On co-evolution, the living kingdoms, what synthetic agriculture broke, and why Stephen Harrod Buhner was right
There is a particular kind of hubris that runs through the modern relationship with the living world.
It shows up in how we talk about bacteria — as enemies to be eliminated. In how we approach pests — as problems to be eradicated rather than signals of imbalance. In how we wage war on disease — as if the body were a battlefield and health were the temporary absence of losing.
I have watched this framework operate from inside a pharmacy for years. And I have watched, with increasing unease, the consequences stack up.
We are living through a global antibiotic resistance crisis of our own making. We are surrounded by evidence that our synthetic agricultural system is degrading the very biological infrastructure that human health depends on. We have plants that cannot reproduce, soils that cannot sustain life, and microbiomes — inner and outer — that are less diverse, less resilient, and less capable of protecting us than they were a generation ago.
This is not an accident. It is the predictable outcome of a species that forgot, somewhere along the way, that it did not arrive on this planet alone.
Life on Earth is organized into five kingdoms: animals, plants, fungi, bacteria (prokaryotes), and protists. Humans belong to one of them. We co-evolved alongside all of the others.
That word, co-evolved, matters more than it might first appear. It does not simply mean we existed in proximity. It means that our biology developed in relationship with the biology of other species, over hundreds of millions of years, in ways that are written into our physiology at the deepest level.
The Human Microbiome Project, published in Nature in 2012, gave us the first population-scale portrait of what that relationship looks like in the human body. The study characterized microbial communities across five body habitats in a healthy cohort and found that even healthy individuals differ remarkably in their microbial composition — shaped by diet, environment, host genetics, and early microbial exposure.¹ We carry, on and inside us, an ecosystem of trillions of microorganisms. The gut microbiome alone contains an estimated 38 trillion microbial cells — roughly equal to the number of human cells in the body.² And these microbes are not merely passengers. They are metabolic partners. They synthesize vitamins, regulate immune function, produce neurotransmitter precursors, protect the gut lining, and train the immune system to distinguish between threat and non-threat.
We did not develop the capacity to do these things ourselves because, across evolutionary time, we never had to. Our microbial partners were always there to do them with us. The relationship is that old, and that fundamental.
Long before the animals, including the human animal — there were plants.
Plants have been producing complex chemical compounds for over 450 million years. Secondary metabolites — the alkaloids, terpenes, flavonoids, phenols, and thousands of other compounds that give medicinal plants their medicinal properties — were not produced for human use. They evolved as a living chemical language: communication between plants and the organisms they co-evolved with, defense against threats, signals to pollinators and seed dispersers, responses to environmental stress.
Stephen Harrod Buhner, in his foundational work The Lost Language of Plants (Chelsea Green Publishing, 2002), documented this with extraordinary depth.³ Buhner argued — and backed with extensive research — that plant phytochemistry is not incidental. It is the original communications network of Earth’s ecosystems: a biochemical conversation running between species that is billions of years old, and that has shaped the immune systems, nervous systems, and metabolic capacity of every organism on this planet, including us.
When we replace botanical diversity with monoculture; when we spray living soils with broad-spectrum herbicides; when we isolate single active compounds from plants and discard the rest as irrelevant; when we treat the pharmacy as the replacement for the plant kingdom rather than its inferior imitation… we are severing a conversation we did not invent and cannot replicate.
The pharmacological model of medicine is extraordinary at doing certain things. But it is structurally incapable of doing what four hundred and fifty million years of plant-animal co-evolution produced.
The discovery of penicillin in 1928 was genuinely one of the most significant moments in medical history. Antibiotics have saved hundreds of millions of lives. This is not in question.
What is in question is what happened next: the industrialization of antibiotic use, the routine administration of antibiotics to livestock at subtherapeutic doses to promote growth, the reflexive prescription of antibiotics for viral infections they cannot treat, and the wholesale adoption of antibacterial everything — soaps and sanitizers, cleaning products, personal care products — as a cultural norm.
The result is the antibiotic resistance crisis we are now living through. The WHO’s Global Antibiotic Resistance Surveillance Report 2025, drawing on data from over 104 countries, found that one in six laboratory-confirmed common bacterial infections worldwide were resistant to antibiotic treatment in 2023. Between 2018 and 2023, antibiotic resistance rose in over 40% of the pathogen-antibiotic combinations monitored, with an average annual increase of 5-15%.⁴ The WHO has identified antimicrobial resistance as one of the top ten global public health threats facing humanity.
This is the cost of treating bacteria as an enemy to be eliminated rather than an ecosystem to be maintained in balance.
The war metaphor encompasses more than our relationship to bacteria – it includes cancer, autoimmune conditions, and any other “disease” we try to eradicate, but most often end up suppressing the symptoms of. It also expands beyond health – to women’s rights, to inequality and inequity, political strife and actual wars plaguing our world today.
And this context shapes what solutions we reach for. If bacteria are enemies, the correct response is weapons: stronger antibiotics, broader-spectrum agents, more aggressive eradication protocols. If bacteria are partners in a disrupted relationship, the correct response is restoration: supporting microbial diversity, protecting the conditions that allow healthy microbial ecosystems to thrive, and using targeted antimicrobial therapy judiciously when genuinely needed rather than reflexively.
The second framing is not softer. It is more accurate. And it is increasingly what the science supports.
Here is something that tends to stop people: the relationship between soil bacteria and human mental health.
Dr. Christopher Lowry at the University of Colorado Boulder has spent decades studying Mycobacterium vaccae, a bacterium found naturally in healthy soil. His research has shown that exposure to M. vaccae activates serotonergic neurons in the brain — specifically in the dorsal raphe nucleus, a region involved in mood regulation — and produces effects on stress resilience, anxiety, and cognition that parallel those of antidepressant medications.⁵ His 2016 research and subsequent work demonstrated that immunization with heat-killed M. vaccae in mice produced anti-inflammatory effects in the brain, reduced stress-induced colitis by 50%, and promoted proactive coping behaviors in the face of a social stressor.⁵
The traditional practice of getting your hands in the soil is now backed by science. Gardening, walking barefoot, working the land — was literally biological maintenance. Contact with healthy soil microbiota was a regular, ongoing input into the immune and nervous systems of every human being who lived close to the earth. Connected to seasons, cycles and rhythms of nature, the sun, and the moon.
We have largely severed that contact. We live on sealed surfaces, in climate-controlled environments, eating food grown in soils increasingly depleted of microbial diversity by decades of synthetic agriculture. We lead sedentary lifestyles under fluorescent lighting day and night. And we are surprised by an epidemic of anxiety, depression, autoimmune dysfunction, and inflammatory disease.
The connection is not metaphorical. It is mechanistic.
No conversation about the disruption of our co-evolved microbial partnerships is complete without addressing glyphosate, the active ingredient in Roundup, and the most widely used herbicide in human history.
Glyphosate works by inhibiting the shikimate pathway — a metabolic route used by plants and microorganisms to synthesize aromatic amino acids. Human cells do not use the shikimate pathway, which is why glyphosate was initially classified as minimally toxic to mammals. What this classification failed to account for is that the gut microbiome — which is not human cells but microbial cells, are profoundly affected.
Samsel and Seneff, in a 2013 review published in Entropy, proposed that glyphosate’s suppression of CYP enzymes and disruption of amino acid biosynthesis by gut bacteria represents a pathway to a wide range of modern chronic diseases.⁶ It should be noted that this paper is a hypothesis-generating review and some of its specific claims remain contested in the peer-reviewed literature. What is not contested is the broader question it raised: that a compound designed to kill plants by targeting a pathway shared with gut microbes is not biologically neutral to the organisms that carry those microbes.
Subsequent research has continued to examine glyphosate’s effects on gut microbiota composition and tight junction integrity. The question of dose, exposure level, and the specific mechanisms of human harm is an active area of research — one that the original regulatory classifications did not adequately anticipate.
The gut microbiome was not seriously characterized until the early 21st century. Glyphosate was approved for agricultural use in the 1970s. We approved a compound designed to disrupt microbial metabolism before we understood what our own microbial partners were doing for us.
There is one more dimension of this that I cannot leave out, because it sits at the intersection of ecology, food sovereignty, and reproductive biology in a way that feels important to name clearly.
The development and widespread adoption of genetically modified crops engineered for herbicide resistance (what Monsanto marketed as “Roundup Ready”) brought with it a specific agricultural model: seeds that are patented and cannot be saved, replanted, or reproduced by farmers. One-time-use biology. Living systems designed to not self-perpetuate.
I find it difficult to look at that model without wondering what it means that we built our food system around organisms engineered to end their own lineage. There is something in that — philosophically, ecologically, symbolically — that feels continuous with everything else we have been exploring in this post. We have applied the logic of industrial production to living systems that do not operate by that logic. Seeds reproduce. Soil ecosystems regenerate. Bacterial communities maintain dynamic balance. These are not failures of efficiency. They are the features that make life possible.
When we engineer them out, we do not gain control. We lose relationship.
I want to be precise about what I am and am not arguing here.
I am not arguing for the abolition of antibiotics or the rejection of pharmaceutical medicine. I am a pharmacist. I understand what these tools can do, and I use them judiciously in my own practice and life.
What I am arguing is that the framework of war, applied to bacteria, to pests, to weeds, to disease — has produced predictable and serious consequences that we are now living with at a population level. And that the alternative framework of ecological relationship, of co-evolution, of working with the living systems we are embedded in rather than against them — is not soft sentiment. It is better science.
It is what Stephen Harrod Buhner spent his life documenting. It is what the microbiome research is increasingly confirming. It is what indigenous agricultural traditions maintained for thousands of years before industrial monoculture made them seem obsolete.
Returning to plant medicine is not as a rejection of modern science but a reclamation of a relationship that is older, broader, and more intelligent than the pharmaceutical model alone. So is tending your gut microbiome with the same care you bring to a garden. So is choosing organic food when possible, not as a luxury but as a vote for a different kind of agriculture.
So is putting your hands in the soil and remembering what you are made of.
Ready to start rebuilding your relationship with the plant kingdom? The Natural Medicine Cabinet Remake Guide is a first step — and the Herbalism starter guide goes deeper.
This is Post 3 of the Born of the Earth series. Next: the root cause beneath the root causes — the worldview that made all of this possible, and what a different one looks like.
Works Cited
→ Want more herbal wisdom like this? Start here.
If you’re feeling stuck, overwhelmed, or unsure where to start on your herbal journey, I’m here to help.
Let’s talk it through together.
I offer a free discovery call where we’ll explore your health or holistic professional career goals and map out supportive first steps tailored just for you.
Book a Complimentary Health Consultation
Book a Holistic Professional Tea Chat
Ready to transform your medicine cabinet? The Natural Medicine Makeover Guide helps you swap synthetic fixes for safe, effective natural remedies. Packed with expert tips from a pharmacist + herbalist, it’s your go-to resource for a healthier, holistic lifestyle. Plus, see my favorite products in my herbal dispensary.
