Why We Keep Getting Human Diet Wrong — Part 1

Walk into almost any modern nutrition conversation and you will more than likely bump into a familiar claim, that plants are trying to poison you. This language is often compelling and, at first glance, it seems like it could be biologically grounded. Compounds like oxalates bind minerals. Lectins disrupt your gut lining. Phytates can interfere with nutrient absorption. Eating these things causes inflammation, and inflammation is the devil.

These compounds are framed as hidden liabilities embedded within otherwise “healthy” foods, quietly undermining human physiology, and ultimately human history.

None of these statements are entirely false, and I think that is what makes them so appealing to some people. Plants do produce defensive compounds, this is completely true. Plants want to produce offspring, and continue their genetic lines the same way that animal species do. Just because they are plants doesn't mean that they don't have ways to defend themselves from predation. Look at cactus and desert plants. They have specific designs to keep them from being eaten by their "predators" and other plants are not different. But that doesn't make them the devil, nor does it mean that humans should not consume them at all. Yes, some of these defensive compounds can interfere with human biological processes under very specific conditions. But the conclusion that increasingly follows this particular myth is that plant foods are fundamentally mismatched to human biology, and that is built on a critical conceptual error.

The presence of a biologically active compound is not the same as the presence of pathology.

More importantly, this myth ignores a deeper and more consequential reality, that humans did not evolve in the absence of plant defense chemistry.

We evolved in continuous interaction with it.

Any framework that attempts to evaluate plant foods outside of that relationship is not just incomplete, it is fundamentally misaligned with the conditions under which human physiology developed.

Plants are not passive entities in the ecological landscape. They are chemically sophisticated organisms that produce a wide array of certain substances called secondary metabolites. These are compounds like alkaloids, phenolics, terpenes, glycosides. They each serve functional roles in defense, signaling, and environmental interaction. From the plant’s perspective, these compounds can deter herbivory, inhibit microbial growth, and regulate internal processes. From the human perspective, they are often labeled as “toxins,” a term that carries a specific implication with it, and it is that their primary relationship to the body is harmful.

But this type of framing collapses a far more nuanced biological reality. Many of these compounds do not simply disrupt human physiology; they can interact with it. In low to moderate doses, they can influence cellular signaling pathways, modulate oxidative stress responses, and alter gene expression. This is the basis of something called hormesis, which is a well-established biological principle in which low-level exposure to stressors induces adaptive, beneficial responses. The same class of compounds that can be harmful at high doses may, under different conditions, contribute to resilience and regulation.

The modern discourse around plant “toxins” tends to flatten this complexity into binary categories.... This is either safe or dangerous, beneficial or harmful, acceptable or to be avoided. But biology does not operate in binaries like this. It operates in gradients, thresholds, and context-dependent interactions.

Take oxalates for example, often cited as a reason to avoid a wide range of plant foods. It is true that oxalates can bind calcium and contribute to kidney stone formation in susceptible individuals, particularly when consumed in extremely high amounts, or in the context of poor mineral balance. However, oxalates are also a normal component of many diets and are routinely processed through renal and intestinal pathways without issue in most individuals eating moderate amounts. Their impact is shaped not only by intake, but by hydration status, mineral availability, gut microbiota composition, and overall dietary pattern. To isolate oxalates as inherently pathological is to remove them from the biological system that determines their effect. In a human population that is chronically dehydrated, we should see higher amounts of issues with oxalates, but does that actually make oxalates the problem?

Lets use a different example of a popular "culprit" called Lectins provide another example. In their raw or improperly prepared forms, certain lectins can indeed interfere with things like gut integrity and nutrient absorption. But this is precisely where preparation becomes biologically decisive. The act of cooking denatures lectins. Traditional processing methods such as soaking and fermenting further reduce their activity, which is something that has been happening with most of the foods that are high in lectins for most of human history, or at least since we discovered fire. The difference between a harmful and a harmless lectin is not then theoretical, it is procedural. What appears, in isolation, to be a “toxin” becomes, within the context of human behavior and cultural practice, a manageable and often negligible factor.

Phytates follow a similar pattern. They can bind minerals such as zinc, iron, and calcium, reducing their bioavailability under certain conditions. Yet they also function as antioxidants, influence glucose metabolism, and may exert protective effects in specific physiological contexts. Once again, the biological impact is not fixed. It is mediated by preparation methods, dietary diversity, and overall nutritional status.

This is where modern interpretations often diverge most sharply from actual historical reality. Traditional human societies did not encounter plant foods as isolated biochemical problems. They engaged with them through established practices that functioned as biological interface strategies. Soaking, fermenting, sprouting, and cooking were not arbitrary cultural artifacts; they were adaptive responses to the chemical properties of plants. These methods altered the structure, concentration, and activity of plant compounds in ways that made them compatible with human physiology.

Cassava, for example, contains cyanogenic glycosides in its raw form, and these are compounds that can release cyanide and pose a serious risk if consumed improperly. Yet cassava has served as a dietary staple for millions of people. The difference lies entirely in preparation. Through soaking, fermenting, drying, and cooking, these compounds are reduced to safe levels. The plant itself is not inherently inappropriate for human consumption; it requires an interaction that aligns with its chemistry.

Similarly, the processing of maize through nixtamalization (a method involving alkaline treatment) actually enhances nutrient availability and reduces anti-nutritional factors. These practices illustrate a broader point, and that is that humans did not passively consume plant foods. They co-evolved behavioral strategies that allowed them to extract value while minimizing risk.

Layered onto this relationship is a factor that is often overlooked in modern diet debates, is the gut microbiome. Human digestion is not a closed system. It is a collaborative process involving a complex ecosystem of microorganisms that participate in the breakdown and transformation of food. Plant compounds, particularly fibers and polyphenols, are central to this interaction. They serve as substrates for microbial fermentation, leading to the production of short-chain fatty acids such as butyrate, which play critical roles in gut health, immune function, and metabolic regulation.

When plant foods are removed completely from the diet, this microbial ecosystem shifts. Diversity may decrease, and its functional capacity changes. The system adapts to the available inputs. If plant foods are later reintroduced after a prolonged absence, the resulting symptoms are often interpreted as evidence of inherent toxicity. But this interpretation confuses cause and effect. What is being observed is not necessarily a harmful property of the food, but a change in the system’s ability to process it.

Tolerance, in this context, is not something that is static. It is an adaptive process that has been fine tuned over thousands of years. If humans were not able to consume plants safely, the human species would have been extinct thousands of years ago.

This brings us to an often-overlooked aspect of human dietary evolution, and that is the role of roots and tubers. Much of modern nutritional discourse emphasizes leafy greens as foundational components of a healthy diet. Yet from an evolutionary and energetic perspective, underground storage organs (like roots, tubers, and rhizomes) likely played a far more substantial role. These foods are energy-dense, rich in carbohydrates, and relatively reliable sources of calories across seasons and environments. They require effort to obtain and process, but they provide a return that aligns with the metabolic demands of a large-brained, highly active species like humans.

Cooking further amplifies their value, increasing their digestibility and caloric availability. This has led some researchers to propose that the incorporation of cooked starches may have contributed to the energetic support necessary for brain expansion in early humans. While the specifics remain debated, the broader pattern is clear. Not all plant foods function identically within the human diet. Leaves, stems, roots, seeds, and fruits each occupy different ecological and physiological roles.

Leafy greens, while rich in certain micronutrients and phytochemicals, are typically low in caloric density and often higher in specific defensive compounds. They were not easy to store, and they were very seasonal due to their decreased tolerance for cold and frost. Their role appears to be more supplemental (providing signaling molecules and micronutrients) rather than serving as primary energy sources. In contrast, roots and tubers offer a more direct contribution to energy balance. This distinction does not render leafy plants unimportant, but it does challenge the modern tendency to elevate them as dietary cornerstones while overlooking the significance of other plant categories.

Herbs further complicate the simplistic framing of plant compounds as “toxins.” Used in both culinary and medicinal contexts, herbs are concentrated sources of bioactive molecules. Many contain compounds that, in higher doses, would exert strong pharmacological effects. Yet in the quantities typically consumed, they function as modulators and subtly influence digestion, inflammation, microbial balance, and even nervous system activity.

This is where the boundary between food and medicine begins to blur. Herbs illustrate that biological activity is not inherently problematic. It is, instead, the basis of interaction. Plants do not merely provide macronutrients and vitamins; they deliver signals that the human body interprets and responds to.

When viewed through this lens, the modern narrative that positions plant foods as inherently dangerous begins to lose coherence. It isolates a single dimension of plant biology (it's defensive chemistry) and elevates it above the broader context in which human-plant interactions evolved. It removes variables such as preparation, dose, diversity, microbial mediation, and cultural practice, and then draws conclusions from that stripped-down model.

It is also important to acknowledge why this narrative has gained traction. Many individuals do experience improvements in symptoms when they remove plant foods from their diet. Digestive issues may resolve. Inflammation may decrease. Energy may stabilize. These outcomes are real, and they should not be dismissed.

But the interpretation of these outcomes is where the error often occurs.

Removing plant foods simplifies the system. It reduces variability, lowers exposure to certain compounds, and decreases digestive demand. For a system that is very likely already dysregulated (whether due to gut dysfunction, chronic stress, or a metabolic imbalance) this reduction in complexity can provide relief. It is analogous to reducing the number of variables in an equation. The system itself becomes easier to manage.

What it does not necessarily reveal is the underlying reason why the system was unable to handle those variables in the first place.

Symptom relief is not the same as identifying root cause. It is an indicator that something has changed in the system’s load, not a definitive statement about the inherent nature of the removed foods.

This distinction becomes critical when short-term strategies are interpreted as long-term truths. An elimination approach can be an effective tool for stabilizing a dysregulated system. But when it is reframed as evidence that entire categories of food are fundamentally incompatible with human biology (and should therefore be eliminated entirely), the conclusion extends beyond what the data supports.

Humans are not a species defined by dietary rigidity. In fact across geographic regions, climates, and historical periods, human diets have varied widely. Some populations have consumed diets rich in animal products, while others have relied heavily on plant-based foods. What unites these patterns is not uniformity, but variability. Seasonal shifts, ecological diversity, and cultural practices created a dynamic nutritional landscape. We developed the ability to digest what was available to us, not the other way around.

This variability likely contributed to metabolic flexibility, microbiome diversity, and resilience in the face of changing conditions. In contrast, modern dietary frameworks often emphasize consistency, restriction, and identity. Foods are categorized, eliminated, and then appear to be moralized. Diet becomes not just a means of nourishment, but a structured system of control and regulation.

Within this context, the idea that plants are inherently problematic offers a kind of clarity. It provides a simple explanation for complex symptoms and a clear set of rules for navigating food choices.

But simplicity is not the same as accuracy.

The core misunderstanding is not that plant compounds can be biologically active or even harmful under certain conditions. It is the assumption that this activity defines their role in the human diet.

Humans evolved not by avoiding plant chemistry, but by interacting with it. They modulated it through preparation, adapting to it through physiology, and integrating it within a broader ecological system that included microbes, animals, and environmental variability. In order to survive, they had to find ways to eat both plant and animal products. There were no other options. It was eat, or starve. And humans found ways to eat what was available to them safely, or we would not be here to talk about it.

When the system that was developed is disrupted, plant foods can become more difficult to tolerate. But this does not mean they are inherently mismatched to human biology. It means the conditions that support that interaction have shifted.

The more productive question, then, is not if plant compounds are harmful in isolation. It is under what conditions the human system is able to engage with them effectively.

This reframing moves the conversation away from avoidance and toward capacity. It recognizes that biology is not defined by the elimination of challenges, but by the ability to respond effectively to them. This is truly finding the "root cause" of many of the issues that we see in the modern culture.

And it sets the stage for the next question in this series.....

If removing plant foods can produce such profound improvements for some individuals, what is actually driving that change?

Because what looks like nutritional superiority is often something else entirely.

And it has far less to do with food than most people think.

If this conversation interests you, please make sure to check back for parts 2 and 3 of the series, and feel free to check out my other articles on topics like this one

• What's the Deal with Organic

• You didn't Evolve to Eat a Diet

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