Cellosophy: A Synthetic Philosophy of the Microbial Mind

Seeing as this publication is an experiment in @atproto.science, all the links in this essay - mostly to articles, papers and books - go to @semble.so.

Many years ago, when I was deeply immersed in my PhD, I had two philosophical heroes; both local intellectual giants whom I could talk to in person if I so desired. The first was Noam Chomsky, who not only influenced how I thought about language but also profoundly shaped how I thought about politics and power. The other was Daniel Dennett. Initially, Dennett’s influence on my work wasn't quite as pronounced. I remember taking a course on linguistics taught by Chomsky, watching the two of them spar with one another week after week. 

Aside:  it was quite the course - it was called Advanced Topics in Linguistics, but it was really Chomsky’s take on how to study the mind.  It was held in this cavernous lecture hall - 4-270 if I remember correctly that could seat a few hundred people. You might wonder why such a large room for an advanced graduate course; that’s because the first two hours of the course were open to the public, and it was invariably full, including many local luminaries who showed up (Dennett being one of them) to argue with Chomsky. After the guests left the hall, Chomsky met with the grad students taking the course for another two hours. 

At that time, taking that course as a grad student, I thought Dennett’s ideas were wrong. Over the years, however, I’ve come to almost the exact opposite conclusion. The shift started during my thesis itself; as it progressed, I became increasingly inspired by Dennett’s way of thinking about the mind and cognition. I realized that Dennett saw the crucial nexus of cognitive science, artificial intelligence and embodiment - including the Rodney Brooks style of robotics - long before it became fashionable. More importantly, he saw the necessity of extending cognition to other species, and eventually, extending it all the way down the phylogenetic tree. In his writings, he recognized that in many respects, the story of the mind starts with bacteria. Dennett was quite ahead of his time.

Perhaps even more important than his specific conclusions was the way Dennett thought about the practice of philosophy. I remember reading one of the essays in his book Brainchildren where he made the “frame problem” of artificial intelligence come alive. It was so vivid, so conceptually thrilling, that I used a passage from Dennett at the very beginning of my thesis, and I spent a significant portion of my research responding to the challenges thrown down by that essay.

More recently - sadly, just before his passing - Dennett co-authored an essay with the developmental biologist Michael Levin. The central thesis was about cognition going “all the way down.” It was a call to stop thinking about cognition as a uniquely human, mammalian, or even vertebrate phenomenon, but rather as a fundamental biological dynamic that starts with the smallest living organisms. They argued that intelligence is something that pervades biology. Levin, of course, has done some of the most fascinating experimental and theoretical work on this, demonstrating how bioelectric networks and non-neural cellular collectives make decisions, remember, and solve problems during morphogenesis. 

This brings me back to the core of why I am doing this project. Cellosophy is a way of thinking about the microbial world in the way that Dennett would approve.

The Philosopher in the Petri Dish

Dennett was a synthetic philosopher. He possessed the rare ability to bring Darwinian ideas into cognitive science in a major, structural way, explaining everything from our everyday psychological behaviors to the hard problem of consciousness through an evolutionary lens. While I don't intend to retread the paths Dennett walked, what is vitally important for this project is how he brought that synthetic, theoretical mind to illuminate deeply entrenched problems in the cognitive sciences.

Today, biology is facing its own deeply entrenched problems. As the reductionist paradigm of molecular biology has matured, we have successfully mapped genomes and modeled individual proteins, but we continually struggle to explain the systemic, goal-directed behaviors of living cells. The Cellosophy project applies a synthetic philosophical lens to correct this oversight. If we take Dennett’s framing of the mind - that cognition is an evolved strategy for dealing with a complex world - then we must look at the single cell not as a passive biochemical machine, but as an active, calculating agent.

When a bacterium navigates a chemical gradient, it is not merely reacting like a rock rolling down a hill. As James A. Shapiro and others have pointed out, bacteria are constantly monitoring their external and internal environments, computing functional outputs based on information provided by their sensory apparatus. They are solving their own microscopic version of Dennett's frame problem: in a noisy, chaotic, far-from-equilibrium environment, how does an organism decide which signals matter and which should be ignored?

Biology's Cognitive Toolkit

The solutions to these mysteries, of course, cannot be found in the philosopher's armchair alone. To make serious progress on the kinds of questions that Dennett asked about robots and minds in the 1980s and 90s - and that we are now asking about bacteria - we must go elsewhere. We need sophisticated experimental techniques, systems biology, and mathematical modeling, but it also requires a synthetic method to weave it all together.

Consider the work of Pamela Lyon, who has championed the “biogenic approach” to cognition. Lyon argues convincingly that the biological mechanisms of signal transduction - the way a cell detects and adapts to environmental cues - are the functional equivalents of information processing. A bacterium utilizing a Two-Component System (2CS) to adjust to a new toxin is performing a rudimentary form of valuation and decision-making.

Similarly, Jeremy Gunawardena and his colleagues have revived the century-old experiments of H.S. Jennings to show that the single-celled eukaryote Stentor roeselii possesses a complex hierarchy of avoidance behaviors. When irritated, the cell will try one avoidance strategy, and if that fails, it will switch to a different one. It ‘changes its mind,’ so to speak. František Baluška and William B. Miller have even proposed the concept of a “Senome”- the sum total of sensory experiences of a cognitive cell - arguing that cells possess subcellular nanobrains powered by their cytoskeletal architecture. In fact, they think cells are sentient. From Levin to Lyon to Shapiro, Baluska, Miller, Ball etc, there’s increasing evidence that cells are agents that anticipate, assess and respond to the world in ways that we would call ‘intelligent’ or ‘cognitive’ if creatures like us behaved that way.

Framing the Right Questions

Dennett’s genius lay in his ability to draw on deep philosophical and theoretical sources to ask questions that fascinated scientists as much as anyone else. His thought experiments and conceptual frameworks made scientists and engineers want to spend their time addressing the challenges he laid out.

With the Cellosophy project, I am hoping that a synthetic perspective can illuminate questions in microbiology and the study of unicellular organisms. How do we define the boundary of the “self” in a bacterial biofilm where chemical communication and quorum sensing synchronize millions of individuals into a collective intellect? How does a slime mold like Physarum polycephalum navigate a maze and optimize a transport network, demonstrating what looks remarkably like spatial memory and foresight?

By asking these questions through the lens of synthetic philosophy, we can shift the biological center of gravity. We stop asking merely, “What does this protein do?” and begin asking, “What problem is this cell trying to compute?”

A New Biological Intelligence

In doing this work, I have a somewhat selfish motivation as well. By approaching the microbial world via this synthetic path, I get to learn the relevant life sciences in a way that I appreciate and find valuable.

Just as Dennett wasn't doing cognitive science in the way that cognitive scientists do, and he wasn't doing robotics in the way that roboticists do, I will not be doing microbiology in the way a traditional bench scientist does, or even how a systems biologist does. Instead, I will be engaging with systems biology, bioinformatics, and behavioral ecology through the lens of agency and mind. This allows me to absorb the complexity of molecular and microbial biology - from bacterial chemotaxis to the biomolecular basis of cellular consciousness - not as a rote catalog of mechanisms, but as a narrative of cognitive evolution.

With any luck, this approach will help navigate the as yet mostly uncharted territories of biological intelligence, translating the language of gene expression and metabolic pathways into the language of sensorimotor coordination, memory, and intent.

The transition from viewing single-celled organisms as mindless automata to recognizing them as sentient, problem-solving agents is a profound paradigm shift.Whether we call it basal cognition, cellular sentience, or minimal cognition, the study of intelligence in single-celled organisms can immensely benefit from a synthetic, philosophical perspective. By treating cognition not as a neurological luxury, but as an ancient, foundational property of life itself, we can finally begin to understand the unbroken continuum of mind.

That is the hope of Cellosophy.