‘The botanist is he who can affix similar names to similar vegetables, and different names to different ones, so as to be intelligible to every one,’ observed the great Swedish taxonomist Carolus Linnaeus, a botanist himself. It might strike us as a limited ambition today, but in classifying the living world according to the traits of species, Linnaeus laid the foundations of modern biology. He was certainly proud of his achievements. ‘God creates, Linnaeus organises,’ he liked to say; and he would doubtless think it only proper that scientists still use his system today, subdividing all life into kingdom, phylum, class, genus and species.

This urge to categorise, to draw order from chaos, begins to make sense of the world around us and lies at the root of a number of sciences. Where would chemistry be without its periodic table? Or geology, without its eras and epochs? But there is a striking difference with biology. Only in biology is such classification still an active part of mainstream research. How the ‘tree of life’, that great chart plotting out the relatedness of all living organisms, should be structured is the source of rancour, even rage, among otherwise mildmannered scientists. One article by Ford Doolittle, most urbane of scientists, conveys the mood in its title – ‘Taking an axe to the tree of life ’.

The problem is not one of arcane subtleties, but concerns the most important of all distinctions. Like Linnaeus, most of us still instinctively divide the world into plants, animals and minerals – they are, after all, the things we can see. And what could be more different? Animals charge around, guided by their sophisticated nervous systems, eating plants and other animals. Plants produce their own matter from carbon dioxide and water, using the energy of sunlight, and are rooted to the spot; they have no need of a brain. And minerals are plainly inanimate, even if the growth of crystals persuaded Linnaeus, a touch embarrassingly, to categorise them too while he was at it.

The roots of biology as a subject likewise split into zoology and botany, and for generations never the twain did meet. Even the discovery of microscopic life forms did little to break down the old division. ‘Animalcules’ like amoeba, which move around, were dropped into the animal kingdom, and later on took the name protozoa (literally, ‘first animals’), while coloured algae and bacteria were added to the plants. Yet if Linnaeus were to be pleased to find his system still in use, he would be shocked by the degree to which he had been deceived by outward appearances. Today the gap between plants and animals is perceived as quite narrow, while a dreadful gulf has opened up between bacteria and all the rest of complex life. It is the crossing of this gulf that causes so much disagreement among scientists: how exactly did life go from the primitive simplicity of bacteria to the complexity of plants and animals? Was it always likely to happen, or shatteringly improbable? Would it happen elsewhere in the universe, or are we more or less alone?

Lest the uncertainty play into the hands of those who would like to ‘add a little God’ to help out, there is no shortage of plausible ideas; the problem lies in the evidence, and specifically in the interpretation of evidence relating to deep time, a time perhaps 2,000 million years ago, when the first complex cells are thought to have emerged. The deepest question of all relates to why complex life arose only once in the whole history of life on our planet. All plants and animals are undoubtedly related, meaning that we all share a common ancestor. Complex life did not emerge repeatedly from bacteria at separate times – plants from one type of bacteria, animals from another, fungi or algae from yet others. On the contrary, on just one occasion a complex cell arose from bacteria, and the progeny of this cell went on to found all the great kingdoms of complex life: the plants, animals, fungi and algae. And that progenitor cell, the ancestor of all complex life, is very different from a bacterium. If we think about the tree of life, it’s as if bacteria make up the roots, while the familiar complex organisms make up the branches. But whatever happened to the trunk? While we might consider single-celled protists, such as amoeba, to be intermediate forms, they are in fact in many respects nearly as complex as plants and animals. Certainly they sit on a lower branch, but they’re still well above the trunk.

The gulf between bacteria and everything else is a matter of organisation at the level of cells. In terms of their morphology at least – their shape, size and contents – bacteria are simple. Their shape is usually plain, spheres or rods being most common. This shape is supported by a rigid cell wall around the outside of the cell. Inside there is little else to see, even with the power of an electron microscope. Bacteria are pared down to a minimum compatible with a free-living lifestyle. They are ruthlessly streamlined, everything geared for fast replication. Many keep as few genes as they can get away with; they have a propensity to pick up extra genes from other bacteria when stressed, bolstering their genetic resources, and then lose them again at the first opportunity. Small genomes are copied swiftly. Some bacteria can replicate every 20 minutes, enabling exponential growth at astounding rates, so long as raw materials last. Given sufficient resources (obviously an impossible demand) a single bacterium weighing a trillionth of a gram could found a population with a weight equal to that of the earth itself in less than two days.

Now consider complex cells, which rejoice in the formidable title eukaryotes. I wish they had a friendlier name, for their importance is second to none. Everything that is anything on this earth is eukaryotic – all the complex life forms that we’ve been talking about. The name derives from the Greek, eu meaning ‘true’ and karyon meaning ‘nut’, or ‘nucleus’. Eukaryotic cells, then, have a true nucleus, distinguishing them from bacteria, which are termed prokaryotes for the lack of one. In a sense, the prefix pro- is a value judgement, for it proclaims the prokaryotes evolved before the eukaryotes. I think this is almost certainly true, but a few researchers would disagree. Regardless of exactly when it evolved, though, the nucleus is the defining feature of all eukaryotic cells. We can’t hope to explain their evolution without understanding how and why the nucleus came to be, and conversely why no bacteria ever developed a true nucleus.

The nucleus is the ‘command centre ’ of the cell, and is packed with DNA, the stuff of genes. Beyond its very existence, there are several aspects of the eukaryotic nucleus that are alien to bacteria. Eukaryotes don’t have a single circular chromosome, like bacteria, but a number of straight chromosomes, often doubled in pairs. The genes themselves are not strung out along the chromosome like beads on a string, as in bacteria, but are broken up into bits and pieces, with great expanses of non-coding DNA in between: we eukaryotes have ‘genes in pieces’, for whatever reason. And finally, our genes don’t lie ‘naked’, like those of bacteria, but are fantastically bound in proteins, an arrangement as impervious to tampering as modern plastic gift-wrapping.

Outside the nucleus, too, eukaryotic cells are a world apart (see Fig. 4.1). They are usually much bigger than bacteria – on average, 10,000 to 100,000 times their volume. And then they are full of all sort of things: stacks of membranes; sealed vesicles galore; and a dynamic internal cell skeleton, which provides structural support, while at once being able to dismantle and rebuild itself around the cell, enabling changes of shape and movement. Perhaps most important of all are the organelles. These microscopic organs are devoted to particular tasks in the cell, just as the kidney or liver carry out their own specialised tasks in the human body. Most significant are the mitochondria, known as the ‘powerhouses’ of the cell, which generate energy in the form of ATP. An average eukaryotic cell harbours a few hundred mitochondria, but some contain as many as 100,000. Once upon a time they were free-living bacteria, and the consequences of their entrapment will loom large in this chapter.

These are merely differences in appearance. In behaviour, eukaryotic cells are equally arresting, and again utterly different from bacteria. With a few fiddling exceptions, so to speak, practically all eukaryotes have sex: they generate sex cells like the sperm and egg, which fuse together to form a hybrid cell with half the genes of the father, and half of the mother (more on this in the next chapter). All eukaryotic cells divide via a spellbinding gavotte of chromosomes, which double up and align themselves on a spindle of microtubules, before retiring to opposite ends of the cell, as if with a bow and a curtsy. The list of eukaryotic eccentricities goes on, and I want to mention just one more: phagocytosis, or the ability to gobble up whole cells and digest them within. This trait seems to be an ancient one, even if a few groups, such as fungi and plants, have lost it again. So, for example, although most animal and plant cells don’t troop around engulfing other cells, immune cells do exactly that when they consume bacteria, drawing on the same apparatus as an amoeba.

All this relates equally to all eukaryotic cells, whether plant, animal or amoeba. There are, of course, many differences between them too, but set against their shared properties, these pale into insignificance. Many plant cells contain chloroplasts, for example, organelles responsible for photosynthesis. Like mitochondria, chloroplasts were once free-living bacteria (in this case cyanobacteria), which were swallowed whole by a common ancestor of all plants and algae. For whatever reason, this ancestral cell failed to digest its dinner, and through a case of indigestion acquired everything needed to become self-sufficient, powered only by sun, water and carbon dioxide. In one gulp, it set in motion the entire train of circumstances that ultimately separates the stationary world of plants from the dynamism of animals. Yet peer within a plant cell, and this is but a single difference set against a thousand traits in common. We could go on. Plants and fungi rebuilt outer cell walls to reinforce their structure; some have vacuoles, and so on. But these are all no more than trifling differences, as nothing compared to the empty void that separates eukaryotic cells from bacteria.

Yet it is a teasing void, at once real and imaginary. There is some degree of overlap between bacteria and eukaryotic cells in almost all of the traits we’ve considered. There are a few large bacteria, and a good many tiny eukaryotes: their size range overlaps. Bacteria have an internal cell skeleton, alongside their cell wall, composed of very similar fibres to the eukaryotic cell skeleton. It even appears to be dynamic, to a point. There are bacteria with straight (not circular) chromosomes, with structures that resemble a nucleus, with internal membranes. A few lack cell walls, at least for part of their life cycle. Some live in sophisticated colonies that might pass as multicellular organisms, certainly for bacterial apologists. There are even one or two cases of bacteria harbouring other, even smaller, bacteria inside them – an enigmatic finding, given that no bacterium is known that can swallow cells by phagocytosis. My sense is that bacteria made a start along the trail to almost all eukaryotic traits, but then stopped short, unable to continue the experiment, for whatever reason.

You may feel, not unreasonably, that an overlap is the same thing as a continuum, and therefore there is nothing to explain. There can be no void between bacteria and eukaryotes if there is a continuum from simple bacteria at one end of the spectrum to complex eukaryotes at the other. This is true in a sense, but I think it is misleading, for although there is indeed some degree of overlap, it is really an overlap of two separate spectra – a truncated one for bacteria, which runs from ‘extreme simplicity’ to ‘limited complexity’, and a vastly longer one for eukaryotes, which runs from ‘limited complexity’ to ‘mind-boggling complexity’. Yes, there is overlap, but bacteria never made it very far up the eukaryotic continuum; only the eukaryotes did that.

The difference is illustrated forcibly by history. For the first 3,000 million years or so of life on earth (from 4,000 to 1,000 million years ago), bacteria dominated. They changed their world utterly, yet barely changed themselves. The environmental changes brought about by bacteria were awesome, on a scale that even we humans find hard to conceive. All the oxygen in the air, for example, derives from photosynthesis, and early on from cyanobacteria alone. The ‘great oxidation event’, when the air and sunlit surface oceans became flooded with oxygen, around 2,200 million years ago, transfigured our planet forever; but the shift didn’t make much of an impression on bacteria. There was merely a shift in ecology, towards the kind of bacteria that like oxygen. One type of bacteria came to be favoured over another, but all of them remained resolutely bacterial. Exactly the same is true of other monumental shifts in conditions. Bacteria were responsible for suffocating the ocean depths with hydrogen sulphide, for a little matter of 2,000 million years; but they always remained bacteria. Bacteria were responsible for oxidising atmospheric methane, precipitating a global freeze, the first snowball earth; but they remained bacteria. Perhaps the most significant change of all was brought about by the rise of complex multicellular eukaryotes, in the last 600 million years. The eukaryotes offered up new ways of life for bacteria, like causing infectious diseases; but bacteria are still bacteria. Nothing is more conservative than a bacterium.

And so history started with the eukaryotes. For the first time, it became possible to suffer ‘one damned thing after another’, instead of the interminable sameness of it all. On a few occasions, things happened damned fast. The Cambrian explosion, for example, is an archetypal eukaryotic affair. This was the moment – a geological moment, lasting perhaps a couple of million years – when large animals abruptly materialised in the fossil record for the first time. These were not morphologically tentative forms, this no procession of worms, but an astonishing catwalk of weird body plans, some of which vanished again almost as swiftly as they had appeared. It was as if a deranged creator had woken up with a start and immediately set about making up for all those aeons of lost time.

The technical term for such an explosion is a ‘radiation’, in which one particular form suddenly takes off, for whatever reason, and embarks on a short period of unbridled evolution. Inventive new forms radiate out from the ancestral form like the spokes on a wheel. While the Cambrian explosion is the best known, there are many other examples: the colonisation of the land, the rise of flowering plants, the spread of grasses, or the diversification of mammals, to mention but a few. These events tend to occur when genetic promise comes face to face with environmental opportunity, as in the wake of a mass extinction. But regardless of the reason, such magnificent radiations are uniquely eukaryotic. Each time, only eukaryotic organisms flourished; bacteria, as ever, remained bacteria. One is forced to conclude that human intelligence, consciousness, all the properties that we hold so dear and seek elsewhere in the universe, simply could not arise in bacteria: on earth, at least, they are uniquely eukaryotic traits.

The distinction is sobering. While the bacteria put us eukaryotes to shame with the cleverness of their biochemistry, they are seriously stunted in their morphological potential. They seem to be incapable of producing the marvels we see around us, whether hibiscus or hummingbird. And that makes the transition from simple bacteria to complex eukaryotes perhaps the single most important transition in our planet’s history….