Imposing Limits
THE PCR POLICE
By the mid- to late 1990s, a number of extraordinary publications on the recovery of ancient DNA had attracted widespread suspicion from researchers within and even outside of the ancient DNA community. As the discipline developed, practitioners began to respond to the hype that had been building up around it. This took form as an enthusiasm and confidence in the ability of scientists, with the aid of PCR, to consistently and reliably sequence DNA from a range of fossils, then to use that genetic information to learn about species origins, evolution, and migrations across time and space. Hype also manifested as speculation concerning scientists’ potential to one day use DNA to resurrect extinct creatures, including dinosaurs. In responding to hype in both its forms, researchers felt the need to address the field’s technological challenges and status as a public-facing practice. In fact, several researchers took it on themselves to address the discipline’s ever present contamination concerns. They also sought to push back against what they viewed as disproportionate or undeserved publicity. As they saw it, too much media coverage, especially directed at studies making exceptional but questionable claims, was a second source of contamination that could challenge the legitimacy of the science.
In 1993, Tomas Lindahl, a well-known expert in DNA decay and repair at the Imperial Cancer Research Fund in the United Kingdom, spoke out publicly on these contamination concerns. As a specialist in the molecular behavior of DNA, Lindahl was highly suspicious of recent evidence that seemed to suggest the extremely long-term preservation of DNA. Such findings defied all past and current research on the principles of DNA degradation. It seemed to defy the chemical composition of DNA itself. In two separate articles, both published in Nature, Lindahl made these points and more, highlighting that processes such as hydrolysis, a chemical reaction that occurs to break down the compounds of a substance when exposed to water, posed serious problems for the preservation of DNA in fossil material.1 He argued that DNA’s biochemistry could not support such longevity, and in the event that it could, he was deeply worried about contamination. To control for contamination, he suggested using negative controls, conducting appropriate chemical analyses, and reproducing the results. This last recommendation was especially important but difficult to achieve because it required conducting the experiment again, using the same sample or a separate one, and obtaining the exact same results.
For these reasons, Lindahl found the work on multimillion-year-old DNA—or “antediluvian DNA” as he called it—to be particularly problematic.2 As far as he was concerned, the credibility of such studies depended on proof of the authenticity of the DNA itself and the reproducibility of results. He cited two studies that claimed to have recovered multimillion-year-old DNA from amber insects—one by David Grimaldi and colleagues in New York and the other by Raúl Cano, George Poinar, and Hendrik Poinar in California—which he felt did not have adequate evidence to support their bold claims. In one of his papers published in Nature, Lindahl directly insinuated that the rather outstanding results these scientists had obtained were very likely the product of contamination. “It is hardly surprising,” noted Lindahl, “that insect-like DNA can be detected by PCR in experiments carried out in a department of entomology.”3 In a clearly open attack on both of these recent amber studies, George Poinar set out to defend his team’s work. In a reply to Lindahl, also published in Nature, Poinar argued that this “ ‘off the cuff’ ” comment about contamination was not only uninformed but misplaced. “In our experiments,” he explained, “none of the extraction, amplification or sequencing was conducted in a department of entomology, or of botany for that matter.”4 Poinar stood by the authenticity of their findings, but regardless of his defense, the question of contamination was out in the open.
Not only did Lindahl think that such studies were problematic but he also believed they distracted attention from other research: “Recent claims of recovery of 100-million-year-old DNA have overshadowed the valuable and important studies on moderately ancient DNA.” For Lindahl, the next step in this field must be a conservative one: “Rather than proceed spectacularly further and further back in time with anecdotal reports on single samples, using the notoriously contamination-sensitive PCR, I suggest that the next goal be a convincing report on the amplification of small DNA fragments, say, 100,000 years old.”5 From his view, it was a matter of establishing DNA authenticity through the defining of criteria and a matter of redirecting research toward more promising avenues of study, even if that meant redirecting research away from the media spotlight.
In fact, there were several practitioners who welcomed Lindahl’s criticism concerning ancient DNA authenticity. According to his memoir, Svante Pääbo especially applauded Lindahl’s use of the term “antediluvian DNA”—initially used as a pejorative form of ridicule of studies reporting the recovery of very ancient, prehistoric DNA. Pääbo later recalled that he and his own lab at the time at the University of Munich in Germany loved it and used it because they felt it accurately characterized a growing body of unreliable research in the discipline.6 From their perspective, this rhetoric was one way to separate their own work from what they viewed as more sensational and less credible research.
Pääbo welcomed Lindahl to the conversation about contamination because he felt that many in the developing discipline of ancient DNA research were not paying close enough attention to it. As early as 1989, Pääbo, along with Russell Higuchi and Allan Wilson, suggested a short list of criteria, from control extracts and independent extracts to phylogenetic comparison, to be implemented in laboratories in order to circumvent contamination.7 However, Pääbo and others were increasingly frustrated with some studies that did not take these criteria as seriously as they suggested. Over the previous five or so years, the search for DNA from ancient and extinct organisms had brought together scientists from disparate disciplines. Those interested in the new field brought different scientific and epistemic cultures with them. At the intersection of these diverse backgrounds, researchers were faced with the need to merge various disciplinary values in order to reliably recover DNA from fossils and apply the results to a range of biological or historical questions. For several researchers, including Pääbo, it was crucial to standardize the practice, and this, as he emphasized, required specialized knowledge and solid training in molecular biology. “It was a great help to have a respected scientist from outside the field point this out,” Pääbo wrote in his memoir, “especially given my concern that the ancient DNA field tends to attract people without a firm background in molecular biology or biochemistry who, lured by the media attention that accompanies many ancient DNA results, simply apply the PCR to whatever old specimen they happen to be interested in.” This, as far as Pääbo was concerned, was “ ‘molecular biology without a license.’ ”8 According to both Lindahl and Pääbo, experts in molecular biology themselves, ancient DNA authenticity was a prerequisite for credibility on which both the success of the field and the reputation of the practitioners promoting it depended.
As excited scientists joined the hunt for ancient DNA, Pääbo became just as much a regulator of the new field as he was a researcher in it. According to a former doctoral student in his lab, Pääbo and the researchers and students working with him took on the role of “the PCR police” (Interviewee 12). They embraced a much more critical and conservative attitude, particularly regarding the work of their peers. They did so through advocating for criteria and openly demonstrating evidence that others’ results were the product of contamination.
DEBUNKING DINOSAUR DNA
While Lindahl, Pääbo, and some other scientists found the results of these amber studies problematic, their distrust of multimillion-year-old DNA hit new heights when Scott R. Woodward, a microbiologist at Brigham Young University in Utah, and colleagues announced the recovery of 80-million-year-old DNA from bone.9 In a paper published in Science in 1994, Woodward and colleagues were careful not to claim that the bone or the DNA from it were dinosaurian in origin, but they did suggest it, and the media reinforced the idea with newspaper headlines reading “Bone Yields Dinosaur DNA, Scientists Believe,” and “Scientist Says He Has Isolated Dinosaur DNA.”10
The sensationalism quickly turned to skepticism as several independent studies called into question the authenticity of these results.11 Science, the same journal that first published Woodward’s study, published a report by science writer Ann Gibbons titled “Possible Dino DNA Find Is Greeted with Skepticism,” which covered several researchers’ initial concerns and their evidence.12 For example, S. Blair Hedges, a biologist at Pennsylvania State University, and Mary Schweitzer, the paleontologist at Montana State University, critiqued the study on the grounds that it lacked appropriate phylogenetic analyses and additional attempts to replicate results prior to publication. According to Woodward’s team, they had recovered evidence of several mitochondrial DNA sequences and determined them to be just as distantly related to birds and reptiles as to mammals. However, when Hedges and Schweitzer conducted an independent investigation, their phylogenetic analyses suggested that the DNA sequences were not dinosaurian but mammalian in origin, thus likely the product of contamination, specifically human contamination.13 Other studies suggested this conclusion too.14
Like Hedges and Schweitzer, Pääbo’s new lab at the University of Munich, where he had been recently appointed professor, strongly suspected that the DNA recovered by Woodward’s team was actually a contaminate. In fact, it was his lab that provided clear evidence for it.15 Hans Zischler, a postdoctoral researcher at the time, took the lead on this case. After conducting phylogenetic analyses, he too found that the supposed dinosaur sequences were more closely related to mammals than to reptiles or birds, but it was still not clear exactly to whom or what the sequences belonged. They appeared to be mammalian, perhaps human, but it remained to be definitively demonstrated. Pääbo and his lab thought on this, particularly on the nature of mitochondrial DNA. They knew that sometimes segments of the mitochondria can be transferred for various reasons from the mitochondrion to the nucleus of a cell, resulting in a special sequence referred to as a nuclear mitochondrial DNA segment. Pääbo’s lab hypothesized that Woodward’s lab had extracted a nuclear version of mitochondrial DNA with an unusual mutation, thus explaining the unidentifiable sequence (the supposed dinosaur sequence). To test this, Pääbo’s lab devised a clever, and rather bizarre, experiment. Human DNA contains a mix of mitochondrial DNA and nuclear DNA sequences, the former inherited from the mother and the latter from the father. What they needed, explained Pääbo in his own record of events, was nuclear DNA, and nuclear DNA alone. The one way to get it would be from male sperm. As Pääbo recalled in his memoir, he asked his male graduate students to contribute to the cause by donating their own sperm from which Zischler would then isolate the head from tail to extract the nuclear DNA. He would sequence it for comparison with the suspected dinosaur sequence. In the end, they obtained a number of nuclear mitochondrial DNA sequences from the sperm samples, two of which they found to be nearly the same as the suspected dinosaur sequence.16
They wrote up their findings and conclusions for publication in Science and, in a rather sarcastic fashion, tried to rationalize the striking similarity between their results and the supposed dinosaur sequences. First, they proposed that if Woodward’s dinosaur DNA was in fact dinosaur DNA, then it must mean their sequences were similar because their own lab in Munich was actually contaminated with dinosaur DNA. They found this scenario highly unlikely. Second, they hypothesized that dinosaurs and mammals might have hybridized at some point before their extinction, therefore exchanging their DNA, thus explaining why the supposed dinosaur sequence looked more mammalian than dinosaurian. This too they found highly unlikely. Finally, they suggested that the extracts or equipment used in Woodward’s lab were not clean but contaminated by human DNA. Quite obviously, Pääbo’s lab found this conjecture most convincing: “In conclusion, these results strongly suggest that Woodward et al. accidentally amplified nuclear copies of human mitochondrial DNA.”17
Dinosaur DNA, in this case, was debunked. And the news of it, of course, played out publicly. A Science News headline read, “Dinosaur DNA Claim Dismissed as a Mistake.”18 A reporter for New Scientist wrote, “ ‘Jurassic DNA’ Looks Distinctly Human.”19 In an article for the New York Times, “Critics See Humbler Origin of ‘Dinosaur’ DNA,” Malcolm Browne covered the story in detail. He discussed the issues of authenticity and reproducibility, as well as the caution that some scientists thought ought to be exhibited before making such big claims about truly ancient DNA. On this point, Browne quoted Hedges, who spoke to the caution he displayed in one of his own early experiments regarding the preservation and extraction of dinosaur DNA: “ ‘We were working on an astonishingly well preserved fossil of a Tyrannosaurus rex, in which the bones themselves have survived without becoming mineralized into stone,’ Dr. Hedges said. ‘We found DNA sequences in the dinosaur bone that were in the right places and really looked like what we expected dinosaur DNA to be.” According to Hedges, they submitted their results for publication in Nature, but when they found they could not replicate the results, they pulled the paper from publication. “Replication,” as Hedges put it, “is one of the key essentials of scientific method.”20 Indeed, some scientists—especially those who played a role in demonstrating that the presumed dinosaur sequences were actually a case of contamination—believed that extraordinary claims should be accompanied by extraordinary evidence in order to prevent erroneous, and what many viewed as publicly embarrassing, results.
Clearly, the early studies on long-term preservation of DNA from amber insects fell into this category of extraordinary claims. And Pääbo’s lab, not surprisingly, was one that questioned these studies and set out to test their validity. In 1994, Hendrik Poinar moved to Munich to join Pääbo’s lab for his doctoral degree. While there, Poinar carried out research to try to understand the biochemical behavior of DNA and the particular environments in which it was more likely to preserve. Specifically, the goal was to create an independent experiment that could be used to confirm ancient DNA authenticity. In the lab, Poinar, Pääbo, and colleagues worked on a method called amino acid racemization, a test that used amino acids as biomarkers to determine DNA decay and its potential preservation in fossils. In an article entitled “Just How Old Is That DNA, Anyway?” science writer Robert F. Service explained the experiment: “An international team of researchers reports that a chemical change that converts amino acids in proteins from one mirror-image form to another—a process known as racemization—takes place at virtually the same rate as the degradation of DNA.” Therefore, “if the amino acids show this conversion to even a modest degree, then the original DNA in the sample is likely long gone, suggesting that any remaining genetic material is a contaminant.”21 In other words, these scientists suggested that if the amino acids had been altered or could not be detected, then it could be safe to say that any accompanying DNA would also be altered or even nonexistent. Undamaged DNA would be a sign of recent DNA and therefore an indication of contamination.
In this specific study, the team tested the racemization of amino acids against the degradation of DNA using twenty-six different specimens ranging from several thousands to several millions of years old. Specimens included a mammoth as well as humans remains, dinosaur bones, and amber insects. For the most part, they found that multimillion-year-old specimens like dinosaur fossils showed extensive racemization. They even tested the fossil from Utah from which Woodward and his team claimed to have recovered DNA. This sample showed extensive racemization too. Indeed, other million-year-old organisms revealed similar results. They tested both fossil leaf remains and sediments from the Clarkia deposit in northern Idaho, the same place from where Edward Golenberg and his team claimed to have recovered the first evidence of multimillion-year-old DNA. Like the dinosaur fossils, these fossil leaf remains showed extensive racemization and therefore extensive DNA degradation. The results in the end suggested that retrieving DNA sequences from extremely ancient material was highly unlikely.22
However, there seemed to be an exception to the rule. In this same study, practitioners found that amber samples exhibited a lower level of racemization. Indeed, they detected amino acids that seemed to be endogenous to the organism. Although they did not also detect any DNA, they hypothesized that amber resin, due to low water content, could provide conducive conditions for molecular preservation. Even Pääbo reasoned that the retention of amino acids, and perhaps nucleic acids, could be attributed to the preservative properties of the resin itself.23 Dinosaur DNA was out of the question, but based on these research results, the preservation of DNA from amber insects was open to debate.
In the wake of Jurassic Park, the United Kingdom’s Natural Environment Research Council (NERC) funded the Ancient Biomolecules Initiative (ABI).24 This initiative represented NERC’s second funding strategy to expand on research that started with the Biomolecular Palaeontology Special Topic from 1988 to 1993. The ABI—chaired by chemist Geoffrey Eglinton at the University of Bristol and archeologist Martin Jones at Cambridge University—would fund three rounds of research projects to investigate the preservation and evolution of biomolecules across time from DNA to proteins, lipids, and carbohydrates.25 According to several interviewees, the initiative was rumored to have been granted at that time in part because of Jurassic Park (Interviewees 9, 25, 46). One media article suggested as much: “The world-wide success of the film Jurassic Park has highlighted the need for projects funded by the Ancient Biomolecules Initiative.” The piece continued, “Partly in response to the high profile that the film brought, the Natural Environment Research Council is providing the Ancient Biomolecules Initiative with about £2m for this area of research over a period of around five years.”26 Out of the three application rounds, the ABI granted money to twenty-one research projects, fifteen of which focused on ancient DNA from plant, animal, and human remains.27 It also included funds to test the Jurassic Park hypothesis.28
The group that set out to test the Jurassic Park hypothesis—the reality of the long-term preservation and extraction of multimillion-year-old DNA from amber insects—was from the Natural History Museum (NHM) in London. In their application to the ABI, researchers outlined their objective to test the validity of such claims published in high-profile scientific journals against the hype. “Our work to date has shown that ancient DNA from four fossil insects, if it is present at all, is in exceedingly low copy number and/or highly degraded,” they explained in their application. “We now wish to carry out the necessary detailed laboratory investigation to show, beyond reasonable doubt, whether any ancient DNA fragments exist whatsoever within amber-entombed fossils.”29 According to one researcher who worked on the project, there was a direct connection between this project and the film hype. “My job that I got at the Natural History Museum was all down to Jurassic Park,” they explained. “The museum probably would never have got the funding to try and do this DNA from amber if it hadn’t been for Jurassic Park in the first place. Part of my kind of entry into the ancient DNA world was all due to a movie; a fanciful fictional movie.” Their objective, however, was not to recover dinosaur DNA and bring them back to life. “We weren’t trying to get dinosaur DNA,” clarified this interviewee. “We were trying to get insect DNA out of insects in amber” (Interviewee 25). Their project—“Ancient DNA and Amber-Entombed Insects: A Definitive Search”—was determined to produce a closed case either for or against the preservation and extraction of DNA from amber-preserved fossils.30
At the NHM, researchers including Richard Thomas, Andrew Smith, Richard Fortey, Andrew Ross, and Jeremy Austin undertook a comprehensive experiment to recover DNA from fifteen samples of amber insects, each from different resin types and time periods.31 George and Hendrik Poinar supplied some of the samples, including the bee specimen that provided the initial evidence for the preservation and extraction of DNA from ancient amber.32 After performing DNA extractions and PCR amplifications on the fifteen amber insects, the research group carried out negative controls and conducted phylogenetic analyses to check for ancient DNA authenticity. In reminiscing on the study, one researcher recalled how they “did all the protocols” and “jumped through all kinds of hoops” to ensure they had “believable results” (Interviewee 24). Despite such extensive experiments, however, they were unsuccessful in identifying any evidence of DNA from these multimillion-year-old insects in ancient amber.
In 1997, they published their findings in the Proceedings of the Royal Society, announcing that they had “singularly failed to recover authentic ancient DNA from amber fossils.”33 They explained that their results, coupled with previous research by two additional teams, provided convincing evidence that amber-preserved insects were not a consistent and reliable source of molecular preservation.34 Their findings concluded, “The incompatibility between these and our negative results and previous reports of ancient DNA from amber-preserved insects is difficult to reconcile without suggesting some form of cryptic contamination in the latter.” As far as these researchers were concerned, the existence of DNA from amber fossils was not much more than a “biological curiosity.”35
Following years of speculation and even scientific evidence in support of it, the Jurassic Park hypothesis appeared debunked at last. “ ‘No Go’ for Jurassic Park–Style Dinos,” reported Science.36 “Lights Turning Red on Amber,” stated Nature.37 Although the scientists searching for multimillion-year-old DNA were only a small subset of the overall community, the whole of the field was affected by the high-profile nature of their claims and the equally high-profile responses to their refutation. This led to a dramatic drop in public and professional confidence in the field’s credibility related to ancient DNA authenticity and the reproducibility of results.
The problem of contamination had come to the forefront just a few years earlier in 1995 at the Third International Ancient DNA Conference at Oxford University in England.38 Together, Tomas Lindahl and Svante Pääbo tried to enforce professional and philosophical values of protocols and precision. According to one of the early leaders in the discipline, “Lindahl gave his talk about it being impossible for DNA to survive for too long, and Svante made a really eloquent talk about the need for rules and rigor within the field.” Consequently, “everybody went away really impressed with the fact that we had to sort of self-regulate ourselves.” As far as Lindhal and Pääbo were concerned, there was a lot at stake if scientists in this new field did anything otherwise. “And I think the message that Svante was trying to get across was that if we don’t self-regulate ourselves then we will lose credibility and the field will completely die” (Interviewee 4). However, the need to self-regulate was not just a private plea to the community. It was a public one too. A Science report read, “But the hype—and the embarrassment when some claims did not hold up—is causing ancient DNA researchers to fear that their field won’t be taken seriously.”39
As early as 1992, the community of ancient DNA researchers was conscious of their tendency to search for DNA from specific specimens that would be sure to appeal to the public, as well as popular but prestigious research journals. Robert Wayne, then at the Zoological Society of London, and Alan Cooper, a doctoral student at Victoria University of Wellington in New Zealand, were the initial editors of the Ancient DNA Newsletter, and in one of the first issues they highlighted this phenomenon. Over the previous few years alone, more than 35 percent of ancient DNA papers had been published in high-profile and high-impact research journals such as Nature, Science, and Proceedings of the National Academy of Sciences. “However, before we bask in self-congratulatory splendor,” Wayne and Cooper wrote, “we should realize many of the papers concern just a few samples of disco species.” The disco species, according to their view, were the flashy and iconic multimillion-year-old specimens often featured in studies as being the first or the oldest DNA. “The novelty of ancient DNA will soon disappear, requiring that we address more fundamental evolutionary questions.”40 Even at the height of hype, researchers recognized that the excitement of the practice and its time as a science in the spotlight might dissipate sooner rather than later.
Amid reports for the first and the oldest DNA came a more conservative movement as researchers were encouraged to set their sights on less geologically ancient specimens. Lindahl was one of the earliest proponents for this move. In fact, he—along with Pääbo—had argued since the early 1990s for the defining of criteria and a refocusing on younger samples. As he saw it, the flashy, headline-grabbing studies on multimillion-year-old DNA ultimately detracted attention from other more relevant and valuable work in the field, often work conducted on less ancient but more scientifically interesting specimens. Here, Lindahl argued that instead of focusing efforts on reaching further back in time, practitioners should attempt to generate convincing evidence for authentic DNA 100,000 years old or younger.41 In such specimens, DNA was both more likely to be preserved and scientists would be more likely to be able to extract enough of it for meaningful analysis. From his view, it was more important, if not arguably necessary, to establish reliable evidence for ancient DNA authenticity.
Although not all scientists heeded Lindahl’s advice, there were a few that did. In 1994, two back-to-back publications in Nature reported the recovery of DNA from the extinct woolly mammoth. This is certainly a “disco species” of its own, and both studies drew on Lindahl’s suggested criteria in hopes of demonstrating the authenticity of their results and, by extension, the broader possibility of reliably recovering DNA from specimens that were tens of thousands of years old. One study—by Pääbo and Matthias Höss at the University of Munich and in collaboration with Nikolai Vereshchagin at the Institute of Zoology in Saint Petersburg, Russia—claimed to have sequenced DNA from five mammoths ranging from 9,700–50,000 years of age.42 The other study—led by Erika Hagelberg, Mark Thomas, and Charles Cook Jr. of the University of Cambridge, in collaboration with colleagues Andrel Sher, Gennady Baryshnikov, and Adrian Lister—recovered DNA from two mammoths, one of which was at least 47,000 years old and presumed to be the oldest DNA from a vertebrate to date.43 Interestingly, these achievements came nearly two decades after Allan Wilson at Berkeley, arguably one of the founders of ancient DNA research as a field, had attempted to identify genetic information from a frozen baby mammoth carcass found in Russia. Although Wilson and his lab extracted evidence of ancient proteins, they were not successful in extracting and identifying DNA. Consequently, these two studies provided the first evidence for this type of preservation. Together, they suggested the reliable recovery of DNA from organisms that has been dead for thousands of years without the contamination concerns that plagued those studies claiming to have discovered multimillion-year-old DNA.
As researchers turned their sights to less geologically ancient specimens, the specimens they studied were not necessarily less newsworthy from either a public or professional perspective. Indeed, there were other studies that enjoyed a good deal of media exposure and that simultaneously validated the potential of obtaining and using ancient DNA data to answer some of evolutionary biology’s most complex questions.44 One of the best-known studies of this decade was none other than the recovery of DNA from our ancient and extinct cousin, the Neanderthal.45
Over a century ago, in the mid-1800s, the first Neanderthal specimen was found in a cave in the Neander Valley, Germany.46 At the time, no one knew this would become one of the first and most famous Neanderthal specimens in the history of paleoanthropology, and it was not until ten years after its discovery that researchers formally recognized the skeleton as such and declared it a separate species. This discovery, among others throughout the nineteenth and twentieth centuries, garnered extensive scientific and public interest around the study of human origins.47 Since then, the Neanderthal’s place in human history—and its extinction nearly forty thousand years ago—has provoked heated debates among scientists and the public alike. Up until the late twentieth century, however, the Neanderthal’s relationship to modern humans remained unresolved.48 Now, a century or so after the original Neanderthal specimen was found, Ralf Schmitz—curator at the Rheinisches Landesmuseum in Bonn, Germany, where the remains were housed—sought to change that. He knew there was work going on in the field of ancient DNA research that could potentially shed light on the Neanderthal’s origins and evolution, and he thought that Pääbo, one of the leaders of the new field, might be up for the challenge.
After enlisting Pääbo’s assistance, Schmitz provided a small sample of bone, which Matthias Krings, a graduate student conducting the study, then ground into a fine powder to extract DNA from it. Following a successful DNA extraction and PCR amplification, they were able to obtain 379 nucleotide base pairs of mitochondrial DNA, which they then compared to more than 2,000 mitochondrial DNA sequences from modern humans to determine its authenticity. What they found was good news. The Neanderthal DNA sequence varied from the modern human DNA sequences at an average of 27 positions. By comparison, modern humans differed by an average of just 7 positions. This meant that the Neanderthal DNA sequence was four times as different from the modern human DNA sequences and unique to the Neanderthal itself. The result was extraordinary, and they knew they needed further evidence in support of it. They needed to reproduce these results, preferably in a different lab independent of their own.
For the job of reproducing the results, they turned to Mark Stoneking, a geneticist specializing in human evolutionary history who had studied with Wilson at Berkeley for both his graduate and postdoctoral work in the 1980s. Stoneking, now a professor at Pennsylvania State University, had been involved in a number of landmark studies on the molecular evolution and origins of humans. One such study, led by Rebecca L. Cann and published in Nature in 1987, provided genetic evidence for the “Mitochondrial Eve” and “Out-of-Africa” hypotheses.49 By comparing the mitochondrial DNA sequences of nearly 150 modern humans from across five regions of the world, they were able to determine their relatedness to one another and that they shared a maternal ancestor, popularly referred to as “Mitochondrial Eve.” They also demonstrated that their common origin could be traced back to a single location, Africa. This lent support to the idea that humans first evolved in Africa, then migrated out of Africa to eventually populate the rest of the globe. The prospect of extracting genetic evidence from a Neanderthal, thought to be an extinct and distant cousin to living humans, was naturally exciting to Stoneking. In fact, it had been something of a dream for Wilson and his lab to use DNA to understand the relationship between modern humans and other early and extinct hominids such as Neanderthals.50
Stoneking agreed to attempt to replicate the results; a doctoral student, Anne Stone, who had spent a year in Pääbo’s lab and was familiar with their protocols, took on the task. Here, Stone’s goal was to extract, amplify, and sequence Neanderthal mitochondrial DNA that would be identical to select regions of the mitochondrial DNA sequences recovered by Pääbo’s lab. She would attempt to achieve this by doing so in a different lab and by using a different piece of bone from the same Neanderthal specimen. The success of all this, of course, depended on precautions to minimize or avoid contamination. Unfortunately for these researchers, the first round of results was disappointing. Stone extracted and sequenced DNA, but it looked distinctly human, which obviously suggested that the equipment, reagents, or sample had been contaminated at some point in the process. If Neanderthal DNA were present, even in the smallest amounts, the PCR technique would have likely detected and amplified the contaminating DNA instead. According to Pääbo’s memoir, he hoped this was the case and that there was still a chance to recover Neanderthal DNA. To test this, the lab came up with a new plan. Stone would use a different primer—a short, single-stranded DNA sequence used in the PCR technique to begin DNA synthesis—which would likely pair with the Neanderthal DNA, if it was indeed present, and not the modern DNA. Stone performed the study again, and this time the second round of results proved more promising.51
However, Stone was still not sure if the sequence from her lab matched the sequence from the Munich lab. The two teams would have to compare them to confirm their authenticity. Over an anxious phone call, they compared the differences in sequences one by one. “I called and read off the differences to [my colleague] on the phone,” recollected one of the scientists involved. “I would say one and [my colleague] would say, ‘Yay!’ ” (Interviewee 30). The reading of the sequence, as well as the celebratory responses to it, went on, one by one. With match after match, they concluded that both labs, independently of each other, had recovered authentic Neanderthal DNA.
In 1997, Krings and his colleagues from the Pääbo lab published their paper in Cell on the first evidence of Neanderthal DNA.52 The publication was important for a number of reasons. Most obviously, the research shed light on the evolutionary relationship between humans and their Neanderthal ancestors. The researchers explained how they sequenced DNA, which they then compared with that of modern humans. Through such comparisons, they were looking for evidence of genetic similarity between the two, but based on the sequence data and subsequent analysis they found no evidence of genetic contribution. Specifically, they argued that Neanderthal mitochondrial DNA, when compared with mitochondrial DNA of primates and modern humans from Africa, Europe, Asia, and across the world, demonstrated significant differences, and they interpreted this as evidence that Neanderthals had lived, then died, without contributing any of their DNA to modern humans. In other words, they found no evidence that Neanderthals and our ancient human ancestors had interbred thousands of years ago. However, they also noted that this conclusion could not be definitively determined by mitochondrial DNA alone. These results also suggested that modern humans had their origins in Africa, not Europe. At the same time, the researchers reasoned that these findings did not completely rule out the possibility of a genetic contribution from extinct Neanderthals to extant humans; further data would be necessary to fully resolve this question. Nonetheless, this study and its attempt to use molecular data to inform a history that had traditionally relied exclusively on morphology added heat to an already virulent debate in evolutionary anthropology about our own origins and evolution over time.53
Further, this paper was noteworthy for where they chose to publish it. In his memoir, Pääbo recalled the reason for submitting this paper to Cell instead of to Nature or Science, as had been the tradition in the field of ancient DNA research: “Publication there would send a signal to the community that the sequencing of ancient DNA was solid molecular biology and not just about the productions of sexy but questionable results.”54 As far as Pääbo was concerned, a paper on ancient DNA research, published in a highly respected journal like Cell, but one that was in his view less about the headlines and more about the rigor, would work wonders for the field, especially at a time when its integrity was so openly contested. Pääbo wanted to show that their work was rigorous and relevant to evolutionary biology. Sure enough, this paper was intensely technical and methodological. Pääbo hoped to demonstrate that ancient DNA research was a serious business.
Despite Pääbo’s decision to publish in Cell, the study did not escape press and public attention. Indeed, the celebrity that accompanied the science, the fossil itself, as well as the study’s conclusions and implications for human evolutionary history were all reasons to expect an onslaught of media coverage. Science, for example, called it “a technical tour de force.”55 A report in Nature declared, “Given the quality of the new molecular findings, the study of ancient human DNA can, at long last, be said to be on a secure footing.”56 The Guardian of London spotlighted the research conclusions with the following headline: “We’re African, No Bones About It.”57 Roger Lewin also published a piece in New Scientist—“Back from the Dead”—where he explored the research implications. Lewin quoted Tomas Lindahl, a notorious critic of ancient DNA activity, who said the study was a “landmark discovery” and “the greatest achievement so far in the field of ancient DNA research.”58 Ancient DNA always ran the risk of contamination, but for Lindahl this paper was “compelling and convincing” in its validity.59 In light of these new results and the newfound confidence that scientists seemed to throw behind the science of ancient DNA research, Lewin brought back the idea of resurrection, saying, “We’ll never resurrect dinosaurs but what about Neanderthals?”60
The recovery of Neanderthal DNA was a highlight of the decade, but it was also just one of many studies that addressed major questions in human evolutionary history, especially regarding the migration and admixture of past populations. Hagelberg, for example, had provided some of the earliest evidence for the fact that DNA could be preserved in and extracted from human bone.61 Later, she and colleagues demonstrated the ability to amplify DNA from ancient human remains of Polynesia and then used this DNA to inform hypotheses about the migration and occupation of past peoples on these and other islands.62 In the United Kingdom, Terence Brown and Keri Brown at the University of Manchester were instrumental in furthering the exploration of ancient DNA methods as applied to archeological specimens.63 From this nexus, ancient DNA activity flourished as practitioners tried to learn more about human evolution, populations, migrations, diet, and disease as well as to determine the sex, ages, and kinships of past people. For example, researchers across the United Kingdom, France, Germany, Israel, and the United States began to investigate the preservation and extraction of DNA in ancient humans in terms of its application to questions in human evolutionary history.64 Practitioners also published on evidence of leprosy and tuberculosis in ancient humans.65 Together, these works seemed to suggest the utility of ancient DNA research as applied to archeological, anthropological, and epidemiological specimens, but contamination again was a worry.66
These concerns over contamination as it related to the study of ancient humans played out publicly. Here, the issue was not necessarily about whether DNA could last for several thousand years but whether the DNA that was preserved and extracted could be demonstrated to be authentic human DNA and not a contaminate. In this context, with humans working on ancient human remains, it was especially difficult to determine whether modern DNA could be contaminating whatever ancient DNA might be left in these samples.
In 1995, just a few years before the Neanderthal DNA discovery, Stoneking wrote an article for the American Journal of Human Genetics, “Ancient DNA: How Do You Know When You Have It and What Can You Do with It?” He wrote the article in response to both the professional development and popular attention that the field had achieved. As Stoneking noted, there were numerous articles on the topic, research funding opportunities, international conferences, newsletters, textbooks, and even rumors of a journal. In addition to all of this, there was “public notoriety,” much of which centered around the book and movie Jurassic Park. Indeed, taken together, it seemed the search for DNA from fossils had, as Stoneking claimed, “ ‘arrived’ as a legitimate field of inquiry.”67 At the same time, however, he conceded there were more than just a few kinks to be worked out first. Sure enough, the field faced two troubling issues, namely the question of ancient DNA authenticity and the perceived value of ancient DNA data to broader research in evolutionary biology.
To address these issues, Stoneking considered a case by Elaine Béraud-Colomb of the Institute of Developmental Biology in Marseille, France, and colleagues who reportedly recovered DNA from several human specimens up to twelve thousand years of age.68 He commended the “exhaustive procedures” the team took in order to control contamination, noting that the study seemed to meet the “informal guidelines” suggested by researchers like Pääbo. According to Stoneking, “This may seem like over kill to the uninitiated, but the ancient DNA community tends to be a rather suspicious lot and likes to see some evidence that people are paying attention to the concerns that have been raised about avoiding contamination and authenticating results.” Although Stoneking agreed that independent replication in a separate lab was definitely preferable, he believed it was unrealistic. Here, he argued that it would be far from practical to make this kind of replication a requirement for every study produced by every lab. In practice, it would “cause more problems than it would solve” because independent replication on this scale would be expensive, destructive, and ultimately restrictive. He instead explained that “precautions” as well as “multiple independent extractions from each sample” would “suffice.”69
In addition to issues of authenticity, Stoneking spoke to the utility of ancient DNA data and particularly the novelty and celebrity of the field: “After all, isn’t it a neat enough trick to show that DNA can indeed be obtained from ancient specimens?” In answering his own question, Stoneking wrote, “Alas, if ancient DNA is to become a legitimate field of scientific inquiry, then the answer must be no.” He pointed out that recent research in the field, including Béraud-Colomb and colleagues’ work, simply showcased the anomaly of ancient DNA from one or several samples with little insight or impact into the larger looming questions in evolutionary biology. Stoneking insisted that the authenticity and utility of ancient DNA research must extend beyond its novelty: “If ancient DNA is to be more than a technological curiosity, then we don’t need any more such papers.”70 With increasing interest in ancient human DNA came increasing issues regarding authenticity as well as utility. As an alternative to one-off extractions from supposed “disco species,” he recommended producing more sequences from many samples to tackle anthropological questions on a population rather than individual level.
During this decade, researchers were responding to credibility concerns, induced by both contamination and celebrity, by constructing criteria that would help to transform the hunt for DNA from fossils from an emergent into an established practice. Alan Cooper, now a postdoctoral researcher in the Department of Biological Anthropology at Oxford University, was becoming a dominant researcher in the field and a major critic of other colleagues’ studies. In 1997, he replied to Stoneking in the American Journal of Human Genetics, reinforcing independent replication in light of ancient DNA’s short but sensational history: “Several ancient DNA ‘triumphs’ . . . that have turned out to be embarrassingly unrepeatable, or contaminated, might have been prevented if independent verification had been sought prior to publication.” Cooper argued that adherence to hard-and-fast criteria ensured credibility: “In summary, there are currently several methods available to test the authenticity of ancient human DNA sequences. I suggest it is the responsibility of the ancient-DNA community, and archaeologists working with them, to insist that they are fully utilized. Failure to do so threatens the credibility of ancient-DNA research.”71 Ancient DNA’s credibility was at stake, no doubt. As far as he was concerned, all studies must perform all tests and checks in order to demonstrate their reliability. Although Cooper and Stoneking agreed contamination was a problem, they differed in the extent to which criteria should be required.
After nearly a decade of headline-grabbing and contentious publications, the problem of contamination, one exacerbated by the celebrity that surrounded the science of ancient DNA research, began to divide the community. The field had made great strides, but its technical difficulties were more than apparent. Indeed, the community’s credibility was on the line and some took the task of self-regulation into their own hands. This became more obvious at some of the later ancient DNA conferences toward the end of the decade. A biomolecular archeologist and early researcher in the field, for example, recalled these tensions: “I remember there was a conference where Alan [Cooper] was fourth or fifth speaker in a session and he was going to present some of his work. And he changed his talk. I saw him redoing his slides just before his talk. And he stood up and instead of talking about the work he was doing, he talked about how rubbish the field was and how human ancient DNA was becoming completely discredited.” According to this interviewee, “Everybody hated him for it because he was just so rude. But it needed to be done. We’d just listened to four talks by people who . . . said, ‘We’ve done this’ and ‘We’ve done that.’ Is it actually genuinely true?” (Interviewee 4).
In addition to addressing the community at this conference, Cooper, along with Robert Wayne and Jennifer Leonard at the University of California, Berkeley, published publicly on the discipline’s increasing professional and popular appeal: “From the beginning, ancient DNA research was a populist science. Reports of DNA from ancient remains led to wild speculation in the press and film that life could be restored to ancient creatures. Each new discovery served to reconfirm the public impression that scientists were moving quickly toward this goal. New reports of ancient DNA, although often of limited evolutionary significance, were published in the most prestigious journals.” These researchers, among others, clearly realized that popular enthusiasm had been a major player in their early history. At the same time, they also believed that this interest alone was not enough: “The honeymoon period has passed for ancient DNA research, and the difficulties associated with a maturing field need confronting.”72 By the end of the decade, it was more than obvious that contamination was one of those difficulties. It was a call that the novelty of the practice must give way to its eventual maturity.
THE ROLE OF HYPE
Throughout the 1990s, a handful of practitioners had tested the limits of DNA preservation in what became a decade-long debate. This debate was initiated, and also very much kept alive, by a number of practitioners who sought to reach further back in time to the days of the dinosaurs in attempts to extract DNA from various specimens. This race for the oldest DNA, and in some cases dinosaur DNA, was influenced by the hype around Michael Crichton’s book and Steven Spielberg’s movie Jurassic Park, both released early in the decade. In light of this interplay between science and the media, interviewees characterized this decade and the search for DNA from fossils as the “Wild West” and even “the Jurassic Park phase” (Interviewees 10, 4).
By the end of the 1990s, however, contamination concerns as they related to ancient DNA authenticity placed the practice’s credibility on the line. Here, the issue of contamination was illustrated most clearly, and most publicly, through those same research papers claiming to have extracted and sequenced multimillion-year-old DNA. Not long after these papers were published, other practitioners challenged the authenticity of their findings. In fact, some practitioners demonstrated that such bold claims were either irreproducible or the outright product of contamination. The overturning of these research results had devastating consequences for the community’s reputation, so much that researchers had to work to establish their legitimacy in light of failed expectations. Crucially, the ancient DNA community was responding not just to these failures, but to the very public nature of those expectations. This was because the very studies that were demonstrated to either be irreproducible or the product of contamination had been published in high-impact journals such as Nature and Science and broadcast across mass media.73
Researchers felt a need to respond, to defend their credibility. In response to this, some scientists sought to impose limits by defining criteria to minimize contamination in the lab and by redirecting research toward more promising avenues of study on less geologically ancient specimens that would be more likely to preserve DNA and have preserved enough of it to be used for meaningful analyses. Lindahl, Pääbo, and to a certain extent Cooper and Stoneking were chief proponents of this conservative movement from the onset.
After nearly two decades of research into the long-term preservation of DNA from ancient remains, it was clear that the field faced severe technological limitations, resulting in community division and widespread skepticism in its potential to deliver on initial promises. Indeed, ancient DNA’s disciplinary development had followed a similar trajectory to that of other scientific ideas and technological innovations. This trajectory—“the hype cycle”—characterizes the lifespan of an idea or innovation as a series of highs and lows in correspondence to the successful or unsuccessful attainment of expectations.74 More specifically, the hype cycle is often described as moving from an initial trigger and peak of expectations followed by a trough of disillusionment, and at last a slope of enlightenment and a plateau of productivity. As science historian Elsbeth Bösl explicitly argues, the search for DNA from fossils followed this pattern of development.75 In fact, a biomolecular archeologist who joined the search for ancient DNA early in the discipline’s formation offered this observation too: “I’d say this research discipline has developed the way that all science—new scientific disciplines—develop in that you have an initial wonderful discovery, you have lots of hype and high expectations, and then you come down to it with a bump, and then you do the hard work of working out what it all means and what you can really do: what is realistic and what isn’t” (Interviewee 5). According to this scientist, hype had become a driving feature in the search for DNA from fossils. Crucially, however, researchers were responding to more than just failed expectations as they related to limitations of the PCR technique and the longevity of DNA preservation.
As the new field neared the turn of the century, its practitioners found they had to work around and against two different but not unrelated problems affecting the credibility of the search for DNA from fossils: the problem of contamination and the problem of what they viewed to be too much undeserved or disproportionate publicity. In the first instance, hype took form as a confidence and enthusiasm, on behalf of both scientists and media reporters, in the ability to consistently and reliably sequence DNA from a range of fossils, then to use that genetic information to learn about species origins, evolution, and migrations across time and space. In the second instance, hype was projected as speculation concerning scientists’ potential to one day use DNA to resurrect extinct creatures, including dinosaurs.
Hype, in both forms, was instrumental in the ancient DNA’s disciplinary development.76 In the early years, hype was performative in that it generated interest and guided activity that led scientists to experiment with novel ideas in order to establish evidence for their feasibility.77 In the early stage of any innovation, the utility and reliability of the new technology or technique is not a given but must be demonstrated. “Hype corresponds to a particular phase in the career of innovations,” explains sociologist of science Nik Brown. “The whole language of novelty, newness and revolutionary potential is actually part and parcel of the hyperbolic discourse surrounding the early or opening moments of resource and agenda building.”78 Indeed, it is often pragmatic, even necessary, to engage in hype to attract further attention from professional and public audiences alike in order to marshal interest and resources. In the case of the emergence of ancient DNA research, the press created opportunities for publicity but scientists also fashioned their own opportunities for attention. The interchange between scientists and the media, specifically around the idea of discovering dinosaur DNA, influenced publication timing, grant funding, research agendas, and professional recruitment. During this decade, some scientists were savvy in capitalizing on the celebrity of their fast-growing field in order to secure their success.
At the same time, hype—or too much of it, or not the right kind of it—posed a problem to the field’s growth and acceptance as a credible and legitimate approach to studying evolutionary history. Brown captures this tension between hope and hype, explaining that while hype plays a role in generating activity and sustaining interest in new technologies and their applications, hype can lead to overshoot, which can result in damaged reputations. It is more than scientists’ reputations at stake but the reputation of an entire research practice that can suffer from failed expectations: “In so many cases, the present fails to measure up to the expectations once held of it. This can have disastrous consequences for the reputation not only of individuals but entire innovation fields.”79 Sure enough, ancient DNA researchers felt that celebrity was a further form of contamination which could reduce the legitimacy of the new field.
The failed expectations of PCR technology as applied to very ancient fossil material were compounded by the intense public interest in the search for ancient DNA. In responding to hype, researchers felt the need to address the field’s technological challenges and status as a public-facing practice. Specifically, a handful of researchers took it on themselves to address these ever present contamination worries. They also pushed back against what they viewed as disproportionate or undeserved publicity. The skepticism surrounding the ability to recover DNA from ancient human remains exacerbated these issues. As the discipline developed, contamination concerns challenged the authenticity of results. More broadly, these concerns deeply challenged the credibility of the practice. Given the discipline’s short but sensational history, it seemed difficult, if not impossible, for scientists to move toward community consensus regarding ancient DNA authenticity. From enthusiasm to cynicism, ancient DNA research had emerged, evolved, and now struggled to become an established practice within evolutionary biology. The field’s credibility was on the line, and according to scientists, contamination and celebrity were to blame. As a consequence, there was mounting distrust and discord among ancient DNA researchers. After two decades, three newsletters, and four conferences, the ancient DNA community was growing but clearly growing in different directions.