Ideas to Experiments
DISCOVERING ANCIENT DNA
Ideas about the theoretical preservation and potential extraction of DNA from fossils originally arose outside the traditional laboratory research setting, but it was at the University of California, Berkeley, that ancient DNA research became a localized, specialized, and more widely recognized activity. Allan C. Wilson, a professor of biochemistry at Berkeley, was primarily responsible for transforming the idea of recovering DNA from fossils into experiments with evidence for the long-term preservation of molecules. Born in New Zealand in 1934, Wilson moved to the United States for his graduate studies, ultimately completing his Ph.D. at Berkeley in 1961, where he would spend the rest of his career. Over the years, Wilson earned a reputation as a pioneering scientist in evolutionary biology for his use of molecular data to reconstruct patterns and processes in evolutionary history.1
Specifically, Wilson was interested in using molecular biological techniques to study human evolution. One of his most well-known studies, published by Science in 1967, forced the scientific community to reconsider the way human evolutionary history was understood.2 This article, co-authored with his graduate student Vincent M. Sarich, was considered a landmark paper in the field for its use of molecular evidence from humans and apes to suggest a much more recent common ancestry than previously thought based on paleontologists’ estimates using fossil evidence. In this paper, Wilson and Sarich relied on a comparison of protein sequences to determine that humans and primates split from one another approximately 4–5 million years ago.
While Wilson and Sarich’s conclusion was groundbreaking, so was their methodology. At the time, their study lent support to a new and highly controversial hypothesis—the molecular clock hypothesis. This concept—introduced by Linus Pauling, a physical chemist at the California Institute of Technology, and his postdoctoral student Émile Zuckerkandl—suggested that molecules evolve over time at a steady rate, and because of that, they proposed using molecular data and their mutation rates to date divergences of one species from another in their evolutionary history.3 As historians of science Marianne Sommer and Elsbeth Bösl both note, the molecular clock hypothesis essentially argues that history, specifically evolutionary history, is recorded in molecules, written in our DNA.4 Zuckerkandl and Pauling suggested this concept in general, but it was Wilson and Sarich who demonstrated evidence of it as applied to the evolutionary history of primates and humans.
Wilson had long sought to apply molecular biological techniques and data to study evolutionary history, and he soon thought to extend this research to ancient organisms too. In fact, doing so appeared a natural extension of his expertise and visionary tendency. Poinar and Hess’s publication in Science in 1982 on the exceptional cellular preservation of a 40-million-year-old insect in amber garnered widespread attention from many, including Wilson. Whether Wilson contacted Poinar, or whether Poinar contacted Wilson, is not entirely clear.5 What is clear, however, is that Wilson’s lab and Poinar’s lab—both at Berkeley at the time—eventually established a collaboration.6
In 1983, Poinar and Hess, together with Russell Higuchi—a molecular biologist and postdoctoral researcher working with Wilson—set out on the first experiment to actually test ideas about the preservation and extraction of DNA from insects in amber. The challenge was clear, as preparation alone was a tedious task. First, Poinar began by selecting amber specimens that would potentially offer optimal preservation of DNA. Next, the three sterilized all the lab equipment in order to avoid contamination. Even as early as the 1980s, they all realized the risk of contaminating their results with their own DNA merely through handling the specimen during preparation and extraction. Therefore, they took precautions to minimize contamination, thus maximizing the chances of recovering DNA from the organism itself. Meanwhile, Hess began to section and take samples of the specimens by cutting into their amber capsules, then carefully removing the insects’ tiny tissues.7
After specimen preparation was completed, they performed a template assay test on the tissues, an experiment that made a radioactive copy and gave a radioactive signal in the presence of even the most miniscule amounts of DNA. If DNA were present, it would be copied and a signal would be emitted. In the end, they found evidence of DNA in two of the seven specimens sampled—a moth and a fly. They appeared to overcome the biggest challenge, how to get DNA from multimillion-year-old amber insects, but another issue soon emerged, namely how to determine to whom or what the DNA belonged. Was the DNA from the insect itself or was it a contaminant from the environment? At the time, no other experiments were done to determine the authenticity of the DNA, and the results were never published.8
Following this initial experiment to recover DNA from amber insects, Higuchi and Wilson shifted their efforts to a much younger specimen, the extinct quagga that once roamed the plains of South Africa over a hundred years ago. Equus quagga was an enigmatic species primarily because of its unusual appearance: its backside and hind limbs were solid brown, resembling a horse, while its neck and face were covered by brown and white stripes, resembling a zebra. By the late 1800s, however, the entire species had become extinct. In fact, humans had hunted the quagga to extinction, leaving behind the skeletons and skins of only twenty specimens, now stored in museums across the world.
There were a number of reasons behind Higuchi and Wilson’s decision to study the quagga. The first was born out of a sentimental motivation. Reinhold Rau, a taxidermist and conservationist at the South African Museum in Cape Town, near where quagga once lived a hundred years ago, felt a sense of guilt about the role humans played in the species’ demise. Indeed, Rau was interested in bringing the quagga back to life in order to rectify its extinction. His plan was to use selective breeding processes with living zebras to recreate the quagga’s unique striping pattern. Although Rau did not plan to use DNA to try to clone the quagga, he did need its DNA to determine its phylogenetic relatedness to extant horses and zebras so his breeding program could be successful.9 During his career, Rau visited several museums looking for suitable samples for DNA analysis. He ultimately took a soft tissue sample from a 140-year-old quagga specimen on display at the Natural History Museum in Mainz, Germany. Rau sent the sample to Oliver Ryder at the San Diego Zoo, an expert in molecular evolution and conservation. It was Ryder who offered the sample to Wilson and Higuchi at Berkeley for DNA analysis.10
Equus quagga. This mare lived at the London Zoo from 1851 to 1872. (Reprinted by permission from Springer Nature: Nature’s News and Views, “Raising the Dead and Buried” by Alec Jeffreys, copyright 1984)
While there were sentimental motivations for studying the quagga, there was also a scientific interest in its evolutionary history. At the time, paleontologists who used morphological data, such as fossil data, disagreed over the quagga’s relatedness to living horses and zebras. Some argued it was more closely related to horses than zebras. Meanwhile, others argued it was more closely related to zebras but constituted a separate species. Some disagreed with both interpretations, proposing that the quagga was not a separate species of zebra but a subspecies of the Plains zebra.11
Finally, there were practical reasons for studying the quagga. Sure enough, Higuchi and Wilson thought it would be much more likely to recover DNA from material a few hundred years old than trying to gather DNA from material millions of years old. And if they were successful in doing so, they could much more easily verify the authenticity of the extinct quagga’s DNA, as well as determine its evolutionary history, by comparing it to DNA sequences of extant horses and zebras of today.
In the spring of 1984, Higuchi, Wilson, and their team of researchers successfully extracted DNA from the 140-year-old remains of a quagga. In taking a sample from a small piece of dried muscle, Higuchi and colleagues were able to recover sequences of mitochondrial DNA, a type of DNA inherited on the maternal line and found in abundance in plant and animal cells. To do so, they used standard methods of DNA extraction, but the process was complicated by the fact that the quagga DNA was old, degraded, and fragmented. In fact, they were only able to recover approximately 1 percent of that expected from fresh muscle. In order to better study these DNA fragments, Higuchi and colleagues cloned and amplified single fragments of the DNA using a phage vector—a type of DNA molecule that naturally replicates itself in bacteria. Just as clones of a single human, if they existed, would share the same DNA sequence, clones of a single fragment of quagga DNA would also have identical DNA. Of all the clones made—nearly 25,000 total—just two could be demonstrated to be mitochondrial in origin and were subsequently sequenced. The two clones together included 229 nucleotide base pairs of quagga DNA. Although short strands, the DNA sequences were similar enough and yet different enough from zebra, horse, cow, and human mitochondrial DNA sequences to show that they had successfully obtained, for the first time, ancient DNA from an extinct creature.12 At the same time, the sequences were most similar to the plains zebra of all the zebras tested, and least similar to the horse of all the equine species tested. This was evidence for including the quagga as a subspecies of the plains zebra. With this molecular data, they were also able to determine that the quagga had diverged from the zebra approximately 3–4 million years ago.
Higuchi and colleagues took a number of steps to announce their discovery. First, they wrote up their research results and submitted an article for publication in Nature, a renowned British journal and century-old competitor with the American journal Science. While they waited for their paper to be reviewed, Higuchi and colleagues worked quickly to write and submit a grant proposal to the National Science Foundation (NSF), one of the largest federal government agencies responsible for funding scientific research across the United States. The application they submitted—“Molecular Paleontology: Search for Fossil DNA”—requested $330,000 to be distributed over three years and represented the first official research proposal of its kind. Wilson and Higuchi would head the research with Poinar, Hess, Alice Taylor (an electron microscopist), and Barbara Bowman (a graduate student who worked on the quagga study). Their goal was to continue the search for DNA from the quagga and other extinct species including bison, mammoths, and moas—an extinct and flightless bird of New Zealand. They even proposed to continue searching for multimillion-year-old DNA from amber insects.
In their application, Wilson and colleagues stated that this research, if funded, could mark the start of a new way to study evolutionary history and give rise to a new field of scientific inquiry, molecular paleontology. “This is the first proposal to study the possible utility of DNA to paleontology,” they wrote. “If clonable DNA is present in many fossil bones and teeth and in insects included in amber, a new field, molecular paleontology, can arise.” However, the quagga data alone formed both the preliminary and primary evidence on which the proposal stood.13 The application was a bold one, especially given the available evidence on which it rested. Indeed, they conceded in their application the “exotic” and “speculative” nature of their project, but they remained optimistic that their work could be a revolutionary approach to studying ancient and extinct life. They had high hopes for this new venture, but their proposal was in the hands of other scientists and a decision panel who would either accept or reject it.
NSF reviewers were intrigued by the prospect of searching for DNA from fossil material, but caution colored their feedback. One reviewer, for example, called the proposal “interesting, significant, even exciting.” Another called it a “pioneering effort” at the interface of “molecular systematics and paleontology.” Meanwhile, another reviewer was not as optimistic: “Discovering and extracting DNA from fossil species is a very interesting and technically difficult biochemical feat, but it is certainly not clear to me how this approach will broaden our perspective on any major evolutionary problems.” Other referees recognized the difficulty of the task Wilson and colleagues proposed but were not as quick to give up on it. Sure enough, they felt the challenge was worth the effort. “I refuse to gaze into a crystal-ball and reject the possibility a priori,” wrote a reviewer. “It is clear that looking for fossil DNA is worth the trials and tribulations, particularly if so distinguished [a] researcher as Wilson wishes to undergo the trauma.” A different reviewer made a similar comment: “I am not convinced that selection of these organisms will demonstrate the universal applicability of recombinant DNA technology to systematic evolutionary studies. . . . However, at one time it was common knowledge that the earth was flat and the moon was made of green cheese.” Despite all the technical obstacles, a handful of reviewers seemed confident that Wilson and colleagues would overcome them. “If it is possible to do,” wrote one last reviewer, “they can do it.”14
Despite the mostly positive reviews, the decision panel unanimously rejected the proposal for funding. Their first reason for rejecting it came down to a matter of tangible research outputs: “The proposal is not designed to develop a new technology which when developed would be broadly applicable to a wide range of specimens.” The second reason came down to the practicality of the research itself. “At most the project will provide that some fossil remains contain clonable DNA,” explained panel members. “If clonable DNA is obtained, its usefulness for phylogenetic studies remains to be shown, given the likelihood of the occurrence of unquantifiable diagenetic change and the presence of contaminating DNA.” Overall, the panel was far from convinced that the search for DNA from fossils would prove a worthwhile endeavor: “The Panel does not consider that obtaining clonable DNA from a 140-year-old museum specimen, however interesting, provides sufficient preliminary evidence that DNA from 10,000 or 26-million-year-old specimens is likely to yield valuable information.”15 With that, the search for DNA from fossils seemed at a standstill.
MUMMY DNA
While Wilson and Higuchi were experimenting with amber fossils and quagga remains, similar studies regarding the long-term preservation of molecules were being pursued elsewhere. Svante Pääbo, a doctoral student at the University of Uppsala in Sweden, had recently begun exploring the idea of recovering DNA from ancient Egyptian mummies. Although a student of molecular biology, Pääbo had always been interested in Egyptology. Indeed, ancient Egyptian mummies and culture had fascinated archeologists, anthropologists, and linguists, as well as scientists and the broader public, for centuries.16 Pääbo was determined to somehow couple his passion for ancient Egyptian culture with his studies in molecular biology, and his knowledge of current research from prominent scientists in the field inspired him to do just that. Pääbo was well aware of Wilson’s work on molecular evolution, and like Wilson, he was attracted to applications of molecular biological techniques to study evolutionary history, especially human evolutionary history.17 Pääbo also knew of another researcher, Alec J. Jeffreys, a prominent molecular biologist at the University of Leicester in England studying the genetic evolution of humans and apes.18 According to Pääbo, both Wilson’s and Jeffrey’s respective works prompted him to speculate on how molecular biological techniques could be used to study ancient life, and in this case to study life in ancient Egypt.19
In the summer of 1981, Pääbo went to the store to buy a piece of liver. He was interested in the theoretical preservation of DNA in ancient Egyptian mummies, and he knew that mummification involved dehydration, which would likely prevent DNA degradation. Thus, mummification could prove an ideal process for long-term DNA preservation. Given this reasoning, Pääbo decided to replicate the procedure, to some extent, by cooking the liver in an oven. Pääbo wanted to conduct this work in the lab, but he made sure to keep it secret for fear of being reprimanded by his supervisor or humiliated in front of his colleagues should the experiment turn out to be a total failure. According to Pääbo’s memoir, he went to the lab and began baking the liver in an oven, heating it up and drying it out over the course of a few days. By the second day, the smell was so strong and repulsive that he became worried his colleagues, or even worse his supervisor, would investigate and discover the source. Fortunately for Pääbo, as he recalled in his memoir, the smell subsided after another day or two, with no questions asked. In the clear, Pääbo assessed the liver—now a hard, dry, shriveled substance—and attempted to recover DNA from it. According to Pääbo, he was instantly successful. The DNA was certainly fragmented, including just a few hundred nucleotide pairs, much less than the thousands of nucleotide pairs to be expected from fresh tissue. Still, in theory, the study was successful. Pääbo felt “vindicated.”20
Although this experiment was successful, the preservation and extraction of DNA hundreds to thousands of years old remained to be tested. To satisfy his curiosity, Pääbo asked a curator of a small local museum who also happened to be a close friend if he could take samples from several mummy specimens to try to discover DNA. Although Pääbo was not allowed to take direct samples from some of the most prized and well-preserved mummies, the curator did allow him to sample previously detached or already damaged skin and muscle tissue from three mummies in the collection. Pääbo was appreciative of the opportunity, and back in the lab he applied standard DNA extraction techniques to each of the three samples. To his disappointment, he was unsuccessful in recovering any DNA samples.21
Despite this setback, Pääbo was determined not to give up. With help from his museum curator friend, Pääbo approached the Berlin State Museums asking for more and better samples of mummy material. The curators were agreeable, and after a two-week trip to Berlin, he returned to Sweden with more than thirty samples. He continued to work nights and weekends in the lab to keep his study a secret, but this time he decided to investigate each sample for cellular preservation before trying to extract DNA. If there was evidence of cellular preservation, then there might be evidence of DNA preservation. Using a standard technique in microscopy, Pääbo prepared and placed the mummy samples on small glass slides, then stained the samples with a dye. Looking at the slides under a microscope, the dye would emit a color and enhance the visualization of cells or cell parts if any were preserved in the samples. Out of all thirty samples, Pääbo found only three showing even the slightest evidence of cellular preservation. He hoped that at least one of these samples would show signs of DNA preservation too.22
Under the microscope, Pääbo further assessed a sample of skin taken from the left leg of a mummified child that had showed very clear evidence for the preservation of cell nuclei. The cell nucleus was particularly interesting because of its role as the command center for cell growth and as a storage unit for the majority of its genetic material, including its DNA. Pääbo applied a second stain to the sample, this time in search of evidence of DNA. According to him, the test was positive, emitting color and therefore evidence that at least some DNA remained intact. Pääbo was elated. As far as he was concerned, this was a sure sign of ancient and authentic DNA. “Since this DNA was in the cell nuclei, where the cellular DNA is stored,” he explained in his memoir, “it could not possibly be from bacteria or fungi because such DNA would appear at random in the tissue where the bacteria or fungi were growing.” As far as he was concerned, this was “unambiguous evidence” that the DNA observed was that from the mummy child itself and not a contaminant from the environment.23 Pääbo then attempted to extract the DNA. To his surprise, he was successful.
Pääbo quickly began writing up his research methods and findings for publication. To acknowledge the East German curators who allowed him to sample the specimens, he chose to publish the first recovery of DNA from two-thousand-year-old mummies in an East German journal called Das Altertum. His paper was published in 1984, but its reception was anticlimactic. According to Pääbo, this research, which he considered groundbreaking, received no attention at all. The first formal report on the preservation and extraction of DNA from ancient Egyptian mummies received no response—no letter, no question, not even a reprint request. Pääbo, disappointed and discouraged, reasoned the lack of attention was due to publication in a lesser-known journal. “I was excited,” he recalled, “but no one else seemed to be.”24
In an attempt to reach a wider audience and attract greater attention, he sent a second manuscript for review to the Journal of Archaeological Science. The journal received the manuscript in October 1984, and although the article was accepted, the review process was slow and the paper was not published until later the following year. Between low readership in the first case and slow publication in the second, Pääbo questioned if anyone cared at all about the prospect of procuring DNA from ancient or extinct material and the implications for paleontology, archeology, and evolutionary biology more broadly.25
PUBLISHING ANCIENT DNA
In 1984, the same year Pääbo sent his work out for publication, Nature published Higuchi, Wilson, and colleagues’ article on the recovery of DNA from the extinct quagga. This piece stood as the first recorded evidence for the long-term preservation of DNA and its successful extraction from the remains of an ancient and extinct species.26 Their paper and its presentation in an esteemed journal such as Nature was noteworthy for three reasons.
First, the quagga study outlined the theoretical and technical procedures for identifying, extracting, amplifying, and sequencing DNA from ancient and extinct material. This was something that had not been previously demonstrated. Second, the study showcased how ancient DNA sequences could be successfully analyzed and applied to phylogenetic problems. It also lent support to the molecular clock hypothesis, an increasingly popular idea that proposed molecules and the rates at which they mutate over time could be used to date the split of one species from another in their evolutionary histories. Finally, the quagga study was a conceptual contribution to the fields of evolutionary biology and molecular biology. Although some of the questions asked and methods used were not necessarily groundbreaking for the time, the fact that Higuchi and colleagues undertook experiments to test ideas about the theoretical preservation and potential extraction of DNA from ancient and extinct specimens made this work significant and its implications enticing. This publication was essential in bringing this new line of research to the attention of the scientific community. Indeed, ancient DNA research could be a way to travel back in time to study evolution in action.
Pääbo was shocked to learn of a successful study so similar to his own, and surprised at its publication in an esteemed journal such as Nature. At the same time, he appreciated this work because it validated his own. “If Allan Wilson was studying ancient DNA, and if Nature considered an article about 120-year-old DNA interesting enough to publish,” wrote Pääbo in a memoir, “then surely what I was doing was neither crazy nor uninteresting.”27 Wilson, an established experimentalist well-known for his molecular work in evolutionary biology, certainly lent credibility to the speculative idea of recovering DNA from fossils. A researcher like Wilson at an institution like Berkeley possessed the authority, security, and resources to test such abstract ideas, while a renowned journal like Nature carried the prestige to generate attention and influence over other scientists and the public.
To be clear, publication of the quagga study in Nature was effectively an endorsement of its legitimacy. While the evidence in support of the study was important and necessary, it was how the professional scientific community reacted to the evidence—in this case its acceptance and publication—that gave the study the stamp of credibility it needed. This was especially valuable considering the highly speculative nature of the research in the first place. Further, publication in top-tier journals like Nature and Science carried clout with more than just the scientific community. In fact, the high-profile and high-impact nature of the research these journals published appealed to the wider public. Media reporters were apt to cover them. Given this, scientists worldwide started to think twice about the prospect of DNA hidden away in ancient skins and tissues. In other words, place and power of place mattered to the reception and exploration of speculative ideas.28
Inspired, Pääbo wrote a third and final paper on the recovery of DNA from ancient Egyptian mummies, this time submitting it for publication in Nature.29 Lucky for him, it was quickly reviewed and printed in April 1985. In this article, Pääbo argued that DNA could provide genetic answers to historical and archeological questions about Egyptian culture, evolution, population, and disease. However, like Wilson’s 1983 amber study and the 1984 quagga study, in Pääbo’s study DNA was only partially preserved and only in some samples. In this case, only one mummy exhibited evidence of DNA. If paleontological and archeological specimens were to be reliable data resources for molecular evolution studies, then DNA’s survival in specimens would need to be a repeatable, not a rare, occurrence. Ancient DNA would need to be more than an anomaly. Pääbo hoped this publication in Nature would finally attract the attention he originally anticipated and encourage further exploration on a much more significant scale.
As Pääbo recalled in his own later account of events, he was excited to see another scientist, especially a scientist as prominent as Wilson, invested in exploring the long-term preservation of DNA: “I thought about how to approach Allan Wilson—a demigod, in my view—to ask if I might work with him at Berkeley after my PhD defense.” Indeed, Pääbo was unsure how to introduce himself and his work, so he settled on sending Wilson a copy of his Nature paper. Wilson had no knowledge of Pääbo as a researcher, but the manuscript made a considerable impression. Pääbo recalled, “I received a response from Allan Wilson, who addressed me as ‘Professor Pääbo’—this was before both the Internet and Google, so there was no obvious way for him to find out who I was.” “The rest of the letter was even more amazing. . . . He asked if he could spend his upcoming sabbatical year in ‘my’ laboratory!” For Pääbo and his lab mates, it was all a “humorous misunderstanding.” “I joked with my lab mates,” he wrote, “that I would have Allan Wilson, perhaps the most famous molecular evolutionist of the time, wash gel plates for me.”30 Pääbo quickly replied to Wilson to explain that he was not a professor but a student still working on his doctorate. Instead, Pääbo asked if there would be an opportunity after his graduation to join Wilson in Berkeley for his postdoctoral training.
Although ideas regarding the theoretical preservation and potential extraction of DNA from fossils arose outside the traditional laboratory setting, the circulation and reception of those ideas largely depended on evidence produced inside the lab. In other words, the acceptance of these ideas heavily depended on scientists’ ability to turn them into experiments with evidence. This was vital, especially considering the idea of discovering DNA from ancient and extinct species was one that many, including researchers themselves, considered wildly speculative. The lab—specifically Wilson’s lab in Berkeley and, to a certain extent Pääbo’s lab in Uppsala—became the first sites of ancient DNA activity to provide the earliest evidence in support of a new line of research.
In the mid-1980s, the search for DNA from fossils, mainly a private affair, went public. Along with the published quagga article, Nature also issued a “News and Views” commentary to go with it. The review—titled “Raising the Dead and Buried”—was written by Alec Jeffreys, a respected geneticist, and in it he speculated on the significance of this new line of research. “Is the quagga as dead as a dodo? Not entirely, and nor indeed might be the dodo, if the remarkable findings of Russell Higuchi, Allan Wilson and co-workers . . . are anything to go by.” Based on the research findings, the extinct quagga’s DNA had survived intact for more than a hundred years, and there was enough of it for scientists to clone and study. For Jeffreys, these findings were certainly preliminary, but they also pointed toward the beginning of something exciting and revolutionary. “Any hopes that molecular biology and paleontology can be fused into a grand evolutionary synthesis by studying fossil DNA, still look like nothing more than a glorious dream,” noted Jeffreys. “However, it is far too early to give up, and it might just be possible that DNA has survived in some fossilized material.”31
For Wilson, the quagga study was his first to exhibit evidence of DNA from an ancient and extinct organism, but he and his lab were no strangers to the study of ancient molecules, nor were they strangers to the press and public attention associated with it. Before both the amber and quagga experiments, Wilson and colleagues had attempted the extraction of proteins and even DNA from woolly mammoths. In the summer of 1977, the opportunity presented itself when an approximately forty-thousand-year-old baby mammoth was found preserved in permafrost near Magadan in Siberia. Named Dima, the baby mammoth was an exceptional fossil find for two reasons. First, it was the most complete mammoth discovered since the 1800s. Second, it was the only complete mammoth to be excavated, then immediately refrigerated in a lab, thus preventing the specimen from thawing and decomposing. Wilson heard about the find and was especially interested for the latter reason, since refrigeration might prevent the degradation of cellular and molecular material. In the spring of the next year, after a series of inquires that eventually resulted in an American-Soviet scientific collaboration (an interesting collaboration for an unusual time of American-Soviet political conflict), a sample of muscle from the carcass was packed in dry ice and shipped to Berkeley from the Soviet Union.32 Being frozen for thousands of years, Dima the baby mammoth presented a unique opportunity for immunological, chemical, and molecular research of an ancient and extinct species.
Dima’s discovery and delivery to Berkeley was of immediate interest to scientists and the public alike, making headlines across multiple newspapers.33 Indeed, there were good reasons behind all the attention. For starters, humans have long been captivated by mammoths in terms of their existence and extinction approximately ten thousand years ago.34 For the most part, the mammoth’s evolutionary history and its relationship to extant elephants were uncertain, and the reasons for its extinction also remained a mystery.35 Before Wilson and colleagues even began their work, much less published the results of it, media reporters began to speculate on the implications. Reporter Walter Sullivan for the New York Times, for example, conceded that the main goal of the scientists’ work was to search for mammoth proteins and perhaps mammoth DNA, with the hope that molecular evidence would shed light on the relationship between the extinct mammoth and extant elephant. At the same time, Sullivan entertained the idea of bringing mammoths back to life, hinting that while the possibility of cloning a mammoth was improbable, at least right now, it was not entirely impossible.36
A few years later, Wilson and colleagues were ready to publish, and in 1980 their paper in Science appeared. Ellen M. Prager, a molecular biologist and postdoctoral researcher with Wilson, and Alice Taylor, an electron microscopist, had found evidence of ancient proteins from Dima along with well-preserved microscopic muscle structure.37 Reporter John Noble Wilford, also writing for the New York Times, described their research as an “exploratory tool in the emerging science of fossil genetics” but also speculated on its use as a potential tool for resurrecting the mammoth if only its DNA could be found: “If they could find intact strands of DNA . . ., the raw material of heredity, they could conceivably reconstruct the long-extinct species through cloning, though the chances of doing this are considered quite remote.”38 To be clear, Prager and colleagues did not find mammoth DNA, nor did they attempt to look for it in this specific study. It was not until five years later that Wilson and Higuchi attempted the task, and they only did so with difficulty. In the end, they were able to detect the presence of DNA from the baby mammoth but were unable to replicate or authenticate the DNA.39 Nonetheless, early evidence for the preservation of molecules in ancient and extinct creatures, be it proteins or DNA, generated much speculation across the media about scientists’ potential to bring extinct animals back to life.
It was not long before this far-out speculation about mammoth resurrection looked like a reality, at least according to the media. In April 1984, MIT Technology Review reported a story declaring that the mammoth, extinct for the past tens of thousands of years, had been brought back from the dead. A Dr. Yasmilov of the University of Irkutsk and a Dr. Creak from the Massachusetts Institute of Technology were the alleged masterminds behind this feat. According to the article, Yasmilov had recovered a frozen mammoth egg from a carcass in Siberia and sent the sample to Creak. Creak recovered DNA from the frozen mammoth egg, then combined the sequences from the extinct mammoth with sequences from the sperm of an extant Asian elephant. The resulting product was implanted into the wombs of several Indian elephants that served as surrogates for these elephant-mammoth hybrids. Although a number of the surrogates miscarried, two gave birth to the first elephant-mammoth hybrids. Scientists called them a new species, Elephas pseudotherias.40
The news went viral. The Chicago Tribune, for example, reprinted the report, which was subsequently sensationalized by hundreds of newspapers across the United States. In the end, however, the entire story was a hoax, written by an undergraduate student, Diane Ben-Aaron, for an undergraduate course. Although it was published on April 1, 1984, April Fool’s Day, reporters had not noticed or made the connection. Regardless, the tale’s instantaneous popularity across media outlets made it clear that the idea and perceived reality of bringing extinct species back to life was something the public wanted, or even needed, to know about. It spoke to the press’s and public’s simultaneous fascination with and fear of genetic engineering and technology, thus provoking a host of ethical, moral, political, and environmental arguments both for and against it.41
The potential to resurrect extinct species continued to hit headlines, with reports ranging from the wildly speculative to the more subdued. The weekly tabloid National Examiner, for example, published a report claiming, “Mad Scientists Are Cloning Dinosaurs as Weapons of the Future.” The report contained a mostly false story combining mammoth cloning and American-Soviet nuclear warfare conspiracies with actual scientific research going on at Berkeley.42 At the same time, there was more accurate reporting. The magazine New Scientist, for example, noted that “stories that the quagga, the dodo, and the mammoth might be about to rise and stalk the Earth once more are somewhat exaggerated,” but “resurrecting the quagga” might one day “indeed be possible.” In fact, the report’s title—“The Resurrection of the Quagga”—hinted at as much.43
Importantly, media reporters were not the only ones talking about the resurrection of extinct species. Indeed, some scientists entertained the idea too. In another New Scientist article—“To Clone a Dinosaur”—Mike Benton, a paleontologist then at the University of Belfast and now at the University of Bristol, directly attended to the topic of resurrection, specifically dinosaur resurrection: “Will we ever be able to clone a dinosaur?” Benton’s answer was not yes but neither was the answer no. Although it would not be easy to reliably recover dinosaur molecules, Benton suggested that very small amounts of protein are likely to remain intact in fossils as old as the dinosaurs that existed 65–245 million years ago. More likely than discovering ancient dinosaur proteins, however, was the prospect of bringing the quagga back to life. According to Benton, it might be possible to resurrect the extinct quagga by inserting its DNA into the embryo of a mountain zebra to create some sort of quagga-zebra hybrid.44
THE ROLE OF SPECULATION
Speculation was a central feature guiding various scientists’ early research efforts to test the theoretical preservation and potential extraction of DNA from fossil species. Scientists from Poinar and Pääbo to Wilson and Higuchi clearly speculated about the recovery of DNA from fossil material hundreds to millions of years old. They wondered about its application to questions in evolutionary biology. They also wondered about its implications for changing how researchers study the past. Such conjectures were typical, even necessary, for generating and testing hypotheses, especially the most unconventional ones. In fact, philosophers of science have proposed that speculation is a useful and essential component of the scientific process. Adrian Currie and Kim Sterelny, for example, argue that speculation can be particularly productive in moving scientific inquiry forward. Although speculation by definition exceeds available evidence in support of it, “productive speculation” can be empirically grounded and hypothesis-generating.45 It can increase interest and traction around an idea to ultimately produce convincing data in support of it. In these early research efforts to discover DNA in fossils, speculation motivated practitioners to undertake experiments that could generate evidence.
At the same time, there were more overt expressions of far-out speculation, namely around the hypothetical idea of species resurrection. Speculation extended beyond immediate research practices or potential. For example, media reporters, as well as some scientists, openly entertained the potential to use ancient DNA to not only study evolutionary history but to maybe one day bring back extinct species. To a certain degree, this type of speculation was productive in creating an awareness of and excitement for this new line of research for both public and professional audiences.
But speculation can only be so useful in promoting research. Moreover, speculation, or rather too much or the wrong kind of it, may even frustrate research efforts. Currie and Sterelny make this point, arguing that speculation, if idle, can be a vice. In these circumstances, idle speculation takes place when speculation cannot or does not advance research efforts by producing alternative scenarios or providing additional evidence needed to support those scenarios.46 In fact, in these early years, scientists feared exactly this outcome, that too much speculation with too little evidence could harm their research and reputation in terms of credibility. Even Wilson, a visionary for his time, confessed that the search for DNA from fossils was an exotic and speculative undertaking. From the outset, Higuchi was concerned with contamination that would affect DNA authenticity and consequently its credibility. Yet even with reliable evidence, albeit preliminary evidence, for the successful extraction of DNA from the quagga, the NSF funding panel rejected Wilson and Higuchi’s proposal on the grounds that the research and evidence for it was underdeveloped and not widely applicable across the sciences. Moreover, Pääbo conducted his study of ancient Egyptian mummies in secret for fear of failure and subsequent reprimanding or ridiculing. This tension between science and speculation—most notably scientists’ awareness of and ability to engage or disengage as necessary—was an equally important element that colored ancient DNA’s emergence and evolution into a new way to study evolutionary history.
This is not to underestimate the importance or impact of the quagga study, nor that of the mummy study, in marshaling wider attention and support for the search for ancient DNA. In the quagga and mummy studies, the evidence was impressive for the time, but within the bigger picture the evidence was also weak. A couple of short DNA strands from a single sample of an extinct quagga and one ancient mummy were exciting but not extra-ordinary. The preservation of DNA in some fossils did not guarantee the preservation of DNA in all fossils. Ancient DNA, at least at this time, was an anomaly. And the science behind it was more of a spectacle and a rarity than a predictable method of obtaining data. What was important about these studies was the acceptance of the evidence, however weak, by prestigious scientists and esteemed journals. Evidence, and professional publication of it, played a role in establishing a certain degree of credibility behind these novel ideas. However, in order for scientists to transform the search for DNA from fossils into a legitimate scientific research program, they would need better-preserved fossils, better techniques and technologies, more funding, more evidence, and lots of luck.