From Aggregation to Strategy
In the earliest phases of the universe, matter existed in a relatively undifferentiated state. Particles such as protons, neutrons, and electrons floated freely, with no stable connections to one another. Even when atoms formed, they were simple, uniform, and interchangeable. A single hydrogen atom is much like any other, and without lasting arrangements between them, there was little in the way of meaningful difference.
As the universe cooled and expanded, something profound began to happen: particles started to stick together. Atoms formed bonds to become molecules. Not all combinations were possible. Some were unstable and broke apart, but others held. The rules of physics didn’t just allow aggregation, they favored certain arrangements over others. The universe began to explore what was stable.
This principle, aggregation guided by stability, is the first step in the emergence of complexity. Simple units join to form larger structures, but not at random. The interactions are constrained by properties like charge, shape, and energy minimization. These constraints act like filters, selecting for some patterns while excluding others. Out of this selective process, structure begins to emerge.
But structure alone is not yet enough. Two molecules might be stable when bound together, but without any variation in form or function, the system remains uniform, flat, featureless. As we saw in the previous chapter, complexity needs gradients: differences that can drive process and transformation. What unlocks the next stage here is a different kind of gradient, not one of energy or concentration, but of sequence. When molecules, especially long, chain-like ones, can join in different orders, each with different properties, structure becomes capable of carrying difference. And when differences in structure lead to differences in behavior, we begin to see the glimmer of something more: information.
From Sequence to Encoding
A long chain of molecules arranged in a specific order is not just a bigger molecule, it’s a pattern. And once patterns can differ, they can also begin to matter.
Imagine a soup of monomers, simple molecular building blocks, each capable of bonding to others in a linear chain. If every chain is identical, the system contains no usable difference. But if some sequences are more chemically reactive than others, if one sequence can catalyze a reaction that another cannot, then the system begins to respond to variation. A chain’s structure now determines its function.
This is the beginning of encoding. The order of elements in the chain encodes a specific potential: what the sequence can do, what it might trigger, what outcomes it makes more likely. A single change in that sequence might render it inert, or alternatively, make it dramatically more effective at catalyzing a reaction, binding to a partner, or triggering a downstream effect. At this point, the system is no longer operating purely on the level of physical assembly; it has entered the realm of representational structure. One thing now stands for another: a pattern stands for a possibility.
It’s worth emphasizing that this is not yet symbolic representation in the way humans use language. There is no external interpreter reading the molecule like a sentence. But the functional consequences of variation serve as a primitive kind of semantics. Different arrangements lead to different effects, and that is enough to begin building a logic of selection.
Some sequences persist not just because they’re stable, but because they’re useful. This is the first glimmer of memory in nature: a structure that carries the record of past interactions in its form. If a sequence helps speed up a useful chemical reaction (a kind of catalyst) it may persist longer simply because the reaction it enables tends to recreate or preserve the conditions that favor its own survival.
It does not yet replicate, but it endures, not through copying, but through continued relevance. Usefulness, in this early context, is what allows structure to persist.
Catalysis and the Foundations of Memory
At this stage, we do not yet assume reproduction or heredity. Even in a world of random molecules, not all patterns behave the same. Some chains fold into stable shapes that resist degradation and persist longer. Others may have a different kind of advantage: they can catalyze reactions, helping nearby molecules form bonds more efficiently. This does not guarantee that the catalyst itself survives, but in some cases, its activity changes the environment in ways that support its continued presence. If a molecule helps stabilize its surroundings, or even contributes, directly or indirectly, to the formation of more molecules like itself, it may begin to persist through feedback, not just durability.
These are fragile steps, but important ones. They show how functional patterns, those that do something, can begin to shape the conditions of their own survival, even before life exists. In this sense, chemistry begins to favor function before biology formalizes it.
For example, in a reaction known as the formose reaction, simple molecules like formaldehyde can spontaneously form sugars (Breslow 1959). As the reaction proceeds, some of the intermediate sugars begin to catalyze later steps, creating a self-reinforcing loop. It is not life, but it is a hint of something life-like: a feedback cycle where products help sustain the process that produces them.
Beyond purely chemical reactions, the environment itself also supplied catalysts.
Even without biology, the early Earth offered natural catalysts that could give molecules a head start. Clay minerals, with their layered structures, can adsorb (bind onto their surfaces) and align simple organics, effectively bringing them into close proximity. In doing so, clays can act a bit like primitive enzymes, holding molecules in place long enough for reactions to occur that might otherwise be too slow or unstable (Cairns-Smith 1982). Metal sulfides such as iron and nickel sulfide, abundant in the crust, can drive redox chemistry, providing a spark for the formation of more complex organic molecules (Wächtershäuser 1988). These geochemical catalysts don’t guarantee survival, but they do demonstrate how simple molecules could have been nudged toward persistence. Under the right conditions, the environment itself supplied scaffolding that allowed helpful configurations to stick around longer, adding to their stability.
Scaffolding Complexity
What makes this kind of persistence important is not only that patterns stick around, but that they begin to stack. A molecule that catalyzes another’s formation does more than survive; it participates in a network. A primitive vesicle, a tiny bubble of fat molecules, can shield fragile molecular structures from the external environment. In doing so, it doesn’t merely contain; it selects, helping certain configurations persist while others degrade. A clay surface, with its finely layered structure, is more than a passive foundation: it actively binds certain molecules and encourages others to form in place. By templating, it participates in the system, biasing the landscape toward some structures over others.
As these effects accumulate, they begin to interlock. Catalysts shape the chemical environment; the environment shapes which catalysts persist. Compartments isolate reactions; those reactions in turn alter the compartments. What starts as a scattered set of interactions gradually becomes a coordinated system, where the parts reinforce and constrain each other in stable, repeatable ways.
This is how constructive emergent complexity begins. It has no master plan, but rather, it has layers of feedback that preserve structure, amplify function, and scaffold new possibilities. Once structures begin to affect their own survival, the system is no longer passively shaped by the laws of chemistry. It becomes historically shaped. The present carries traces of what has worked before, and those traces condition what can happen next.
At a certain point, the interactions among structures become rich enough that the system as a whole behaves differently than any of its parts. New patterns of organization emerge, ones that cannot easily be reduced to the components alone. These emergent levels are not arbitrary; they are real thresholds, each marking a step in the architecture of complexity.
These networks of catalysts and compartments laid the groundwork for something even more powerful. Once patterns were not only stabilized but also copied, a new dynamic entered the scene. Stability alone could not explain the richness of life. What was needed was a mechanism that could harness variation and accumulate it across generations. This is where Darwin’s great insight enters: the principle of natural selection.
Natural Selection: The First Strategy
What transforms persistence into evolution is replication. Once a structure can not only endure but also be copied, a new logic takes over. This is Darwin’s great insight: when replicators vary, and when those variations affect how successfully they are copied, the world begins to change in a systematic way. Natural selection is the process by which patterns that are better at surviving and being copied become more common over time.
It is simple in form, almost trivial:
When copies of a structure are made, they are rarely perfectly exact; some variations make further copying more likely, and those variations, carried forward, accumulate over time.
And yet from this humble algorithm comes the full diversity of life.
What makes natural selection so powerful is that it uses history as fuel. Each generation carries forward the traces of what worked before. Molecular sequences that were copied reliably became genes. Genes, bundled into organisms, were tested not only against chemistry but against the demands of environments. Behaviors that aided copying spread. Slowly, the strategies of life accumulated through iteration, without foresight.
Daniel Dennett has called natural selection “Darwin’s dangerous idea” and “the universal acid”: an insight so simple and substrate-neutral that once grasped, it eats through every domain of thought (Dennett 1995). The same algorithm recurs wherever patterns can be copied, varied, and retained. It does not depend on carbon chemistry, DNA, or even biology at all. It is a blind but inexhaustible generator of design.
This is why the Darwinian logic extends far beyond biology. Richard Dawkins emphasized that genes themselves act like “selfish replicators,” spreading if they are good at making more of themselves, regardless of the fate of the organism (Dawkins 1976; 1989). The same perspective applies at higher levels: brains shape their own neural circuits through reinforcement, strengthening connections that prove useful while others fade. What is “copied” here are the connections between neurons, reinforced if useful and pruned if not. Cultures evolve too, as behaviors and beliefs spread unevenly across minds. Even technology, from stone tools refined across countless generations, to machines built on previous designs, to computer code rewritten and repurposed, follows this path of iteration, variation, and retention.
In each case, the core is the same: copying plus selection turns mere persistence into strategy. It allows a system not only to endure, but to adapt.
Natural selection is the first ratchet of strategy in the universe, but it is not the last. Once copying and selection are in play, the door opens to richer forms of memory and adaptation. Patterns can begin to do more than survive, they can respond, adjust, and refine themselves. From this point forward, persistence is no longer passive. It becomes strategy.
From Memory to Strategy
With persistent structures and functional feedback loops in place, systems begin to do more than endure, they begin to respond, adjust, and adapt. When a configuration of molecules influences which reactions occur, and those reactions in turn affect which configurations persist, the system is doing something remarkable: it is processing information. Not in the symbolic way a computer does, but in a chemical way, by allowing structure to shape future structure through feedback.
This is the essence of strategy: a system that modifies its own behavior based on what has worked before. Even before life, even before genes, we see the embryonic form of purpose emerge, not because the system has goals, but because the selective reinforcement of useful patterns creates direction. The past begins to constrain the future by reinforcing patterns that endure.
This, too, is a kind of encoding. The structure of a molecule does not just persist, it means something, because it causes something. Its pattern encodes a function. Once such patterns can be preserved, combined, and reused, the system has entered the realm of functional memory: the foundation of learning, adaptation, and ultimately, agency.
We can now see the larger arc: aggregation yields structure, structure permits variation, variation creates the potential for function, function leads to persistence through feedback, persistence accumulates as a form of memory, and memory enables response, coordination, and strategy.
This layered architecture repeats across nature. The earliest life built on the scaffolding of catalytic networks. Brains built on the architecture of living cells. Human culture built on the architecture of brains. At each level, the capacity to encode difference, preserve it, and use it to shape future behavior is what drives complexity forward.
In the next chapter, we’ll explore how this logic of layered function and memory plays out in the brain, a system that not only remembers, but anticipates; not only adapts, but imagines. The story that began with aggregation will now shift from the evolution of structure to the evolution of mind.