Deep Nutrition by Catherine Shanahan
Name: Deep Nutrition
Author(s): Shanahan, Catherine
Published: 2017
The Core Problem: In a world dominated by a modern diet that causes chronic disease, how can we use food as a strategic tool to communicate directly with our genes and build a stronger, healthier, and more resilient body?
The Bottom Line
- What it is: Deep Nutrition is a guide that bridges ancestral wisdom with modern science to explain how food acts as information that directs our genetic expression.
- Why it matters: It matters because the modern diet, high in sugar and processed vegetable oils, sends the wrong signals to our genes, leading to chronic inflammation and disease.
- What you’ll get: From this Note, you will get a framework for understanding epigenetics, a clear indictment of the “two toxic substances” in the modern diet, and a practical blueprint—The Four Pillars of the Human Diet—for eating in a way that optimises your health and genetic potential.
Time Commitment:
Disclaimer: This content is intended for educational, commentary, and review purposes only. All opinions expressed are my own and are not affiliated with the author or publisher of the book. Any copyrighted material, including quoted excerpts, is used under the principles of fair use for criticism and analysis. For further information or to support the author, please refer to the links mentioned at the beginning of this page.
The Strategist’s Briefing
This book promises: “By eating the foods described later in this book, you will be talking directly to your genes. Your foods will tell your epigenome to make your body stronger, more energized, healthier, and more beautiful. And your epigenome will listen.“.
The big idea is that our health, physical and mental, is much more in our control than we think.
And it’s not that we need to rely on expensive drugs to make it so, instead it’s just about the epigenetic signalling we do via the environment we place our bodies in. “Environment” being an umbrella term for the food we eat, the exercise we do, the habits/routines we follow, the rest we get, the air we breathe, and the social relations we maintain.
The book is divided into three parts: (1) The Wisdom of Tradition, (2) The Dangers of the Modern Diet and (3) Living the Deep Nutrition Way. It is part three that we are most interested in because that contains the actionable steps one can take to achieve what is highlighted above. The healthy eating habits in the book are covered under the umbrella of the “Human Diet”.
Core Frameworks Deconstructed
Citation: All text highlighted in yellow in this section is cited from – Shanahan, Catherine. Deep Nutrition: Why Your Genes Need Traditional Food. Kindle Edition.
Your gene expression matter a lot for your health
The effect that your environment has on your gene expression is called epigenetics.
Genes are what tell your body how to operate, they are basically code/instructions, if a gene gets turned “on” or “off” at the wrong time then you’ll notice it in the form of a health concern.
These can be benign things such as getting a mild allergy during spring, to life threatening such as cancer.
“On” means the body takes note of that instruction and does what it says.
“Off” means it ignores the instruction.
Genes get turned “on” and “off” all the time inside your body, and the things that allow this are called histones, which are proteins around which DNA can wind for compaction and gene regulation.
In simple terms, as you can see in the image below, histones can allow for genes to be accessible (switched “on”, instructions read and executed) or not.
The way histones know which genes are to be made accessible are through things called epigenetic factors/tags, basically think of them as chemical instructions that tell a histone to unwrap when certain conditions are met.
This is posited by the author as the “genetic brain“, if right tags are present in the right configuration then the body will “remember” to do things (like build stronger bones in response to tags that activate with presence of Vitamin D and Calcium) or, in their absence, “forget” to do things.
How does this “genetic brain” remember and forget; through the signals that you give it through your environment and diet.
If there is an environment of optimal abundance then it will remember to do the right things, else it will forget.
Note, there is also a more permanent form of remembering and forgetting, a genetic mutation, that changes the literal instructions in the DNA (and not whether those instructions are being read or ignored).
Why did we evolve like this? According to one doctor this ability provides a “rapid mechanism by which [an organism] can respond to the environment without having to change its hardware” – Makes sense to me, yeah.
Concept 1: Food as Information
Principle: Your diet is not just fuel; it is information that communicates directly with your genes. The foods you eat provide chemical signals (epigenetic tags) that instruct which of your genes to turn “on” or “off”. This process of gene expression, far more than your static DNA code, determines your day-to-day health, allowing your body to adapt to its environment without changing its fundamental hardware.
Application: Histones are proteins that DNA wraps around for regulation. Epigenetic tags from your diet and environment tell these histones when to unwrap DNA (turning a gene “on”) or keep it tightly wound (“off”). This “genetic brain” remembers what to do based on the signals it receives; for example, the presence of Vitamin D and Calcium signals it to build stronger bones.
Strategist’s Note: This framework shifts the perspective on health from one of genetic determinism to one of profound personal agency. As the author notes, our ancestors understood this intuitively, designing their lives around customs that ensured superior health. Your family’s physiologic destiny is largely under your control.
Our ancestors were wise
Far from being uneducated, our ancestors knew pretty well about optimal nutrition and designed their lives around customs and techniques (often kept secret, passed within generations) that ensured superior health well into old age. They may not have been sophisticated (compared to today) about acute injury or insult to the body. But when it came to the long game, from pre-birth to birth to infancy to childhood to adulthood to old age, ensuring that healthy people stayed healthy, they were mostly knew what they were doing.
Beauty is not just skin deep
When someone is healthy from the inside, their DNA makes beautiful faces and bodies. The author talks about “Marquardt face mask” or “repose frontal mask”, a drawing which is said to represent the proportions of an ideal human face and which makes use of the golden ratio. And we have evolutionarily used symmetry, proportion, evenness and texture as a subconscious shorthand to figure out who is worth mating with i.e. healthy enough to give birth to/care for offspring.
Our diet today is not great; cut out the sugar and vegetable oil
The S.A.D. has been widely criticised for its “meat-sweet” characteristics: high intakes of processed/pre-packaged foods, red meat and sugary snacks.
Excess of anything is bad, but excess sugar is especially bad.
Vegetable oils, the fat base used widely for cooking, are also bad because they contain polyunsaturated fatty acids (PUFAs) that are particularly prone to oxidative damage (leads to creation of AGEs), especially when exposed to heat (and surprise surprise, it takes comparatively more heat to extract vegetable oils).
Further, the sources of our foods are no longer local (or organic) and instead we consume “foods made in distant factories“. Even if we consume raw, unprocessed or minimally processed food, it is widely known that modern farming practices have led to nutrition erosion from the soil.
Plus, our macros breakdown today is wildly different from what our ancestors were used to, which means that our bodies are designed for something else than what we give it.
All in all, what we consume today in the name of food is not helping us live to our fullest potential.
Concept 2: The Two Toxins
Principle: The Standard American Diet (“SAD”) is fundamentally at odds with our genetic programming, primarily due to the overconsumption of two key substances: excess sugar (and cheap carbohydrates) and industrial vegetable oils.
Application:
- Sugar & Carbs: As far as your body is concerned, cheap carbohydrates like bread, pasta, and rice are little more than “containers for sugar”. Whether you eat sugar or starch, your body ultimately absorbs sugar, which disrupts metabolism and promotes inflammation.
- Vegetable Oils: These oils are high in unstable polyunsaturated fatty acids (PUFAs) that oxidize easily when heated, creating harmful free radicals and Advanced Glycation End-products (AGEs). This is contrasted with stable, traditional fats like butter and lard that can withstand heat without degrading.
Strategist’s Note: These two ingredients act as “chemical static,” blocking the clear signals your body needs to function correctly. Removing them from your diet is the most critical defensive action you can take to reclaim your health.
Use your diet as a strategic tool to enhance your life
And the way you do it is by basing what you eat on four pillars: (1) meat cooked on the bone, (2) organs and offal, (3) fresh (raw) plant and animal products, (4) fermented and sprouted foods.
Meat cooked on the bone
“When cooking meat, the more everything stays together—fat, bone, marrow, skin, and other connective tissue—the better.”.
Do not overcook your meat: Overcooking can lead to harmful chemicals building up in the meat. There should at least be a tricks of juice that runs down when you slice the meat.
Use the fat while cooking: Your cuts of meat should have their lean muscle/protein covered under a layer of fat that will protect it during cooking.
Make bone stock: Not only is it a great base for soups, gravies and stews, it is very beneficial for bone and joint health
Cook it slowly: And with moisture (by Making soup, stewing, keeping a top on to trap the steam, basting often when cooking in the oven) so that hydrolytic cleavage can happen to make the meat taste good and easier to digest while preventing protein tangles present in overcooked meat. Water also releases glycosaminoglycans that help in joint strengthening.
Organs and offal
They might look gross and eating them may not be for everyone, but offal meats like liver, brains, tongue, heart, kidneys, eyes and such provide a variety of nutrients that we lack today in our modern diets. Indeed it is true that many of the so called “backward” tribes all over the world regularly consume offal.
Getting offal should be easy on the wallet since these are otherwise discarded because nobody likes to eat them, but getting to the place where you can get them will be the challenge.
You will need to find a reliable and quality butcher for the best quality.
Also, making offal taste good is a challenge. The author includes a list of recipes at the end of the book.
Eat fresh
Yeah this is a no-brainer. Try to get fresh greens, fresh milk and fresh meat from quality sources.
The author presents data on how raw milk (obtained from a well managed dairy farm) is better than pasteurised milk. Pasteurisation is required especially in farms where living conditions for cows are such that can give rise to diseases that can get transmitted through their milk. Pasteurisation kills pathogens in milk, but also “fundamentally alters this micro-architecture and diminishes nutritive value significantly.“.
Fermented and sprouted foods
Fermentation sees the yeast or bacteria chomp on the simple sugars in the food and convert them into nutrients for their own growth (which we then eat). While during sprouting the new seedling converts its stored starch into more important things it will need during its growth (which we then eat). So, basically, when we eat fermented or sprouted foods, we take the things that someone else makes for their own use and eat them. You can sprout any kind of seed you want.
Concept 3: The Four Pillars of Health
Principle: The optimal human diet is based on four foundational pillars derived from ancestral eating patterns, which provide the necessary building blocks and information for genetic health.
Application:
- Meat on the Bone: Cooking meat slowly and with moisture, while keeping the bone, fat, and connective tissues intact, releases beneficial compounds like glycosaminoglycans for joint health. Making bone stock is highly recommended.
- Organs and Offal: Nutrient-dense organ meats like liver, heart, and kidneys provide a variety of essential nutrients that are lacking in modern diets focused only on muscle meat.
- Fresh (Raw) Products: Prioritise fresh greens, meat, and milk from quality, local sources. Raw milk, from well-managed farms, has a superior nutritive value that is diminished by pasteurization.
- Fermented and Sprouted Foods: Fermentation (e.g., yogurt, miso, real sourdough) and sprouting (e.g., sprouted grain bread) enhance nutrient bioavailability and can neutralize harmful compounds found in seeds and legumes.
Strategist’s Note: This is not a restrictive diet but a strategic framework for food selection. The focus is on nutrient density, bioavailability, and traditional preparation methods that our genes are adapted to recognize and use effectively
Send the right signal to your body
Indeed, the human body is a process that responds to the environment it finds itself in; so what we breathe in, or eat, or put on our skin, or hear, or see will have an impact on the body. In so far nutrition is concerned the author advises us to send the right signal by:
Consuming sources of Omega-3 fat: Fat in itself is not bad as I have written before here, but the fat composition of the modern diet is different from what our bodies grew to operate optimally on. Far more Omega-6 and too little Omega-3 among other things.
Building structural strength by consuming collagen: “One of the best ways to help collagen heal is, not surprisingly, to eat some. Eating collagen-rich organs (like tripe and tendon) or using bone broths in soups, stews, and sauces floods your bloodstream with glycosaminoglycans …”.
Not eating pro-inflammatory foods: Acute inflammation that we get when hurt is good, since it enables the body to heal itself. But chronic inflammation that we subject our bodies to by eating pro-inflammatory foods (like these) you “block chemical signals required for normal, healthy cellular growth.“.
Exercising: Especially weight training that will tell your body to build muscle instead of fat. Also, muscles act as sinks that can soak up excellent calories that would otherwise have become body fat.
Groups of nutrients that can help prevent against oxidative stress: Omega-3, vitamin-E, cysteine, antioxidants.
Majority of the detail on the Human Diet in the last two chapters (13, 14) – So these are the most important from a tactical standpoint.
- Macros as per the Human Diet should be as follows, compared with the average American diet this is a drastic shift.
- Plan your weekly meals in advance (like, every Sunday for the week ahead) and then go shopping mindfully, else you will buy whatever looks enticing at the moment.
- Remove all the junk from your kitchen. Indeed it is harder to resist temptation to drink a soda kept in the fridge than to not have the option in the first place.
- Rules for shopping for food:
- Natural: If something couldn’t have existed 200 years ago, skip it.
- Variable: If all units (chickens, eggs, tomatoes, etc.) are identical in size and shape, that’s a bad sign.
- Flavourful: Intense flavour indicates nutrient density, but not when it comes from ingredients like sugar, MSG, or hydrolysed protein.
- Seasonal: Avoid foods that are frozen or canned.
- Buy local: Packages should identify the source of the item.
- Suggested basic supplementation: Standard multivitamin, Vitamin-D, Magnesium Oxide, Zinc Gluconate. Additional supplementation recommended for individuals that do not eat meat, dairy, fish.
Link to the author’s website for recipes and other tips
High-Signal Quotations
Citation: All text in the following section is cited from – Shanahan, Catherine. Deep Nutrition: Why Your Genes Need Traditional Food. Kindle Edition.
- Two toxic substances present in our food that are incompatible with normal genetic function: sugars and vegetable oils.
- But you do have control over what may be the most powerful class of gene-regulating factors: food.
- Medical school doesn’t teach doctors to address the root of the problem. It teaches doctors to treat the problem. It’s a practical science with practical aims.
- Medicine is different from other sciences because, more than being a science, it is first and foremost a business.
- Every bite you eat changes your genes a little bit.
- Biologists had long assumed that letter substitution was the only way to generate such physiologic change. Epigenetics has taught us that more often, the reason different individuals develop different physiology stems not from permanent letter substitutions but from temporary markers—or epigenetic tags … epigenetic tagging occurs in response to chemicals that form as a result of nearly everything we eat, drink, breathe, think, and do.
- It seems our genes are always listening, always on the ready to respond and change.
- Failure to attend to the proper care and feeding of our bodies doesn’t just affect us, it affects our genes—and that means it may affect our offspring.
- The phenomenon wherein specific traits are toggled up and down by variations in gene expression has recently been recognized as a result of the built-in architecture of DNA and dubbed “active adaptive evolution.”
- And if women wrote more of our history books, schoolchildren might learn something with more practical application than lists of battles won by various kings.
- As unfair as it seems, less attractive people have more health problems.
- Sugar and vegetable oils act like chemical static that blocks the signals our bodies need to run our metabolisms smoothly.
- Who knows what else is in that pill? The entire supplement industry is essentially unregulated.
- No longer insisting on fresh food from small farmers right in our neighborhoods, we’d been convinced that products made in distant factories were safer, healthier, and better.
- Naturally occurring fatty acids contain bonds in a cis configuration. In this configuration, fatty acids are highly flexible, which prevents crystallization (solidification), and so the molecules behave as liquids. Partial hydrogenation does two things: it irons some cis-configuration bonds completely flat (by saturating the bond with hydrogen) and switches others around to trans. Converting a cis fatty acid to saturated or trans makes it a stiffer and more stackable molecule.
- Unlike sugar—which offers no nutrition—a meal complete with animal fat actually helps us absorb and taste other nutrients.
- For the purposes of cooking, we want to pick the kinds of fats that can take heat. On that count, saturated fats (present in butter, coconut oil, lard, and traditional fats) win hands down. Why? Because they can resist a kind of heat-related damage called oxidation.
- Olive oil … have mostly saturated and monounsaturated fatty acids, which are not so fragile. They are also easily extracted at low temperatures. Vegetable oils come out less readily, and are more prone to side reactions that polymerize and mutate the fat molecules.
- Frying in vegetable oils doesn’t so much cook your foods as blast them with free radicals—fusing molecules together to make the material stiff and inflexible.
- Traditional cooking methods often make nutrients more bioavailable and are, for that reason, anti-inflammatory. Cooking with vegetable oil, on the other hand, destroys complex nutrients.
- Your cholesterol profile contains four different numbers: total cholesterol, LDL, HDL, and a triglyceride value. … HDL should be over 45 in men and over 50 in women. … LDL less than three times the HDL value … triglyceride levels less than 150 … if triglycerides are above 150 and/ or the HDL level is below 40 … very likely that your lipoprotein cycle is disrupted.
- Remember, I said manufacturers play the sugar shell game. If they can’t sell you sugar, they’ll happily sell you the next best thing, dirt-cheap carbs. Pasta lovers aren’t going to want to hear this but, as far as your body is concerned, carbohydrates are sugar.
- This means that if you’ve ever sat down and finished off a box of crackers you’ve essentially eaten a box of sugar. The take-home point is, whether you eat sugar or starch, your body winds up absorbing sugar.
- Foods like bread, pasta, potatoes, and rice are little more than containers for sugar.
- Unfortunately, as the mega-industries grow stronger, they are changing the rules to make it easier to put the word organic on the label. The best bet is to get friendly with your local farmers.
- Getting adequate protein is more challenging on a plant-based diet since even the most protein-rich plants also contain a good deal of blood-sugar–elevating carbohydrate, whereas most high-protein animal foods are zero carb.
- Soybeans contain chemicals called goitrogens and phytoestrogens, which disrupt thyroid and sex hormone function. The Chinese and Japanese who traditionally ate soy would soak, rinse, and then ferment the beans for extended periods, neutralizing the harmful compounds and using the fat- and protein-rich beans as a substrate for microbial action. Traditional tofu, natto, miso, and other cultured soy products are incredibly nutritious. Commercially made soymilk, tofu, and soy-based infant formulas, on the other hand, are not.
- Today we have simpler options for preserving our food, including canning, refrigeration, freezing, pickling (steeping in vinegar), and drying. But in terms of nutrient conservation, each pales in comparison to fermentation,
- Whether you suffer from wheat allergies or you just want to buy the healthiest bread available, bread made from sprouted wheat (or other grains) is your best bet.
- If you can’t find sprouted grain breads, the next best thing is sourdough.
- What the nutraceutical industry doesn’t want you to know is that there’s nothing unique about any of their “unique” formulations; all fresh fruits and vegetables contain antioxidants, flavinoids, and other categories of chemicals used as selling points on nutraceutical packages.
- Remember, cooking burns up antioxidants and damages many vitamins. So the more you eat cooked foods, the more you need to balance your diet by eating fresh, uncooked, pungent-tasting herbs and vegetables.
- While gaining access to many of the nutrients in plants often requires (judicious) use of heat, many animal products are so abundant in nutrients that adding thermal energy risks fusing them together.
- Milk may be the single most historically important food to human health.
- Our bodies continue to be a work in progress throughout our lives, every cell in our body guided by what our diet is telling us about the outside environment.
- If you can’t find a good source of fresh, unprocessed milk, what can you do? Get the next best thing: yogurt made from organic, whole milk.
- Far more realistic and useful way to think about food is as information, the chemical language with which nature speaks directly to our bodies.
- Our cells are extremely sensitive to the specific nature of the chemical messages we send them every time we eat. By altering the blends of nutrients (or toxins) in our food, we can actually control whether our cells function normally, or convert to fat, or turn cancerous … key to being healthy, then, is eating foods that send the right messages.
- To Avoid Inflammation, Keep Total Daily Sugar Intake Under 100 Grams.
- If you’re overweight, your body is almost certainly suffering under a constant state of low-level inflammation.
- Calorie restriction without exercise tells your body to convert stem cells into fat cells as soon as you start eating again.
- The more aware we are of the act of exercising, the more we engage our muscles.
- Use your body consciously. The best exercises involve the entire body.
- Because when it comes to staying young and feeling young, collagen is a big deal. If your parents aged well or lived a long time, you can be sure they had good, strong collagen.
- If I can’t put it on my skin, I won’t put it in my mouth.
- Health is beautiful. Food informs physiology. Source matters. Your family’s physiologic destiny is largely under your control.
- Protein is the “Goldilocks” macronutrient. Unlike carbohydrates, which have no minimum requirement, and unlike fat, which has no maximum (as long as you aren’t generally overeating), when it comes to protein, you need to get enough and not too much.
The Takeaways
This could have been a much shorter book if the author did not get into the science of it, that makes a book a chore to read sometimes.
There are many topics, studies and compounds mentioned in the book and I have only covered the main ones.
If you are interested in the science of how our bodies nourish us then this book is a high level primer on that, with a lot of alleyways that you can go down if you’re interested in learning more about something.
For me though, the last two chapters is where the action is at.
The first one is about the habits, routines, ingredients and recipes that the Human Diet entails. And the next one is a long list of FAQs.
They are dense with practical information, and should be referenced time and again as you go on to live healthier.
Indeed they are a complete guidebook and can easily be a standalone book on their own.
Following them one can get a long way along the healthy way of living before they need to go elsewhere for more info.
Your 3-Point Action Plan
- Eliminate the Two Toxins. Immediately begin purging your kitchen of industrial vegetable oils (e.g., canola, soy, corn) and added sugars/refined carbohydrates (e.g., bread, pasta, crackers). This is the most impactful defensive step you can take.
- Adopt the Four Pillars. Reorient your grocery shopping around the four pillars: incorporate bone broth and slow-cooked meats ; seek out high-quality organ meats like liver ; prioritize fresh/raw produce and dairy from local sources ; and add fermented and sprouted foods to your diet.
- Think Like a Genetic Communicator. Treat every meal as an opportunity to send positive signals to your genes. Prioritise anti-inflammatory Omega-3 fats, eat collagen-rich foods for structural strength, and pair your nutritional strategy with weight-bearing exercise to tell your body to build muscle, not fat.
The principles of Deep Nutrition provide the ‘what’ and ‘why’ of healthy eating. To understand how these dietary choices impact the aging process at a cellular level, see the Field Note on Lifespan by David A. Sinclair.
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Aviral Prakash
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