What If We Are the Bacteria

Shit that keeps me awake

In 1676, a Dutch draper named Antonie van Leeuwenhoek scraped some plaque from his own teeth, placed it under a lens he had ground himself, and became the first human being to see a living microorganism. He called them animalcules — little animals. He was so startled by what he found that he wrote to the Royal Society in London describing “many very little living animalcules, very prettily a-moving.” The Royal Society sent a delegation to verify he wasn’t lying or hallucinating. He wasn’t.

In a single afternoon, the known world doubled. Not in size — in depth. It turned out that underneath the world humans could see with their eyes, there was another complete world, operating by its own rules, populated by its own entities, with its own ecology of competition and cooperation and predation and reproduction. It had been there the entire time. It was causing plague and fermentation and infection and digestion and the souring of milk and the death of children. It was inside us, on us, around us, outnumbering our own cells by a factor that is still being revised upward. And we had had absolutely no idea. Not because we were stupid. Because we did not have the instrument.

We invented the microscope and found a world below us.

We never invented the reverse.

The Asymmetry Nobody Talks About

Think about what the microscope actually does, because it is easy to misunderstand it as simply a magnification device — something that makes small things look bigger. That is true as far as it goes, but it misses the deeper point. The microscope does not just resize things. It reveals an entirely different scale of organisation. It shows you that reality is not just structured at the level you can see. It is structured at multiple levels simultaneously, each level with its own entities, its own dynamics, its own forms of complexity. The human scale is not the only scale at which interesting, consequential things happen. It is just the one we happen to occupy.

The telescope does something different. It is genuinely just a magnification device — it brings distant things closer. When you look at Saturn through a telescope, you are seeing Saturn at human scale, just from much closer than your eyes could manage unaided. The telescope extends the reach of your existing scale. It does not reveal a new layer of organisation. You point it at the sky and you see planets and stars and galaxies — and all of those things, as far as we can tell, are operating at more or less the same scale of organisation as the things we can already see. They are bigger, yes. But a galaxy is not to the universe what a bacterium is to a human body. A galaxy is just a lot of stars. It does not appear to be an entity in any stronger sense than that.

The microscope revealed that the world has more structure going downward than we knew. What we have never had is an instrument that reveals whether the world has more structure going upward.

And here is the thing. There is no logical reason to assume it doesn’t.

What Scale of Organisation Actually Means

Before going further, it is worth being precise about what I mean by a scale of organisation, because the concept is doing a lot of work here.

A bacterium is not just a small human. It is an entity operating at a completely different scale, with a completely different relationship to its environment. It has behaviour — it moves toward nutrients and away from toxins, a process called chemotaxis. It communicates with other bacteria through chemical signals in a process called quorum sensing, effectively taking a census of its local population and changing its behaviour based on the results. Bacteria form biofilms — structured communities with differentiated roles, something that looks uncomfortably like the early stirrings of multicellularity. They compete for resources. They cooperate. Some engage in what looks very much like warfare, producing bacteriocins that kill competing strains. They have been doing all of this for approximately four billion years, which is longer than anything else on Earth has been doing anything.

The point is that at the bacterial scale, there is genuine complexity. Genuine organisation. Genuine dynamics that cannot be reduced to simple physics — or rather, that are not usefully described at the level of physics even though they are, ultimately, physical. You need the concept of “bacterium” to describe what is happening. You need the concept of “quorum sensing.” You need the vocabulary of biology, of behaviour, of ecology. The phenomena at that scale are real phenomena, not just approximations or conveniences.

Now go up a scale. A human body is not just a large bacterium. It is an entity operating at a completely different scale, with a completely different relationship to its environment. It contains approximately 37 trillion human cells and somewhere between 38 and 100 trillion bacterial cells, all operating in an intricate, interdependent system that we are still far from fully understanding. The body has specialised organs, a nervous system capable of generating consciousness, an immune system that can distinguish self from non-self with extraordinary precision, a hormonal system that modulates everything from mood to metabolism. It is, from the perspective of the bacteria living inside it, essentially incomprehensible. Not because bacteria are stupid. Because the human is operating at a scale — and with a kind of organisation — that simply does not map onto anything in the bacterial conceptual universe, to the extent that bacteria can be said to have a conceptual universe at all.

The bacteria in your gut right now have no perception of you as an entity. They perceive gradients. Chemical signals. Surfaces. Other bacteria. The vast organised system they inhabit — you — registers for them only as environment. As local conditions. As the source of nutrients and the context of competition. That you are a thinking, feeling, organised being with intentions and a history and a future is not information available to them. The scale at which you exist as a coherent entity is simply not a scale they can access.

Now. Why do we assume this stops at the human scale?

The Candidates

There are some obvious candidates for larger-scale organisation, and it is worth considering each of them before getting to the stranger possibilities.

The most immediate candidate is the ecosystem. An ecosystem is not just a collection of organisms living in the same place. It has structure — trophic levels, nutrient cycles, predator-prey dynamics, feedback loops that regulate population sizes, successional patterns that drive change over time. Remove a keystone predator and the whole system reorganises. Introduce an invasive species and you can watch the cascading effects ripple through the food web for decades. An ecosystem behaves, in some ways, like an entity — it has states, it responds to perturbations, it has something like homeostasis. The ecologist Aldo Leopold was writing about the “land organism” in the 1940s, and James Lovelock’s Gaia hypothesis, proposed in the 1970s, suggested that the Earth’s biosphere actively regulates conditions in ways that maintain its own habitability.

The Gaia hypothesis has had a complicated reception. In its strong form — the idea that the Earth is, in some meaningful sense, a living organism with something like intention — most scientists find it unpersuasive. In its weaker form — the idea that the biosphere involves complex feedback loops that regulate atmospheric composition, temperature, and ocean chemistry in ways that are not reducible to simple geophysics — it is largely accepted. The Earth’s atmosphere is not in chemical equilibrium. It should be. The fact that it is not, and has not been for billions of years, suggests that biological activity is continuously maintaining it out of equilibrium in ways that happen to be conducive to life. Whether that constitutes the Earth “doing” something is a question about how you define agency, and those arguments can go on forever.

Human civilisation is another candidate. Cities, economies, legal systems, cultural traditions — these are structures that persist across individual human lifetimes, that have dynamics of their own, that shape the behaviour of the humans within them in ways that the humans often do not fully understand or control. An economy is not simply the sum of individual economic decisions. It has emergent properties, feedback loops, crises that arise from the interactions of millions of actors none of whom intended the crisis. A language shapes the thoughts of the people who speak it in ways they are largely unaware of. A culture reproduces itself across generations, using individual humans as its medium the way a virus uses cells. The philosopher Daniel Dennett has written about memes — units of cultural information that propagate, mutate, compete for mental real estate, and evolve by a process analogous to natural selection. Whether or not you accept the specific meme framework, the observation that cultural entities have dynamics that are not fully controlled by any individual is clearly right.

But here is my dissatisfaction with all of these candidates. They feel like extensions of the human scale rather than genuinely above it. Ecosystems, biospheres, civilisations — these are made of things we can see and study and participate in. We can, with effort, perceive them as systems. We can think about civilisation as an entity, even if we are inside it. A bacterium cannot think about the human body as an entity. It has no mechanism for doing so. That asymmetry — the complete unavailability of the higher level to the lower level as a concept, let alone as a percept — is what I am really interested in.

What would be genuinely above our scale in the way that we are above bacteria?

The Instrument We Do Not Have

Here is the problem with thinking about genuinely larger scales of organisation. We can only think about them using a mind that operates at the human scale. This is not a minor technical limitation. It is a fundamental constraint on what kinds of things we can even conceive of.

A bacterium, if it could think — which it cannot, but follow the thought — could not conceive of a multicellular organism. Not because the concept is too complicated, but because the bacterium has no experience of anything that would give rise to that concept. It has no perception of a boundary that defines a self. It has no experience of specialised cells with differentiated functions working in coordination. The concept of “organ” would be as meaningless to it as the concept of “galaxy” is to a medieval peasant — not just unknown, but outside the entire framework within which concepts form.

We are in the same position with respect to whatever might be above us.

We have mathematics, which is the main tool humans use to reason about things outside direct experience. Mathematics got us to quantum mechanics, to general relativity, to the existence of black holes before we had any observational evidence for them. It is a remarkable instrument for extending understanding beyond the senses. But even mathematics requires that you are asking the right questions, constructing the right frameworks. We cannot use mathematics to discover a scale of organisation we have not yet conceived of, because we do not know what equations to write.

We have the analogy, which is the other tool — and the one I am using throughout this piece. The microscope analogy suggests there might be a level of organisation above us the way there is a level below us. But an analogy is not evidence. It is a prompt to consider a possibility, not a demonstration that the possibility is real.

What we do not have is the instrument itself. The reverse microscope. The thing that would let us perceive structure at scales above the human the way the microscope let us perceive structure at scales below it.

And here is the question that follows. What would such an instrument even look like? What are we actually asking for?

The View from Below

Let me stay with the bacterium analogy for a moment longer, because I think it has more in it.

If you are a bacterium inside a human body, here is your situation. You are embedded in an environment of extraordinary complexity. That environment has regular patterns — rhythms of nutrient availability, temperature fluctuations, chemical signals that modulate your behaviour, periodic disturbances, changing conditions in different locations. You navigate this environment. You respond to it. You are causally shaped by it at every moment.

But the environment is not random. It has structure. The nutrient rhythms are not noise — they reflect the human’s eating patterns. The temperature fluctuations reflect fever, exercise, the time of day. The chemical signals are part of a vast hormonal and immune communication system. The periodic disturbances are heartbeats, peristalsis, breathing. All of this structure comes from somewhere. It is generated by the organised activity of the entity you inhabit.

The bacterium has no way of knowing this. From inside, the environment just is what it is. Complex, patterned, sometimes predictable, sometimes not. The idea that all of these patterns are generated by a single organised entity operating at a completely different scale — that there is a unified source of the structure you inhabit — is simply not available.

Now ask. From our perspective, does the universe we inhabit look random? Or does it have patterns?

It has extraordinary patterns. Physical constants that are precisely tuned — or appear to be — to allow the existence of complex matter. The emergence of life, and then of intelligence, apparently from simple initial conditions. The consistent laws of physics, operating identically across billions of light years. The arrow of time, moving in one direction for reasons that are still not fully settled in physics. The fact that the universe is comprehensible at all — that mathematics, invented by human minds, describes physical reality with unreasonable effectiveness, as Eugene Wigner put it.

These patterns might be just what a universe is like — a complex, law-governed system that inevitably produces structure at every scale. That is the standard scientific view, and it is a completely reasonable one.

But the bacterium’s environment also looks like just what the inside of an environment looks like — complex, patterned, sometimes predictable. The bacterium has no way to distinguish “environment generated by an organised entity operating at a higher scale” from “environment that is just complex.” From inside, they look the same.

We might be in exactly that position.

The Fermi Paradox as a Scale Problem

There is a famous problem in astrobiology called the Fermi Paradox, named after the physicist Enrico Fermi, who supposedly asked over lunch one day. Given the vast age and size of the universe, and the apparent abundance of potentially habitable planets, where is everybody? The universe is roughly 13.8 billion years old. There are hundreds of billions of galaxies, each containing hundreds of billions of stars, many of them with planets. Even if the probability of life arising on any given planet is very small, the sheer number of opportunities suggests there should be intelligent civilisations scattered throughout the galaxy. And some of them should be billions of years older than us — plenty of time to have spread across the galaxy, or at least to have made their presence known. But we see nothing. We hear nothing. The sky is silent.

There are many proposed solutions to the Fermi Paradox — the Great Filter, the Zoo Hypothesis, the idea that interstellar travel is harder than we think, the idea that civilisations inevitably destroy themselves before they can expand. But there is one class of solution that bears on our topic here.

What if sufficiently advanced civilisations — or sufficiently advanced forms of intelligence — are not detectable to us because they operate at a scale we cannot perceive? What if the transition from civilisation to something beyond civilisation involves a shift in the scale of organisation, the way the transition from single-celled to multicellular life involved a shift in scale — and that beyond a certain point, the entity is simply no longer visible to instruments calibrated to the human scale?

This is not a new idea. Thinkers from Teilhard de Chardin to Frank Tipler to Ray Kurzweil have speculated about consciousness or intelligence expanding to operate at cosmic scales. What I am suggesting is something slightly different — not that intelligence expands, but that the scale of organisation shifts in a way that makes it unrecognisable to us, the way a human body is unrecognisable to a bacterium. Not bigger intelligence operating at our scale. Something genuinely above our scale, the way we are genuinely above the bacterial scale.

If that were true, we would not detect it. We would look at the universe and see galaxies and empty space and the cosmic microwave background, and the thing we were looking for — the organised entity at the higher scale — would be as invisible to us as we are to the bacteria. The sky would be silent. And the silence would prove nothing.

The Hard Version of the Question

I want to push to the hardest version of this question, the one that I find genuinely difficult to think about.

If there is a level of organisation above us — genuinely above us, in the way that we are above bacteria — then we are inside it right now. We are part of it. We are, in some sense, constituent elements of it, the way bacteria are constituent elements of us.

This means that the thing we are trying to perceive is not out there somewhere, at a distance, in the way that a distant star is out there. It surrounds us. It pervades us. It is the context in which everything we do takes place. And we have no instrument to perceive it, because every instrument we have built is calibrated to the human scale — to detect things at our level of organisation or smaller.

The bacteria in your gut cannot build a microscope that reveals the human body. They cannot build any instrument at all. But they are in an even worse epistemic position than that. They do not know what they are missing. They have no concept of the human body to know that they are failing to detect it. The unknown unknown is the most complete kind of unknown.

We might be in exactly that position. Not failing to detect something we know about. Failing to conceive of something that would explain patterns we cannot account for, structure that seems to come from somewhere, consistency that exceeds what we would expect from a universe of pure chance.

Or we might not be. The universe might simply be what it appears to be — law-governed, complex, and not organised at any scale above the one we can perceive.

I genuinely do not know. I do not think anyone does.

What We Can Say

There are a few things that seem clear to me after sitting with this question.

The first is that the argument from silence — we do not perceive any higher-scale organisation, therefore there is none — is not valid. We did not perceive bacterial organisation for most of human history, and it was there the entire time, operating at a scale just below our perceptual threshold. The argument from silence only works if you have a reliable instrument calibrated to the relevant scale, and we do not have one for scales above us. The silence is not informative.

The second is that the universe does, observationally, have a nested structure of organisation — quarks inside protons, protons inside nuclei, nuclei inside atoms, atoms inside molecules, molecules inside cells, cells inside organisms, organisms inside ecosystems. Each level has its own emergent properties, its own dynamics, its own relevant concepts. There is no reason in principle why that nesting should stop at the human scale, or at the scale of the biosphere, or at the scale of the galaxy. The universe seems to like building structure at multiple scales simultaneously. Why would it stop?

The third is that the question is not merely philosophical. If there is organisation at scales above us, it is presumably causally affecting us, the way we causally affect the bacteria inside us. The structure of our environment — physical, chemical, biological, perhaps informational — comes from somewhere. Most of it, we think we understand. But there is structure in the universe that we do not yet have satisfying explanations for. The fine-tuning of physical constants. The arrow of time. The emergence of consciousness from matter. These might all have eventual explanations within our current framework. Or some of them might be the signal, barely legible, of something operating at a scale we cannot yet see.

The fourth is that if we cannot perceive it directly, our best hope is to reason toward it — to notice patterns that seem to require explanation at a higher level of organisation, the way the early epidemiologists noticed patterns in cholera outbreaks that seemed to require explanation at a level below the visible. John Snow did not need to see bacteria to infer that something too small to see was causing cholera. He needed to think carefully about the patterns. Inference from pattern is the reverse microscope we actually have available to us.

The Instrument We Would Need

What would it actually take to perceive the level above us, if it exists?

I think it would require, at minimum, the ability to process information at timescales and spatial scales far beyond the human. The human body’s processes operate at timescales from milliseconds to decades — a neuron fires in a millisecond, a human lives for decades. Bacteria experience the world at the timescale of minutes and hours. If there is an entity operating at scales above the human, its characteristic timescales might be centuries or millennia or geological epochs. We would be to it as a bacterium is to us — a tiny, rapid, local process, there and gone in an instant from its perspective.

Perceiving at those timescales would require either living long enough to observe processes that unfold over geological time, which no individual human does, or having instruments that record and integrate information over those timescales. We have some of this — geology, archaeology, cosmology are all disciplines that work to reconstruct processes operating over deep time. But reconstructing a process is not the same as perceiving it. We are reading the fossil record, not watching evolution happen.

Spatially, an entity operating at scales above the human might be structured at the scale of the biosphere, or the solar system, or the galaxy. To perceive structure at those scales as structure — as organisation, as entity, rather than just as big — would require a perspective we cannot occupy. We are inside it, which is precisely the problem.

There is a sense in which what I am describing as the reverse microscope is not a physical instrument at all. It is a conceptual instrument. A way of thinking that allows you to perceive organisation at scales you cannot directly observe. We have proto-versions of this — systems thinking, complexity theory, the study of emergence. These are attempts to develop frameworks that allow us to reason about organisation at scales above the individual component. But they are early and incomplete, and they are constrained by the fact that the minds using them are themselves operating at the human scale.

The bacterium cannot conceive of the human body. But the human can conceive of the bacterium. The asymmetry runs in one direction — higher scales can comprehend lower scales, but lower scales cannot comprehend higher scales. If there is something above us, it can presumably perceive us with perfect clarity. We are the ones in the dark.

We Are the Middle

Here is the thing that I keep coming back to. We tend to think of ourselves as occupying either the top of the scale of complexity — the most organised, most conscious, most capable things we know of — or, in more humble moments, somewhere in the middle of a range that extends from simple to complex. But in both cases, we imagine ourselves as the reference point. The scale runs from below us to above us, and we are the centre.

The history of science has been a continuous process of decentring. We are not at the centre of the solar system. The solar system is not at the centre of the galaxy. The galaxy is not at the centre of the universe, which has no centre. We are not the pinnacle of evolution — evolution has no pinnacle, it has no direction, and the bacteria we emerged from are still here, vastly outnumbering us, enormously more ancient, and arguably more successful by most objective measures. Our consciousness, which feels to us like the most important thing in the universe, may be one instance of a more general phenomenon, or it may not be special at all in the way we imagine.

Each of these decentrings was resisted, and each was correct.

The next one might be this. We are not at the top of the scale of organisation. We are somewhere in the middle. Below us, an entire world of organisation that took us until the seventeenth century to discover. Above us, possibly, another entire world of organisation that we have not yet begun to perceive. We are the bacteria looking at the cells looking at the organ looking at the body — except we are the bacteria, and we think the cells are the whole story.

We invented the microscope and found out we were wrong about how full the world was, going down.

We have not yet invented the reverse.

Originally written 2024.

What do you think? Are we the bacteria? Let us know in the comments below.