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Comment to the reader.
The previous three entries in the How We Came About series have laid out the mechanism by which life on Earth changes: the origin of the first replicators, the molecule that carries hereditary information, and the process of natural selection by which heritable variation accumulates into adaptation. From here on, the series turns from mechanism to history. The remaining entries describe what in fact happened on this particular planet — what species arose, in what order, by what particular events — over the four billion years from the first cells to the species writing these words.
This entry covers the longest single stretch of that history. By word count, it is comparable to the entries that will cover the last six hundred million years. By duration, it covers more than three times as much real time. The reason for the asymmetry is simple: for most of life's history on Earth, life was microscopic, and the events that mattered most are recorded as chemical signatures in rocks rather than as fossils a reader could recognise. Dates given here are approximate, and several of them are still debated by working scientists in the early twenty-first century. I have flagged the more contested ones in the prose.
I write in the spring of 2026 of the Common Era. The figures and frameworks used here are those broadly accepted at this moment; later entries in this series will pick up where this one ends.
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What did life on Earth do for the first two billion years of its existence?
The question seems narrow, but the answer turns out to be most of what matters. By the time the period covered in this entry ends, the air had been remade, the ozone layer had formed, the oceans had begun to clear of dissolved iron, an entirely new kind of cell had been invented, sexual reproduction was in operation, and the first organisms had begun to live in cooperative bodies of many cells working as one. None of the species a casual modern observer would recognise existed yet. There were no animals, no land plants, no macroscopic fungi. There were only microbes, in unimaginable numbers, in seawater and shallow lagoons and damp rock and the cracks of the early crust. And yet by the time microbes were finished with the planet, almost every condition required for the later world was in place.
This is the story of how a young, alien planet became Earth as we now know it.
By around 3.5 billion years ago, and possibly considerably earlier, the surface of Earth was already inhabited.
The earliest direct fossil evidence consists of stromatolites — layered, dome-shaped structures formed by mats of single-celled organisms, generally interpreted as the ancient equivalents of the cyanobacterial mats still found in a few protected modern environments such as Shark Bay in Western Australia [1]. Stromatolites of comparable form, well preserved in the rock record, appear in roughly 3.5-billion-year-old strata in the Pilbara region of Western Australia and in possibly older strata in Greenland; the biological origin of the very oldest examples remains contested at the edges, but a substantial fraction of the geochemistry community accepts them as genuine biosignatures. Earlier traces of life — chemical signatures in carbon and sulphur isotopes, rather than morphological fossils — push the appearance of microbial life back further still, to within a few hundred million years of the planet's surface becoming habitable.
What lived in those mats was a prokaryote: a single-celled organism whose DNA floats freely in the cell's interior, not enclosed in any internal compartment. Prokaryotic cells are the simplest cells we know. They have an outer membrane, a single circular chromosome, ribosomes for making proteins, the molecular machinery for energy production, and at most a few accessory structures — flagella for movement, pili for attachment, a capsule for protection. They have no nucleus. They have no organelles. They are small — typically a few micrometres across — and reproduce asexually by simple division into two daughter cells.
Modern prokaryotes are split into two great branches: the Bacteria and the Archaea. The two branches diverged extraordinarily early in the history of life, possibly very close to or even before the last universal common ancestor described in the previous entry, and have followed independent trajectories ever since. Bacteria and archaea look superficially similar under a microscope, but the molecular details of their cell membranes, their gene-expression machinery, and their characteristic enzymes show that they are deeply distinct lineages. The archaea include many of the organisms found in extreme environments — boiling vents, salt flats, the gut of cattle, the depths of the crust — and the bacteria include essentially everything else, from the cyanobacteria that fill the surface oceans to the gut microbes living in the body of any reader of this entry.
For at least the first two billion years of life on Earth, and arguably more, these were the only kinds of cells that existed. The planet was a microbial planet. There was no soil in the modern sense. There were no animals, no land plants, no macroscopic fungi, no reefs of coral, no insects — nothing a casual modern observer would recognise as a creature. The only structures of biological origin large enough to see with an unaided eye were the layered domes and mats built by single cells living together in their countless billions: stromatolites, now recognised as the oldest tangible fossils of life on Earth, and the cyanobacterial sheets from which they grew. Behind that quiet architecture, the planet was running an enormous and unwitnessed experiment in chemistry.
This was not a stalled period. It was a period of profound chemical innovation. Most of the core metabolic pathways that life on Earth still relies on today were invented by prokaryotes during this stretch. Glycolysis, the citric acid cycle, the use of ATP as the cell's energy currency, the basic decoding of the genetic message into protein, the fixation of atmospheric nitrogen, the various fermentation pathways, the family of photosynthetic systems, the chemistry of methane production: all of these were prokaryotic innovations, refined over hundreds of millions of years, and inherited largely unchanged into every later form of life. When a human cell breaks down sugar for energy, the chemistry it uses is essentially identical to the chemistry of bacteria several billion years ago. The molecular toolkit on which all later life would be built was assembled during the prokaryotic age.
The single most consequential prokaryotic innovation, measured by its long-term effect on the planet, was photosynthesis — the trick of capturing energy directly from sunlight and using it to drive chemistry inside the cell.
The earliest forms of photosynthesis did not produce oxygen. They were anoxygenic: they used sunlight to extract energy from compounds such as hydrogen sulphide, dissolved hydrogen, or ferrous iron in seawater, leaving sulphur or rust as waste. Anoxygenic photosynthesis is still practised today by certain green and purple bacteria living in oxygen-poor environments, and it was almost certainly the older form of the trade. It freed life from total dependence on the chemical energy already dissolved in ocean water, and it spread.
At some point — current estimates centre somewhere between roughly three billion and 2.4 billion years ago, with substantial uncertainty — a lineage of bacteria refined the photosynthetic apparatus to use a more abundant electron donor: water itself [2]. Splitting a water molecule (H₂O) requires more energy than splitting hydrogen sulphide (H₂S), but water is essentially limitless on a planet covered in oceans. The pay-off, for any cell that managed it, was enormous. Water-splitting photosynthesis — oxygenic photosynthesis — was a metabolic windfall, and the lineage that invented it inherited the surface ocean.
That lineage is the cyanobacteria. They are still here today; they are responsible, along with their descendants the chloroplasts of plant cells, for the great majority of the oxygen produced on Earth at every moment. From their first appearance, the cyanobacteria began to alter the chemistry of the planet, slowly at first, then irreversibly.