Barcoding Nature

Shifting Cultures of Taxonomy in an Age of Biodiversity Loss

Claire Waterton

• Publisher: Routledge
• Year: 2017
• Print ISBN: 9781138146334
• eBook ISBN: 9781351574778
• Edition: 1
• Topic: Social Sciences
• Subtopic: Sociology
• Index: Social Sciences

DNA Barcoding has been promoted since 2003 as a new, fast, digital genomics-based means of identifying natural species based on the idea that a small standard fragment of any organism's genome (a so-called "micro-genome") can faithfully identify and help to classify every species on the planet. The fear that species are becoming extinct before they have ever been known fuels barcoders, and the speed, scope, economy and "user-friendliness" claimed for DNA barcoding, as part of the larger ferment around the "genomics revolution", has also encouraged promises that it could inspire humanity to reverse its biodiversity-destructive habits.

This book is based on six years of ethnographic research on changing practices in the identification and classification of natural species. Informed both by Science and Technology Studies (STS) and the anthropology of science, the authors analyse DNA barcoding in the context of a sense of crisis concerning global biodiversity loss, but also the felt inadequacy of taxonomic science to address such loss. The authors chart the specific changes that this innovation is propelling in the collecting, organizing, analyzing, and archiving of biological specimens and biodiversity data. As they do so they highlight the many questions, ambiguities and contradictions that accompany the quest to create a genomics-based environmental technoscience dedicated to biodiversity protection. They ask what it might mean to recognise ambiguity, contradiction, and excess more publicly as a constitutive part of this and other genomic technosciences.

Barcoding Nature will be of interest to students and scholars of sociology of science, science and technology studies, politics of the environment, genomics and post-genomics, philosophy and history of biology, and the anthropology of science.

1 Introduction

The Natural History Museum in London (hereafter the NHM) curates and displays one of the most comprehensive and world-famous collections of specimens of once-living forms. Many people who walk into the museum are lured in, enchanted but also bewildered by life’s variety. Some perhaps tune into a sense of reverence towards several millennia of life on the planet, only some of it coincident with human existence. Many natural history aficionados herald such museums as examples of precious ‘secular cathedrals’ of our time (NHM 2003). Fragile butterflies and moths carefully pinned and aligned in mahogany cabinets compete for space and attention with glass dioramic cases of perching birds and numerous other displays. The more conventional historical collections of dried, pressed, pinned and stuffed organisms spanning all five of nature’s kingdoms today compete with the new Darwin Centre’s spirit collection. This houses what, for some people, is perhaps the most exotic specimen of all – a giant squid, once holding a place in the human imagination as a mythical being – suspended in formol-saline within an acrylic tank, nine metres long. Contributing to the sensation conjured by the ghostly and fleshy presence of the squid is the fact that the tank was built by the same company furnishing the artist Damien Hirst with containers for his exhibits. Embodied memories and traces of lost and still-living species are ordered, preserved and classified in every corner of the vast museum. These stand for at least part of the planet’s biodiversity, some of which continues to flourish in living form beyond the walls of the museum.

Less apparent to the public eye are the labyrinthine corridors, impossibly steep and twisting, narrow staircases and rows of offices, storage cabinets and laboratories behind the scenes. This is the setting for a hive of taxonomic activity. The taxonomists working at the museum – scientists who devote their activities to identifying organisms and tracing the evolutionary and bio-geographical relationships between them – draw upon the vast collections of over 60 million life-science specimens. The Natural History Museum is known, for example, amongst the world’s community of cryptogrammic specialists – those individuals with an interest in lower plants such as mosses, liverworts and ferns – to house a significant collection of specimens of the delicate and endangered Killarney fern, the idiosyncrasies of which are close to the heart of one of our museum colleagues. Today the museum’s specimens consist of whole organisms and of fragments of DNA cryogenically stored at −180°C. Each taxonomist tends to specialize in a particular group of organisms, but each knows that their specific expertise and breakthroughs in understanding contribute to the greater understanding of relations between living (and extinct) organisms on the planet.

Between 2002 and 2005 we had the privilege of working behind the scenes with a number of museum scientists. Our research at that time – a multi-sited ethnography, at the museum but also in the field with various groups – was exploring the relationships between amateur naturalists in the UK and the broader domain of biodiversity science and policy.¹ Towards the end of this research, we found ourselves, as was often the case, relaxing and chatting in the Botany common room at the top of the building. We had become accustomed to participating in conversations on broad-ranging topics, including sometimes quite heated discussions on the controversies around moss and algae identification. Such conversations were also a kind of fieldwork for us. But on this occasion we were informed of a discovery just announced which was potentially revolutionary for taxonomy writ large. Paul Hebert, leading a team of taxonomists, molecular biologists and bioinformaticians at the Ontario Biodiversity Institute in Guelph, Canada, was the protagonist here, and a very energetic and articulate one. He had discovered – we were told in a mixture of animated and skeptical tones – that not only could DNA be a key to understanding the similarities, differences and evolutionary relationships between species (a method established in taxonomy since the 1950s), but that a small fragment of any organism’s DNA – a so-called ‘micro-genome’ – could be translated into a digital artefact that would look very similar to a conventional product ‘barcode’. This barcode, in turn, could be banked in a global library which, when full of barcodes, could serve as a reference point for the rapid identification of every species on the planet! Paul Hebert, in interview with us in 2006, referred to this vision as one gene = all species = all life. The global scale of the claim and the language of renaissance, revolution, global reach, precision and speed that it promised for the science of taxonomy, sounded exciting. Hebert had introduced a palpable acceleration of rhythm and energy to the debates around this science that we had not hitherto witnessed. Taxonomy was a field with a reputation for deliberate craft-intensive attention to minute detail, especially of morphological characters, comparisons and changes. It was not known for its animation, speed and desire for dramatic centre-stage influence.

One of our colleagues at the NHM had an uncanny ability to keep his finger on the pulse of his own shifting scientific culture but also to tune into our own imaginations and referents as anthropologists and sociologists of science. He suggested to us that if we were really interested in understanding contemporary cultures of taxonomy, we should find out more about these new proposals, which he believed were set to rock the foundations of taxonomy, as he then knew it. We were inevitably enticed by this prospect, and this book is the result of a three-year (2006–2009) ethnographic study of DNA barcoding and its evolution through the development of what became known as the Barcoding of Life Initiative (BOLI).²

Informed both by science and technology studies (STS) and the anthropology of science, our methods and modes of analysis commit us to investigate the emerging innovation of DNA barcoding as history and culture in-the-making. The present study has interpreted this innovation as belonging to wider shifts underway in taxonomic and related scientific cultures, whilst keeping a close eye on the specific changes it is propelling in the collecting, organizing, analysing, archiving and imagined use of biological specimens and biodiversity data. We have thus explored the intimate and fluid connections between the minutiae of biological organisms (their DNA) and hopes, dreams and visions for future human and planetary existence. We observe ways in which the taxonomic community, which inherits several centuries of tussling with approaches to classification of the natural world, now finds itself caught up in the whirl of two wider intersecting domains – of the big hyper-genomic life sciences, and biodiversity science and policy.

We note here that STS/anthropology of science studies of the genomic sciences and their publics have mostly focused on the field of red genomics (the bio-medical sciences and technologies) and the therapeutic human bodily futures they conjure. Our research, on the other hand, has explored the domains of non-human biology or ecology which intersect with genomic approaches – the so called ‘green genomics’. With exceptions in the area of genetically modified organisms, green genomics seems to have been largely neglected in STS/anthropology of science. Taking many cues from STS/anthropology of science research in red genomics, therefore, we look closely at the pursuit of classifying biological organisms and we consider the relevance this may have for re-thinking past, present and future relationships between humans and the multitude of organisms with which we co-habit the planet. Our attempt to understand the science of genomics (through a ‘green’ rather than a ‘red’ lens) leads us to connect hopes for human survival and betterment with the (future) health of biodiversity and the planet as a whole. The kinds of questions we ask in this book range from those concerning the smallest details of changes in knowledge production and practice within the taxonomic community, to broader ranging questions about biology, ‘life’ and the human position within this more comprehensive ontological frame. What specific organic fragments, for example, do scientists trust, selected from the entire biological make-up of organisms, to communicate appropriate information and promise for the contemporary purposes of the taxonomic and biodiversity sciences, here re-rendered through genomics? What does ‘life’ become as it is encountered, classified, selectively represented, manipulated and mobilized within the speedy, almost frenzied, ‘technopreneurial’ context of contemporary genomic life-sciences? What reciprocities are crafted to maintain relationships between the innovation of DNA barcoding and long-established continuing taxonomic methodologies for ordering life? In what ways are human subjectivities – ways of being human – imagined and woven together with hopes for biodiversity protection, in a genomic barcoded future? What deep intuitions around the protection of species, but also their loss and destruction, inform the urge to archive – for universal access and use – the DNA barcodes of all species on the planet?

The research has required us to zoom in to the micro-scale of understanding the making of a digital genetic artifact – the DNA barcode – and out again, globally, as barcoders have attempted to press a single gene fragment, found in all eukaryotic organisms,³ to reveal the diversity of all life on earth. It has involved, for example, navigating the complex geo-bio-political histories of specimen collection and archiving up to the present time, and gaining an understanding of the protocols being established to regulate the global access to and mobilization of genetic material for taxonomic research. Although sometimes overcome by the scale and heterogeneity of the sites of our new research, we also felt very lucky! It allowed us to continue working with the rich imaginative worlds of taxonomists and their organisms and we continued to frequent specimen collections around the world. It sent us to robotic sequencing laboratories and international meetings where we witnessed bioinformaticians, laboratory and database managers deep in discussion concerning the data standards required for DNA barcoding to become established taxonomic practice. It also took us to meetings of the Convention of Biological Diversity (CBD) – the powerhouse of the turbulent domain of global biodiversity policy and politics. In other words, we experienced first-hand the proliferation of intersections between taxonomic science, molecular biology, biodiversity genomics and global policy, just at the time when all of these were shifting and emerging in more intensified forms, creating a platform for new ways in which global science, and society encounters the natural world (Fischer 2005).

Paul Hebert, the lead player introduced above, provided unreserved support for our ethnography of an enterprise – DNA barcoding – that he believed would, as he put it, ‘remake our relationship with life’. At the time this seemed like a grand claim coming from the traditionally quite humble domain of taxonomic science, but it whetted our appetites for more. It was with some puzzlement therefore that we soon witnessed a dampening of the energy resonating from Paul Hebert’s hopeful and tantalizing promise. We had been invited to the first International Annual Barcoding Meeting held in August 2006 at the NHM, to give a short presentation on our proposed research. The atmosphere in a room packed with an international crowd of taxonomists, was a mixture of intrigue, caution and perhaps even a little contempt. What was immediately apparent to us as we grappled with difficult questions and listened to further talks, was that the taxonomic community writ-large was not going to be easily seduced by what appeared on first impression to be Paul Hebert’s sound-bite approach to life. We had immediately to wake up to the fact that – perhaps inevitably – the vision which had so far captivated us would be refracted through the hopes, sensitivities and commitments of a long-established, highly diverse and fragmented global discipline.

Paul Hebert was not in fact present at this meeting but his and his team’s ideas were communicated through talks provided by other taxonomists. Some individuals present wanted to know more, some wanted desperately to hold Paul Hebert to account and ask him to reduce his vision to a more realistic and modest offering to the intersecting fields of taxonomy and biodiversity science and policy. The latter group demanded an acknowledgement that DNA barcoding could not be hailed as revolutionary, but was actually a rather humble evolution of taxonomic practice in one particular direction. All that was realistically on the table, they felt, was a very simple tool which may speed up species identification and mobilize data for all to use – but this was by no means set to change our relationship with life! Crucially also, in order to make its contribution, DNA barcoding was dependent upon conventional long-established taxonomic resources (such as material voucher-specimens and existing infrastructures).

The meeting was, however, an invaluable portent for our research to come. Although slightly surprised, perhaps by our own naivety more than anything else, we were not disheartened by the potentially numbing ambivalence expressed by the taxonomists present. The sense we grasped was that if we were to step into the world of DNA barcoding, the journey would require us to navigate the eddies and flows of an entangled and emergent set of relationships between promise and tangible achievement. We had come face-to-face with one of many ambiguities that should here set the tone for what is to be explored in this book. Indeed we knew from STS and anthropology of science that it is these very sites of often unspoken tension, contradiction, ambiguity and paradox that offer rich seams for further insight – something to which Mike Fortun, more than any other STS scholar of genomics, bears witness (Fortun 2009). It is in these ‘chiasmic’ spaces that the richest inter-connections between past, present and future; material and virtual forms; the objective and the subjective; the universal and the particular; and the global geo- and bio-political relationships in the making of technoscience can be explored. In STS terms we must look then at the politics, oscillations and frictions that constitute the barcoding network (Barry 2001; Dugdale 1999; Tsing 2005). We need to ask how evident contradictions – for example between promise and tangible achievement – might be contained within a ‘project’. We also need to consider how such contradictions and ambiguities perhaps exceed any given ‘project’, their substantive technoscientific contours more powerfully shaped by the wider cultural context? Furthermore, what does their navigation by scientists as public knowledge producers, thus also as material social world-producers, reveal about the current shaping and experience of so-called modernity writ large?

We hope that the memories, reflections and questions provided above offer a sense of the challenge and excitement with which we began our research into DNA barcoding and BOLI – the multi-pronged institution that has supported this emerging technoscience and its promotion in worlds of practical applications and public policy. Needless to say, much detail will follow about barcoding and BOLI in the chapters of this book. The remainder of our introduction will locate our study within sociological and anthropological approaches to the phenomenon of classification and within the history of the intersections between the taxonomic and biodiversity sciences. We will then provide chapter outlines with which readers can navigate the book.

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Sociologists, anthropologists and historians have long been rightly fascinated by human classification practices. What holds such interest, perhaps, is the idea that classifications of things do not in themselves exhibit only a pre-existing logic in nature: rather they are of social origin and perform social roles and meanings, even while reflecting systematic attention to selected salient qualities in nature. The relationships between classes, then, are not simply to do with the correspondence between the world and the classificatory scheme but also concern the collective construction of meaning (Durkheim and Mauss 1963; Bowker and Star 1999). Such processes also deserve to be interpreted historically: whilst the making of collective meaning through classification endures as a human pursuit, it also changes in its historical detail and anchoring over time. In her essay on the history of naming the diversity of life-forms on our planet, historian of science Lorraine Daston (2004) explores precisely this point.

Daston opens her essay with a rendition of the biblical story of the Tower of Babel, from The Book of Genesis. The story reads as a warning of the ultimate human hubris in pretending that all of humankind could create, out of a context of multiple linguistic classifications, a single harmonious language. According to the story, the people of this world would build a single city-state, live together there and speak a single language comprehensible to all. Beholding this activity as an act of ultimate vanity, God put an end to it, confusing language and scattering people into their separate cultures, all over the face of the earth. The resulting chaos he named ‘Babel’.

The curse of Babel reverberates powerfully in many dystopic cultural fables, including scientific ones, and perhaps most tellingly in taxonomy. The urge to discover unity in nature has been a defining epistemic and normative feature of scientific modernity; and of course, this urge has been animated by an original drive to escape religious dogma’s own visions of a different unity. Daston describes the fear afflicting eighteenth- and nineteenth-century plant taxonomists, for example of the catastrophic confusion that could be wrought by the proliferation of different names for the same plant species or genus – a confusion known within taxonomy as ‘synonymy’. This fear, of a bewildering lack of correspondence between names and kinds – a modern Babel – continues within contemporary taxonomy. As a retired Director of the Oxford Museum of Natural History recently expressed it, ‘without a permanent single system of names, how could there ever be permanence of knowledge?’

The Director’s lasting concern here reminds us of the metaphysical responsibility that taxonomists (including DNA barcoders) shoulder and of the work that has gone on, over time, to achieve collective meaning. Daston describes precisely how taxonomists actually manage the tension between, on the one hand, keeping names for organisms stable (and therefore able to be collectively known and understood) and, on the other hand, allowing for change in naming and classification, as understanding of species, their boundaries and their inter-relations developed. This tension has to be actively managed through collectively agreed conventions. The ‘type specimen’ is one such convention, designed to maintain a stable, collectively understood correspondence between a name and a natural kind, and as such an essential part of taxonomic practice with significant symbolic value. Without such conventions, what Daston calls the ‘St Vitus’ dance of scientific change’ – the inevitable theoretical and technological shifts in the bases of classification – would corrode delicately transmitted common understandings, and Babel would return.

In what follows in this book we see BOLI as a contemporary taxonomic initiative shouldering complex ongoing histories of shifting taxonomic practice and commitment, all of them replete with intricate conventions enabling collective work. Such taxonomic histories are elaborate and complex and we do not enter into their details here. We note, however, that so-called natural order(s) have historically been perceived and generated through quite different lenses of enquiry, reflecting different combinations of purpose, and through different conventions, with implications for collective meaning. This historic reality has contributed to a certain epistemic turbulence which continues today as a characteristic feature of taxonomic cultures (Foucault 1966; Dean 1979; Hull 1988; Stemerding 1991; Ridley 1986).

Scholars reveal, for example, that the portrayal of natural order(s) by taxonomists depends very much upon what properties of organisms are considered to be indicative of order (Hesse 1974). As Foucault’s (1966) oft cited work on the history of natural historical pursuits demonstrates, the classification system developed in the seventeenth and eighteenth centuries known as the Linnaean hierarchy⁴ essentially operated – and continues to do so today – as a linguistic device equipped to lay out a grid of the observable (morphological) physical qualities of organisms, organized according to the measurements of similarities and differences between them. It is this visually perceived ordering of similarity and difference that Foucault se...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• List of figures
• Acknowledgements
• 1 Introduction
• Technical interlude
• 2 DNA barcoding: revolution or conciliation?
• 3 What’s in a barcode?: the use, selection and (de)naturalization of genetic markers
• 4 ‘A leg away for DNA’: mobilizing, compiling and purifying material for DNA barcoding
• 5 Extending the barcoding frontier
• 6 Archiving diversity: BOLD
• 7 BOLI as redemptive technoscientific innovation
• 8 What is it?: identifying nature and valuing utility
• 9 Barcoding nature: final reflections
• Notes
• Bibliography
• Index