by Martin Jones
DNA and its fellow travellers
DNA has been the flagship in a fleet of molecules that are moving our understanding of the human past forward. In the future, we are likely to see the different biomolecules brought together to elucidate that past. Three of these molecules are currently being used to investigate the prehistoric origins of dairying–the DNA of the cattle themselves, and the characteristic lipid and protein signatures left behind in the milk pots. DNA and lipid analysis have been brought together in the study of disease. A few ancient cemetery studies are now bringing together DNA analyses and isotopic studies of bone collagen.
We have perceived the limits of looking at ancient DNA alone. If Matthew Collins’s thermal projections of burial conditions are right, only nine known Neanderthal individuals are expected to retain sufficient intact DNA in a form that is accessible with our existing techniques. Indeed, they may be the only nine individuals of any hominid species other than our own to do so. This brings our thoughts back to the proteins that played such an important role in helping us construct a picture of human genetic diversity in the first place. There is a reasonable case for the persistence of some recognizable protein fragments in dinosaur bones tens of millions of years old, and in marine invertebrates hundreds of millions of years old. Perhaps we shall before long learn something of the proteins of Homo erectus and other key species, and assemble new stories around that. However, the latest suggestions are that the whole biomolecular picture could in any case be changed yet again.
a solid state future
The major enemy of ancient molecules is undoubtedly water. Chemists describe it as the ‘universal catalyst’, the trigger whose presence is needed for so many of the chemical reactions we encounter, particularly those within living systems. We have seen how the very dry sites have conserved a rich array of biomolecules, and the same is true on a microscopic scale. If a solid tissue such as wood or bone excludes water by its dense internal structure, then biomolecules can persist even when, the bone or wood fragment has spent thousands of years immersed in soggy peat. At an even smaller scale, the power of solidity in protecting molecules from water becomes yet more marked. This can be observed as we move from a solid bone to a tiny particle of hydroxy-apatite mineral, or from a piece of wood to phytoliths and phytocrystals. The long-chain molecules that are particularly vulnerable to prolonged contact with water can form weak bonds along the chain’s edges. These bonds collectively become strong when they wrap the molecule across the surface of a mineral particle, or become consumed by it. Wholly immersed, or clinging on tightly to these solid state sanctuaries within a world of breakdown and decay, these biomolecules may last indefinitely. The problem is that they are not currently within the range of analytical methods commonly in use. So tightly are they bound, prising them off would probably destroy them anyway. It is the slightly freer, and consequently more vulnerable, molecules that are being detected by present methods. However, a start has now been made in seeking those in hiding in the solid state zone.
At Menez-Dregan in Brittany, a collapsed cave encased a series of hearths and bone fragments left behind after the visits of Homo erectus half a million years ago. The bones did not look exceptional, except for the manner of their burial. The cave’s collapse had greatly compressed them, and they had rapidly desiccated under high ionic pressure. As the site was excavated, molecular biologist Eva-Maria Geigl came across from Paris to extract the bones carefully and put them in cold storage. Aware of the problems outlined above, Geigl decided to try to detect any surviving DNA in situ in the bone tissue. She attempted this by hybridizing DNA probes on to the bone surface, without trying to remove the molecules–and she got a positive result. It appeared that in the right circumstances (and high pressure may be key), the possibility of really ancient DNA might once again be opened up. It is too early to say how well her results will be received, but at least there is not the mismatch between empirical results and theoretical kinetics that there was with the earlier amplifications from dinosaur bone. Whatever the fate of Geigl’s results, tightly attached biomolecules that effectively persist in solid state have a promising future.
Something similar is happening within ancient protein work, where again the best survivors are probably clinging on tight to a solid surface. At Newcastle, Matthew Collins’s team realized this when they embarked on their search for ancient dairying. They were targeting residues of the milk protein casein in pottery fragments. Not long ago, I heard one of the group, Oliver Craig, give a talk on their ingenious approach to tracking down casein molecules tightly adsorbed on to the pottery surface. They had reasoned that if this tightly bound protein could not be detached intact from the pottery fabric, then the pottery fabric had to be detached from the protein. The method they developed entailed placing the pot fragments in a very particular kind of tube whose inner surface acted like a molecular ‘fly-paper’ for free proteins. They then set about dissolving the pottery by adding the powerful solvent hydrofluoric acid to the tube. As soon as any surviving proteins were free of their pottery attachments, they clung to their new home on the side of the tube. Here, they could be identified by monoclonal antibodies.
As I listened, fascinated, my mind drifted back to that first experience of practical archaeology in a Somerset field in the 1960s. What Oliver was describing was a complete inversion of our data collection then. We had sat between the excavation trench and the site hut, nailbrushes in hand, scrubbing away the dirty, smelly biomolecules from the inert sherds of pottery. At Newcastle, thirty years or so later, the priorities had completely changed. It was now the pottery that was being chemically scrubbed away from the biomolecules. It was a passing thought, and I do not intend to suggest that our entire ceramic heritage should be plunged into a vat of hydrofluoric acid. But looking back on that prehistoric village, I am struck by how much our perception of what remains of the past has changed. In many ways, the visibility and the durability of the finds has proven a poor reflection of the range of information accessible by first bio-archaeological and then biomolecular means.
When David Clarke reconsidered the renowned prehistoric lake villages of Somerset just over twenty-five years ago, he set his sights beyond pottery typologies and metalwork affinities to what life was actually like in the first millennium BC. He speculated about a community adapting to a watery world in which the water was both friend and foe. It was friend in providing a host of resources–shellfish, water plants and rhizomes, nuts, fuels, reeds and sedges. It was a foe in harbouring foot rot, parasites and insect-borne diseases, and forcing the farmers to move their herds around the landscape to graze on different pastures in different seasons. He considered how these lives were put together and how the village communities connected with their neighbours, but he had very little evidence with which to explore any of his suppositions. In the following years, the bio-archaeologists working in John Coles’s Somerset Levels Project would provide some of that evidence, in the form of organic remains that could be studied either with the naked eye or under an optical microscope. Today, virtually every avenue of his speculations could be followed through biomolecules. DNA could reveal much about the local human community, its pattern of kinship, and its interrelations with its more distant neighbours. The same molecule could probe the water-borne diseases suffered by both the farming families and their herds. Isotopic studies of bone proteins could track the dietary journey of those travelling herds, and piece together the diet of their human owners. Lipid studies could be targeted upon that long list of plant and animal resources, many of which fail to show up in any other way. These are possibilities yet to be realized, but the scientific foundation for their realization is in place.
afterword
Is it possible for a novel suite of methods, such as those of biomolecular archaeology, in themselves to drive our ideas about humanity and its history? I don’t think so, but neither does it seem to me those ideas directly drive the novel methods. These so often come from left field, or
derive from some kind of serendipity. However, our ideas are by no means immune from our methods. Instead the histories of methods and of ideas come together in a continuously entangled conversation, constantly responding to one another, sometimes reinforcing, sometimes challenging.
In the time when archaeological methods were about tangible physical things, ideas about the human past were also expressed in terms of physical things; the labels ‘Stone Age’, ‘Bronze Age’ and ‘Iron Age’ make that very clear. I had argued in the introductory chapter of The Molecule Hunt that the utility of those conceptual containers had already been fading as biomolecular archaeology was gathering momentum. Looking back over the text, with a hindsight of years, I am struck by how many conventional conceptual containers were still in place. Although the chapter headings were not specifically articulated in that way, it is not difficult to pick out such themes as plant domestication, animal domestication, the origin of the human species, and the identification of ethnic groups. Much of what has happened over the last fifteen years has further challenged each of those conceptual containers, perforating and blurring their boundaries, dissolving their integrity. That process of dissolution is not in itself the generation of new ideas, more of a challenge, pressing us to think of the human past in novel ways.
The dissolution of the ‘domestication’ container is the easiest to discern, in large part because the boundaries of that particular container have long been ruffled; a number of gradual evolutionary approaches that were pitched against the ‘neolithic revolution’ had been mentioned in the original chapters.
To take the example of the horse, and the way we can currently narrate its engagement with humans over time. Such a narrative embraces a Quaternary world experiencing pronounced and sometimes rapid climatic fluctuations, sweeping away forest and coastlines, lifting every natural boundary to a state of flux. Two large mammals, one on two legs, one on four, continuously renegotiate these changing boundaries, crossing continents in the process, the two-legged one entering Eurasia from Africa, the four-legged one from America. Smaller organisms travel with them, as diseases or parasites. These food webs stretched out across fast-changing environments comprise taxa in a constant state of evolution and co-evolution, adapting to a changing suite of challenges, from leaving their ancestral continents, through to jointly winning the Derby on a European racecourse. Now that we can follow those narratives all the way through, and the various interesting entanglements on the way, a simple two-episode story of ‘wild’ and ‘domesticated’ is not so much wrong as an oversimplification; the terms may remain useful but as two attributes among many that are of interest and evolutionary significance.
The challenge to the ‘human species’ container is in many ways more novel and radical, a point well made at the end of Svante Pääbo’s 2014 review. In terms of porous boundaries in a state of dissolution, his observation that ‘or much of the genome, some humans today are more closely related to the Neanderthals and Denisovans than to other living humans’ is poignant indeed. It is easy now to step back and look critically at the reception of the nineteenth-century discovery of unusual bones in the Neanderthal Ravine, and to reflect on their considerable impact. It is simply too early to reflect in the same way upon equally ground-breaking findings of the early twenty-first century.
This leads directly on to a third conceptual container, the notion of ‘identities’ on a scale smaller than the humanity as a whole, that have variously been labelled ‘culture groups’, ‘ethnic groups’, ‘tribes’, or ‘races’, and have been treated at various times as reproductive populations. As repeatedly alluded to in Chapter Seven and its afterword, these are the narratives that are the most ideologically charged, and in which the narrative of origin and becoming (including the biomolecular narrative) is the most active and conspicuous in informing the notion of identity itself. In relation to this, I would make two observations. First, it still seems comparatively straightforward to get a scientific paper on human genetics published in which such identities are employed as unproblematic labels for human reproductive populations. Second, we do actually have ways of employing biomolecular techniques to look more critically at the relationship between genetic lineage and the construction of identity and a number of interesting papers are already doing that.
As ever, we may have lost some of the simplicity of the patterns in the past as perceived by earlier generations of archaeologists. Nonetheless, it seems fair to say that the global human family is now looking more like many of the families it contains. It may indeed have a core identity, but it also has ambiguous relationships, messy boundaries, and from time to time, a long lost relative comes knocking on our door. Moreover it is far from static in evolutionary terms. The genes that help us digest other species (e.g. those producing lactase and amylase), and the genes that hinder other species from digesting us (immunity and skin characteristics) have been very actively evolving; millennial stories rooted deep in our species’ past can be followed through to the present day. Similar things may be said of the species with whose evolutionary fates we have most directly engaged, the domesticated taxa below us in our chain, and the parasites and disease organisms above us. The other exciting thing about this less pigeonholed, more dynamic narrative of the human past is that it is about evolution in action, and we now have ways of homing in directly on that action.
In the early days of the field, action was about the branching of a tree, typically revealed by sequence variations in non-coding DNA. With time, the emphasis moved to expressed genes, that other biomolecules could help connect to the changing environments in which those genes were expressed. The form of expression could change by mutation on an intergenerational timescale, generating different sorts of proteins and setting in chain different biochemical pathways. We now understand how the pattern of expression may change within the timescale of a single generation, by processes now described as ‘epigenetic’. These processes act by minor chemical alteration of the DNA strands within a living cell, with the effect of switching some genes on and off, and leaving others on as a template for RNA, and protein production, thus determining the actual biochemical pathways enacted. That is how cells within a multicellular organism take on the form of distinctive tissues. Epigenetic processes take the evolutionary circus right down to the lifetime of individual cells.
The earlier quest to detect RNA activity that featured in the early days of biomolecular archaeology has been revived as one of several new approaches to unravelling the epigenetic profiles of various members of the human family, and of the many other species in their food chains. In the future, biomolecular archaeology will explore the core DNA blueprint as its starting point, continue through to the epigenetic control of its expression as different organisms grow, and on to the other biomolecules they produce. It will achieve these on several timescales to the multimillennial lifetime of a taxon to the growth of an individual cell.
What is ensured is a great deal of unimagined detail about our pasts, and the pasts of taxa around us, but will that detail remain essentially material in kind? Will we move to a point of minutely observing past bodies in motion, but leave those bodies mute?
In Chapter Five of the original text, I hinted at the souls of those long gone, and things in their minds that may stay beyond reach, by musing that owners of the the first hand-axes may have been accomplished wood-carvers, leather-workers, and poets. The first two of these could well at some point come to light, should a waterlogged or desiccated site of sufficient antiquity be located and dug. I added ‘poets’ as a bit of rhetorical flourish, not really supposing that this lay within the reach of biomolecular research. It seemed reasonable to be circumspect about how far a very material scientific approach could reach into the ancient creative mind. Now I’m not so sure.
Poetry is about many things, imagination and meaning, encapsulated in speech, rhythm, and musicality. It is now clear that many great apes have an extensive vocabulary of meaningful vocalizations, and that i
n an even wider range of animals, some form of gestural rhythm as central to their behaviour. To look for origins of any of these in the close locality of our own genus is simply looking in the wrong place. However, this in itself doesn’t add up to poetry.
One rather intriguing piece of ancient DNA research may at least have added some rhythm and musicality to the vocalizations. It concerns a gene with the delightful name ‘Forkhead Box Protein P2’.
Individuals carrying a disabled version of the FOXP2 gene experience a variety of problems with their spoken language. They find difficulty in moving their mouths in the very complex ways necessary to for human speech and language. They also have great problems with something called ‘prosody’. This is a term that relates to intonation, rhythm, and the general musicality of human speech, something as important to poetry as the actual meaning of the words. Chimpanzees have much of the apparatus to learn and vocalize a large number of meaningful sounds, but they lack the form of the FOXP2 gene found in humans. The intriguing result to come from ancient DNA studies is that Neanderthals and the individuals from Denisova Cave share that form.
Neanderthal and Denisovan poetry? An engaging notion, but at this point perhaps no more than that. The FOXP2 gene acts in a fairly complex way; the protein it produces is a ‘transcription factor’, moderating a wide range of distinct physiological pathways in a manner compared in Chapter Eight to the conductor of an orchestra. It can also be regulated by other gene sequences, and Svante Pääbos’s group have published evidence that modern humans have a form of regulation distinct form that of their close cousins.
