CHAPTER 5

Little Life and the Biosphere

To give Estha and Rahel a sense of Historical Perspective… Chacko… told them about the Earth Woman. He made them imagine that the earth—four thousand six hundred million years old—was a forty-six-year-old woman.… It had taken the whole of the Earth Woman’s life for the earth to become what it was. For the oceans to part. For the mountains to rise. The Earth Woman was eleven years old, Chacko said, when the first single-celled organisms appeared.

—ARUNDHATI ROY, THE GOD OF SMALL THINGS

Together, Earth and life make up the biosphere.1 The word biosphere was coined by the Austrian geologist Eduard Suess (1831–1914). Suess saw Earth as a series of overlapping and sometimes interpenetrating spheres that included the atmosphere (the sphere of air), the hydrosphere (the sphere of water), and the lithosphere (the rigid, upper levels of the Earth, including the crust and the top layers of the mantle). But it was the Russian geologist Vladimir Vernadsky (1863–1945) who first showed that the sphere of life has shaped planetary history as powerfully as the other, nonliving spheres. We can think of the biosphere as a thin wrapping of living tissue (and the remains and imprints of living tissue) that reaches from the depths of the oceans to Earth’s surface and up into the lower atmosphere. In the 1970s, James Lovelock and Lynn Margulis showed that the biosphere can be thought of as a system with many feedback mechanisms that allow it to stabilize itself in the absence of major shocks. Lovelock called this vast, self-regulating system Gaia, after the Greek goddess of the Earth.

Geology: How Planet Earth Works

Life took some time to get going, so we will begin by considering planet Earth as a purely geological system, like a stage set before the actors have arrived. That should make it easier to understand the complex dramas acted out later by living organisms.

The violent processes of accretion and differentiation, which had forged the young Earth, left a chemically rich ball of matter separated into distinct layers. There was a hot, semimolten core, made mostly of iron and nickel, that generated a protective magnetic field around Earth. Wrapped around the core was a three-thousand-kilometer-thick layer of gas, water, and semimolten rock, the mantle. The lightest rocks rose to the surface and formed Earth’s crust. Gases and water vapor bubbled up through volcanoes to create Earth’s first atmosphere and oceans. Meteors and asteroids ferried in new cargoes of rocks, minerals, water, gases, and organic molecules.

About 3.8 billion years ago, when the bombardment from space eased up, the main driver of geological change was the heat buried in Earth’s core. That heat seeped up through Earth’s mantle, to the crust, and into the atmosphere, churning up the material in each layer, transforming it chemically, and moving vast amounts of matter and gas around in huge, slow convection cycles. Like the evolution of stars, the geological evolution of our Earth was driven primarily by simple processes that fed on an initial, nonrenewable store of energy. Earth changed as it sweated heat from the core through the mantle and crust and out into space.

Heat from the core still drives a lot of geology and will continue to do so for billions of years. But not until the 1960s did geologists figure out how this huge geological machine worked. Their new understanding of geology was based on one of modern science’s most important paradigms: plate tectonics.

Humans have been able to visualize Earth’s surface only in the past five hundred years, when, for the first time, they were able to sail all around it. But most people continued to assume that at large scales, the world’s geography was more or less fixed. Volcanoes might erupt and rivers change course, but surely the layout of continents and oceans, of mountains, rivers, and deserts, of ice caps and canyons, was unchanging. Some, though, began to have doubts. And, just as Darwin showed that life had changed profoundly over the eons, evidence began to accumulate that Earth, too, had a history of profound change.

In 1885, Eduard Suess suggested that about two hundred million years ago, all the continents had been joined together in one supercontinent. We now know he was dead right. Three decades later, Alfred Wegener, a German meteorologist who had done research in Greenland, assembled a lot of evidence that supported Suess’s idea. Wegener published that evidence in 1915, the middle of World War I, in a book entitled (perhaps with a nod to Darwin’s Origin of Species) The Origin of Continents and Oceans. Just as Darwin proposed that living organisms had evolved, Wegener proposed that continents and oceans had evolved, by a mechanism he called continental drift. Once joined in the supercontinent of Pangaea, or Pan-Gaia (a Greek word meaning “all Earth”), they had gradually diverged and moved to their present positions.

Wegener offered plenty of evidence. On a world map, many parts look as if they once fit together, something people had noted since the creation of the first world maps in the sixteenth century. Just before 1600, a Dutch mapmaker, Abraham Ortelius, commented that the Americas seemed to have been “torn away” from Europe by some catastrophe.2 If you look at a modern world map, you’ll see that the shoulder of Brazil fits nicely into the armpit of western and central Africa, while West Africa looks as if it would fit snugly into the huge arc of the Caribbean. In the 1960s, geologists realized that the fit is even better if you focus on the edges of the continental shelves.

Wegener showed that there were almost identical fossils of ancient reptiles in South America and central and South Africa. The early nineteenth-century German scientist Alexander von Humboldt, one of the first scholars to write a modern, science-based origin story, had also noticed similarities between the coastal plants of South America and Africa.3 Then there were rock strata that seemed to start in West Africa and continue in eastern Brazil without missing a beat. As a meteorologist, Wegener was particularly interested in climatic evidence. In tropical Africa, you could find the telltale scratches and gouges of moving glaciers. Could tropical Africa once have hovered over the South Pole? In Greenland, Wegener had found fossils of tropical plants. Something had certainly moved over long distances in the deep past.

But it takes more than some suggestive evidence to make a good scientific hypothesis. Publishing in the middle of World War I didn’t help Wegener’s case, and the fact that he was German and not a geologist ensured that few geologists in the English-speaking world took his ideas seriously. Was it really possible that whole continents could plow through the oceans? Wegener had no idea what force could have pushed them around, and in the eyes of most professional geologists, the absence of an explanation was enough to kill off his hypothesis. In November 1926, Wegener’s theory of continental drift was decisively rejected by the influential American Association of Petroleum Geologists. And that seemed to be that.

Except that a few geologists were intrigued. A British geologist, Arthur Holmes, argued in 1928 that the interior of Earth might be hot enough to act like a slowly moving liquid, like lava. If so, perhaps the motion of material inside Earth could float entire continents around the globe. But not until the 1950s would new evidence show that Wegener, Holmes, and other supporters of the idea of continental drift had been following the right geological scent.

That’s where sonar (the word comes from “sound navigation ranging”) enters the story. Sonar technology can detect and locate objects underwater by bouncing signals off them and analyzing the returning echoes. Many animals use sonar, including dolphins and bats. Human sonar technology, like radiometric dating, was a product of wartime science, in this case attempts to detect enemy submarines. Harry Hess, a geology professor at Princeton, was a naval commander during World War II, and he had used sonar to track German submarines. After the war, he used sonar to map the seafloor, which was still unknown territory to marine geologists. Most expected the seafloor to consist of a flat ooze washed off the continents. Instead, Hess found chains of volcanic mountains running through the Pacific Ocean. No geologist had expected that. After discovering a similar chain running through the middle of the Atlantic Ocean in the early 1950s, he began to develop a theory to explain these mid-oceanic ridges. His task was helped by paleomagnetism, or studies of the magnetism of the seafloor. It was already known that at intervals of up to a few hundred thousand years, Earth’s north and south magnetic poles had swapped places many times. These flips left their traces in lava that seeped up through the ocean floor and took on the prevailing magnetic orientation as they solidified. Measurements of the magnetic orientation of rocks on either side of the volcanic ridges showed a series of north/south flips as you moved away from the ridges. This puzzled Hess.

Eventually, Hess figured out that the undersea mountain chains were being created by magma squeezed up through cracks in the oceanic crust. This made sense, because oceanic crust is thinner than continental crust, so it can be punctured easily by hot magma. As magma climbed through cracks in the seafloor crust, it elbowed the crust apart, creating new seafloor that was imprinted with the magnetic orientation of the period when it formed. The alternating magnetism of mid-oceanic rocks provided a way of dating the formation of these underwater mountain ranges.

Lurking in these discoveries lay the driver of continental drift that Wegener had looked for in vain. Mountain chains, continents, and the seafloor were created and pushed around by huge amounts of hot magma that rose from Earth’s mantle and squeezed through cracks in the seafloor crust. The magma was heated by radioactive elements and by heat from Earth’s core, which retained much of the energy stored during the violent processes of accretion and Earth building. And there in the planet’s core lay the missing driver. Like fusion at the center of a star, heat leaking from the center of the Earth drives most important geological processes on the surface.

We now have abundant evidence that Earth’s crust, both oceanic and continental, is broken into distinct plates that jostle for position as they are dragged back and forth by the semimolten magma on which they float. Hot magmas rising from deep within the Earth circulate under the crust, like water boiling in a saucepan. It is these convection currents of semiliquid rock and lava that move the tectonic plates floating above them. Detailed studies of paleomagnetic bands have allowed earth scientists to trace the movements of plates over hundreds of millions of years, giving us an increasingly precise idea of Earth’s changing geography over the last billion years or so. We now know that these movements have created supercontinents like Pangaea and then broken them up several times in a cyclic process that probably began early in the Proterozoic eon, about two and a half billion years ago. Before that, there were probably no large continents. But some geologists argue that the machinery of plate tectonics may have powered up much earlier. Evidence from the Hadean eon suggests that some form of plate tectonics was already at work 4.4 billion years ago, as soon as Earth differentiated into distinct layers.4

Like big bang cosmology, plate tectonics was a powerful unifying idea. It explained and showed the links between many different processes, from earthquakes to mountain building and the movement of continents. It explains why so many violent geological events take place where tectonic plates meet and grind their way past, over, and under each other. Plate tectonics also explains why Earth’s surface is so dynamic, as it is continually renewed by the arrival of new materials from the mantle, while surface material, in turn, is subducted deep into the Earth.

To understand how plate tectonics works in detail, it helps to focus on the borders between tectonic plates. At divergent margins, like those described by Harry Hess, material rises from the mantle and pushes plates apart. Elsewhere, though, at convergent margins, plates are pushed together. If the two plates have about the same density—if, say, they both consist of granitic continental plates—then, like two bull walruses competing for mates, they will rear up. This is how the Himalayas formed; within the past fifty million years, the fast-moving Indian plate traveled north from Antarctica and smashed into the Asian plate. But if two converging plates have different densities—if, say, one consists of heavy, basaltic oceanic crusts and the other of lighter granitic continental crust—the story is different. The heavier oceanic plate will dive under the lighter plate at a subduction zone. It will travel downward, like a runaway elevator crashing through a concrete floor, carrying crustal material back into the mantle, where it dissolves. As the descending plate drills into the mantle, it will generate so much friction and heat that it can melt the crust above it, splitting it and punching up new volcanic mountain chains. This is how the Andes formed, as the Pacific plate burrowed beneath the plate carrying the west coast of South America.

Finally, there are transform margins. Here, plates grind their way past each other like two pieces of sandpaper jammed together but pushed in opposite directions. Friction will stop the plates sliding until so much pressure builds up that there is a sudden, violent lurch. This is the source of the pressure building up along the San Andreas Fault on the western coast of North America. (Living for a while in San Diego, I occasionally felt tremors, and, like many Californians, I had to buy earthquake insurance.)

The circulation of materials between the atmosphere, the surface, and the mantle had a profound impact on the chemistry of Earth’s upper layers. It generated new types of rocks and minerals. By the time life began to flourish on land, chemical processes within the mantle had already created as many as fifteen hundred distinct types of minerals.5 Plate tectonics give planet Earth an exceptional chemical and geological dynamism.

Plate tectonics also affected temperatures at the young Earth’s surface, and we have already seen how crucial the right temperature was to the history of life on Earth. Two major forces determine average temperatures at Earth’s surface: heat from the interior and heat from the sun. These we can roughly calculate. But the composition of the atmosphere helps determine how much heat is retained at Earth’s surface and how much leaks away into space. Particularly important is the proportion of greenhouse gases. These are gases like carbon dioxide and methane that trap the energy of sunlight rather than reflecting it back into space. Large amounts of greenhouse gases generally mean a warmer Earth. So what controls levels of greenhouse gases?

The astronomer Carl Sagan (one of the great pioneers of a modern origin story) pointed out that answering this question is vital because it may solve another puzzle. Stars like our sun emit more and more energy as they age, so the amount of heat arriving on Earth has slowly increased. When Earth was young, the sun was emitting 30 percent less energy than today. So why was the early Earth not a ball of ice and far too cold for life to form, like Mars today? Carl Sagan called this problem the “early faint sun paradox.”

The answer, it turned out, was the amount of greenhouse gases in the early atmosphere. Their levels were high enough to warm the young Earth so that life could evolve. There was hardly any free oxygen in Earth’s first atmosphere, but there were lots of greenhouse gases, particularly water vapor, methane, and carbon dioxide, belched up from the mantle through volcanoes or ferried in by asteroids. A greenhouse atmosphere was one more important Goldilocks condition for life on the young Earth.

But how stable was this early greenhouse atmosphere? Or, to put it more generally, what ensured that as the sun began to emit more energy, Earth’s surface would remain within the magical temperature range of zero to one hundred degrees Celsius? In the 1970s, James Lovelock and Lynn Margulis argued that there seemed to be powerful self-regulating mechanisms that kept Earth’s surface within the Goldilocks range. As we have seen, they called that something Gaia. Gaia consisted of the sum total of relationships between Earth’s geology and its living organisms that was keeping Earth life-friendly. Many scientists remain skeptical of the Gaia hypothesis. But what is clear is that there are indeed feedback mechanisms within the biosphere, and many do act like thermostats to partially regulate the temperature at Earth’s surface. Some mechanisms are geological, but others work through living organisms.

One of the most important of these thermostats is purely geological, so it would have begun to work even before there was life on Earth. It links tectonics and another driver of planetary change: erosion. While tectonics builds mountains up, erosion grinds them down. Wind and water and chemical flows of various kinds break down the rocks of mountains and move them down a gravitational gradient into the oceans. Erosion explains why mountains aren’t much higher than they are; tectonics explains why they haven’t all vanished into a single, vast global plain. Erosion is itself a by-product of tectonics, of course, because both the wind and rain were burped up from Earth’s innards. And mountain building can speed up erosion as gravity turns high mountain rivers into destructive torrents that gouge the land and transport soils fast toward the ocean.

Here’s how the geological thermostat works. Carbon dioxide, one of the most powerful of the greenhouse gases, dissolves in rainfall and reaches the Earth in the form of carbonic acid. It dissolves material in rocks, and the by-products of these reactions, which contain lots of carbon, are swept into the ocean. Here, some of the carbon gets locked up in carbonate rocks. Where tectonic plates dive back into the mantle at subduction zones, some of this carbon (much of it in the form of limestone) can get buried in the mantle for millions, even billions of years. In this way, the tectonic conveyor belt removes carbon from the atmosphere, and that should eventually reduce carbon dioxide levels and generate colder climates. Today we know that much more carbon is buried within the mantle than is present on Earth’s surface or in its atmosphere.

Of course, if too much carbon dioxide was buried in this way, Earth would freeze. That was prevented (most of the time) by the second feature of the geological thermostat. Driven by plate tectonics (a mechanism that is probably not working on icy Mars), carbon dioxide can return to the atmosphere at divergent zones, where material from the mantle, including buried carbon dioxide, rises to the surface through volcanoes.6 There is a balance between the two halves of this mechanism because higher temperatures generate more rainfall, which accelerates erosion, moving more carbon back into the mantle. But if the Earth cools too much, rainfall will dwindle, less carbon dioxide will be buried, carbon dioxide levels will build up as it is pumped up through volcanoes, and that will warm things up again. The geological thermostat has been adjusting to the increasing warmth of our sun over four billion years.7

We know of nothing like this happening on other planets in our solar system. Venus suggests what Earth could have been like if too much carbon dioxide had remained in the atmosphere. Today, Venus’s atmosphere contains huge amounts of carbon dioxide, and the planet seems to have suffered from a runaway greenhouse effect. Its surface is hot enough to vaporize water and melt lead. Mars took the other wrong turn. It was too small for its gravity to hold on to greenhouse gases, so they leaked away; the planet cooled, and most of its water now exists in the form of ice. Curiosity Rover, as it crawls across the surface of Mars, has shown that there was a time, billions of years ago, when water flowed across its surface and simple life-forms might have flourished. But that time is long past. In any case, neither Mars nor Venus seem to do plate tectonics, which deprives them of a key component of our planet’s thermostat. Mars was too small to retain the internal heat needed to drive tectonics, and Venus, by boiling most of its water away, may have deprived tectonics of the watery lubricant that helped plates move past and over and under each other.8

The geological thermostat was far from perfect, and there were times when it threatened to break down, which would have had dire consequences for the biosphere. But eventually, other, backup thermostats evolved. These were created by the activities of living organisms. So now we must return to the role of life in the biosphere as living organisms stepped onto Earth’s geological stage and began to explore and eventually transform its many different ecological nooks and crannies.

The Unity of Life

Despite the profound differences between Tyrannosaurus rex and an E. coli bacterium, in important respects, life is remarkably unified. All organisms alive today are related genetically. And they share many genetic gadgets, particularly those that, like subroutines in computer software, handle basic housekeeping tasks. In cells, these tasks include jobs such as breaking down food molecules for their energy or their chemical components or moving energy and atoms around. This is why, if you zoom down to the level of cells, it’s hard to distinguish between a human being and an amoeba.

Today, biologists can track the genetic relationships among all living organisms by comparing the huge sequences of As, Cs, Gs, and Ts in their DNA. The basic rule is that the more divergence there is between two genomes, the longer it’s been since those two species shared a common ancestor, and we know roughly the speed at which different types of genomes diversify. So we can say with some confidence that humans and chimps shared a common ancestor about seven or eight million years ago, while humans and bananas have followed different genetic paths for about eight hundred million years. Comparing the DNA of different living species allows us to construct family trees that are much more detailed, and probably more precise, than those based just on the fossil record.

Today, biologists classify all living organisms into three great domains: Archaea and Eubacteria, which consist entirely of single-celled prokaryotes, and Eukarya, which consists of more complex single-celled organisms and also multicelled organisms such as ourselves. The modern classification system has evolved from the taxonomic (classificatory) work of the eighteenth-century Swedish biologist Carl Linnaeus. He grouped all organisms into nested classes. The lowest taxonomic level, the species, contains just one entry. The next level up is the genus, a group of closely related species. Humans, for example, belong to the genus and species Homo sapiens; the genus Homo includes our now-extinct ancestors Homo habilis and Homo erectus (also known as Homo ergaster). The taxonomic levels become increasingly capacious from there; in ascending order, they are family, order, class, phylum, kingdom, and domain. So we can say that humans belong to the species sapiens, the genus Homo, the family Hominidae, the order Primates, the class Mammalia, the phylum Chordata (vertebrates), the kingdom Animalia, and the domain Eukarya.

The first living organisms surely diversified fast, as they entered new evolutionary territory. Many zombies may have survived among them. Here’s one description of the strange world of early life from a recent history of life on Earth:

Sometime early in the Archean eon (which started four billion years ago), reproductive mechanisms got more precise, genes got more stable, and the borders between the living and the almost-living got clearer. That is the point at which natural selection, in Darwin’s sense, really took off. Once life got going, there were no guarantees it would survive. Mars and Venus may once have hosted simple life-forms. But if they did, life was soon extinguished on both planets. Even on Earth, the survival of a thin scum of life for almost four billion years depended on lots of things going right.

Prokaryotes: A World of Single-Celled Organisms

The first living organisms probably belonged to the domain of Archaea, though organisms from the second domain, the Eubacteria, also appeared early. Both domains consist entirely of prokaryotes, minute single-celled organisms that have neither a distinct nucleus nor other specialized cellular organelles. Prokaryotes would dominate the biosphere for more than seven-eighths of its history, until about six hundred million years ago. If we meet living organisms elsewhere in our galaxy, we probably won’t be shaking hands with them but peering at them through a microscope.

So small are prokaryotes that one hundred thousand of them could have a party inside the dot at the end of this sentence. Prokaryote genes float freely in rings and filaments inside the salty molecular sludge of their cytoplasm, so their DNA is constantly buffeted, like everything else in the cytoplasm, and can easily be damaged or altered. Bits of genetic material could even float through the cell membranes and migrate to other cells. In the prokaryotic world, many genetic ideas spread sideways, among unrelated individuals, as well as vertically, from parent to offspring. Prokaryotes trade genes as we humans trade stocks and shares, which is why the idea of a distinct species is harder to define in the prokaryotic world than in our world.

Today, prokaryotes still dominate the biosphere. On and within your body, there are probably more prokaryotic cells than cells with your own DNA. But we ignore them (until they give us a stomachache or cold) because they are so much smaller than our own cells. This vast shadow world that we share with prokaryotes is known as the microbiome.

Until recently, it was tempting to think that the history of single-celled organisms was boring, so we could happily skip the first three billion years of the biosphere’s history. Today we are learning that we can’t make sense of the biosphere’s recent history without understanding the much longer era of little life. As they evolved, prokaryotes developed many new tricks that let them exploit different environments, and we still use several of the biochemical techniques they pioneered.

All prokaryotes can process information. In a sense, they can even learn. Embedded in their membranes are thousands of molecular sensors that can detect gradients of light and acidity, sense when there are potential foods or poisons nearby, and tell if they have bumped into something hard. The sensors are made of proteins, which, like all enzymes, have binding sites that glom on to particular molecules outside the cell or react to changes in light, acidity, or temperature. Once these proteins detect something, their shape changes slightly, which sends a signal to the inside of the cell. The much-studied E. coli bacterium, for example, has four different types of sensor molecules embedded in its membranes, and together they can detect about fifty different types of good or bad things in the neighborhood.10 Once the sensors have detected something, the cell can make choices. For example, it can decide to let particular molecules through its membrane walls (because they look like food) or keep them out (because they look like poison). The decision-making can be very simple. It may be based on a tiny number of inputs and require only yes/no answers. “Should I let this molecule in or not?” Or “It’s getting too hot on this side, yikes! Should I move?” But even the simplest sensors are, in effect, creating basic sketches of a cell’s environment. Once a decision to move has been reached, any equipment the cell has to control motion will be activated. For many bacteria, that is a sort of rotating tentacle, or flagellum, that can act like a propeller. E. coli has six of these whiplike appendages embedded in its membranes. Each is constructed from twenty different components and can rotate several hundred times a second, powered by energy from proton gradients across its membranes. When needed, the flagella can rotate together to give a more directed motion.11 The link between sensors in the membrane and the flagella means that, in effect, E. coli has a short-term memory. It may last for just a few seconds but is powerful enough to say either “No problem, nothing to do!” or “This is not good, flagella, start flailing!” The short-term memory is based on tiny changes in the sensors and the chemicals they emit.

This is simple information-processing equipment, but already we have the three key components of all biological information processing: inputs, processing, and outputs.

Information management gave prokaryotes more control over local flows of energy. Over time, prokaryotes evolved to get, control, and manage energy in many of the diverse environments of Earth’s oceans. The first prokaryotes were probably chemotrophs. That means they got their energy from geochemical reactions between water and rocks that released simple substances such as hydrogen sulfide and methane, chemical energy they could tap.12 But easily digestible chemicals that could release drip-feeds of energy were in limited supply in the earliest oceans; they were readily available only in rare environments such as suboceanic vents. Those limits would have narrowed the possibilities for life on Earth. Quite early on, some prokaryotes learned how to eat other prokaryotes. These were the biosphere’s first heterotrophs, the prokaryotic equivalent of carnivores such as T. rex. You and I are also heterotrophs; we get our food energy by consuming other organisms, not by eating chemicals. But even eating other organisms has its limits if the entire biosphere depends on an energy chain anchored within the oceans.

Photosynthesis: An Energy Bonanza and a Revolution

By about 3.5 billion years ago, a new evolutionary innovation, photosynthesis, was letting some organisms tap into flows of energy from the sun. This was life’s first energy bonanza, and its impact was the prokaryotic equivalent of a gold strike.

Photons of light from the sun have thousands of times more energy than the tired old photons from the cosmic background radiation. Tapping into that colossal flow of energy was a game changer. From now on, though life would continue to recycle all the matter it used (hence the interest of scientists in flows of carbon, nitrogen, and phosphorus), energy seemed to be more or less limitless.13 Living cells now had the energy to reorganize themselves and their surroundings on an entirely new scale. They spread more widely and the amount of life surely increased by several orders of magnitude.

How did living organisms use sunlight? There are several types of photosynthetic reactions that convert sunlight to biological energy with varying degrees of efficiency and release different by-products. All of them use energetic photons newly arrived from the sun to goose electrons inside light-sensitive molecules such as chlorophyll. This gives the electrons such a shock that they jump out of their home atoms and then get kidnapped, wriggling all the time, by proteins. The proteins pass the high-energy electrons through cell membranes in a sort of bucket brigade. This creates an electrical gradient across the membrane that can be used to charge up energy-carrying molecules such as ATP. This is chemiosmosis again, but this time, the energy that charges up molecules of ATP comes not from food molecules but from that vast generator in the sky, the sun.

That’s the first stage in all forms of photosynthesis. In the second stage, the captured energy is used, in a series of complex chemical reactions that vary greatly in their efficiency, to do work inside the cell or to form molecules such as carbohydrates that can warehouse energy for future use. The earliest forms of photosynthesis did not produce oxygen as a by-product, and they worked well in a world without free oxygen. They may have used energy captured from sunlight to steal electrons from hydrogen sulfide (rotten-egg gas) or from iron atoms dissolved in the early oceans.

Even the simplest early forms of photosynthesis provided a revolutionary new supply of energy, and the amount of life in the early oceans may have increased to as much as 10 percent of today’s levels.14 Prokaryotes that made their living from photosynthesis had to be near the surface of the oceans or on seashores. Many formed coral-like structures known as stromatolites, which grew into reefs at the edges of continents as billons of organisms accumulated over thickening layers of their dead ancestors. Stromatolites still exist in a few special environments, such as Shark Bay, off the coast of Western Australia. They are rare today, but from the time when they first appeared, more than 3.5 billion years ago, until about 500 million years ago—significantly more than half the history of our planet—they were probably the most visible form of life on Earth. If aliens had come looking for life on this planet, they would have found stromatolites. And perhaps that’s what we’ll find when we first detect life on rocky planets in other star systems.

Eventually, new forms of photosynthesis evolved in a group of organisms known as cyanobacteria. These forms of photosynthesis could extract more energy by using water and carbon dioxide as their primary raw materials. Prying electrons loose from water molecules was tougher than capturing them from hydrogen sulfide or iron. But if you could do it, you got more energy, and of course in water, you had a much more abundant source of energy. Using the energy captured from sunlight, these sophisticated photosynthesizers zapped water molecules and stripped electrons from their hydrogen atoms. Then they added the captured electrons to carbon dioxide molecules to form carbohydrate molecules, which acted as huge energy barns. The oxygen from broken water molecules was released as waste. The general formula for this oxygen-generating form of photosynthesis is H2O + CO2 + energy from sunlight → CH2O (carbohydrates that act as stores of energy) + O2 (molecules of oxygen that are released into the atmosphere). Oxygen photosynthesis was much more efficient than earlier forms but still could extract only about 5 percent of the energy in sunlight, which is less than the most efficient modern solar panels. Photosynthesis pays a substantial garbage tax to entropy in the energy wasted inside the cell and the energy and materials carried away by oxygen.

Oxygen-producing photosynthesis, the sort of photosynthesis used by all modern cyanobacteria, may have evolved as early as three billion years ago. This is suggested by evidence for brief “whiffs” of increased oxygen levels even before the end of the Archean eon, two and a half billion years ago. But at first, any oxygen they released would have been quickly absorbed by iron or hydrogen sulfide or free hydrogen atoms, because oxygen is an electron thief and will combine eagerly with any element that has spare electrons. That is why atoms that have had their electrons stolen are said to have been oxidized. (Atoms with spare electrons are said to be reduced, and the many chemical reactions that involve both processes are known as redox reactions.) Powerful evidence for the evolution of the first cyanobacteria is the disappearance from three billion years ago of sedimentary rocks rich in pyrite (fool’s gold), which, like iron, rusts in the presence of free oxygen. But there was a limit to how much oxygen these mechanisms could absorb, and starting about 2.4 billion years ago, levels of atmospheric oxygen began to rise fast, from less than 0.001 percent of today’s levels to perhaps 1 percent or more.

The appearance of an oxygen-rich atmosphere beginning about two and a half billion years ago (the “great oxygenation event”) transformed the biosphere. Rising oxygen levels altered the chemistry of the biosphere and even of the upper levels of Earth’s crust. The exceptional chemical energy of free oxygen powered new chemical reactions that created many of the minerals on today’s Earth.15 High up in the atmosphere, oxygen atoms combined to form three-atom molecules of ozone, O3, that began to shield Earth’s surface from dangerous solar ultraviolet radiation and have continued to do so ever since. Protected by the ozone layer, some algae may have started colonizing the land for the first time. Until then, bathed in solar radiation that would have ripped apart any bacteria brave enough to venture onto land, the continents of planet Earth had been more or less sterile.

The oxygen buildup was a profound shock to living organisms because, for most of them, oxygen was poisonous. So rising oxygen levels caused what the biologist Lynn Margulis called an “oxygen holocaust.” Many prokaryotic organisms perished, and those that didn’t die retreated to protected environments in the deeper, oxygen-poor levels of the oceans or even into rocks.

Rising oxygen levels messed up Earth’s thermostats because as yet there were no mechanisms that could absorb excess oxygen, so the buildup threatened to run out of control. Free oxygen broke down atmospheric methane, one of the most powerful of greenhouse gases, while photosynthesizing cyanobacteria consumed huge amounts of the other crucial greenhouse gas, carbon dioxide. As oxygen levels rose and levels of greenhouse gases fell, early in the Proterozoic eon, Earth froze in the first of several snowball-Earth episodes. Glaciers spread from the poles to the equator, turning the Earth white, and a white Earth reflected more sunlight, cooling it even further in a terrifying positive-feedback loop. Eventually, most of Earth’s oceans and continents were covered by ice. The Makganyene glaciation lasted for one hundred million years, from around 2.35 to 2.22 billion years ago.

This was a close shave. Organisms for which oxygen was a poison perished or hid deep in the oceans. But even organisms that could cope with oxygen suffered in a world where glaciers covered both the land and the oceans, blocking the sunlight needed for photosynthesis. Life hung by a thread, as most life-forms retreated beneath the ice and huddled around the warm fires of suboceanic volcanoes.

But Earth did not go the way of Mars and get too cold for life. This was thanks to the geological thermostat driven by plate tectonics, now renovated and supplemented by new biological techniques that depended on the activity of photosynthesizing organisms. Glaciers blocked photosynthesis, which slashed oxygen production. Meanwhile, under the glaciers, oceanic volcanoes kept pumping carbon dioxide and other greenhouse gases back into the oceans. Greenhouse gases began to accumulate beneath the ice until, eventually, they broke through the glaciers, and Earth’s surface warmed again. Oxygen levels plummeted to about 1 or 2 percent of the atmosphere, and there followed a long period, almost a billion years, during which oxygen levels remained low and climates remained warm. Earth’s ancient thermostats seemed to have been reset to cope with the presence of significant levels of atmospheric oxygen produced by cyanobacteria.

Eukaryotes to the Rescue

Was this a long-term solution? Didn’t these mechanisms promise a biosphere that would fluctuate dangerously between extreme heat and extreme cold? If so, why were climates relatively stable for a billion years between about two billion and one billion years ago? Now biology came to the rescue by evolving new types of organisms that could supplement Earth’s thermostats by sucking oxygen out of the air. These organisms, the first eukaryotic cells, didn’t just help stabilize global temperatures. They also marked a biological revolution that would eventually allow the evolution of large organisms such as you and me.

So far, all living organisms had been single-celled prokaryotes in the domain of either Archaea or Eubacteria. The appearance of a third domain of life-forms, Eukarya, matters a lot to us because all large organisms, including ourselves, are built from eukaryotic cells. These were the first cells that could use oxygen systematically, exploiting its fierce chemical energy in a process known as respiration, which is what we do when we breathe. Respiration is the reverse of photosynthesis and is really a way of releasing solar energy that has been captured and stored within cells through photosynthesis. While photosynthesis uses energy from sunlight to turn carbon dioxide and water into energy-storing carbohydrates, leaving oxygen as a waste product, respiration uses the chemical energy of oxygen to pilfer the energy warehoused in carbohydrates, leaving carbon dioxide and water as waste products. The general formula for respiration is CH2O (carbohydrates) + O2 → CO2 + H2O + energy.

Like photosynthesis, the evolution of respiration by eukaryotes counts as an energy bonanza, because it gave these new organisms access to the huge chemical energies of oxygen but in tiny, gentle doses that didn’t blast them apart. Respiration gives you the energy of fire without its destructiveness. By using oxygen cleverly, respiration can extract at least ten times as much energy from organic molecules as earlier non-oxygenic ways of breaking down food molecules.16 With more energy to power their metabolism, rates of primary production—the production of living organisms—may have increased by anything from ten to a thousand times.17

Genetic evidence suggests that the first eukaryotes evolved about 1.8 billion years ago.18 As they proliferated, taking in more and more oxygen, they pumped carbon dioxide back into the atmosphere as a waste product. And here we see the beginnings of a new, biologically controlled planetary thermostat. Eukaryotes began to remove much of the atmospheric oxygen generated by cyanobacteria. This may help explain why climates were relatively stable for much of the Proterozoic eon. Indeed, they were so stable that some paleontologists refer to the period between about two and one billion years ago as “the boring billion.”

Modern biologists regard the distinction between eukaryotic and prokaryotic cells as one of the most fundamental divides in biology. Eukaryotic cells are much larger than most prokaryotic cells. They can be ten or a hundred times as wide, so their total volume can be many thousands of times as large. In eukaryotes, membranes form inside cells as well as around them, creating separate compartments, like rooms in a house, in which different activities can take place. This allows specialization, an internal division of labor that was impossible for prokaryotes. One of these compartments, the nucleus, protects the genetic material of all eukaryotes. Indeed, the word eukaryote comes from the Greek for a “shell” or “kernel.” The protected container of the nucleus ensured that eukaryotic DNA was generally more stable than that of prokaryotes. It could also be stored in larger amounts and copied more easily, so eukaryotes generally have more genetic toys to play with. That explains why they would eventually evolve even more exuberantly than prokaryotes. Eukaryotes also contain many internal organelles, like cut-down versions of the hearts, livers, and brains of animals. The most important of these are the mitochondria that some eukaryotes use to tap the rich energy of oxygen, and the chloroplasts that other eukaryotes use to tap the energy of sunlight through photosynthesis.

Eukaryotes also had new information-processing and body-control capabilities, which meant they could respond in more complex ways to changes in their surroundings.19 The single-celled eukaryote paramecium has a neat trick for dealing with obstacles. If it hits one, it backs off, turns a few degrees, and moves forward again, repeating the toing-and-froing, like a bad driver trying to parallel-park, until it is no longer hitting anything. In effect, it is mapping its environment and learning what to do next. It is using information about its surroundings to orient itself in the world, to avoid dangers, and to find energy and food.

How did the first eukaryotic cells evolve? The biologist Lynn Margulis showed that they evolved not through competition but rather by a sort of merging of two existing prokaryotic species. It is common for different species to collaborate through what is known as symbiosis. Today, humans have vital symbiotic relationships with wheat, rice, cattle, sheep, and many other species. But Margulis was talking about a much more radical type of symbiosis, one in which once independent bacteria, including the ancestors of modern mitochondria, ended up living inside a cell from the Archaea. Margulis called the mechanism endosymbiosis. At first, her idea seemed crazy, because it ran counter to some of the most fundamental concepts about evolution by natural selection. But most biologists now accept her arguments.

The most important evidence for endosymbiosis is the odd fact that some of the organelles inside eukaryotes contain their own DNA, and that DNA is quite different from the genetic material in the nucleus. Margulis realized that organelles such as the mitochondria that manage energy in animals and the chloroplasts that manage photosynthesis in eukaryotic plants look as if they were once independent prokaryotic cells. Exactly how they ended up inside other cells remains unclear, and some have argued that such mergers must be extremely rare. If so, that probably means that even if bacterialike organisms are common in the universe, large organisms like us may be extremely rare, because, on our planet at least, only eukaryotes can build large organisms.

Margulis’s discovery of endosymbiosis tells us something more about the history of life. Evolution is not just a matter of competition. Nor is it just a matter of constant divergence as new species appear. We also see collaboration, symbiosis, and even convergence. This means we have to reconsider the conventional metaphor of a tree of life, because even if we still think of three domains of life, it looks as if the third domain, the Eukarya, evolved not by increasing divergence but by the convergence of Archaea and Eubacteria—rather as if two branches of an ancient tree joined up again.

As if that were not strange enough, eukaryotes had one more trick up their sleeve: sex. Like all species, prokaryotes pass their genes on to their offspring. Most just split in two and pass on their genes through asexual reproduction. But, as we have seen, prokaryotic genes can also travel sideways as bits of DNA and RNA jump ship, go on the road, and find new homes inside other cells. Prokaryotic cells share genes the way humans share library books. But eukaryotes have a different and more complex way of passing on their genes, and they pass them on only to their offspring, never to strangers.

In eukaryotes, the genetic material is locked inside the protected vault of the nucleus. That material is released only under the most stringent conditions, using rules less promiscuous and more orderly than those of prokaryotes, and these rules affect how eukaryotic cells evolve. When eukaryotes produce germ cells—eggs and sperm, the cells from which their offspring will be formed—they don’t just copy their DNA. They stir it around first. They swap some of their genetic material with another individual of their species so that the offspring of the two parents gets a random selection of genes, one half from one parent and the other half from the other parent. Both the genetic and the physical mechanisms involved in this elaborate dance are exquisitely complex. But the result was to add a new twist to evolution. Slight but random genetic variations were guaranteed every generation, because even if most of the genes were the same (after all, both parents are from the same species), a tiny number were always slightly different. With more variation to select from, evolution had more options. That’s why evolution seems to have sped up in the past billion years. The boring billion years of the Proterozoic eon prepared the way for a much more exciting time—the Phanerozoic eon, the era of big life.