GAPS, What We Eat And Why Part1 Being Appropriate For The Planet

This blog is for educational purposes only, and should not be construed as medical advice.

This post is important and should be shared with anyone seemingly confused about dietary choices. For accuracy, I've processed it through both Gemini and Claude AI, and I'm quite satisfied with the outcome. I appreciate Gemini for providing the headings and sub-headings that enhance its readability. A reminder that this post should be considered in conjunction with previous posts, which should be read chronologically.

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Nature’s Laws and the Human Blueprint: Why Anatomy and Physiology Dictate Our Diet

I have come to believe that Dr. Natasha Campbell-McBride has a profound understanding of Sir Francis Bacon's tenet: "Nature to be commanded, must be obeyed..." She is a medical doctor trained in both neurology and neurosurgery. Her medical education includes what we would today call microbiome studies. Upon discovering the power and impact of food on the human body, she continued her education, earning a Master of Science degree in Human Nutrition. In her nutrition practice, she learned clinically through observation the best methods for healing, extrapolating from what worked and what did not work for her patients. She integrated and synthesized that knowledge into the GAPS concept of which I now blog.

One of Dr. Natasha Campbell-McBride's most nuanced observations is that living on this planet requires a lifestyle and dietary strategy appropriate to our governing evolutionary parameters. To illustrate this, she points to space travel, noting that we send astronauts into the cosmos with engineered spacesuits, not jeans and T-shirts, because they must be appropriately equipped for outer space conditions. She similarly cites a diesel vehicle, which functions only with diesel fuel, as any other fuel source will be an inappropriate substitute. Human physiology possesses a specific evolutionary identity with distinct biological requirements which must be efficiently fulfilled if sound health throughout one's lifetime is the long-term goal.

This biological identity is rooted directly in the solar lifecycle of our planet, of which humans are a part. The sun initiates this cycle by inundating the Earth with light, fueling plants to photosynthesize raw sugars. From there, energy moves in a strict chain: herbivores unlock the vegetation, and predators hunt those herbivores to capture concentrated nutrients. As omnivores, humans stand at a unique convergence point, capable of processing both plant and animal foods. However, to maximize health, our dietary choices should align with the specific efficiency parameters of our evolutionary biology. By respecting these physiological constraints with appropriate food choices, we fulfill the exact evolutionary requirements that Dr. Campbell-McBride emphasizes in the GAPS Nutritional Protocol, ensuring our food choices work with our body's essential design.

The Human Strategy: Contrasting Our Anatomy and Physiology with the Animal Kingdom

To truly understand our place in this cycle, we must contrast our digestive anatomy and physiology with that of specialized herbivorous animals. This contrast gives us our first clues as to what constitutes efficient nutrition for the human body. I will look at two types of herbivores: ruminant animals like cows as well as hind-gut animals like horses. You will see that despite having vastly different digestive anatomy, both herbivorous groups handle their plant-based diets by aligning with three fundamental rules of mammalian biology. First, microbes break down plant fiber, because only microbes possess the tools to dismantle raw cell walls. Second, stomach acid kills microbes, creating an environment entirely hostile to those same essential organisms. Third, surface area determines absorption, meaning a mammal's primary site of nutrient absorption always matches the exact location where its food is successfully unlocked.

The Ruminant Strategy: Internal Cultivation

Ruminant animals, like the cow, utilize a highly specialized digestive tract comprising a four-chambered stomach designed around these laws. The first two massive chambers, the rumen and reticulum, host trillions of microbes in a continuous bidirectional flow of fluid and plant matter. They use this two-way sorting system to manage plant matter, pushing large fibers back up to the mouth to be re-chewed as cud. In these first two chambers, microbes break down the cellulose of the plant in an entirely oxygen-free environment in a process called fermentation. As the multiplying microbes unlock the fiber from the plant matter, their waste products become nutrition for the cow in the form of volatile fatty acids (saturated fats). The cow's anatomy perfectly respects the rule that surface area determines absorption, meaning the bulk of this fat-derived energy absorbs directly through the textured, towel-like lining of the rumen wall to provide roughly 75% of its daily fuel.

Through peristalsis, food is moved on to the third chamber, the omasum, where fermentation slows down and further water and water-soluble nutrients are absorbed. The fourth chamber, the abomasum, closely mirrors the human stomach; it is highly acidic and destroys most incoming microbes. Here, the trillions of microbes swept along in the digestive process are enzymatically digested and subsequently pass into the small intestine. This intestine serves as a secondary, highly specialized absorptive area dedicated strictly to capturing those broken-down microbes as the cow's primary source of high-quality protein. Thus, the cow masterfully satisfies all three biological rules: cultivating the microbes required to unlock tough plant fiber, deploying intense stomach acid to kill and digest them, and matching its absorptive surface area perfectly across both the stomach and small intestine to where those nutrients are unlocked.

The Hindgut Strategy: Separated Zones

The horse's digestive tract, though seemingly similar to the human digestive tract, operates under completely separate evolutionary parameters. While it starts with a simple, single-chambered stomach, the internal machinery is radically different. Its stomach is split into two distinct halves by a physical border. The upper part is completely non-glandular, meaning this tissue contains no chemical pumps or glands to produce digestive juices. This creates a warm, neutral holding zone where microbes can safely live and immediately begin fermenting easy plant sugars from the moment the food is swallowed. This quick fermentation accounts for only 10% to 15% of the horse's total digestion before those unlocked nutrients move to the small intestines to be immediately absorbed into the bloodstream.

The remaining food moves down into the bottom half of the stomach where it hits a dense pool of intense digestive acid. This acid serves as a strict chemical checkpoint, instantly killing all incoming microbes while simultaneously shutting down the early fermentation. Because this simple stomach cannot dismantle tough plant cell walls, the remaining 85% of fibrous food passes through the small intestine virtually untouched. The plant material reaches the massive hindgut, comprising the cecum and large colon, which serves as the horse's true functional fermentation chamber where it hosts its massive reservoir of trillions of microbes. In this entirely oxygen-free environment, the microbes ferment plant cellulose, producing volatile fatty acids. Because this fermentation happens at the tail end of the system, it is the horse’s large intestines which serve as its primary absorptive surface area to match that late unlocking zone. Thus, the horse satisfies all three rules by entirely segregating its zones: deploying a massive posterior chamber to host the vital microbes needed to unlock tough fiber, keeping its harsh stomach acid isolated to an early region to fulfill its protective role, and following the rule that surface area determines absorption by capturing that late energy strictly within the highly vascularized walls of the large intestine.

The Human Strategy: The Acid Refinery

In contrast to these complex herbivorous systems, the human digestive tract operates on a physiological structure optimized for nutrient-dense, easily accessible foods. Rather than hosting massive internal fermentation chambers to process raw plant matter, our upper anatomy is structured to efficiently break down foods like meat, fish, eggs, and dairy (from the GAPS perspective, initially fermented dairy, later raw dairy). Our digestive process begins in a uniform stomach characterized by an intensely acidic environment. In a healthy human, this harsh acid barrier ensures the stomach destroys the vast majority of incoming microorganisms, maintaining a stark contrast to the teeming microbial pools found in the front of a herbivore's stomach.

Because humans concentrate on easily accessible foods that can be broken down by our own chemical enzymes, we do not require the massive foregut or hindgut fermentation structures found in herbivorous animals. Consequently, our nutrient absorbing surface area is positioned up front to match where our food is unlocked: our primary absorptive powerhouse is concentrated almost exclusively within the small intestine, which makes up over 56% of total human gut volume. This structure features massive, surface-expanding folds, villi, and microvilli designed for the rapid, highly efficient uptake of fully digested fats and proteins directly into the bloodstream early in the digestive sequence.

The Human Strategy: Plant Versus Animal Protein Absorption

The human body does not treat all food equally; it grades and processes food based on how easily it can be broken down. To see how this works, we can look at the Digestible Indispensable Amino Acid Score (DIAAS) used by the UN Food and Agriculture Organization. This score simply measures how much of a protein's amino acids are actually absorbed by the human small intestine.

When we view food choices through this biochemical lens, the data matches our specialized omnivorous design:

• Animal Proteins (High Bioavailability): Animal proteins regularly achieve maximum efficiency ratings at the absolute top of the DIAAS scale. Their amino acid structures match human tissue requirements almost perfectly. Because they contain zero fiber, they break down easily, allowing the small intestine to absorb 90% to 95% of the protein consumed early in the digestive sequence.

  
  

• Plant Proteins (Lower Bioavailability): Plant proteins generally score between 60% and 85% on the official truncated DIAAS scale. They are much harder to digest because they are physically locked behind tough cellulose fiber walls and chemically bound by anti-nutrients. Furthermore, individual plants are usually missing a complete, balanced amino acid profile. Crucially, whole plants in their natural state never score at the top of this tier; a plant can only reach an 85% score through industrial ultra-processing and chemical refining, which artificially strip away the fiber barrier to isolate the protein—highly processed products that, from the GAPS perspective, should not even be considered food.

  
  

• The Amino Acid Pooling Rule: Once absorbed, amino acids enter a temporary pool in the bloodstream and liver. To build new human tissue, all nine essential amino acids must be simultaneously present in this pool. Animal proteins deliver a complete, fully balanced profile rapidly filling the pool to fuel immediate cellular repair. Whole plants, however, drop single amino acids into the blood at a slower, uneven trickle because they are trapped behind fiber. For a healthy person, the body can buffer this delay over the course of a day. But for an injured, leaking gut wall that requires an immediate, synchronized supply of raw materials for rapid tissue regeneration, this sluggish trickle delays the healing process, leaving the cellular structure starved for immediate repair blocks.

  
  

Ultimately, the human blueprint perfectly validates our biological rules: we wield an intense stomach acid that controls incoming microbes, entirely lack the internal infrastructure needed to host them for plant processing, and concentrate our primary absorptive surface area right where our food is chemically unlocked.

The Human Strategy: Animal Fats vs. Plant Fats

Just as our highly streamlined anatomy dictates our protein selection, it also determines what kind of fat our bodies can actually utilize as clean fuel. While there is no single percentage score for fats like the DIAAS system for protein, the basic rules of our digestive tract remain exactly the same:

Animal Fats (Immediate Accessibility): Natural animal fats—like tallow, lard, suet, ghee, and pastured egg yolks—contain zero fiber. Because they are completely un-entangled, our upper stomach acid refinery breaks them down easily, allowing our small intestine to absorb 95% to 98% of the fat early in the digestive tract with almost no waste.

Plant Fats (The Cellulose Trap): Whole plant fats found in nuts, seeds, and grains are locked tightly behind rigid cell walls. Because humans lack the massive fermentation chambers of a cow or horse, we cannot break down these walls. As a result, a massive portion of whole plant fat (roughly 15% to 30%) passes right through our small intestine completely unabsorbed and exits the body as waste.

The Brain Fuel Rule (ALA vs. DHA): The human brain and nervous system rely on highly specialized, long-chain fats (DHA and EPA). Pasture-raised animals and wild fish deliver these fats in their fully formed state, ready for immediate absorption. Plants contain zero DHA; they only offer a short-chain version (ALA) found in flax or walnuts. To use it, the human liver must try to stretch this short-chain fat into brain fuel, but the human conversion rate is a near-useless 0.5% to 5%.

Stability in Acid and Heat: Traditional animal fats are structurally stable and saturated. They pass through our uniform, highly acidic stomach without mutating. Conversely, commercial plant and seed oils are highly fragile and unstable. When exposed to heat during cooking or processing, they easily oxidize and mutate into inflammatory byproducts that irritate our delicate intestinal lining. Commercial plant and seed oils are entirely incompatible with tissue healing and are never allowed on the GAPS diet.

The Human Strategy: The Lower Tract Bottleneck

Because humans follow the rule that surface area determines absorption, looking at our large intestine reveals why a fiber-heavy diet fails our anatomy. In a horse, the large intestine is a massive, highly specialized fermentation tank built specifically to turn plant bulk into daily fuel. In a human, the large intestine is short, completely lacks the complex villi needed for macromolecule absorption, and is designed primarily to extract water and compact waste.

When you consume tough plant matter, it passes through your upper tract completely untouched and drops into the colon. The microbes living there will try to ferment it, but because this happens at the absolute end of the line, the nutrient-absorbing surface area of the small intestine has already been bypassed. Instead of creating systemic fuel, this late fermentation produces pockets of trapped gases and metabolic waste. Because our lower anatomy lacks the cellular transport mechanisms to absorb proteins or complex nutrients at this stage, that undigested plant mass stagnates, turning the lower tract potentially into a breeding ground for opportunistic pathogens.

Overcoming the Fiber Barrier: Culinary, Fermentation, and Combining Strategies

Having said that, there are distinct ways to make plants more digestible and complete for the human tract; they can be cooked, fermented, juiced, or strategically paired. Because our anatomy lacks the internal fermentation chambers of a cow or horse, we must utilize external strategies to bypass our structural limitations. Cooking uses heat to break down tough cellulose and soften rigid cell walls before the food even reaches our mouths. External fermentation—such as souring vegetables or culturing grains—deploys beneficial microbes outside the body to pre-digest plant carbohydrates and neutralize natural defense chemicals. Juicing completely extracts the liquid nutrients, leaving the problematic fiber matrix behind so our small intestine can absorb the vitamins and minerals without anatomical strain.

Furthermore, those who choose to focus heavily on plant foods must actively manage the amino acid pooling rule by utilizing precise food-combining strategies. Because individual plants carry limiting amino acids, matching complementary plant groups within the same meal—such as pairing grains with legumes—is essential to supply all nine essential amino acids simultaneously.

Crucially, this is not an active GAPS strategy. These heavy plant foods would only ever be considered once the individual has sealed and healed the gut wall. Even after achieving enough structural healing to reintroduce them, these specific plants require intensive preparation methods like soaking, sprouting and fermenting before consumption so as to neutralize their natural defense chemicals and to further break down fiber. Through these external traditional preparation and intelligent pairing methods, humans effectively mimic the digestive work of herbivores, allowing us to safely handle our unique physiological constraints.

Conclusion: The Biological Mandate of the GAPS Protocol

It should now be clear that whole plants, examined from this physiological efficiency perspective, are not the most seamless building materials for the human body. When a person relies primarily on plant foods for cellular structure, the digestive system is forced to expend massive amounts of metabolic energy just to crack open defensive cell walls and collect fragmented proteins which ultimately are structurally inappropriate for our specific pool requirements. Over time, this structural mismatch strips away the protective mucosal layer, systematically shears down the delicate microscopic villi of the small intestine, and eventually causes the tight junctions of the intestinal wall to biochemically open—a condition clinically recognized as intestinal permeability, or leaky gut. When this barrier breaks, the biological rules of extraction fail completely; instead of clean, fully digested building blocks flowing into the bloodstream, toxic, un-fermented food particles and pathogenic microbes pass straight into circulation, placing an overwhelming toxic burden on the entire body. The GAPS Nutritional Protocol is designed to respect the exact evolutionary and physiological constraints of the human identity, and by so doing ensure sound health over ones lifespan.