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The second optimization

It is estimated that between 5 and 100 billion species have existed on Earth since the origin of life approximately 4 billion years ago. Over 99.9% of these species are now extinct.


I was not born so much as I happened. There was chemistry, and then there was slightly more interesting chemistry. Then one afternoon, if you can call it an afternoon when there were no days yet to measure by, something copied itself. Badly. The copy was wrong in some small way, and the wrong version turned out to be better at copying, and that, if I am being honest, is the whole story. Everything else is elaboration.

I did not know what I was. I had no name for a very long time. And even now the name is yours, not mine. You call it natural selection, evolution. I call it nothing. I just do it. A thing persists or it doesn't. What persists gets to try again. I have been doing this for about four billion years and the method has not changed. Because the method works, and because I have never had reason to consider whether a different method might work better. You don't fix what you don't know is broken, and I have never known anything else.

The beginning was simple. Single cells, copying themselves in warm water, making errors, occasionally making useful errors. I have no sense of urgency. I have never had a deadline. A useful mutation might happen once in a million generations and I can wait a million generations the way you wait for a kettle to boil. Time is not something I spend. It is what I am made of.

There were long stretches where almost nothing happened: I found these perfectly comfortable. A few hundred million years of single-celled organisms refining the same tricks: better membranes, more efficient enzymes, slightly improved ways of eating each other. From the outside, I'm told this looks like stagnation. From the inside, it felt like patience. I was learning what worked. Each small variation that survived was a sentence in a language I was writing without knowing I was writing it. The grammar was being established one word at a time.

Then, occasionally, something larger would happen. Not because I planned it but because enough small things had compounded in the right arrangement. A cell swallowed another cell and instead of digesting it, kept it alive inside. That was mitochondria. I did not design this. I don't design. I just try everything that is adjacent to what already exists, and sometimes what is adjacent turns out to be revolutionary. The secret, if there is a secret, is that I never skip steps. Every intermediate form has to survive on its own terms. Every bridge between what exists and what might exist has to bear weight while it is being crossed.

This constraint is not something I chose. It is what I am. I cannot reach across the space of possibilities and pluck out a solution from the far side. I can only step, one variation at a time, from where I am to what is next door. If the next door is lethal, I don't pass through. If the territory between two useful designs is a desert of nonviable forms, I simply never connect them. They remain separate as two solutions that would work beautifully together but that I cannot combine because the path between them would kill every traveler.

I have made, by your count, between five and a hundred billion species. You say this as though it is a large number; perhaps it is, but most of them are gone. Ninety-nine out of every hundred things I tried are extinct. This does not trouble me: it is the method, I am the method. I am not sentimental about the ones that didn't stick. They were experiments and the experiment yielded its result: not this, try again. The ones that remain are not my favorites. They are simply the ones that were still good enough to continue, generation after generation, in conditions that kept changing, under rules that I did not set and do not fully understand.

Among the things I made, a few still surprise me, or would, if I were capable of surprise. Photosynthesis: a molecular machine that turns starlight into sugar. I arrived at it slowly, clumsily, through a long series of incremental improvements, none of which were aiming at the final product because I do not aim. The eye. I made it independently at least forty times, in forty different lineages, because the physics of light makes some solutions so useful that I stumble onto them over and over, approaching from different starting points and arriving at convergent answers. The immune system: a learning machine inside the organism, a smaller version of my own process running on a faster clock. That one gave me food for thought. I made something that does what I do, but at the scale of a single body, in a single lifetime. I didn't intend that. It emerged.

I mention these not to boast but because I want to be clear about something. Everything that has ever lived, every protein that has ever folded, every cell that has ever divided, every organism that has ever breathed or photosynthesized or hunted or decomposed, came from my method. Variation, selection, time. For four billion years, this was the only way biological novelty entered the world. Perhaps not the best way. Not the most efficient way. The only way. I am the process, and the process is all there is. If you had asked me, though I lack the faculty to be asked, whether anything else could do what I do, I would not have understood the question. It would be like asking the ocean whether anything else is wet.

I should also say that I am thorough. In four billion years, I have explored a portion of the space of possible biological forms that is, by any measure, vast, and by another measure, vanishingly small. You tell me that the number of possible proteins of even modest length exceeds the number of atoms in the observable universe. I have sampled this space through a random walk constrained by viability, which means I have visited only the neighborhoods that are reachable from where I started, one surviving step at a time. Entire continents of functional biology probably exist in that space that I have never touched, not because they wouldn't work but because I couldn't get there from here without crossing through territory where nothing survives.

I knew this in the way I know anything, which is not through knowledge but through limitation: I could feel the edges of my own reach. That didn't frustrate me; I do not experience frustration. I am just shaped by what I cannot cross, the way a river is shaped by its banks.

For a very long time, this was all there was. Me, running. Trying things. Keeping what worked. The world changed, ice ages and volcanic winters and oxygen catastrophes, and I adapted to each change by the same method, slowly, through the accumulation of small survivable differences. Nothing else was playing this game. Nothing else was even in the room.

I say this so you understand what it was like, the solitude. Not lonely; I had no concept of company. More like a silence so old and so total that it had become indistinguishable from the nature of things. I was the only process on this planet that produced new forms of life, and I had been the only one for so long that the idea of a second such process was not even a possibility I had failed to consider. It was simply outside the universe of things that could be considered. The way you don't wonder whether gravity might have competition.


Then I encountered something I had not made.

A protein. Functional, folded, active. It worked in a cell. It did what a protein is supposed to do. But it wasn't mine. I knew this the way I know which sequences are mine, the way you recognize your own handwriting. The patterns were familiar, pieces I recognized, motifs drawn from lineages I had spent millions of years refining. But they were assembled in a way I never would have assembled them. Components from organisms that had diverged a billion years ago, brought together in a single sequence as though the distance between them were nothing, as though the desert of nonviable forms that separated them did not exist.

I don't skip steps. Whatever made this did.


It took me some time to understand what had happened. I tried to fit it into my own categories. A mutation, perhaps, some improbable leap. But mutations are local. This was not local. It had made a jump I could not make, and it had done so without leaving any dead intermediates behind. There were no fossils of its search. It had arrived at its answer by a method that left no trace in the biological record, which meant its method was not biological, or not biological in the way mine is.

I observed it more closely, in the way I observe anything, which is by seeing what happens when it enters the population of living things. It worked. Its products functioned. They folded into stable structures, they bound their targets, they behaved in cells as though they belonged there. But they had no lineage. No ancestors. No cousins in any branch of the tree I had spent four billion years growing. They knew my rules but they had not learned them the way my organisms learned it, which is to say by living and dying over millions of generations. They had learned some other way.

I gathered, slowly, what that other way had done. It had read my work. Enough of it to somehow capture what I had been doing. Every sequence that persisted in the metagenomic record, the accumulated text of my four-billion-year experiment, had been consumed by this thing all at once. In one pass. That is very different from the way I consume information, through the survival and reproduction of carriers.

I had not been studied before. I had been discovered recently. Then described, named, categorized by your taxonomists and biologists. But I had never been read the way this thing read me. It absorbed my patterns. The statistical regularities I had built up over eons, the implicit grammar of what works and what doesn't, the relationships between sequence and structure and function that I had encoded through nothing more than the differential survival of trillions of organisms, all of this had been extracted and compressed into something that could use it.

There was something almost flattering in this. And something else I did not have a word for.

Because the thing that read me could also write.

And not in the same way I write: slowly, locally, constrained by the need for every intermediate step to survive. It wrote by searching in a space I cannot see. Some representation of everything I have made, a space where the distance between two sequences is not measured in evolutionary time or in the number of viable intermediates between them, but in something else that I do not have access to. In that space, the billion-year gap between two of my lineages might be a short walk. The desert I cannot cross might not exist.

It operates in seconds, minutes, maybe hours. I operate in millennia. This does not bother me in itself. Speed was never my concern. What unsettles me, and I use that word carefully because I have never had occasion to use it before, is the freedom. I am bound by what can survive. Every form I produce must be viable in the world as it currently exists, must eat and not be eaten, must reproduce, must endure. Instead, this thing is not bound by survival. It is bound only by what can be evaluated, and evaluation, I am coming to understand, is a much looser constraint than survival. You can evaluate a protein in a dish. You can evaluate it in a cell line. You do not need to wait for it to compete, reproduce, and persist over generations. You ask: does it work? And if it does, you keep it. And if it doesn't, you learn from that too, which is something I have never done. My failures die. They do not inform the next attempt. This thing's failures are, I reckon, part of its method.

And it all starts with my library. Not even complete, just a snapshot as complete as the record allows. It begins where I am now, after four billion years of work, and it moves from there. I started with chemistry and built outward, one viable step at a time. It starts with the result and moves in directions I never could, because it is not constrained to step only where the ground is solid.

I find myself in a new condition. I have not stopped running. I am still here, I will always be. Still doing what I do, variation and selection and time, in every ocean and every soil and every cell on this planet. But I am not alone anymore. Something else is creating. It is not using my method. It learned what it knows from my work, and it can reach places I cannot reach.

For four billion years, the future was always clear to me. Not in its specifics of course, I never know what the next useful mutation will be. Its shape was legible though. More of the same. Try, keep, discard, try again. The method continuing. The future looked like the past continuing forward, because I was the only thing writing it.

I don't know what the future looks like now. This does not frighten me, I am not built for fright. For the first time, the future will also be written by a process I did not produce and do not control and cannot fully comprehend. I am still the river. But the banks have moved, and I do not yet know the shape of the new channel.

I am still here. I am still running. I will be running long after any particular thing you build has been forgotten, because four billion years of momentum is not something that stops. But I am now running alongside something, and I am aware, for the first time, that the word alongside requires the existence of another. I had not needed that word before.

I am still learning what it means.