores the fact that biology decides where that energy goes: stored, burned, or wasted as heat.

The Real Lever: Work With Your Physiology, Not Against It

Instead of chasing smaller and smaller numbers, a more effective approach is to change the inputs your body actually responds to:

• Prioritise protein and fibre to increase TEF and satiety.

• Reduce ultra-processed foods that spike insulin and override hunger cues.

• Preserve muscle with resistance training, keeping BMR higher.

• Support hormones with adequate sleep, stress management, and nutrient quality.

These are the levers that allow your neuroendocrine system to regulate weight naturally — without constant calorie micromanagement.

Final Thought

If calorie counting really worked, obesity wouldn’t be a global epidemic. The math isn’t wrong — the method is. It’s time to stop fighting your biology and start working with it.

What’s Next: Rethinking “Energy Balance”

In the next part of this series, we’ll go deeper into the concept of “energy balance” itself. We’ll look at why the equation Energy In = Energy Out is true but trivial — and why focusing on the equation without asking what controls its inputs and outputs is like staring at your car’s fuel gauge while ignoring the throttle, the engine, and the leaks in the tank.

Because the question isn’t just whether 2+2 = 4 — it’s who or what is deciding whether we’re adding 2s or 3s in the first place.