Unlocking the Past

by Martin Jones

  At one time, the archaeological record seemed for the most part to be reduced to durable mineral items, nature having long before done its job of recycling the living and organic elements of our world. Subsequently, it seemed there were pockets, culs-de-sac, in which nature had been switched off or excluded, odd places where organic remains could be found in pristine condition. Now it appears that neither of these visions was accurate. Nature and its forces are everywhere, penetrating far further into the Earth’s surface than we had imagined. Yet nowhere does Nature complete the job. In all kinds of contexts, some sorts of molecular traces slip out of the grand recycling process and linger on as fading signatures of lost worlds.

  afterword

  In the final chapter of The Molecule Hunt, I had mused upon an inversion between ‘sample’ and ‘noise’, drawing a contrast between the scrubbing of surface adherents from a potsherd, that I remember from my first dig, and Oliver Craig scrubbing the potsherd away from its surface adherents. I must stress it was a comment on the shifting focus of enquiry, rather than a call for the wholesale destruction of our material cultural heritage.

  In a similar fashion, biomolecular archaeology started with the tacit premise that the visible, tangible object was still key. We wanted to know the DNA of this particular skull, or that particular plant. It took a bit of time to think of the biological container of the DNA as interesting indeed, but not entirely necessary, and for some palaeogenetic studies, not as relevant as it first would seem. If we reflect on the hominin fragments from Denisova cave, it is certainly true that the teeth as physical objects provided much for the archaeologists to discuss in terms of the implications of the radical findings. The finger and toe bones that generated so much exciting genetic information, as actual physical objects, have rather less to contribute. Once liberated from such biological containers, ancient biomolecules might find some other places to hide, and retain for us their testimony of a distant past.

  Even if the Denisova finger bone as a physical object was comparatively mute, its contained DNA allowed completely novel evolutionary and biogeographical inferences to be drawn on at least three hominin taxa, including that of the finger’s owner. At least in this case, the evidence was derived from human skeletal evidence of some sort. By the time of the Denisova work, other groups had begun examining DNA with an even greater separation from living tissue, and to follow their work, we return to the cold Northern Arc across the Bering Straits, which had attracted visits by the likes of Cooper, Shapiro, and Willerslev.

  For eight months of the year, the Kolyma River that drains northeastern Siberia is frozen to depths of several metres. Within its catchment, mammoths once roamed and polar bears are believed to have evolved. Between this river and the Lena River to the west, a series of cores was taken by Willerslev’s team into the permafrost sediments, cores in some cases reaching over thirty metres in depth, and up to two million years in antiquity. Locked to those sediment particles were strands of DNA. Those strands may have ‘lost’ their plant or animal host, but found instead clay minerals on which to attach. Such minerals are well known to have adsorptive properties commensurate with biomolecules.

  In those deep Siberian cores, sedimentary DNA could be detected going back 400 millennia, and which, before the publication of the Thistle Creek horse, represented a new maximum in the far reach of ancient DNA. Making sense of this novel evidence was much facilitated by the growing number of master sequences accumulating in genome libraries. Using an established procedure called Basis Local Alignment Search Tool (BLAST), DNA sequences could be run through these ever extending libraries looking for matches, and then their statistical significance could be calculated.

  Matches were indeed found. These permafrost sediments retained DNA fragments from woolly mammoth, steppe bison, horse, reindeer, musk ox (and an unknown relative), brown lemming, and hare. Alongside these animals, sediments going back 400,000 years retained DNA fragments from just short of 300 taxa of plants. A whole new branch of palaeoecology had opened up around ‘sedimentary DNA’.

  A number of sedimentary sequences that once would have been explored through macrofossils are now also being understood through ancient DNA, and these are not just in cold environments. The freezing temperatures are certainly advantageous, but stratified ancient DNA has also been usefully recovered from sediments accumulating in the bottom of temperate region lakes, and also in ocean cores. The method can even be used when the sediments themselves seem sparse, which brings us back to the ice.

  The vast sheet of ice that covers 80 percent of Greenland’s land surface to a depth of two to three kilometres is a repository, not just for the occasionally frozen human body, as mentioned in this chapter, but also of detailed climate history going back 100,000 years and beyond, as revealed by the chemistry of the strata of frozen water and of the gases dissolved within them. That chemistry generates a detailed history of climatic fluctuations over the half million years during which the ice sheet has grown. Apart from these contained gases, the frozen water is at first glance, a rather unlikely source for ancient biomolecules. Towards the base however, the ice is a little dirtier, with dispersed particles of silt. These it seems, are sufficient to capture fragments of DNA that reveal a whole ecosystem perhaps half a million years old.

  Applying a range of DNA recovery methods from cores taken deep into the ice, Willerslev and colleagues assembled a picture of the woodland that existed before Earth’s second largest ice sheet had begun to grow. The woodland comprised alder, spruce, pine, birch, and aspen. Between the trees were grasses, interspersed with yarrow, chickweed, plantain, saxifrage, and clumps of snowberry. Beetles, spiders, and butterflies moved among them, and flies gathered in the wake of the larger animals. His richly forested landscape where now there is just ice has all been gleaned from dispersed particles of silt within that ice, and the molecules discreetly attached to them. The early targets of biomolecular archaeology were whole bodies, in which the flesh, the skin, and the hair remained attached, so maybe the informative molecules as well. With confidence, the field moved to the more familiar remains, teeth and bones, from which the soft tissue has decayed. The target fragments got smaller and smaller and stretched beyond organisms to the particles making up sediments. Now in this extraordinary study of the contents of an ice sheet, a vibrant ecosystem is reimagined, from half a million years ago, from a small sample of slightly murky water.

  5

  gaining control

  did human evolution stop?

  We could be excused for thinking so. Until it comes to the decline of the Neanderthals, archaeology seems to have a lot to say about skulls, brow-ridges, genetics, hominid species’ names and the like. After that time, the narrative takes a quite different form, shifting to art and artefacts, burial ritual and monuments, landscapes, social complexity and so on. It seems as if a seismic shift in the human past has left Nature on the far side of a ravine and allowed Culture to take over. An illusion of course, but one with a foundation in a clear pattern in the data. First of all, after the disappearance of our last hominid cousins, it is certainly the case that genetic diversity of the human line was left greatly diminished. Variations in human mitochondrial DNA may be enough to cast light on human migrations, but they are tiny in comparison with what is encountered even among our primate relatives. Two gorillas dwelling in the same small West African woodland could quite easily be separated by a mitochondrial variation beyond that encompassing the entire human race. Within our own species, there is very little genetic variation at all.

  Yet while that genetic shrinkage has happened, the cultural diversification among human societies has been phenomenal. There seems to have been an inverse relationship between culture and genes. As the latter narrowed in range, so the former blossomed into an unprecedented variety of forms. The last few thousand years have left behind a greater range of artefacts and artifice than all of the previous 2 million years of Homo put together. We are, of course, rather biased in this obs
ervation by what survives and what archaeologists have traditionally collected. It would be more accurate to say there has been a blossoming of the more durable things–fired clay, metal, and monuments. For all we know the owners of the first hand-axes were also accomplished wood-carvers, leather-workers and poets, the fruits of whose creativity have failed to survive.

  Culture did not really spring from nothing as the first of a series of ‘great civilizations’ was established, any more than Nature and evolution came to a halt when the global expansion ended and the last fellow hominid disappeared. Nevertheless, at various stages after that time, the material residue of past human societies begins to take on a quite different shape. Large and complex built environments were created within bounded and controlled landscapes. A vast range of raw materials was fashioned into artefacts, sometimes involving the manipulation of fire within carefully constructed kilns.

  Alongside all these changes was a shift in the way in which people fed themselves. They changed what they ate and made fundamental changes to how that food was acquired. The way in which many of their food plants and animals grew and reproduced had changed. It was now rigorously controlled within plots in which everything, from the boundaries to the plants within and the soil beneath them, was fixed by human action. For many, the origin of farming lies at the root of all the technical, cultural and social changes that followed. Rather than biological change coming to a halt, the main evolutionary action had passed from our own species to the animals and plants that were maintained within these plots.

  Most of the conspicuous civilizations of the last few thousand years have depended upon an increasingly small number of these animals and plants. Prominent among them is a handful of annual plants, whose hard seeds can be softened by grinding or cooking. In the distant past people gathered numerous species of wild fruits, nuts, fish, shellfish, birds and game. In recent millennia their food sources have dwindled to the monotonous expanses of grain crops that still carpet much of the world today. Cultural diversification took place in the context not only of a shrinking genetic range, but also of a dwindling food base. Across the Old World and the New, a series of major civilizations have been built on a narrow range of these cultivated grasses. In east Asia it was rice, further to the west and in Europe it was wheat and barley, in sub-Saharan Africa sorghum and millet, and in America maize. Moving to evolutionary trajectories of the last 10,000 years, our attention has increasingly been drawn from the humans themselves to the plants, in particular to those key seed plants on which many came to depend.

  in search of seeds

  The rather antiquarian response to the pot of cereal grain recovered from the 1960s excavation described in the opening chapter was quite typical of archaeology at that time. Few archaeologists thirty years ago had a clear idea of what plant tissues survived in the archaeological record, let alone what molecular evidence they might retain. One might think that something the size of an ancient cereal grain would be easily picked out from the excavated soil, but most were missed. Only when they occurred in very dense concentrations were they recovered. The great majority were tossed aside unnoticed. Once archaeologists had embarked upon their concerted effort to find out more about everyday lives and what people were eating, they began to look more closely at the sediments they excavated, passing them through sieves. On dry and sandy sites, it was possible to pass a fair amount of sediment through large screens. This yielded a number of ancient maize cobs from sites in the south-west of the United States and in Central America. However, if the sediments were at all clayey and damp, and if the food plants were small grains rather than large maize cobs, there was very little that sieving could achieve. That all changed, following the simple expedient of mixing the excavated sediments with water.

  When mixed with water, what first appears to be an unremarkable sediment, taken from an excavated living floor, hearth or rubbish pit, separates out into two components. Most of the sediment sinks, the mineral part of a soil being over twice as dense as water. A separate fraction rises to the water’s surface. It might contain fragments of root, tiny snail shells and the lighter bones of rodents and birds. Most of all it would be composed of dark fragments of plant tissue, blackened pieces of wood, and seeds. The simple process of flotation transformed plant remains from an archaeological oddity to the source of its largest potential data-set. Excavations that were yielding potsherds and bones in their tens of thousands were now yielding ancient plant remains by the million. Here was a form of evidence that could find its way past buildings and potsherds, right through to the prehistoric stomach.

  During the 1960s and early 1970s, flotation was carried out in a variety of rather makeshift devices. They acquired names like the ‘Siraf machine’, the ‘Ankara machine’ and the ‘Cambridge machine’, depending on where the device had been put together by a combination of local plumbing and abandoned oil drums, all designed to operate in remote locations with minimal facilities. The aim was to keep pace with the excavation of a site, mixing vast quantities of archaeological dirt with water, in order that the precious ‘flot’ could be separated, bagged up and labelled, for study back in the lab. I well remember my surprise on seeing under the microscope what had emerged from these dark flots. What to the naked eye were amorphous black pellets, under low magnification revealed structure in astonishing detail. Intricate surface forms were clearly visible, and several separate layers of cellular tissue could be seen through their eroded and broken surfaces. Some oozed a spongy, honeycombed material which provided evidence of the fire that had contributed to their survival, carbonizing and distorting them in the process. At that stage, little attention was paid to their chemical or molecular structure; there was sufficient work to do recording and interpreting the wealth of physical variation in the plant remains. There was enough physical evidence to identify a whole range of ancient food plants among the debris and, by comparison with modern seeds, a wide range of crops was charted through time. In particular the cereals and legumes appeared to survive reasonably well. A category that was even more intriguing than the food plants themselves was the chaff and secondary tissue cleaned from these grain crops and also discarded.

  Particularly well preserved were the fragments of seed-head stalk or ‘rachis’ upon which the ancient cereals had grown. Their form was characteristic to such a degree that they were often easier to identify than the grains themselves. Although these stalk fragments were only a few millimetres long, it was possible to make out where the grains and the surrounding chaff were attached, and how the different sections of the seed-head were linked together. In the most ancient rachis fragments that have been recovered, from wild cereals from sites in Israel, the clean breaks can be seen on each fragment. They are rather like the neat scars left on a branch when leaves fall, a reflection that the seed-head had broken up on ripening, allowing the seed to disperse naturally. On rachis fragments from the last 10,000 years, something quite different is seen. Under the microscope, these natural break points can be seen. The rachis follows a characteristic dog-leg at this point. But the rachis is unbroken here, and instead the untidy breaks are at arbitrary weak points elsewhere. What can be seen in the difference between the two rachis forms is the disablement of a fragmentation pattern fundamental to the natural dispersal of seeds. Looking down the microscope upon flots of small blackened fragments, we can observe the precise genetic modification that transformed wild grasses into cereals and, in doing so, formed the basis for a remarkable range of transformations in human society.

  The difference between the brittle rachis that allowed wild grasses to disperse, and the tough rachis that held cereal grains in place and at the mercy of their human predators and guardians, is a fundamental one. The small but visible evolutionary step between the two has intrigued evolutionary scientists ever since Darwin’s theory was in print. In the opening chapter of the Origin of Species, Darwin concerns himself with the issue of domesticated species, a theme he later developed into a treatise in its
own right. Foremost in his thinking was the idea of the ‘civilized’ breeder who, in contrast with ‘savages’, could control nature, setting the evolutionary agenda and creating genetic diversity among plants and animals in the human sphere. He had not seen the ancient rachis fragments under the microscope. Neither did he have the archaeological or the genetic understanding we have today. He therefore remained suitably circumspect about how this novel human engagement with evolution had come about, and whether it had happened once, or several times, in one place or in many parts of the world. By the 1920s, the archaeological and genetic pointers that Darwin lacked were available. The question of agricultural origins could be freshly attacked by the Australian archaeologist, Vere Gordon Childe.