Contamination
DO IT RIGHT OR NOT AT ALL
In the summer of 2000, scientists convened for the Fifth International Ancient DNA Conference at the University of Manchester in England.1 According to a meeting report published in Science, the discipline seemed to have emerged from its race for the oldest DNA and was entering a new phase of methodological development and scientific maturity. The author, Eric Stokstad, highlighted several studies that seemed to confirm this assessment.2
One study that Stokstad featured was by Svante Pääbo and Hendrik Poinar, at that time a doctoral researcher studying with Pääbo in Munich, whose recent research had found that coprolites, the scientific term for fossilized poop, were great sources of DNA.3 In this study, they tried to extract DNA from approximately twenty-thousand-year-old fossilized feces found in a cave outside of Las Vegas, Nevada. Standard methods for extracting and amplifying DNA from modern fecal material were unsuccessful, so they used another approach involving a chemical compound, N-phenacylthiazolium bromide, which breaks down sugar-derived protein cross-links in order to release the DNA. By adding this compound to the extraction process, they were able to recover DNA and then determine, based on sequence comparison, that these coprolites were left behind by an ancient and extinct ground sloth, Nothrotheriops shastensisthus. From this data, scientists were given a glimpse into the diet of a long-lost species. Based on this study, caves seemed to be a unique site for molecular preservation, while the application of this method to fossilized feces revealed a unique source of molecular information.
Stokstad also spotlighted recent research led by Alex D. Greenwood and Ross D. E. MacPhee at the American Museum of Natural History, who claimed to have recovered the first evidence of nuclear DNA, not just mitochondrial DNA, from the extinct woolly mammoth.4 In this same study, Greenwood and colleagues also claimed to have salvaged partial sequences of an endogenous retrovirus found in the DNA.5 Stokstad explained that although endogenous retroviruses are common across all creatures and unlikely to offer information or insight about the life of a particular organism, this finding led the team to consider the possibility of tracing the evolution and extinction of species through ancient pathogens. Prior to this specific study, MacPhee and Preston A. Marx of the Aaron Diamond AIDS Research Center in New York City hypothesized that pathogens from encroaching humans or animals arriving in North America via the Bering Strait could be in part responsible for the mammoth’s eventual extinction.6 If viruses could be detected in the fossil record, then this could be the start of a new field dedicated to the search for, and the study of, paleoviruses. According to Stokstad, the scientists behind this research admitted that finding evidence of an Ice Age pathogen would come down, basically, to luck.7 In highlighting new methods and sources of DNA, however, Stokstad portrayed the practice at the beginning of the twenty-first century as one ready to make some serious, cutting-edge contributions to our knowledge and understanding of evolutionary history.
A month after the meeting, however, Science published another article with a very different view on the state of the field. This article—“Ancient DNA: Do It Right or Not at All”—painted a picture of skepticism, criticism, and frustration with the discipline’s development. The article was written by Alan Cooper—recent founder and director of the Henry Wellcome Ancient Biomolecules Lab at the University of Oxford—and Hendrik Poinar, recently graduated from Pääbo’s lab in Munich and by this time a postdoctoral researcher at Pääbo’s new lab at the Max Planck Institute for Evolutionary Anthropology (MPIEVA) in Leipzig. The publication was a direct response to the conference, and one presentation in particular that Cooper and Poinar thought had all too “boldly opened with the claim that the field was now mature and could move ahead with confidence.” Indeed, Cooper and Poinar strongly disagreed with this assessment: “This optimism is unfounded,” they argued, “as demonstrated by the notable absence of ‘criteria of authenticity’ from many presentations at the conference.”8 Although standards for ancient DNA authenticity had been suggested over the decade, and while some scientists had adopted them, Cooper and Poinar felt that many others still ignored them. The authors even noted that editors and reviewers of prestigious journals continued to publish work without proper controls that would ensure the findings were both authentic and reproducible. They blamed the collective scientific enterprise—scientists, editors, and reviewers alike—for failing to employ or enforce criteria to standardize the practice and restore its reputation as a credible discipline.
To combat contamination concerns, Cooper and Poinar proposed a list of nine rules for “criteria of authenticity.” First, every study had to be conducted in a “physically isolated lab”—a lab specially dedicated to ancient DNA activity in order to circumvent any contamination from modern material. Drawing on guidelines outlined in previous publications, Cooper and Poinar argued that labs handling ancient material must be physically isolated from other molecular or microbial labs containing modern material.9
In the “Ancient DNA Lab,” Cooper and Poinar recommended that “control amplifications,” or multiple extractions, be performed to test for contamination. Other required controls included “quantitation” to first determine if enough DNA was available for amplification, as well as “cloning” to estimate the amount of endogenous DNA (DNA originating from the organism) in the PCR product. Further, they argued that sequences should show “appropriate molecular behavior” or evidence of degradation. In other words, ancient sequences were expected to be short sequences of less than five hundred base pairs. Longer sequences were assumed to be the result of contamination, or at least required justification to demonstrate that contamination had not occurred. Additionally, Cooper and Poinar suggested employing indirect evidence of DNA preservation via “biochemical preservation” of other molecules like amino acids. And in the case of human ancient DNA, where contamination concerns particularly ran rampant, they insisted that sequences should be extracted and analyzed from “associated remains” or from animal remains to confirm molecular preservation from the same environmental setting. They also argued for “reproducibility,” namely that practitioners should be able to produce the exact same results from the initial extraction, as well as additional extractions, of the same specimen. Finally, Cooper and Poinar maintained that scientists should reproduce their findings through “independent replication.” This meant that a second sample of the specimen should be taken, extracted, sequenced, and confirmed in an independent lab by independent researchers. Although they admitted that completing all nine criteria would be expensive and time-intensive, Cooper and Poinar believed doing so was vital to the future of the field.10
Other practitioners expanded on these newly proposed expectations, particularly regarding requirements for the ancient DNA lab.11 For example, some scientists suggested that ancient DNA research be conducted in a physically isolated lab, ideally located in a building without a PCR lab, and fitted with specific ventilation systems with positive air pressure to prevent contamination via airflow when entering or exiting. Further, all equipment brought into the clean lab should be decontaminated with bleach or ultraviolet (UV) irradiation as appropriate. With each person’s entry into the clean lab, researchers would be required to dress in full-body suits complete with gloves, shoe covers, hairnets, and facemasks to avoid contamination during experimentation. Afterward, UV lights are used to sterilize the space in preparation for the next use. Researchers were also advised to never enter the clean lab after working in the PCR lab to avoid cross-contamination between these workspaces. Ultimately, the physical separation of the ancient DNA lab from other labs, as well as the precautions that researchers are required to take when working in the lab, became a hallmark of the proper practice of ancient DNA activity. The presence or absence of a clean lab became a way in which some scientists measured the credibility of research results within this community.
Overall, Cooper and Poinar’s “Ancient DNA: Do It Right or Not at All” was an influential though not isolated effort to address contamination concerns. Sure enough, their criteria of authenticity drew on various publications introduced over the years, some of which dated back to the late 1980s or early 1990s.12 One much more recent paper published by Pääbo’s lab in 1997 on Neanderthal DNA, for example, outlined in detail the methodological and technological precision that they thought necessary for demonstrating ancient DNA authenticity.13 But still there was a sense of frustration on behalf of some scientists, including Cooper and Poinar, who felt that others in the field were not taking contamination concerns and standardization seriously. One interviewee explained the frustration and subsequent publication this way: “Various people—like Svante [Pääbo] and Tomas Lindahl and Alan Cooper and Hendrik Poinar—said there are issues and most people listened to them, who were actually published in the early papers or the erroneous early papers. . . . But a few people didn’t and carried on ignoring them and so on. Then, in frustration, these criteria get published” (Interviewee 6). For Cooper and Poinar, it was more than the credibility of just one or two or even a handful of studies at stake. Indeed, they believed the credibility of the discipline as a whole was in jeopardy. The one way to fix this, as far as they were concerned, was for fellow colleagues in the field to strictly adhere to the criteria of authenticity: “Failure to do so can only lead to an increasing number of dubious claims, which will bring the entire field into further disrepute.” The future of the field depended on it: “If ancient DNA research is to progress and fulfill its potential as a fully-fledged area of evolutionary research, then it is essential that journal editors, reviewers, granting agencies, and researchers alike subscribe to criteria such as these for all ancient DNA research.”14 For Cooper and Poinar, enforcing criteria was necessary in terms of standardizing the field and establishing its credibility within evolutionary biology more broadly.
Several years after Cooper and Poinar published their criteria of authenticity, Pääbo and Poinar, along with other colleagues, reiterated the importance of guidelines, especially in terms of reproducibility and replication. In a hefty thirty-page review paper for the Annual Review of Genetics, they reflected on the field’s nearly twenty-year-history.15 Looking back to the early days, Pääbo and co-authors recalled the early studies in the mid-1980s that first claimed to have demonstrated the discovery of DNA from ancient and extinct organisms, namely the discovery of DNA from the quagga and the ancient Egyptian mummy.16 But they also brought attention to the fact that the findings in these studies, the first of their kind, had not been successfully reproduced to guarantee authenticity. Pääbo later noted that even his initial research on mummy DNA likely contained modern contamination.17 As Pääbo and co-authors argued, “They were in a sense precocious, since the amounts of DNA present in the old tissues were so small that the isolation of bacterial clones carrying the same DNA sequence was essentially impossible. The results could therefore not be repeated in order to verify their authenticity. Thus, the litmus test of experimental science—reproducibility—was hard or impossible to achieve.”18 In this article, the authors explained that the advent and adoption of PCR in the late 1980s to ancient DNA studies changed this by offering scientists opportunities to exponentially amplify the given DNA sequence under investigation. But at the same time, this ability to amplify and analyze more than a single sequence exposed evidence of two challenges for the search for DNA from fossils, namely sequence errors via molecular damage or modern contamination.19 According to Pääbo and colleagues, two decades later, “Contamination remains the single most serious concern in the study of ancient DNA . . ., a reality reflected in the continuous evolution of techniques to avoid contamination as well as the addition to and modification of criteria of authenticity.”20
In their review paper, Pääbo and colleagues listed the criteria of authenticity, insisting that following them was of “paramount importance” in order to uphold the discipline’s credibility.21 At the same time, however, these authors also argued that completion of the criteria alone was not enough and “cannot be taken as proof that a DNA sequence is genuinely ancient.”22 In fact, it was entirely possible that a result could be a false positive. They noted that if an organism is contaminated with a specific DNA sequence, in theory the criteria of authenticity may be satisfied but the result itself may still be inauthentic. To explain this point, they provided an example of a case where DNA was extracted from a nearly thirty-thousand-year-old bear tooth found in China. From this tooth, researchers were able to amplify human DNA sequences (sequences that were clearly not authentic in origin to the bear tooth), which they were then able to reproduce. In this case, the criteria of authenticity were satisfied but the sequence that was first produced, then subsequently reproduced, was contaminated from the start.23 In light of this, the authors added that “the most important prerequisite for successful ancient DNA research is a highly skeptical attitude to one’s own work.”24 The criteria, they explained, were more of a framework for conducting and validating research results. Scientific reasoning, or a critical attitude, toward the research must be a part of the process too. In other words, criteria were important, but criteria alone were not enough.
The extreme efforts that some scientists took to emphasize the importance of authenticity and reproducibility of ancient DNA analyses, not to mention the efforts they took to try to achieve both, was not unusual or unreasonable. Indeed, sociologists of science Harry M. Collins and Trevor J. Pinch, for example, investigated the variety of ways in which a number of practitioners have depended on replication as a hallmark of successful experimentation in their own scientific endeavors. In addition to the how, Collins and Pinch also investigated the reasons why these practitioners depended on replication. Drawing on cases ranging from parapsychology to the detection of gravitational waves and solar neutrinos, Collins and Pinch argued that for many practitioners, replication of results—the ability to generate the exact same finding again and again—was the cornerstone of scientific validity.25 Collins specifically explained that for the majority of practitioners, “reproducibility” was understood as evidence that what they were doing in the lab corresponded to reality and the “universality” of science.26
However, Collins and Pinch also noted that replication in practice is far from straightforward. In fact, it is often a serious source of controversy. In the early stages of a new research field, it is nearly impossible to know whether the methods employed or results produced are indeed reliable. In the beginning, the correctness of the outcome is open to debate, as are the means for producing, then reproducing, that particular outcome, whatever it may be. In one of his works, Collins put the point this way: “Usually, successful practice of an experimental skill is evident in a successful outcome to an experiment, but where the detection of a novel phenomenon is in question, it is not clear what should count as a ‘successful outcome’—detection or non-detection of the phenomenon.”27
In the case of ancient DNA research—even after nearly two decades of exploration into the subject—the very presence or absence of DNA in fossil material was subject to debate. Researchers were divided over both the theoretical existence of and potential evidence for ancient DNA. They were divided over the possibility that DNA could exist intact for hundreds, thousands, or even millions of years in the first place, and they were divided over the proof required to demonstrate that authentic and ancient DNA from fossil material could be reliably as well as repeatedly recovered. Consequently, the act of replication—initially intended as a standard of success—was instead a source of never-ending disagreement.
Collins described this dilemma in terms of a kind of regress. Specifically, he called this the “experimenters’ regress”—a “paradox which arises for those who want to use replication as a test of the truth of scientific knowledge claims.”28 In other words, “To know whether an experiment has been well conducted, one needs to know whether it gives rise to the correct outcome. But to know what the correct outcome is, one needs to do a well-conducted experiment.”29 And on and on the regress goes until scientists decide, by whatever means, on what qualifies as a correct outcome of a properly conducted experiment.
But overcoming this regress is hardly easy. Not only is the validity of methods or results vulnerable to disagreement but the actual ability to reproduce those same results with the same methods is often riddled with debate: “The problem is that, since experimentation is a matter of skillful practice, it can never be clear whether a second experiment has been done sufficiently well to count as a check on the result of a first. Some further test is needed to test the quality of the experiment—and so forth.”30 Therefore, even if researchers are satisfied with the first experiment, they may not be persuaded that the second experiment, initially intended to replicate the results, was carried out in a competent manner.
In theory and in practice, there can always be disputes over how an experiment was conducted. Replication of scientific experiments is an arduous business. For Collins, “experiments are difficult” because “much experimental skill is tacit.” As Collins explained, tacit knowledge is unarticulated knowledge involving matters of intuition, judgment, and experience, all of which are affected by more tangible resources such as time and money. When it comes to experiments, tacit knowledge is both essential and elusive. Indeed, the very nature of experiments, how they are conducted and reported, can be the crux of the problem. “Therefore, an experiment cannot be fully described in print even with the best will in the world,” argued Collins. “That the conventions of scientific writing and publishing prevent the promulgation of intimate details of experimental trials, errors, and fudges, only makes things worse. Thus, an experimenter who wishes to test another’s findings by replicating the experiment finds it hard to know whether any failure to find the same result is a consequence of the result not being robust or the replication being unlike the original in some crucial way.”31
PCR, although an invaluable technique that facilitated the growth of the field, was also the source of its many problems. Considering PCR’s drawbacks in regard to contamination, a younger scientist explained, “It’s a mess. Half the time nothing happens. If something does happen, you can’t repeat it. You get contamination you can’t get rid of and you have no idea where it’s coming from.” The entire process is like “voodoo in the lab” with “all these rituals,” but in the end “you can’t figure out where anything is coming from,” this scientist said, laughing. “It’s so frustrating!” (Interviewee 27). Even the Leipzig lab—a frontrunner in the world of ancient DNA research—struggled with technological limitations too. According to another researcher, a colleague at the MPIEVA in Leipzig warned against working in the field of ancient DNA research: “Whatever you do, don’t get into this. It’s a completely dead-end thing” (Interviewee 42). As time went on, and despite the huge strides that have been made in the field, many practitioners felt that one step forward almost always meant two steps back. “And we were kind of stuck,” one recalled. “You had a whole generation of researchers—this is what they wanted to do—but they were bound up by the limits of the technology” (Interviewee 27).
The Fifth International Ancient DNA Conference was an obvious nexus of contention regarding contamination, and Cooper and Poinar’s publication “Ancient DNA: Do It Right or Not at All” forcefully put the issue, as well as their solution to it, out in the open for researchers internal and external to the practice. Their criteria of authenticity became a hallmark of credibility, and the acts of reproducing and replicating results became measures of experimental expertise. For many practitioners, contamination was a highly technical issue, and Cooper and Poinar’s criteria functioned as a gatekeeper in the process of determining the reliability of results.
DUAL CONTAMINATION
Criteria of authenticity were more than a response to the developing discipline’s technical challenges. The criteria were also a response to its status as a public-facing science, or even arguably a celebrity science. To be clear, scientists were concerned about “contamination” in both a literal and figurative sense as it related to ancient DNA authenticity and the intense press and public interest that surrounded the science.
In the literal understanding of the term, contamination referred to a specimen’s exposure to DNA from other sources such as the environment or bacteria. Human handling in the field, lab, or museum was a further problem that scientists had to be aware of and avoid. This was all complicated by the highly damaged nature of DNA from organisms hundreds to thousands of years old. Yet as this reality of contamination became more pervasive and more publicized, researchers became cognizant of a different but not entirely unrelated form of contamination. In the figurative understanding of the term, some scientists saw the media as having a negative influence. More specifically, they viewed the hype and growing celebrity of ancient DNA research, especially related to disproportionate or undeserved media attention, as something that was contaminating their credibility as a legitimate approach to studying evolutionary history. Such hype was instrumental in the search for ancient DNA research’s emergence and evolution into a new scientific field. At the same time, however, the failed expectations, and the very public nature of them, became interpreted by those internal and external to the field as overshoot, which ultimately damaged the reputations of not just a handful of practitioners but the overall discipline.
Indeed, the turn of the century was a critical period for the field, and the Fifth International Ancient DNA Conference, as well as Cooper and Poinar’s “Do It Right or Not at All” article, were the ultimate illustrations of the need for change and the impetus for it. It was a turning point as ancient DNA researchers were forced to face years of concerns regarding contamination, celebrity, and what some viewed as a general lack of regard for either. At the Ancient DNA Conference in Manchester in 2000, a scientist recalled that conference organizers assumed the audience would ask questions about the validity of results. “But nobody did,” said this scientist. “Everybody was very British and polite and just sat there” (Interviewee 5). Another senior scientist offered a similar perspective: “We were at the lunch of an ancient DNA meeting bitching away about how most reports were repeating the same errors that we’d seen in the late ’80s and in the mid ’90s. It was just like, ‘Ah, for fuck’s sake, we’re doing it again!’ ” (Interviewee 32). For this interviewee, contamination concerns coupled with the growing celebrity nature of the field were the reasons for their discontent, explaining that some scientists were “attracted by the sexiness of the work” and the opportunity of “publishing in Science or Nature” (Interviewee 32). As one practitioner explained, contamination and celebrity were also the motivating factors behind researchers’ decisions to advocate criteria of authenticity: “So, this is why Cooper and Poinar published that paper. That’s where it all came from and it’s this lack of self-criticism . . ., standing back from your work and saying, ‘Is this believable? Is this right?’ I think most scientists do, but some don’t because they just think, ‘Wow, this is great! I’ve got a great result and I can get a paper in Nature or Science’ ” (Interviewee 5). “Do It Right or Not at All” was not just a call for criteria but a demand to discipline the search for DNA from fossils as it developed into a celebrity science.
Just as media attention empowered the young field, it seemed to undermine it, too. Sure enough, some researchers—working both in and outside the discipline—viewed the ever present attention around the search for DNA from fossils as a further and more figurative source of contamination. As far as one senior researcher was concerned, these reactions were tied to deeply seated worries about the discipline’s corresponding credibility: “I think [it] was not just a defense against Jurassic Park,” explained this interviewee. “It was a defense against the rest of the scientific community who were starting to look at ancient DNA as, like I said, a sort of charlatan type of research” (Interviewee 4). According to some scientists, too much media interest or influence in the face of failed expectations could be seriously damaging.
In a way, however, celebrity was embedded in the science and publication practices around it. Reflecting on the history of the ancient DNA community, for example, one geneticist presented this perspective: “I do think it was a community that was distorted by the probability of getting spectaculars. It was interested in getting spectaculars; famous fossil, bit of DNA, Nature or Science.” Both scientists and scientific institutions, along with the media, played a part in encouraging and producing headlining research: “So, I think it was distorted by the attention that Nature and Science give, and maybe those journals deserve a little bit of criticism because they like the headlines and let some things in that weren’t that scientifically interesting because they had the ‘wow’ factor.” For this interviewee, the publicity associated with an exciting young discipline of study had an effect on the type of research personalities attracted to it: “If you work in a more mature field, the route to a big paper in Nature and Science is years of painstaking work. We had phases where you get your bone, do your PCR, sequence it, send your paper off—so it attracted and rewarded people who liked a short-cut to success, as papers in Nature and Science are perceived as a success.” However, this interviewee also conceded having previously capitalized on the celebrity of the science by publishing a paper in Nature on a very small amount of mitochondrial DNA mainly because it was DNA from an iconic, newsworthy specimen: “I can’t preach and I don’t mean to be preaching, but I think it was a distortion” to publish minimal results in such a high-profile journal. When asked if it felt like this in retrospect, the interviewee replied, “Oh no. It felt like it then. We knew. So, in some ways it attracted some crazy dudes—some successful crazy dudes and some unsuccessful crazy dudes” (Interviewee 21).
In reaction to credibility concerns, ancient DNA researchers engaged in “boundary-work” as an attempt to separate their work from other research that they viewed as less credible. Thomas F. Gieryn, a science studies scholar, initially introduced this concept of boundary-work by drawing on a historical analysis of early natural philosophers’ and scientists’ struggles to achieve authority in the face of opposition.32 In his complete treatment of the idea, Gieryn described boundary-work as a “sociological explanation for the cultural authority of science itself” via the “discursive attribution of selected qualities to scientists, scientific methods, and scientific claims for the purpose of drawing a rhetorical boundary between science and some less authoritative residual non-science.”33 According to Gieryn, there is no one way to do science but different ways to draw and redraw the boundaries of what we view as science.
As Gieryn aptly noted, scientists often engage in boundary-work when they feel their credibility, and by extension their authority, is under attack. When threatened by internal or external interests, scientists defend their research by drawing a line, or multiple lines, between their work and other activities—scientific or not—that they consider a challenge to their reputation. When this happens, boundary-work is a vital factor in the contest for credibility: “Boundary-work becomes a means of social control: as the borders get placed and policed, ‘scientists’ learn where they may not roam without transgressing the boundaries of legitimacy, and ‘science’ displays its ability to maintain monopoly over preferred norms of conduct.”34 Indeed, boundary-work is a process by which scientists continuously construct, deconstruct, and negotiate definitions of what counts as science.
In the history of ancient DNA research, practitioners felt the need to respond to credibility concerns on two fronts: in response to the literal worry regarding the contamination of fossil or genetic material in the lab and in response to the figurative worry regarding the contamination of their reputation through excessive press and public attention. In other words, ancient DNA researchers engaged in “double boundary-work” in which researchers build boundaries on two fronts in response to two different but not unrelated issues that appear to affect their autonomy, authority, and legitimacy.35 In one sense, researchers responded to contamination concerns by building technical boundaries around the practice through the implementation of criteria via the use of certain technologies and techniques. Cooper and Poinar’s “Do It Right or Not at All” article was an example of this on paper, while the presence or absence of an “Ancient DNA Lab” was a physical boundary used by some scientists to help demarcate reliable from less reliable work.
In another sense, they felt the need to respond to the celebrity status of the field by building boundaries through rhetorical strategies in an attempt to isolate their work from media interest or influence—something that scientists were starting to feel was contaminating the quality of the science. In light of contamination and celebrity concerns, researchers realized that the integrity of their work depended on a policing of it. For some this necessitated a public response. Rob DeSalle and David Lindley, for example, wrote The Real Science of Jurassic Park and The Lost World in an attempt to address the scientific versus fictitious aspects of Jurassic Park and its successful sequel, The Lost World (1997).36 David Norman, a paleobiologist at the University of Cambridge, reviewed the book and claimed, “It debunks the whole scenario very effectively and is a perfect antidote to all the ridiculous hype surrounding these films. Steven Spielberg is a fantastically successful film-maker; he has created some of the best fantasy movies ever; and that is all that Jurassic Park and The Lost World are—pure fantasy, no more, no less.”37 Indeed, DeSalle and Lindley set out to draw a line between the movies and ancient DNA activity as a real scientific and technological practice. To be sure, their intent was directly motivated by the consistent publicity that surrounded the science of ancient DNA research. According to a practitioner involved in the early ancient DNA research studies, “That book comes directly from the media interest in ancient DNA work” (Interviewee 18). Other scientists responded similarly but through more conventional means. Adrian M. Lister, for example, a paleontologist and close collaborator with ancient DNA researchers, wrote an article called “Ancient DNA: Not Quite Jurassic Park,” while Mary Schweitzer and science writer Tracy Staedter published a piece entitled “The Real Jurassic Park.”38 In both these works, the researchers alluded to the blockbuster movie but highlighted the fickle nature of molecular preservation and the predominant problem of contamination. Given these issues, among many others, they argued that the idea of bringing dinosaurs back to life was out of reach, at least for now, all in an effort to set the record straight.
DO IT WITH ME OR NOT AT ALL
While initially intended to reduce controversy regarding authenticity and reproducibility of findings, criteria of authenticity as articulated in the “Do It Right or Not at All” article effectively provoked further debate and division in the community. In the attempt to control contamination and celebrity concerns, some also tried to control competition by making it more difficult to participate in the practice, limiting access to the technique and to success in the field. Indeed, the criteria of authenticity, and the degree to which scientists observed or did not observe these standards, divided the community into different collaborations, conferences, and even places of publication. According to one of the earliest researchers in the field, “Ancient DNA: Do it Right or Not at All” was the ultimate embodiment of a new, conservative, and exclusive philosophy of how to conduct scientific research on ancient and extinct specimens. As this interviewee noted, a more apt title for this paper would have been “Do It with Me or Not at All” (Interviewee 11).
By the turn of the century, Pääbo and Cooper had become scientifically and politically powerful players in the field. Both had become directors of generously funded labs at top-tier research institutions. Their credentials and experience had earned them reputations as cutting-edge, even cut-throat pioneers in the search for DNA from fossils. Both researchers had started off as students with Allan Wilson in the late 1980s and early 1990s at Berkeley, the lab recognized as the birthplace of ancient DNA research. And early in their careers they were both published authors in the new field and vocal spokespersons on the direction in which the search for DNA from fossils should go. Inside the community, Pääbo became known as the “Dark Lord of Ancient DNA” (Interviewee 12) and Cooper as the “Chief Challenger” (Interviewee 28). In their own ways, they established their own schools of thought and schools of followers.
As prestigious and prolific centers of ancient DNA activity, Pääbo’s and Cooper’s labs exercised their authority over the future of the field, and their ideologies specifically influenced a younger generation of rising practitioners. Here, they were influential in the developing discipline of ancient DNA research, particularly in regard to their conservative stance on contamination issues, but they differed in their interactions with, or rather reactions to, the rest of the community. “I think they, together, had a pretty strong influence on this conservatism,” recalled one of Pääbo’s former students, “with the difference that Alan [Cooper] propagated more aggressively than Svante [Pääbo] did” (Interviewee 15). At Oxford, for example, one scientist recalled exposure to and interaction with the ancient DNA community: “I did my PhD with Alan, and being fairly naive and unprepared, I listened to what Alan was saying about everybody doing it wrong. And he would occasionally send me to conferences . . . and give talks basically about how people should be doing it properly, and that probably didn’t start me off as being popular with people” (Interviewee 6). According to interviewees, Cooper’s involvement with the community was much more active and assertive, while Pääbo took a different, but not less effective, stance toward research in the field.
At Leipzig, Pääbo—despite his role as a founder of the field—intentionally isolated himself, his work, and his lab from the rest of the community. His disassociation came through his absence at conferences and disregard for most, although not all, work outside of his lab. An earlier student of Pääbo’s recalled the community schism through the deliberate negation and resulting ignorance of other research in the field: “It was present, definitely, but it took me some years to realize it because I started in Svante Pääbo’s lab. . . . For some time, I didn’t even realize that the other part of the community existed. . . . In Svante’s world, it basically didn’t exist. It was nothing one needed to cite, nothing one needed to read. So, I kind of knew there was something, but it was something completely unimportant” (Interviewee 15). Pääbo and Cooper, along with their schools of thought and followers, both promoted conservatism via hardline devotion to criteria of authenticity, but they used different strategies to separate their work from what they viewed as less credible efforts in the ever growing field of ancient DNA research. Together, this conservative philosophy shaped how their students, as well as colleagues and collaborators, viewed their own research in relation to the rest of community.
According to one of the early researchers in the field, ancient DNA appealed to practitioners across disparate disciplines, but as it did, it drew in a group of practitioners that, as far as this interviewee was concerned, were “amateurs,” ill-equipped in the specifics and nuances of molecular biology. “The trouble with ancient DNA is that you get people thinking they can do it; people who were forensic scientists, people who were doctors, the sort of doctors who like to retro-diagnose what Mozart died from. [Laughs]” For this researcher, as well as others, the amateur interest in the field was a challenge to the ancient DNA community’s credibility and the boundaries they tried to place around the practice. “So, you get these people who think they can do DNA and they don’t have the right facilities or the right knowledge or the right understanding of ancient DNA” (Interviewee 5).
Concerns for contamination, or a lack thereof, ultimately divided members of the community. Reflecting on the conflict at this time, this researcher described the divide as embodied by “two different types of scientists: the ones who do proper work in laboratories in clean rooms and the other ones who work in forensic labs or even medical labs where there is no proper thinking about controls and contamination.” Their differences in practices resulted in a “division” between what many in the community referred to as “believers” and “non-believers” (Interviewee 5). Specifically, this division centered around debates about contamination and scientific standards for avoiding it.39
While both sides of the schism were aware of contamination, these groups differed in the degree to which they employed certain methods to test for ancient DNA authenticity. Roughly, the non-believers were suspicious, even outright dismissive, of research produced by the believers. These non-believers—which included individuals such as Pääbo and Cooper, as well as their students and closest collaborators—viewed research by the believers as less rigorous and therefore less credible, less believable. Interestingly, these terms—believers and non-believers—were categories that scientists on both sides of the schism used in reference to themselves and others (Interviewees 6, 23, 28, 36). Some also referred to the schism as a difference between the “haves” and “have nots” (Interviewee 11). Although not all interviewees used both or even one set of terms to describe the split, they all recognized the split, though to differing degrees, and its influence on the sociology of their science.40
Most noticeably, this community schism took form by way of separate conferences, collaborations, and places of publication. At the Fifth International Ancient DNA Conference, the tension was tangible. One epidemiologist and self-subscribed believer recalled the event: “I went to this awful conference . . . and none of us were invited to talk, so we all had to have posters and they ignored the posters.” As far as this interviewee was concerned, the overall conference “looked like a closed shop.” Indeed, this scientist “came away with a very strong message—‘Don’t bother coming back!’ ” (Interviewee 23). This skepticism was more than obvious, to the point where some felt more than unwelcome. In response to this and other issues, believers and non-believers alike went their separate ways.
As a consequence of differences, the ancient DNA community schism grew into two different conferences: the International Conference on Ancient DNA and Associated Biomolecules (an extension of the original conference, primarily attended by the believers) and the International Symposium for Biomolecular Archaeology (a new and distinct event for the non-believers). This split was first and most apparent in 2002, when the Sixth International Conference on Ancient DNA and Associated Biomolecules, a continuation of the early meetings, was hosted at the Hebrew University of Jerusalem in Israel.41 According to a scientist and self-described non-believer, “There was a divide—there was a split—because you had the next ancient DNA conference going to Israel with people who published some very poor work on paleodisease DNA and so, you know, [my colleague] and I said, ‘Well, we’re not going to that one’ ” (Interviewee 5). Indeed, various researchers in epidemiology were interested in using genetic techniques to study the evolution of disease throughout history. Helen Donoghue and Mark Spigelman in the United Kingdom, as well as Susanne Hummel and Bernd Herrmann in Germany, for example, had been trying to extract evidence of ancient pathogens, such as tuberculosis and leprosy, from human skeletons and other remains.42 Their work seemed to suggest the success of the ancient DNA techniques as applied to anthropological and epidemiological questions, but contamination, of course, was a concern. According to Cooper and colleagues, this body of research hinted at the “potential field of genetic paleopathology,” but for them, this sort of work came with real reservations: “Unfortunately, some pathogens are common in the extant human population (e.g. M[ycobacterium] tuberculosis) or have congeneric relatives common in soil or other animal hosts (e.g. Mycobacterium bovae), raising the possibility of contamination through handling, burial, or the use of animal products.”43 In other words, there was more than one reason to be suspect of this type of work unless practitioners could demonstrate otherwise.
According to interviewees, those who identified as non-believers formed a different conference that they thought would better represent their desired epistemic standards for the practice of ancient DNA research. In 2004, this separate conference—the First International Symposium on Biomolecular Archaeology (ISBA)—was hosted at the University of Amsterdam as an alternative avenue for the non-believers who doubted the authenticity of work by the believers.44 “The ISBA only started off because of the ancient DNA meetings” and “the split in the community,” recalled one researcher and non-believer. According to this practitioner, the split came down to differences in perceptions of what really qualified as credible research: “Apparently, it’s [the ancient DNA meetings] still going. And apparently, people are still publishing stuff about insane stuff which is completely wrong!” (Interviewee 22). Another scientist on the side of the believers also reflected on this schism. For this interviewee, the search for DNA from fossils was about the battle for and burden of proof. The 1990s was a “period of confirmation,” and to a certain extent the believers feel their work is still being challenged today. “The bastards out there,” laughed this scientist, “who say, ‘We don’t really believe’ ” (Interviewee 28). This schism was certainly acknowledged at the time but also expanded on and reinforced by interviewees’ memories and retelling of it.
Although conferences were loci of community conflict, contamination concerns further divided the discipline into different places of publication. Another non-believer offered a similar story about how this all played out professionally. “There are two major divisions,” explained this scientist. “You can see where they publish. The people on the more critical side [non-believers] tend to publish in higher-impact journals. The people who are less critical [believers] tend to publish in journals no one has ever heard of” (Interviewee 6). In particular, the believers claimed it was hard to publish through the more well-known outlets such as Nature and Science. Some said it was rumored that reviewers would reject or negate their findings when their research went under review. One scientist on the side of the believers said, “They [non-believers] threw the baby out with the bath water and they just disregarded any work that didn’t have dedicated air-conditioned facilities for the sole use of ancient DNA work. They just negated anything that people like me found.” This same scientist explained, “They would say, ‘Well, of course you can’t believe that because they don’t do this and they don’t do that.’ It got very annoying.” Given this perceived rejection or negation, the believers turned to alternative avenues for publication and recognition: “We just ignored them and published in medical microbiology journals or multidisciplinary journals” (Interviewee 23). The split, based on different groups of scientists from differing scientific traditions and of differing epistemic standards, ultimately impacted the community culture, from conferences and collaborations to the publication process.
For the most part, the community divide came down to whether one decided to adopt and adhere to the “criteria of authenticity” as outlined in Cooper and Poinar’s article. A younger researcher recalled this particular phase of this discipline’s development: “ ‘[Ancient] DNA: Do It Right or Not at All’ is like the nucleus of one era of total proprietary: ‘Ancient DNA belongs only in Ancient DNA Labs. If you don’t have this—if you don’t do it exactly as we say—you’re out. We won’t publish your research’ ” (Interviewee 27). One leading practitioner, for example, compared the divide to a “religious schism” where people “stopped talking to each other” and “dissed each other” and “sabotaged each other.” This resulted in “different conferences” with “different prophets” (Interviewee 6).
In their attempt to control contamination in light of celebrity concerns, certain scientists were also attempting to control community competition by making it more difficult for some to participate in the practice. According to a molecular evolutionary biologist in the field, for example, “criteria of authenticity” seemed to be, at least to a certain degree, “a means to control or limit access” to search for DNA from fossils (Interviewee 2). Another early researcher in the 1990s explained it this way: “Ancient DNA has really been run by . . . Svante [Pääbo] and [Alan] Cooper. Cooper’s role in steering things or pushing things in certain ways, criteria of authenticity, or ‘Do It with Me or Not at All School of Ancient DNA’ . . . —I find it very annoying because it’s not a nice field to work in when everybody is saying, ‘You can’t!’ ” For this scientist, this exclusive attitude was a problem, even unscientific: “There is no ‘one way’ because science doesn’t go the way ‘one person’ says it” (Interviewee 11). As one practitioner observed, “For some time many people thought—and a few people inside the field tried to make people think—that ancient DNA was kind of something magic, and that only two or three labs in the world can do it” (Interviewee 15). A leading geneticist confirmed just as much: “A lot of people know Svante Pääbo and two or three other people and they completely ignore the other ones” (Interviewee 48). For these interviewees, criteria functioned to control success in the field.
Overall, boundary-work was most evident by way of the division between believers and non-believers—a split that manifested itself via the formation of different associations, conferences, and publication strategies. An unpublished paper, initially intended as a chapter of an unpublished book on ancient DNA research, offers an especially illustrative example of the presence and consequence of boundary-work. According to the chapter’s authors, Bernd Herrmann at Georg August Universität Göttingen in Germany and Charles Greenblatt of the Hebrew University of Jerusalem, “The scientific community has not acted optimally in establishing a supporti[ve] and cooperative system, but has pretty early started in splitting up in schools of the ‘haves’ and the ‘have-nots’ instead.” For Herrmann and Greenblatt, both of whom found themselves on the side of the believers (or have-nots), the non-believers “partially defined themselves more in terms of expert knowledge by self allocation of scientific standards.” Specifically, they argued that in the field’s contest for credibility, the believers turned “basic epistemological standards of experimental design and falsification” into a “battlefield.”45 In an interview, another practitioner offered a similar sentiment, humorously describing the field as a “feudal system with lords battling each other,” “trying to gain control,” and “setting forth on horses to destroy each other’s kingdoms” (Interviewee 25). Indeed, boundaries, intended for disciplining the discipline, were more than a means to address concerns about contamination and celebrity.
For practitioners, boundaries were also a means of controlling competition, thus shaping ancient DNA’s disciplinary development, community culture, and even how scientists approached the writing of its history. In certain cases, practitioners constructed their own history by dismissing other research they disagreed with but that was nonetheless a part of the field’s past. Herrmann and Greenblatt, for example, argued that “different positions were not discussed in terms of scientific standards but were ignored rather by strategic behavior” like “citation cartels” and “self referential structures.”46 Indeed, the first textbooks in the field, such as one by Herrmann and Susanne Hummel, cite several different studies as compared to research literature reviews written by Pääbo, Cooper, and students trained in their tradition.47 Some non-believers—like Pääbo, Cooper, and others—disregarded research by the believers, who included scientists like Herrmann and Hummel. As one senior practitioner explained, “I think we would certainly have a feeling that there is a kind of body of work that we simply don’t believe, in the past, and that we don’t cite rather than spending a lot of time saying we don’t believe it” (Interviewee 36). In an article, Eske Willerslev, a student of Alan Cooper, and Cooper himself also noted the tendency to exclude certain studies, for a number of reasons, from the literature: “Perhaps unsurprisingly, many of the most extravagant a[ncient] DNA reports have since been either disproved or effectively disregarded. . . . Many other claims remain in limbo, where a lack of appropriate methods or replication renders them effectively meaningless.”48 The writing in, or writing out, of certain studies and their authors from the history of the discipline was a further form of boundary-work that some scientists sought in an effort to establish their preferred version of the field as well as their own places within it.
In the wake of contamination problems at the turn of century, researchers felt their credibility was compromised. For some scientists, such as Cooper and Poinar, it was more than the credibility of one or two or even a handful of studies at stake. Rather, they believed the credibility of the discipline as a whole was in jeopardy. The one way to fix this, as far as they were concerned, was for fellow colleagues in the field to strictly adhere to the criteria of authenticity. Here, ancient DNA researchers engaged in boundary-work through the publication of criteria of authenticity and a mandate that fellow colleagues, editors, and reviewers alike adhere to these standards. In some ways, a handful of practitioners advocated for technical boundaries around the practice through the implementation of criteria via the use of certain technologies and techniques. In other ways, this boundary-work was quite literal as the presence or absence of an “Ancient DNA Lab” was a physical boundary used by some scientists to help demarcate credible from less credible work. The criteria of authenticity, and the call to reproduce results, became a hallmark of experimental expertise by which ancient DNA research was judged.
By 2005, however, researchers were realizing that the criteria for ancient DNA authenticity were not infallible. Practitioners, for example, were finding that DNA degradation patterns and processes were not well understood despite technological and conceptual advances. In response to this, Thomas Gilbert and Michael Hofreiter, former students of Cooper and Pääbo, respectively, along with Hans-Jürgen Bandelt and Ian Barnes, challenged the use of criteria that had been introduced in Cooper and Poinar’s landmark paper. In this new article, the authors noted that Cooper and Poinar had initially intended the criteria as a guide for ancient DNA authenticity. In practice, its use had turned into a checklist that some thought actually guaranteed authenticity of research results. According to Gilbert and colleagues, what began as a guide became a “religious doctrine” that some “blindly followed.” This was particularly a problem because researchers were beginning to realize that these parameters did not always ensure authenticity. In fact, they could, in certain cases, produce false results. Although the criteria were useful, these authors argued that treating criteria as a checklist had become an inappropriate substitute for critical thinking and scientific reasoning: “Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies.”49
Such dogmatic adherence to the checklist criteria had produced two problems. In an interview, one scientist explained the issue, saying that in many cases, papers had been published by scientists who had fulfilled all the criteria but despite this, they were still “publishing bad results.” At the same time, papers were not being published because scientists had not fulfilled all the criteria, and in some of these instances they were actually “failing to publish good results” (Interviewee 6). This concern was mirrored in Gilbert and co-authors’ argument that completion of criteria should not, and in fact could not, serve as the be-all and end-all of ancient DNA research. According to the authors, the “authenticity and reliability of ancient DNA data arise from a complex interplay of several poorly understood areas of knowledge,” and “no clear-cut answer exists as to what makes a study reliable.”50 Even after years of debate and disciplinary development, there seemed to be no definite community agreement on what really makes a “good” or “bad” ancient DNA study.
This counterclaim was not necessarily a rejection of criteria for ancient DNA authenticity. Rather, these researchers were bringing attention to the fact that the criteria were imperfect and that rigid dedication to them was problematic. Gilbert and co-authors suggested a solution: “It is our opinion that ancient DNA researchers should take a more cognitive approach with regards to assessing the reliability and conclusions of their data. Suggested criteria remain important, and should not be lightly discarded, but we advocate that, in place of planning or assessing studies by using criteria as check-lists, consideration should be given on a case-by-case basis as to whether the evidence presented is strong enough to satisfy authenticity given the problems.”51 The authors argued that scientists should assess their projects by asking questions about feasibility. For example, does the age and environment of the sample suggest DNA preservation? Or is there information about the handling history of the sample that might suggest prior contamination which might be difficult to detect and therefore jeopardize ancient DNA authenticity?
Interestingly, Pääbo and Hendrik Poinar, as well as Cooper and Willerslev, had made similar suggestions in the years following the publication of “Ancient DNA: Do It Right or Not at All” as they too began to realize the inherent issues with their criteria.52 Reflecting on the article’s publication, an influential scientist in the field said, “And the big mistake . . . with that paper—huge mistake . . . with that paper—was not putting at the end of that list: ‘If the result passes the criteria, it’s probably still wrong. It’s just that you failed to disprove it’ ” (Interviewee 32). Nonetheless, these criteria and the severity with which they had been enforced continued to provoke further debate in the community.
Although controversy over what counts as a thorough experiment is common across the sciences, this is a particular problem for new fields of science or in areas of controversial science. “The problem with experiments,” Harry Collins and Trevor Pinch write, “is that they tell you nothing unless they are competently done, but in controversial science no-one can agree on a criterion of competence. . . . Thus, in controversies, it is invariability the case that scientists disagree not only about results, but about the quality of each other’s work. This is what stops experiments being decisive and gives rise to the regress.”53 Ideally, “reproducibility” should serve as evidence for the “universality” of science: “Anybody, irrespective of who or what they are, in principle ought to be able to check for themselves through their own experiments that a scientific claim is valid.”54 However, in the case of an emerging science or an area of controversy within a science, the “who” and “what” and “how” of an experiment become subjects of debate. The intensity of this debate around contamination was compounded by the celebrity that surrounded the science.
As researchers engaged in boundary-work, they did so on two fronts and in response to two separate but intertwined issues impacting their legitimacy with the broader public and their authority in the scientific community.55 While they were concerned about contamination in the literal and technical understanding of the term, they were also concerned about the influence of celebrity. On one hand, some researchers working both in and outside of the discipline viewed the ever present media attention around the search for DNA from fossils as a further and more figurative source of contamination but one that was no less real. They felt that disproportionate and undeserved media interest or influence had the adverse effect of contaminating their credibility, thus their scientific authority. On the other hand, media attention had been a crucial component of the field’s growth in terms of its initial formation and overall identity. Over the years, the press consistently publicized the nascent science. Meanwhile, scientists also fashioned their own opportunities for exposure. This intentional exchange between scientists and the media—specifically around the idea of discovering DNA from some of the world’s most ancient and charismatic creatures, such as dinosaurs or mammoths—influenced scientific practices from research agendas and student recruitment to publications and further funding. In fact, the public’s interest in the search for DNA from fossils and the attention the media gave to it were instrumental in its birth and growth into a scientific discipline.
Consequently, researchers were torn between their need to appeal to the press and public for support while simultaneously distancing themselves from the hype that had come to characterize the field. In speaking of science in general, cultural studies scholar Peter Broks summarizes the dilemma: “To maintain its authority it needs to be set apart from the general public, but to maintain its legitimacy it needs to appeal to the general public.” However, in practice, this presents an unavoidable tension: “Being set apart increases its alienation; making it more ‘popular’ undermines its authority.”56 Indeed, ancient DNA researchers found themselves walking a fine line. It was difficult for researchers to balance legitimacy and authority, especially in light of increasingly apparent technological limitations and contamination issues. At the turn of the twenty-first century, members of the ancient DNA community found themselves facing a paradoxical situation as the celebrity of the science simultaneously empowered and undermined it.