The Human Operating Manual

Macronutrient & Hydration Basics

As you may or may not be aware, reducing the complexity of a topic tends to result in the exclusion of seemingly important details. This is one of the reasons why communicating scientific ideas leads to misinterpretation and public (and often professional) false confidence. As a side note, this way of communicating is also how people can weaponize “facts” for personal gain and for wide-scale persuasion. Keep this in mind while going through this section, and other sections for that matter, and acknowledge that the chosen explanations are there to give you a greater understanding of what your body needs, with as little nutritional dogma woven in as possible.

As always, keep an open mind, but do your own research and personal experimentation.       


Macronutrients are the bulk fuel and structural materials that allow the body to recover and grow stronger. The big buckets. Protein, carbohydrates, fat, fibre, and water make up nearly all of what you eat by weight, and the balance between them shapes everything from how energetic you feel to how your body handles stress to how long you live.


Tragically, the simplest concept in nutrition is also the most misunderstood. One decade saturated fat is killing you; the next it’s safe; the next it’s actively beneficial. One year, carbohydrates are essential fuel; the next, they’re metabolic poison. Protein is either insufficient in the modern diet or dangerously over-consumed, depending on which book you read. Fibre went from “essential” to “questionable” to “essential” again. The whiplash appears to be because nutrition science is genuinely difficult to do well, and most of what reaches the public has been filtered through layers of commercial interest and reductionist storytelling before it gets there.


This page covers the basic biology of each macronutrient: what your body actually does with the food, how it gets digested, how much you need, and where the popular framing tends to go wrong. The clinical territory of food sensitivities, antinutrients, and specific dietary patterns lives on The “Natural” Diet page. The microbiome’s role in fibre metabolism gets a more comprehensive explanation in Microbiome Basics. The fasting and metabolic flexibility material lives in Fasting in Part II. Here we focus on the underlying mechanisms.


A note before we start: nutrition research has problems that don’t apply to most other areas of human biology. John Ioannidis at Stanford has documented that single-paper findings in nutrition epidemiology often fail to replicate, and that the field’s reliance on observational data with massive confounders produces conclusions that are more fragile than the popular presentation suggests. Edward Archer has gone further, arguing that the entire body of NHANES self-reported food frequency data is “physiologically implausible” and shouldn’t be used to derive guidelines. Kevin Hall at the NIH has quietly transformed the field by running metabolic ward studies (keeping subjects in research facilities for weeks, controlling and measuring everything they eat), which bypasses the self-report problem entirely, but more on that later.


Protein

What is Protein?

Of all the macronutrients, protein is the one whose role is least disputed. Your body needs it constantly: to repair tissue, build enzymes and hormones, maintain immune function, produce neurotransmitters, and replace skin and hair cells. Unlike carbohydrate and fat, protein can’t be stored in any meaningful long-term reserve. Whatever you don’t use within roughly a day either gets converted to glucose (gluconeogenesis), used for energy, or excreted. This means protein intake needs to be a daily affair, not a once-a-week stockpiling exercise. Protein also has a greater thermic effect than fat and carbohydrates, and improves satiety by lowering ghrelin (hunger hormone) and increasing leptin (satiety hormone).   


Proteins are chains of amino acids. Twenty different types are used to build the proteins in your body, of which nine are “essential” because your body can’t synthesize them and you need to get them from food (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine). The rest, your body can make from other amino acids if necessary.


Different food sources have different amino acid profiles. Animal proteins (meat, fish, eggs, dairy) generally provide a “complete” profile. All nine essential amino acids in proportions roughly suited to human requirements. Plant proteins are typically incomplete in some specific amino acid (lysine in grains, methionine in legumes), which is why traditional cuisines often combine grains with legumes (beans and rice, hummus and pita, lentils and bread) without anyone needing to know the underlying amino acid chemistry.


A note on methionine and glycine balance. Methionine is one of the essential amino acids and is concentrated in muscle meat. Excess methionine produces reactive oxygen species and may accelerate aging in some animal models; Brian Kennedy and others have published extensively on methionine restriction and lifespan. Glycine appears to counterbalance some of methionine’s pro-aging effects and is concentrated in connective tissue, skin, bone, tendon, and ligaments – the parts of the animal that get thrown out in modern muscle-only meat consumption. Eating “nose to tail” (bone broth, skin-on cuts, organ meats, marrow) better matches the amino acid balance our ancestors got from whole-animal consumption. Chris Masterjohn has compiled the most accessible practitioner-level resources on this balance, including a comprehensive food database.


Digestion

The cells in your stomach lining produce an inactive enzyme called pepsinogen, which gastric acid converts to active pepsin. Pepsin starts breaking proteins into shorter chains (peptides). The work continues in the small intestine, where pancreatic enzymes (trypsin, chymotrypsin) finish the job. By the time amino acids reach your bloodstream, they’ve been broken down to their individual molecular units (amino acids).


All proteins are digested down into amino acids (a nitrogen-containing amine group connected to a carboxyl acid). Amino acids are distinguished by their tails, which are always some configurations of carbon, hydrogen, and oxygen atoms. There are hundreds of amino acids on Earth, but only twenty-one are used to build proteins in living plants and animals. Nine of these are considered essential for humans, meaning our bodies can’t make them on their own; we need to get them from our diet. The others your body can make by itself if needed, usually by breaking down and reformulating other amino acids.


Amino Acids

Amino acids are absorbed through the intestinal wall and travel via the bloodstream to the liver, where they’re either used immediately to build new proteins, converted to glucose for energy, or (if there’s an excess) broken down. The nitrogen-containing amine group is converted to urea (this conversion happens in the liver and is genuinely consequential; without it, ammonia would accumulate and kill you), which then travels to the kidneys for excretion in urine.


Amino acids and some peptides can self-regulate their time in the intestines. For example, the digestive hormone cholecystokinin (CCK) can slow down the contraction speed of the intestines in response to protein intake. CCK gets released when you eat dietary protein, and it slows down your digestion so that you can absorb it better.


Leucine stimulates a complex in muscle called mTOR (mammalian target of rapamycin), and this initiates a signaling cascade that increases muscle protein synthesis (MPS). Leucine is an essential amino acid, not extracted from the gut and liver on first pass metabolism, and has a concentration-dependent, passive diffusion across the cell membrane. So, the amount of it in the cell reflects the quantity in the diet. However, it only increases muscle protein synthesis (MPS) in the short-term. You need all the essential aminos for it to be sustained.


Waste Not, Want Not

We pee out the equivalent of fifty grams of protein each day. Exercise adds to that total by increasing muscle breakdown. We have to eat enough protein to replace what we lose each day, lest we find ourselves in a protein deficit. If we eat more protein than we need, the extra amino acids are converted to urea and cleared out by the urine. 


After the nitrogen-containing head is chopped off, converted to urea, and sent on its way, the tails are used to make glucose (gluconeogenesis) or ketones, both of which can be used for energy. Proteins are typically a minor part of the daily energy budget, providing around 15 percent of our calories each day. But they are a vitally important emergency energy supply if we’re starving.


Protein Types

Different proteins are absorbed at different rates. Whey protein is absorbed quickly; casein is absorbed slowly. Whole-food protein from a steak or a piece of fish is absorbed more slowly than either, because it’s bound up with fat, fibre, and connective tissue that slows digestion. The popular framing of “fast” versus “slow” protein has some validity, but is often oversimplified. For most practical purposes, whole-food protein produces sustained amino acid availability that supports protein synthesis throughout the day. However, many other factors determine protein absorption, such as the pH levels of the gut, the permeability of the intestinal lining, protein sensitivity, and the presence of hormones related to gastric emptying.


Whole-food protein sources, roughly ranked by quality and bioavailability:

  • Pasture-raised eggs: close to the gold standard for protein quality, plus fat-soluble vitamins and choline
  • Wild fish: particularly fatty fish like salmon, sardines, and mackerel for omega-3s, alongside protein
  • Pasture-raised meat: beef, lamb, game animals, poultry, with grass-fed where available
  • Organ meats (offal): liver, heart, kidney; nutrient density per gram of protein is exceptional
  • Bone broth and slow-cooked stocks: particularly important for the glycine balance covered above
  • Full-fat dairy from healthy animals: raw and fermented preferred (kefir, yogurt, cheese)
  • Shellfish, particularly oysters: extraordinarily nutrient-dense
  • Plant proteins from properly prepared sources: sprouted/soaked legumes, fermented soy products, quinoa


The “properly prepared” caveat for plant proteins matters because of antinutrients (lectins, phytates, oxalates) that can interfere with mineral absorption. Traditional preparation methods (soaking, sprouting, fermenting) reduce these compounds substantially. The full breakdown lives on The “Natural” Diet page.


A note on A1 versus A2 dairy. Most modern dairy cattle (Holsteins, particularly) produce milk containing the A1 beta-casein protein, which produces the digestion peptide BCM-7 in some people. Older European breeds and most Asian cattle produce A2 beta-casein, which doesn’t produce BCM-7. The A1/A2 difference has been associated in some research with digestive discomfort and possibly other effects, though the human evidence is mixed and A. Stewart Truswell published a critical review challenging the strength of the original claims.9 If you experience GI discomfort with dairy but tolerate cheese (which has lower BCM-7) or A2 milk where available (Guernsey, Jersey, Charolais, Limousin breeds), that’s a reasonable adjustment.


How Much Protein Do We Need?

The official RDA (0.8 g/kg body weight) is calibrated to prevent deficiency in sedentary adults, not to support optimal body composition or performance. Most active adults benefit from substantially more than this.


The more lean muscle mass that you have, the more protein you need to sustain that amount of muscle. A higher bodyweight requires more building blocks due to the increased mass. However, for optimal health and body composition, you’d want to focus on your lean muscle mass. The idea is to lose the fat and maintain the muscle, rather than feeding fat stores with extra calories from unnecessary protein.


Stuart Phillips at McMaster University has been the most influential researcher on protein and muscle metabolism, with decades of work characterizing how dietary protein supports muscle protein synthesis (MPS). Luc van Loon at Maastricht has done complementary work, particularly on the per-meal threshold for triggering MPS.

  • Active adults benefit from roughly 1.4–2.0 g/kg/day of protein, distributed across multiple meals
  • The per-meal threshold for triggering muscle protein synthesis is approximately 0.4 g/kg of high-quality protein, with leucine being the primary trigger (roughly 2–3 g of leucine per meal)
  • Older adults need more protein than younger adults to achieve the same MPS response (anabolic resistance)
  • The “30 grams per meal absorption limit” widely cited in popular nutrition is more flexible than the original framing suggests. There’s no hard ceiling, but there is a diminishing-returns point above ~0.4 g/kg per meal


Brad Schoenfeld has done the most comprehensive meta-analytic work on the so-called “anabolic window.” The supposed 30-minute post-workout protein deadline. His 2013 meta-analysis showed the window is much wider than originally thought, with protein synthesis remaining elevated for roughly 24 hours after resistance training. You can stop worrying about chugging protein shakes immediately after the gym; getting adequate protein across the day matters far more than precise timing. 


A note on protein intake and aging. The popular wellness discourse has produced two contradictory positions: that older adults need more protein (which is correct based on Phillips’ anabolic resistance research) and that protein intake should be restricted for longevity (based on the Walter Longo and Valter Longo work on mTOR and IGF-1). The honest synthesis is that adequate protein matters for maintaining muscle mass and function in aging, and that “longevity protein restriction” claims are based on extrapolations from rodent and worm models that don’t translate cleanly to humans. Sarcopenia (age-related muscle loss) is a substantial cause of disability and mortality in older adults, and protein adequacy is a meaningful protective factor.


Protein can’t be stored long-term

  • Carbohydrates can be stored as liver and muscle glycogen (100- 500 grams). Extra carbs will be burned off as energy or converted into triglycerides to be stored as body fat.
  • Fat and extra carbs can be stored in near infinite amounts as body fat in the adipose tissue. 
  • Protein intake will be used for elevating muscle protein synthesis and activating mTOR, which will help to maintain your current lean muscle mass. To activate these pathways, you need only a certain amount of protein, and more won’t have a dose-increasing effect.
  • Starvation may cause the breakdown of muscle for energy, as well as excess protein intake (specifically glucogenic amino acids).  


In the short term, an influx of increased protein supply won’t trigger gluconeogenesis in your own muscle tissue because there is no demand there. The body will have met its need for amino acids and thus doesn’t require additional glucose. Temporary protein stores fluctuate throughout the day, and they’re connected to the feeding and fasting cycles.


However, if you eat more protein than your body needs right now, it slows the digestion of the excess and gradually releases amino acids into the blood over the next few hours, when your protein synthesis decreases. Some amino acids can even be temporarily stored inside muscle cells for future use, whether for maintaining amino acid homeostasis or for energy production. The reason it’s thought that you can only absorb 30 grams of protein in one sitting is that you only need about 20-30 grams of protein to trigger muscle protein synthesis and actually build muscle. 


Thermal Effect

The thermal effect of protein is 30% more than carbs. Protein turnover is an energy dependent process that requires ATP. It also may activate the “futile cycle” where synthesis and protein degradation both increases, leading to a greater dissipation of energy. The act of preserving lean body mass during dieting is important as it slows the drop in metabolism. It is also more satiating because they are not very energy dense (voluminous) and it triggers a signaling that is favorable for satiety in the brain. Whey protein absorbs faster than casein so it has a faster detectable change in amino acid blood concentration. High protein increases anorexic hormones like GLP-1, glucagon, CCK, and PYY.


Carbohydrates

What are Carbohydrates?

Carbohydrates are the macronutrient where the field has been most dishonest with the public. Three decades of public health messaging that treated carbs as the foundation of a healthy diet (the food pyramid) was followed by a low-carb counter-revolution that treated them as metabolic poison. Both positions oversimplify dramatically. 


Carbohydrates break down into glucose, which fuels essentially every cell in your body. The brain alone uses roughly 120g of glucose per day under normal conditions; red blood cells (which lack mitochondria) require glucose because they can’t use ketones or fatty acids. Glucose is stored as glycogen in the liver (~100g) and skeletal muscle (~300-500g), with excess converted to triglycerides and stored as body fat.


When blood sugar is too high is can be toxic to blood vessels and endothelial cells. When it is low, there may be nausea, fainting, coma, etc. Insulin also helps to take in amino acids and lipids, particularly in peripheral tissue. It also inhibits lipolysis and fat oxidation. Carbs actually contribute very little to stored fat. They just inhibit fat oxidation and lipolysis.


Carbohydrates that are lower on the glycemic index (GI), such as complex carbohydrates, help us to produce slower-release energy for our brains and bodies, improve satiety, manage weight gain, create healthier skin, stabilize our mood, store fuel, and often come with a healthy dose of fibre, vitamins, and minerals. 


Crucially, carbohydrates aren’t strictly “essential” the way protein and certain fats are. Your liver can produce all the glucose your body needs through gluconeogenesis from amino acids and the glycerol backbone of fats. Populations have lived for extended periods on near-zero carbohydrate diets (traditional Inuit populations, some pastoralist societies) without developing carbohydrate deficiency. This doesn’t mean carbohydrates are unnecessary; it means they’re contextually useful rather than strictly required. 


Digestion

In the mouth, amylase in your saliva begins the digestive process. Once in the stomach, the hydrochloric acid kills off bacteria, and it is then pushed on. In the small intestine, the starches and sugars are hit with enzymes produced by the intestine and pancreas to break them down further. The pancreas sits just beneath the stomach and is attached to the small intestine with a short duct. It’s most famous for its production of insulin, but the pancreas also produces most of the several dozen enzymes used in digestion (along with bicarbonate, which neutralizes the stomach acid as it enters the intestine).

If your genes no longer produce lactase, the lactose cannot be broken down into glucose and galactose, and the bacteria in the large intestine eat it, producing gas and the side effects of lactose intolerance.

Since much of the carbohydrate in your diet comes from starch, and starch is made entirely from glucose, about 80 percent of the starches and sugars that you eat end up as glucose. The rest is broken down to fructose (about 15 percent) or galactose (about 5 percent). Of course, if you eat a diet high in processed foods full of sugar (i.e., sucrose, which is glucose plus fructose) or high-fructose corn syrup (which is about 50 percent fructose and 50 percent glucose mixed with water), the percentage of fructose might be a bit higher for you, and the percentage of glucose a bit lower.

These sugars are absorbed through the intestinal wall and into the bloodstream. The walls of our intestines are full of blood vessels, and blood flow to our guts more than doubles after a meal to carry away nutrients. The result is a rise in blood sugar after a meal, particularly one high in carbs. If the food you eat is highly processed, low in fibre, and easily digested, the carbs are digested quickly, and the sugars rush into the bloodstream, creating a huge spike in blood sugar. Those foods are said to have a high glycemic index, which is the rise in blood glucose measured two hours after ingesting a particular food, relative to the rise you’d experience from eating pure glucose. Foods that are harder to digest (more complex carbohydrates, fewer sugars, more fibre) take longer to digest and absorb, resulting in a long, low rise in blood sugar, and a low glycemic index.

But glycemic index doesn’t tell the full story, because individual responses to identical foods vary dramatically. Eran Segal and Eran Elinav at the Weizmann Institute published a landmark 2015 paper showing that two people eating the same food can have meaningfully different blood glucose responses. One person might spike on bananas but be fine with cookies; another, the reverse. The variation is driven by genetics, microbiome composition, sleep quality, recent activity, and other factors. This is the foundation of personalized nutrition projects like ZOE (Tim Spector at King’s College London). The glycemic index is a reasonable rough guide; continuous glucose monitoring (or paying attention to how you actually feel) is a better individual guide.


Timing

A high-carbohydrate diet has more than 45% of calories coming from carbs. A low-carb diet needs to include less than 130g of carbs per day (less than 26% of a typical 2000-calorie-per-day diet). Active people’s needs vary. They require adequate carbohydrates to fuel their liver and muscle glycogen stores and to maintain joint health. 

Active people should consume carbs before, during, or after a workout. A post-carb serotonin release can help with sleep. Get at least 20-30g of carbs from dietary sources.

Higher seasonal fruits, berries, vegetables and limited meat during the summer months. Higher carbohydrate intake, whilst also consuming fat sources, promotes fat storage to increase survival odds during the winter months. 

A note on fruit specifically. The popular wellness discourse has produced an odd convergence: fruit gets demonized by the carnivore/keto crowd as “nature’s candy” and praised by the plant-based crowd as essential. The honest position: whole fruit comes packaged with fibre, vitamins, polyphenols, and water, which dramatically alters its metabolic effect compared to the equivalent grams of sugar from a soda. Fruit juice is much closer to soda than to fruit; the fibre matrix matters substantially. Seasonal whole fruit consumption appears in most traditional human diets and isn’t problematic for most people in moderation. The “promotes fat storage” framing common in some popular sources overstates what the actual research supports.


Examples

  • Organic fresh fruits and vegetables. Lightly cook the greens to maximize their longevity-boosting effects and to destroy goitrogens
  • Soaked, sprouted, or sour-leavened whole grains, legumes, and nuts. These processes eliminate antinutrients like phytic acid and enzyme inhibitors
  • Frequent consumption of lacto-fermented fruits, vegetables, drinks, and condiments (more to match physical demands and less if sedentary) 
  • Frequent consumption of tubers, such as potatoes, kumaras, yams, taro, and Jerusalem artichokes
  • Moderate use of traditional, natural sweeteners such as raw honey, maple sugar, maple syrup, dehydrated cane sugar juice, stevia powder, and date sugar
  • Strictly limited consumption of unpasteurized beer and wine (the resveratrol effects of wine are exaggerated dramatically)

Why Carbs Get Demonized

The current anti-carb wave has legitimate roots and legitimate overreach. The legitimate part: the food industry has spent decades replacing fat with sugar in processed foods, with the clearest documented case being Cristin Kearns and Stanton Glantz’s 2016 JAMA Internal Medicine analysis of internal sugar industry documents from the 1960s. The Sugar Research Foundation paid Harvard researchers (whose names ended up on a 1967 NEJM review) to redirect dietary blame from sugar to fat. The review shaped fifty years of public health policy. 


More recently, Coca-Cola funded the Global Energy Balance Network (GEBN) starting around 2012, with the explicit goal of shifting public obesity discourse from sugary drinks to physical inactivity. Marion Nestle at NYU has been the most rigorous documenter of these patterns; the 2015 New York Times exposure of the GEBN funding caused Coca-Cola to disband it.


On the other side of the coin: turning anti-sugar findings into anti-all-carbohydrate framing, treating broccoli and table sugar as nutritionally equivalent because both are “carbs,” ignoring the varied metabolic effects of different food matrices. Robert Lustig’s Sugar: The Bitter Truth lecture and broader work on fructose are well-grounded research; the popular extrapolations that all carbs are sugar in disguise go well beyond what Lustig himself argues.


Fibre

Fibre is technically a subcategory of carbohydrates: the carbohydrate fraction your digestive enzymes can’t break down. But it functions so differently from digestible carbs that it warrants its own treatment.


What Fibre Does

Fibre comes in two basic forms:

  1. Soluble fibre dissolves in water, forming a gel-like substance in the gut that slows nutrient absorption (which moderates blood glucose response), feeds gut bacteria, and helps lower LDL cholesterol. Found in oats, beans, apples, citrus fruits, and psyllium husk.
  2. Insoluble fibre doesn’t dissolve, instead acting as bulk that helps maintain regular bowel transit and feeds different gut bacterial populations. Found in whole grains, vegetables, nuts, and seeds.


Both types matter. The most powerful fibre effects in the research come from what your gut microbiome does with it. Justin and Erica Sonnenburg at Stanford have been the most influential researchers on the microbiome-fibre relationship, with their work showing that fermentable fibres feed bacterial populations that produce short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate. These SCFAs feed the cells lining your colon, regulate immune function, and have systemic effects extending far beyond the gut.


The full microbiome treatment lives in Microbiome Basics. The relevant fibre summary here: feed your microbiome with diverse fibrous foods, and the downstream effects include better blood glucose regulation, reduced inflammation, more resilient gut barrier function, and probably a meaningful amount of your overall health that doesn’t get attributed to fibre in the popular framing.


How Much You Actually Need

The official US recommendation is 25-35g daily, with most adults getting 15-20g. The Hadza hunter-gatherer baseline (when comparable measurements have been done) is roughly 100g daily. This is a level that would produce significant GI distress in most modern Westerners who suddenly attempted it.


Most adults benefit from increasing fibre intake gradually toward the 30-40g range, with diversity of sources mattering as much as total grams. Sudden large increases produce bloating, gas, and digestive distress as the microbiome adjusts. The goal is to feed a diverse microbiome with varied fermentable substrates over time.


When Fibre Is Bad

There are situations where fibre should be temporarily reduced:

  • Active inflammatory bowel disease flare: high fibre can aggravate symptoms during acute episodes
  • Small intestinal bacterial overgrowth (SIBO): fermentable fibres feed the wrong populations; treatment often involves a low-FODMAP phase
  • Severe IBS: particularly fructans and FODMAPs may need temporary restriction
  • Post-surgical recovery: bowel rest may be appropriate


Fibre Sources

  • Vegetables: leafy greens, cruciferous (broccoli, cauliflower, Brussels sprouts), root vegetables, alliums (garlic, onions, leeks)
  • Tubers: potatoes, sweet potatoes, yams, kumara, taro, Jerusalem artichokes
  • Fruits: berries, pears, apples, citrus, with skin where applicable
  • Legumes: beans, lentils, chickpeas (properly prepared)
  • Whole grains: oats, quinoa, buckwheat, properly prepared rice
  • Nuts and seeds: almonds, chia seeds, flaxseeds, hemp seeds (in moderation)
  • Resistant starch: cooked-and-cooled rice and potatoes, green bananas


Fat

Fat is the macronutrient that has undergone the most dramatic public reputation reversal in recent decades. Three generations of public health messaging that treated dietary fat as the primary cause of cardiovascular disease has given way to a more nuanced picture, partly through the work of researchers who challenged the prevailing view at significant career cost.


What is Fat?

Fats serve several essential functions:

  • Cell membrane structure (every cell in your body is bounded by a fat-based membrane)
  • Hormone production (steroid hormones, including testosterone, estrogen, and cortisol, are made from cholesterol)
  • Fat-soluble vitamins (A, D, E, and K all require dietary fat for absorption)
  • Energy storage (adipose tissue can store essentially unlimited energy reserves)
  • Insulation and protection of organs
  • Myelin synthesis (the fatty sheaths around nerves)
  • Brain structure (the brain is roughly 60% fat by dry weight)

Dietary fats break down into three main categories based on chemical structure:


Saturated fats
have no double bonds in their fatty acid chains and are typically solid at room temperature. Found in animal fats, coconut oil, and dairy fat. Once considered the primary dietary villain, current research presents a more complex picture.


Monounsaturated fats (MUFAs)
have one double bond. Found in olive oil, avocados, nuts, and some animal fats. Generally regarded as beneficial across most research traditions.


Polyunsaturated fats (PUFAs)
have multiple double bonds and are divided further into:

  • Omega-3 fatty acids: particularly EPA and DHA from marine sources, ALA from plants. Anti-inflammatory effects, beneficial for cardiovascular and cognitive function.
  • Omega-6 fatty acids: found in most vegetable oils, nuts, and seeds. Essential in moderate amounts but problematic in excess (covered below).


Trans fats
are unsaturated fats with hydrogen bonds in the trans configuration rather than the natural cis configuration. Almost entirely industrial in origin (partially hydrogenated vegetable oils). Substantial evidence for cardiovascular harm; largely banned from the US food supply since 2018 but still present in some processed foods globally.

 

The Saturated Fat Story

The original case against saturated fat traces to Ancel Keys and the Seven Countries Study from the 1960s, which found correlations between saturated fat intake and cardiovascular disease. Keys’ work shaped public health policy for the next half-century. The methodological critiques that emerged later (particularly Nina Teicholz’s The Big Fat Surprise, which traces how Keys’ methodology selectively excluded countries that didn’t fit the hypothesis) have shifted the conversation considerably.


The evidence:

  • Saturated fat consumption raises LDL cholesterol modestly in most people
  • LDL cholesterol is associated with cardiovascular disease, but the relationship is more complex than the “LDL = bad” simplification
  • Ronald Krauss’s lipid subfraction research showed that LDL particles vary in size and atherogenic potential – small dense LDL is more strongly associated with cardiovascular events than large fluffy LDL
  • Allan Sniderman has argued that apolipoprotein B (apoB) is a better cardiovascular risk marker than LDL cholesterol alone
  • Replacing saturated fat with refined carbohydrates worsens cardiovascular risk markers
  • Replacing saturated fat with whole-grain carbohydrates or unsaturated fats improves cardiovascular risk markers
  • The 2020 Bazinet review and several subsequent meta-analyses have failed to find strong evidence that saturated fat per se causes cardiovascular disease in the absence of other dietary factors

Saturated fat in the context of a whole-food diet is probably fine for most people; the apocalyptic framing of saturated fat from the 1980s and 90s was overcooked; chronic high intake of any single nutrient in isolation is rarely optimal. People with familial hypercholesterolemia or other genetic lipid disorders may need to be more cautious.


The Cholesterol Story

Dietary cholesterol (the cholesterol in food, primarily eggs and shellfish) affects blood cholesterol much less than the original framing suggested. The 2015 US Dietary Guidelines removed the longstanding 300mg daily cholesterol limit, acknowledging that for most people, dietary cholesterol intake doesn’t substantially affect blood cholesterol. This was a significant shift after decades of contrary advice.


What affects blood cholesterol significantly:

  • Saturated fat intake (modestly)
  • Refined carbohydrate intake (significantly raises triglycerides and small dense LDL)
  • Sugar intake (similar effects)
  • Genetic factors (familial hypercholesterolemia, APOE variants)
  • Inflammation status
  • Metabolic health overall


If you’re concerned about cholesterol, the leverage points are mostly upstream of dietary cholesterol: reducing refined carbohydrates and sugar, improving overall metabolic health, increasing potassium-rich foods, and getting adequate omega-3s. The classical advice to “avoid eggs” was based on a model of cholesterol biology that turned out to be wrong.


Digestion

Bile is a green juice produced by your liver and stored in your gall bladder, which is a small, thumb-sized pouch that sits between the liver and small intestine, connected to both with short ducts. When fats enter the small intestine from the stomach, the gall bladder squirts bile onto the mush of food. Bile acids (also called bile salts) act like detergents, breaking up the globs of fat and oil into tiny emulsion droplets. Once the fat is emulsified, enzymes called “lipases,” produced by the pancreas, are added to the mix and break these emulsion droplets down to an even smaller size, to microscopic droplets called micelles, just a hundredth the diameter of human hair. These micelles form, break apart, and form again like the bubbles in a fizzy drink. Each time they break apart, they release the individual fatty acids and glycerides (which are fatty acids attached to a glycerol molecule) they were holding, the basic building blocks of fats and oils.


Fatty acids and glycerides are absorbed into the intestinal wall and re-formed into triglycerides (three fatty acids attached like streamers to a glycerol molecule), the standard form of fats in the body.


The evolved solution to preventing lumpy blood (due to fat not mixing in water-based solutions) is to pack triglycerides into spherical containers called chylomicrons. This keeps the fats from clumping together, but results in a package too big to be absorbed through capillary walls and into the bloodstream, where they need to go for distribution throughout the body. The fat molecules, packed in chylomicrons, are dumped into the lymphatic vessels. Part surveillance system, part garbage collection, the lymphatic vessels have their own network throughout your body, picking up debris, bacteria, and other detritus and bringing it to the lymph nodes, spleen, and other immune system organs to be dealt with. It’s well-suited to pick up big particles like chylomicrons stuffed with fat. The lymphatic vessels also collect all the plasma that leaks out of your blood vessels and return it to your circulatory system, so it offers a port of entry into the bloodstream. Specialized lymph vessels called lacteals, embedded in the intestinal wall, pull chylomicrons into the lymph system and then dump them directly into the circulatory system, just upstream of your heart.


White, fat-filled chylomicrons are so big after a fatty meal that they can give the blood a creamy hue. Eventually, they are ripped apart and their contents pulled into waiting cells for storage or use. Lipoprotein lipase enzymes in the blood vessel walls first break the triglycerides into fatty acids and glycerol, which are pulled into waiting cells by aptly named fatty acid transporter molecules, before being reassembled into triglycerides. Most fat is stored in fat cells (adipocytes) and muscles, forming a reserve fuel tank. These stored triglycerides are the fat that we feel in our belly and thighs, or see marbled into a nice cut of steak.


Timing

Higher fat meat, fish, shellfish, and fermented vegetables would be more likely to be eaten during the winter (depending on the culture and geography of your ancestors), and a ketogenic diet loosely adhered to. Not necessarily for the supposed weight loss, but because agriculture is limited in colder climates, and food scarcity would result in fasting and preserved meat where possible. In the case of cultures that sailed large distances, they may have acquired a set of genes that enabled enhanced fat storage, allowing for greater survival by fasting and relying on fat stores when no food was available. 

If possible, try to limit your consumption of foods that are both high glycemic and high in fat during a single meal.

For example: Lean meat goes great with complex carbohydrates. As does fatty meat with green vegetables.

Fat-soluble vitamins are often found in nutrient-dense and colourful vegetables, so it is worthwhile consuming them with foods that are higher in saturated fat.    


Examples of Fat         

  • Liberal use of animal or animal-derived fats, including lard, tallow, egg yolks, butter, and cream
  • Traditional oils like extra-virgin olive oil and expeller-pressed sesame oil, and limited amounts of expeller-pressed flaxseed oil, as well as coconut oil, palm oil, and palm kernel oil. Aim for oils that have a high burn point for cooking
  • Cod liver oil, enough to provide 10,000 IU of vitamin A and 1,000 IU of vitamin D
  • Fish oil or krill oil, if a higher fish and shellfish intake is not feasible
  • Limit trans fats and vegetable oils as much as possible. Some people can be able to handle greater quantities of omega-6s than others (those with ancestral ties to heavy plant eaters), but it is more likely that we will currently eat too much omega-6s and not enough omega-3s


The Seed Oils Question

This is the macronutrient debate that’s currently hottest in popular discourse, and the honest position is more nuanced than either the maximum-concern or the dismissal positions suggest.


The case against industrial seed oils (soybean, corn, canola, sunflower, safflower, cottonseed):

  • They’re high in omega-6 linoleic acid, which competes with omega-3s for the same enzymatic pathways
  • The omega-6:omega-3 ratio in modern Western diets is often 15:1 or higher, compared to estimated ancestral ratios of 1:1 to 4:1
  • Industrial extraction processes use high heat, hexane solvents, and refining steps that can produce oxidized fats and trans fat byproducts
  • Repeatedly heated seed oils (deep fryer oils used over multiple cooking cycles) produce substantial oxidized lipid products with documented cardiovascular harm
  • Population-level consumption of seed oils tracks closely with rising rates of metabolic disease, though correlation isn’t causation


The case for moderation rather than maximum concern:

  • Linoleic acid in moderate amounts is essential and not directly harmful
  • Some long-term cohort studies show neutral or even beneficial outcomes for moderate seed oil consumption (often confounded by overall diet quality)
  • The “seed oils cause everything” framing common in some wellness circles outruns the actual research
  • Cold-pressed and unrefined versions of these oils have meaningfully different oxidation profiles than industrially processed versions


The reasonable synthesis: minimize industrial seed oils, particularly heavily processed and repeatedly heated versions; replace with traditional fats (olive oil, butter, ghee, avocado oil, coconut oil for high-heat cooking); aim for an omega-6:omega-3 ratio closer to 4:1 than to 15:1; recognize that fixing seed oil intake alone won’t fix a broader inadequate diet, and obsessing over occasional restaurant exposure is probably counterproductive.


A note on omega-3s. Most adults benefit from increased EPA/DHA intake, which is most reliably achieved through fatty fish (salmon, sardines, mackerel) two to three times weekly. ALA from plant sources (flaxseed, walnuts, chia) converts to EPA and DHA inefficiently. Typically, only 5-10% of ingested ALA gets converted in adults. Vegetarians and vegans typically benefit from algae-based DHA supplementation. Fish oil supplements work but oxidize quickly; storage in dark glass with refrigeration matters.


Water and Hydration

After all the macronutrient complexity, water is refreshingly simple. Your body is roughly 60% water by weight; you lose water continuously through respiration, perspiration, urination, and digestion; you need to replace what you lose. The official guidelines (1.5-2L daily for sedentary adults, more for active people or hot environments) are roughly correct as starting points.


What’s Going On With Water


Water serves essentially every physiological function:

  • Blood plasma (transport of nutrients, gases, hormones)
  • Cellular fluid (the medium for every metabolic reaction)
  • Lubrication of joints and mucous membranes
  • Temperature regulation through perspiration
  • Waste excretion through urine
  • Maintenance of blood pressure and circulatory volume


Hydration status affects cognitive function meaningfully. Even mild dehydration (2-3% of body weight) impairs attention, working memory, and mood. Athletes performing at higher dehydration levels show measurable performance decrements.


8-Glasses-A-Day?

The “8 glasses of water per day” rule has surprisingly weak research backing. The actual evidence base for any specific water intake target is limited; Heinz Valtin at Dartmouth published a comprehensive review in 2002 documenting that the 8-glasses claim has no clear scientific origin. The rough physiological reality is that most healthy adults regulate hydration well through thirst, supplemented by water in food (vegetables, fruits, soups) and other beverages.


That said, certain populations benefit from more deliberate hydration:

  • Older adults (whose thirst sensitivity declines with age)
  • People in hot climates or hot work environments
  • Athletes and physically active people
  • Pregnant or breastfeeding women
  • People recovering from illness with fluid losses


Electrolytes Matter

Pure water without adequate electrolytes can actually impair hydration in some contexts. Sodium, potassium, magnesium, and calcium are all required for proper fluid balance. The popular wellness framing that “we eat too much salt” obscures the fact that most active people, particularly in hot climates, may benefit from more sodium than the standard guidelines suggest. The guidelines were calibrated to populations with hypertension; healthy, active adults often need substantially more.


Practical hydration approach:

  • Drink to thirst as a baseline
  • Supplement with electrolytes during intense exercise, hot weather, or extended sweat exposure
  • Recognize that water from food (soups, fruits, vegetables) counts toward total intake
  • Consider sodium intake more carefully if you’re an active person eating a whole-food diet (you’re probably under-consuming sodium relative to your needs)
  • Reduce caffeine, alcohol, and high-sugar beverage intake (all have net dehydrating effects in various contexts)


Quality of Water

Drinking water quality varies significantly by source and infrastructure. 

  • Most municipal tap water in developed countries is reasonably safe but contains chlorination byproducts, fluoride, and trace pharmaceutical residues
  • Filtration (activated carbon, reverse osmosis, ion exchange) addresses most concerns at modest cost
  • Well water and spring water vary by source. Testing is essential before relying on these
  • Bottled water in plastic exposes you to phthalates, BPA, and microplastics, particularly when stored warm
  • Glass-bottled spring water is the cleanest commercial option, but expensive
  • Heavy chlorination, fluoridation, and infrastructure leaching (lead pipes in older buildings) are real concerns, warranting investigation in specific contexts


For most adults, filtered tap water from a reasonable municipal source through a basic activated carbon or reverse osmosis filter is fine. Obsessive water optimization beyond this is mostly diminishing returns.


Sports and Exercise Hydration

For workouts under an hour at moderate intensity, water alone is usually sufficient. For longer or more intense sessions, particularly in heat:

  • 0.1-0.2L every 15-20 minutes during the workout
  • Sodium replacement (0.5-1% concentration) for sessions over an hour or in hot conditions
  • Carbohydrate intake (6-8% concentration) for sessions over 90 minutes when not keto-adapted
  • Coconut water with added salt is a reasonable natural sports drink alternative
  • Avoid commercial sports drinks with high-fructose corn syrup and artificial dyes

Resources

  • Ioannidis, J.P. (2018). The challenge of reforming nutritional epidemiologic research. JAMA, 320(10), 969–970. See also Ioannidis, J.P. (2013). Implausible results in human nutrition research. BMJ, 347, f6698.
  • Archer, E., Hand, G.A., & Blair, S.N. (2013). Validity of U.S. nutritional surveillance: National Health and Nutrition Examination Survey caloric energy intake data, 1971–2010. PLoS One, 8(10), e76632. Archer’s broader critique of self-report nutrition data has been controversial but methodologically substantive.
  • Hall, K.D., Ayuketah, A., Brychta, R., et al. (2019). Ultra-processed diets cause excess calorie intake and weight gain: an inpatient randomized controlled trial of ad libitum food intake. Cell Metabolism, 30(1), 67–77. The first true RCT comparing ultra-processed and unprocessed diets in a metabolic ward setting.
  • Sun, L., Sadighi Akha, A.A., Miller, R.A., & Harper, J.M. (2009). Life-span extension in mice by preweaning food restriction and by methionine restriction in middle age. Journals of Gerontology Series A, 64(7), 711–722. Multiple subsequent papers have explored methionine restriction and lifespan in animal models.
  • Masterjohn, C. (2017). Balancing methionine and glycine in foods. Available through Chris Masterjohn’s database resources at chrismasterjohnphd.com. Masterjohn’s database resources represent practitioner-level synthesis grounded in primary biochemistry.
  • Phillips, S.M. (2014). A brief review of higher dietary protein diets in weight loss: a focus on athletes. Sports Medicine, 44 Suppl 2, 149–153. Phillips’ broader research output on muscle protein synthesis is foundational.
  • Witard, O.C., Jackman, S.R., Breen, L., Smith, K., Selby, A., & Tipton, K.D. (2014). Myofibrillar muscle protein synthesis rates subsequent to a meal in response to increasing doses of whey protein at rest and after resistance exercise. American Journal of Clinical Nutrition, 99(1), 86–95. Van Loon’s broader work on protein and muscle metabolism is widely cited.
  • Schoenfeld, B.J., Aragon, A.A., & Krieger, J.W. (2013). The effect of protein timing on muscle strength and hypertrophy: a meta-analysis. Journal of the International Society of Sports Nutrition, 10, 53.
  • Truswell, A.S. (2005). The A2 milk case: a critical review. European Journal of Clinical Nutrition, 59(5), 623–631. The A1/A2 debate continues; Truswell’s review remains the most cited critical synthesis.
  • Zeevi, D., Korem, T., Zmora, N., et al. (2015). Personalized nutrition by prediction of glycemic responses. Cell, 163(5), 1079–1094.
  • Berry, S.E., Valdes, A.M., Drew, D.A., et al. (2020). Human postprandial responses to food and potential for precision nutrition. Nature Medicine, 26(6), 964–973. The PREDICT studies and ZOE project work from Tim Spector’s group.
  • Ludwig, D.S., Aronne, L.J., Astrup, A., et al. (2021). The carbohydrate-insulin model: a physiological perspective on the obesity pandemic. American Journal of Clinical Nutrition, 114(6), 1873–1885.
  • Hall, K.D., Bemis, T., Brychta, R., et al. (2015). Calorie for calorie, dietary fat restriction results in more body fat loss than carbohydrate restriction in people with obesity. Cell Metabolism, 22(3), 427–436.
  • Gardner, C.D., Trepanowski, J.F., Del Gobbo, L.C., et al. (2018). Effect of low-fat vs low-carbohydrate diet on 12-month weight loss in overweight adults and the association with genotype pattern or insulin secretion: the DIETFITS randomized clinical trial. JAMA, 319(7), 667–679.
  • Kearns, C.E., Schmidt, L.A., & Glantz, S.A. (2016). Sugar industry and coronary heart disease research: a historical analysis of internal industry documents. JAMA Internal Medicine, 176(11), 1680–1685.
  • O’Connor, A. (2015). Coca-Cola funds scientists who shift blame for obesity away from bad diets. The New York Times, August 9, 2015. Marion Nestle’s Food Politics and Soda Politics provide comprehensive treatment of these patterns.
  • Lustig, R.H. (2009). Sugar: The Bitter Truth. University of California Television lecture; broader research published in multiple peer-reviewed papers including Lustig, R.H., Schmidt, L.A., & Brindis, C.D. (2012). The toxic truth about sugar. Nature, 482(7383), 27–29.
  • Sonnenburg, E.D., & Sonnenburg, J.L. (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism, 20(5), 779–786. The Sonnenburgs’ broader research output is foundational.
  • Teicholz, N. (2014). The Big Fat Surprise: Why Butter, Meat and Cheese Belong in a Healthy Diet. Simon & Schuster. Teicholz is an investigative journalist; her treatment of the saturated fat history is well-researched if necessarily polemical.
  • Krauss, R.M. (2010). Lipoprotein subfractions and cardiovascular disease risk. Current Opinion in Lipidology, 21(4), 305–311. Krauss’ broader research output on lipid subfractions is foundational.
  • Valtin, H. (2002). “Drink at least eight glasses of water a day.” Really? Is there scientific evidence for “8 × 8”? American Journal of Physiology – Regulatory, Integrative and Comparative Physiology, 283(5), R993–R1004.