The Ghost in the Machine is a Garden: An Engineer's Guide to Our Inner Ecosystem

Omer Ozkan On the DNA of Things

Jul 05, 2025

The Hook

As a young man, Omer Ozkan felt the future’s shadow. An industrial engineer by training, he turned his systems-thinking mind to the world’s most pressing external problem: climate change. He founded Turkey’s first solar energy company, building complex grids to harness the power of the sun and save the planet from itself. But after years of optimizing external systems, a pivot—both jarring and profound—turned his gaze inward. Spurred by the disruptive power of AI and the birth of his daughter, he dove into the enigmatic world of biotechnology. He discovered an ecosystem more complex than any power grid, an internal universe that held, he believed, “the door for life.” The engineer who tried to save our outer world realized the next frontier of human resilience was hidden within.

Central Idea

For over a century, Western medicine has operated on a warfare model, born from the triumphs of germ theory. We see the body as a fortress to be defended, pathogens as enemies to be eradicated, and drugs as our chemical artillery. Yet, as chronic diseases escalate, this paradigm shows its limits. Omer Ozkan’s journey from engineering planetary systems to microscopic ones offers a powerful alternative: health is not a battle to be won, but an ecosystem to be managed. His work reframes disease as a breakdown in communication within our vast microbial society. The future of medicine, he argues, lies not in being a better warrior, but in becoming a wiser gardener—cultivating balance in the rich, complex soil of our own gut.

Exploration and Evidence

The modern medical narrative began with a clear hero and villain. Louis Pasteur and Robert Koch gave us germ theory, identifying specific microbes as the cause of specific diseases. The discovery of penicillin was our silver bullet, an antibiotic "nuclear bomb" that could wipe out bacterial invaders. This model was stunningly effective against acute infectious diseases and built the foundations of our healthcare system. But its very success created a blind spot. In our quest to kill the "bad bacteria," we waged an indiscriminate war on all bacteria, forgetting that for every foe, there were a thousand friends. The result is an epidemic of chronic conditions—IBS, autoimmune disorders, allergies—that the warfare model cannot explain. These are not diseases of invasion, but of imbalance.

This is where the pivotal partnership between two minds comes into focus. The technological engine of their company, Enbiosis, was built by co-founder and Chief Technology Officer, Ufuk Nalbantoğlu, PhD. A computer engineer with deep expertise in artificial intelligence, machine learning, and bioinformatics, Dr. Nalbantoğlu is the architect of the core science. It was Omer Ozkan, the entrepreneur, who recognized the genius in Dr. Nalbantoğlu's work, grasped the philosophy behind it, invested in it, and has been leading the idea into the world. As Ozkan himself describes the dynamic, if Ufuk is the Leonardo da Vinci, he is the Medici; if Ufuk is the Steve Wozniak who single-handedly builds the revolutionary computer, Ozkan is the Steve Jobs who understands how it can change the world and builds the company to do it.

Ozkan saw that Dr. Nalbantoğlu's technology could solve a key problem in gut health. He observed that in patients with Irritable Bowel Syndrome, the rich diversity of the microbiome often collapses into an oligarchy, where a single group of bacteria seizes power and destabilizes the entire population. The solution, powered by Dr. Nalbantoğlu's science, is elegantly simple in concept: stop feeding the oligarchs. By identifying which foods fuel the dominant, problematic bacteria, they can be selectively starved. Simultaneously, by providing nutrients for the beneficial, suppressed microbes, the system can be nudged back toward a healthy, diversified state. It is a restoration of democracy at the microbial level, made possible by Dr. Nalbantoğlu's bioinformatics engine and Ozkan's entrepreneurial vision.

Of course, managing this society of trillions is a task of staggering complexity. This is where Dr. Nalbantoğlu’s scientific engine and Ozkan's leadership become indispensable. The process, which Ozkan provocatively calls a "digital fecal transplant," uses the proprietary AI that Dr. Nalbantoğlu developed to achieve the goal of a physical transplant without the risks. The system, built upon his sophisticated mathematical and machine learning models, identifies a healthy donor microbiome profile to use as a target. Then, the AI he architected acts as a master strategist, simulating how different combinations of foods and supplements can shift the patient's unbalanced microbiome toward that healthy target. This is not the generalized intelligence of a chatbot; it is a powerful, specialized computational tool—Dr. Nalbantoğlu's creation—being directed by Ozkan's strategic vision to manage a living system of near-infinite variables.

Counterpoints and Complexity

This revolutionary vision is not without its hurdles. Ozkan is the first to admit the primary challenge is resistance from the very people he hopes to help. Most clinicians were not trained in microbiome science, which was largely absent from medical school curricula until recently. To them, the field is noisy, filled with conflicting claims, and lacks the regulatory approval they rely on. The idea of modulating the microbiome with food sounds more like wellness marketing than serious medicine.

Furthermore, the metaphor of a "digital fecal transplant" risks sounding like a science-fiction overreach. However, it serves as a crucial bridge to understanding a complex biological process. It is not a literal digital transfer, but a data-driven strategy to replicate a clinical outcome—rebalancing a microbial community—through a non-invasive, personalized nutritional plan.

Finally, Ozkan offers a stern warning against viewing this approach as naively innocent. "If something has a serious positive effect," he cautions, "the opposite application of the same thing might have a very negative effect, too." Food and supplements, when used with this level of precision, are not benign. They are powerful tools that can heal or harm, and should be treated with the same respect as a prescription drug.

Closing Insight

When asked what drives him, Ozkan speaks of the future and his daughter. His mission is not just to fix digestive issues but to prepare humanity for the difficult days that may lie ahead. Whether facing climate change on Earth or the challenge of living on Mars, our ability to survive will depend on our resilience. That resilience, he believes, begins with the ecosystem we carry within us. We cannot always change the world outside, but we have an astonishing ability to change the world inside. By learning the language of our microbes, we are learning to adapt faster and more effectively than ever before. The engineer’s journey from solar panels to the gut reveals a profound truth: perhaps our greatest technology is not the one we build, but the one we learn to cultivate. In tending to our inner garden, we may find the strength not just to survive the future, but to truly flourish in it.

Actionable Bonus

Questions for Reflection:

In what ways does the "warfare" model of health (fighting disease, killing germs) appear in your own thoughts or actions regarding your well-being?
If you were to view your body as a garden instead of a fortress, what is one small, nurturing act of "gardening" you could perform for it this week?
What part of your identity would feel reshaped after a major physical transformation?

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