Unlocking the Past

by Martin Jones

  This issue has taxed archaeologists and anthropologists ever since the bones came to light. First it was tackled simply by looking at the bones themselves, then attention moved to the stone tools and the archaeological sites they left behind. It has not been an issue simply about a few long-dead relatives. Underlying the issue of how different we are from our curious cousins is a far more fundamental debate about the evolutionary dynamic of the natural world around us, and the nature of our place within it. To understand that underlying debate, and the place of ancient DNA in resolving it, let us look back to the bones from which those fragmentary molecules came.

  once upon a time in the west

  The bones in question were unearthed in 1856 from the Feldhof Cave, above the Neander valley near Dusseldorf. To the quarrymen who found them they appeared almost human–but not quite. There were a number of significant differences. The thigh-bones were too thick and curved, and most strikingly of all there was a sizeable ridge of bone protruding from the brow. A local schoolteacher was alerted; fortunately he realized they were something quite unusual. Speculation ensued. Perhaps they belonged to a congenital idiot, or a foreigner. The tough bandy legs were reminiscent of horse-riding Cossacks, the intense brow-ridge brought stress and disease to mind. These were weak explanations for highly distinctive features. What is more, these bones were not the only unusual things coming out of the ground at the time.

  As Christians, those quarrymen had very likely learnt that God had created the world at nine o’clock in the morning on the 23rd of October in the year 4004 BC. Yet as the scale of quarrying grew with the progress of nineteenth-century industry, things were appearing from beneath the Earth’s surface that were increasingly difficult to contain within this story. Sediments were cut through that surely had taken a great deal longer than 6,000 years to accumulate–but maybe geologists had got their timing wrong. Fossils of weird animals appeared–well, maybe Noah’s Flood could account for their absence today. Occasionally, those animals were found at the same level as worked tools–this was getting tricky, but could we be sure those hand-axes were fashioned by humans? As the quarrymen dug deeper, so the biblical counter-arguments became strained. With the Industrial Revolution continuing apace, quarrying on a considerable scale, and the counter-arguments at the point of collapse, the sheer weight of evidence for a deep and complex Earth history was crying out for a different story. Now, in a valley called Neanderthal, the quarrymen had found something that seemed to be only partly human.

  It was only three years later that Charles Darwin was to bring the whole creationist story to its knees. In its place, he offered a new, coherent story into which all the new information arising from decades of digging into the Earth–slow sedimentation, fossils, extinction, and species transformation–could reasonably comfortably fit. The story was one of evolution by natural selection. It explained how, over a very long period of time indeed, going back far beyond 4004 BC, species of plants and animals changed in form, as a result of a rather unpleasant process, the struggle for survival. Over the next few years, Darwin and his colleague Thomas Huxley hammered home the implications for humanity. We were not created ah initio, but had instead descended from apes. A century and a half later, the shock waves have yet to settle.

  The find of Neanderthal man played, and continues to play, a key role in this new world-view. Huxley argued that its strange form was to do, not with idiocy, horse-riding or disease, but with evolutionary change. Here was a ‘half-human’ who bore direct witness to the mechanisms that, Darwin argued, had underpinned natural history. The bones had only remained a puzzling enigma for a few years before taking their place as part of the foundation of a radically new view of the world and of our place within it. The varnished bones became an important museum specimen.

  Once the idea of a half-man midway between animals and ourselves had sunk in, attention turned to the novel concept of linear, directed evolution. The quarrying activity that had exposed so much of the new information was part of a wider economic revolution. Those at the heart of the revolution warmed to the optimistic idea of universal human progress, a progress of which they now occupied a vanguard position. The gradual evolution that Darwin had explained formed a basis for their status, for their premier position in the natural order of things. Deep in the mists of time were undifferentiated species without specialized senses, without sensibility. Slowly but surely, they acquired backbone, structure, a nervous system and brain. Then they stood upright, became self-conscious and acquired dexterity and language. Ascending this path, climbing the evolutionary tree, they could still see the offshoots of these various stages, whose progress had stopped at a lower level: worms, insects, vertebrates, mammals and apes. At the tree’s crown were those epitomes of progress, humans. If one looked more closely at the crown, the process of natural selection could be viewed in detail. Some humans were a little below the crown’s tips, looking up with awe to the Victorian men of capital and enterprise who embraced the new ‘Darwinism’ which in turn endorsed their position closest to the sun.

  The Neanderthals, as those skeletons closely resembling the original find from Neanderthal came to be called, were well beneath the shade of the crown. As the years progressed, other lowlier beings were added to those shady positions. In the 1890s, a Dutch doctor found bones of what would later be called Homo erectus on the island of Java. These were the skulls with the strong brow-ridge that had persisted to a late date in south-east Asia. In 1907, a jawbone was recovered from Mauer, near Heidelberg, from a species that would later be named Homo heidelbergensis. Elsewhere in Europe, the number of Neanderthal finds was growing. Indeed, some examples had clearly come to light prior to the Neanderthal Valley example, but simply a little too early for the concept of a ‘proto-human’ to be considered. However, the Neanderthals have never perched very comfortably on the evolutionary tree directly below us, for a variety of reasons, not least because on average their brains were larger than ours.

  At first, these linear stories of evolution and progress had addressed some of the mismatches between the biblical account and the data emerging from quarrying beneath the ground. But, as that database grew, so simple linear evolution came under strain. The diversity found in nature increasingly resisted being ordered in a single straight line. All the elements of Darwin’s own mechanism of evolution have survived, and still survive in a robust state, but they needed a ‘bush’ rather than a ‘tree’ to turn them into an effective account. Each group of plants and animals led its observers along a similar line of reasoning. There was so much variety in nature, it simply couldn’t be constrained within a single axis of variation. There had to be offshoots, side-branches, dead ends all over the place on this spreading evolutionary bush. That was a reasonably painless modification of the story when dealing with insects, starfish, ferns or whatever, but when it came to humans something still jarred.

  Even having been absorbed into Darwin’s biological world, we have remained in awe of ourselves and our species. It has seemed to us that our powers of perception, our conscious thought and creativity, and our sheer ability to control nature, are attributes of such magnitude that they are a case apart. How could our hominid cousins, so close to us on the evolutionary bush, avoid being drawn on to our path? So much human evolution continued to read like a multi-millennial quest to lift those forelimbs off the ground, to open up that brain cavity in preparation for thought and to stretch that larynx out in anticipation of speech, so that music, art and civilization would one day blossom forth. The subtext of human evolution remained a drive for progress, a collective struggle for betterment of the species. In explaining these fossil bones, both the Neanderthals of Europe and the late Homo erectus fossils from China and Java were repeatedly drawn back into the story. This continued to be the case, even as other evolutionary trees were changing from skyward pines to untidy bushes. Franz Weidenreich, writing in the 1940s, and Carlton Coon, writing in the early 1960s, were able to organize the known hominid fossi
ls into one global story in which the watchwords were ascendancy and slow, gradual progress. For these authors, the Neanderthals, Peking Man and Java Man were all part of one common species. The variety between them reflected deep-seated racial differences across the different continents of the world, differences that have endured until the present day.

  As they developed their ideas and brought them into print, another continent was yielding up a remarkable series of hominid fossils that could be taken to suggest a quite different story of origins. As Coon was preparing his manuscript, the African hominid record was about to explode, as Louis and Mary Leakey started to find the first of a series of key fossils where the Rift Valley split the Earth open at a gorge called Olduvai. As scientific dating methods came on stream to put these fossils in order, so their dates as well as their form changed the global focus of human evolution. Europe and Asia became outliers to the main action. The earliest dates were to be found in East Africa, as was the greatest diversity of fossil types. An alternative to the multi-regional argument was emerging, which gave primacy to one particular continent, Africa.

  enter the molecules

  Something else was happening in the 1960s that would eventually point in the direction of Africa. While the Olduvai Gorge was yielding fossils that would change the whole story, a young New Zealand scientist called Allan Wilson was wondering whether these fossils on their own could hold the key. Wilson’s laboratory would subsequently hold a central place in the growth of ancient DNA science. Back in the 1960s, he was one of the pioneering figures to shift the focus from whole fossils to molecules. At this stage, the double helix was little more than a decade old. It was too early to explore its fine structure as we are able to do today. At that point, Wilson examined a better understood group of molecules, the proteins. He was growing sceptical about the way primate anthropologists were trying to relate different fossils according to differences in skeletal form. The small sample sizes worried him, as did the vagueness about the links with genetics, and with the difference between sexes. Neither did he like the jargon physical anthropologists used, which struck him as a bit of a smoke screen. Molecular science had moved forward enough to take what seemed to him a more transparent and testable approach. Together with Vincent Sarich, at the time a graduate student in anthropology, he attempted to uncover the family tree of humans and other primates by comparing the structures of serum albumins, the predominant proteins in blood plasma. What they did was develop some antiserums to a human serum albumin, and then test the extent to which they cross-reacted with the serum albumins of a whole range of other species. None cross-reacted as if it was identical to humans but a fairly strong cross-reaction was achieved with chimpanzees, regarded by primatologists as our closest living relative. Other apes, including the gorilla, orangutan, gibbon, and siamang, also gave moderate cross-reactions. The strength of the cross-reaction progressively weakened as the tests moved to Old World monkeys, New World monkeys, more distant primates, and non-primates. The molecular variation among the albumin proteins seemed to make evolutionary sense, and open up a new route to our phylogeny. So far, so good–but things quickly became more contentious with another property of the molecules. They could be used to generate a measure of time.

  The pace of evolution can vary. Some disease organisms can evolve into new forms faster than we can develop remedies against them, while a marine invertebrate called a brachiopod has retained much the same form for hundreds of millions of years. There is no in-built evolutionary rate for organisms as a whole. Molecules are different. Their change is more directly governed by rates of chemical reaction. Those rates may vary, for example according to the temperature and the presence or absence of catalysts, but they remain rates that are broadly determinate.

  Let us take the example of the serum albumins studies by Sarich and Wilson. The strength of the cross-reaction between human antiserum and chimp serum provided a measure of the sequence similarity of two proteins that performed precisely the same function, but in different, albeit related, species. Those differences are not the outcome of differential natural selection, as nothing functional has changed. Instead they are to do with accumulating chemical aberrations, or mutations, along bits of the molecule away from the main functional areas, away from the powerful forces of selection that would otherwise erase them. These mutations simply accumulate like dust on an unswept surface, away from the main ecological action.

  If chimps and humans do have a common ancestor, then there must have been a particular point in time when the two lines of descendants began to diverge. From that point onwards, the random mutations along the chimp line will accumulate independently from the random mutations in the human line. So long as there is some steady probability of mutations occurring through time, the number of sequence differences will be a measure of how long ago that divergence happened. This is the logic that Sarich and Wilson employed. By considering a variety of species, they demonstrated that the levels of difference between albumin proteins seemed well ordered, and came up with series of time estimates for different episodes in the human evolutionary story. Drawing on all the measures of albumin dissimilarity among the primates, they concluded that the common ancestor of all primates was around six times as ancient as the common ancestor of humans and our closest living relatives, the chimps. The oldest fossil Old World monkeys go back 15-20 million years, and combining fossil and immunological arguments the authors favoured a primate ancestor at 30 million years. This implied that we split from the chimp and gorilla lines as recently as 5 million years ago.

  Eyebrows were raised across the hominid fossil fraternity who had been getting increasingly confident about their own scientific dating methods and their broadening range of hominid fossils from secure, dated contexts. One small assemblage of fossils came from the Siwalik Hills of northern India. It was labelled Ramapithecus, and dated to 14 million years before the present. There seemed to be a clear contradiction between this tangible, datable fossil and the rather novel argument from a quite separate discipline, about albumin proteins, that seemed to float free of the archaeological record. The scholars who knew about the fossils did not feel ready to collapse their global picture of human evolution to a particular part of East Africa. Neither were they persuaded by a time scale that had shrunk to a third of the age of its oldest fossil. They were not prepared to ditch the received wisdom of human evolution as a story of long, slow progress. Sarich and Wilson initially came in for a lot of criticism.

  They only had to wait a few years, and for the recovery of new specimens, for the fossil evidence itself to remove its own barriers to the shorter time scale. In 1976, David Pilbeam found a better Ramapithecus fossil near to the original find, and detailed enough to allow the species to be gracefully ‘retired’ to the orangutan line. In the subsequent years, the time estimate of 5 million years for a common ancestor with chimps has broadly survived, and given great strength to a powerful tool of molecular evolutionary science, the so-called ‘molecular clock’.

  molecular clocks

  Archaeologists and earth scientists looking back into the past are accustomed to working with a variety of natural clocks. The basic requirements of such clocks are that they proceed at a knowable pace, as do very many natural processes, and that their pace does not get deflected by what is happening around them. The most important of these are the so-called radiometric clocks. These use radioactive breakdown in one form or another, suitably triggered by some archaeological or geological event. Much of the dating of early hominids, for example, has made use of the slow breakdown of one form of potassium to argon gas, a valuable means of dating volcanic deposits in Africa’s Rift Valley. Similarly, the prehistory of the last 20,000 years or so is now reconstructed around carbon dates, derived from the slightly faster breakdown of a certain form of carbon to nitrogen gas. Archaeologists also make use of a series of chemical processes to supplement these radiometric timekeepers. An example of these is the measurement of a layer of hydrated
silica that gradually deepens on the surface of stone tools after exposure. In some respects, molecular clocks are similar, involving a triggered, time-dependent chemical reaction. In other respects, they are rather different. First, the chemistry behind mutations and altered DNA and protein sequences is very complicated. The same could be said of radiometric dating, but here the complexities are rather better charted and understood. We would not expect molecular clocks ever to come anywhere near to rivalling the precision possible with radiometric clocks. Second, molecular clocks, as part of reproducing organisms, are subject to natural selection. Chance mutations may progressively distance the molecular sequences of two relatives, but we can rarely be sure that natural selection will not then steer them back again towards an ecologically favoured format. The basic processes of evolution can thus distort and confuse the time scale used to measure its pace.

  This is invariably true of any biomolecule with a significant influence on the form the whole organism takes. In whole organisms, redundant structure is uncommon. Everything seems finely tuned by the brutal rigours of natural selection. There are no spare limbs to be found and hardly any dispensable organs. This forced economy of whole-organism design has always limited the use of bodily form as an evolutionary timepiece. If selection pressure is strong enough to mould one lineage in a certain way, then many lineages may be so moulded. A shared physical feature may either result from common ancestry, or from convergence in a tough, competitive environment. It is not always easy to separate the two.

  Proteins are not totally immersed in this environmental drama. True, they each have their functional regions somewhere along their length, conducting precise, crucial biochemical tasks. However, there does seem to be considerable arbitrary baggage within these long-chain molecules. It is not always easy to draw a line between functional and non-functional sequences, between the stretches faced with natural selection and those undergoing .neutral’, that is random, evolution. Allan Wilson was acutely aware that this could apply to molecules as much as it did to whole organisms. Later in his career he published some elegant examples of convergent evolution among proteins. To approach a more ideal molecular clock, the molecules had to distance themselves from the environment and from natural selection, and that is where DNA comes in.