Introduction
The Age of Reptiles ended because it had gone on long enough and it was all a mistake in the first place.-- Will Cuppy, How to become extinct (1941)
It is hard to make sense of the history of life on Earth. A mass of strange and extraordinary animals and plants perhaps flits before our eyes when we think of prehistory: Neanderthal man, mammoths, dinosaurs, ammonites, trilobites . . . and of course a time when there was no life at all, or at least merely microscopic beasts of extreme simplicity floating in the primeval ocean.
These impressions come from many sources. Children today are weaned on dinosaur books, and the images of living, breathing dinosaurs are everywhere, in movies and television documentaries. Then, too, as children, many people have gone to coastal cliffs or quarries and collected their own fossil ammonites or trilobites. These common fossils, as well as many much more spectacular and beautiful examples, such as petrifactions of exquisite fishes showing all their scales, still shiny after millions of years, may be seen in fossil shops, or in lavish photographs in coffee table books and on the web.
Most people are aware that dinosaurs, despite their ubiquity in modern culture, lived a long time before the first humans, and there were untold spans of time before the dinosaurs existed that were populated by ever-more unusual and strange animals and plants. How are we to make sense of all of this?
Fossils
The keys to understanding the history of life are fossils (Fig. 1). Fossils are the remains of plants, animals, or microbes that once existed. Fossils may be petrifactions, which means literally ‘turned into rock’, and these are some of the commonest examples. Petrified fossils may be of two kinds, first, those that are literally turned to rock, and where none of the original organism remains. The leaf or tree trunk, or shell, or worm, has completely disappeared, and the cavity left behind has been replaced by grains of sand or mud, or more often by minerals in solution that have flowed through the spaces in the surrounding rock and have then infiltrated the space and crystallized.
The second, and commoner, kind of petrifaction still retains some of the original material of the animal, perhaps the calcium carbonate that made up the shell, or some cuticle or carbonized relic of the plant. Rock grains or minerals then merely fill the cavities. So, many people might be surprised to realize that common fossils, such as a 400-million-year-old trilobite or a 200-million-year-old ammonite, are actually largely made from the original calcium carbonate of their external skeleton or shell, as in life. Similarly, by far the majority of dinosaur bones are still made of the original calcium phosphate (apatite), the main mineralized constituent of bone then and today. If you look closely at the outer surface of these fossils, perhaps with a magnifying glass, you can see extremely fine features, such as pimples and growth lines on the trilobite carapace, original multicoloured mother-of-pearl on the ammonite shell, and muscle scars or tooth marks on the surface of the dinosaur bone. If the fossil shells or bones are cut across and examined under the microscope, all the original growth layers and internal structures are still there. So, a section cut through dinosaur bone looks just as fresh today as a section through a modern bone.
Every plant or animal that has ever lived has not turned into a fossil. Indeed, if this were the case, the surface of the Earth would be covered in avalanches of fossils everywhere, great mounds of dinosaur bones, trilobites, giant coal forest trees, ammonites, and the like, probably extending to the moon. No one knows what proportion of life has ended up fossilized, but it is clearly a tiny fraction, much less than 1 per cent. Plants or animals must at least have hard parts such as a skeleton, a shell, or a toughened, woody trunk to be readily preservable. Even so, the majority of animal carcasses and dead plants enter the food chain almost immediately, being scavenged by animals or decomposed by bacteria. Dead organisms can only turn into fossils if sedimentation is happening, that is, sand or mud are being dumped on top of the remains, perhaps on the floor of a deep lake, under a sand bar in a river, or deep in the ocean, below the zone that is constantly churned up by currents and tides.
Worms and feathered dinosaurs: exceptional preservation
Other fossils may be preserved in slightly unusual conditions that may, on occasion, provide unique and unexpected insights into ancient life, so-called exceptional preservation. Exceptionally preserved fossils may show soft structures, such as flesh, eyes, stomach contents, feathers, hair, and the like. Sites of exceptional fossil preservation are sometimes called ‘windows’ on the life of the past. They allow palaeontologists, the scientists who study fossils, to see a snapshot of everything that existed at particular times and in particular places. These at least allow palaeontologists to see the soft-bodied worms, jellyfish, and other creatures that are rarely preserved in normal circumstances.
The Burgess Shale in Canada is one of the most famous of these sites of exceptional preservation. These rocks are 505 million years old, so they document some of the oldest animals. Without the Burgess Shale, and similar sites of about the same age in Greenland and China, palaeontologists would know only about shelled and skeletonized organisms such as brachiopods (‘lamp shells’), trilobites, and sponges. The Burgess Shale has increased our knowledge of life in the Cambrian many-fold: it has revealed whole clans of worm-like creatures, some related to modern swimming and burrowing worms, others seemingly unique and hard to link to modern animals. The Burgess Shale also shows the feathery legs and gills of the trilobites, their mouths, guts, and sense organs, and it reveals strange tadpole-like swimming animals that have primitive backbones and so are close to our own ancestry.
Equally famous are the sites of exceptional preservation in Liaoning Province in north-east China. These date back to 125 million years ago, and they have produced spectacular fossils of birds (and dinosaurs) with feathers and internal organs, mammals with hair, fishes with gills and guts, and any number of worms, jellyfish, and other soft-bodied denizens of those ancient Chinese lakes (Fig. 2).
There are dozens of other such sites of exceptional preservation scattered pretty randomly through time and space. But why do they exist and how are the soft structures preserved? Most of these sites come from times and places where oxygen was limited. Deep lakes and deep oceans sometimes lose the normal oxygen content of the waters, if, for example, there is a dramatic growth of algae and other floating plants at the surface, a so-called algal bloom. These occur in warm conditions, and the lakes and oceans may become temporarily stagnant. The stagnation of the waters may itself kill swimming creatures, and beasts that crawl around on the bottom muds. The lack of oxygen can also mean that the normal scavenging creatures cannot survive, and the carcasses do not have all their flesh stripped.
Experiments show that, in oxygen-poor, or anoxic, conditions, soft tissues, even muscles, guts, and eyeballs, can be invaded by minerals that come from the body fluids of the animals, or from the surrounding sediments. These are typically flash-mineralizing processes, where the fibres of a muscle, or the complex tissues of a gill or a stomach, are invaded and replaced within hours or days at most. Once mineralized, the replicas of soft tissues can then survive to the present day.
Living blimps? Quality of the record
Like most palaeontologists, I sometimes sit bolt upright in bed at night and worry whether the fossil record is informative or not. Charles Darwin wrote about the ‘imperfection of the geological record’, and he was well aware that most organisms are never fossilized, and so palaeontologists miss so much of ancient life.
The question though is: how much is missing? Is it 50 per cent or 90 per cent or 99.99999 per cent? This can never be determined, of course. A more sensible question might be: how adequate is the fossil record?
Palaeontologists have speculated that there might be whole sectors of extinct life that we know nothing about. What if there were a diverse class of floating animals that were constructed of extremely lightweight materials, and provided with great air bladders that filled with gases lighter than air? These creatures might have been many metres long, perhaps as large as dirigible aircraft, sometimes called blimps during the Second World War. These blimp beasts could well have dominated the Earth, if they were so large, and yet they might have entirely escaped fossilization. Their bodily tissues might have been so lightweight that they rotted away when they died. Their gas bladders would clearly burst and disappear during decay. Living in the air, in any case, means their carcasses might have generally fallen onto the surface of the Earth, and so they might not often have been covered with sediment in any case.
Palaeontologists have no way of detecting such hypothetical extinct beasts. Other soft-bodied creatures can be assumed to have existed, though. For example, there are many phyla, or major groups, of worm-like creatures today, nematodes, platyhelminths, gastrotrichs, sipunculids, and others, that have no known fossil representatives. And yet, because they exist today, and because we can establish their evolutionary relationships to other organisms with shells or skeletons, we know the length of their missing fossil record. If a soft-bodied worm group is the closest relative of another wormy creature with a shell, both groups must have existed for the same length of time; their common ancestor must have lived at a particular time, and the fossil record of the shelled group establishes a minimum age for both groups. The known missing record of the soft-bodied group is called a ghost range, a part of the missing fossil record we can predict with some certainty.
What do the sites of exceptional preservation tell us? If they preserve more or less everything that lived at the time, soft- and hard-bodied, they can be used as a yardstick against which to test the ‘normal’ fossil record. It seems that the ancient exceptional sites, such as the Burgess Shales, tell us more about unknown groups than the more recent ones, such as the Liaoning beds in China. In fact the soft-bodied organisms from Liaoning, worms, jellyfish, insects, and the like, are all entirely predictable from other known fossils and from ghost ranges.
Palaeontologists have been pretty assiduous in retrieving fossils. As time goes on, it now seems to take much more effort than it took a century ago to find something new. Indeed, not much has changed in our knowledge of the fossil record since the time of Darwin. In the 1850s, palaeontologists knew about trilobites and ammonites, fossil fishes, dinosaurs, and fossil mammals. They did not know anything about the first life from the Precambrian, nor did they know much about human evolution. But the fact that neither trilobites nor humans have been found in the age of the dinosaurs, nor have any other fossils been found in seriously unexpected places, suggests that the record is known more or less well. Our work now is merely to flesh out the details.
But that still says nothing about the giant blimps . . .
Molecules and the history of life
It might seem unexpected to introduce molecular biology at this point. But, just as historians have parallel sets of evidence from artefacts and from written records, so too do students of the history of life. Until the 1960s, there were only fossils; after that there were also molecules – even though most palaeontologists at the time probably did not appreciate it.
In an extraordinary paper published in 1962 by Emil Zuckerkandl and Linus Pauling, in a rather obscure conference volume, the molecular clock was born. Molecular biology had arisen ten years earlier when, in 1953, James Watson and Francis Crick announced the structure of deoxyribose nucleic acid, DNA, the chemical that makes up genes and is the basis of the genetic code. By 1963, several proteins, such as haemoglobin, the protein that carries oxygen in the blood and makes it red, had been sequenced, that is, the detailed structure had been determined, and the new breed of molecular biologists had noted something extraordinary. The proteins of different species of animal were not identical, and their structures differed more between distantly related species. In other words, the haemoglobin molecules of humans and chimpanzees were identical, but the haemoglobin of a shark was very different.
Zuckerkandl and Pauling took the brave leap of suggesting, on rather limited evidence then, that the amount of difference was proportional to time. The negligible difference between the haemoglobins of humans and chimpanzees showed these two species had diverged only a short time ago, geologically speaking, whereas the 79 per cent difference between human and shark haemoglobin pointed to a divergence 400 million years ago, or more.
In the 1960s, protein sequencing was a laborious process, and the new data came slowly, but by 1967 the haemoglobin of the great apes was known sufficiently that the first attempt was made to produce an evolutionary tree. The science of molecular phylogenetics was born. Vincent Sarich and Allan Wilson, in a three-page paper in the American journal Science, plotted the relationships of humans and apes, and showed that our nearest relative was the chimpanzee, then the gorilla, and then the orang-utan. This was not so unexpected, and it agreed with the pattern of relationships established from studies of anatomy. The shocking part of the paper was that the molecular clock said humans and chimps had diverged only 5 million years ago.
Palaeontologists were variously bemused and horrified. Most dismissed the new technique: after all, if it produced such ludicrous results, it was clearly not working. Everyone knew that humans and chimpanzees had split some 15–20 million years ago, based on studies of Proconsul and other early human-like fossils from the Miocene of Africa. Others took the method seriously, but were equally unhappy about the result.
As the protein data sets grew, more mammals were added to the tree, and the branching dates seemed quite reasonable for most other groups. This increased the nervousness of the palaeontologists, who then faced a conundrum: do we accept the new molecular date, or insist on the established fossil evidence? Slowly, they came to realize the molecular date was probably right. Closer study of the fossils showed that they had been over-interpreted. The supposedly ‘human’ characters of Proconsul and its kin were not really human at all. This fossil was related to the common ancestors of humans and the African apes, and so said nothing about the true timing of divergence. Since the 1970s, new finds in Africa have shown that the divergence date between humans and chimps must be at least 6–7 million years ago.
Now, molecular biologists interested in the tree of life, the great pattern of relationships linking all species, use DNA sequences. Protein sequencing is slow, and the evidence limited. DNA, the genetic code, offers much more information, and new techniques developed in the 1980s have made sequencing almost automatic. Computers can also crunch enormous masses of data these days, so sequencers are happy to run lengthy segments of the genetic code, consisting of many genes, and for dozens, or even hundreds of species, to produce patterns of relationships for specific groups or for large sectors of life. It is possible to assess the genome of, say, twenty species of lizards, and draw up a tree that documents evolution over a span of perhaps 10 million years. Equally, the analyst can select, say, twenty species across all of life – a human, a shark, a mollusc, a tree, a fern, a bacterium – and find a tree of relationships that extends deeply back in time.
But where do the fossils fit into all this?
Cladistics
I remember when I attended my first scientific meeting, as an undergraduate, a session of the Society for Vertebrate Palaeontology and Comparative Anatomy at University College, London, in 1976, I wondered if I would ever go back. As I looked on nervously, the big beasts of the subject were bickering and squabbling appallingly over something called ‘cladistics’. I’d heard nothing about this – it wasn’t taught then as part of my degree. One person would assert with fervour that everyone should adopt this new technique. Another would say it was all nonsense – even a Marxist plot to overthrow the scientific method. I stumbled back to the train, wondering whether my decision to become a professional palaeontologist was mistaken. Were they all mad?
On reading around, I discovered that cladistics had been promulgated by a German entomologist, Willi Hennig. He had written about the technique in the 1950s, but it had only really attracted attention when the book was translated into English and reissued in 1966. But, from 1966 to 1980, only a rather small group of true believers espoused the method, and it had not in any way become mainstream. Hennig argued passionately that systematists, the biologists and palaeontologists who were interested in species and the tree of life, should be more objective in their methods.
Until Hennig’s time, systematists had attempted to draw up trees of relationships based on a judicious sifting of the character evidence. A biological character is any observable feature of an organism – ‘possession of feathers’, ‘possession of four fingers’, ‘iridescent blue feathers on top of the head’, ‘multiple flower heads on each stem’ – and systematists had long understood that if two organisms share a character they might well be related. The problem was always convergence, the well-known observation that unrelated organisms might evolve similar features independently. Insects, birds, and bats have wings, but no one ever suggested that this was sufficient evidence to group these organisms together as close relatives: in detail, their wings are anatomically quite different in structure, and so they evolved them independently, but for the same purpose. But how were systematists to distinguish convergence from truly shared, evolutionarily identical, characters?
This was Hennig’s point: objective techniques were required to distinguish truly shared characters from convergences, but also to distinguish inherited ‘primitive’ characters from those that truly marked a particular branching point. So, while it is true that humans and chimpanzees share the character ‘hand with five fingers’, and this is not a convergence, the character is not helpful at the level of the branching point between the two species.
In fact, all land-living vertebrates basically have a five-fingered hand – lizards, crocodiles, dinosaurs, rats, bats, whales, and so on. Hennig had identified the critical point, that anatomical characters had to be evolutionarily unique (not convergent) and they had to be assessed at the correct level in the tree before they could be considered useful. He termed such characters synapomorphies, sometimes rendered in English as ‘shared derived characters’. (Hennig’s writing, in any language, is heavy going, and he liked inventing long words – neither of which helped gain him converts.)
Hennig’s concept of a synapomorphy is more or less the same as the classic notion of a homology, that is, any structure that shares a common fundamental pattern because of common ancestry – such as the human arm, the wing of a bat, and the paddle of a whale. These limbs may have different functions today, but they all share the same bones and muscles inside, and we now know they evolved from the ancestral front limb of the first mammal.
Since the 1970s, systematists have increasingly switched to using cladistics in their work. After all, there was no alternative – the older techniques were really inspired guesswork. Acceptance came largely for a reason Hennig could not have predicted, namely the growth in power and ease of use of computers. The secret to cladistics is the character matrix, a listing of all the species of interest, and codings of their characters (1 for presence, 0 for absence). Multiple cross-checking over the matrix, and repeated runs of the analysis, provided statistical methods of assessing which tree or trees explained the data best, and the probability that synapomorphies were correctly identified or not. In practice, there have been many problems, but cladistic methods are ubiquitous, and repeat analyses by different analysts allow published trees to be tested and confirmed or rejected.
The great leap forward
Palaeontologists are aware that their field has transformed itself immeasurably since the 1960s, but public attention has focused elsewhere – the space race, genetic engineering, computer technology, nanoscience, global change. But, cladistics and molecular phylogeny have introduced new rigour into the field of drawing up evolutionary trees. Whereas in the 1950s and 1960s a palaeontologist did his or her best to make a tree by ‘joining the dots’ – linking similar-looking beasts through time – today there are many independently derived trees of the evolution of different groups, some based on different genes, others on different combinations of fossil and recent data on anatomy. But do they agree?
The astonishing discovery is that molecular and palaeontological trees agree with each other more often than not. The two approaches are pretty well independent, so it is possible then to compare, say, a tree based on molecular sequences of modern rodents with a tree constructed by measuring the teeth and other anatomical features of living and extinct species. Inevitably, everyone hears about the cases where the results disagree. In the early days of molecular sequencing, some bizarre results emerged, but the methods were young, and mistakes were easy to make. Such bizarre results are rare now. In some cases, palaeontologists have humbly accepted that they have been entirely unable to resolve certain parts of the evolutionary tree, and the molecules give an unequivocal answer straight away. In other cases, there is no resolution yet, and more work is required. Some parts of the great tree of life may remain forever mysterious, perhaps because rates of evolution were so fast that characters did not accumulate, or the branching points are so ancient that subsequent evolution has obliterated the clues to relationship.
The third methodological or technological advance has been in dating the rocks. Since the 1960s, the accuracy of dating has improved greatly, and sequences of rocks and sequences of events can be compared more accurately than before. But we can look at that later. Let’s begin the story.
Chapter 1 : The Origin of Life
As a general rule, then, all testaceans grow by spontaneous genera-tion in mud, differing from one another according to the differences of the material; oysters growing in slime, and cockles and the other testaceans above mentioned on sandy bottoms; and in the hollows of the rocks the ascidian and the barnacle, and common sorts, such as the limpet and the nerites.-- Aristotle, History of Animals
From the earliest days people have wondered about the origins of life. The ancient Greeks and Romans considered the topic, and had many ideas. Most, like Aristotle (384–322 BC), focused on the idea of spontaneous generation, a process that they believed happened today, and that had presumably happened when life first arose. As Aristotle wrote above, he believed that marine shellfish all arose spontaneously from the mud, sand, and slime on the seabed and among the coastal rocks. He made similar assumptions about other forms of life: moths arose from woollen garments, garden insects arose from the spring dew or from decaying wood, and many fishes arose from froth on the surface of the ocean. Such views held sway until the nineteenth century.
Louis Pasteur (1822–95) famously showed conclusively that life could not arise spontaneously. He repeated experiments that had been performed before, but took great pains to exclude all possibility of contamination. Earlier workers had gone through the process of boiling a broth of water and hay in sealed flasks so that anything living in the water or the air within the flasks would be killed. But, despite these precautions, they still found microscopic organisms living in the water, and Pasteur argued that the germs entered the vessels when they were being cooled in a mercury trough. So he repeated the experiments, sterilizing the glassware and the water in the flasks, but ensuring also that laboratory air could not enter the cooling mixtures. With the air excluded, nothing living was detected in the boiled water even many months later.
The age of the Earth
The death of spontaneous generation was not the only problem for scientists interested in studying the origin of life about 1900. They also had no truly ancient fossils to work with, and no real idea of the age of the Earth, nor of the major events that might have preceded the origin of life. There was a widely held view that the Earth was something like a huge ball of iron – iron is one of the commonest elements – that had once been molten, and had been cooling down. Indeed, the eminent late Victorian physicist William Thomson, later Lord Kelvin (1824–1907), used this assumption, and his knowledge of thermodynamics, to speculate that the Earth formed only 20–40 million years ago.
Kelvin’s view that the Earth was relatively young influenced many people at the turn of the twentieth century. No matter that the biologists and geologists were quite unhappy with this estimate; the leading physicist of the day had pronounced, and he had based his evidence on clear calculations. Charles Darwin had long assumed, for example, that the Earth must be hundreds or thousands of millions of years old, although he never speculated more closely than that. Nonetheless, he could see how the rocks of the south coast of England had accumulated rather slowly, made up from many millions of thin layers, each perhaps representing a year or a century. Other geologists held similar views, whether based on their calculations of the time taken for sedimentary rocks, such as limestones and mudstones, to accumulate, or the time it might have taken for the oceans to separate from the initial molten rock, and then to become salty.
Ironically, Kelvin lived through the crucial discoveries that were to show that his physical view of the Earth was too simplistic, but he was reluctant to shift. The discovery of radioactivity by Henri Becquerel (1852–1908) in 1896, the property of certain elements, such as uranium, radium, and polonium, to emit rays and to change their atomic number, changed everything. Radioactive elements may decay into another element, with the emission of rays. In radioactive decay, the parent element, such as uranium, would decay into another element, called the daughter, such as thorium, over a certain amount of time.
The discovery of radioactivity caused excitement throughout the world of physics, and only four years later, Ernest Rutherford (1871–1937) and Frederick Soddy (1877–1956) showed that radioactive decay is exponential – that is, the quantity of radioactive material halves over fixed amounts of time. In other words, 1,000 atoms of uranium reduce to 500 in a certain span of time, those 500 to 250 in the same amount of time, then to 125, and so on. Three years later, and in the hearing of an ageing and somewhat crotchety Lord Kelvin, Ernest Rutherford suggested that radioactive decay might provide a geological clock. He argued that, if scientists measured the time it takes for half the quantity of the parent radioactive element to decay to the daughter element, a span since called the half life, measurements of the proportions of parent to daughter element in a suitable rock sample could then give an estimate of the age of the rock.
Rutherford’s suggestion was put into practice remarkably rapidly. In a bravura performance, the young British geologist Arthur Holmes (1890–1965), aged only 21 at the time, published the first age estimates for rocks in 1911: his estimated dates ranged from 340 million years (a Carboniferous rock), to 1,640 million years (a Precambrian rock). These are not far off the modern age estimates (Fig. 3). Note that the first nine-tenths of the history of the Earth is called the Precambrian, because it precedes the Cambrian period: this is rather an apologetic, or negative term, for such a vast span of the Earth’s history, but the term is established now and cannot be readily changed.
After the first very crude estimates had been made, Holmes, and many others, worked hard to improve their understanding of age measurements, and the chemistry and physics were much revised, so that by 1927 Holmes was able to produce a reasonable summary of key dates for the history of the Earth. Holmes suggested that the age of the Earth was between 1,600 and 3,000 million years. In the same year, Rutherford suggested 3,400 million years, and by the 1950s, the age of the Earth was estimated at 4,500–600 million years, the currently accepted figure. It was, and still is, hard to date the exact origin of the Earth because rocks were presumably molten then, and so there are no solidified crystals that may be dated.
Making the Earth habitable
There is some debate about when the Earth became habitable: did it take 200 or 600 million years? Most geologists have favoured the latter view: after all the initially molten surface had to cool to below 100 ◦C, or any organic compounds would have been burnt off. Life is based on carbon, hydrogen, and oxygen, and these all remain in a gaseous state at high temperatures. Of course water boils at 100 ◦C, and life is essentially water (H2O) with carbon.
The Sun and its accompanying planets formed some 4.6 billion years ago from gas into which earlier generations of stars had spewed not only hydrogen and helium but small amounts of carbon, oxygen, and other elements forged in their cores. At first, the Earth was a molten mass, but it cooled, separating into an outer cool crust and an inner molten mantle and core. The heavier iron sank to the core, while lighter elements such as silicon rose to the surface. It took some 50 million years for the separation to occur, and the Moon may have spun off at this time, the result, it is thought, of a collision with an enormous planetoid. Massive volcanic eruptions rent the semi-molten silicon-rich rocks at the Earth’s surface, and produced great volumes of gases: carbon dioxide, nitrogen, water vapour, and hydrogen sulphide. Temperatures on the Earth’s surface were too high, and the crust was too unstable, for any form of carbon-based life to exist. At this time, the record of craters on the Moon suggests that there were a few huge impacts on Earth, impacts from large comets or asteroids that would have provided enough energy to turn the ocean into steam. Thus, if life had got started before 4 billion years ago, it would probably have been wiped out, only to start afresh.
As the Earth’s surface cooled, the lithosphere, the rocky crust and outer mantle, began to differentiate as a cooler upper layer above the underlying asthenosphere. As the rocky lithosphere formed, and the upper crust divided into plates that were moved by mantle convection, slow-moving gyres of heat rising from the depths of the mantle moved laterally as they came close to the base of the cooler solid crust, and began the stately journey of the Earth’s tectonic plates.
Geologists keep searching for the oldest rocks on Earth, and they are at all times pushing the limits of what might be possible (molten rocks cannot be dated, and error bars on dates become quite large when such ancient dates are attempted).
The oldest rock unit on Earth is said to be the Acasta Gneiss from the Northwest Territories, Canada, dated at up to 4.0 billion years old. This is a metamorphic rock, and the date is assumed to reflect the age of the older granite from which the gneiss was formed. Even older are zircons, isolated mineral grains, from the Jack Hills in Australia, which have yielded a date of 4.4 billion years. Could these minerals really have been solid, and even accumulating under water, at that point? Their discoverers claim this is the case, while others are sceptical that the Earth could have been cool enough for water to exist so soon after its formation.
The oldest sedimentary rocks have been reported from the Isua Group in Greenland, dated at 3.8–3.7 billion years ago. There is no doubt that water existed on the Earth by this point, and that some of the Isua Group rocks really are formed from accumulated sand, laid down under water, and deriving from older rock sources. It has even been claimed that these oldest sedimentary rocks also contain traces of life, but this claim is still much debated.
Traces of early life
In 1996, Stephen Mojzsis, then a graduate student at the Scripps Institution of Oceanography at La Jolla, California, made a startling announcement in the journal Nature. He claimed to have identified a clear chemical signature for life in carbon compounds from Isua Group rocks. He had analysed minute grains of graphite, a form of carbon, in the rocks, and found an unusually high proportion of carbon-12. The carbon atom has two stable isotopes, carbon-12 and carbon-13. The ratio of these two forms of carbon can indicate the presence or absence of organic residues of previously living organisms: enrichment in carbon-12 relative to carbon-13 is characteristic of photosynthesizing organisms, and the organisms that eat them. Mojzsis was confident he had identified life: ‘Our evidence establishes beyond reasonable doubt that life emerged on Earth at least 3.85 billion years ago, and this is not the end of the story. We may well find that life existed even earlier.’
If the interpretation is correct, then the grains of graphite in the Isua rocks prove that photosynthesis was happening 3.85 billion years ago. Photosynthesis is the process by which green plants convert energy from sunlight into food. Carbon dioxide and water combine, and produce oxygen, usually given off as a gas, and sugars, which form the building blocks of the plant. Now, in the early part of the history of the Earth, these photosynthesizing organisms were not trees or flowers, but presumably simple microbes known as cyanobacteria.
Other researchers have argued strongly against this interpretation. They noted, for example, that the Isua graphite was not in the sedimentary rocks of the area, but in the metamorphic rocks. Indeed, the Isua sedimentary rocks contained relatively low proportions of graphite. The alternative argument was then that the Isua graphites were of secondary, inorganic origin and might have formed by heating of iron carbonate. One of the critics, Roger Buick of the University of Washington, Seattle, said that ‘These rocks have been buried and cooked at least three times. They’ve been severely squashed and strained and tied in knots at least three times too.’
The Isua graphites are still held as evidence for early life, and the debates continue to rage. But how does this chime with current theoretical views about the origin of life?
The biochemical theory for the origin of life
There are many models for the origin of life, all based on an understanding of how the simplest living organisms today operate. The first ‘modern’ model for the origin of life was presented in the 1920s independently by two remarkable scientists, the Russian biochemist A. I. Oparin (1894–1980) and the British evolutionary biologist J. B. S. Haldane (1892–1964). Oparin and Haldane share the distinction of being independent co-founders of the so-called biochemical theory for the origin of life, as well as being known normally only by their initials.
According to the Oparin–Haldane model, life could have arisen through a series of organic chemical reactions that produced ever more complex biochemical structures. They proposed that common gases in the early Earth atmosphere combined to form simple organic chemicals, and that these in turn combined to form more complex molecules. Then, the complex molecules became separated from the surrounding medium, and acquired some of the characters of living organisms. They became able to absorb nutrients, to grow, to divide (reproduce), and so on. The Oparin–Haldane model was not tested until the 1950s.
In 1953, Stanley Miller (1920–2007), then a student of Harold Urey (1893–1981) at the University of Chicago, made a model of the Precambrian atmosphere and ocean in a laboratory glass vessel. He exposed a mixture of water, nitrogen, carbon monoxide, and nitrogen to electrical sparks, to mimic lightning, and found a brownish sludge in the bottle after a few days. This contained sugars, amino acids, and nucleotides. So Miller had apparently recreated the first two steps in the Oparin–Haldane model, mixing the basic elements to produce simple organic compounds, and then combining these to produce the building blocks of proteins and nucleic acids.
It should be noted that critics have said that the mixture of gases that Miller used (with high percentage concentrations of hydrogen and methane) was rather different from the likely atmosphere of the early Earth. Atmospheric hydrogen is ultimately replenished from the mixture of gases released from the solid Earth; but the geochemistry of the subsurface means that the mixture generally should contain the oxidized form of hydrogen, namely water vapour, H2O, rather than the large proportion of free hydrogen gas in Miller’s model atmosphere.
Further experiments in the 1950s and 1960s led to the production of polypeptides, polysaccharides, and other larger organic molecules, the next step in the hypothetical sequence. Sidney Fox at Florida State University even succeeded in creating cell-like structures, in which a soup of organic molecules became enclosed in a membrane. His ‘protocells’ seemed to feed and divide, but they did not survive for long, so they were not living, despite the hype made by the press at the time.
In a recent twist to the classic Oparin–Haldane biochemical model, Euan Nisbet (University of London) and Norman Sleep (Stanford University) proposed the hydrothermal model for the origin of life in 2001. In this model, the ancestor of all living things was a hyperthermophile, a simple organism that lived in unusually hot conditions. The transition from isolated amino acids to DNA may then have happened in a hot-water system associated with active volcanoes, rather than in some primeval soup at the ocean surface. There are two main kinds of hot-water systems on Earth today, ‘black smokers’ found in the deep oceans above mid-ocean ridges where magma meets sea water, and hot pools and fumaroles fed by rainwater that are found around active volcanoes.
RNA world
Biologists have long been unhappy with aspects of the Oparin–Haldane model. They have pointed out, for example, that the two fundamental functions of any living thing are that it must have some form of genetic code, the ability to pass on information from one generation to the next, and it must be able to perform chemical reactions, to break down food, for example. These are, respectively, the functions of genes and enzymes. Genes are the segments of the genetic code, written in the sequence of bases in the DNA (deoxyribose nucleic acid), that specify particular functions. Enzymes are chemicals that stimulate, or catalyse, chemical reactions. The conundrum was to determine whether life originated according to a ‘genes first’ or ‘enzymes first’ model.
The solution seems to be that perhaps both functions arose at the same time. In 1968, Francis Crick (1916–2004) suggested that RNA was the first genetic molecule. He argued that RNA could have the unique property of acting both as a gene and an enzyme, so RNA on its own could be a precursor of life. RNA (ribonucleic acid) is one of the nucleic acids and it has key roles in protein synthesis within the cells. The genetic code, the basic instructions that contain all the information to construct a living organism, is encoded in the DNA strands that make up the chromosomes. Different forms of RNA act as the template for translation of genes into proteins, transfer amino acids to the ribosome (the cell organelle where protein synthesis takes place) to form proteins, and also translate the transcript into proteins.
When Walter Gilbert from Harvard University first used the term ‘RNA world’ in 1986, the concept was controversial. But the first evidence came soon after when Sidney Altman of Yale University and Thomas Cech of the University of Colorado independently discovered a kind of RNA that could edit out unnecessary parts of the message it carried before delivering it to the ribosome. Because RNA was acting like an enzyme, Cech called his discovery a ribozyme. This was such a major finding that the two were awarded the Nobel Prize for Chemistry in 1989; Altman and Cech had confirmed part of Crick’s prediction.
But how could naked RNA molecules exist, and how could they act as a foundation for life? The argument was that the simple RNA molecules may have assembled themselves by chance in rock pools, more or less following the assumptions made by Oparin and Haldane, and as shown in the Stanley Miller experiment. These simple naked RNA molecules mainly existed and then disappeared, but perhaps one or two were able to copy themselves, and they could have become dominant.
To take this forward to create a living cell, there might have been two stages, the production of a protocell by combination of two components, an RNA enzyme and a self-replicating vesicle (Fig. 4). This satisfies the minimum requirement that two RNA molecules should interact, one to act as the enzyme to bring together the components, and the other to act as the gene/ template. Together the template and the enzyme RNA combine as an RNA replicase. But these components have to be kept together inside some form of compartment or cell, or they would only occasionally come into contact to work together. This is the second pre-life structure, termed a self-replicating vesicle, a membrane-bound structure composed mainly of lipids (organic compounds that are not soluble in water, including fats) that grows and divides from time to time. The RNA replicase at some point entered a self-replicating vesicle, and this allowed the RNA replicase to function efficiently (Fig. 4).
This is a protocell, but it is not yet living. It is just a self-replicating membrane bag with an independent self-replicating molecule inside. To make the protocell function both components have to interact, the vesicle protecting the RNA replicase, and the RNA replicase perhaps producing lipids for the vesicle. If the interaction works, the protocell has become a living cell. The cell is alive because it has the ability to feed itself, to grow, and to replicate. Evolution can happen because the cells show differential survival (‘survival of the fittest’), and the genetic information for replication is coded in the RNA.
Some aspects of the RNA world hypothesis have been tested, but much remains to be done. And in any case, the model remains hypothetical, because none of these stages would be likely to be fossilized. If the RNA world existed, it had to pre-date the oldest fossils, and the Earth had to be cool enough for the organic elements to survive being burned off. Some estimate that this might have been a time of 100–400 million years, somewhere between 4.0 and 3.5 billion years ago.
The first fossils
The oldest fossils appear to date from about 3.5 million years ago. Fossils of this age have always been controversial, but there are two kinds, microfossils and stromatolites. The first truly ancient fossils were reported in the 1950s, and the pressure to find ever-older specimens is intense. Mistakes have often been made, and that is no surprise because the oldest fossils are bound to be from extremely simple organisms, and microscopic ones at that. So it’s no wonder that great experts have often been caught out over-interpreting a chance bubble or mineral fragment in a microscope slide, even a bit of fluff or a modern plant spore.
It is probably unexpected that the most convincing truly ancient fossils are large structures called stromatolites. These are mounds made partly from living organisms and partly from sediment, and they still exist today. Stromatolites (Fig. 5a) are made from many thin layers that apparently build up over many years or hundreds of years to form irregular mushroom- or cabbage-shaped structures. They are built from microbial mats composed of some of the simplest of living organisms called cyanobacteria, and these have sometimes been called, rather misleadingly, blue-green algae. Algae, like seaweeds, have advanced cells with nuclei, whereas cyanobacteria, like ordinary bacteria, are made from the simplest of cells, without a nucleus.
Typical cyanobacteria photosynthesize, so they live in shallow water, near the water’s edge. Today, they are found generally in highly saline waters, often in tropical regions, where pools of seawater have partly evaporated. In less saline waters, herbivorous animals eat them up. The thin microbial mat may sometimes then be swamped by fine grains of mud, and the cyanobacteria grow up through the sediment to keep in touch with the sunlight. Over time, extensive layered structures may build up. In most fossil examples, the constructing microbes are not preserved, but the layered structure remains. Many early examples have proved controversial, but the oldest that are generally accepted come from Australia, and are dated as 3.43 billion years old.
Perhaps the oldest currently accepted microfossils other than stromatolites date from 3.2 billion years ago. They were reported in 2000, from a massive sulphide deposit in Western Australia. The fossils are thread-like filaments (Fig. 5b) that may be straight, sinuous, or sharply curved, and even tightly intertwined in some areas. The overall shape, uniform width, and lack of orientation all tend to confirm that these might really be fossils, and not merely inorganic structures. If so, they confirm that some of the earliest life may have been thermophilic (‘heat-loving’) bacteria that lived near a hot, sulphur-producing structure under the sea, as predicted by Euan Nisbet and Norman Sleep’s model for the origin of life.
There is a long gap in time after the 3.4-billion-year-old stromatolites and microfossils before more convincing fossils are found. There are some specimens from rocks dated at 2.5 billion years old in South Africa, and then the famous Gunflint Chert of Canada, dated at 1.9 billion years ago. The Gunflint microfossils include six distinctive forms, some shaped like filaments, others spherical, and some branched, or bearing an umbrella-like structure. These Precambrian cells resemble in shape various modern bacteria, and some were found within stromatolites. Most unusual is Kakabekia, the umbrella-shaped microfossil; it is most like rare micro-organisms found today at the foot of the walls of Harlech Castle in Wales. These modern forms are tolerant of ammonia (NH3), produced by ancient Britons urinating against the castle walls. So were conditions in Gunflint Chert times also rich in ammonia?
Strange things were happening on the Earth 2 billion years ago, apart from the ammonia-loving Kakabekia. The atmosphere suddenly seemed to carry oxygen, there are organic traces of quite diverse life, and new kinds of microfossils appear, some of them with nuclei. If this is true, these mark the origin of the eukaryotes, and so the origin of sex.
Chapter 2 : The Origin of Sex
What use is sex?-- John Maynard Smith, ‘The origin and maintenance of sex’ (1971)
It has often been noted that sex is a ludicrous and messy business. Simple organisms seem to be able to reproduce perfectly successfully by splitting or budding: amoebas go on feeding until they are quite large, and then one individual splits into two; a yeast or a sponge buds off side shoots that eventually break free as separate little organisms. So what’s the point of sex?
In his book The evolution of sex, the noted British evolutionary thinker John Maynard Smith (1920–2004) wrote in 1978 about the twofold cost of sex. He pointed out that asexual organisms, those that have only one gender and that reproduce by splitting or budding, can increase their population sizes rapidly. Because each individual is effectively a female, each of the offspring is capable of reproducing independently. Sexual organisms, those that reproduce following exchange of genetic material, have two sexes, female and male, and it’s the males (of course) that are the problem. So if each female produces two offspring, and there is 1 : 1 sex ratio, then on average the two offspring will consist of one female and one male. The rate of doubling of the population size is half that of an equivalent asexual organism.
