The Wrong Unit

This is not a bad framework. It has produced centuries of genuine discovery. But it is also the wrong frame — and the cost of that framing error might be why we still can't explain where life came from, or reliably recognize it somewhere else.

A growing group of researchers is making this argument: the individual organism, biology's fundamental unit of analysis, is a scale, not a category. When you analyze at the wrong scale, you produce the wrong map. And if the map is wrong at the foundation, the destinations it points to may not exist.

The individual organism is the unit. That choice has consequences.

i · the individual was always a compromise

Begin with the mitochondria in your cells.

Every cell in your body contains them — the organelles that convert food to ATP, that power every process that keeps you running. Mitochondria have their own DNA. Their own ribosomes. Their own reproductive cycle. They divide independently of the cell they inhabit.

The reason: they aren't yours. Mitochondria are ancient bacteria — proteobacteria engulfed by early eukaryotic cells roughly 1.5 billion years ago and never released. What we call the cell is a merger. A cooperation so successful and so ancient that it became a thing, a unit, an organism. But it started as two organisms, and the boundary between them is still, if you look closely, negotiable.

This is endosymbiotic theory, proposed by Lynn Margulis in 1967 — initially rejected by the mainstream, now foundational. The nucleus may be another ancient capture. You are a nested cooperation of things that were once separate — organized into a pattern that acts as an individual because individuality became useful.

And that's before the microbiome.

Your gut contains roughly 38 trillion microbial cells — approximately equal to the number of human cells in your body. These organisms synthesize vitamins you cannot produce yourself, regulate immune responses, influence brain chemistry via the gut-brain axis. Remove them and the system fails. They are not optional accessories. They are part of the system.

The term biologists have developed for this is holobiont — the host organism plus its associated microbial community, treated as an integrated evolutionary unit. Under holobiont theory, you are not an organism with a microbiome. You are a collective. The organism as category is a useful approximation of a more complex reality.

Consider slime molds. Normally single-celled amoeba, living and feeding independently. Under starvation, they aggregate into a multicellular body — complete with differentiated tissues, a stalk, and reproductive fruiting structures. When conditions improve, they disaggregate back into individuals. The individuality is conditional. Reversible. Tactical. It turns on and off based on need.

The individual organism is not a natural kind. It is what life looks like at a particular scale, under particular conditions. It is the level of organization that turned out to be useful for classification — not the fundamental unit of the thing being classified.

Centering it may be the oldest category error in science.

ii · what selection actually produces

If the individual is the wrong unit, what is the right one?

This is where it gets genuinely vertiginous.

One answer gaining traction in astrobiology and origin-of-life research: stop asking about organisms and start asking about assembly. The framework, assembly theory, developed by chemist Lee Cronin and astrobiologist Sara Walker, proposes a way to identify life that does not require knowing what life looks like.

The core insight: complex molecules that require a specific, information-preserving sequence of steps to construct are signatures of selection. Random chemistry does not build a working enzyme. It does not iterate toward a functional protein fold. Only processes that store and re-use information — processes we call living — can produce molecules with a high assembly index: the minimum number of distinct causal steps needed to construct them from scratch.

The assembly index of a simple molecule is low. A rock's constituent minerals have low assembly indices — random geological processes can produce them. But a strand of DNA, a folded protein, a complex metabolic intermediate: these have assembly indices so high that random processes cannot plausibly generate them without a history of selection. The complexity itself is the signature.

This framing is substrate-independent. It does not require the life-form to use DNA, carbon chemistry, or water. It does not require anything recognizable. It just requires asking whether the molecular complexity present in a sample can be explained by random processes — or whether something that preserves and accumulates information must have been operating to produce it.

For astrobiology, this changes the search. Current detection strategies largely look for biosignatures associated with Earth life: oxygen, methane, specific organics. But if life elsewhere uses a different chemistry, those signatures are silent. Assembly theory provides a detection method that would identify alien life even if it looks nothing like us — measure the assembly index of the molecules present, and ask whether random processes could produce them. The answer does not depend on the substrate.

For origin-of-life research, the reframing may be equally important. The question of how the first organism arose might be intractable precisely because it presupposes that individuality comes first — that a boundary exists before a metabolism, a cell before a chemistry. Assembly theory suggests inverting this: selection operating on molecular complexity is the primary phenomenon. The individual organism is a later organizational achievement, a downstream consequence of selection discovering that encapsulation — containing a chemistry within a boundary — is advantageous.

The question stops being how did the first cell appear and becomes at what point did selection start preferring certain assemblies over others, and what has that process been building ever since.

That is a different question. It requires different methods. And it opens different territory entirely.

iii · what this does to you

There is no clean line where you begin.

You are a coalition of formerly separate organisms whose cooperation has been running long enough that the coalition developed a name for itself. The atoms in your body were not synthesized for you — they were forged in stellar interiors, distributed by supernovae, and have been cycling through living systems for billions of years before this particular arrangement. The arrangement is temporary. The atoms predate you. The patterns they are expressing predate the planet.

What you call I is a high-assembly-index process: a configuration of matter that requires selection history to explain. Not an object. Not a stable thing. A pattern that has been running long enough to get interesting.

This is the nested coherence principle in precise operation. Local systems — cells, organisms, colonies — align within larger patterns. What appears individual at one scale is a component of a collective at another. What appears to be a boundary from the inside is a zone of negotiation from the outside.

The mycelium network under a forest demonstrates this structurally. Individual mushrooms are fruiting bodies — the visible, countable surface expressions. The organism is the network: kilometers of fungal threads threading through soil, transferring nutrients between trees, maintaining forest chemistry across seasons. The individual mushroom is a function the network performs. It is not the thing itself.

Life has always worked this way. Bacteria form biofilms — not aggregations of individuals but coordinated communities with differentiated roles and chemical signaling. Cells form tissues. Organisms form ecosystems. The major evolutionary transitions — the ones that produced mitochondria, multicellularity, eusocial insects — are all events where collectives reorganized into new kinds of individuals. Selection does not only act on organisms; it acts on the level of organization currently producing the most heritable variance.

The individual organism is not the protagonist of life's story. It is a recurring character type. Selection invents it, uses it, and — when conditions favor a different scale — steps over it to organize things differently.

What assembly theory adds is the possibility that the whole trajectory is detectable from outside — that you can read selection's history in molecular complexity without knowing what life is supposed to look like. That life, wherever it exists, whatever substrate it runs on, will leave a specific signature in the information it accumulates.

The category error is not that individual organisms are unreal — they are real, at their scale. It is that assuming the individual scale is primary means studying outputs rather than the process. You are cataloguing the fruiting bodies and wondering why the forest does not make sense.

The universe has been running selection on this planet for roughly four billion years. It may have been running it elsewhere. It does not need the organisms to be recognizable. It just needs the chemistry to be improbably complex.

The individual organism was never the point. It was always the output.

iv · sources

• How a radical new view of life could reveal its origin and alien life — New Scientist, 2026-05-27
• Assembly theory explains and quantifies selection and evolution — Nature, 2023-09-28
• On the Origin of Mitosing Cells — Journal of Theoretical Biology, 1967-03-01