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Electronic Theses, Treatises and Dissertations The Graduate School

2012 The Search for Ancient DNA, the Meaning of , and in the Modern Evolutionary Synthesis Elizabeth Dobson

Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY

COLLEGE OF ARTS AND SCIENCES

THE SEARCH FOR ANCIENT DNA, THE MEANING OF FOSSILS,

AND PALEONTOLOGY IN THE MODERN EVOLUTIONARY SYNTHESIS

By

ELIZABETH DOBSON

A submitted to the Program in History and Philosophy of in partial fulfillment of the requirements for the degree of Master of Arts

Degree Awarded: Summer Semester, 2012 Elizabeth Dobson defended this thesis on March 26, 2012.

The members of the supervisory committee were:

Frederick Davis

Professor Directing Thesis

Michael Ruse

Program Director

Gregory Erickson

Committee Member

Scott Steppan

Committee Member

The Graduate School has verified and approved the above-named committee members, and certifies that the thesis has been approved in accordance with university requirements.

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To my fiancé,

Patrick Jones

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ACKNOWLEDGMENTS First, I would like to thank my former professor, Mary Schweitzer, who first inspired my passion for paleontology. Without her love and support, the following work would not have been possible. I would also like to thank my former professor and advisor, William Kimler, who first taught me to think, research, and write as a historian of science. I am indebted to these two mentors, for without them I may have never learned to merge my passion for history with my love of paleontology. Next, I would like to thank my committee members who contributed to this work in many ways. I am especially grateful for my current professor and advisor, Frederick Davis. Your attentive guidance and constant encouragement helped to make this project a reality. Thank you for believing in me. Thank you also to Michael Ruse for your philosophy and support of my studies. I have grown so much under your guidance. Thank you for all you have taught me. Many thanks go to Gregory Erickson who has been a most valuable mentor over the past two years. Thank you for your direction and for further inspiring my research in paleontology. I would also like to thank Scott Steppan for clarification and careful comments on chapter three and the work as a whole. Special thanks also go out to a number of admirable scientists: Mark Norell, Jack Horner, Hans Larsson, Peter Dodson, and Brent Breithaupt. I appreciate your time, your insights, and your interest in the construction of this work. I am especially appreciative of Derek Turner who has proved an essential sounding board from afar. I want to also thank Ronald Doel, Kristine Harper, and Paul Brinkman for helpful suggestions. Many thanks go to my friend, Lindsey Newberry, for her thorough edits on every chapter. Most importantly, I am forever grateful for my and their unfailing love and support. Thank you to my parents, Allen and Martha Dobson, and also my siblings, Robert and Sara. Finally, I want to offer a special thank you to my fiancé, Patrick Jones. Your love and patience over the last two years will always be remembered. I cannot begin to thank you enough.

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TABLE OF CONTENTS

Abstract ...... vi

INTRODUCTION ...... 1

CHAPTER ONE: LITERATURE REVIEW ...... 5

CHAPTER TWO: PALEONTOLOGY FROM DARWIN TO DNA ...... 21

CHAPTER THREE: THE SEARCH FOR ANCIENT DNA (1984-1991) ...... 47

CHAPTER FOUR: THE SEARCH FOR ANCIENT DNA (1991-1999) ...... 68

CHAPTER FIVE: MAKING SENSE OF ANCIENT DNA ...... 91

CONCLUSION ...... 115

REFERENCES ...... 123

BIOGRAPHICAL SKETCH ...... 132

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ABSTRACT

Reflecting on the , historian Martin Rudwick claimed, “The ‘meaning’ of fossils has been seen in many different ways in different periods.” This insight rings true today as the search for ancient DNA has provided a deeper meaning of the term and offered paleontology a more expansive role in the molecular age. In this work, I provide a historical account of ancient DNA research from 1984 to1999 and discuss the implications of ancient DNA research as a new approach to fossil studies for the science of paleontology. The emergence of ancient DNA research over the past several decades has introduced a fresh and quantitative methodology for studying fossils and a new means through which to discover and decipher our evolutionary past. Ancient DNA research has revolutionized how scientists view and study ancient and fossil specimens. In doing so, the search for ancient DNA has transformed what was once a purely historical approach to fossil studies into a more experimental one. In this thesis, I argue that the early history of ancient DNA research, when appropriately situated in the overall history of paleontology, is best understood as an extension and realization of the modern evolutionary synthesis and a step toward bridging the gap between historical and experimental science.

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INTRODUCTION

In February 2012, a team of Russian scientists announced the resurrection of an Ice Age plant from ancient tissue, frozen and preserved, in the nest of squirrel that lived some 30,000 years ago. In this report, Svetlana Yashina, of the Institute of Biophysics at the Russian Academy of Sciences, and colleagues announced, “Late plant tissue of S. stenophylla, naturally preserved in , can be regenerated using tissue culture and micropropagation to form healthy sexually reproducing plants…At present, plants of S. stenophylla are the unique representative of ancient higher plants to be cultivated successfully.”1 The Russian scientists’ report captured the imagination of the world press. USA Today, The London Telegraph, and Discover all carried the story. The prospect of bringing ancient and even extinct creatures back to is an idea that first became a conceivable reality with the advent of ancient DNA research in the mid-1980s. Shortly after, the idea of resurrecting the past gained popular appeal when Michael Crichton published his highly sensational science-fiction thriller, Park. However, the scientists behind this specific study were more realistic about the implications of the ancient Ice Age plant and what this report means for science. Reflecting on the study’s findings, Yashina and fellow researchers claimed, “This natural cryopreservation of plant tissue over many thousands of years demonstrates a role for permafrost as a depository for an ancient pool, i.e., preexisting life, which hypothetically has long since vanished from the earth’s surface, a potential source of ancient germplasm, and a laboratory for the study of rates of .”2 This mildly fantastical account of the Ice Age plant resurrection, when compared to the imaginative world of Jurassic Park, is perhaps indicative of the past several decades of ancient DNA research and a more realistic vision of the potential of this type of inquiry. Nevertheless, the idea that we can successfully recreate the past remains a hot – though controversial – topic even thirty years after the first ancient DNA study which suggested that raising the dead and buried may in fact be an obtainable scientific reality. In this work, I cover new ground in the history of paleontology. My argument, although spread across five chapters, is three-fold. First and foremost, I provide a historical account of

1 Svetlana Yashina, Stanislav Gubinb, Stanislav Maksimovichb, Alexandra Yashina, Edith Gakhovaa, and David Gilichinsky “Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost,” Proceedings of the National Academy of Sciences (2012): 4. 2 Ibid., 1. 1

aDNA research from its inception in the 1980s until the turn of the twenty-first century. To develop this point, I must situate aDNA research into the broader history of paleontology. Chapter one provides a literature review of the history of the life sciences with an emphasis on paleontology. This historiography establishes a backdrop from which to understand the more general trends in the history of the life sciences from Darwinian , classical , and the modern evolutionary synthesis to , molecular paleontology, and . More importantly, I note how these trends were critical influences on the development of paleontology as a science and profession and how they affected paleontology’s role in evolutionary discussion from the mid-nineteenth to late twentieth century. In chapter two, I discuss more specifically paleontology’s significance in evolutionary theory from Darwin to DNA. This chapter explores paleontology as evidence of evolution and its role in Darwin’s argument for evolution by . I also cover paleontology’s waning influence in evolutionary theorizing at the turn of the twentieth century with the rising popularity of experimental biology. At the same time, however, paleontology remained an active science through the development of field techniques and also the maturation of the field paleontologist as best exhibited through the rise of paleontology, and more specifically paleontology in the American West. This chapter sets up a background for understanding paleontology as a historical science while discussing the bias of experimental scientists towards more traditional, inferential approaches that emerged over the last century. My focus narrows to the history of aDNA research in chapters three and four. Chapter three presents a history of aDNA research from 1984 to 1991. From a Kuhnian perspective, I view the history of aDNA as the investigation of a scientific anomaly, namely the existence of DNA in ancient and fossil organisms. However, it is not my intention to either prove or disprove Kuhn’s argument as presented in The Structure of Scientific Revolutions. Rather, I incorporate his notion of anomaly as a guide for organizing aDNA research. In this chapter, I mainly focus on early efforts to reproduce and authenticate results. I also explore the growing acceptance of aDNA as a viable field of research and its potential impact on a number of disparate disciplines from to paleontology. In chapter four, I continue the historical account of aDNA research from 1991 to 1999. I extend Kuhn’s notion of anomaly into this section and primarily analyze scientists’ attempts to reproduce claims of aDNA, especially in ancient and fossil organisms older than one million years of age. This section addresses the use of aDNA in the

2 construction of phylogenies, or evolutionary histories, and also explores the benefit of dating. Finally, chapter five is an analysis of the previous four chapters in which I attempt to make sense of the early history of aDNA research and its significance for the history of paleontology. I begin this chapter with a discussion of the philosophical distinction between historical and experimental science, and further suggest that the early history of aDNA research represents a transition from a traditionally historical to a more experimental approach to fossil studies. I then consider the changing meaning of the term “fossil” in light of recent advances in aDNA studies. The early history of aDNA research also raises important questions of disciplinary boundaries, and I conclude this chapter with an analysis of these boundaries and the implications for the field and the future of paleontology. Thus, I argue that the early history of aDNA research from 1984 to 1999, when appropriately situated in the overall history of paleontology, is best understood as an extension of the modern evolutionary synthesis and a step toward bridging the gap between historical and experimental science. Ancient DNA research remains an active area of research today and numerous advances have been made within the past decade. Technological achievements have improved the process and accessibility of aDNA studies. Furthermore, a number of exciting, and often controversial, reports have been published over this ten year period. I recognize that aDNA, as a young and burgeoning field, has diversified in a myriad of ways and that these more recent developments are also an integral part of the story of aDNA research. Nevertheless, I have chosen to limit my review of aDNA research to the first two decades of its development only. As a historian and philosopher of science, I hope to provide an accurate history of aDNA with a meaningful analysis of the ramifications for paleontology and larger evolutionary synthesis. Yet I realize that the last decade of aDNA study will be a necessary component for future scholarship. My review of this history is portrayed almost entirely through the science itself as evidenced through scholarly scientific articles and the very few, but significant, memoirs of scientists and science writers over these years. My conclusions are based on these primary articles and other scholars’ historical and philosophical reflections. These conclusions have also been informed and guided by interviews with current scientists and paleontologists. In sum, the following work is an honest attempt to capture some of the most provocative research in the history of modern science. I hope to provide a careful synthesis of aDNA research and a thoughtful analysis of its

3 consequences for the history of paleontology, the future of paleontology in a molecular age, and the overall impact this novel approach to fossil studies has on the larger modern evolutionary synthesis.

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CHAPTER ONE

LITERATURE REVIEW

Introduction

Ancient DNA (aDNA) research, the search and recovery of genetic material from ancient and fossil creatures, is an outgrowth of years of scientific and technological achievements and an even longer history of conceptual evolvements. As a product of decades of research, aDNA research is most appropriately understood in light of those scientific advancements that over the past century or so have made this novel, yet controversial approach to fossil studies a possibility. A quote from the late David Hull, historian of science, captures this point:

If one is interested in science as a process, conceptual systems cannot be viewed as seamless wholes. Science is a cooperative affair, each scientist contributing his or her special combination of abilities and areas of knowledge. A more appropriate picture is scientists casting their patchwork nets, one after the other, retrieving them, reworking them piecemeal on the basis of the most recent fit, and then casting them again.1

Science is a process of discovery and development and in the life sciences, this discovery and development is often interdisciplinary. This review will cover major milestones in the from Darwinian evolution, , and the dawning of the modern evolutionary synthesis to the advent of molecular biology, molecular paleontology, and the creation of paleobiology. With an emphasis on paleontology, the goal of this historiography is to provide a backdrop which will help us appreciate how the recent practice of aDNA research fits into the larger history of biology. I also hope this review of the history of biology will prepare us for a deeper analysis of how aDNA relates even more specifically to the history of paleontology and its meaning for the field of paleontology as a science and profession. The theory of evolution by natural selection has had an outstanding impact on the birth and growth of biology and more

1 David Hull, Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science, (Chicago: The Press, 1988), 493.

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importantly, it has come to operate as the cornerstone for every biological discipline from and paleontology to genetics and molecular biology. For this reason, our story will start and end with evolution.

Theory of Evolution by Natural Selection

In November of 1859, published his book. Darwin had become convinced of the transmutation of following his voyage on the Beagle in the 1830s, but sat on his theory for nearly twenty years after. During this time, Darwin was constructing one long argument for the evolution of species by natural selection. He argued that all of today’s creatures, diverse in form and function, all evolved from a common ancestor. Darwin also argued that in this world there is competition for resources and a struggle for existence. He explained, “Owing to this struggle for life, any variation, however slight from whatever cause proceeding, if it be in any degree profitable to an individual of any species…will tend to the preservation of that individual, and will generally be inherited by its offspring.”2 Darwin proposed that the “preservation of favourable variations and the rejection of injurious variations” occur under the principle of Natural Selection.3 His theory was an immediate sensation. Although many had qualms with the specifics of natural selection, most naturalists quickly converted to the new theory. The formation of Darwin’s theory of evolution first depended on a changing world view in favor of an ancient earth as inferred from geology and paleontology. The old world view believed in a young earth only several thousand years old. Additionally, the old world view argued that the earth was unchanging, all creatures were designed by the Creator, and that man stood at the pinnacle of the “.”4 This transition from the old to the new world view, and specifically the acceptance of evolution, had much to do with the major breakthroughs in late eighteenth century geology and paleontology.5 Historian Peter Bowler noted, “The theory of biological evolution is really only part of a whole new approach to the study of the earth’s past

2 Charles Darwin, , in From So Simple a Beginning, ed. Edward O. Wilson (New York: W. W. Norton & Company, Inc., 2006), 489. 3 Darwin, On the Origin of Species, 502. 4 Arthur O. Lovejoy, The Great Chain of Being: A Study of the History of an Idea (Cambridge, Massachusetts: Press), 1936. 5 Edward J. Larson, Evolution: The Remarkable History of a Scientific Theory (New York: The Modern Library, 2004), xvi. 6

that has been developed over the last few centuries.”6 In the early 1800s, geology became organized as a new science, and its dramatic new discoveries challenged traditional views of the earth. Among the most well-known and influential geologists of the period was Sir (1797-1875). The publication of the first volume of his seminal work in1830 quickly became one of the most fundamental texts for nineteenth century geology. The startling new conclusion among professional geologists was a consensus for a very ancient Earth with successive epochs of life. Meanwhile, paleontology was an emerging field of in the early nineteenth century. Although it lagged behind geology in its development as a professional field, recent discoveries in paleontology served to reinforce the ancient earth view. Paleontology and the fossil record clearly showed many forms now extinct, and that life on earth had changed over what had to be a long time period. French naturalist (1769-1832) was one of the most prominent paleontologists of the early1800s. Later christened the founder of paleontology, Cuvier was a champion of , and his work led him to radical conclusions for establishing as fact. Cuvier entertained ideas of species diversity as evidenced through the fossil record, and furthermore, his work in paleontology rejected the long standing belief that species, as a special and perfect creation from above, were exempt from extinction.7 The emergent disciplines of nineteenth century geology and paleontology had much to do with increasing evidence in favor of an ancient and dynamic earth and much to do with the development of Darwin’s argument for evolution. As historians of evolutionary theory have shown, Darwin was not the first to propose a theory of evolution. Although hailed as the founder of modern evolutionary theory, there were several precursors who helped pave the way for both the development and reception of his ideas. Nineteenth century naturalists were aware of ideas of evolution, and although some entertained such ideas and even published on the subject, they were by no means generally accepted. These men included French naturalists Georges-Louis Leclerc, Comte de Buffon, Jean-Baptiste Lamarck, and the Scottish geologist Robert Chambers. Even Darwin’s grandfather, Erasmus

6 Peter Bowler, Evolution: The History of an Idea, revised ed. (Berkeley: University of California Press, 1989), 4. 7 , Life of the Past: Introduction to Paleontology (New Haven: Press, 1953), 140-141; Bowler, Evolution, 112-118. 7

Darwin, postulated the evolution of organisms.8 However, what Darwin’s precursors lacked in their theories of evolution was strong evidence in favor of its reality. As paleontologist George Gaylord Simpson put it: Darwin’s precursors were “long on speculation and short on facts.”9 Darwin’s precursors also failed to give any explanation of a mechanism which could account for evolutionary change. In fact, Darwin and – co-discoverer of evolution by natural selection – were the first to propose a mechanism for evolutionary processes. The impact of Darwinian evolution was far reaching. Darwin’s On the Origin of Species (1859) had in part such an enormous impact because it was not only a theory but also a very general theory that touched on nearly every branch of science. Darwin compiled his evidence for evolution by natural selection through a number of sciences from geology and paleontology to and . He probed these sciences for evidence for the geographical distribution of species, , and the meaning of species. One of the most striking features of Darwin’s theory, and also its success, was its unificatory power. As philosopher of science Michael Ruse claimed, “Above all else, Darwin’s theory exhibits this value, unifying into one whole all of the hitherto disparate areas of biology: paleontology, , behavior, , , , and more.”10 Nearly every scientific discipline, in some way or another, was impacted by the Origin. Darwin’s theory, as a new comprehensive vision of life, became the foundation in which biology and all subsequent developments depended on. However, that is not to say that his theory was void of difficulty. Interestingly, because Darwin’s theory of evolution relied so much on evidence from other sciences, the full power and scope of his theory was only as strong as the sciences behind it. In many cases, Darwinian evolution had to wait for the sciences it depended on for evidence to catch up with theory. Bowler eloquently explained:

Disciplines from geology and paleontology to the science of experimental genetics had to be created before the modern form of became possible. Small wonder that it took a long time for the framework of these new sciences to be established and that in the process many different kinds of ideas were tried out. The scientific debates that

8 Bowler, Evolution; Michael Ruse, The Darwinian Revolution: Red in and Claw, 2nd ed. (Chicago: University of Chicago Press, 1999). 9 Simpson, Life of the Past, 142. 10 Michael Ruse, Mystery of Mysteries: Is Evolution a Social Construction? (Cambridge: Harvard University Press, 1999), 66. 8

surrounded the emergence of evolution theory were not just the products of a revolution within a single science. Rather, they were the result of complex interactions between a whole series of emerging scientific disciplines, which had to be fitted together before the Darwinian revolution could be completed.11

Bowler’s point is well taken, especially when we consider the role that genetics has played in the success of evolutionary theory. For example, nineteenth century naturalists had no clear understanding of how worked and Darwin, very much in tune to some of the difficulties of his theory, “candidly admitted great ignorance of the process of heredity.”12 The best working hypothesis at the time was of “” which explained the offspring’s features as a blending of parental characteristics. From this view, Darwin developed his own theory of inheritance known as “pangenesis” which was later determined by the development of modern genetics to be in severe error. Bowler explained, “Darwin’s thinking on the link between growth, heredity, and evolution remained grounded in a conceptual system that would only be overthrown with the emergence of Mendelian genetics.”13 However, in time and with the rediscovery of Mendelian genetics, evolutionary theory was strengthened and flourished.

Classical Genetics

Austrian friar and naturalist (1822-1884), now considered the father of genetics, first published the results of his famous pea pod experiments in 1866. This work, what we now recognize as significant research on the laws of inheritance and the foundation of modern genetics, was in fact largely ignored and instead, regarded as a piece on hybridization rather than inheritance. For this reason, among many others, Mendel’s paper was essentially neglected until its rediscovery in the early 1900s. Bowler attributed part of this neglect to Mendel’s approach being “out of touch with the prevailing conceptual framework.” Expanding on this point, he claimed, “Only when that framework changed would it become possible for a new generation of biologists to look back and see that inheritance of characters in peas offered a

11 Bowler, Evolution, 18. 12 Ruse, The Darwinian Revolution, 210. 13 Bowler, Evolution, 210. 9

model upon which to build a whole new theory of heredity.”14 When this happened nearly thirty- five years later, the field of what is now known as classical genetics was born. In 1900, according to the traditional and somewhat controversial account, three men – , Carl Correns, and Erich Tschermak – independently rediscovered Mendelian-like results and conclusions. Soon after, they also recovered Mendel’s own research and writings on the same conclusions.15 The rediscovery of Mendel’s work as applied to inheritance did not, however, immediately result in the field of classic genetics as we now know it. Lacking total consensus, the field found itself split between two schools of thought; the Mendelians and the biometricians. The Mendelians, led by , argued for an inductivist methodology while the biometricians, guided by Walter Raphael Weldon and Karl Pearson, approached heredity from a mathematical perspective. Bateson, evolutionary morphologist and ardent Mendelian of the early twentieth century, coined the term ‘genetics’ in 1905.16 (1866-1945), an American embryologist and once staunch opponent of Mendelism, was a converted supporter by the 1920s and became a major figure responsible for the field’s advancement. Morgan’s ground breaking quantitative and experimental research on the fruit fly had much to do with his change of opinion.17 In the early 1900s, Walter Sutton and Theodor Boveri created the “ theory” which proposed as the mechanism of heredity and the transferor of . Morgan and his colleagues’ fruit fly studies at Columbia University confirmed this hypothesis. Bowler stated, “Modern genetics only emerged when T. H. Morgan and his colleagues finally identified the Mendelian factor as a material unit or ‘gene’ in the chromosome, thereby opening up a cornucopia of insights that would explain a host of complex phenomena and clear up once and for all the confusion over unit characters and genetics factors.”18 Yet, despite major strides in genetics, the field as a whole remained largely divided. It took just over a decade to resolve their differences and through the work of , John Haldane, , and Sergei Chetverikov, the field of genetics was brought under one cohesive, theoretical framework by the

14 Peter Bowler, The Mendelian Revolution: The Emergence of Hereditarian Concepts in Modern Science and Society (London: The Athlone Press, 1989), 108. 15 Bowler, The Mendelian Revolution, 113. 16 Garland Allen, Life Science in the Twentieth Century (New York: John & Sons, Inc., 1975), 50-51. Bowler, The Mendelian Revolution. 17 Allen, Life Science in the Twentieth Century, 57. 18 Bowler, The Mendelian Revolution, 128. 10

early 1930s.19 Thus, the field of classical genetics was born and with it, the foundation from which modern molecular biology was to be built.

The Modern Evolutionary Synthesis

Theodosius Dobzhansky, esteemed and evolutionary biologist, produced his inspirational work, Genetics and the Origin of Species, in 1937. Following in Morgan’s footsteps and his work in of fruit flies, Dobzhansky’s main purpose in this book was to merge Darwinism and Mendelism under one unified framework. Dobzhansky’s efforts were far reaching and were soon recognized as relevant by other disciplines like paleontology and systematics. This culminated into what we now call the “Modern Evolutionary Synthesis.” Paleontologist and historian of science claimed, “Like most great books, Dobzhansky’s volume is not merely a review and categorization of existing data. It is a long argument for a general attitude toward nature and a specific approach that might unite the disparate elements of evolutionary theory.”20 This “general attitude toward nature” was eagerly embraced and advanced through the works of several influential figures from a variety of disciplines, namely the evolutionary biologist (1942), paleontologist George Gaylord Simpson (1944), and botanist and geneticist George Ledyard Stebbins, Jr. (1950). G. G. Simpson, professor of zoology at Columbia University and also Curator of the Department of Geology and Paleontology at the American Museum of Natural History, was a chief contributor to the modern evolutionary synthesis. Two of his books in particular, Tempo and Mode in Evolution (1944) and The Meaning of Evolution (1949), became fundamental works in paleontology and evolutionary theory. Simpson’s role in the new evolutionary synthesis was to bring the field and recent works of paleontology into larger discussion with the evolutionary theory and in particular, the biological community. At the same time, Simpson hoped to raise the status of paleontology as both a profession and a science. He believed that the key to doing so relied on a more quantitative and analytical approach to paleontological research.21 For Simpson, our life’s past was a necessary condition for understanding evolutionary processes. In his

19 Bowler, The Mendelian Revolution, 128-152; Walter M. Fitch and Francisco Ayala, eds., Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson (Washington, D. C.: National Academy Press, 1995), iv. 20 , Genetics and the Origin of Species (New York: Columbia University Press, 1982), xxvi. 21 David Sepkoski and Michael Ruse, eds., The Paleobiological Revolution: Essays on the Growth of Modern Paleontology (Chicago: The University of Chicago Press, 2009), 20. 11

introduction to Tempo and Mode in Evolution, Simpson announced, “The basic problems of evolution are so broad that they cannot hopefully be attacked from the point of view of a single scientific discipline. Synthesis has become both more necessary and more difficult as evolutionary studies have become more diffuse and more specialized.”22As an ardent advocate for a more integrated and multidisciplinary approach to the study of evolution, Simpson urged the seemingly disparate disciplines of genetics and paleontology to “realize that we do have problems in common” and “that difficulties encountered in each separate type of research may be resolved or alleviated by the discoveries of the other.”23 Likewise, Ernst Mayr was another critical promoter of the modern evolutionary synthesis. Playing on Dobzhansky’s former work, Mayr’s Systematics and the Origin of Species (1942) sought to promote the role of systematics in evolutionary theory. Mayr’s book as a critical part of the evolutionary synthesis represented “a self-conscious effort to explicate the significance of population variation in the understanding of evolutionary processes and the origin of new species.”24 Mayr’s contribution was significant for many reasons, but most important for his definition of species. Before Darwin, and even since Darwin, the species concept was a major difficulty. William Herschel, nineteenth century mathematician, astronomer, and later botanist, captured the enigma of species as the great “mystery of mysteries.”25 Yet Mayr, in his 1942 work, attempted to find clarity and defined species as “groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.”26 While Mayr’s delineation was a step forward and his Systematics and Origin of Species remains one of the most foundational works of evolutionary theory, his proposed definition of species was not entirely satisfactory.27 The lack of a precise understanding of species plagues not only biologists, but also paleontologists, taxonomists, and alike. Nonetheless, evolutionary theory brought a number of disparate fields together in an effort to answer some of life’s most pressing question.

22 George Gaylord Simpson, Tempo and Mode in Evolution (New York: Columbia University Press, 1944), xv. 23 Simpson, Tempo and Mode in Evolution, xvi. 24 Jody Hey, Walter M. Fitch, and Francisco Ayala, Systematics and the Origin of Species: On Ernst Mayr’s 100th Anniversary (Washington, D. C.: The National Academies Press, 2005), vii. 25 John Herschel, quoted in Cannon, “The Impact of ,” 305. 26 Ernst Mayr, “ and Systematics,” in Genetics, Paleontology, and Evolution, eds. Glen Jepsen, Ernst Mayr, and George Gaylord Simpson (Princeton: Press, 1949), 284. 27 For example, asexual organisms, creatures that produce offspring from a single parent, pose a significant problem and find themselves excluded under this description. 12

Dobzansky, Simpson, and May’s efforts, among others, helped to consolidate the diverse field of biology under Darwin’s grand and unifying theory of evolution. As Hull noted, “The intent of the founders of the Modern Synthesis was to bring together the best in population genetics, systematics, paleontology, and so on into one grand theory.”28 Reflecting on the progress and current standing of evolutionary theory, evolutionary biologist Jody Hey, the late molecular evolutionist Walter Fitch, and biologist Francisco Ayala put it this way:

It [modern theory of evolution] is not one single theory with its corroborating evidence, but a multidisciplinary body of knowledge bearing on biological evolution: an amalgam of well established theories and working hypotheses together with the observations and experiments that support accepted hypotheses (and falsely rejected ones), which jointly seek to explain the evolutionary process and its outcomes. These hypotheses, observations, and experiments originate in disciplines such as genetics, , neurobiology, zoology, botany, paleontology, and molecular biology.29

Such a synthesis was an arduous, but not an impossible task. Indeed, paleontology as a professional discipline – despite Simpson’s efforts to revitalize the field – still awaited full recognition from the biological community as a serious and rigorous participant in evolutionary discussion. Historian David Sepkoski and philosopher Michael Ruse noted, “It would be a mistake, however, to conclude that paleontology was, in the late 1940s or afterward, a fully equal and respected partner in the new-Darwinian community.”30 Nonetheless, Simpson’s efforts were a step forward in the right direction for bringing paleontology into fuller conversation with the rest of the life sciences and uniting them under one common factor, namely evolutionary theory. As Dobzhansky famously stated, “nothing in biology makes sense except in the light of evolution.”31

28 Hull, Science as a Process, 34. 29 Hey, Fitch, and Ayala, Systematics and the Origin of Species, v. 30 Sepkoski and Ruse, The Paleobiological Revolution, 22. 31 Theodosius Dobzhansky, “Nothing in Biology Makes Sense Except in the Light of Evolution,” The American Biology Teacher 35 (1973): 125-29. 13

Molecular Biology

James D. Watson and , researchers at the , wrote in an article that would forever change the direction of biology, “We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.”32 True to their words, Watson and Crick’s proposal, published in Nature on 25 April 1953, solved the mystery of inheritance, namely, the structure of genetic material and how this information was stored and passed on from one generation to the next. Watson, at the young age of twenty-two, obtained his PhD in Zoology at Indiana University under the direction of Salvador Luria, an accomplished geneticist. Crick, eleven years Watson’s senior, earned his PhD in physics at the University College of London, but soon turned his interests to biology. Together, and with the help of their colleagues, physicist Maurice Wilkins and chemist and crystallographer , Watson and Crick transformed the field of biology. Watson and Crick’s discovery united the current biological practices of the day with a true understanding of the structure of DNA and the process of inheritance. The discovery of the DNA double helix soon gave way to the new field of research called molecular biology. Crick defined molecular biology as follows:

The term is used in two rather different ways. First, in a very general sense it can mean almost anything – the attempt to understand any biological problem at the level of atoms and molecules. You could talk about the molecular biology of behavior – and that’s not so far-fetched as you might imagine; some senior molecular biologists are getting close to that. Second, there is a classical sense of the term, and this is much narrower: classical molecular biology has been concerned with the very large, long-chain biological molecules – the nucleic acids and proteins and their synthesis. Biologically, this means genes and their replication and expression, genes and the gene products.33

32 and Francis Crick, “Molecular Structure of Nucleic Acids,” Nature 171 (1953): 737. 33 Horace Judson, The Eighth Day of Creation: Makers of the Revolution in Biology (New York: Cold Spring Harbor Laboratory Press, 1996), 178-179. 14

The field of molecular biology opened up a completely new way in which to study life and the evolution of organisms. The three main approaches, now fused into one general approach, were structural, biochemical, and informational. Historian Garland Allen explained that today, “Current ‘molecular biology’ includes not only a structural and functional element, but also an informational element…concerned with the structure of biologically important molecules (such as proteins or nucleic acids) in terms of their function in the of the cell and how they carry specific biological information.”34 Yet, the discovery and development of molecular biology into a truly cohesive and fertile discipline was very much a process. When interviewing Crick about the discovery of the structure of DNA, historian Horace Judson mentioned that discovery “seemed curiously difficult to pin to a moment or to an insight or even to a single person.” Crick’s perceptive response was to say, “I think that’s the nature of discoveries, many times: that the reason they’re difficult to make is that you’ve got to take a series of steps, three or four steps, which if you don’t make them you won’t get there, and if you go wrong in any one of them you won’t get there.” He concluded, “It isn’t a matter of one jump – that would be easy. You’ve got to make several successive jumps. And usually the pennies drop one after another until eventually it all clicks. Otherwise it would be too easy!”35 , a French biologist and participant in the biological revolution, expressed a similar sentiment when he said, “No one man created molecular biology.”36 Certainly, the creation of molecular biology did not happen overnight. Instead, molecular biology was the result of years of research made possible by decades of conceptual and technological developments. Philosopher of science Thomas Kuhn argued a similar line in his The Structure of Scientific Revolutions. In this work, Kuhn claimed, “That is a new theory, however special its range of application, is seldom or never just an increment to what is already known. Its assimilation requires the reconstruction of prior theory and the re-evaluation of prior fact, an intrinsically revolutionary process that is seldom completed by a single man.”37 Kuhn makes a strong point in that new theories and even new sciences emerge by way of a consolidation of knowledge. The history behind evolutionary theory, the emergence of classical genetics, the development of the modern evolutionary synthesis, and the coming of molecular biology are all

34 Allen, Life Science in the Twentieth Century, 189. 35 Judson, The Eighth Day of Creation, 155-156. 36 Judson, The Eighth Day of Creation, 178. 37 Thomas Kuhn, The Structure of Scientific Revolutions (Chicago: The University of Chicago Press, 1962), 7. 15

the result of the accumulation of conceptual, intellectual, and technological advancements over time. Hull echoed this sentiment, stating, “Science is not a process by which we go from no knowledge to some knowledge or from some knowledge to total knowledge. Rather it is a process by which scientists go from some knowledge to more knowledge.”38 Molecular biology was but another way to knowledge. More importantly, it was a new facet for which to directly study evolution on a much finer scale through the details of organismal DNA, RNA, and proteins. Ayala wrote, “Molecular biology, a discipline that emerged in the second half of the twentieth century, nearly one hundred years after the publication of The Origin of Species, has provided what many scientists consider the strongest evidence yet of the evolution of organisms.”39

Molecular Paleontology

In 1954, just a year following Watson and Crick’s report on the structure of DNA, Philip H. Abelson, a physicist by training but at the time the director of the Carnegie Institution of Washington’s Geophysical laboratory, announced the astonishing discovery of amino acids in fossil shells over 300 million years old.40 Prior to this study, it was presumed that the organic components of organisms, such as amino acids (what had been discovered as the basic building blocks of proteins essential for life), did not survive fossilization, especially in fossils millions of years old. Abelson’s research proved different. Speculating on the significance of his discovery, he announced in Scientific American, “The biochemical approach was largely limited to the study of living organisms…Now, however, it has been shown that the hard parts of many ancient creatures contain appreciable amounts of their original organic substance!”41 Abelson’s study merged the new and innovative techniques of molecular biology with the traditional fossil materials of paleontology. Abelson, recognizing molecular biology’s potential, ventured to apply molecular studies to not just living or more recent organisms, but fossils as well, and in doing so, introduced paleontology to a new approach to fossil studies. Soon after, others followed suit and their

38 Hull, Science as a Process, 26. 39 Ayala, “ vis- à-vis Paleontology,” in Paleobiological Revolution, 176. 40 Philip H. Abelson, “Organic constituents of fossils,” Carnegie Institute of Washington Yearbook 53 (1954): 97– 101; Philip H. Abelson, “Amino acids in fossils,” Science, 119 (1954): 576. 41 Philip H. Abelson, “Paleobiochemistry,” Scientific American 195 (1956): 83. 16

research endeavors would culminate in the beginnings of a new field of science, first termed paleobiochemistry, but more aptly known today as molecular paleontology. G. B. Curry, Department of Geographical and Earth Sciences at the University of Glasgow, wrote, “In its widest sense, molecular paleontology embraces the study of intact molecules in living organisms, as well as the investigation of the variably decayed remnants of ancient molecules which occur in great abundance in rocks and fossils.”42 Molecular paleontology has grown tremendously since its first emergence in the mid-1950s. Abelson’s 1954 study, the first in molecular paleontological research, was so groundbreaking because it demonstrated that organic material, such as amino acids, not only existed in fossil shells, but were capable of preservation over millions of years. Such a discovery could yield important information regarding past and present organismal structure and history. In the 1954 article “Organic constituents of fossils,” Abelson claimed, “It therefore seems likely that these fossils originally contained proteins which played the same important role in the of ancient creatures as they do in today’s organisms.”43 Despite the excitement of this recovery, Abelson recognized the contingencies that this study and other molecular studies faced. The preservation of organic molecules requires extremely unique and favorable conditions, but even then, adventitious contamination remains an issue during the extraction process.44 Multiple, successful studies would be necessary to confirm the reality of Abelson’s initial research. In keeping up with the new molecular age, Abelson and others explored the recovery of amino acids in fossilized specimen, both and vertebrate.45 His discoveries opened unparalleled options for the study of past life, and furthermore, introduced a new method for studying molecular evolution of long dead, or even extinct organisms directly.46 Fitch and Ayala wrote in reference to Simpson’s justified failure to anticipate molecular biology’s development and influence, “It would be unfair to claim lack of vision here, where nothing short of a

42 G. B. Curry, “Molecular Paleontology,” in Paleobiology: A Synthesis, eds. and Peter Crowther (Oxford: Blackwell Scientific Publications, 1990), 95; also see Bruce Runnegar, “Molecular Palaeontology,” Palaeontology 29 (1986): 1-24. 43 Abelson, “Organic constituents of fossils,” 99-100. 44 Ibid, 98, 100. 45 Abelson, “Amino acids in fossils”; Abelson, “Organic constituents of fossils”; Abelson, “Paleobiochemistry.”; Abelson, “Some Aspects of Paleobiochemistry”; also see Gordon J. Erdman, Everett M. Marlett, and William E. Hanson, “Survival of Amino Acids in Marine ,” Science 23 (1956): 1026. 46 Erdman, “Survival of Amino Acids in Marine Sediments”; Ho, “ composition of and tooth proteins in late Pleistocene ”; De Jong, “Preservation of antigenic properties of macromolecules over 70 Million Years Old”; Weiner, “Soluble Protein of the Organic Matrix of Mollusk Shells”; Westbroek, “Fossil Macromolecules from Cephalopod Shells”; Armstrong, “Fossil Proteins in Vertebrate Calcified Tissues.” 17

sorcerer’s clairvoyance could have anticipated the magician’s tricks of molecular biology and its boundless contributions to elucidating the history of evolution.”47 In 1980, Stephen Weiner, structural biologist of the Weizmann Institute of Science, published an article titled “Molecular evolution from the fossil record – a dream or reality?” Following Abelson’s footsteps, Weiner and fellow colleagues produced several successful studies on amino acids from fossil shells. Although amino acids are rather easily recovered, the reconstruction of entire proteins from amino acid sequences is a much more difficult task. Weiner eloquently explained: “An analogy illustrating the difficulty, is the reconstruction of words from a printed page which has been thoroughly shredded. The problem at hand is perhaps even more complex.”48 Despite the formidable task ahead, Weiner perceived the recent advancements of molecular biology as a sign of hope for the future of molecular paleontological research. He concluded his article on a more positive note, exclaiming, “Our dream is not quite as farfetched as it seemed just a few years ago.”49 Weiner’s article was published in the journal of Paleobiology; a relatively young journal that had just started publication five years previously. The development of this journal and the placement of Weiner’s molecular paleontology article within it were perhaps indicative of another simultaneous development in biology and paleontology.

The Paleobiological Revolution

In preparing their book, The Paleobiological Revolution, Sepkoski and Ruse sought to capture some of the most critical moments in the new field of paleobiology through the memoirs of some of the field’s most influential characters. In general, the paleobiological revolution can be viewed as a movement from strictly descriptive, taxonomic questions to a more quantitative and theoretical approach that focused more on questions of an evolutionary nature. In defining paleobiology, Sepkoski noted the difficulty in finding “one single definition that would be agreed upon by all paleobiologists.” Instead, Sepkoski described the nature of paleobiological research, broadly speaking, as research directed towards “biological questions about fossils and the fossil record” with a “focus on the evolution, adaptation, , function, and behavior of extinct

47 Walter M. Fitch and Francisco Ayala, eds. Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson (Washington, D. C.: National Academy Press, 1995), vi. 48 S. Weiner, “Molecular Evolution from the Fossil Record – A Dream or a Reality?” Paleobiology 6 (1980): 4. 49 Ibid, 5. 18 organisms.”50 Encouraged by Simpson’s earlier influence towards an evolutionary synthesis, paleontology began to reevaluate itself as a discipline and a profession. In his article, “The Emergence of Paleobiology,” Sepkoski noted that “During the 1950s and 1960s a major transformation was quietly taking place in paleontological approaches to evolutionary theory and the fossil record”51 Paleontologists first began to reevaluate the status of their discipline and its relation to geology and biology. Secondly, they began to associate their research more directly with the modern evolutionary synthesis, and lastly, paleontologists started to apply quantitative methods, such as statistical analysis, to their research.52 Early campaigners for the paleobiological approach marshaled their efforts towards asking and answering questions of an evolutionary nature (like extinction) by applying new quantitative methods to the fossil record and urging fellow paleontologists to do the same. With the diligence and direction of such men, Richard Rambach, paleontologist of the , wrote, “The transition from traditional paleontology to modern paleobiology was well underway by the early 1960s.” The palebiological approach, interested in quantifiable studies of fossils, was dedicated to raising the next generation of paleobiologists. The most notable among them were and Stephen Jay Gould and their proposal of in 1972.53 Eldredge and Gould’s groundbreaking concept of punctuated equilibrium suggested that the , as inferred from the fossil record, was better understood by “rapid and episodic events of speciation” as opposed to the Darwinian view of a “slow and steady transformation of an entire population.”54 The argument was so significant because it not only questioned the long standing assumption of , but because it sought to overthrow this particular view of evolutionary processes by reinterpreting the fossil record and using paleontological evidence in favor of a different theoretical, and perhaps more accurate, understanding of how evolution occurs. Philosopher Derek Turner noted that Eldredge and

50 David Sepkoski, “The Emergence of Paleobiology,” in The Paleobiological Revolution: Essays on the Growth of Modern Paleontology (Chicago: The University of Chicago Press, 2009), 15-16. 51 Sepkoski, “The Emergence of Paleobiology,” in The Paleobiological Revolution, 26. 52 Ibid., 26-27. 53 Richard Rambach, “From Empirical to Evolutionary Paleobiology: a Personal Journey,” in The Paleobiological Revolution: Essays on the Growth of Modern Paleontology (Chicago: The University of Chicago Press, 2009), 400-401; Sepkoski, “The Emergence of Paleobiology,” in The Paleobiological Revolution, 29. 54 Stephen Jay Gould and Niles Eldredge, “Punctuated Equilibria: An Alternative to Phyletic Gradualism,” in Models of Paleobiology, ed. Thomas J. M. Schopf (San Francisco: Freeman, Coopers & Company, 1972), 84. 19

Gould’s paper “sparked a debate about what, if anything paleontology has to add to evolutionary theory.”55 Eldredge and Gould’s punctuated equilibrium represented a bold effort to bring theoretical paleontology to the high table and into . Three years later, in 1975, the growing discipline of paleobiology established their first scholarly journal. Both events stood as landmark achievements in paleontology’s history and signified a serious transformation of paleontology as a discipline and its role in evolutionary theory.

Conclusion

If we recall Hull’s point regarding science as a process, “If one is interested in science as a process, conceptual systems cannot be viewed as seamless wholes,” then two overarching themes should become apparent from our review of the history of biology. First, we see science as a process dependent on both discovery and development over time. Second, we see that discovery and development in science, and specifically in the life sciences, is often an interdisciplinary effort. For example, recent strides in paleobiology were first and foremost made possible by Darwinian evolution yet also relied on future advances in the modern evolutionary synthesis. These two themes, science as a process and the interdisciplinary nature of science, will become increasingly obvious as we continue into our study of the history and significance of aDNA research. Knowledge of the history behind these landmark achievements in biology allows us to have an enriched understanding of future developments, particularly in instances where the full significance of a new science has yet to be realized. Understanding the conception of aDNA research and discovering its consequences, particularly as an extension of the modern evolutionary synthesis, is especially dependent on an appreciation of the this background of information. Before turning our attention to the early history of aDNA research and our analysis of its significance for the science of paleontology, we should first focus more specifically on the history of paleontology in to understand its early role in evolutionary theory and its development in practice and theory over the past century or so.

55 Derek Turner, Paleontology: A Philosophical Introduction (Cambridge: Cambridge University Press, 2011), 16. 20

CHAPTER TWO PALEONTOLOGY FROM DARWIN TO DNA

Introduction

In Fossils and the History of Life, Simpson defined paleontology as the “the science of discovering and studying the fossil record and from it deciphering the history of life.”1 Early on paleontology was a major source of evidence for evolutionary theory. Discovery after discovery offered more evidence of past life forms, extinct and living, and the development of practices such as morphology and helped to decipher their evolutionary relationships and find their place among the great . The rise experimental science in the early 1900s posed a threat to paleontologists and the traditional way of studying evolution. Analytical methods and quantifiable evidence was preferred to more historical and inference-based sciences like paleontology. Though paleontology continued to advance as a scientific field in its own right, it did so on the outskirts of the major developments in experimental and evolutionary biology in the first half of the twentieth century. Paleontology, still a discovery driven field, found itself at a crossroads with the growing popularity of the modern evolutionary synthesis and the advent of molecular biology. This chapter is a review of the history of paleontology from the 1800s and onwards into the early twentieth century with an emphasis on , and specifically dinosaur paleontology. This review will discuss paleontology’s development as a discipline and a profession in regards to its early role in evolutionary theory, its relation to experimental biology, and the rise of the field paleontologist – as most popularized through dinosaur fossil discoveries – with specific attention to the growth of field methods and techniques.

Natural History

Natural history, the scientific and systematic study of plants and , yields a rich and extensive past. fascination with the earth’s diversity of organisms dates back to antiquity and is evidenced across the world. Similarly, the study of fossils, the remains of past

1 George Gaylord Simpson, Fossils and the History of Life (New York: Scientific American Books, 1983), 4. 21

plant and animal life forms, has a long history both far reaching in time and space. Over the centuries, the study of natural history slowly evolved to incorporate the study of fossils, and by the early 1900s, fossils had become to be understood as a record and reflection of the history of life. At the same time, natural history began to emerge from its adolescence as the field grew into a mature science. For this reason, our story begins in Europe, where natural history first and most fully realized itself as a professional, scientific discipline. Before its professionalization however, and despite such widespread interest, natural history primarily remained an activity of leisure. Most amateur naturalists were either self-trained through experience, or they found some sort of informal training in medical school where they received an education in anatomy, physiology, and botany. Two natuarlists in particular, and Georges Louis Leclerc, comte de Buffon, were largely responsible for both the foundation and development of natural history as it stands in its modern form today.2 Carl Linnaeus (1707-1778), a Swedish gentleman, was formally trained in medicine, but his passion for natural history soon eclipsed his medical profession and turned to the naming and classification of plants and animals. Faced with an ill-fitting and rather haphazard procedure for classifying organisms, Linnaeus sought to clarify the existing system. In 1735 Linnaeus published his famous , in which he introduced the first standardized system of classification for plants, animals, and also minerals. That following year, Linnaeus presented his principles for classification; binomial nomenclature. This system assigned two Latin or Greek names to each natural object, the first indicative of the and the second, of the species within the genus. For Linnaeus, and many other budding naturalists of the time, the true value in classification was in discovering the order of nature, or the order of God’s creation. Linnaeus’ system of classification was chiefly important because it was simple and accessible, transforming the classification of plants and animals, for the first time, into a standardized enterprise that was easily shared among naturalists across the board. South of Sweden and sharing a similar curiosity for the order of things, Linnaeus’ contemporary Georges Louis Leclerc, comte de Buffon (1707-1788) first discovered his love for natural history through a political assignment as director of King Louis XV’s Royal Garden, a

2 Paul Farber, Finding Order in Nature: The Naturalist Tradition from Linnaeus to E. O. Wilson (Baltimore: The Johns Hopkins University Press, 2000); Martin Rudwick, The Meaning of Fossils: Episodes in the History of Palaeontology (London: MacDonald & Company, 1972); Simpson, Life of the Past.

22

placement which served him well throughout the remainder of his life. Buffon, given the task of sorting the royal natural history collection, fashioned a much more ambitious project; his goal was to deliver the first complete record of all natural history. In 1749 Buffon published the first of his thirty-six volume . The impact of the entirety of his work, a project not yet attempted by anyone before, had far reaching implications both at home and also across the Atlantic in . Buffon’s work was not only novel in its attempt to create a comprehensive study of all creatures, but conceptually, Buffon broke from the traditional Christian view of nature in favor of a more “nonreligious interpretation” and “new vision of the living world.”3 In later years, Buffon expanded the scope of study to include fossils which, despite their long history of discovery and speculation, were in fact not well understood. Yet Buffon’s conjectures about fossil forms only went so far. The mystery of fossils, and more importantly their implications for the history of life, was a project bequeathed to the next generation of rising naturalists. Embracing the study of fossils, another French naturalist, Georges Cuvier (1769 -1832) was the first to practice comparative anatomy and as a champion of this new approach, his methods transformed the study of natural history. Cuvier desired more than just the classification of the plants and animals of the world, but rather he was much more interested to discover their form and function and more broadly, their relationship to one another. In 1796, Cuvier wrote two papers that revolutionized the way naturalists would study and interpret fossils and the earth’s history. His first paper, a study of the fossile from Paraguay, , suggested that the “huge fossil beast” was actually an extinct species distinct from any living animal today. Cuvier’s second paper, a comparison of African and Indian skeletons, fossils from Siberia and Northern Europe, and the American from Ohio, proposed a similar conclusion. While Cuvier’s first paper was a remarkable piece, the second paper really validated his argument and secured his conclusion for the reality of extinction.4 Outside of theory, Cuvier also used comparative anatomy in the reconstruction of fossil animals from whole or even partial skeletons. These wondrous fossil creatures, unprecedented to man’s knowledge, quickly consumed the public’s attention. Cuvier’s reconstructed creatures popularized the growing science of paleontology in the public’s eye, but more significantly, his

3 Farber, Finding Order in Nature, 18; Rudwick, The Meaning of Fossils, 93-95. 4 Rudwick, The Meaning of Fossils, 101. 23

comparative anatomy demonstrated time and time again the power behind this methodology and paleontology itself.5 Leaving France, but following the Cuverian tradition, English naturalist Sir (1804-1882) assumed his role as the foremost comparative anatomist of the nineteenth century. As a notable comparative anatomist, Owen also stood as one of the world’s first and most brilliant paleontologists. By the mid-1800s, natural history had diverged into more specialized areas of study, such as zoology, botany, and geology.6 Paleontology, often considered geology’s twin, soon followed suit. In fact, Charles Lyell, one of the most influential figures in the early , coined the term paleontology in 1838. While Cuvier, pioneer of paleontology, never lived to see his efforts materialize into a distinct field of its own right, his successor Owen helped to unify the efforts of Linnaeus, Buffon, and Cuvier, among others, into the formal discipline of paleontology that we have today. Owen, dedicated to the study of fossils, is perhaps most well remembered for his coinage of the term Dinosauria (“fearfully great lizard”) in 1842. Although speculative, the first known discovery of a dinosaur fossil was in North America. Found in the state of New Jersey in 1787, the fossil was brought to the Academy of Natural Sciences in Philadelphia which was at that time the New World’s center for intellectual and cultural life. However, the fossil’s identity perplexed society members and remained a mystery. Crossing back over the Atlantic, Mary Ann Mantell, wife of the physician and amateur fossil hunter , stumbled across a strange - like object in a forested region of . The fossil, first found in 1822, was later interpreted by Mantell as a new animal which he named “.” At the same time, Reverend reported on the finding of a different, but similarly large -like animal, which he called “.” As Simpson stated, “Thereafter the rate of discovery accelerated, reaching an early high point in the late 1870s.”7 Over these years, paleontologist were becoming more interested in uncovering the true nature and existence of these unusual fossils. A notable theorizer, Owen was particularly curious about the world’s many disparate creatures, alive and dead, and in 1848 he published his classic piece titled Archetype and Homologies of the Vertebrate Skeleton.8 In this work, Owen presented his theory of “archetype”

5 Farber, Finding Order in Nature, 39. 6 Farber, Finding Order in Nature, 33. 7 Simpson, Fossils and the History of Life, 28-29. 8 Bowler, Evolution, 131-132. 24

and concepts of analogous and homologous structures. According to Owen, the archetype was the basic blue print for which all were modeled after. He believed that all organisms, when exposed of their varying, external traits, shared the same, rudimentary . This idealized archetype also inspired Owen’s relating ideas of analogy and . Owen noticed that some organisms have dissimilar structures serving the same function; these he termed analogous structures. While the bat wing and wing may look alike and both fulfill the function of flight, their wings are actually fundamentally different in structure. Conversely, homologous structures were similar in structure but dissimilar in function. The classic example of the bat wing and the human arm illustrates similar structure but different use. Owen’s work on the archetype supplied natural history with a frame of reference from which to study and understand life’s creatures. However, his framework was soon surpassed and reinterpreted under a new theory of life. Charles Darwin (1809-1882), an English gentleman, naturalist, and good friend of Owen, soon emerged as a prominent figure in natural history. In the twenty years of the development of his theory of evolution, as presented in the Origin (1859), Darwin drew on the research and conclusions of fellow naturalists trained in geology, botany, zoology, and paleontology. Owen’s own paleontological work and idea on analogous and homologous structures proved particularly useful. For his argument, Darwin took Owen’s evidence and interpreted it under a different framework, namely his theory of evolution by natural selection. Under this view, Darwin inferred similar structures among organisms as evidence of a common ancestor from which all of today’s forms have evolved. Although Owen disliked much of Darwin’s argument and its conclusions, he admitted that his own work fit Darwin’s purposes rather well. In the end, Darwin’s theory of evolution eclipsed Owen’s interpretation of the natural world.9 The profound success of Darwin’s theory of evolution, then and even more so now, rested in its unificatory power to bridge together the disparate areas of classification, paleontology, biogeography, behavior, embryology, systematics, and morphology, among others.10

9 Martin Rudwick, The Meaning of Fossils: Episodes in the History of Palaeontology (London: MacDonald & Company, 1972), 207. 10 Ruse, The Darwinian Revolution. 25

Fossils and Evolution

The growing science of paleontology as realized through comparative anatomy studies of fossil and living specimens became instrumental in revealing the history of life. Fossils were of special importance because they provided our only direct evidence of the past. As our understanding of fossils matured, the fossil record became an increasingly valuable tool for discovering our past and making sense of the history of life. The fossil record showed us evidence of many creatures once living but now extinct and furthermore, that the earth and life itself had been changing and for a much longer period of time than previously imagined. Reflecting on paleontology’s early significance in the nineteenth century, Rudwick explained:

It [paleontology] had shown that that history had been of almost inconceivable length; that life on Earth had passed through many strange phases, becoming progressively more complex, more varied, and more like the living world present; that Man, although the most recent newcomer to the scene, could be interpreted as the supreme and crowning feature of entire history; and above all, that this history was essentially intelligible and meaningful.11

Paleontology, along with geology, played a major role in naturalists’ developing concept of an ancient world. The advent of Darwin’s theory of evolution by natural selection in 1859 provided the discipline with an over-arching system from which to better understand fossil data and the history of life. Evolutionary theory gave meaning to the fossil record and, in turn, the paleontological record offered some of the greatest evidence in favor of evolution. Darwinian evolution suggested a new world view for naturalists. His theory shed light on and gave explanation to many aspects of geology and the fossil record. For example, the process of extinction and the existence of fossils could be explained as a consequence of evolution.12 Darwin’s theory provided paleontology with a model for understanding both species change and species lineage. However, the fossil record’s inherent imperfections also served paleontology a major disservice.

11 Rudwick, The Meaning of Fossils, 265. 12 Ronald Rainger, An Agenda for Antiquity: & Vertebrate Paleontology at the American Museum of Natural History, 1890-1935 (Tuscaloosa: The University of Alabama Press, 199), 9. 26

In chapter nine of the Origin, “On the Imperfections of the Geological Record,” Darwin addressed one of the most pressing concerns of evolutionary theory, the problem of transitional forms. Quite candidly, Darwin conceded that “the distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty.”13 Simply put, if Darwin’s argument that more primitive species have evolved over extended periods of time, manifesting themselves in the new and varied forms seen today, then we should expect to find the intermediate forms – the transitional links – in the fossil record. Unfortunately, we are not as fortunate and Darwin admitted this. He explained, “Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.”14 Darwin recognized three causes for the “poorness of our paleontological collections.” The first explanation denoted our lack in quantity and quality of available fossil specimens. Although the last 150 years of fossil hunting have substantially improved the fossil record, during Darwin’s time, the paleontological evidence was sparse. Darwin attributed the second explanation for the absence of forms to the rarity of their preservation. He understood fossil preservation to be a unique occurrence requiring nearly ideal conditions. This remains just as much of an issue for paleontology now as it did in Darwin’s day. However, the third and perhaps most important explanation, at least according to Darwin, were the extensive intervals of time separating one geological formation from another. Darwin explained that upon viewing the layers of rock formation, resting very close on top of one another, it is hard to avoid assuming that they are also close in time. Rather, if we take a more serious look, we will see that the rock layers are actually separated by widespread periods of time. For evolution to occur as a slow and gradual process, Darwin needed to show that the world was millions, if not billions of years old. After all, time is the key ingredient for change.15 Despite the jarring incompleteness of the paleontological evidence, Darwin argued that the difficulties did not warrant immediate refutation of his theory. All things considered, Darwin aptly described the fossil record through his famous metaphor of a book, explaining, “I look at the natural geological record, as a history imperfectly

13 Darwin, On the Origin of Species, 627. 14 Ibid., 628. 15 Ibid., 632-634. 27

kept, and written in a changing dialect; of this history we possess the last volume alone, relating only to two or three countries.” Furthermore, “Of this volume, only here and there a short chapter has been preserved; and of each page, only here and there a few lines.”16 Darwin argued that the fossil record was clearly an incomplete one, and for this reason, we should not expect more from it than could be offered. Transitional forms are few because fossil preservation is rare, but just because the fossils are absent does not necessarily entail that they never existed at all. While these gaps may eventually be filled by future discoveries, we should not expect a flawless record of life. A patchy history of life, Darwin understood that paleontology was limited in information and explanations, but the evidence for evolution based on the record we do have should not be underestimated. Thus, he concluded, “On this view, the difficulties above discussed are greatly diminished, or even disappear.”17 Not everyone was as confident, including Darwin himself, to dismiss the fossil record’s imperfections altogether. Sepkoski and Ruse wrote, “Despite the fact that paleontological evidence played a vital role in demonstrating evolutionary succession, in what appears in retrospect to be a profound irony, even as Darwin elevated the significance of the evidentiary contributions of paleontologists, he also had a major hand in condemning paleontology to second- disciplinary status.” Sepkoski and Ruse succinctly captured this paradox, explaining that “Darwin’s dilemma, however, was that he both needed paleontology and was embarrassed by it.”18 Because of the imperfect nature of the fossil record, paleontology as a field was severely limited by the sorts of questions one could ask and, more importantly, answer. Rudwick claimed that “once our attention turned to the means by which new kinds of life had come into existence, paleontology proved unable to supply the insights that thinking men demanded.”19 The fossil record demonstrated, on some level, that evolution in fact did occur. But following the Origin’s publication, and upon the rapid and widespread acceptance of evolution, the questions of “why” and “how” evolution occurs became of primary interest. Thus, paleontology’s waning influence in the latter half of the nineteenth century was in part due to its inability to address the more exciting questions that had begun to be asked.

16 Ibid., 647. 17 Ibid., 647. 18 David Sepkoski and Michael Ruse, “Introduction: Paleontology at the High Table,” in The Paleobiological Revolution: Essays on the Growth of Modern Paleontology, eds. David Sepkoski and Michael Ruse (Chicago: University of Chicago Press, 2009), 2. 19 Rudwick, The Meaning of Fossils, 265. 28

The Rise of Experimental Biology

Despite the change in emphasis to questions of how and why evolution occurred, some naturalists continued to focus their attention on reconstructing the history of life primarily through the disciplines of comparative anatomy, embryology, and morphology. Over the next several decades from 1860-1880, naturalists dedicated themselves to these pursuits. By the late nineteenth century the new science of morphology – the study of organism forms – soon became a central component of natural history and more specifically paleontological research. Morphologists were primarily interested in discovering a basic unity of type. They were also interested in searching for the common ancestor. Paleontological, anatomical, and embryological reconstructions were especially useful for discerning ancestry. Lastly, morphologists were interested in phylogenies, or evolutionary family trees. Here again fossils, comparative anatomy, and embryology proved essential in the reconstruction of the great tree of life.20 (1834-1919) and August Weismann (1834-1914), both German naturalists, became leading figures of the morphological tradition. As a converted Darwinian, Haeckel infused fossil evidence with both comparative anatomy and embryonic studies for constructing the evolutionary histories of organisms. He was also instrumental in popularizing the morphological approach.21 Weismann, who specialized in cytology, the study of cells, was another considerable influence in morphological research. Like Haeckel, Weismann was interested in how embryology could shed light on evolutionary history, but more importantly, he focused his research on heredity and made several sweeping contributions to the field. However, soon both Haeckel and Weismann took their research to the next level and began to theorize more broadly about morphology’s role in evolutionary processes. Many were skeptical and as Allen explained, “Yet, like Haeckel’s, Weismann’s theories went far beyond the available facts and as such ultimately came to be regarded by workers of the twentieth century as too morphological and too speculative.”22 Those opposed to seemingly unfounded theorizing were the rising generation of experimental biologists and their new approach to the study of life and evolution.

20 Allen, Life Science in the Twentieth Century, 2-4. 21 Bowler, Evolution, 201; Allen, Life Science in the Twentieth Century, 6-8. 22 Allen, Life Science in the Twentieth Century, 8. 29

Since the 1800s, experimental methodologies were prevalent among the physical sciences. Yet it was not until nearly the turn of the twentieth century that experimental methods found their way into the life sciences.23 The rise of physiology – the study of organism function and their physical and chemical processes – embraced the new experimentalism and developed both rigorous and extensive methods for understanding processes of life. Historian Paul Farber explained, “Impressed by the rise of experimental physiology and its spread throughout the scientific world from Baltimore to Kiev, naturalists sought to import the experimental method into areas of natural history where certain questions appeared intractable or where new questions could be profitably asked.”24 Many young naturalists – to become the new generation of biologists – were growing discontent with more traditional subjects of and approaches to natural history and the study of evolution. These biologists sensed more important areas for research such as embryology and heredity and also more productive methodologies such as experimentation. The rising generation of experimental biologists’ skepticism of the morphological tradition stemmed from this approach’s inability to test many of its hypotheses and its reliance on indirect evidence instead. Morphology was too speculative to provide satisfactory answers to more pressing evolutionary questions.25 The imperfection of the fossil record remained an issue for many experimentalists. This growing attitude among a number of biologists led to the emergence of new research areas such as embryology, heredity, and . Although such fields as embryology had existed, these research areas began to incorporate new techniques like experimentation and new evidence in the form of quantitative data. Farber echoed this point and more:

The physiological tradition has significance for natural history in ways more important than just an initial hostility to Darwin’s theory. For it represented a competing tradition in the life sciences that not only held its perspective to be more valuable one in shedding light on the nature of life but also claimed to deserve a larger share of the institutional

23 Farber, Finding Order in Nature, 73. 24 Ibid., 81. 25 Allen, Life Sciences in the Twentieth Century, 9. 30

resources because of its superior intellectual claims and its potential practice value for medicine and agriculture. 26

Although, natural history, and paleontology specifically, continued traditional and historical research on evolution and grew in public popularity, support came mainly from museums. Farber wrote, “As natural history achieved a popular triumph it experienced a scholarly decline. Universities and research institutes increasingly abandoned traditional activities of naming and classifying in favor of investigating issues in heredity and development using experimental methods.”27 As biologists turned their attention to new questions and new methods, it seemed that paleontologists and their more traditional, historical approaches to studying evolution had been left in the dust and rubble with their fossils. Yet paleontology, committed to its tradition in morphology and taxonomy, probed forward despite its marginalization in favor of the rise of experimental biology. Perhaps, as Bowler argued, a portion of paleontology’s neglect in the history of evolutionary biology comes from the historian’s neglect. Bowler argued that even in the face of pressures to go experimental, the disciplines of evolutionary morphology, paleontology, and biogeography remained confident in their ability to explore and explain the course of evolution. Bowler urged that “the standard histories of the impact of Darwinism have been skewed by a concentration on the debate over mechanisms at the expense of the debates that arose over how to interpret the course of life’s evolution.”28 While neglected by the new movement towards experimental science, paleontology continued its historical approach in recreating the past through an influx of fossil discoveries and the rise of the field paleontologist especially in the American West.

Paleontology in America

While the fossil hunt was very much a global enterprise, and collecting techniques were certainly fashioned and practiced in Europe among other places, the accounts left behind by some of the earliest and most prominent American paleontologists provide the most telling record of early, traditional field techniques. Furthermore, many American paleontologists –

26 Farber, Finding Order in Nature, 79. 27 Ibid., 98. 28 Peter J. Bowler, Life’s Splendid Drama: Evolutionary Biology and the Reconstruction of Life’s Ancestry, 1860- 1940 (Chicago: The University of Chicago Press, 1996), 2. 31 especially in the late eighteenth and early nineteenth centuries – were vertebrate paleontologists; many who were interested in some of the more charismatic vertebrate creatures like the . Although paleontology overall, as a budding discipline, encompassed other areas of study like invertebrate and plant paleontology, some of the most informative histories regarding the practice and perfection of field techniques are exhibited through accounts of vertebrate paleontology, and specifically dinosaur paleontology in the American West. Historian Robert Kohler noted, “In the United States alone dozens or scores of collecting expeditions were dispatched each year to the far corners for the world between 1880 and 1930; hundreds in all, or thousands – perhaps as many as in the previous two hundred years of scientific expeditioning.”29 The American West was an unchartered territory for exploration and harbored treasure beds of fossils. No place other than the American frontier was the fossil hunt more rigorous and rewarding. Henry Fairfield Osborn (1857-1935), Curator of the Department of Vertebrate Paleontology at the American Museum of Natural History (AMNH) in New York City, was one of the most eminent American paleontologists of the twentieth century. In the introduction to Charles Sternberg’s Life of a Fossil Hunter, one of the first memoirs of a paleontologist’s life and work in the field, Osborn eloquently captured the uniqueness of the American paleontological tradition: “The richness of the great American fossil fields, which extend over the vast arid and semi-arid area of the West, scattered over both the great plains region and the great mountain region, has resulted in the creation of a distinctively American profession: that of fossil hunting.”30 American vertebrate paleontology specifically became a vital part of paleontology’s larger history and development as a profession, complete in methodology and best practices.31 Three men in particular, , , and , were primarily responsible for the field’s foundation through their scholarship and sponsorship of paleontological endeavors. , paleontologist, friend, and colleague of Osborn, wrote, “At that time and for some years later, the science [paleontology] was almost exclusively in the hands of three uncommonly able and distinguished

29 Robert Kohler, All Creatures: Naturalists, Collectors, and Biodiversity, 1850-1950 (Princeton: Princeton University Press, 2006), 8. 30 Henry Fairfield Osborn, introduction to Life of the Fossil Hunter, by Charles Sternberg (San Diego: Jensen Printing Company, 1931), xi-xii. 31 While invertebrate paleontology is also important to the history of paleontology and to studies in molecular paleontology, I have chosen to focus on specifically on vertebrate paleontology because its history provides the most detailed documentation on early paleontological practices. 32

men. Dr. Joseph Leidy and Professor E. D. Cope, of Philadelphia, and Professor O. C. Marsh, of Yale.”32 American vertebrate paleontology as a scientific profession truly began with the life and career of Joseph Leidy (1823-1891). Leidy, born and raised in Philadelphia, is considered to be the father of American paleontology.33 As in Europe, most American naturalists and budding paleontologists were initially trained in medicine, seeing that it was the most common means of graduate study at the time, before turning their full attention to the study of fossils. Schooled as a physician, Leidy practiced medicine for two years before giving up his medical career for studies in paleontology which would prove to be not only his greatest life’s work, but also some of the greatest in the history of paleontology.34 However, Leidy’s career in paleontology was more akin to the lifestyle of the arm-chair naturalist. Leidy never ventured out into the field mainly because he had no reason to; hundreds upon hundreds of fossils were shipped directly to him for comparison, identification, description, and classification. While Leidy made invaluable contributions to paleontology, the tradition of the field paleontologist was really best exemplified through the work of Leidy’s younger, and perhaps more ambitious contemporaries, Marsh and Cope. In 1860, a year after the Origin’s publication, Othniel Charles Marsh (1831-1899) graduated from Yale College and entered the world as an ardent proponent of Darwin’s theory. He pursued degrees in paleontology and anatomy overseas in Germany and upon his return six years later, was appointed Professor of Vertebrate Paleontology at Yale. During his career as an eminent American paleontologist, Marsh’s team recovered an astounding collection of fossils, high in quantity and also quality. With hundreds of publications, he was a prolific researcher and writer, well known in both America and Europe.35 Most notably, he was responsible for establishing the adventure and successes of the field paleontologist. Marsh’s most curious and memorable discoveries are attributed to the Yale expeditions of 1870-1873. Marsh, like Leidy, was fascinated with the variety and abundance of fossils of the American West and in 1868 he was extended an invitation to travel to the Western United States

32 William Berryman Scott, Some Memories of a Palaeontologist (New York: Arno Press, 1980), 57. 33 Leonard Warren, Joseph Leidy: the last man who knew everything (New Haven: Yale University Press, 1998); Henry Fairfield Osborn, Impressions of great naturalists; Darwin, Wallace, Huxley, Leidy, Cope, Balfour, Roosevelt, and others (New York: Scribner, 1928). 34 Warren, Joseph Leidy: the last man who knew everything, xv, 47, 53. 35 and Clara LeVene, O.C. Marsh: Pioneer of Paleontology (New Haven: Yale University Press, 1940). 33

along the Missouri River in Omaha, Nebraska.36 During this first expedition Marsh discovered fossils which would prove “the first in a long series of fossil horse remains that was to form one of the chief jewels in Marsh’s scientific work.”37 The fossil horse remains also proved some of the strongest evidence for evolutionary theory. Enthralled with the experience, Marsh immediately planned his next expeditions. His subsequent trips out West, known as the Yale expeditions, yielded an abundance of fossil horses, fossil turtles and , numerous fossil and , the interesting new , Palaotherium (Titanotherium) prouti, and most exciting of all a new dinosaur named by Marsh, Pterodactylus oweni. 38 The mass yield of fossils was certainly not due to Marsh’s strategic planning, efforts, and personal financial advantage alone, but his team of Yale students, researchers, and government/university patronage made it all possible.39 These expeditions were responsible for an impressive collection of fossils, but his dinosaur remains stood as the most fascinating objects from his travels and the most popular items in his museum. The successful results attracted the attention of others and the need for standardized collecting practices. Edward Drinker Cope (1840-1897), born in Philadelphia and to a family of great fortune, quickly came to the forefront of American vertebrate paleontology and the greater as a highly influential paleontologist and prominent member of both the American Philosophical Society and the Academy of Natural Sciences.40 Although of little formal scientific training but much experience, Cope researched at the Smithsonian Institution and later studied under the prestigious direction of Leidy.41 By the late 1860s, Cope had written an astonishing thirty-seven scientific papers within five years.42 Cope’s achievements thus far foreshadowed a rigorous and prolific scientific career particularly as a field paleontologist. Cope spent some of his early career surveying the fossil beds of eastern North America, particularly the era of New Jersey, but he was eager to join the fossil hunt in the

36 Ibid., 96. 37 Ibid., 99. 38 Ibid., 106-107, 120. 39 Ibid., 137-138. 40 Henry Fairfield Osborn, “Edward Drinker Cope” in Impressions of Great Naturalists: Darwin, Wallace, Huxley, Leidy, Cope, Balfour, Roosevelt, and others (New York: Scribner, 1928), 169-171; Url Lanham, The Bone Hunters (New York: Columbia University Press, 1973), 60. 41 Rainger, An Agenda for Antiquity, 11. 42 Mark Jaffe, The Gilded Dinosaur: the fossil war between E.D. Cope and O. C. March and the rise of American science (New York: Crown Publishers, 2000), 12. 34

West.43 In the meantime, Marsh and his team were discovering complete skeletons from the fossil beds of the American West. Such news prompted Cope to travel west in 1867 in search of greater, more complete fossil species and received further opportunities in 1871 when he was appointed principal paleontologist on the U.S. Geological trip to Yellowstone.44 During his expeditions, he “brought back remains of carnivorous dinosaurs, extinct sea serpents, and flying reptiles.”45 He was also extremely gifted in his interpretation and reconstruction of the fossil materials he and others recovered. Overall, Cope was one of the most impressive paleontologists in American history. His intelligence and financial state gave him great advantage. As Rainger claimed, “Because of his financial resources Cope and his collectors were able to obtain more fossils than Leidy had received.” Cope’s monetary advantage allowed him to hire one of the best collectors in the States, Charles Sternberg.46 As a result, Cope “identified 1,282 new species and genera of fossils” and his “private collection of fossils was much larger than the academy’s and included remains of flying reptiles, bizarre horned mammals, and huge sauropod dinosaurs…”47 His high productivity in the field and his analyses of fossils made him a leading field paleontologist. Both Marsh and Cope established and mastered the career of the field paleontologist. Their ambitious personalities and significant financial endowments allowed them to effectively organize and execute some of the earliest and most successful fossil digs in the States, if not the world. Historian Warren Leonard eloquently wrote:

As the nineteenth century drew to a close, the field of paleontology was prominently represented by Americans. Leidy had helped to provide the indispensable foundation, but it was Cope and Marsh who raised American paleontology to a position of international eminence with their discoveries of immense, fossilized dinosaurs and mammals, their

43 Howard, The Dawn Seekers: The First History of American Paleontology (New York: Harcourt Brace Jovanovich, 1975), 191. 44 Ronald Rainger, “The rise and decline of a science: vertebrate paleontology at Philadelphia's Academy of Natural Sciences, 1820-1900,” Proceedings of the American Philosophical Society 136 (1992): 14; Lanham, The Bone Hunters, 65-66, 95--98; Howard, The Dawn Seekers, 214; Rainger, An Agenda for Antiquity, 12. 45 Rainger, An Agenda for Antiquity, 12. 46 Lanham, The Bone Hunters, 165. 47 Rainger, “The Rise and Decline of a Science,” 14. 35

description of large numbers of new genera and species, and the working out of their affinities and phylogenies.”48

Marsh’s and Cope’s growing prestige in paleontology attracted a cohort of budding fossil collectors and future paleontologists. The American West provided the landscape for the development of the field paleontologist, a now iconic image in paleontology. Marsh’s and Cope’s efforts were instrumental in building opportunities for potential field paleontologists to mature. This next generation of field paleontologists would be primarily responsible for the creation of early field techniques and carrying these practices into the next century.

Paleontology in the Field

The history of paleontology is colored with many memorable characters, but Charles Sternberg, Barnum Brown, Roland T. Bird, and Roy Chapman Andrews stand among the most influential. As several of the most notable fossil hunters, these men are exemplars of the field paleontological tradition. Their expeditions and memoirs capture both the adventure and hardship of the field paleontologist and also the establishment of many standard field techniques still used today. Their records demonstrate the professionalization of the field and more notably, the maturation of a specific set of practices in paleontological research; practices which will serve to compare and contrast to the later methodologies such as experimentation and quantitative analyses that come to be a part of paleontology in the latter half of the twentieth century. Charles Sternberg (1850-1943), enamored with natural history from the start, was primarily a self-trained fossil collector but undoubtedly one of the best in paleontology’s history. After a brief time at the university, Sternberg, passionate for field paleontology, left school and headed into the Kansas field sites on his first official expedition in 1876, under the support of the famous Cope.49 Sternberg worked the field under Cope’s provision for four years “full of countless hardships and splendid results.”50 The life of the fossil hunter was both rewarding but rough. Every day in the field was spent patiently prospecting for not only fossils but water for

48 Warren, Joseph Leidy: the last man who knew everything, 190. 49 Charles Sternberg, Life of a Fossil Hunter (San Diego: Jensen Printing Press, 1931), 19-20, 30, 32; Lanham, The Bone Hunters, 165. 50 Sternberg, Life of the Fossil Hunter, 34. 36

survival. It was a good day if you came across both. The fossil hunt, driven by curiosity and passion, also required endurance and patience. As Sternberg recalled, some days the search over “barren land” and “miles and miles of blistering chalk” yielded “nothing to show for our trouble.”51 However, when a fossil find did occur, it was celebrated with much enthusiasm, even in spite of the intensive labor ahead for its safe recovery. The fossil find was followed by long, hard “work in the hot sun” in which “[e]very blow of the pick loosens a cloud of dust…carried by the wind into your eyes.” The day is spent “lying there on the blistering chalk in the burning sun, and working carefully and patiently with brush and awl.” After hours, and sometimes days of work, when the fossil was sufficiently exposed, the bone and encompassing is isolated by digging a ditch around the specimen. After the bone was traced, a ditch was dug around the fossil and immediate surrounding sediment. The isolated fossil, situated on a pedestal of earth, was then cut from the ground by “repeated blows of the pick” and “securely wrapped and strengthened with plaster or with burlap bandages that have been dipped in plaster.” The plaster jacket protected the fossil during transportation and sometimes, when working with larger specimens, “boards are put length-wise to assist in strengthening the material, so that it will bear transportation.”52 Despite the hardships, the toil was well worth the reward. The three decades Sternberg worked in the fossil fields yielded multiple, marvelous discoveries. His first expedition to the badlands in 1876, accompanied by Cope himself, was one of the most satisfying with the “stupendous cliffs and ranges” that inspired a sense of “awe at the power here displayed.”53 It was on this expedition that Sternberg, Cope, and the rest of the crew discovered a remarkable number of fossil specimens ranging from , turtles, , and sharks54 to some of the earliest finds of the famous saurian or “long-necked” dinosaurs and the first discoveries of the ceratopsian or great horned dinosaurs.55 Sternberg’s adventures continued well beyond his time with the Cope expeditions. An avid fossil collector, Sternberg sought the beloved in numerous localities over several expeditions ranging from Kansas and the badlands, to the Oregon and Texan frontiers. Sternberg’s life is most assuredly the embodiment of the true and rustic field naturalist and his legacy far exceeds his prolific discovery of fossil

51 Ibid., 46. 52 Ibid., 41-42. 53 Ibid., 62. 54 Lanham, The Bone Hunters, 164. 55 Sternberg, Life of the Fossil Hunter, 78, 88. 37

plants and animals. Inspired by prominent paleontologists Marsh and Cope, and also by his innate love for natural history, Sternberg became a notable fossil collector in his own right. Osborn, first and foremost a biologist but also a skilled paleontologist, was perhaps one of the most successful administrators and promoters of paleontology in the early twentieth century. Like Sternberg, Osborn fell under Cope’s influence. But whereas Sternberg was a free- lance fossil collector, Osborn received a more formal training in paleontology and evolutionary biology during his early studies at Princeton. Following graduation in 1877, Osborn seized a spot on a field expedition out west to Wyoming where he first met Cope, who proved a significant mentor for the budding scientist. As a biologist and paleontologist who specialized in comparative anatomy and morphology, Osborn later secured a position at both Columbia University and the AMNH as curator of paleontology.56 As a curator of the museum, Osborn was a serious advocate for paleontological research and its practical application to evolution. By the mid-1880s, Osborn had struck a close relationship with both Cope and colleague William Berryman Scott. Like Cope, Osborn and Scott were interested in evolutionary questions in regards to the fossil record. Rainger explained, “While each provided morphological and taxonomic information on the extinct animals they examined, Osborn and Scott concentrated on the study of evolutionary questions pertaining to fossil vertebrates.”57 Paleontologists like Osborn, Scott, and Cope believed that the fossil record had something important to say about evolution. Osborn, studying closely with Cope, adopted many of his ideas on evolution and became an active supporter of vertebrate paleontology and the contributions the field could make to the study of evolution. Much of Osborn’s theorizing revolved around human origins. As Osborn developed his theory of , “Asiatic origin of mammalian life,” he was equally determined to prove it through the fossil record.58. Roy Chapman Andrews (1884-1960), one of the most famed fossil hunters, became Osborn’s leading explorer on his “Central Asiatic Expeditions” and into the Gobi Desert and Mongolia. Under Osborn’s provision, Andrews organized and executed multiple expeditions in search of fossil evidence to support Osborn’s theory of human origins. Though the evidence never

56 Rainger, An Agenda for Antiquity. 57 Ibid., 37. 58 Rainger, An Agenda for Antiquity, 100; Osborn’s motive behind Chapman’s Asiatic expeditions was more than scientific. Osborn was interested in fossil evidence of human origins for verification of his own evolutionary and biogeographical theories, but he was also interested for religious reasons and the search for the “missing link.” Imperialism was also a driving force behind the expeditions. 38

materialized as Osborn hoped, Andrews helped sensationalize several astounding discoveries like the first ever dinosaur .59 Nonetheless, Osborn’s administrative skills and passion for paleontology resulted in many field expeditions both at home and frontiers overseas. Osborn was particularly skillful in securing some of the best burgeoning fossil hunters of the West. Barnum Brown (1873-1963), one of the most dedicated and successful paleontologists of the twentieth century, is most famously remembered for his discovery of the second Tyrannosaurus rex specimen from the badlands of the Hell Creek Formation in Montana. Like many of the naturalists and paleontologists discussed, Brown also shared an innate passion for natural history and exploration in particular. Brown later sharpened his interests and skills in natural history at the University of Kansas where he studied under the direction of Samuel Wendell Williston, a former student of Marsh. Brown entered the university in 1894, the same year that Williston was organizing an expedition to the badlands of South Dakota and drafting any willing students to “help transport gear, collect fossils, and keep camps operational” during the journey. Brown immediately jumped at the opportunity.60 Brown fell naturally under Williston’s guidance and his first expedition in 1894 truly shaped his love for the field and his talent for finding and excavating fossil specimens. Brown, utilizing the same techniques documented in Sternberg’s account, became a master in fossil excavation and soon became “chief excavator” for Williston’s specimens as well as his own. The following summer of 1895, Williston and his crew headed out to Wyoming in search of dinosaurs where Brown served as his right hand man for the expedition. The Wyoming expedition, like the previous dig in South Dakota, proved highly successful, yielding a wonderful and invaluable skull.61 By Williston’s recommendation, Brown spent the next several years with the field crew from the AMNH where his skill was noticed by Osborn. In 1897, Osborn extended an invitation for Brown to attend Columbia University where he could continue his degree and simultaneously work at the AMNH where he would learn the growing “museum paleontological technique.”62 Brown proved an indispensable crew member, particularly in the excavation of some of the largest sauropod bones discovered.

59 Ibid. 60 Lowell Dingus and Mark Norell, Barnum Brown: The Man Who Discovered Tyrannosaurus rex (Berkeley: University of California Press, 2010), 24-25. 61 Ibid., 31-32, 36, 38. 62 Dingus and Norell, Barnum Brown, 49. 39

With nearly four field seasons under his belt, Brown had become a master field paleontologist. Still under Osborn’s supervision, Brown set to work on excavating the massive bones of Diplodocus at the Como Bluff quarry in Wyoming. Diplodocus, a large and long- necked sauropod, was one of the largest dinosaurs dominating the world nearly 150 million years ago. The excavation of this immense creature was beyond tedious, and the transportation of the bones was an even more arduous task. Fossil bones, depending on the size of the specimen, along with the added weight of the plaster jacket, could easily weigh anywhere from fifty to several hundred pounds.63 The colossal size of the Diplodocus bones presented a particularly delicate and difficult task. Brown’s method was to “expose some of the bones on top and sides of the vertebral column, cover these with paper, then run cement and plaster over them, strengthening the whole with boards, then digging underneath.” All the while “being careful to brace the section well” and to then wrap it “with rawhide drawn tightly and nailed to the boards” making the specimen secure and “firm as rock.”64 Brown’s work on the Diplodocus skeleton, the first to be recovered by the AMNH, “launched the development of what would quickly become the world’s best and most famous collection of dinosaurs.” Lowell Dingus and Mark Norell added, “And beyond that, by covering the fragile, 150-million year-old hindquarters of his Diplodocus in a sturdy plaster jacket reinforced with wooden struts, he helped establish a critical collecting technique that is still used today by paleontologists around the world.”65 Brown believed himself the creator of the plaster jacket technique and although he certainly had a hand in popularizing the practice, the plaster jacket actually originated back during Cope’s and Sternberg’s fossil digs in 1876. Soon after, Marsh’s fossil collector, Williston, adopted a similar method of wrapping fossils with strips of paper soaked in flour paste. The technique caught on quickly and soon both Cope’s and Marsh’s field crews used this method.66 Nonetheless, the plaster jacket, among other field techniques, is still the most popular among field paleontologists today, dating back to the late 1900s with some of the earliest American paleontologists. Roland T. Bird (1899-1978), though lacking any formal training in paleontology, was one of the most rigorous and passionate fossil collectors of the twentieth century. In 1932, Bird made

63 Ibid., 27. 64 Ibid., 55. 65 Ibid., 57. 66 James Farlow, introduction to Bones for Barnum Brown: Adventures of a Dinosaur Hunter, ed. V. Theodore Schreiber (Fort Worth: Texas Christian University Press, 1985), 213; Dingus and Norell, Barnum Brown, 57. 40

a rather significant fossil find while journeying through Arizona on his Harley.67 In the outcrop of a hill, Bird stumbled across the skull imprint of a mysterious creature. He shipped the fossil to his father in New York who had the skull identified by Brown, “the dinosaur and fossil reptile man at the American Museum.”68 Bird finally had the opportunity to meet Brown in person in 1933, and the following year he received a personal invitation from Brown to join the AMNH crew on an expedition led by Carl Sorenson to the Howe quarry of Wyoming.69 The journey proved one of the most fruitful of Brown’s young but promising career as a fossil collector. The Howe quarry on the Wyoming expedition, one of Bird’s field experiences with Brown, epitomizes the field paleontologist’s life. The original mission at Howe quarry was to recover two dinosaur skeletons, but as the dig ensued and five scapulas were revealed, the crew soon began to suspect that much more was hidden below the rock beds than they had anticipated. The quarry had already yielded several partial skeletons and Bird and the others continued to dig in hopes of recovering the rest of the bones to make up the complete skeleton. However, the crew “came upon the vertebral column of another individual that led to another ” and beside these remains was “an assorted mass of packed bones that seemed to have no bottom.” Meanwhile, the other end of the quarry showed “vertebrae of a great neck, either to ten feet long.” Bird exclaimed, “I could hardly bear to take time out for eating and sleeping; not in wildest dreams had I pictured such a mass of fossils, such a paleontological jackpot.”70 After being called to the quarry, Brown described the find as “an absolute, knockout dinosaur treasure trove.”71 However, the trove begged hard work with long and tedious hours in the field. The mass of bones – layers upon layers of disarticulated skeletons – called for the crew to construct a grid map of the entire area to be excavated. Bird directed the task by stretching strings, each about a yard apart, across the length and width of the quarry. After the grid was laid down, Bird set about sketching each bone within every grid of the quarry site. The purpose of the quarry map was to record the position of each fossil and its relation to the other surrounding bones. As Bird mapped, Brown and the crew members followed behind with brush and pick, carefully exposing

67 Roland T. Bird, Bones for Barnum Brown, 19-22. 68 Dingus and Norell, Barnum Brown, 252. 69 Roland T. Bird, Bones for Barnum Brown: Adventures of a Dinosaur Hunter, ed. V. Theodore Schreiber (Fort Worth: Texas Christian University Press, 1985), 41-45, 47. 70 Bird, Bones for Barnum Brown, 53. 71 Ibid., 54. 41 the mass of bones for excavation. The treasure trove attracted much attention from local visitors to the press and radio. The Howe quarry represented a historical and scientific wonder, but it also pushed the patience and tested the talents of the paleontologists working there. Bird reflected on the experience:

It’s a good thing 1934 came around only once in my lifetime; I couldn’t have taken it twice. I began it as a wandering motorcycle cowboy, looking for almost anything to happen. And it had happened in spades…and awls and prospecting picks and dust brushes…on the most interesting job in the world. I was working with and for the top man in his field. And he was working on the biggest job of his life…fifteen dinosaurs, more or less, in one fantastic graveyard. And it had all happened because a fossil I had stumbled over happened to be the first of its kind ever found.72

The stories of Sternberg, Brown, and Bird illustrate the establishment of a paleontological tradition couched in a love for fossils and the field. These early field paleontologists helped popularize the romantic image of paleontology in the field; an image that continues to attract both serious paleontologists and amateur fossil hunters alike. In their biography of Brown, Dingus and Norell noted, “From the outside, paleontological expeditions seem like adventurous, romantic treasure hunts. But this image doesn’t take into account the hard work and often tedious daily routines and hardships of working in desolate regions, where blistering heat can make finding water a life-and-death concern…”73 While these memoirs broadcast adventure and inspiration, the stories also highlight the hardships of fieldwork and the development of field processes, techniques, and practices to overcome those obstacles. The explosion of field and survey collecting in the late 1800s and early 1900s is evidence of the growing popularity of fossilized creatures and increasing interest in natural history. Kohler noted that natural history surveys of the late nineteenth and early twentieth century differed from previous collecting procedures in that “It was organized, systematic, and sustained in contract to sporadic individual efforts…” He continued, “But whether it was the private passion of one man or an official government project, and whether it lasted months or decades, natural history survey

72 Ibid., 61. 73 Ibid., 25. 42

was organized, planned, and long-term. It aimed at a comprehensive, total inventory.” 74 Universities, museums, and governments alike commissioned multiple survey collecting expeditions. Marsh, Cope, and Osborn played a critical role in the organization, execution, and promotion of field expeditions on behalf of their respective institutions. The primary objective of early paleontological digs was to discover and describe new fossil specimens. As fossils poured in from the American West and across the world, collections grew bigger and bigger. Farber claimed, “Nowhere did the glory of natural history appear more evident than in the construction and expansion of natural history museums in that late 1800s.”75 By that time, museums had a long standing tradition as a storehouse for natural history collections. In light of the outpouring of fossil specimens from around the world, fossils – particularly dinosaur fossils – became the main museum attraction. As museum fossil collections attracted the fascination of the public, the collections also served research needs for the naturalist. Paleontologists specifically were interested in the traditional description, naming, and cataloguing of new fossil finds, as well as fitting them into the evolutionary tree of life. Fossils were then cleaned and prepped for museum displays. The intense outburst of field collecting and the dramatic increase in fossil collections encouraged the established tradition of the field paleontologist and the early objectives of paleontology in general. The influx of fossils from the American West and other places around the world required museums to acquire more storage, more work space, and more hands. The major American museums such as the AMNH were receiving great numbers of fossils that they were quickly running behind on their preparation and study. Historian of science Paul Brinkman noted, “The need for greater speed and accuracy drove the development of a number of innovative techniques.”76 Before these new innovations though, fossil preparation was only done by hand. Brinkman highlighted this often long, arduous task, explaining, “Preparators removed the matrix from the bones by chipping it away with a tedious, repetitive tapping of light shoemaker’s hammers on hardened steel chisels or awls. The work was exhausting for the preparator and too hard on the specimens.”77 The current methods of fossil preparation proved even more inefficient to handle the mass amounts of fossils that were accumulating in museum

74 Kohler, All Creatures, 10. 75 Farber, The Order of Things, 88. 76 Paul D. Brinkman, The Second Jurassic Dinosaur Rush: Museums and Paleontology in America at the Turn of the Twentieth Century (Chicago: The University of Chicago Press, 2010), 228. 77 Brinkman, The Second Jurassic Dinosaur Rush, 228. 43 basements. As a result, new techniques were developed to better handle the increasing amount of work. Brinkman discussed that “Preparators derived new techniques for speeding the work by adapting the technologies of other industries to fossil preparation.” One of the more successful techniques, the pneumatic apparatus, was developed in the early 1900s. The pneumatic apparatus “consisted of an air compressor, air tank, pressure gauge, piping and fixtures, and a suit of air tools, including pneumatic hammers and drills.”78 Such inventions and advancements in technology were critical in keeping up with the outpouring of fossil specimens and the improvement of paleontological data and research. Paleontology was – and still is – a very discovery driven field. In his introduction to Bird’s Bones for Barnum Brown, James Farlow reflected on the early history of field paleontology, explaining: “In many ways Brown was the one of the last and greatest old-time dinosaur hunters. In his time the main effort of field work was to collect new or well-preserved specimens; paleontologists were primarily interested in finding new faunas and working out the evolutionary relationships of the creatures they studied.”79 The history of the field is more than critical to understanding its development and current status as a discipline and profession today. More importantly, the history of field paleontology provides a contrast to the more recent and experimental approaches to paleontology within the past half century. Farlow further explained, “While these goals are still important in fossil hunting, there is an added dimension to field work nowadays. Modern paleontologists are also concerned with questions of how fossil assemblages formed and how they can be used to reconstruct the paleoecology of ancient organisms.” The emergence of molecular paleontology and paleobiology in the latter half of the twentieth century certainly reflected this change in emphasis. Furthermore, Farlow perceptively noted:

Modern field collecting techniques are consequently more sophisticated and quantitative than those of Brown’s day. For studies of this kind, poorly-preserved and fragmentary specimens (which were often ignored in the pioneer era of vertebrate paleontology) can be just as important as the most complete and exquisitely preserved skeleton.

78 Ibid., 229. 79 Farlow, introduction to Bones for Barnum Brown, 6. 44

However, this does not imply that “old-timers like Brown were uninterested in matters of paleoecology,” but rather “such questions were of secondary importance.”80 Modern paleontology has undergone a shift in the kinds of questions they want to ask and a shift in approach in how to answer them. The history of field paleontology provides the context from which to better understand paleontology’s foundation and evolution over the past centuries, particularly since the molecular revolution of the 1950s.

Conclusion

During Darwin’s time, paleontology was one of the strongest lines of evidence for evolution as fact. Yet the excitement about the fact of evolution eventually passed and naturalists began to seek questions more related to the processes of evolution. The rise of experimental biology encouraged an emphasis on analytical studies and quantifiable evidence; a type of quantitativeness that historical sciences like paleontology could not provide at the time. Though pushed to the margins of evolutionary theorizing, paleontology continued to grow and found its identity in the adventurous image of the field paleontologist and through the myriad discoveries of dinosaur fossils in particular. With the professionalization of the field paleontologist emerged a specific set of field practices tailored to the discovery and recovery of fossils; a traditional set of field practices best exemplified through the science and memoirs of vertebrate paleontology, and dinosaur paleontology specifically. At the same time, paleontologists entertained larger evolutionary questions, though ignored because of experimental biases. Simpson’s efforts helped to change this and as Bowler argued, paleontology’s emergence “as an active participant in the Darwinian synthesis of the 1940s” was “because early twentieth-century paleontologists had pioneered new avenues of research on evolutionary issues.”81 However, the molecular biological revolution in the latter half of the twentieth century introduced science to an entirely new way to study life and evolution. The advent of molecular biology as a new avenue of research led not only to great advancements in biology, but also made possible two significant movements; the rise of molecular paleontology and aDNA research. These developments, over the next several decades, began a shift from what could be called classical paleontology to modern paleontology. Though the field paleontologist and historical approaches remained an integral part of

80 Ibid., 6. 81 Bowler, Life’s Splendid Drama, 39. 45

paleontological investigation, molecular paleontology, aDNA research, and also paleobiology – by bringing in experimental methodologies to fossil research – helped to bring the field into larger evolutionary discussion. Paleontologists began to ask new questions of their fossils and answer them using new techniques as well. This resulted in what Ruse might call a “new breed of scientist.”82 In a new molecular age, scientists continued to explore the realms of possibility and soon the field of aDNA research was born. aDNA research taught researchers that fossils were more than just museum displays but rather potential storehouses for genetic information. This next chapter will document the first seven years of aDNA research in hopes of better understanding a novel approach to fossil studies and its implications for the science of paleontology in an experimental and molecular age.

82 Ruse, Mystery of Mysteries, 214. 46

CHAPTER THREE THE SEARCH FOR ANCIENT DNA (1984-1991)

Introduction

aDNA research, the retrieval of nucleic acids from ancient plant and animal remains, continues to be a controversial but also potentially promising area of research. Although a relatively young and developing field, the quest for aDNA yields a sensational history. With its advent in the mid-1980s, aDNA research has proven to be a novel and exciting approach to studying and recreating the past. The following chapter is a historical account of aDNA research from 1984 to1991. Although this history does not cover every aDNA study from this time period, I have selected a number of the most well-known and published case studies for survey. Moreover, from a Kuhnian perspective the early history of aDNA research is the exploration of an anomaly; an unexpected outcome not predicted by the current scientific paradigm. The presence of DNA in ancient and fossil specimens seriously tested the paradigm induced understanding of DNA preservation and fossilization processes, and furthermore, began to revolutionize the way scientists thought about and studied fossils and DNA. Consequently, aDNA refers to DNA samples that have become highly degraded through time and other processes. Such samples need special techniques by way of preparation and extraction to ensure retrieval of reliable DNA sequence data. aDNA samples are usually considered older than material used in forensic studies and may range anywhere from a few years old to millions of years old. In this chapter, I employ Kuhn’s theory of scientific revolutions and specifically his notion of a scientific anomaly as a methodology, or guide, for organizing the early history of aDNA research. It is not my goal to either prove or disprove Kuhn’s overall theory of scientific revolutions. I only use his concept of anomaly as a method for interpreting the history of aDNA research and more importantly, for analyzing the awareness, authentication, and acceptance of a scientific anomaly.

47

Anomaly Awareness

In 1984, an extraordinary discovery was made when preserved DNA was extracted from the museum remains of the long-dead Equus , a zebra-like relative of the horse reported to have gone extinct in 1883.1 The scientists who made the discovery, biochemist Russell Higuchi, evolutionary molecular biologist Allan Wilson, and colleagues, were researching at the University of California, Berkeley. Until this study, the only fossil molecules revealed had been amino acids and proteins. While scientists had been extracting DNA from recent material for nearly two decades since the discovery of the double helix in 1953, researchers had not yet attempted to recover DNA from something long dead. Realizing the magnitude of their study, Higuchi and colleagues sent their results to Nature: “The present report seems to be the first demonstration that clonable DNA sequence information can be recovered from the remains of an extinct species.”2 Had Higuchi and researchers struck a scientific anomaly? The existence of preserved DNA in a 140-year-old museum specimen certainly challenged the current understanding of DNA preservation. Typically, as soon as an organism dies, DNA and other organic components begin to decay rapidly. This process, called autolysis, “occurs because the organism’s own enzymes start to decompose the organic substances of the body.”3 Although an essential component of life, the biological composition of DNA is extremely delicate. Its limited chemical stability makes DNA especially susceptible to external conditions which contribute to, or quicken, the decay process. Environmental conditions such as length of time exposed, sediment type, contact with water, temperature, rate of burial, and onset of fossilization processes all play a critical role in organic and inorganic preservation.4 With internal and external decay processes combined, often little is left in the way of organic substances, like DNA, and typically all that remains is the skeleton of an organism long gone. However, Higuchi and colleagues’ results showed that despite the odds, some DNA could, and in fact did, stand the test of time. The anomaly was the presence of intact DNA in an extinct, 140- year-old specimen. The quagga study seemed to produce results that contradicted our

1 Russell Higuchi, Barbara Bowman, Mary Freiberger, Oliver Ryder, and Allan Wilson, “DNA Sequences from the quagga, an Extinct Member of the Horse Family,” Nature 312 (1984): 282-284. 2 Ibid., 284. 3 Bernd Hummel and Susanne Herrmann, “General Aspects of Sample Preparation,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, eds. Bernd Hermann and Susanne Hummel ( New York: Springer-Verlag, 1991), 60. 4 Refer to Chapter 1 of David Raup and Steven Stanley’s Principles of Paleontology for more information. 48

understanding of DNA preservation. So what was wrong? The results? Or, was it time to rethink the preservation of DNA and its significance for molecular studies? In 1962, Thomas Kuhn published his seminal work, The Structure of Scientific Revolutions, in which he discusses his idea of a scientific anomaly. In this work, Kuhn argued that the is a process first characterized by stable periods of “normal science” in which scientists conduct research under the guidance of an existing paradigm, or framework, that contains specific methods, techniques, rules, and theories for scientific study. Normal science is then interrupted by the incidence of an anomaly, an unexpected result in research not predicted by a current scientific paradigm. The continued occurrence of such anomaly, to the point where it becomes a significant problem for the existing paradigm, then results in a “crisis.” Next ensues a period of “incommensurability” in which groups of scientists continually talk past one another because of growing differences in perception about the crises and paradigm at hand. Kuhn, playing on Gestalt psychology, best captured this stage of incommensurability through the illustration of the “duck-rabbit.” The “duck-rabbit” is a picture in which two observers could perceive two very different images; one may see a duck, while at the same time the other might see a rabbit. Kuhn explained that “[w]hat were ducks in the scientist’s world before the revolution are rabbits afterwards.”5 Thus, a takes place when the old paradigm proves insufficient to answer the science’s questions and a new paradigm, in light of new evidence, eventually comes to replace the former. Though Kuhn’s larger argument will not apply here, his notion of an anomaly is relevant to the recent discovery of DNA in long dead organisms. The 1984 quagga study represented the awareness of an anomaly and the studies that followed throughout the 1980s, and well into the 1990s, signified the exploration of this anomaly. Was aDNA preservation merely a rare and unique occurrence or could Higuchi and others’ study be replicated with other ancient organisms? In The Structure of Scientific Revolutions, Kuhn stated, “Discovery commences with the awareness of anomaly, i.e., with the recognition that nature has somehow violated the paradigm-induced expectations that govern normal science.” Furthermore, “It then continues with a more or less extended exploration of the area of anomaly. And it closes only when the paradigm theory has been adjusted so that the

5 Kuhn, The Structure of Scientific Revolutions, 111. 49

anomalous has become the expected.”6 However, Kuhn also noted that “[a]ssimilating a new sort of fact demands a more than additive adjustment of theory, and until that adjustment is completed – until the scientist has learned to see nature in a different way – the new fact is not quite a scientific fact at all.”7 The quagga study was certainly striking, and the results were even more exciting. With potentially far reaching implications for better constructing and detailing evolutionary histories, this anomaly proved worthy of exploration. With permission from the Museum of Natural History in Mainz, Germany, Higuchi and his team sampled a small piece of dried muscle and some connective tissue from the quagga specimen. Upon investigation, the results showed positive for DNA, but after 140 years, the DNA remnants were small and highly degraded. Regardless, Higuchi’s team attempted to test for quagga DNA first using gel-electrophoresis, a standard DNA technique and process which uses a gel substance subjected to an electric current to separate different sized or charged DNA fragments.8 Following electrophoresis, they attempted to clone, or copy, the mitochondrial DNA (mtDNA) sequences. mtDNA was selected because its abundance in cells makes cloning much easier. Proving successful, the quagga DNA was compared to zebra, cow, and human sequences. The results: the quagga DNA recovered was not only distinct, authentic quagga DNA, but more importantly, the data shed light on the phylogenetic relationship, or the evolutionary history of the quagga. The molecular data complemented fossil evidence which originally suggested the quagga was closely related to the zebra. The study’s molecular analyses confirmed this hypothesis. The quagga study offered one of the first glimpses of the potential use of molecular data for illuminating the evolutionary history of other extinct and extant organisms. Higuchi and his researchers hypothesized, “If the long-term survival of DNA proves to be a general phenomenon, several fields including palaeontology, evolutionary biology, archaeology and forensic science may benefit.”9 In his popular article “Raising the dead and buried,” , Department of Genetics at University of Leicester, United Kingdom, speculated, “Is the quagga as dead as a dodo? Not entirely, and nor indeed might be the dodo, if the remarkable findings of Russell

6 Ibid., 52-53. 7 Ibid., 53. 8 Jörg Epplen, “Simple Repeat Loci as Tools for Genetic Identification,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, eds. Bern Hermann and Susanne Hummel (New York: Springer-Verlag, 1991), 15. 9 Higuchi et al., “DNA sequences from the quagga,” 284; Paleontology will be spelled “palaeontology” only when quoting U.K. based publications. 50

Higuchi, Allan Wilson and co-workers reported on page 282 of this issue are anything to go by.” Jeffreys concluded, “Any hopes that molecular biology and palaeontology can be fused into a grand evolutionary synthesis by studying fossil DNA, still look like nothing more than a glorious dream. However, it is far too early to give up, and it might just be possible that DNA has survived in some fossilized material.”10 Whatever the answer, scientists were interested in making this dream a reality. The 1984 aDNA study suggested that perhaps it was possible for standard DNA techniques and procedures to be applied to not only recent organisms but to much older organisms and even fossil specimens as well. Svante Pääbo, expert in aDNA research, was one of the first to test the anomaly. In 1985, the year following the initial quagga study, Pääbo, biologist and researcher at the Department of Cell Research at the University of Uppsala, Sweden, and colleagues tested for DNA from the remains of ancient Egyptian skin.11 This study involved a number of Egyptian and mummy fragments, ranging from the Sixth Dynasty to late Roman era (approximately 2370-2160 BC). In hopes of producing similar results to the quagga study, Pääbo and fellow researchers examined each mummy sample for DNA content. However, just the skin and “superficial parts of the left lower leg” of a mummified boy, who died before his first year, was the only one of the twenty-three mummies investigated to show evidence of DNA remnants. Nonetheless, Pääbo and colleagues, with the available DNA, prepared to test for authenticity. Like Higuchi’s team, Pääbo and his researchers were interested in testing for endogenous DNA to determine whether or not the genetic material was of true mummy origin or a contaminant. If the alleged DNA was contaminated, then it would be of no use for phylogenetic reconstruction. So, to test authenticity Pääbo and others compared the mummy DNA with sequences from the Alu family, a group of DNA sequences found in the of and other .12 Comparison allowed Pääbo’s team to rule out contamination of the mummy sequence, thus concluding they had recovered original mummy DNA. Furthermore, this mummy study confirmed the feasibility of the original quagga study; that in some cases aDNA preservation was possible. In fact, this study extended the expected preservation of DNA by

10 Alec Jeffreys, “Raising the dead and buried,” Nature 312 (1984): 198. 11 Svante Pääbo, “Molecular cloning of ancient Egyptian mummy DNA,” Nature 314 (1985): 644-45. 12 The Alu family is the most abundant family of repetitive elements in mammalian , including humans. They are speculated to control gene activity. The Alu family sequence is important because it helps explain human population genetics and human evolution in relation to primates. The purpose for comparing mummy sequences to the Alu family was to check for similarity or overlap in sequences. Also refer to Schmid and Jelinek, “The Alu Family of Dispersed Repetitive Sequences.” 51

nearly 2,000 years. Pääbo, in an article he wrote for Nature, confidently concluded, “These results establish the feasibility of faithfully cloning substantial pieces of genomic DNA from biological remains of great antiquity.”13 Pääbo and others’ study reached several other important conclusions. Though the majority of the mummies used in this study showed no evidence of DNA, they concluded, from the one mummy sample in which DNA did exist, that where we choose to look for DNA in our specimens may be of decisive importance. In this case, DNA preservation was more likely to occur in certain parts of the body, the “superficial tissues and peripheral parts,” as opposed to “more deeply situated tissues.”14 In his Nature article, Pääbo explained this as a result of the ancient Egyptian mummification process through dehydration: “Thus the parts of the body in direct contact with the dehydrating agent may have dried out first, thus shortening the time that hydrolytic processes acted upon macromolecules in these tissues.” Knowing where to look for preserved DNA would better guide future research. Secondly, Pääbo concluded that molecular studies of ancient Egyptian mummies was not only possible, but could be particularly useful to historical studies and understanding Egyptian patterns of population and disease. From an anthropological perspective, aDNA studies could provide answers for a “number of Egyptological problems”15 that remained unsolved. The impact of molecular data had far reaching consequences. The quagga study, and also mummy research, marked the first successful attempts to extract, clone, and analyze DNA sequences from ancient specimens and in doing so, set an exciting example for others interested in testing aDNA research to follow. Although these early aDNA studies were indeed successful and demonstrated that molecular studies on ancient specimens could provide direct and quantifiable evidence of evolutionary history, many more studies were needed to further authenticate the results and potential utility of aDNA research overall.

13 Pääbo, “Molecular cloning of ancient Egyptian mummy DNA,” 645. 14 Ibid., 645. 15 Ibid., 645. 52

Appreciating Authenticity

In light of an anomaly, it is sometimes beneficial for scientists to be more skeptical than accepting of new and remarkable results. As Kuhn perceptively noted, “By ensuring that the paradigm will not be too easily surrendered, resistance guarantees that scientists will not be lightly distracted and that the anomalies that lead to paradigm change will penetrate existing knowledge to the core.”16 Though in the case of aDNA research there may not necessarily be a decision between one paradigm over another, Kuhn’s point is still enlightening in explaining both the value of scientific rigor and reproducibility in aDNA studies. When faced with an anomaly, the scientist must distinguish between a true anomaly and what may have been the results of a laboratory contaminant. In the particular case of aDNA research, contamination was – and still is – a serious issue. Although a leading expert in DNA studies, Pääbo – along with other researchers – was also a serious critic and always emphasizing the risk of contamination in molecular studies.17 Fossil DNA specifically was suspect to special contaminates like microorganisms; however, external contamination, like human DNA, could also spoil aDNA samples. Thus, Pääbo advocated using “rigorous precautions” prior to and during testing. Replication of the study was also necessary using “different tissues of the same individual to control for contamination of the specimen.”18 Pääbo in particular was an early advocate for appropriate protocols and techniques in aDNA studies in hopes of yielding original DNA and not artifacts due to contaminated samples or sloppy science in the lab. Moreover, it was especially important to recognize and prevent contamination because aDNA samples are exceptionally rare and delicate. While the mummy and quagga study succeeded in cloning and sequencing available ancient DNA with presumably no contamination, future experiments would be extremely hard to create, much less replicate. Reflecting on the limiting factors of the mummy study, and also Higuchi and his team’s former report, Pääbo and researchers explained, “However, they were in a sense precocious, since the amounts of DNA present in the old tissues were so small that the

16 Kuhn, The Structure of Scientific Revolutions, 65. 17 Svante Pääbo, “Ancient DNA: Extraction, Characterization, Molecular Cloning, and Enzymatic Amplification,” Proceeding of the National Academy of Sciences 86 (1989): 1939-1943; Svante Pääbo, Russell Higuchi, and Allan Wilson, “Ancient DNA and the Polymerase Chain Reaction,” The Journal of Biological 264 (1989): 9709-9712; Alan Cooper and Svante Pääbo, “Ancient DNA: Do It Right or Not At All,” Science 289 (2000): 1139; Svante Pääbo, Hendrik Poinar, David Serre, Wiviane Jaenicke-Deprés, et al., “Genetic Analyses from Ancient DNA,” The Annual Review of Genetics 38 (2004): 645-679. 18 Pääbo, “Ancient DNA: Extraction, Characterization, Molecular Cloning, and Enzymatic Amplification,” 1943. 53

isolation of bacterial clones carrying the same DNA sequence was essentially impossible.”19 For this reason, both studies’ results could not be replicated to validate their legitimacy. As Pääbo and colleagues claimed, “Thus, the litmus test of experimental science – reproducibility – was hard or impossible to achieve.”20 The current molecular cloning techniques, while valuable, were most useful when working with ample amounts of DNA. Over time, DNA breaks down, and often we are left with a degraded and much damaged sequence of genetic material, if anything at all. Such small samples are very difficult, if not impossible, to accurately copy without errors. Technological advancements were necessary to keep up with the ambitions of aDNA research. Nonetheless, these difficulties were not obstacles enough to deter future aDNA research. The British bog body, more popularly known as the Lindow man, was a curious case for an aDNA study. Margaret Hughes, of the Department of Biochemistry at the University of Liverpool, and colleagues took up investigation in 1986. The 2,500 year old body, first discovered in 1984 in a marshy British bog, seemed an unlikely candidate for DNA preservation. For centuries, the Lindow man had been exposed to water with relatively high pH levels that are known to be extremely destructive to the preservation of organic components.21 However, Hughes attempted the task anyway. After securing a muscle sample, Hughes and colleagues ran the standard tests to check for what, if any, DNA remained. All attempts failed. They then attempted to demonstrate signs of DNA degradation, but those trials failed too. Hughes and her colleagues concluded that “while a little DNA may be preserved during the dehydration process of Egyptian mummies, probably none survives the acid, aqueous, anaerobic and virtually sterile preservation conditions of bog-bodies…”22 Although no positive results were reached, the study proved useful for understanding likely and unlikely circumstances for organic preservation. Success or no success, the search for aDNA continued. That same year, Glen Doran, Department of at Florida State University, and colleagues made a remarkable recovery: brain tissue containing preserved DNA from an 8,000 year old human. In 1986, Doran and his team announced, “As this find appears to be the oldest-known example of preserved human cell structure and DNA, it represents a significant

19 Pääbo et al., “Genetic Analyses from Ancient DNA,” 646. 20 Ibid., 646. 21 Margaret Hughes, David Jones, and Robert Connolly, “Body in the bog but no DNA,” Nature 323 (1986): 208. 22 Ibid., 208. 54

resource for both anthropological and genetic studies.”23 Two years earlier in 1984, a swampy cemetery of “preserved human body and soft matter” was discovered out in Brevard County, Florida.24 The site, Windover pond, yielded at least forty individuals, and with X-ray imaging, among other methods, nine of the unearthed skulls were determined to contain soft tissue. Doran and fellow reseachers stated, “The overall impression from physical analysis of these intracranial masses was that, although shrunken and altered in consistency, the gross anatomical features of contemporary brains were present.”25 From the ancient soft tissue, nucleic acids were recovered, tested, and confirmed as human DNA. The Windover site study not only had archaeological significance, but this outstanding discovery contributed much to our understanding of DNA preservation potential. Doran and co- authors reported, “It is especially noteworthy that this material has been preserved in an aqueous environment, suggesting that intact DNA can survive in other than extremely arid conditions, which greatly widens the sites where ancient genetic material may be found.”26 Although the discovery was a rare find, the study challenged the presumed limitations of DNA preservation, particularly when the British bog body seemed to confirm our expectations. Multiple future studies were indeed necessary to construct a more robust and comprehensive understanding of what kinds of environments and influencing factors increase or decrease the likelihood of DNA survival in ancient remains. Speculating on the importance of molecular preservation, Geoffrey Eglinton and Graham Logan at the , United Kingdom, stated, “The interpretation of the new molecular data will require the development of a parallel understanding of molecular , i.e., the process of decay at the molecular level and their consequences in terms of biasing the eventual record. Experiments following decay under different environmental conditions are needed.”27 An explosion of future experiments was soon made possible a few years later with the invention of the polymerase chain reaction (PCR): a technological achievement that dramatically enhanced both the quantity and quality of DNA research. Kuhn claimed, “There are instrumental

23 Glen Doran, David Dickel, William Ballinger, Jr., O. Frank Agee, Philip Laipis, and William Hauswirth, “Anatomical, cellular and molecular analysis of 8,000-yr-old human brain tissue from the Windover archaeological site,” Nature 323 (1986): 803. 24 Ibid,. 803. 25 Ibid., 805. 26 Ibid., 806. 27 Geoffrey Eglinton and Graham Logan, “Molecular preservation,” in Molecules through Time, eds. Gordon B. Curry and Geoffrey Eglinton (Great Britain: University Press, Cambridge, 1991), 325. 55

as well as theoretical expectations, and they have often played a decisive role in scientific development.”28 The development of PCR in 1987, by and fellow colleagues, soon revolutionized not only DNA studies but also had a serious impact on other disciplines such as systematics, molecular and cellular biology, forensics, and medicine.29 In fact, PCR was so revolutionary to molecular research that Mullis, then at the University of California, Berkeley, was awarded the 1993 Nobel Prize for its invention.30 PCR’s primary advantage was its ability to amplify DNA. It could essentially produce limitless (millions or billions) copies of DNA sequences from only a few strands, or even just one strand, of DNA. This technique was extremely useful in circumstances where only microsamples or especially damaged samples were available. In such cases, it was necessary to use PCR to amplify the small amounts of preserved fossil DNA before even undertaking standard DNA research. Furthermore, the process was relatively quick and cheap.31 Shortly after PCR’s invention, Pääbo, Higuchi, and Wilson – aDNA research pioneers – announced in a 1989 article, “The recently achieved ability to study DNA from museum specimens and archaeological finds via PCR opens up the possibility of studying molecular evolution by actually going back in time and directly approaching DNA sequences that are ancestral to their present-day counterparts.”32 The technological advancement of PCR further facilitated the exploration of an anomaly, the existence of DNA in extinct and even ancient organisms. In the spring of 1989, Pääbo tested the reliability of PCR on several ancient specimens. In an article, Pääbo stated, “To make general statements about the state of preservation of DNA in ancient dry remains of soft tissues, I have extracted nucleic acids from 12 specimens

28 Kuhn, The Structure of Scientific Revolutions, 59. 29 Kary Mullis, “Specific synthesis of DNA in vitro via polymerase-catalysed chain reaction,” Meth Enzymol 155 (1987): 335-350; R. K. Saiki, S. Scharf, F. Faloona, K. B. Mullis, and G. T. Horn, “Enzymatic amplification of beta- globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia,” Science 230 (1985): 1350-54; R. K. Saiki, D. H. Gelfand, S. Stoffel, S. J. Scharf, and R. Higuchi, “Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239 (1988): 487-91. 30 George Poinar and Roberta Poinar, The Quest for Life in (Reading, Massachusetts: Addison-Wesley Publishing Company, 1994), 75. 31 PCR uses repeated cycle of heating and cooling to separate double-stranded DNA into single-stranded DNA. The single strand of DNA is then exposed to primers, or short fragments of DNA. The se primers attach themselves to the appropriate sites flanking the section of desired DNA to be amplified. A copy of the desired DNA is produced. Poinar explains, “For each original piece of fossil DNA, there are now two double-stranded pieces of DNA, each with an original piece of DNA and a new piece of amplified DNA” (The Quest for Life in Amber, 74). This process continues as a chain reaction with the desired DNA being exponentially multiplied creating millions to billions of copies. 32 Svante Pääbo, Rusell Higuchi, and Allan Wilson, “Ancient DNA and the Polymerase Chain Reaction,” The Journal of Biological Chemistry 264 (1989): 9712. 56

representing a wide variety of geographical regions and different time periods.”33 This study, involving a range of specimens, successfully extracted DNA from a piece of four year old pork, skin from a wolf, a 13,000 year old , and various body parts and organs of ancient Egyptian mummies. Two of the specimens, the marsupial wolf and the giant ground sloth, were extinct. Standard DNA methods were used and DNA amplification via PCR was also performed. Pääbo announced, “Here I report the nature of the chemical modifications in these DNA samples and show that, whereas these modifications render molecular cloning techniques difficult and possibly error prone, the recently developed polymerase chain reaction (PCR) is likely to produce reliable sequence information from many ancient tissue remains.”34 What was once rendered nearly impossible with previous molecular cloning techniques was now a conceivable reality thanks to the technological advancement of PCR. Pääbo’s 1989 study established that the extent of DNA degradation and size reduction does not necessarily correlate to the age of samples. He explained, “For example, the DNA extracted from the 4-year-old dried pork and the ≈100-year-old Thylacinus samples are degraded to a comparable extent as the DNA from the 13,000-year-old Mylodon extract, whereas the predynastic 5000-year-old Egyptian mummy samples seem to be degraded to a lesser extent.”35 Thus, DNA preservation, sample size and quality, heavily depends on how quickly an organism is dried out immediately following its death. Pääbo explained that “the conditions under which the individual specimens have been preserved may be of decisive importance.”36 A sample’s age is not always indicative of DNA preservation potential; maybe some of our most ancient fossils contain DNA after all. Several months later, with the added convenience of PCR, Richard Thomas, Department of Biochemistry at University of California, Berkeley, and Walter Schaffner, Institute of Molecular Biology at the University of Zurich, Switzerland, along with Wilson and Pääbo, investigated the extinct marsupial wolf, Thylacinus cynocephalus.37 Systematists, scientists dedicated to the classification of organisms, had long argued over the phylogenetic placement of the extinct thylacine. Some argued a closer relatedness to the extinct group of South American

33 Pääbo, “Ancient DNA; Extraction, characterization, molecular cloning, and enzymatic amplification,” 1939. 34 Ibid., 1939. 35 Ibid., 1943. 36 Ibid., 1943. 37 Richard Thomas, Walter Schaffner, Allan Wilson, and Svante Pääbo, “DNA phylogeny of the extinct marsupial wolf,” Nature 340 (1989): 465-467. 57

carnivores, the borhyaenids, while others contended that thylacine was closer to the Australian carnivorous . The molecular data could potentially settle the dispute. Thomas and colleagues applied the PCR technique to several thylacine DNA sequences, one of which revealed human mtDNA and was quickly labeled a contaminant. Another muscle sample showed evidence of both human and marsupial origin, but a third sequence proved authentic marsupial DNA. The molecular evidence from this sequence, when compared to six other marsupial species, showed that the marsupial wolf “falls well within the radiation of Australian marsupials, where it is closely related to the dasyurids, a group that includes the Tasmanian devil and Australian tiger cat.”38 These data and new phylogeny demonstrated that the thylacine and the dasyurids diverged before the other marsupials sampled. Furthermore, the data strongly supported the hypothesis that the thylacine was of Australian origin. Despite the rather definitive conclusions drawn from the molecular data, the morphological data were inconsistent. The morphological evidence suggested that the thylacine was of South American origin, because it shared these unique traits with the South American borhyaenids. This study captured a current difficulty with phylogenetic construction: the inconsistency of molecular and morphological data. While the molecular evidence may suggest one evolutionary story, the morphological evidence might support a different history. When this occurs, the evolutionary history with more supporting evidence is typically favored, although still bearing in mind data inconsistencies. In this case, the molecular evidence won. Thomas and his team concluded, “This statistically significant discrepancy justifies the proposal that the dental and pelvic traits shared uniquely by thylacines and borhyaenids suggests a remarkable amount of convergent or parallel evolution, resulting in the resemblance between these species.”39 Reflecting on Thomas’ conclusions, Pääbo and colleagues announced, “This established the retrieval of DNA from museum specimens by PCR as a viable approach to the study of extinct animals.”40 However, more astonishing news came a year later, in 1990, when an article published in Nature announced “the extraction of DNA from fossil leaf samples from the Clarkia

38 Ibid., 465. 39 Thomas et al., “DNA phylogeny of the extinct marsupial wolf,” 467. 40 Pääbo et al., “Genetic Analyses from Ancient DNA,” 660. 58

deposit (17-20 Myr old)…”41 Edward Golenberg, Department of Botany and Plant Sciences at the University of California, Riverside, and researchers extracted DNA from an exceptionally well-preserved fossil leaf. Jeremy Cherfas, in his article for Science, “Ancient DNA: Still Busy After Death,” claimed, “That DNA could survive for such a staggering length of time was totally unexpected – almost unbelievable.”42 Golenberg’s team reported that the majority of artifacts from this area were fossil leaf compressions with “intact cellular tissue with considerable ultrastructural preservation…”43 Despite exceptional preservation, only one of the ten extracts possessed DNA. Selecting a piece of the chloroplast gene for PCR amplification, Golenberg and fellow researchers explained that “the chloroplast genome occurs in large numbers within plant cells providing greater probability of sampling large, intact molecules.”44 With this approach, they successfully extracted and amplified original DNA sequences from the fossil leaf, and upon comparison with four other extant species, he identified the fossil species as Magnolia latahensis. Speculating on the study’s significance, Golenberg and his co-authors stated, “The work accomplished at Clarkia will hopefully close the circle in the study of evolutionary biology and begin an active dialogue between paleontologists and evolutionary geneticists.”45 This study not only suggested the importance of interdisciplinary cooperation in fossil DNA studies, but that perhaps other paleontologists could get their hands on the DNA of some of their most ancient creatures too. With more studies pushing the age limits of DNA preservation, scientists were beginning to see the potential of aDNA studies as applied to paleontological research. Perhaps paleontology could benefit from aDNA research too. If so, aDNA would prove an unprecedented approach to fossil studies in paleontological history. Overall, the alleged positive results of the Clarkia study suggested new possibilities for DNA preservation that truly tested even our most liberal understanding of DNA preservation potential. Golenberg and fellow colleagues confidently concluded, “At an age estimated 17-20 Myr, these samples have substantially pushed

41 Edward Golenberg, David Giamnasi, Michael Clegg, Charles Smiley, Mary Durbin, et al, “Chloroplast DNA sequence from a Miocene Magnolia species,” Nature 344 (1990): 656-658. 42 Jeremy Cherfas, “Ancient DNA: Still Busy After Death,” Science 253 (1991): 1354. 43 Golenberg et al., “Chloroplast DNA sequence from a Miocene Magnolia species,” 656. 44 Golenberg et al., “Chloroplast DNA sequence from a Miocene Magnolia species,” 658; The decision to amplify chloroplast presided along the same rationale for amplification of mtDNA seen in previous studies. 45 Edward Golenberg, “Amplification and analysis of Miocene plant fossil DNA,” in Molecules through Time, eds. Gordon Curry and Geoffrey Eglinton (Great Britain: University Press, Cambridge, 1991), 426. 59

back the age of DNA that may be recovered and sequenced.”46 Was it too good, or rather too old, to be true?

Anomaly Accepted?

A year later, Pääbo and Wilson published a response and criticism to the Magnolia paper.47 In the review, Pääbo and Wilson recommended that Golenberg and his team’s results be read with caution for the following two reasons. First, they argued that the expected decay rates of DNA did not support DNA preservation in a fossil of such old age. Next, they argued caution based on their own inability to amplify DNA sequences from the Clarkia area and replicate similar results. After all, reproducibility is the litmus of experimental science. Golenberg, taking heed of Pääbo and Wilson’s skepticism, stated, “Both of these concerns question the validity of the present work on the Miocene Clarkia DNA and the future of extended molecular paleontological work.” He then claimed, “Of course empirical confirmation must take precedence over theoretical objections. Yet some discussion of these theoretical objections may be of value in understanding some of the limits of molecular paleontology in the future.”48 Was four million years too old for DNA to survive? While they too pushed the age limit of DNA preservation, Pääbo and Wilson were clearly suspicious about pushing the limits too far. In this case, further convincing was needed before such spectacular results were accepted. It was essential to ensure that good science was being done. Regardless, the rather remarkable Magnolia results pushed the possibilities for DNA preservation far beyond previous limits and scientists interested in aDNA began to look towards even older specimens for research. What was also particularly exciting about this study compared to other earlier aDNA studies was that it involved fossil material. Apart from the ancient age of the specimen, the Magnolia leaf was a truly fossilized object as opposed to the quagga or mummy material. Reflecting on this study in their article “Full of Sound and Fury: The Recent History of Ancient DNA,” Robert Wayne, Jennifer Leonard, and Alan Cooper wrote:

46 Golenberg et al., “Chloroplast DNA sequence from a Miocene Magnolia species,” 658. 47 Svante Pääbo and Allan C. Wilson, “Miocene DNA sequences – a dream come true?” Current Biology 1 (1991): 45-46. 48 Edward Golenberg, “Amplification and analysis of Miocene plant fossil DNA,” in Molecules through Time, 421. 60

The magnolia study broke the million-year barrier, and with considerable excitement researchers turned to long extinct charismatic creatures such as dinosaurs as well as more mundane insects preserved in amber. A strong case could be made for amber preserved specimens because researchers believed that amber rapidly desiccates trapped remains and inhibits bacterial activity, two prerequisites for preservation of ancient DNA.49

At the University of California, Berkeley, aDNA research using amber-embedded specimens became a primary interest. The first attempt to extract DNA from amber inclusions actually occurred in 1983, just a year before Higuchi and others’ initial aDNA study, under a collaborative effort between Wilson, Higuchi, George Poinar, and Roberta Hess. George Poinar, entomologist at the University of California, Berkeley, later campaigned for aDNA research in amber inclusions while also simultaneously popularizing the idea which inspired Michael Crichton’s book Jurassic Park. Roberta Hess, later known as Roberta Poinar through her marriage to George, was an electron microscopist at Berkeley. In 1991, George Ponair and colleagues wrote, “Although extracting DNA from amber inclusions is a relatively recent endeavor which makes crucial use of the rapid developments in the area of cell and molecular biology (especially PCR), reviving simple life forms from fossilized resin has been a dream for some time.”50 Amber inclusions, often whole organisms trapped in sticky liquid tree resin and encased in a hardened amber shell, were appealing subjects of DNA research because of their exquisite state of preservation. Out of eight amber specimens prepped for the 1983 study, only two (a moth and a fly) revealed any DNA. The difficulty of the task ahead was apparent as the preparation alone took several days and the process of extraction was very tedious because external contamination remained a serious issue. This first attempt was little mentioned, possibly because no experiments were conducted to rule out contamination of the alleged DNA and authenticate the results.51 Reflecting on their earlier ambitions, George Poinar and Roberta Poinar explained, “The idea of extracting DNA from amber-embedded insects was perhaps a

49 Robert Wayne, Jennifer Leonard, and Alan Cooper, “Full of Sound and Fury: The Recent History of Ancient DNA,” Annual Review of Ecology and Systematics, 30 (1999): 459. 50 George Poinar, Jr., Hendrik Poinar, and Raul Cano, “DNA from Amber Inclusions,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, eds. Bern Hermann and Susanne Hummel (New York: Springer-Verlag, 1991), 93. 51 Ibid., 93, 95; George Poinar and Roberta Poinar, The Quest for Life in Amber (Reading: Addison-Wesley Publishing Company, 1994), 73-74. 61

little before its time then, possibly because the technology wasn’t yet in place.”52 Nonetheless, this study was an important stepping stone for future research endeavors. Several years later, after technology had caught up, particularly with the invention of PCR, and following numerous DNA studies on ancient museum specimens, archaeological finds, and fossils, the first published study of DNA extraction from amber specimens was reported in 1991. This study by Raul Cano, molecular biologist of the California Polytechnic State University, George Poinar, and his son, Hendrik Poinar, claimed to have found DNA in stingless bees, 24-50 million years old, preserved in Dominican amber.53 Further study ruled out contamination, suggesting the recovered DNA was original genetic material. Subsequent successful studies with amber inclusions soon demonstrated that amber-bedded specimens could be prime objects for molecular research.54 In an article a few years later, Poinar, Poinar, and Cano announced, “What scientists thought impossible some ten years ago, when DNA extraction studies on amber inclusions were first attempted, has now become a reality.”55 A dream turned to reality, with much thanks to technological advancements, aDNA research began to capture more than just the scientific community’s attention. Michael Crichton, famous science fiction writer, captivated the public with a fancied version of aDNA research in his popular novel, Jurassic Park (1990). Ben Waggoner, Department of Biology at the University of Central Arkansas, wrote of Jurassic Park’s overall popularity, “By far the most celebrated development has been the sequencing of ancient DNA… its fame being largely due to the overwhelming popular success of the book and movie Jurassic Park…”56 Jurassic Park, inspired by early aDNA studies with amber inclusions, imagined a science fiction scenario in which scientists resurrected the dinosaurs using ancient dinosaur DNA from the guts of a mosquito remarkably trapped and exceptionally preserved in amber. The novel, and later movie, not only popularized this new approach to fossil studies, but also served as the ultimate illustration of resurrecting ancient life forms. Crichton’s Jurassic Park took the possibilities of aDNA research and pushed them to the extreme, truly romanticizing the idea and

52 Poinar and Poinar, The Quest for Life in Amber, 72. 53 Raul Cano, Hendrik Poinar, D. Roubik, and George Poinar, Jr., “Enzymatic amplification of DNA from the bee Proplebeia dominicana in 24-25 million year old amber,” Med. Sci. Res. 20 (1992): 249-251. 54 Raul Cano, Hendrik Poinar, and George Poinar, Jr., “Isolation and partial characterization of DNA from the bee Proplebeia dominicana in 24-25 million year old amber,” Med. Sci. Res. 20 (1992): 619-623. 55 Poinar et al., “DNA from Amber Inclusions,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, 102. 56 Ben Waggoner, “Molecular Paleontology,” Encyclopedia of Life Sciences (2001): 3-4. 62

potential of aDNA. But, did the popular, romantic image of aDNA match the scientific evidence? Not entirely. While recent aDNA research suggested unprecedented possibilities for studying extinct and ancient organisms in real time, researchers were cautious about jumping to such fantastical conclusions. The year 1991 marked a critical moment in the history of aDNA studies; it was a time to reflect on the past seven years of research and where this research may be headed in the future. Richard Thomas, previously employed at the University of California, Berkeley, and now director of the DNA laboratory at the Natural History Museum in London, organized a small conference dedicated to recent aDNA research. The conference, titled “Ancient DNA: The Recovery and Analysis of DNA Sequences from Archeological Material and Museum Specimens,” was held 8-10 July, 1991 at the University of Nottingham, England. With interesting research in progress, the purpose of the workshop was to congregate with those interested scientists and make sense of what was occurring in aDNA studies. Although Thomas had envisioned a more “quiet, technical meeting” comprised of several dozen researchers, Chefras reported in his article for Science that the conference attracted more attention than anticipated. Chefras explained, “But that was before the science section of The New York Times published a fanciful ‘recipe’ for recreating a dinosaur from ancient DNA – and mentioned Thomas’s upcoming workshop at the University of Nottingham.” Quoting Thomas, Chefras reported: “‘We were inundated by people,’ says Thomas. ‘We were stunned and amazed by the reaction from the press. We had to spend a fair amount of our time telling them, ‘No, we are not going to reconstruct the dinosaur.’”57 Chefras exclaimed, “However much scientists may protest that it cannot be done, the public and the popular press clearly expect ancient DNA to create Jurassic Park for real.”58 While the press and public may have been more than disappointed at the news, the conference’s scientific attendees found the workshop rewarding. Chefras noted, “They found that molecular biology may be on the brink of revolutionizing archeology and paleontology, just as it had earlier revolutionized population genetics and evolutionary biology.” Furthermore:

57 Cherfas, “Ancient DNA: Still Busy After Death,” 1354. 58 Ibid., 1356. 63

Some 40 presentations at the conference showed that students of ancient DNA are overcoming the problems of technique and contamination and turning their pursuit into a full-fledged field that offers unique answers to serious questions about kinship, the migrations of ancient peoples, and the taxonomic relations and rates of evolution of long- extinct species.59

In part, what this conference and article established was that aDNA research was indeed a new field of scientific research. Chefras predicted that archeology and anthropology would be the immediate beneficiaries of aDNA research because recent material is more likely to yield easier experimentation and successful results. However, evolutionary biologists also wanted in, perhaps because they could see the light at the end of the tunnel for the potential of aDNA studies. The previous seven years certainly demonstrated not only the awareness of an anomaly within the existing scientific paradigm, but also a serious exploration of that anomaly by a number of researchers testing a number of specimens all disparate in age and kind. Was it time to make room for a deeper understanding of DNA preservation in ancient material? It seems safe to say that in light of the evidence, aDNA researchers had adopted a more liberal understanding of DNA preservation than before. As more studies were conducted and results of aDNA were authenticated, scientists acknowledged that the preservation of ancient genetic material was indeed possible, and more importantly, that the molecular data recovered was valuable for constructing the history of life in both real and deep time. However, as scientists began to examine the preservation potential of DNA in a new light, their current understanding became more complicated and confused. The exploration of this anomaly was far from over. In the preface to their work Molecules through Time, Gordon Curry and Geoffrey Eglinton wrote:

Despite the spectacular successes of recent years, there is still little known about the extent to which biomolecules are preserved in the fossil record. The geological conditions that are conducive to good biomolecular preservation are something of a mystery: indeed, we simply do not know yet whether such preservation is exceptional rather than commonplace. Further research may well reveal many more examples of excellent preservation; there will surely be spectacular discoveries in the next few decades, as new

59 Ibid., 1354. 64

techniques are applied more widely and as we begin to build up a better understanding of the processes in geological environments.60

More research would be necessary to create a more robust and accurate understanding of the factors affecting the fossilization of genetic material before scientists could confidently conclude the full potential and significance of aDNA research overall. Chefras ended his Science article with a quote from Golenberg: “The object is not necessarily to see who can get the oldest DNA…but actually to start working up research projects that can make sense.”61 Chefras eloquently concluded:

That was the message that participants at the Nottingham conference took away with them: Despite the remaining technical problems, ancient DNA is no longer just a curiosity but an area where systematic studies can produce insights unavailable by any other technique. For archeologists, anthropologists, and paleontologists the message is clear – the time has come to ensure that textbooks on the polymerase chain reaction and gene cloning are on the bedside table.62

All in all, the anomaly remained in part a mystery. Though scientists were fairly confident in the results from the quagga and mummy studies, many were skeptical about twenty-million-year-old fossil leaf DNA. Future study would clarify whether Golenberg’s results and others like it were an artifact of contamination or a true scientific anomaly. Nonetheless, the conference’s overall message optimistically confirmed aDNA as a new, legitimate field of research and a worthy scientific endeavor. This was a particularly important message for the field of paleontology. As we learned in chapter two, paleontology once played a leading role in arguments for evolutionary theory and in particular for Darwin’s theory of evolution by natural selection as first published in the Origin. Fossils were evidence of the extensive and dynamic history of life from past to present. For most of its history, the science of paleontology relied on the morphology and comparative anatomy of

60 Gordon Curry and Geoffrey Eglinton, Molecules through Time (Great Britain: University Press, Cambridge, 1991), 311. 61 Cherfas, “Ancient DNA: Still Busy After Death,” 1356. 62 Ibid., 1356. 65

fossil creatures to piece together the history and evolution of life. Yet the rise and priority of experimental science in the early 1900s, and experimental biology in particular, further marginalized paleontology as a historical science, ill-equipped to answer questions of an evolutionary nature. Thus, aDNA was a particularly inviting field of research for paleontological specimens because if DNA could be preserved in some of the world’s most ancient and curious life forms, then paleontology could directly test and observe evolution in real time, for the first time. For paleontology, aDNA research seemed to suggest that a fossil’s value extended far beyond the museum shelf. Perhaps the answers to our questions are hidden within. As Jack Horner, paleontologist at Montana State University, recently suggested, “Molecules are fossils too.”63 By the early 1990s, it was becoming more apparent that aDNA research was a viable molecular approach to several fields of study from anthropology to evolutionary biology, and researchers continued to test the age limits of DNA preservation. Bruce Runnegar, Professor of Geology at the University of California, Los Angeles, wrote:

I like to take the catholic view that palaeontology deals with the history of the biosphere and that palaeontologists should use all available sources of information to understand the evolution of life and its effect on the planet. Viewed in this way the current advances being made in the field of molecular biology are as important to present-day paleontology as studies of comparative anatomy were to Owen and Cuvier.64

As a reliable approach to fossil studies, aDNA research would revolutionize the once purely historical field of paleontology with the incorporation of experimental techniques and the application of current molecular technology in very exciting, novel ways. Carol Cleland, philosopher of science at the University of Colorado, wrote on the philosophical distinction between historical and experimental science, and her work is useful for exploring this transition from a historical to a more experimental approach to fossil studies. We will discuss her argument further and its implications for paleontology as a historical science in chapter five.

63 Jack Horner and James Gorman, How to Build a Dinosaur (New York: Penguin Group Inc., 2009), 85. 64 Runnegar, “Molecular Palaeontology,” 1. 66

Conclusion

Overall, the early years of aDNA research from 1984 to 1991 signify the exploration of an anomaly, namely the presence of DNA in ancient and fossil specimens. These early years of research demonstrate both the awareness of an anomaly and attempts to authenticate results. Yet, the previous seven years of study did not determine the acceptance of the anomaly among the scientific community. In fact, many remained skeptical. By the early 1990s, however, scientists had begun to realize that aDNA research was a valuable and practical method for studying the past. Specimens up to several thousand years in age seemed acceptable research candidates. Anything older was questionable. Although aDNA research was made possible and further facilitated by technological advancements, such as standard DNA testing techniques and the later development of PCR, aDNA research also relied on scientists’ ability to explore new uses for old specimens. It required learning to think about and study fossils and DNA in a different light. In the case of aDNA research, it was the application of available technology in an innovative way. At the same time, aDNA research required caution and special techniques for preparation and extraction of highly degraded DNA samples. We have only surveyed the first several years of aDNA research, and a much fuller analysis of the outcome of the study of aDNA and its significance for the field of paleontology and also the modern evolutionary synthesis at large will come in the following chapter. As Hull claimed, science is a process and one that often relies on interdisciplinary efforts. All in all, we can say that aDNA research had shown us that our fossils may be more alive than they seem.

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CHAPTER FOUR THE SEARCH FOR ANCIENT DNA (1992-1999)

Introduction Following the first official meeting on aDNA research in 1991, conference participants were filled with a new found confidence in the future of their field. The potential of aDNA research as a viable approach to both archaeological and paleontological specimens would allow scientists to study deep time in real time. However, at the same time, researchers were skeptical of reports claiming DNA from very ancient specimens, namely specimens millions of years old. For this reason, some researchers tested the limits of DNA preservation and focused on the recovery of DNA from some of our most ancient creatures like dinosaurs. Further study soon proved their results unauthentic which suggested that really ancient fossils were an unlikely source of DNA. Instead, pioneers in aDNA research stressed the development and adherence to strict criteria and stringent practices in hopes of producing not only genuine DNA sequences, but evolutionary significant aDNA studies as well. Over these years, aDNA research became a valuable tool for constructing evolutionary histories and molecular clock dating. This chapter is a continuation of the history of aDNA research and an account of its development from 1992- 1999. It is also the further exploration of a scientific anomaly; the existence of DNA in ancient organisms.

Ancient Anomalies Golenberg and fellow researchers’ twenty-million-year-old fossil leaf study surprised many scientists, and the earlier amber studies proved equally interesting. The latest invention of the polymerase chain reaction (PCR) made experiments with only small and even highly degraded samples of DNA possible. Even if really ancient paleontological specimens contained only a miniscule amount of genetic material, then perhaps sequences could be amplified via PCR to make for a substantial study. If DNA existed in fossil material then we would not have to infer patterns and rates of evolution, but we could prove it with quantifiable, molecular evidence. In her article, “The Future of Molecular Paleontology,” Mary Schweitzer, paleontologist at North Carolina State University, argued, “Examination of such molecules may strengthen the

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objectivity of the scientific discipline of paleontology, as well as providing an independent means of testing phylogenetic hypotheses.”1 However, the Magnolia study results remained an ancient anomaly. These studies, and others like them, would need to be reproduced in order to authenticate both the reality and reliably of DNA preservation in objects over the million year mark. Recent amber studies suggested that amber inclusions would be the most likely paleontological specimens to yield intact DNA. In 1992, the year following the first official aDNA conference, Rob DeSalle, Department of Entomology at the American Museum of Natural History, New York, and colleagues decided to further explore the likelihood of DNA in fossilized amber specimens. Amber inclusions seemed ideal candidates for an aDNA study because of the often exquisite preservation of the specimens trapped within the solidified resin. Yet, the likelihood of DNA preservation in fossil amber remained uncertain. DeSalle and others, however, were more interested in what important evolutionary questions could be answered with amber DNA if it did in fact exist. Objective, molecular evidence, in the face of morphological disagreement, might settle any discrepancies. Mastotermes darwiniensis, a termite from northern Australia, was considered the “missing link” between cockroaches and termites. Also dubbed a “living fossil,” it was considered the most primitive living species of termite.2 Living fossil, a term first coined by Darwin in the Origin, refers to any living organism that shares an extreme similarity to a fossil – often extinct – creature. In such cases, most organisms considered to be a living fossil do not possess many derived features by way of form or function, but instead retain the most primitive characteristics of its fossil ancestor. However, the primitiveness of Mastotermes was often debated. Other phylogenetic interpretations had been proposed, yet none of them were in agreement and each interpretation suggested a radically different evolutionary history of the extinct and extant termites. To better assess these inconsistencies between phylogenetic reconstructions, DeSalle and fellow researchers extracted DNA from an extinct three-winged termite exquisitely preserved in 25 to 30-million-year-old amber. DNA sequences from this amber specimen, Mastotermes electrodominicus (an extinct, but close relative of the living M. darwiniensis), were compared with sequences from related insects for phylogenetic analyses in hopes of better understanding termite evolution.

1 Mary Schweitzer, “The Future of Molecular Paleontology,” Palaeontologia Electronica 5 (2003): 1. 2 Rob DeSalle, John Gatesy, Ward Wheeler, and David Grimaldi, “DNA Sequences from a Fossil termite in Oligo- Miocene Amber and Their Phylogenetic Implications,” Science 257 (1992): 1933. 69

Although only an extremely small and highly degraded sample of DNA was recovered from the amber specimen, DeSalle and colleagues were confident in its authenticity. In their article for Science they proudly claimed, “We have sequenced the oldest DNA extracted from a fossil (in 25-million-year-old amber) and have used analyses of this DNA in phylogenetic reconstruction.”3 DeSalle and his team, recognizing contamination as a “major pit-fall of this type of investigation,” were nonetheless self-assured that their results were contaminant-free. They reported confidence in their results based on proper protocol, facility control, and contamination testing. For this study, researchers were interested in using the molecular data to explore several evolutionary questions. First, DeSalle and his colleagues were interested in discerning the evolutionary relationship of M. electrodominicus – the 25-million-year-old amber specimen – to other winged creatures like termites, cockroaches, mantinds, and more specifically, the extant M. darwiniensis. DeSalle’s team also recognized the advantage of incorporating both fossil and extant evidence in phylogenetic construction. Because fossils are crucial for elucidating evolutionary patterns, they wanted to discover the effect of adding the fossil into the overall evolutionary history of these creatures. Furthermore, these researchers were interested in how both the molecular and morphological data interacted in phylogenetic construction with the addition of molecular data from the fossil specimen.4 Based on the molecular evidence, their results (which incorporated both the inclusion and removal of the fossil specimen, M. electrodominicus, with phylogenetic analyses) indicated that incorporation of fossil data significantly affected phylogenetic interpretation and its overall meaning. In closing the article, DeSalle and others noted that using fossil taxa and all available data in phylogenetic studies is important because inclusion of fossil specimens can critically alter our perception of evolutionary relations between past and present creatures. More impressive was the preservation and extraction of DNA from a fossil millions of years old. Although most successful aDNA studies concentrated on more recent fossil material, DeSalle and colleagues claimed, “Among all modes of fossilization, it can be reasonably assumed that preservation in amber will more consistently yield fossil DNA from Tertiary and perhaps older geo-logical periods. In summary, they stated, “Here is an illuminating glimpse into

3 DeSalle et al., “DNA Sequences from a Fossil termite in Oligo-Miocene Amber and Their Phylogenetic Implications,” 1934. 4 Ibid., 1935. 70

the DNA of 25 million to 30 million years ago.”5 DeSalle and his team’s termite study suggested that paleontological material of some of our most ancient organisms could benefit from aDNA research. As the termite study tested the limits on DNA preservation in fossil material, other researchers continued aDNA work on more recently extinct specimens such as the thylacine. The evolutionary history of Thylacinus cynocephalus, the extinct Tasmanian tiger, was a source of much debate over the past century. While native to Australia, the thylacine also exhibited a strong morphological relatedness to borhyaenids, another group of carnivorous wolf-like marsupials which were of South American origin. At the center of the debate was whether the morphological relatedness of thylacines and borhyaenids was evidence of a common ancestor or . While many morphological analyses had been done, the results were ambiguous in that they supported both hypotheses. Though Thomas and others’ 1989 study on the extinct marsupial, one of the earliest aDNA studies, added some clarity to the debate, the issue remained unresolved. In 1992, Carey Krajewski and colleagues set out to further compare DNA sequences of the extinct thylacine with thirteen other Australian marsupials in hopes of truly discovering and settling their evolutionary history. Krajewski, then at the Department of Zoology at Southern Illinois University, and others explained, “The central purpose of this study is to bring DNA sequence data to bear on the phylogenetic position of Thylacinus with respect to dasyurid marsupials.” Moreover, “If thylacines are only ‘specialized’ dasyurids, then they should have a close genetic relative within the family. If, however, they are an ancient lineage, they should appear as a to all dasyurids. To discriminate between these hypotheses, some resolution of phylogeny within Dasyuridae is also required.”6 Krajewski and fellow researchers’ study, extensive in material and methods, sampled DNA sequences from thirteen specimens representing the entirety of the dasyurid family. In addition to the extant specimens sampled, aDNA was extracted – using appropriate protocol as suggested by Pääbo and PCR procedures – from an extinct thylacine specimen from the Smithsonian. Based on a series of phylogenetic analyses, the study concluded that Thylacinus

5 Ibid., 1936. 6 Carey Krajewski, Amy Driskell, Peter Baverstock, and Michael Braun, “Phylogenetic Relationships of the Thylacine (Mammalia: Thylacinidae) among Dasyuroid Marsupials: Evidence from Cytochrome b DNA Sequences,” Proceedings of the Royal Society of London 250 (1992): 20.

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was strikingly different from other dasyurides. This was most likely evidence that the thylacine came from a separate ancestral lineage. However, Krajewski and his team conceded that although this present study did not “completely resolve deep branches of the dasyuroid tree,” it is more clear now that Thylacinus is less related to dasyurids than previously thought.7 This evidence rejected the former hypothesis put forth by Simpson in the early 1940s, that the thylacine represented a more recently derived lineage. Instead, the evidence supported the opposing hypothesis that thylacine was of an older, separate, and distinct lineage. It was not until nearly five years later, in 1997, that the Krajewski and colleagues reached a more definitive resolution about the thylacine’s evolutionary past. In their article, “DNA phylogeny of the marsupial wolf resolved,” they presented strong evidence for Dasyuromorphia as a monophyletic group, or a separate and distinct , thus providing “the best evidence to date for the phylogenetic placement of thylacines with Dasyuromorphia.”8 Krajewski and others, arguing for a thorough study and definitive conclusion, stated, “The result is not an artefact of short DNA sequences,” nor “failure to evaluate alternative hypotheses,” or “limitation to a single gene tree.”9 Their results showed with cautious certainty that the anatomical similarities between the Australian thylacine and South American boyhyaenid were the result of convergent evolution. These studies demonstrated rigor and persistence in solving an evolutionary enigma. It demonstrated the value in assessing both morphological and molecular data when discerning evolutionary histories. In this case, molecular evidence was necessary to test and decide the correct story about the thylacine’s past. The Tasmanian tiger studies from 1989 to 1997 represented one of the most extensive and definitive phylogenetic studies using aDNA research. Another rigorous evolutionary study, and an example of aDNA research at its best, was the extinct study by Alan Cooper, Pääbo, and fellow researchers. The moa was a flightless bird that roamed the forests during the Pleistocene. Unfortunately, the moa, and all eleven species thereof, went extinct by 1400 A.D. Yet, the extinct moa shared several biogeographical and anatomical similarities with the kiwi, another New Zealand native, flightless bird. For this reason, it was thought that extinct moa shared a common ancestor with the modern kiwi. Despite such morphological similarities, the exact relationship between the two flightless

7 Krajewski, “Phylogenetic Relationships of the Thylacine (Mammalia: Thylacinidae) among Dasyuroid Marsupials: Evidence from Cytochrome b DNA Sequences,” 26. 8 Carey Krajewski, Larry Buckley, and Michael Westerman, “DNA phylogeny of the marsupial wolf resolved,” Proceedings of the Royal Society of London 264 (1997): 915. 9 Krajewski, “DNA phylogeny of the marsupial wolf resolved,” 915; Artefact is the U. K. based publication spelling. 72 birds remained uncertain. Cooper, then working in the Department of Biochemistry and Molecular Biology at the University of California, Berkeley, along with Pääbo and other colleagues, attempted to settle the score.10 Using bone and soft tissue samples from five extinct and different moa specimens – all recovered from cave sites – Cooper and fellow researchers applied standard DNA extraction and PCR procedures. DNA sequences were also taken from eight other ratites, the larger group of flightless birds that includes creatures like the , for comparative analyses. Contrary to the biogeographical and morphological evidence, phylogenetic analyses derived from molecular data suggested a different evolutionary story. In their article, Cooper and his co-authors announced, “The most surprising result of the phylogenetic analysis is that the two groups of New Zealand ratites have different origins, the representing an earlier divergence among ratites, whereas the kiwis more recently shared an ancestor with the ostrich and Australian ratites.” 11 Based on comparative analyses of DNA sequences, Cooper and colleagues determined that the moa actually diverged early on from other flightless birds and furthermore, the kiwi was more closely related to the Australian emu and cassowary. This proved that flightless birds had independently settled in New Zealand at two different times. Reflecting on the molecular analysis in light of morphological analyses, Cooper and others commented, “It is interesting to compare this view of ratite evolution with the view that emerges from morphology.” They explained, “A analysis of 83 postcranial skeletal characters agrees with the molecular data in that kiwis, emus, and cassowaries form a monophyletic group and that moas constitute an early divergence among ratites.” Yet other studies’ evidence suggests that kiwis are more closely related to moas than with other ratites of Australian origin. Nonetheless, Cooper and colleagues – confident in their molecular analyses – concluded that because the “majority of the morphological traits shared by moas and kiwis are primitive,” that kiwis and moas must have evolved convergently or independently from a more primitive ancestor.12 Where morphological evidence may be inconclusive, molecular data can be decisive. In this case, using aDNA and DNA sequences were especially valuable in exploring the hypothesis of the “molecular clock”; an innovative idea that uses molecular change in organisms

10 Alan Cooper, Cecile Mourer-Chauvire, Geoffrey Chambers, Arndt von Haeseler, Allan Wilson, and Svante Pääbo, “Independent origins of New Zealand moas and kiwis,” Proceedings of the National Academy of Sciences 89 (1992): 8741-44. 11 Ibid., 8742. 12 Ibid., 8743. 73 to date divergence rates among those organisms. Ayala explained, “If the rate of evolution of a protein or gene were approximately the same in the evolutionary lineages leading to different species, proteins and DNA sequences would provide a molecular clock.”13 In explaining the utility of this approach, Turner noted, “If you know the average rate of change in the genes or proteins, then you should be able to work backwards in order to determine how much evolutionary time it took, at that rate of change, to get from a common ancestor in the past to the living organisms that we observe today.”14 This notion of the “molecular clock” uses molecular change to date past evolutionary events and in particular, dating splits in . For example, molecular clock dating can tell us when two species diverged from one another in the distant past. If we can know when one species diverged from another, it may be possible to further hypothesize about genetic and/or environmental reasons for the divergence. Based on the moa study results, Cooper and co-authors hypothesized, “Under the assumption of a flightless ratite ancestor, the moas, which represent an early divergence among the ratites, and the kiwis, which represent a later divergence, must have been isolated together when New Zealand was separated from Australia at approximately 80 million years ago.”15 Molecular clock dating not only offers a more conclusive phylogenetic history, but knowledge of that history can help us construct a more accurate and robust understanding of a world that existed hundreds, thousands, and millions of years ago. The termite, Tasmanian, and moa studies tested the reality of DNA in ancient and fossil material. Each study focused on using aDNA from extinct creatures in comparison with extant organisms in hopes of illuminating the true story of their past. In each case, morphological evidence and previous phylogentic analyses with morphological data posed considerable confusion about the ancestral state of the termite, thylacine, and moa respectively. However, by employing molecular data, and specifically aDNA sequences from these extinct specimens and their extant relatives, researchers were able to settle the discrepancies. These studies, careful in the precision of their research, claimed confidence in the authenticity of their results. However, the termite DNA, estimated at 25 million years old, was by far the oldest of these studies and

13 Francisco Ayala, “Molecular Evolution vis- à-vis Paleontology,” in Paleobiological Revolution: Essays on the Growth of Modern Paleontology, eds. David Sepkoski and Michael Ruse (Chicago: The University of Chicago Press, 2009), 177. 14 Derek Turner, Paleontology: a Philosophical Introduction (Cambridge, Massachusetts: Cambridge University Press, 2011), 197. 15 Cooper et al., “Independent origins of New Zealand moas and kiwis,” 8743-8744. 74 also the oldest DNA ever sequenced. Despite the assumed rigor behind these studies, the results, especially in DeSalle’s study, would need authentication through further research.

Anomaly or Artifact?

In the year following the termite study, Thomas Lindahl, working at the Imperial Cancer Research Fund in Hertfordshire, United Kingdom, wrote in a review article for Nature about the chemical stability of DNA and its consequences for the future of aDNA research.16 He stated, “Although DNA is the carrier of genetic information, it has limited chemical stability.” Certain processes such as hydrolysis and oxidation, the breaking down or altering of chemical compounds through interaction with water or oxygen, directly affect the chemical composition of DNA. Lindahl explained, “The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.”17 Despite the chemical instability of DNA and its unlikely preservation in fossil material, Lindahl noted that if possible, “Recovery of DNA fragments from extinct animals or plants in museum collections or from archaeological excavations can permit direct comparison with related contemporary material by DNA sequencing.” Such an approach “offers a valuable complement to taxonomic studies.” As noted, even in the rare case that DNA has been preserved, it most likely exists in fragments or is so degraded that it is impossible to use in any evolutionary study. Even though PCR can be helpful in amplifying miniscule amounts of DNA, contamination via PCR remains a problem. Lindahl explained, “A problem with the hypersensitive PCR technique, as encountered by most newcomers to the method, is that trace amounts of contaminating DNA accidentally derived from laboratory glassware, or even the experimenter, readily produce false-positive results.” Moreover, “This is a particularly difficult problem in work with ancient DNA, which is often highly degraded or possibly non-existent in available specimens and the occasional dramatic ‘success’ in this area should be viewed with skepticism.”18 While DeSalle and fellow researchers’ results appeared at first a remarkable feat in aDNA research, its celebration was premature.

16 Thomas Lindahl, “Instability and decay of the primary structure of DNA,” Nature 362 (1993): 709-715. 17 Ibid., 709. 18 Ibid., 713. 75

In 1993, DeSalle and his colleagues published a follow-up to their 1992 termite study. This article, “PCR jumping in clones of 30 million-year-old DNA fragments from amber preserved termites,” retracted their previous claims of authentic DNA sequences from the ancient amber specimen. Instead, DeSalle and his fellow researchers attributed the prior results to extant insect and fungal contamination.19 In a later article, “Problems of reproducibility – does geologically ancient DNA survive in amber-preserved insects?”, Jeremy Austin, Department of Paleontology and Zoology at the Natural History Museum, London, and fellow scientists objected to previous studies claiming to have retrieved authentic DNA sequences from fossil material over several million years old. Austin and co-authors noted, “Whether geologically ancient DNA exists or not remains controversial, largely because previous claims have not been verified by independent replication, a primary criterion of authenticity.”20 Though fossil amber may contribute to the exceptional morphological and biochemical preservation of specimens, it may not be a realistic candidate for the aDNA preservation. To test the validity of prior claims of alleged DNA from amber specimens millions of years old, Austin and fellow researchers, including Richard Thomas at the Natural History Museum, attempted to replicate the results of several aDNA studies. In addition to their efforts to reproduce Cano, Poinar, and Poinar’s 1991 amber study, Austin’s team tested for DNA in fifteen insects in fossilized amber. All attempts to replicate and authenticate DNA results failed. In conclusion, Austin and others claimed:

Whereas ancient DNA sequences from specimens younger than 100000 years old have now been replicated independently, we have singularly failed to recover authentic ancient DNA from amber fossils. Although no negative result can disprove the existence of ancient DNA in amber-preserved fossils, our work shows that isolation of geologically ancient DNA from amber-preserved insects is not reproducible.21

19 Rob DeSalle, M. Barcia, and C. Wray, “PCR jumping in clones of 30 million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus),” Experientia 49 (1993): 906-909. 20 Jeremy Austin, Andrew Ross, Andrew Smith, , and Richard Thomas, “Problems of reproducibility – does geologically ancient DNA survive in amber-preserved insects?” Proceedings of the Royal Society of London 264 (1997): 467. 21 Austin et al., “Problems of reproducibility – does geologically ancient DNA survive in amber-preserved insects?” 473. 76

Other studies also tried to reproduce the amber study findings but could not. Thus Austin and colleagues’ study, in line with other researchers’ unsuccessful efforts, concluded that “in the absence of unambiguous and independent verification, research on geologically ancient DNA will remain little more than a ‘biological curiosity.’”22 Lindahl, reminding us of the unlikely preservation of DNA in anything over several hundreds of thousands years old explained, “Beyond this point, time-dependent chemical decay of DNA structure makes successful retrieval difficult.” Yet regardless of the age of the specimen being subject to DNA testing, Lindahl argued that stringent precautions and procedures be taken. Arguing for experimental rigor, Lindahl noted that both positive and negative results of aDNA studies need to be reported, that reproducibility of results from a number of specimens should be pursued, that negative controls are to be used, and that chemical analysis testing for presence of proteins should be employed as well. If there is no evidence of proteins, then there will be no evidence of DNA either. In closing his article, Lindahl warned:

Recent claims of recovery of 100-million-year-old DNA have overshadowed the valuable and important studies on moderately ancient DNA. Rather than proceed spectacularly further and further back in time with anecdotal reports on single samples, using the notoriously contamination-sensitive PCR technique, I suggest that the next goal be a convincing report on the amplification of small DNA fragments, say, 100,000 years old.23

According to Lindahl, the point was not to see who could recover the most ancient DNA. Rather, Lindahl suggested that we should be more concentrated in creating useful and careful, evolutionary studies when genuinely ancient DNA is available. The following year saw a series of more impressive and reliable aDNA studies. In 1994, Oliva Handt and Pääbo, both researching at the Institute of Zoology at the University of Munich, Germany, along with other colleagues, sampled an assortment of muscle, connective tissue, and bone from the ancient Ice Man for DNA analysis. Three years previously, in the Tyrolean Alps of Italy, a 5,100 to 5,300 year old “Ice Man” was discovered. The Ice Man, because of its frozen

22 Ibid., 473. 23 Lindahl, “Recovery of antediluvian DNA,” Nature 365 (1993): 700. 77 condition from death until discovery, was presumably a prime candidate for DNA study. 24 With a total of eight samples, Handt, Pääbo, and colleagues applied standard DNA extraction and PCR amplification procedures. What they discovered was that any endogenous DNA that did remain was fairly degraded. Using appropriate protocol, they tested for human contamination that may have occurred during the excavation and handling of the Ice Man at the time of discovery. Two samples were chosen for testing of contamination. To further validate the sequence’s authenticity, Handt and colleagues requested independent collaboration with a lab in Oxford. There in England a bone sample from the Ice Man was analyzed twice by two independent researchers and both results in Oxford proved “unambiguous and identical” to the initial result produced in the Munich lab. Thus, Handt and his team confidently concluded that the DNA sequence, uncontaminated, was of original Ice Man material and could be compared to other contemporary human population sequences. Most notable was the study’s overall procedure and attention to detail; what Wayne, Leonard, and Cooper referred to as the “gold standard of authentication in studies of ancient DNA.”25 Caution and thoroughness was the hallmark of a good aDNA study. That same year, Matthias Höss and Pääbo, Institute of Zoology at the University of Munich, and Nikolai Vereshchagin, Institute of Zoology, St. Petersburg, Russia, published an impressive study on mammoth DNA sequences.26 The study involved multiple soft tissue samples from five different all ranging in age from 9,700 to over 50,000 years old. Multiple samples from four out of the five specimens were subjected to further testing. Sampling a number of individuals made for a more well-rounded study. Following proper protocol, DNA was recovered from the ancient mammoths, carefully sequenced, and compared to DNA of African and Indian for phylogenetic comparison. Taking heed of one of Lindahl’s earlier articles on aDNA research criteria, they noted:

Lindahl suggests that sequences should be verified by reproduction from different individuals of a species, that negative results should be reported along with positive ones, and that samples of a moderate age group (up to 100,000 years) should be investigated to

24 Oliva Handt, Martin Richards, Marion Trommsdorff, Christian Kilger, Jaana Simanainen, Oleg Georgiev, Karin Bauer, , Robert Hedges, Walter Schaffner, Gerd Utermann, Bryan Sykes, and Svante Pääbo, “ Analyses of the Tyrolean Ice Man,” Science 264 (1994): 1775-1778. 25 Wayne et al., “Full of Sound and Fury,” 462. 26 Matthias Höss, Svante Pääbo, and Nikolai Vereshchagin, “Mammoth DNA sequences,” Nature 370 (1994): 333. 78

establish if they contain retrievable DNA. We completely agree and believe that it represents a great danger to the field of molecular archaeology if methods and procedures that allow the confirmation of results are not used. For example, sequences retrieved by molecular cloning cannot be reproduced because of the low cloning efficiency of ancient DNA, and are therefore of only limited scientific value.27

Höss and fellow researchers urged other studies, like the previous amber specimen studies, be subjected to the same kind of rigorous analysis and reproduction. Immediately following Höss and colleagues’ Nature article was a second ancient mammoth study. This report, published by and colleagues of the Department of Biological Anthropology at the University of Cambridge, United Kingdom, as well as Adrian Lister, Department of Biology at University College of London, claimed DNA extraction and PCR amplification of ancient genetic material from the bones of two frozen Siberian woolly mammoths. Discovered in the 1970s, both specimens were dated at least 47,000 years old. Hagelberg’s team exclaimed, “To our knowledge, these mammoth bones are the oldest dated vertebrate remains from which DNA has been amplified.”28 Also commenting on Lindahl’s classic 1993 article, Hagelberg and researchers stated, “Lindahl has suggested that moderately ancient DNA (about 100,000 years old) should be targeted for analysis to bridge the temporal gap that exists between DNA sequences from relatively recent biological remains and those many millions of years old.”29 In fact, anything older than about one million years old, termed “Antediluvian DNA” by Lindahl, was expected to be impossible.30 Like Lindahl, Hagelberg and colleagues advised for more aDNA sequencing of both extinct and extant specimens within this recommended age range for a better understanding of the potential of DNA preservation. Despite Lindahl’s advice and a decreasing confidence in the likelihood that DNA could survive over 100,000 years of age, some researchers still clung to the possibility that DNA could endure the million year barrier. In the wake and excitement of Jurassic Park, Scott Woodward and colleagues published a stunning report in November of 1994. Woodward, of the Department of at Brigham Young University, Utah, and scientists announced in Science,

27 Höss et al., “Mammoth DNA sequences,” 333. 28 Erika Hagelberg, Mark Thomas, Charles Cook, Jr., Andrel Sher, Gennady Baryshnikov, and Adrian Lister, “DNA from ancient mammoth bones,” Nature (1994): 333. 29 Hagelberg et al., “DNA from ancient mammoth bones,” 333. 30 Lindahl, “Recovery of antediluvian DNA.” 79

“DNA was extracted from 80-million-year-old [presumed dinosaur] bone fragments found in strata of the Upper Cretaceous Blackhawk Formation…in eastern Utah.”31 This study pushed the limits of DNA preservation even further than 1990 Magnolia article. Woodward and fellow researchers recovered two bone fragments, possibly belonging to two different creatures, from the 80 to 85-million-year-old coal beds in the Upper Cretaceous Blackhawk formation – an area known for dinosaur trackways, but only a few dinosaur fossils. The bones, appearing to have undergone little destruction, were sampled and a total of forty-two DNA extractions were obtained. Of the available extractions, nine DNA sequences proved worthy of study and were compared with all sequences in GenBank and the European Molecular Biology Laboratory databases.32 Although the study claimed to have authentic dinosaur DNA, no phylogenetic analyses were published along with the study to support the claim. Just a year later, in 1995, another report claiming dinosaur DNA came from Peking University in . Zhang Yun and colleagues at Peking University in , China, announced, “Ancient DNA representing parts of genes have been obtained from the flocculent inclusions of the Late Cretaceous dinosaur , collected from Xixia Basin, Henan Province.”33 Although exciting, the results were received with skepticism. Contamination, always an issue when working with DNA studies, became an immediate concern for skeptics. Woodward and colleagues even admitted the high risk of contamination involved in aDNA research: “The possibility of contamination of ancient samples by contemporary DNA is a serious concern when analyzing ancient DNA sequences…It is imperative that every precaution be taken to prevent the introduction of contemporary DNA into the ancient sample.”34 In light of this observation, five other laboratories set out to independently check for DNA authenticity. Each lab determined the alleged dinosaur DNA to be false. Now exposed as a contaminant, researchers suspected the DNA was an artifact of human origin. S. Blair Hedges and Schweitzer soon published further research and a response to the Woodward and his team’s dinosaur study confirming the suspicion. In their article Hedges,

31 Scott Woodward, Nathan Weyand, and Mark Bunnell, “DNA sequence from Cretaceous period bone fragments,” Science 266 (1994): 1229. 32 GenBank and the European Molecular Biology Laboratory databases contain genetic sequences for mammals, birds, reptiles, , and also insects. Comparison with these databases allows recognition of genetic similarities and differences among organisms. 33 Zhang Yun and Fang Xiaosi, “A Late Cretaceous with Preserved Genetic Information,” Acta Scientiarum Naturalium Universitatis Pekinensis 32 (1995): 129-139. 34 Woodward et al. “DNA Sequences from Cretaceous Period Bone Fragments,” 1230. 80

Department of Biology and Institute of Molecular Evolutionary Genetics at Pennsylvania State University, and Schweitzer, then at the Department of Paleontology of the Museum of the Rockies in Bozeman, Montana, reported, “However, our results suggest that the DNA template was not from a Cretaceous organism such as a dinosaur, but rather from an extant organism, most likely a human.” Furthermore, in closing their technical comments, they added, “Although phylogenetic support has been presented for other findings of DNA surviving for millions of years, real advance in this field will come only when it is demonstrated that those studies can be replicated in independent laboratories.”35 Multiple studies endorsed Hedges and Schweitzer’s conclusion that the DNA amplified was not dinosaur but human DNA. Hans Zischler, of the Zoological Institute at the University of Munich, and researchers stated, “In conclusion, these results strongly suggest that Woodward et al. accidentally amplified nuclear copies of human mitochondrial DNA. The fact that a sequence from an ancient specimen is not identical to any hitherto determined sequence cannot be taken as an indication for the ancient origin of that sequence.”36 The same fate befell the dinosaur eggs from China. Regarding this report, Wang and colleagues from the National Key Laboratory of Molecular Virology and , China, established, “Taken together, our results from both the similarity alignment and the phylogenetic analysis clearly show that the Peking University scientists accidentally amplified fungal and plant rDNAs in their PCR experiments attempting to get dinosaur DNA.”37 The probability of recovering any real dinosaur DNA seemed bleak, and the false report added to the skepticism that DNA could survive more than Lindahl’s recommended 100,000 year threshold. Later in 1996, Höss and other researchers, focusing on more moderately ancient specimens, performed another ancient DNA study, this time on the extinct ground sloths.38 Forty-five samples from the remains of thirty-five ground sloths (representative of three families of extinct sloths) from North and South America were investigated for DNA. Although an extensive study, only two of the specimen, from Mylodon darwinii (one specimen from the

35 S. Blair Hedges and Mary Schweitzer, “Detecting Dinosaur DNA,” Science 268 (1995), 1191. 36 Hans Zischler, Matthias Hoss, Oliva Handt, Antoinette van der Kuyl, Jaap Goudsmit, and Svante Pääbo, “Detecting Dinosaur DNA,” Science 268 (1995): 1193. 37 Hai-LinWang, Zi-Ying Yan, and Dong-Yan Jin, “Reanalysis of Published DNA Sequence Amplified from Cretaceous Dinosaur Egg Fossil,” Mol. Biol. Evol. 14 (1997), 590. 38 Matthias Höss, Amrei Dilling, Andrew Currant, and Svante Pääbo. “Molecular phylogeny of the extinct ground sloth Mylogon darwinii.” Proceedings of the National Academy of Sciences 93 (1996): 181-185.

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AMNH, New York, and the other from the Natural History Museum, London), revealed DNA. Even then a large portion of the DNA was bacterial or fungal in origin. However, using PCR, they were able to isolate and amplify some endogenous DNA. Contamination was ruled out because “all bone processing, DNA extraction, and the setup of the PCR were done in a laboratory dedicated exclusively for these purposes.”39 Proceeding with only the small, but quality, amounts of DNA available, Höss and colleagues compared the sloth sequences with extant material. The sloth study’s results were particularly curious for several reasons. First, Höss and his researchers discovered that Mylodon darwinii shared a closer relationship with the two-toed, rather than three-toed sloths. Initially, there were three hypotheses surrounding the evolutionary relationships among extinct and extant sloths, but the molecular data seemed to reject the more widely-accepted hypotheses that the group Mylodontidae, which M. darwinnii is a member, was an outgroup to living sloths. Instead, molecular analyses confirmed the less popular hypotheses that Mylodontidae was more closely related to the two-toed sloth, while group Megatheridae was more associated with three-toed sloths. What this seemed to suggest was that an arboreal lifestyle, or life in the trees, among sloths evolved at least twice. Second, phylogenetic analyses of molecular data allowed the team of researchers to estimate a date of divergence among the sloth and other edentates (a special group of toothless mammal creatures such as armadillos). Using molecular clock dating, Höss’s team determined that the extinct ground sloth differed most from other mammal groups because their lineage diverged before the Cretaceous period ended (and before the ). Conveniently, the molecular evidence agreed with the morphological evidence. Molecular clock dating also allowed Höss and fellow researchers to pose some intriguing questions regarding the sloth’s extinction at the end of the last glaciation. Speculating on the study’s results, Höss and his co- authors surmised, “It is interesting that, in spite of not being closely related, two arboreal genera survived the mass extinction of sloths at the end of the last glaciation, whereas all ground- dwelling sloths, including those more closely related to the tree-living forms and existing in the same areas as these, disappeared.” Furthermore, “One may ask what caused specifically the tree- living forms to survive. An attractive hypothesis would be that humans colonizing the Americas in the late Pleistocene Epoch were responsible for the demise of the sloth radiation, a fate that

39 Höss et al., “Molecular phylogeny of the extinct ground sloth Mylogon darwinii,” 184. 82

only arboreal forms were able to avoid.”40 An elegant study, Höss and his team of workers were able to more accurately determine the evolutionary relationship between the extinct ground sloth and its modern relatives. Furthermore, they were able to estimate a date of divergence and also hypothesize possible reasons for the ground sloths extinction approximately 10,000 years ago. So far, recent studies and results on very ancient paleontological material, over 100,000 years old, had been shown to be more of an artifact due to contamination rather than a true scientific anomaly. The amber aDNA studies had been shown to be the results of contamination. Furthermore, amber specimens were proved to be rather unreliable sources for aDNA research. Additionally, both reports claiming dinosaur DNA were demonstrated to be contaminants. Recall Golenberg’s previous comment in Chefras’ article: “The object is not necessarily to see who can get the oldest DNA…but actually to start working up research projects that can make sense.”41 Unfortunately, paleontological material was not proving as promising as some had hoped. Anything over 100,000 years old was unlikely. Instead, archaeological specimens seemed more appropriate for DNA analyses and were becoming less of an anomaly and more accepted as a reliable source for aDNA research.

Appreciating Authenticity (redux)

The success of Höss and others’ ground sloth study relied on controlled procedures and careful analyses. More importantly, however, and perhaps rather obvious, was the necessary preservation of DNA in the first place. No matter how thorough a study was, any positive result depended on the existence of DNA in the specimen. As previously noted, the chemical instability of DNA naturally makes the preservation of DNA over extended periods of time extremely unlikely. In their case, Höss and fellow researchers attributed this unique occurrence of DNA preservation in the sloth specimens to their cave burial and its “dry and cold, subantarctic conditions in Southern Chile.” They surmised that the “low temperatures may be one condition that is critical for the survival of DNA over long time periods.”42 Low temperatures decrease the rate of chemical decomposition and thus, reduce degradation of DNA. Just a month after

40 Höss et al., “Molecular phylogeny of the extinct ground sloth Mylogon darwinii,” 185. 41 Chefras, “Ancient DNA: Still Busy After Death,” 1356. 42 Höss et al., “Molecular phylogeny of the extinct ground sloth Mylogon darwinii,” 184. 83 publication of the ground sloth study, Höss other colleagues submitted a second article which explored the likelihood of DNA preservation in ancient organisms. In this 1996 article, “DNA damage and DNA sequence retrieval from ancient tissues,” Höss and fellow scientists explored the application of gas chromatography as an effective tool for testing the likelihood of DNA in aged specimens.43 This technique, called gas chromatography/mass spectrometry (or GC/MS for short), can identify a number of chemical substances from a given sample. First developed in the 1950s, gas chromatography was most commonly used in drug investigations where substance detection was critical. As applied to aDNA research, gas chromatography could be used to measure modifications in DNA and thus predict the likelihood of preservation beforehand. Like Lindahl, Höss’s team recognized the two main types of damage, namely hydrolytic and oxidative damage, which negatively affect the DNA preservation especially in organisms over 10,000 years old. Because hydrolytic and oxidative processes had serious damaging effects on nucleic acid, the retrieval of DNA from ancient remains over 100,000 years of age was expected to be very difficult and perhaps impossible. Höss and his co-authors wrote, “Here we describe the detection and approximate quantification of different types of oxidative base damage in samples of different age and the correlation of such damage with the inability to retrieve ancient DNA sequences by PCR.”44 This study included eleven specimens ranging in age from 40 to 50,000 years old and from a variety of “burial conditions and tissue types.”45 Of the eleven specimens, twenty DNA extractions were obtained from both bone and soft tissue. Yet only five of the twenty sequences were of reproducible quality; two from soft tissue samples and three from bone. Only four out of the five sequences proved authentic. Though they were unable to determine a strong correlation between tissue type and DNA preservation, they did note that samples with reproducible amounts of DNA came from specimens found in arctic and subantarctic environments. As Höss and others explained, “The mammoth sample and the Selerikan horse are from permafrost deposits in Siberia, the onager comes from a frozen deposit in Alaska and the giant ground sloth (Mylodon darwinii) is from a cold cave deposit in Southern Chile. In contrast, the samples from Egypt, Europe, South and warm regions of the Americas had large amounts of DNA

43 Matthias Höss, Pawel Jaruga, Tomasz Zastawny, Miral Dizdaroglu, and Svante Pääbo, “DNA damage and DNA sequence retrieval from ancient tissues,” Nucleic Acids Research 24 (1996): 1304-1307. 44 Höss et al., “DNA damage and DNA sequence retrieval from ancient tissues,” 1304. 45 Ibid., 1305. 84

damage and yielded no DNA sequences.” They concluded, “It therefore seems that for the long- term preservation of DNA a cold environment is of critical importance.” 46 Yet given an ideal environment for preservation, DNA survival in much older specimens remained uncertain. Höss and researchers also noted, “Since the archaeological and palaeontological specimens used are valuable and available in limited quantity, the amounts of DNA that could be extracted allowed only two analyses by GC/MS per specimen.”47 Despite the preservation of DNA in much older archaeological and paleontological objects, the low amount of surviving DNA was a limiting factor in the number of samples that could be sequenced. This also posed a problem for attempts to reproduce and verify results. Nevertheless, this report was a valuable step toward a more educated understanding of the opportunities and obstacles in aDNA research. Hendrik Poinar, another integral figure in the search for aDNA, also dedicated his efforts to better understanding the nature and likelihood of DNA preservation. Poinar, in an article for Science co-authored by Höss, Pääbo, and Jeffrey Bada of the Scripps Institution of Oceanography, University of California at San Diego, noted, “Although several ways to authenticate ancient DNA have been suggested, the field is in need of techniques that can indicate whether a particular ancient specimen may contain endogenous nucleic acids.”48 For this study, Poinar and his colleagues tested the extent in which amino acid racemization could be considered a useful indicator of DNA degradation in ancient samples. In brief, amino acid racemization is the process in which one type of amino acid converts to another, different type of amino acid. An amino acid’s conversion from one form to another is dependent on environmental factors. As they further explained, “The rate at which racemization takes place differs for each amino acid and is dependent on the presence of water, the temperature, and the chelation-of certain metal ions to proteins.” Therefore, “Racemization is thus affected by some of the same factors that affect of DNA, the major hydrolytic reaction responsible for the spontaneous degradation of nucleic acids.”49 Because of the similar nature and response to the same factors, amino acids proved an effective means of comparison to DNA. In this study, Poinar and his colleagues applied amino acid racemization to previously examined archaeological specimens from which ancient and authentic DNA had already been

46 Ibid., 1306. 47 Ibid., 1305. 48 Hendrik Poinar, Matthias Höss, Jeffrey Bada, and Svante Pääbo, “Amino Acid Racemization and the Preservation of Ancient DNA,” Science 272 (1996): 864. 49 Poinar et al., “Amino Acid Racemization and the Preservation of Ancient DNA,” 864. 85 sequenced.50 Their results from this application demonstrated that high levels of amino acid racemization were indicative of low and insufficient amounts of DNA in specimens. Although their study did not prove any correlation between the age of the sample and presence of DNA, a similar result and conclusion in Pääbo’s 1989 study, they did find a connection between colder climates and DNA preservation. Results suggested that “the limit for the retrieval of useful DNA sequences implies that the survival of DNA is limited to a few thousand years in warm regions such as Egypt and to roughly 105 years in cold regions.” This conclusion seemed to be confirmed by other studies as well: “Such temporal limits for DNA retrieval are similar to those predicted from laboratory experiments.”51 Overall, Poinar and fellow workers’ study and application of amino acid racemization to DNA studies provided an effective check for confirming or disproving evidence of DNA. Amino acid racemization could serve as a practical indicator of the likelihood that DNA may exist in ancient specimens. Drawing on Poinar and colleagues’ suggested amino acid racemization technique, Matthias Krings, Zoological Institute at the University of Munich, along with fellow researchers published a report the following year on Neandertal DNA.52 The specimen, belonging to the Rheinisches Landesmuseum Bonn in Germany, was first found in Western Germany in 1856. The relatedness of Neandertals to modern day humans had been a source of contention for some time. While Neandertals were contemporaries with modern humans, many presumed that Neandertals were either the direct ancestor of modern hominids, at some point or in some way contributed to the modern hominid gene pool, or lastly, that Neandertals were outlived by modern humans and thus passed on nothing by way of genes to contemporary humans.53 However, the most popular hypothesis was that Neandertals were an entirely separate and distinct species and having gone extinct around 40,000 BC did not contribute any genes to humans. Using standard DNA extraction and PCR amplification procedures, as well as rigorous precautions to control contamination (an especially troublesome issue when working with anthropological material), Krings, Pääbo, and colleagues analyzed bone samples from the 30,000

50 In order to ensure that they were using authentic DNA sequences, Poinar and others only selected samples from nine studies that clearly demonstrated an strict adherence to criteria for authenticity. 51 Poinar et al., “Amino Acid Racemization and the Preservation of Ancient DNA,” 864. 52 Matthias Krings, Anne Stone, Ralf Schmitz, Heike Krainitzki, , and Svante Pääbo, “Neandertal DNA Sequences and the Origin of Modern Humans,” Cell 90 (1997): 19-30. 53 Krings, “Neandertal DNA Sequences and the Origin of Modern Humans,” 20. 86

to 100,000 years old Neandertal man. Krings and colleagues announced, “It is thus among the oldest specimens for which the chemical ability of DNA would seem to allow for the retrieval of endogenous DNA.” They continued, “Furthermore, the extent of amino acid racemization indicated that preservation conditions of the Neandertal fossil have been compatible with DNA preservation.”54 From this data, Krings and his team were able to draw some valuable conclusions pertaining to human evolution. The Neandertal man report presented some interesting evidence for human evolution and furthermore, added to our confidence in archaeological specimens as reliable sources for DNA study. Based on both sequence comparison and phylogenetic analyses, the results suggested that the Neandertal man lies outside the modern human lineage. Krings and fellow researchers explained, “Thus, although based on a single Neandertal sequence, the present results indicate the Neandertals did not contribute mtDNA to modern humans.”55 Even though these results dismissed the notion of Neandertals as early ancestors to contemporary hominids, Neandertals – as a phylogenetic outgroup – can be helpful in addressing human origins and development. In addition to the molecular data, both archaeological and paleontological evidence revealed a similar story. Both the fossil and molecular evidence suggested a similar divergence date between Neandertals and humans. Aside from the impressive quality of research and standing as a significant contribution for illuminating the evolutionary history and origin of modern humans, the Neandertal study added to the growing acceptance of aDNA as not merely an anomaly, but more of a real occurrence and a consistent means of studying ancient organisms in real evolutionary time. A couple years later, scientists met again at the Fifth International Ancient DNA Conference to reflect on the progress of aDNA research over the past fifteen years and future of the field. This conference, held in Manchester, United Kingdom 12 to 14 July 2000, comprised of 110 scientists from a variety of disciplines. In their hardline article, “Ancient DNA: Do it Right or Not at All,” Cooper and Poinar responded to a comment made at the conference that the “field was now mature and could move ahead with confidence.” They countered that such “optimism is unfounded, as demonstrated by the notable absence of ‘criteria of authenticity’ from many presentations at the conference.” Cooper and Poinar further noted that “Ancient DNA

54 Ibid., 26. 55 Ibid., 27. 87

research presents extreme technical difficulties because of the minute amounts and degraded nature of surviving DNA and the exceptional risk of contamination.”56 As seen, the 1990s produced “series of high-profile studies” with big claims that were unable to be reproduced, like the 1994 dinosaur DNA reports. Despite efforts to set strict criteria and stringent practices for aDNA research, bad science was still happening. Cooper and Poinar stated, “Regrettably, despite the recommendation that such criteria be routinely applied, high-profile journals continue to publish studies that do not meet the necessary controls, and many new researchers fail to utilize them.”57 In an effort to advertise, yet again, best practices for aDNA research, they summarized the appropriate protocol: a physically isolated work area, control amplifications, appropriate molecular behavior, reproducibility, cloning, independent replication, biochemical preservation, quantitation, and associated remains.58 If done right, the potential for aDNA study on archaeological and paleontological specimens could be great. In their article, “Full of Sound and Fury: The Recent History of Ancient DNA,” Wayne and Leonard of the Department of Organismic Biology, Ecology, and Evolution at the University of California, Los Angeles, along with Cooper, of the Department of Biological Anthropology at Oxford, also commented on the current state of aDNA research at the end of the decade. Since the first study in 1984, Wayne, Leonard, and Cooper noted that although the new discipline of aDNA research “remains thematically diverse, rigorous authentication procedures provide a unifying methodological focus.”59 Scientists interested in aDNA were concerned with evidence, proper standards of research, authentication of results, also knowledge of the field’s shortcomings. Adherence to “rigorous authentication procedures” would help unify current researchers under a shared standard of science and how proper aDNA research should be done. This was important if scientists were to have any hope of learning the true potential of aDNA research as a practical approach to studying ancient and fossil objects in real evolutionary time. Over the past fifteen years, scientists had explored the anomaly of aDNA in a number of sources from museum, archaeological, and late Pleistocene samples to amber inclusions and even fossils millions of years old. These studies focused on constructing evolutionary histories and using molecular clock dating. As Wayne and colleagues noted, “The questions addressed by ancient

56 Alan Cooper and Hendrik Poinar, “Ancient DNA: Do It Right or Not at All,” Science 289 (2000): 1139. 57 Cooper and Poinar, “Ancient DNA: Do It Right or Not at All,” 1139. 58 Ibid., 1139. 59 Wayne et al., “Full of Sound and Fury,” 458. 88

DNA research concern any issue that benefits from a direct historical perspective.” Such areas included “(a) systematics; (b) changes in as a function of time and environmental change; (c) migration and admixture; (d) ecology and paleoecology; (e) the origin and spread of disease; and (f) tempo and mode of in populations.”60 The research implications are far reaching. In reflecting on the early history of aDNA research, Wayne, Leonard, and Cooper put it this way:

Molecular evolutionary biologists have envied the paleontologist's unique access to historical information and longed to utilize the rich information inherent in ancient DNA sequences. Such was the promise of research on DNA preserved in the remains of extinct organisms. However, the intense excitement at the first reports of ancient DNA greater than a million years old was followed by confusion and disillusionment when the claims were severely criticized.61

By the late 1990s, they argued, “The honeymoon period has passed for ancient DNA research, and the difficulties associated with a maturing field need confronting.”62 Speculating on the past and future of aDNA research, Wayne and colleagues surmised:

The rise and decline of ancient DNA research has been dependent on the development of new techniques, the limits of which subsequently were defined by critical analysis and replication. The development of new techniques and methods of analysis still promises new avenues of research (e.g. sloth dung), but the realm of questions is now circumscribed by the likelihood that DNA will not persist much beyond 100,000 years.63

The most promising potential for aDNA research in regards to genetic diversity rests in the fact that “Ancient DNA analysis can provide a direct record of the tempo and mode of genetic change

60 Ibid., 458. 61 Ibid., 457-458. 62 Ibid., 464. 63 Ibid., 468. 89 within populations, and thus a means of testing and re-fining existing population models.”64 So far, archaeological specimens seemed to be reliable candidates for DNA analyses. Paleontological material, unfortunately, had been repeatedly shown to be too old for DNA to survive. Austin and fellow colleagues noted, “Although the initial optimism that palaeontological research would be advanced by the study of geologically ancient DNA seems to have been unfounded, studies of ‘dead’ DNA from much younger material continue to hold promise for research in archaeology, population genetics, and evolutionary and conservation biology.”65 In conclusion, Wayne and co-authors elegantly captured the future and promise of aDNA research: “Although some may despair over the unlikely prospect of Cretaceous DNA, most will recognize that the study of ancient DNA, if directed toward millennial scale changes, still has the potential to solve evolutionary mysteries. The initial excitement may be gone from the field, but with maturity of purpose, it will come to signify more than sound and fury.”66

Conclusion

The previous fifteen years of aDNA research represents the exploration of a scientific anomaly and the emergence of a scientific field. Over these years scientists tested the age limit for DNA preservation. Several remarkable DNA reports claiming to break the million year mark were published. However, these studies – like the Magnolia fossil leaf, termite amber, and dinosaur bone – were soon proved false and the products of contamination. Instead, ancient and fossil objects under 100,000 years of age proved the most promising subjects for DNA analyses. Yet the potential for aDNA as applied to paleontological material was and still is an enthralling prospective. By bringing together the disparate fields of archaeology, paleontology, and molecular biology, scientists could – for the first time – study the evolution of fossil organisms in both real and deep time. Such a prospect could potentially revolutionize the primarily historical field of paleontology by taking an experimental and non-inferential approach to the study of fossils. Although paleontology may not have come out on top in the search for aDNA, the implications of aDNA research for the field of paleontology are considerable. In the next

64 Ibid., 469. 65 Jeremy Austin, Andrew Smith, and Richard Thomas, “Paleontology in a molecular world: the search for authentic ancient DNA,” TREE 12 (1997): 306. 66 Wayne et al., “Full of Sound and Fury,” 469-470. 90 chapter we will further discuss the significance of aDNA research for paleontology as a historical science in a molecular age and its future role as part of the modern evolutionary synthesis.

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CHAPTER FIVE

MAKING SENSE OF ANCIENT DNA

Introduction

The past fifteen years of aDNA research demonstrated that some of the world’s ancient creatures and fossil specimens not only preserved evidence of DNA, but that scientists could also successfully extract, sequence, and use this ancient genetic material in meaningful, evolutionary studies. The ramifications of this type of study for fossils and for a number of fields, including paleontology, were considerable. However, these years of research also demonstrated that our most ancient paleontological specimens are unlikely to yield any DNA. Thus, the hype of and our hopes for Jurassic Park is likely to remain an idea of fiction. This chapter will attempt to analyze our review of aDNA research and what it means to the field of paleontology as a novel approach to fossil studies. First, I will discuss the field of paleontology as a historical science, its relation to the nature of experimental science, and how the integration of analytical approaches to fossil studies may be transforming the purely historical science of paleontology into a more experimental one. Furthermore, the history of aDNA research also calls us to reevaluate the very meaning of the term “fossil.” As Rudwick claimed, “The ‘meaning’ of fossils has been seen in many different ways in different periods.”1 I cover topics of meaning change in light of this insight and current developments in aDNA. Lastly, I consider the role of disciplinary boundaries in aDNA research and the ramifications for the future of paleontological research.

Historical and Experimental Science

The rise of experimental biology and, more specifically, the new field of genetics at the turn of the twentieth century, led to the increasingly marginalized field of paleontology. Morgan, reigning geneticist of the early 1900s, was one of the most serious critics of descriptive and theoretical paleontology. Rainger succinctly characterized Morgan’s overall attitude, stating:

1 Rudwick, The Meaning of Fossils, 266. 92

“Paleontologists and field biologists could accumulate new data about evolution, but Morgan maintained that descriptive biology could add nothing new to explaining the mechanisms and patterns of evolution.” Additionally, “descriptive work could lead to serious misinterpretations.”2 Rainger explained Morgan’s contempt for theoretical paleontology in evolutionary discussion, noting that “Experimental biologists were interested in casual, not historical, explanations, and by the early twentieth century, some viewed the evolutionary interpretations of paleontologists as speculative and untenable.”3 Morgan’s vehement opposition to theoretical paleontology represented one of the more extreme attitudes towards the field in the wake of experimental biology; however, not all biologists shared this sense of hostility. Nonetheless, Morgan’s attitude towards paleontology at the beginning of the twentieth century was indicative of a very real opposition that paleontology faced at the turn of the century. This disposition continued to grow throughout the century and helped to foster a bias for experimental science over historical science in evolutionary biology. Osborn, leading vertebrate paleontologist and spokesman for the field, imagined a much different role for paleontology in evolutionary theory. Osborn was interested in questions of an evolutionary nature and answering them with paleontological research. However, his primary methodology for exploring such inquiries was through descriptive and theoretical paleontology; precisely what Morgan – Osborn’s rival – argued as “speculative and untenable.” Rainger wrote:

Osborn’s scientific studies reflected the morphologist’s interest in obtaining evidence to document evolution and to construct evolutionary interpretations. In developing umbrella theories that accounted for variation, development, and inheritance, Osborn and other morphologists employed traditional means of investigation: the observation and description of organic forms.4

Keeping with the natural history tradition, Osborn resisted the experimental biological movement. Favoring more traditional and historical methods, he campaigned against the integration of experimental approaches in paleontological research. Rainger explained Osborn’s resistance to the new biology “because it represented a specialized field of study that threatened

2 Rainger, An Agenda for Antiquity, 135. 3 Ibid., 20. 4 Ibid., 132. 93

the work of the naturalist and the traditional way of doing science.”5 Morgan’s and Osborn’s dispositions capture not only a general attitude at the turn of the century, but also a growing rift between the experimental and historical sciences and their respective and expected roles in evolutionary theory. Historical sciences such as paleontology that employed historical approaches of research like morphology were considered subjective and therefore, objectionable. On the other hand, experimental sciences provided testable hypotheses and quantifiable data and were considered more objective. Experimental biology soon became a dominant approach in evolutionary studies, thus pushing paleontology and its historical methodology into the margins of scientific inquiry. With the growing popularity of experimental biology, paleontology soon found itself less in the university and more confined to the museum. Yet, paleontology, and vertebrate paleontology in particular, had always shared an intimate bond with natural history museums; a bond dating back to the founding of Peale’s Philadelphia Museum in the late 1700s. As Simpson pointed out, “This close interrelationship between fossils and museums arose almost at the beginning of scientific vertebrate paleontology in America, and quite at the beginning of public museums.”6 At the turn of the twentieth century, paleontology was almost exclusively limited to the museum setting with little educational and financial support from the university. Nonetheless, paleontology as a discovery driven science flourished under the museum’s direction. In The Second Jurassic Dinosaur Rush, Brinkman noted, “Although marginal relative to other burgeoning subfields of biology or geology at those universities that continued to support it, vertebrate paleontology survived and continued to grow modestly in the academy.”7 In the museum, paleontology pursued the natural history tradition and used morphology and taxonomy to navigate questions of evolutionary nature. Though biologists had formerly relied on morphology and other historical approaches, they broke from the tradition and instead moved to universities where cutting-edge research labs and opportunities for experimental study of evolution were available. As Brinkman put it:

5 Ibid., 142. 6 George Gaylord Simpson, “The Beginnings of Vertebrate Paleontology in North America,” Proceedings of the American Philosophical Society 86 (1942): 157. 7 Brinkman, The Second Jurassic Dinosaur Rush, 18. 94

In museums, vertebrate paleontology was somewhat isolated from the universities and laboratories where earth breaking developments in experimental biology and genetics were then taking place. Conceptually and methodologically, it remained wedded to what historian Ronald Rainger called the morphological tradition.8

Osborn, for instance, strongly believed that paleontology had something important to contribute to evolutionary theory but was fervently committed to traditional paleontological methods such as description and classification. Conversely, Morgan argued that beyond establishing the fact of evolution, paleontology had nothing to say about evolutionary processes. While the science of paleontology succeeded within the natural history museum, its confinement to this institution and partial negligence in university curriculum had its consequences. Ruse noted:

Although the study of fossils is the science ordinary people think of first when they think of evolution, in the professional worth paleontology has low status indeed – far below the work of the fruit fly geneticist. All of those years when paleontology was found less in universities and more in museums, when entertaining or instructing the public was its chief function, when the significant theoretical occupation was making up hypothetical histories of life, have left their mark.9

Gould also speculated on this point, noting that even today the status of the field continues to have a “curiously low and almost ironic reputation” among professional scientists, particularly when the science of paleontology is so “beloved and glamorized by the public” through the iconic images of Indiana Jones or Jurassic Park.10 Despite its growth in the museum throughout the first half of the twentieth century, paleontology slipped into a role of irrelevance in evolutionary discourse among experimental sciences. During this time, a significant and at times antagonistic division between the experimental and historical sciences developed. From this division followed the belief that historical sciences, because of their subjective nature, were inferior to more objective,

8 Ibid., 255. 9 Ruse, Mystery of Mysteries, 143. 10 Stephen Jay Gould, “Tempo and Mode in the Macroevolutionary Reconstruction of Darwinism” in Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson, eds. Walter Fitch and Francisco Ayala, (Washington, D. C.: National Academy Press, 1995), 127. 95 experimental approaches. Recently, scholars have attempted to reevaluate the reasons for this bias. In All Creatures Kohler noted:

Historically it is true that description and inventory did cease to be a high-prestige practice, yielding precedence to more overtly theoretical modes. But to think therefore that one is a lesser preliminary to the other immodestly assumes that change in science is progressive and that what comes after is by definition superior to what came before. It is not, or not always: just different. Each generation of scientists finds it useful to highlight their own novelty and worth by contrasting their practices with those whose imperfections and limits history has already revealed. But that rhetorical gambit is simply an artifice of the process of making new knowledge and careers. A generation of biologists fastened the ‘mere’ onto describing and classifying in part for social reasons.11

Kohler’s insight is astute, and he brings attention to the idea that it may be time to evaluate our biases. He continued, “The view that classification is descriptive and subjective (because it depends on individuals’ experience and judgment), rather than analytic and objective, is the bias of an age that have been persuaded to think of experiment and casual analysis as the only ways to truth.”12 Historical and experimental sciences may be inherently different in nature and practice. However, such dissimilarities do not necessarily warrant one type of science, or one way of discovering truth about the world, as fundamentally superior or inferior to the other. In fact, the discovery and description of fossils remains a critical component to understanding the evolution of life. Allen argued along these same lines:

The emphasis on experimentation and biochemical analysis has often been taken to imply the modern biologists have repudiated the methods of observation and description that were so prevalent a part of natural history in the past. While some biologists in recent years, in the full flush of one or another molecular successor, have spoken

11 Kohler, All Creatures, 228. 12 Ibid., 269. 96

condescendingly about ‘mere observation’ or ‘old-fashioned descriptive methods,’ these processes remain a necessary foundation for any biological (or scientific) inquiry.13

Both Kohler and Allen concede that a bias exists and that this prejudice is undeserved. There seems to be a distinction between a historical and an experimental science but just what that distinction is remains subject to philosophical debate. Allen noted that early experimentalists in the life sciences “sought to test their hypotheses with living systems in which they only studied one variable at a time.”14 Testing of hypotheses – although not without some disagreement – appears to be a major feature and difference between historical and experimental sciences. Furthermore, whether this distinction entitles an experimental science superior to a historical science is a separate question. In her 2002 article, philosopher Carol Cleland discussed both the methodological and epistemic differences between historical sciences (paleontology, archaeology, geology, astronomy, etc.) and experimental sciences (physics, chemistry, etc.). Cleland’s central claim is that “scientists engage in two very different patterns of evidential reasoning, and one of these patterns predominates in historical research and the other in classical experimental research.”15 At the same time, she also argued that while historical and experimental sciences each have distinct patterns of investigation and reasoning, their difference in approach does not warrant historical science as inferior to experimental science. She stated, “Because each practice is tailored to exploit the information that nature puts at its disposal, and the character of that information differs, neither practice may be held up as more objective or rational than the other.”16 Cleland distinguishes the historical and experimental sciences based on the testing of hypotheses. Noting the division and also the tension between the two sciences, Cleland explained, “Scientists are well aware of the differences between experimental and historical science vis-à- vis the testing of hypotheses. Indeed, it is sometimes a source of friction. Experimentalists have a tendency to disparage the claims of their historical colleagues, contending that the support offered by their evidence is too weak to count as ‘good’ science.”17 According to Cleland,

13 Allen, The History of Life Sciences, xv. 14 Ibid., xvi. 15 Carol Cleland, “Methodological and Epistemic Difference between Historical Science and Experimental Science,” Philosophy of Science 69 (2002): 476. 16 Ibid., 476. 17 Ibid., 475. 97 quantifiable data and testing hypotheses in “controlled laboratory settings” is the mark of an experimental science. Cleland argued that a “classical” experimentalist first begins investigation by developing a hypothesis about “regularities among event-types.”18 Next, he makes a prediction about what will occur if the hypothesis is true and will create a set of controlled experiments to test it. Lastly, the experimentalist will execute the series of controlled experiments in order to “prevent the target hypothesis from misleading confirmations and disconfirmations.”19 Reflecting on Cleland’s description, Turner employed the following example to illustrate the process:

For example, suppose that an ecologist wants to test a hypothesis about the effects of deer browsing on local vegetation. She makes a prediction about what sorts of plants would grow in a given spot, were they not browsed by deer, and she tests this hypothesis by fencing off a small plot of forest and waiting to see what happens. The ecologist then repeats the experiment while varying certain conditions, such as the amount of sunlight available to the plants or the acidity of the …20

Turner explained that this experiment would be repeated but manipulated via certain controlled conditions in order to determine the most accurate results about the hypothesis under investigation. On the other hand, a historical scientist proceeds in his inquiry somewhat differently than the experimentalist. Instead, a historical scientist will begin investigation by observing “puzzling traces (effects) of long-past events.” Next, he might form a set of hypotheses to explain these traces through a “common cause,” and lastly, he will test for it. Cleland conceded that it may seem objectionable that historical sciences have anything to test at all, and she explained that “it would be a mistake to conclude that hypotheses about the remote past can’t be ‘tested’.” According to Cleland, “Traces provide evidence for past events just as successful predictions provide evidence for generalizations examined in the lab.” However, unlike the experimentalist, the goal of the historical scientist is to find a “smoking gun” or “a trace(s) that unambiguously

18 Ibid., 476. 19 Ibid., 477. 20 Derek Turner, Making Prehistory: Historical Science and the Scientific Realism Debate (Cambridge, Massachusetts: Cambridge University Press 2007), 41. 98

discriminates one hypothesis from among a set of currently available hypotheses as providing ‘the best explanation’ of the traces thus far observed.”21 For example, as Turner suggested, the discovery of the iridium layer at the Cretaceous-Tertiary boundary along with the massive crater off the Yucatán Peninsula in Mexico, serves as salient illustrations of a “smoking gun” in support of the that an extraterrestrial impact to the earth caused the extinction of the dinosaurs.22 Although Cleland argued that these are the ways in which a historical and an experimental science would proceed in its study, she noted that these are but “ideal types” of sciences. Therefore, some sciences may be experimental but also historical. As Turner reiterated, “Historians often reason experimentally, and experimentalists sometimes reason historically.”23 However, Cleland noted that the acceptance or rejection of a hypothesis may also be influenced by other factors (psychological or sociological) outside of the experiment’s results. Nevertheless, Cleland argued, “I am merely trying to characterize what the scientific community expects of a ‘good’ experimental researcher when she goes about testing a hypothesis in her lab, and I am claiming that it is best understood in terms of an extended series of interdependent experiments, as opposed to the solitary experiment.”24 Philosophically, Cleland claimed that historical and experimental sciences differ in their testing of hypotheses; historical scientists depend upon evidence of a “smoking gun” whereas experimentalists rely on repeated experimentation. Granted Cleland’s argument is not uncontested,25 but for my purposes, her work is a useful guide, and her distinction between historical and experimental science helps to illuminate the significance of the recent development of aDNA research as a new approach to fossil studies for the field of paleontology. The recent history of aDNA research has transformed fossil studies from a once purely historical science into a more experimental science. Horner captured both the distinction between these sciences, as well as the current developments in paleontological research, noting, “The recent technological changes in how bones are studied are profound. For most of the last century the study of dinosaurs was primarily a collector’s game. It certainly was

21 Cleland, “Methodological and Epistemic Difference between Historical Science and Experimental Science,” 480- 481; Turner, Making Prehistory, 39. 22 Turner, Making Prehistory, 39. 23 Ibid., 40. 24 Cleland, “Methodological and Epistemic Difference between Historical Science and Experimental Science,” 480. 25 Turner, Making Prehistory. 99

not an experimental science. But that is changing.”26 He is correct in saying that the progress of science is very much in step with technological advancements. However, do the experimental techniques of aDNA research truly make paleontology an experimental science – at least in the sense that Cleland talks about an experimental science – or is it more of a novel method and more experimental approach to uncovering and discovering our past? I argue the latter applies best in this case. aDNA research changed the way in which scientists view and study fossils.

The Meaning of Fossils

In 1565, Conrad Gesner (1516-1565), Swiss native and foremost naturalist of the sixteenth century, published A Book on fossil Objects, chiefly Stones and Gems, their Shapes and Appearances. After publication, this work became the foundation for fossil studies and what Rudwick argued as a most “appropriate date to choose as a starting point for the history of paleontology.” More notably, however, Rudwick also argued that Gesner’s title, A Book on fossil Objects, chiefly Stones and Gems, their Shapes and Appearances, was a dead giveaway that the term “fossil” has drastically changed in meaning over the past few centuries.27 Reflecting on the history of paleontology, Rudwick claimed, “The ‘meaning’ of fossils has been seen in many different ways in different periods.”28 In The Meaning of Fossils: Episodes in the History of Palaeontology (1976), Rudwick argued that throughout paleontology’s history the term “fossil” has evolved in time and in accordance with cultural and scientific developments from the sixteenth century to Darwin’s publication of the Origin in 1859. I believe this argument still holds true today as the term “fossil” has taken on a new meaning in light of recent developments in molecular paleontology and more specifically, aDNA research. Turner also shares this insight as mentioned in his most recent work, Paleontology: A Philosophical Introduction.29 The original meaning of the word fossil, which dates back to the sixteenth century, refers to anything “dug up.” Such a broad definition of fossil included both organic and inorganic material. During the especially, no distinction was made between organic matter, such as relics of ancient but once living creatures, and inorganic materials like stones and gems. For most of human history, fossil objects were anything considered distinctive in appearance and

26 Horner and Gorman, How to Build a Dinosaur, 7. 27 Rudwick, The Meaning of Fossils, 1. 28 Ibid., 266. 29 Turner, Paleontology: A Philosophical Introduction, 201. 100

a source of curiosity. Consequently, Gesner’s original book on fossils, although appropriate for its time, described many objects such as minerals, crystals, and rocks as fossils. Today, we understand fossils to be any trace of past life, and consequently, we no longer recognize Gesner’s characterization of minerals, crystals, and rocks as fossils. This is because the meaning of terms is subject to change depending on our theories. The meaning of fossils is closely tied to, and often dependent on, our theories about the world and how it works. Humans have long speculated on the significance of fossils and although most theories were more mythical in origin, such an understanding is a reflection of worldview. For example, Simpson noted that one of the most common explanations for the existence of fossils during the Middle Ages was to explain that they either grew from the earth’s crust through some powerful force or that these objects fell directly from the heavens to the earth.30 Other theories of fossils were more sophisticated, however. The Greeks, for instance, hypothesized that the presence of sea shells far from the coast line indicated that the sea had once covered much more ground but has since retreated. Even though such a theory has a modern ring to it, the very existence of fossils remained a source of debate for centuries to come. Simpson explained, “As early as the 6th century before Christ the Greeks knew in a general way what fossils were and what they meant, but as late as the 18th century of our era, some 2200 years later, men of science were still gravely arguing the point.”31 Thus, the term fossil has taken different meanings in light of evolving theories. Our review of the first two decades of aDNA research raises the question of what a fossil is and calls us to make room for molecules as an integral part of fossil research. Today, the term fossil refers to any remains and traces of once living organisms. In light of aDNA research, we now recognize fossils also as storehouses for molecules. Turner’s work on “meaning change” and “theory change” help shed light on this subject. In Paleontology: A Philosophical Introduction, Turner specified two principles among philosophers of science that prove especially useful for analysis of the changing meaning of fossils and ancient DNA research. The first principle, “meaning change,” simply suggests that the “meanings of technical terms in science change over time.” The second principle, “theory-dependence of meaning,” denotes that the “meanings of scientific terms usually depend on scientific theories.” Turner recognized that

30 Simpson, Life of the Past, 6. 31 Ibid., 6. 101

these two notions are very much in line with Kuhn’s reasoning in The Structure of Scientific Revolutions. Although Kuhn argued a hardline that scientific terms can have a dramatic change in meaning when a scientific revolution occurs, Turner suggests that “the meanings of scientific terms can change even without a full-blown scientific revolution.”32 I believe the latter applies to the history of aDNA research as a novel perspective on not only how we study fossils, but how we have grown to think of them as well. Fossils, the remains and traces of past life, take on many forms and over the centuries we have learned to identify and classify their existence and rarity. The most common fossils exist only as parts of a once whole organism. These parts are almost always hard parts such as shells, bones, and teeth. Although they often occur in fragments, we can piece together broken and scattered parts. Sometimes a fossil mold is made when an organism’s body is impressed into sediment, thus preserving shape and detail even upon the organism’s decay. Other sorts of fossils, like trace fossils, are especially interesting and particularly useful for providing information about the creature’s lifestyle and behavior. Trackways, a type of , are the preserved footprints of imprints of a once living animal. For instance, dinosaur trackways, which are abundant across the globe, are frequently footprints and from which we can infer dinosaur locomotion and other behavioral habits. Trace fossils can also include skin, , or shell imprints as well as eggs or (fossilized excrement). These types of fossils are valuable for providing information that hard parts may lack. Because soft parts like skin and do not typically survive fossilization, their imprints tell us more critical details about the creature’s physiology, and in the case of coprolites, we can infer diet. On rare occasions, entire organisms may be preserved. The pristinely preserved mammoths of Siberia and Alaska are salient examples. The ground sloths of South America are other prime examples of nearly perfect fossil preservation. Colder environments contribute to this type of preservation, thus, these types of specimens are ideal for aDNA studies because their exceptional preservation is liable to yield quality DNA. Amber-inclusions are another form of fossilization and are a more frequent occurrence. Most unique, however, is the fossilization of soft parts, or the inorganic components, of plants and animals. These parts typically include soft tissues, cells, proteins, and DNA. As mentioned, these organismal components are usually the first to go once an organism dies. Recent discoveries in molecular paleontology in the last fifty

32 Turner, Paleontology: a Philosophical Introduction, 201. 102

years or so, made possible by developments in molecular biology, have offered evidence that a fossil’s value may be more than superficial and that amino acids and proteins exist intact. More recently, aDNA research has proved the remarkable preservation of DNA. As Horner put it, “Molecules are fossils too.”33 Though molecules are not fossils in the literal sense, Horner’s point still stands as a call to recognize a new significance in our fossils. Molecular paleontology, and more recent advances in aDNA research, suggests that amino acids, proteins, and even DNA may be preserved. Bernd Hermann and Susanne Hummel of the Institute of Anthropology in Gottingen, Germany wrote:

The detections of high molecular organic compounds in ancient remains has turned out to open a new research area with many implications, the most important being the extraction of ancient DNA (aDNA)…from fossils, subfossil remains, artifacts, traces from biological courses, and museum specimens. Since this technique provides access to the basic molecules of organismic evolution, it opens up the possibility of studying evolution at the molecular level over a principally unlimited time scale.34

The history of paleontology has shown that the meaning of fossils has evolved, and more importantly, is still evolving. Turner aptly noted, “The meaning of the term ‘fossil’ depends on one’s theory of fossilization”35 and “Just what counts as a fossil is subject to changes in technology.”36 These two points are of vital importance. The recent emergence and development of aDNA research suggests we make room for molecular preservation in our knowledge of fossils. For the first time, we now recognize that fossils may be bearers of essential information like DNA. The early history of aDNA research, as the exploration of an anomaly made possible by advances in technology, has invited a deeper understanding of fossils by showing us that DNA preservation and extraction is possible in ancient material. Turner elegantly concluded:

33 Horner and Gorman, How to Build a Dinosaur, 85. 34 Bernd Herrmann and Susanne Hummel, “Introduction,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, eds. Bernd Hermann and Susanne Hummel (New York: Springer-Verlag, 1991), 1. 35 Turner, Paleontology: a Philosophical Introduction, 202. 36 Ibid., 203. 103

To summarize: the meaning of the term ‘fossil’ depends to a large extent on going scientific theories as well as on current technology, and it is subject to change. Although these observations may not seem too exciting at first, they have interesting consequences when you combine them with the observation that the fossil record has always been the disciplinary turf of paleontology, as well as the point made early that paleontology’s status has waxed and waned with changing views about the completeness of the fossil record.37

The meaning of fossil is not fixed but probable to change in the face of novel discovery. It is pertinent that we realize the contingency of scientific terms and theories and furthermore, to be open to anomalies in science which may better clarify our past, present, and future. aDNA research suggests that a fossil’s value extends beyond the museum shelf and that perhaps the answers to our questions are hidden within. When scientific terms and theories change, scientific practices change too. aDNA research has altered the way in which one views, studies, and handles invertebrate and vertebrate fossils. Where it has been the museum’s mission to collect and preserve, aDNA research sometimes destroys fossils and specimens once so delicately prepped and displayed for public viewing, in hopes of extracting what, if any, organic molecules may have survived fossilization and geologic time. Cooper, then at the Molecular Genetics Laboratory at the National Zoological Park in Washington, D.C., explained, “A diverse collection of taxonomically identified specimens located in one place creates a range of opportunities for evolutionary and ecological research while avoiding costly field studies.”38 However, this reality presents an interesting issue for the relationship between archaeology, paleontology, and the museum. Gary Graves and Michael Braun of the National Museum of Natural History at the Smithsonian Institution stated, “Traditional museum collections of vertebrates and other organisms increasingly are being viewed by molecular biologists as valuable storehouses of DNA.” In his article, “Raising the dead and buried,” Jeffreys wrote in regards to recent discoveries in aDNA, “The obvious next question is whether other museum specimens will yield

37 Ibid., 205. 38 Alan Cooper, “DNA from Museum Specimens,” in Ancient DNA: Recovery and Analysis of Genetic Material from Paleontological, Archaeological, Museum, Medical, and Forensic Specimens, eds. Bernd Hermann and Susanne Hummel (New York: Springer-Verlag, 1991), 149. 104 up their molecular secrets. One can only hope the museum curators will be reasonably sympathetic to hordes of molecular biologists eager to dismantle their cherished exhibits.”39 Graves and Braun contended that while it is “gratifying that new uses have been found for old specimens,” this “privilege of sampling specimens is accompanied by the responsibility of supporting the maintenance and growth of museums.”40 Retrieving molecular material often entails some extent of destruction to the object. Thus, it is necessary that scientists interested in molecular research, wishing to utilize the luxury of museum collections, communicate with museum curators to minimize conflict of interest between aDNA extraction and museum object preservation. Although current techniques have advanced to the point where scientists can sample museum objects with little to no harm to the specimen, it remains necessary to keep open the line of communication. aDNA research has transformed the meaning of fossils and consequently how scientists view fossils and the information that can be gleaned from within. Fossils are more than meets the eye, but they are also storehouses of molecules and genetically informative material. In Life of the Past (1953), Simpson perceptively wrote, “Over the years it was learned what fossils are and how to find and collect them. Now we are learning how to extract from them all the information they can give us, which is much more extensive than our predecessors dreamed.”41 All in all, aDNA research is a fascinating development of modern science; a development that requires us to reevaluate the meaning of fossils, its larger significance for the science of paleontology, and its greater potential in the modern evolutionary synthesis.

Disciplinary Boundaries

The recent expansion of aDNA research also raises questions of disciplinary boundaries. Two specific questions come to mind. First, what types of scientists were doing aDNA research in those early years? Are these researchers paleontologists? Anthropologists? Or, are they molecular biologists? Second, what science, if any, exercises authority over this new approach to fossil studies? Is it paleontology? Anthropology? Or is it molecular biology? These are complex

39 Jeffreys, “Raising the dead and buried,” 198. 40 Gary Graves and Michael Braun, “Museums: Storehouses of DNA?” Science 255 (1992): 1335. 41 Simpson, Life of the Past, 19. 105 questions and perhaps too challenging to tease apart entirely. However, we can at least begin to search for possible answers and allude to their significance. To address the first question, in our review of the early history of aDNA research, we find that the majority of research was primarily undertaken by molecular biologists and biochemists. Recall the first aDNA study of 1984. Russell Higuchi, first author on the quagga DNA paper, was a skilled biochemist. One of his co-authors, Allan Wilson, a New Zealand native and leader in molecular studies, was trained in molecular evolutionary biology. At the time, both researchers were employed by the Department of Biochemistry at the University of California, Berkeley. Likewise, Svante Pääbo was working as a molecular biologist in the Department of Cell Research at the University of Uppsala and in partnership with Institute of when he first began his studies in aDNA. Although initially trained in humanities, Pääbo went molecular with his graduate studies in biology. Currently, Pääbo is Director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology, one of the leading labs for anthropological aDNA research. Similarly, Margaret Hughes, first author of the British bog body study of 1986, was a researcher in the Department of Biochemistry at University of Liverpool. Edward Golenberg, lead author on the twenty-million-year-old Magnolia DNA paper, was employed by the Department of Botany and Plant Sciences at University of California, Riverside. Although an anthropologist at Florida State University, Glen Doran teamed up with an array of researchers experienced in pathology, radiology, biochemistry, molecular biology, and immunology and medical microbiology for his aDNA study on the archaeological site at Windover. Additionally, Richard Thomas, who – along with fellow researchers – fist recovered DNA from the extinct Tasmanian devil, worked in the Department of Biochemistry at the University of California, Berkeley. His colleague, Walter Shaffner, was a molecular biologist at the University of Zurich in Switzerland. A survey of the early participants in aDNA research reveals two things. First, aDNA research was not being done by paleontologists but by biologists. At least in the early years, aDNA research seemed to be distinctively tied to molecular biology as research, for the most part, was conducted by biologists, biochemists, and molecular biologists. Yet it seems peculiar that paleontologists would be so slow to embrace such a revolutionary approach to fossil studies. It strikes me that there are three reasons for the paleontologist’s reluctance to embrace aDNA research as an integral part of paleontological research. First, I think paleontologists were not

106 among the early participants in aDNA research mainly because most paleontologists lacked sufficient training in molecular biology and also access to the appropriate lab equipment for DNA research. Even though many paleontologists today, as a product of the paleobiological revolution, embrace more quantitative and analytical approaches to paleontological data, this breed of paleontologist still lacks the knowledge and expertise of the molecular biologist in an area like DNA research. Thus, molecular biologists and biochemists who were skilled in DNA lab work were the first to pilot such studies. A second explanation for the paleontologist’s hesitancy may stem from the uncertainty surrounding aDNA research as an entirely legitimate field of research, especially for working on fossils over 100,000 years of age. Our review of aDNA research has shown us the exploration of a scientific anomaly; the existence of DNA in ancient and fossil organisms. Before aDNA research could be taken seriously as a reliable approach to studying fossils, studies had to be performed and published, reproduced and reported again. Best practices had to be established and authentication was required. Reports of DNA from ancient specimens were viewed with skepticism until tested for contamination and successfully repeated. After years of research and reproduction, the existence of DNA in ancient and fossil organisms up to 100,000 years of age was accepted. Yet reports of DNA from fossils exceeding this threshold, no matter how pristine the preservation, were still regarded with suspicion. Moreover, all reports claiming DNA from ancient creatures, like the dinosaurs, had been proven the results of contamination. Thus by the late 1990s, there was no standing report on the successful extraction and sequencing of DNA from anything over 100,000 years old. Although the novel field of aDNA had proven a valid research tool for more modestly ancient subjects, this approach to fossil studies as applied to ancient paleontological material remained exceedingly controversial. For the most part, aDNA research was not useful to paleontologists interested in studying much older creatures and looking at the much bigger picture of evolutionary history. I believe this was a large reason for the paleontologist’s slow response to the practice of aDNA research. However, a negative cannot be proven, and though it is highly unlikely, it could be possible that someday DNA will be shown to exist in fossils millions of years old. Finally, perhaps paleontologists were cautious about aDNA research as applied to paleontology because it posed a threat to the traditional ways of doing paleontology and studying evolution. We can recall Osborn’s suspicion of experimental biology and his resistance to the

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integration of experimental techniques in paleontological research. As Rainger remarked, Obsorn’s opposition to experimental biology was “because it represented a specialized field of study that threatened the work of the naturalist and the traditional way of doing science.”42 Perhaps paleontologists are more interested in just studying the fossils and less interested in biology and genetics; therefore, less willing to learn a new science and to apply it and integrate it with their own work on fossils. While this could be the case, I do not think most paleontologists today would share the opinion that aDNA research poses a serious challenge to paleontology or the traditional ways of doing science. Paleontology has advanced remarkably over the past century thanks to the efforts of Simpson and Gould to bring paleontology back to the high table and into the larger discussion of evolutionary biology. The advent of molecular paleontology in the 1950s and the emergence of paleobiology several decades later have challenged the traditional methods of paleontological research. However, the rise and success of these fields were not to the detriment of other traditional methods of inquiry like morphology, taxonomy, and systematics. In fact, research efforts in molecular paleontology and paleobiology have added to paleontology’s information sources and development as a science; especially as a science in a molecular age. Therefore, though some may view aDNA as a threat coming from outside of their field, I do not think this is the primary reason for the paleontologist’s absence in early aDNA studies. Nonetheless, I feel that this could be a potential part of the story of aDNA research that would be intriguing to further investigate. Overall, we find that the majority of aDNA research in its first two decades of development was dominated by biologists interested in working on much older anthropological and paleontological material. This brings us to our second question: who claims authority over aDNA research? Before we try to answer this question, we should mention the role of disciplinary boundaries. First, disciplinary boundaries tell us much about the nature of a scientific field and how its research and practices differ and distinguish it from other sciences. Each scientific discipline has a special set of inquiries and also distinctive procedures and standards of investigation. According to Kuhn, scientific communities, or scientific disciplines, consist of “practitioners of a scientific specialty” who are “[b]ound together by common elements in their education and apprenticeship” and “see themselves and are seen by others as the men responsible

42 Rainger, An Agenda for Antiquity, 142. 108

for the pursuit of a set of shared goals, including the training of their successors.”43 For example, paleontology is interested in discovering and deciphering the history of life. To do this, paleontologists take fossils as their primary source of evidence and use morphology, taxonomy, and systematics, among other approaches to recover and reconstruct the history of life and evolution. Sometimes, however, disciplines are after similar questions despite their disparate methods of examination. For instance, paleontology and molecular biology are both interested in the study of life and evolution. Whereas paleontology focuses primarily on fossil evidence, molecular biologists are concerned with life at the cellular and molecular level and use proteins, RNA, and DNA as study subjects. Though paleontology and molecular biology have radically different methods of research, they are in some ways interested in the same questions about life and the evolution of life. Disciplinary boundaries are useful demarcations between one science and another but at the same time, these boundaries should not inhibit crossover or collaboration. In fact, often times these lines become blurred, especially in instances where two or more disciplines are interested in answering the same question. Instead, sciences such as paleontology, systematics, genetics, and biology, among others, should encourage the transcendence of those boundaries in favor of interdisciplinary communication and cooperation. As Ruse aptly noted, “collaboration is very much of the nature of modern science.”44 One of the main themes of the modern evolutionary synthesis was, and still is, to promote interdisciplinary scholarship towards the study of evolutionary biology. The history of aDNA research suggests a movement towards more cross- disciplinary discussion of evolutionary theory. aDNA research is a unique interface between a number of varying disciplines. In transcending discipline boundaries, aDNA research unites a number of sciences from anthropology and biochemistry to paleontology and molecular biology, in which each bring its own tools and sources of information to the table. As Muller suggested, “On each method alone, it is evident, the complexities and uncertainties of the problems are very great, and far better results could be achieved by a pooling of the evidences.”45 If this is the case, it may be difficult to discern disciplinary boundaries.

43 Ibid., 296. 44 Ruse, Mystery of Mysteries, 124. 45 Hermann Joseph Muller, “Reintegration of the Symposium on Genetics, Paleontology, and Evolution,” in Genetics, Paleontology, and Evolution, eds. Glen Jepsen, Ernst Mayr, and George Gaylord Simpson (Princeton: Princeton University Press, 1949), 421-422. 109

Interdisciplinary research between the paleontologist and biologist is especially appropriate. After all, paleontology functions between the two sciences of geology and biology. James W. Valentine of the Department of Integrative Biology at University of California, Berkeley, wrote, “From its inception as a science, paleontology has drawn upon both geological and biological sciences, and its findings have been applied to problems in each of those fields.”46 In a recent interview at the annual Society for Vertebrate Paleontology (SVP) conference in fall of 2011, Mark Norell – Curator of Paleontology at the AMNH – made a similar point. Norell, who described himself as a “biologist who studies fossils,” claimed that there exists a kind of trichotomy among paleontologists. He explained that there is a cohort of scientists, like himself, who consider themselves first and foremost biologists. He also noted a second cohort who views themselves primarily as geologists, and the third group he identified as a blending of the two. According to Norell, each type of paleontologist looks at the world very differently and consequently, approaches the world differently too.47 Nonetheless, conversation between disparate perspectives should be encouraged. We should recognize those differences in view and approach them not as a disjunction between paleontologists, but as an advantage and a coming together of multiple lines of evidence towards a common goal and a fulfillment of the modern evolutionary synthesis. The possibility that some of our most ancient fossils could yield DNA was – and still is – an exciting prospect. For the first time, paleontologists might not be entirely dependent on inferences about the history and evolution of life from an incomplete and biased fossil record. Instead, we could obtain quantifiable evidence of evolutionary history from fossils. But do we see paleontologists responding to aDNA research? Were they attempting to integrate this new tool into fossil studies? At least in this review of the history, paleontologists were not experimenting with aDNA. As mentioned earlier, this is perhaps because paleontologists were not trained and equipped to carry out such studies. Or perhaps it is because really ancient paleontological specimens, which most paleontologists are interested in, were proven unlikely candidates for DNA study. In a more recent article, Schweitzer and colleagues noted, “The recovery of DNA sequences from fossil tissues has the greatest potential for elucidating

46 James Valentine, “ to Paleobiology,” in Paleobiology: A Synthesis, eds. Derek Briggs and Peter Crowther (Oxford: Blackwell Scientific Publications, 1990), 547. 47 Mark Norell, interview by author, 4 November 2011, Las Vegas, recording, Society of Vertebrate Paleontology, Las Vegas. 110

evolutionary relationships, and hence, has been the focus of many molecular efforts with fossils and subfossil material. But it has been hypothesized that DNA analyses are useless for extremely ancient specimens (i.e. greater than ∼1 Ma).”48 Norell shared a similar opinion:

Is there DNA from ancient animals? I would say “probably yes.” Does it exist in fragments which are ever big enough to contain meaningful sequence? I would say “probably no.” Also…deciding what is a fossil, I say up to perhaps 350,000 years…going older than that though is a pretty slippery slope. You might be able to isolate something from something…and say, “yes, we have nucleic acids which are here”…but as far as it being informative for any scientific question or any hypotheses you might want to test, I just don’t see it.49

Even if DNA over 100,000 years old did exist, it is likely too fragmented and degraded to sequence and further produce any evolutionary significant study from. Thus, aDNA research is not likely to be useful to paleontologists interested in much older organisms. In an interview, Horner echoed Norell’s concern:

But after the answer is found, the question is what we do with this stuff? What do we do with this DNA? We’re not going to make a dinosaur with it. We’re not going to clone it and make a dinosaur. We just don’t have enough of it. We don’t know enough to know what the whole three trillion strand looks like.50

According to Horner, DNA from million-year-old material – if it does exist – is not going to give us the information we need to answer the important evolutionary questions we should find interesting. Any hopes that scientists will retrieve truly ancient DNA from million- year-old animals or plants remains bleak.

48 Mary Schweitzer, Recep Avci, Timothy Collier, and Mark Goodwin, “Microscopic, chemical and molecular methods for examining fossil preservation,” C. R. Palevol 7 (2008): 160. 49 Mark Norell, interview by author, 4 November 2011, Las Vegas, recording, Society of Vertebrate Paleontology, Las Vegas. 50 Jack Horner, interview by author, 2 November 2011, Las Vegas, recording, Society of Vertebrate Paleontology, Las Vegas. 111

I have identified several possible deterrents that may shed light on reasons why paleontology was slow to respond to such a groundbreaking research tool. From the start, DNA research was a job for the molecular biologist, not the paleontologist. Next, it was shown very improbable that DNA could survive in paleontological material over the 100,000 year threshold. Lastly, it is possible that some paleontologists viewed new experimental and molecular research as a threat to traditional paleontological approaches. It may be that aDNA work will remain the jurisdiction of molecular biological programs and as a job for the molecular biologist, not the paleontologist. However, there are attempts towards integration. Ancient archaeological material has proved some of the most successful materials for extracting aDNA and the Max Planck Institute of Evolutionary Anthropology, directed by Pääbo, seeks to integrate scientists of various training to better research aDNA:

The Max Planck Institute for Evolutionary Anthropology unites scientists with various backgrounds (natural sciences and humanities) whose aim is to investigate the history of humankind from an interdisciplinary perspective with the help of comparative analyses of genes, cultures, cognitive abilities, languages and social systems of past and present human populations as well as those of primates closely related to human beings.51

A move towards a synthesis of evolutionary knowledge involves an integration of scientists from multiple backgrounds and disciplines. Maybe similar efforts can be made to integrate molecular biology and paleontology with aDNA study to further explore its benefits. Despite the poor outlook, the curiosity that DNA may remain in some of our older and more charismatic creatures lingered. Can DNA survive over 100,000 years, let alone millions of years? If not, then paleontology will certainly be limited in the breadth of DNA research as applied to fossils. If it is possible, then paleontology will have much to gain. This question might still be worth asking. Recently, however, there is a group of scientists from Ancient DNA Centre at McMaster University in Hamilton, Ontario, Canada looking to push the envelope. Though a research lab within the Department of Anthropology, the McMaster Ancient DNA Centre investigates DNA in a variety of material, including paleontological specimens:

51 “Max Planck Institute of Evolutionary Anthropology,” last modified February 2012, http://www.eva.mpg.de/. 112

The McMaster Ancient DNA Centre approaches a wide range of evolutionary and molecular biological questions using DNA and proteins from archaeological, paleontological, and forensic remains. We use state-of-the-art techniques to extract and sequence these molecules, discerning origins and population histories of a wide range of species, both extinct and extant. This allows us to follow evolution in action, directly testing models based on modern theory and observation.52

The McMaster Ancient DNA Centre, headed by Hendrik Poinar, operates on a collaborative scale by drawing upon a number of researchers and research institutions from anthropology and paleontology to biology and biochemistry. The McMaster lab is a prime example of aDNA research at its best and a pluralistic science willing to push the boundaries of possibility. Thus, the history of aDNA is not a success story for paleontology, but I doubt this means that paleontologists should give up on the new science. In fact, some of the greatest scientific discoveries and revolutions have been the result of scientists pushing the possibilities even in the face of cynicism. Schweitzer and fellow researchers, for example, have published some remarkable but controversial studies in dinosaur science. In the early 1990s, at the height of aDNA research, Schweitzer, after examining tissue from a Tyrannosaurus rex bone, observed red, spherical shapes that looked strikingly similar to red blood cells. Multiple tests attempting to falsify this blood cell hypothesis failed and Schweitzer published her conclusions. Despite the controversial nature of her work, Horner defended Schweitzer’s research arguing, “Regardless of whether [Schweitzer’s] hypotheses turn out to be correct, she followed the strict procedures of scientific inquiry and proposed hypotheses that are both testable and repeatable.” In sum, Horner claimed, “In my opinion, Mary Schweitzer is currently at the head of the high table in dinosaur paleontology. As for her detractors, I doubt the table is in view.”53According to Horner, the recent strides taken in molecular paleontology represent cutting edge research in paleontology. Though Schweitzer does not conduct aDNA research, her work on dinosaur blood cells and proteins stems from a similar vein; that of molecular paleontology and the idea that fossils, like living organisms, can be studied for genetically valuable information. Her work, despite it being highly contested, represents some of the most revolutionary and technologically advanced

52 “McMaster Ancient DNA Centre,” last modified February 2012, http://socserv.mcmaster.ca/adna/About-us/. 53 Jack Horner, “Dinosaurs at the High Table,” in The Paleobiological Revolution: Essays on the Growth of Modern Paleontology, eds. David Sepkoski and Michael Ruse (Chicago: The University of Chicago Press, 2009), 119. 113

research in paleontology and dinosaur paleontology specifically. Paleontologists and other scientists interested in studying fossils should keep an open mind and feel encouraged to push the parameters. Conclusion

In sum, the recent expansion of aDNA research, when appropriately situated in the overall history of paleontology, beckons us to reconsider the nature and role of historical and experimental sciences. It also requires us to reassess our understanding of the term fossil, especially in relation to how we think about and study fossils. Moreover, aDNA research asks us to reexamine disciplinary boundaries among the sciences of biology and paleontology. In this chapter, we discovered that paleontologists were not major participants in the early years of aDNA study, and we explored several explanations for their absence. The early history of aDNA research demonstrated that more modestly ancient organisms – those under 100,000 years of age – were more ideal candidates for aDNA study. Overall, aDNA research was not useful to paleontologists interested in studying our most ancient creatures and discovering the big picture of evolutionary history. Nonetheless, the history of aDNA represents an outstanding conceptual breakthrough; it is a history that shows us that our fossils may be more alive than they seem, that scientists can take our fossils beyond description and classification, and by incorporating experimental techniques and objectively quantifiable data, researchers can begin to ask and answer more evolutionary stimulating questions. aDNA research challenges our traditional interpretations of historical and experimental sciences, as well as our notions of disciplinary boundaries. Together, molecular paleontology, paleobiology, and aDNA research represent a move toward a larger evolutionary synthesis – perhaps even a new synthesis in biology – and also a step toward bridging the gap between historical and experimental science.

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CONCLUSION

Continuing the Modern Evolutionary Synthesis

In a 1983 conference on evolution, Gould gave a talk titled, “Irrelevance, Submission and Partnership: The Changing Role of Paleontology in Darwin’s Three Centennials and a Modest Proposal for .” In this talk Gould argued that “palaeontology has a new role to play in the third centennial” and one of “neither irrelevance, nor subservience, but true partnership.”1 He explained that at the time of the first centennial in 1909 – marking the birth of Darwin – that paleontology, despite its “vigorous role in evolutionary theory for the first two or three decades after 1859,” had fallen into a state of irrelevance. At the turn of the century, paleontologists had “waned along with the entire school of speculative ,” and most paleontologists “returned to their ancient métier of correlating rocks for geologists.”2 Gould, however, noted that fifty years later, paleontology’s status in regards to evolutionary theory had taken a turn for the better. He described that by the second centennial in 1959 – in honor of the 100th anniversary of the Origin’s publication – that this celebration “featured plenty palaeontology and precious little disagreement.”3 In the two decades prior, Simpson adamantly campaigned for paleontology as a part of the evolutionary synthesis. Thus, the bulk of paleontology’s shifting status and role in evolutionary discussion had much to do with his efforts in bridging the gap between evolutionary biology and paleontology. Gould announced, “For 1959 represented the heyday of the hard version of the Modern Synthesis, a movement that brought such traditional fields as palaeontology and systematics under the explanatory aegis of Darwin’s original hypothesis of natural selection, finally united fruitfully with the Mendelian genetics of micromutation.”4 At the same time, paleontology, though moving out of irrelevance, had adopted a tone of submission: “It had relinquished the idea that a direct study of vast times and changes might contribute new principles to a larger synthesis, and had

1 Stephen Jay Gould, “Irrelevance, submission, and partnership: the changing role of palaeontology in Darwin’s three centennials and a modest proposal for macroevolution,” in Evolution from Molecules to Men, ed. D. S. Bendall (Cambridge: Cambridge University Press, 1983), 353. 2 Ibid., 349. 3 Ibid., 349. 4 Ibid., 349. 115

opted for satisfaction that its phenomena could be rendered consistent with a body of theory presented as a package by colleagues in other disciplines.”5 Now, upon the third centennial in 1982 – in remembrance of Darwin’s death – Gould contended that paleontology had evolved from irrelevance and subservience into an age of true partnership. He claimed, “Evolutionary theory at the third centennial is bursting with new life and excitement. We are experiencing none of the anarchy of 1909, since Darwinism is now secure as a centerpiece. But we are also moving away from the smugness of 1959 and considering a flood of useful expansions and additions.”6 Earlier, Simpson had argued in his book Fossils and the History of Life that “What is needed, and what has been widely pursued during the present century, is a synthesis of evolutionary theory involving all levels, from molecules through whole organisms and specific populations to multispecific biotas, at all times from the origin of life to now.”7 What is needed is a merging of multiple lines of evidence, and as a novel approach to fossil studies, aDNA is a useful expansion and addition to our existing knowledge of evolutionary theory. Viewed from this framework of synthesis, the history of aDNA research is most appropriately recognized as an extension of the modern evolutionary synthesis and part of the molecular and paleobiological movement towards integrating more experimental and quantitative approaches in paleontology. However, this trend toward more experimental methodology in paleontology poses an issue for Cleland’s distinction between a historical and an experimental science. Turner argued that while Cleland’s argument has merit, there is a great deal of recent work in paleontology that does not entirely fit her mold of a historical science. For example, the late J. John Sepkoski, Jr., an invertebrate paleontologist at the University of Chicago, was one of the first paleontologists to employ a statistical approach to paleontological research.8 A leading figure of the paleobiological revolution, Sepkoski popularized a more quantitative approach to fossil studies. Ruse, in his chapter “Crunching the Fossils,” described Sepkoski as a “new breed of scientist” as he suspected that Sepkoski had never dug up a real fossil in his life but rather was “happiest when collecting vast libraries of data and then crunching the numbers through the computer,

5 Ibid., 352. 6 Ibid., 363. 7 Simpson, Fossils and the History of Life, 152. 8 Derek Turner, personal communication, 19 January 2012. 116

seeing what patterns emerge at the other end.”9 This is part of Turner’s disagreement with Cleland’s description of historical science. Sepkoski’s work, among others, was interested in testing hypotheses through quantitative methods in hopes of finding evidence of larger evolutionary processes and patterns. Turner argued that the search for a “smoking gun” is not involved in this kind of research. This is contrary to what Cleland would suspect of a historical science. I believe this is an indication that something more complex and interesting is developing within the field of paleontology. This conflict also suggests that Cleland’s distinction between historical and experimental science, as being a difference in the testing of hypotheses, is inadequate. Turner’s concern with Cleland’s description of a historical science in regards to paleontology could be suggestive of a trend in paleontology towards the incorporation of experimental methods and even a new synthesis in biology. aDNA challenges the traditional interpretations of historical and experimental science. However, I do not want to argue that paleontology in its entirety is becoming an experimental science in Cleland’s sense. As the late evolutionary biologist Antoni Hoffman claimed, “Yet palaeontology is first and foremost a historical science. Palaeontologists are primarily historians of the biosphere and must focus on reconstructing history.”10 Indeed, paleontology is a historical science in this manner, and thus I think we can more aptly recognize that the emergence of aDNA research, as a part of the larger movement of molecular paleontology and paleobiology, has introduced scientists to new tools and new questions that may be applied to paleontological study. In becoming more cosmopolitan, scientists are beginning to appreciate and incorporate experimental procedures and more objective evidence in research on fossils. As a science, paleontology is becoming more of a of historical and experimental approaches and thus, blurring the lines and perhaps biases between historical and experimental sciences. Perhaps this is suggestive of a new synthesis in biology; one that makes room for new approaches in molecular paleontology, molecular systematics, paleobiology, integrative biology, aDNA, and evolutionary developmental biology. The traditional view of the field paleontologist, as best exemplified through the memoirs vertebrate paleontologists such as of Sternberg, Brown, Bird, and Chapman is changing. Some paleontologists, like Sepkoski, are satisfied working with numbers and large data sets. Some

9 Ruse, Mystery of Mysteries, 214-215. 10 Antoni Hoffman, “History of Palaeontology,” in Paleobiology: A Synthesis, eds. Derek Briggs and Peter Crowther (Oxford: Blackwell Scientific Publications, 1990), 554. 117 paleontologists take their studies into the lab for molecular analyses. But this is not to say that the field paleontologist has become obsolete. Rather paleontology is still very much a discovery driven field. Some paleontologists are content spending months in the field, discovering and describing new species. A move towards more experimental and analytical techniques in paleontology does not have to be to the exclusion of more traditional practices. Instead, the desire for quantifiable evidence and the integration of quantitative analyses has produced a new type of paleontologist, or “new breed of scientist.” As Turner put it:

In many respects, the paleobiological revolution represented a move in the direction of evolutionary paleontology. In saying this, I don’t mean to suggest that the scientists necessarily wanted to move away from organismic paleontology. The study of particular kinds of prehistoric life remains an important and lively part of paleontology…Rather, the major players of the “revolutionary” period – the 1970s and 1980s – sought to establish evolutionary paleontology as an important part of the field, without necessarily edging out other things.11

Experimental movements in paleontology should be viewed as a blending of the old with the new towards a more robust view of both paleontology as a science and evolution as an all- encompassing theory. As Rudwick stated, “It would be salutary for the historians to be reminded by the palaeontologists that most of the earlier frames of reference are still being utilized – even if unrecognized – in modern palaeontology: the insights and methods of one ‘paradigm’ of interpretation have not been wholly abandoned, but absorbed into the next.”12 Rudwick was correct in noting older paradigms are not necessarily to be ignored and left behind as modern science moves forward. In fact, as Allen argued, “While some biologists in recent years, in the full flush of one or another molecular successor, have spoken condescendingly about ‘mere observation’ or ‘old-fashioned descriptive methods,’ these processes remain a necessary foundation for any biological (or scientific) inquiry.”13 At the same time, paleontology – among other biological sciences – should be open to a more cosmopolitan view of science. This is not only beneficial but necessary if we hope to truly

11 Turner, Making Prehistory, 10. 12 Rudwick, The Meaning of Fossils, 267. 13 Allen, The History of Life Sciences, xv. 118

move nearer an evolutionary synthesis. If not, we will remain stagnant in our own, old ways of doing science, blind to novel tools that may be fruitful to future research. For instance, Horner proposed, “In my mind, the future of dinosaur paleontology is multidisciplinary synthesis, with teams of senior researchers and students tackling problems using a wide variety of methods, but beginning in the field with the collection of new specimens.”14As a new avenue towards cross- discipline inquiry, I think aDNA research can be viewed in a similar vein as molecular paleontology and paleobiology. Aside from interdisciplinary scholarship, it is also undeniable that technology has played a critical role in the development of science and the growth of paleontology specifically. Science tends to progress alongside those technological advancements. In a recent interview at the SVP conference, fall of 2011, Hans Larsson, paleontologist and evolutionary biologist at McGill University, Canada, reflected on the history of paleontology. In response to the question whether the emergence of quantitative studies in paleontology has helped to bring the field into larger discussion with evolutionary biology, Larsson replied:

Absolutely. By bringing in new methods and new sciences to paleontology, it’s done a couple things. One, it has allowed the field to grow…paleontology is becoming more interdisciplinary…the field is becoming much more diverse. It also has more technology. So now we have computers, we have CT machines, we have the ability to make immunohistochemical stains and images…very easily. Twenty years ago that was extremely hard and only hardcore molecular biologists could do that. Now, someone like myself could do that.15

Over the past several decades, since the molecular revolution and the introduction of novel technologies, paleontological practices have moved beyond description and classification. Paleontologists have learned the benefit of co-opting technologies from other fields for their own purposes. They have also learned that fossils may contain precious material within, be it amino acids, proteins, or even DNA. The molecular and technological revolution of the past century has taken paleontology into another realm of possibility as far as research tools and agendas.

14 Horner, “Dinosaurs at the High Table,” in The Paleobiological Revolution, 119. 15 Hans Larsson, interview by author, 4 November 2011, Las Vegas, recording, Society of Vertebrate Paleontology, Las Vegas. 119

Technology is imperative to the direction of science, but progress also depends on the scientist’s ability to envision novelty in their research, such as taking an old tool and using it in a new way. For example, aDNA research required learning to take techniques common to DNA analysis and apply it to fossils. However, these kinds of innovations may be difficult to see at first. Schweitzer wrote, “Data derived from multidisciplinary, non-traditional techniques can be difficult to decipher, and without a basic understanding of the type of information provided by these methods, their usefulness for fossil studies may be overlooked.”16 Once recognized, however, the advantages can be vast. Objective and quantifiable evidence appeared one of the greatest benefits of molecular research on ancient specimens. Praising the benefits of aDNA research, Cooper wrote:

aDNA methods provide an opportunity to characterise the genetic composition of species and populations in the past, and to actually observe evolutionary change through real time. Such a record has great potential to reveal the processes that have generated the diversity and distribution of taxa in our modern environment, and to examine phenomena such as speciation, domestication, morphological evolution, and the impacts of major environmental changes. aDNA data also provide an important opportunity to test our ability to accurately reconstruct evolutionary history via the fossil record or via extrapolation from the genetic data of modern species.17

Historical sciences like paleontology and archaeology could profit greatly by objectively testing historical inferences. As Ayala claimed, “Thus, the inferences from comparative anatomy and other disciplines that study evolutionary history can be tested in molecular studies of DNA and proteins by examining the sequences of and amino acids.” Furthermore, he wrote, “The authority of this kind of test is overwhelming: each of the thousands of genes and thousands of proteins contained in an organism provides an independent test of that organism’s evolutionary history.”18 According to Ayala, molecular evolutionary studies presented a serious advantage over “paleontology, comparative anatomy, and other classical disciplines.” Ayala exclaimed that the

16 Schweitzer, “Microscopic, chemical and molecular methods for examining fossil preservation,” 1. 17 Alan Cooper, “The Year of the Mammoth,” PLOS Biology 4 (2006): 0311-0313. 18 Ayala, “Molecular Evolution vis- à-vis Paleontology,” in The Paleobiological Revolution, 177. 120

advantage here is that information from molecular evolutionary studies is “readily quantifiable.” Second, “comparisons can be made between very different sorts of organisms,” and finally, such studies have the advantage of “multiplicity.”19 For example, the discrepancy of the morphological data in regards to the phylogenetic placement of the extinct thylacine was eventually clarified using molecular analyses of aDNA. Turner observed: “To all appearances, the debate seems to pit paleontology against molecular biology. Each discipline has its own source of evidence – the fossil record vs. the genes and proteins of living creatures – and the issue is which of these sources of evidence can tell us more about the past.”20 However, we can also learn to view these multiple lines of evidence, both historical and experimental, as valuable paths of scientific inquiries in their own right. The past century represents decade upon decade towards evolutionary synthesis among a myriad of sciences. It would be a shame to undo this progress. Sepkoski and Ruse reflected on Morgan’s low opinion of paleontology nearly a century ago. Quoting Morgan, they wrote, “Paleontologists have sometimes gone beyond this descriptive phase of the subject and have attempted to formulate ‘causes,’ ‘laws’ and ‘principles’ that have led to the development of their series.” Morgan continued:

The geneticist says to the paleontologist, since you do not know, and from the nature of your case you can never know, whether your differences are due to one chance or to a thousand, you can not with certainty tell us anything about hereditary units which have made the process of evolution possible. And without this knowledge there can be no understanding of the causes of evolution.21

Unfortunately this attitude towards paleontology persisted for the better part of the last century until Simpson published his famed book, Tempo and Mode in Evolution, in 1944. A continuation of Dobzhansky’s initial vision for an evolutionary synthesis, paleontology resurfaced and slowly but surely found itself as a viable discipline in evolutionary discourse. Four years following Simpson’s Tempo and Mode in Evolution, the late Hermann Joseph Muller, wrote the following illustrative metaphor:

19 Ibid, 177. 20 Turner, Paleontology: A Philosophical Introduction, 199. 21 Sepkoski and Ruse, The Paleobiological Revolution, 3. 121

That great complex beast called Life, which is so subject to both inner and outer conflicts, has left behind him a long and devious though often ill-marked trail. Poring over the footprints, the marks where he has lain down or struggled or undergone digressions or reverses, the paleontologists have tried to reconstruct the story of his wanderings and to interpret what features of his nature and what characteristics of the terrain led to his following the routes that he did. On the other hand the geneticists, coming upon the creature himself apparently slumbering (his motions being so much slower than theirs), have tried, together with the taxonomists and physiologists, to penetrate into his present nature and therefrom to infer the manner of his movement, what paths he is likely to have taken and why, and what future directions of travel might be expected of him. On each method alone, it is evident, the complexities and uncertainties of the problems are very great, and far better results could be achieved by a pooling of the evidences.22

A “pooling of the evidences,” although ideal, may be easier said than done; especially, when such disparate disciplines face a long standing divide between the historical and experimental sciences. Hopefully we have moved past such patronization and now realize through the technological advancements of molecular biology and the conceptual developments in molecular paleontology, paleobiology, and even aDNA research that paleontologists have a vital role in our understanding of evolutionary processes. More broadly, the early history of aDNA research, along with other recent developments such as molecular paleontology, molecular systematics, paleobiology, integrative biology, and evolutionary developmental biology, can be viewed as part of a new synthesis in biology.

22 Muller, “Reintegration of the Symposium on Genetics, Paleontology, and Evolution,” in Genetics, Paleontology, and Evolution, 421-422. 122

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BIOGRAPHICAL SKETCH

Elizabeth Dobson graduated from North Carolina State University of Raleigh, North Carolina in 2010 with a Bachelor of Arts in Honors History and a Bachelor of Arts in Philosophy. She is a current Master’s student in the Program for the History and Philosophy of Science at Florida State University of Tallahassee, Florida. Elizabeth is from Mount Pleasant, North Carolina.

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