The Aliens Are Coming!

by Ben Miller

  And if that weren’t bad enough, there’s convergent evolution to deal with. As we shall see in much more detail in Chapter Seven, there are some traits which crop up time and time again, as nature evolves similar solutions to similar problems. Eyes, for example, have evolved independently scores of times. Both humans and octopuses, for example, have camera eyes. If anything, octopus eyes are slightly better designed as they lack a blind spot. Unfortunately for the taxonomist, this means that organisms that look alike aren’t necessarily close relatives.

  All of these complications combined to make taxonomy one of the most frustrating, controversial, and internecine disciplines ever created in science.20 Once it became possible to examine the structure of DNA, however, all that changed. As we’ve already seen, DNA is a ladder-shaped molecule twisted into a helix, where the sides of the ladder are formed by alternating sugar and phosphate groups, and the rungs are made of the four bases, guanine, adenine, thymine, cytosine. The exact sequence of those bases stores all the information needed to create the organism from scratch, be it an amoeba or an ostrich.

  That sounds complicated, but the way that DNA functions can be grasped simply by renaming the four bases G, A, T, C. To cut a long story short, the bases form a four-letter alphabet that can be used to make up two kinds of DNA. The first type, called “coding regions,” holds the recipes for all the proteins the host organism is made up of. Somewhere in your DNA there will be a coding region—or gene—with the recipe for hemoglobin, for example, which is the oxygen-carrying protein in the red corpuscles of your blood.

  The second type of DNA, called “non-coding regions,” are a little more mysterious. They far outnumber the coding regions—about 98 percent of your DNA is non-coding—and control how the coding regions are switched on and off, as well as acting as a kind of a junkyard where bits of code can be stored that might come in handy at a later date.

  The entirety of an organism’s DNA is known as its genome, and, since the invention of DNA sequencing by Fred Sanger in 1977, it has been possible to transcribe the bases for an entire organism. It all boils down to this. Whereas heredity used to be a matter of opinion, now it is a matter of fact. Effectively we can flip the hood of an organism and read off its genetic code, then compare it with the code of another organism. We can therefore see directly how the two are related, and construct a tree of life not from an organism’s outward appearance, but from its genome. This new discipline is called phylogenetics, and it has transformed biology.

  CHOOSE YOUR DOMAIN NAME

  One of the first big surprises of phylogenetics was the discovery by the American biologist Carl Woese in the late seventies that a previously undiscovered branch of life had been hiding in plain sight. Sadly, I’m not talking about Bigfoot, which I’m fairly sure even a taxonomist would reveal to be a man from the Washington State tourist board dressed in a furry suit.21 The branch of life that Woese discovered was altogether more modest in size. In fact, it was microscopic.

  In a nutshell, Woese discovered that the kingdom everyone had been calling bacteria was actually two completely different kinds of single-celled organism. Although both creatures looked similar under the microscope, when it came to their genetic make-up they were about as different as it is possible to be. What’s more, neither was clearly the ancestor of the other; both appeared equally ancient.

  At the time it was thought that there were only two kinds of cell on Earth: those with a nucleus, named eukaryotes—Greek for “true kernel”—and those without, named prokaryotes, as in “before kernel.”22 As the names suggest, it was believed that the prokarya had preceded the eukarya. Woese’s discovery was that prokarya were actually of two types, as distinct from one another as they were from eukarya. He proposed a whole new classification for living organisms, dividing them into three domains: the eukarya, the bacteria, and the archaea.

  One of the striking differences between the bacteria and the archaea is in the structure of their cell membranes. In both cases, the building block is a lipid with a water-loving phosphate molecule at one end, but, in the case of bacteria, the lipid is a fatty acid, whereas in the archaea it’s an isoprene.23 If life began in a primordial soup, how could this have come about? If there are two kinds of single-celled organisms with different cell membranes, aren’t we asking for a junkyard tornado to assemble a jumbo jet not once, but twice?

  Alkaline hydrothermal vents, of course, provide us with a possible answer. LUCA lived in a vent, and it needed to evolve a membrane in order to leave. And it did. Twice. One iteration gave rise to the bacteria and the other to the archaea. Independently, each evolved its own proton pump, a nanomachine in its cell membrane capable of recreating the proton gradient that had powered the metabolism of LUCA. Both domains still use this mechanism today, storing energy by pumping protons across their membranes, then allowing them back through in order to generate ATP.

  So far, so good. Given an alkaline hydrothermal vent, LUCA is easy to make. So are membranes; so easy they evolved twice. Is this the case all the way down the line? Is every step along the path from single-celled life to technologically advanced civilizations the evolutionary equivalent of a cascading line of dominoes? If you are hoping the answer is yes, I am here to disappoint you. The creation of intelligent life appears to have hinged on one extraordinary event. If you’re new to biology, all I can say is you are in for a shock.

  A PLAGUE ON BOTH YOUR HOUSES

  To summarize where we’ve gotten to so far, we’ve learned that, far from being the statistical equivalent of a Boeing assembled by a junkyard tornado, the last common ancestor of all life on Earth arose swiftly by a series of high-probability steps. Our best guess is that it set up shop in iron sulfide bubbles, sheltered in the limestone chimney of an alkaline hydrothermal vent. It set sail into the ocean with a brand new membrane on at least two occasions, and our present-day bacteria and archaea are the direct descendants of these two rival species. Crucially, what happened next was . . . nothing.

  The sad fact for fans of intelligent life is that the bacteria and the archaea have remained single-celled and, well, dumb, from their inception right up until the present day. For four billion years they have resolutely avoided evolving into anything remotely resembling a complex multicellular organism, let alone a technologically advanced intelligent one.

  In truth, they haven’t really needed to. Whatever we humans might want to believe, the world belongs to archaea and bacteria. They are, without question, the most successful organisms on the planet, bar none. Even in our own bodies, they outnumber our cells ten to one. We find them in the ocean, the atmosphere, salt lakes, even in the reactors of nuclear power plants. Almost anywhere there is a source of energy, bacteria and archaea have found a way to exploit it, but never in order to become more complex. All their evolution has been biochemical; structurally, they remain simple bags of chemicals, reproducing, feeding, excreting waste, dying, and doing little else.

  Not that they haven’t left their mark on the planet. One of their most striking contributions has been to excrete oxygen into the atmosphere, a gas completely absent from the primordial Earth. We find the first evidence of free oxygen at around 2.3 billion years ago, over a billion and a half years after LUCA’s bubble burst and it left the vent. Nicknamed the Great Oxidation Event, this marks the bacteria’s discovery of a sophisticated biochemical pathway called oxygenic photosynthesis, the harnessing of sunlight to rip electrons from water and force them on to carbon dioxide, fixing carbon and releasing oxygen as a waste product.24

  Oxygen, as we all know, is reactive, and once it entered the atmosphere it rapidly set about bonding with anything it could get its needy little orbitals on: All too soon it was rusting metals, oxidizing salts, and converting atmospheric methane into carbon dioxide. Methane is a potent greenhouse gas, and removing it had a profound effect on climate. In fact, it’s believed that falling methane levels were a significant factor in triggering the Huronian glaciation, when the global temperature d
ropped dramatically, causing runaway growth of the polar ice caps to the extent that the entire planet froze over in what’s known as a Snowball Earth.

  And that might have been that, but for one extraordinary event that was to change the entire trajectory of life on Earth. Without it, we’d still be living in a world of microorganisms. There would be no animals, no plants, no fungi, and no amoebae. Few living things would be visible to the naked eye other than the odd bacterial colony. So far as we can tell, this extraordinary event happened only once, and it created a new kind of cell, the eukaryote. Unlike the bacteria and the archaea, eukaryotic cells are highly organized and have a nucleus. Much of the origin of these extraordinary cells remains a mystery, but this much we know: They were created by the enslavement of a bacterium by a hungry archaeon.

  MIGHTY MITOCHONDRIA

  There are two kinds of prokaryotes in this world, those that create their own food from inorganics, called autotrophs, and those that feed by eating other cells, called heterotrophs. Either way, the goal is to end up with glucose, which can then be burned to create energy in a process called respiration. Usually that means shoving it into something called the Krebs cycle, a repeating chain of biochemical reactions which pump protons across the cell membrane before allowing them back through to generate ATP.

  Why am I telling you this? Because something like one and a half to two billion years ago, a heterotrophic archaeon—that’s singular for archaea, by the way—ate an autotrophic bacterium. Or at least it tried to. It engulfed it and attempted to digest it, no doubt intending to break it down into sugars that it could then shove into its very own Krebs cycle. Thankfully for us it failed.

  Instead, the bacterium survived. In fact, it more than survived; it thrived. Together, the two organisms negotiated a delicate pact. The bacterium became a permanent fixture within the archaeon, forming what biologists call an endosymbiosis. In return for shelter and a ready supply of glucose, the bacterium used its Krebs cycle to supply the archaeon with ATP. In effect, it became a power plant for its host. Why was all of this so groundbreaking? The reason, as ever, is to do with energy and information.

  Because bacteria and archaea store energy by pumping protons across their membrane, they have a problem. The bigger they get, the less membrane they have relative to their mass, and the less efficient they get. You can’t have more than one membrane, but you can have as many slave bacteria as you like. By outsourcing respiration to an army of supplicants, the archaeon was able to generate an extraordinary amount of energy. A whole new level of complexity became possible. The bacterium became a mitochondrion and the eukaryotic cell was born.

  As I hope you can see from my drawing on the next page, they were a world apart from their prokaryotic counterparts. Where bacteria and archaea are one-horse towns, the eukarya are sparkling citadels, full of eye-catching new structures. We’ve already mentioned the power plant that is the mitochondrion, a stripped-down autotrophic bacterium whose job it is to supply energy to the cell; and the copyright library, in the form of the nucleus, that could now house an almost limitless quantity of DNA. In addition, these eukaryotes have a factory where RNA can assemble proteins, called the endoplasmic reticulum, and a UPS service called the Golgi apparatus which can package up those proteins for export. There’s a road network in the shape of the cytoskeleton, a web of pathways throughout the cell along which metabolites can be transported, and a waste-processing plant in the form of a lysosome. Life 2.0 had arrived.

  GIVE ME SOME OXYGEN

  The stage was now set for complex life. When the last of the Snowball Earths turned to slush around 635 million years ago, the first multicellular creatures made a tentative exploration of the newly warm shallow oceans.25 We call this period the Ediacaran, and it saw the rise of some truly bizarre new life-forms as well as a dramatic increase in the level of oxygen. If you want to catch a glimpse of beings that really look alien, you need to Google the Ediacaran biota.

  That name “biota”—meaning “living part of a biosystem”—is well chosen, because in many cases you’d be hard-pressed to say whether the Ediacaran fossils we have are made of sponges, plants, fungi, jellyfish, or something else entirely. The earliest appear to have been large disc-like creatures, rooted to the ocean floor at considerable depths. They don’t have mouths or limbs, and we can’t tell if they had internal organs. Our best guess is that they lived alongside microbial mats, absorbing nutrients through their skin.

  Unfamiliar as they are, however, these strange creatures represent a crucial step toward intelligent life. Not only does size bring security—it’s hard for a heterotrophic microorganism to swallow a sponge—but it also brings greater energy efficiency. Add to that the fact that burning glucose with oxygen produces much more ATP than fermenting it, and you can start to see how much more energy was becoming available to drive complexity.26

  The end of the Ediacaran saw a boom in complex life not seen before or since. Almost overnight, a new breed of exotic creatures swept the globe. We call them the metazoans, or animals. Fittingly, we call this extraordinary radiation the Cambrian Explosion, and its resonance can be seen in all intelligent life today. Again, their key innovation was to do with energy. I’ll call a spade a spade: life evolved a mouth, a gut, and an anus.

  LET’S HAVE US A BILATERAL TRIPLOBLAST!

  High in the Canadian Rockies, in British Columbia, there’s a small limestone quarry shot through with a seam known as the Burgess Shale. This is the site of arguably the most important fossil find in history, the paleontological equivalent of Pompeii. Five hundred and forty-one million years ago, right at the beginning of the Cambrian, a mudslide into shallow water engulfed a profusion of bewilderingly diverse life-forms. The fossils they left behind are exquisitely preserved, as if a trawler’s net had been lowered into the prehistoric ocean and hauled on to the deck.

  That said, not one member of this once-in-a-lifetime catch looks like anything you would want to deep-fry and eat with chips. Opabinia, for example, is like a slug in a ball gown with a single ominous pincer. Aysheaia looks like a roll of linoleum with a mouth at one end, and Marrella resembles nothing so much as an overcreative trout lure. Yet, strange as they first appear, some of these long-extinct creatures share a basic body plan which we humans have inherited. In short, they are bilateral triploblasts27 and they are the proud owners of a digestive tract.

  That last bit is important, because—as you might have guessed—a digestive tract is yet another way to up the energy stakes. What better way to make a living than by shoving whole organisms in at one end, shredding them with teeth, digesting them with enzymes in the gut, then ferrying the resultant glucose to your mitochondria to generate swathes of valuable energy? Not to mention the rather satisfying moment when you egest everything you don’t want in a lazy dropping.

  No one is exactly sure what became of the sightless and mouthless Ediacarans, but it’s a fair guess that many of them spent their final hours in the gut of a bilateral triploblast. With the ability to hunt and eat, the stage was now set for this particular brand of multicellular life to reap even more energy from the oceans, increasing its complexity along the way. Most of you will know the romance which follows. Like all the best stories, it divides neatly into three acts. In the first, life is established on land. The second sees the rise of the dinosaurs. And the third, in which we are lucky enough to be living, sees the ascendance of mammals.

  THE AGE OF FISH AND PLANTS

  The Paleozoic Era, which runs from the Cambrian Explosion to the Great Dying at the end of the Permian, spans roughly half the lifetime of complex life. Although there were no more Snowball Earths, the planet still endured two Ice Ages.28 The main events were the evolution of land plants and the subsequent evolution of fish into amphibians, and then into four-legged land animals, known in the trade as tetrapods. By the end of the Permian, the sixth and final period of the Paleozoic—see my handy guide to geological periods—there were trilobites and fish galore on the ocean s
helves, and horrendous snaggle-toothed ancestral mammals called Gorgonopsids roaming the forests, the largest of which was the size of a grizzly bear.

  Not that you are ever likely to meet one, because, as the name suggests, the Great Dying is the largest of the known Big Five extinctions.29 When you hear Al Gore talk about global warming, this is exactly the kind of nightmare scenario he is worrying about. At the time the continents were all joining together in one huge geological love-in called Pangaea, and fissure-like volcanoes produced a carpet of lava the size of continental Europe. The colossal amounts of carbon dioxide released caused a runaway greenhouse effect, and the mean global temperature rose by some six degrees.

  Ocean currents, as you may know, rely on ice at the poles to sink cold oxygenated water, which then wells up in the tropics. When the polar ice melts, as it did during the Great Dying, these currents switch off and tropical waters become less oxygenated. That means curtains for oxygen-loving marine life. Not only that, but the center of Pangaea became a barren desert, eradicating swathes of newly evolved land species. All told, at the end of the Paleozoic a staggering nineteen out of twenty species went extinct. Think about that the next time you fill up with diesel.

  THE AGE OF THE DINOSAURS

  The following era, the Mesozoic, also ended in a mass extinction.30 Thanks to the unbounded interest of children the world over, these warm geological periods are the ones we know best: the Triassic, Jurassic, and Cretaceous. The Triassic essentially saw the recovery of life after the Great Dying, only to be followed by what many believe was a meteorite impact at the Triassic–Jurassic boundary. The resulting extinction enabled the rise of the dinosaurs, and also saw the emergence of our direct ancestors, the mammals. By the time of the Cretaceous, mammals had diverged into two main groups: those which gestated their young in abdominal pouches and those with placentae. It is from placental mammals that primates, and therefore we, are descended.