“Some of these stories are closer to my own life than others are, but not one of them is as close as people seem to think.” Alice Murno, from the intro to Moons of Jupiter

"Talent hits a target no one else can hit; genius hits a target no one else can see." Arthur Schopenhauer

“Why does everything you know, and everything you’ve learned, confirm you in what you believed before? Whereas in my case, what I grew up with, and what I thought I believed, is chipped away a little and a little, a fragment then a piece and then a piece more. With every month that passes, the corners are knocked off the certainties of this world: and the next world too. Show me where it says, in the Bible, ‘Purgatory.’ Show me where it says ‘relics, monks, nuns.’ Show me where it says ‘Pope.’” –Thomas Cromwell imagines asking Thomas More—Wolf Hall by Hilary Mantel

My favorite posts to get started: The Self-Righteousness Instinct, Sabbath Says, Encounters, Inc., and What Makes "Wolf Hall" so Great?.

Sunday, March 30, 2014

The Better-than-Biblical History of Humanity Hidden in Tiny Cells and a Great Story of Science Hidden in Plain Sight

            Anthropology enthusiasts became acquainted with the name Svante Pääbo in books or articles published throughout the latter half of this century’s first decade about how our anatomically modern ancestors might have responded to the presence of other species of humans as they spread over new continents tens of thousands of years ago. The first bit of news associated with this unplaceable name was that humans probably never interbred with Neanderthals, a finding that ran counter to the multiregionalist theory of human evolution and lent support to the theory of a single origin in Africa. The significance of the Pääbo team’s findings in the context of this longstanding debate was a natural enough angle for science writers to focus on. But what’s shocking in hindsight is that so little of what was written during those few years conveyed any sense of wonder at the discovery that DNA from Neanderthals, a species that went extinct 30,000 years ago, was still retrievable—that snatches of it had in fact already been sequenced.

Then, in 2010, the verdict suddenly changed; humans really had bred with Neanderthals, and all people alive today who trace their ancestry to regions outside of Africa carry vestiges of those couplings in their genomes. The discrepancy between the two findings, we learned, was owing to the first being based on mitochondrial DNA and the second on nuclear DNA. Even those anthropology students whose knowledge of human evolution derived mostly from what can be gleaned from the shapes and ages of fossil bones probably understood that since several copies of mitochondrial DNA reside in every cell of a creature’s body, while each cell houses but a single copy of nuclear DNA, this latest feat of gene sequencing must have been an even greater challenge. Yet, at least among anthropologists, the accomplishment got swallowed up in the competition between rival scenarios for how our species came to supplant all the other types of humans. Though, to be fair, there was a bit of marveling among paleoanthropologists at the implications of being some percentage Neanderthal.

            Fortunately for us enthusiasts, in his new book Neanderthal Man: In Search of Lost Genomes, Pääbo, a Swedish molecular biologist now working at the Max Planck Institute in Leipzig, goes some distance toward making it possible for everyone to appreciate the wonder and magnificence of his team’s monumental achievements. It would have been a great service to historians for him to simply recount the series of seemingly insurmountable obstacles the researchers faced at various stages, along with the technological advances and bursts of inspiration that saw them through. But what he’s done instead is pen a deeply personal and sparely stylish paean to the field of paleogenetics and all the colleagues and supporters who helped him create it.

It’s been over sixty years since Watson and Crick, with some help from Rosalind Franklin, revealed the double-helix structure of DNA. But the Human Genome Project, the massive effort to sequence all three billion base pairs that form the blueprint for a human, was completed just over ten years ago. As inexorable as the march of technological progress often seems, the jump from methods for sequencing the genes of living creatures to those of long-extinct species only strikes us as foregone in hindsight. At the time when Pääbo was originally dreaming of ancient DNA, which he first hoped to retrieve from Egyptian mummies, there were plenty of reasons to doubt it was possible. He writes,

When we die, we stop breathing; the cells in our body then run out of oxygen, and as a consequence their energy runs out. This stops the repair of DNA, and various sorts of damage rapidly accumulate. In addition to the spontaneous chemical damage that continually occurs in living cells, there are forms of damage that occur after death, once the cells start to decompose. One of the crucial functions of living cells is to maintain compartments where enzymes and other substances are kept separate from one another. Some of these compartments contain enzymes that break down DNA from various microorganisms that the cell may encounter and engulf. Once an organism dies and runs out of energy, the compartment membranes deteriorate, and these enzymes leak out and begin degrading DNA in an uncontrolled way. Within hours and sometimes days after death, the DNA strands in our body are cut into smaller and smaller pieces, while various other forms of damage accumulate. At the same time, bacteria that live in our intestines and lungs start growing uncontrollably when our body fails to maintain the barriers that normally contain them. Together these processes will eventually dissolve the genetic information stored in our DNA—the information that once allowed our body to form, be maintained, and function. When that process is complete, the last trace of our biological uniqueness is gone. In a sense, our physical death is then complete. (6)

The hope was that amid this nucleic carnage enough pieces would survive to restore a single strand of the entire genome. That meant Pääbo needed lots of organic remains and some really powerful extraction tools. It also meant that he’d need some well-tested and highly reliable methods for fitting the pieces of the puzzle together.

            Along with the sense of inevitability that follows fast on the heels of any scientific advance, the impact of the Neanderthal Genome Project’s success in the wider culture was also dampened by a troubling inability on the part of the masses to appreciate that not all ideas are created equal—that any particular theory is only as good as the path researchers followed to arrive at it and the methods they used to validate it. Sadly, it’s in all probability the very people who would have been the most thoroughly gobsmacked by the findings coming out of the Max Planck Institute whose amazement switches are most susceptible to hijacking at the hands of the charlatans and ratings whores behind shows like Ancient Aliens. More serious than the cheap fictions masquerading as science that abound in pop culture, though, is a school of thought in academia that not only fails to grasp, but outright denies, the value of methodological rigor, charging that the methods themselves are mere vessels for the dissemination of encrypted social and political prejudices.

Such thinking can’t survive even the most casual encounter with the realities of how science is conducted. Pääbo, for instance, describes his team’s frustration whenever rival researchers published findings based on protocols that failed to meet the standards they’d developed to rule out contamination from other sources of genetic material. He explains the common “dilemma in science” whereby

doing all the analyses and experiments necessary to tell the complete story leaves you vulnerable to being beaten to the press by those willing to publish a less complete story that nevertheless makes the major point you wanted to make. Even when you publish a better paper, you are seen as mopping up the details after someone who made the real breakthrough. (115)

The more serious challenge for Pääbo, however, was dialing back extravagant expectations on the part of prospective funders against the backdrop of popular notions propagated by the Jurassic Park movie franchise and extraordinary claims from scientists who should’ve known better. He writes,

As we were painstakingly developing methods to detect and eliminate contamination, we were frustrated by flashy publications in Nature and Science whose authors, on the surface of things, were much more successful than we were and whose accomplishments dwarfed the scant products of our cumbersome efforts to retrieve DNA sequences “only” a few tens of thousands of years old. The trend had begun in 1990, when I was still at Berkeley. Scientists at UC Irvine published a DNA sequence from leaves of Magnolia latahensis that had been found in a Miocene deposit in Clarkia, Idaho, and were 17 million years old. This was a breathtaking achievement, seeming to suggest that one could study DNA evolution on a time scale of millions of years, perhaps even going back to the dinosaurs! (56)

            In the tradition of the best scientists, Pääbo didn’t simply retreat to his own projects to await the inevitable retractions and failed replications but instead set out to apply his own more meticulous extraction methods to the fossilized plant material. He writes,

I collected many of these leaves and brought them back with me to Munich. In my new lab, I tried extracting DNA from the leaves and found they contained many long DNA fragments. But I could amplify no plant DNA by PCR. Suspecting that the long DNA was from bacteria, I tried primers for bacterial DNA instead, and was immediately successful. Obviously, bacteria had been growing in the clay. The only reasonable explanation was that the Irvine group, who worked on plant genes and did not use a separate “clean lab” for their ancient work, had amplified some contaminating DNA and thought it came from the fossil leaves. (57)

With the right equipment, it turns out, you can extract and sequence genetic material from pretty much any kind of organic remains, no matter how old. The problem is that sources of contamination are myriad, and chances are whatever DNA you manage to read is almost sure to be from something other than the ancient creature you’re interested in.

            At the time when Pääbo was busy honing his techniques, many scientists thought genetic material from ancient plants and insects might be preserved in the fossilized tree resin known as amber. Sure enough, in the late 80s and early 90s, George Poinar and Raul Cano published a series of articles in which they claimed to have successfully extracted DNA through tiny holes drilled into chunks of amber to reach embedded bugs and leaves. These articles were in fact the inspiration behind Michael Crichton’s description of how the dinosaurs in Jurassic Park were cloned. But Pääbo had doubts about whether these researchers were taking proper precautions to rule out contamination, and no sooner had he heard about their findings than he started trying to find a way to get his hands on some amber specimens. He writes,

The opportunity to find out came in 1994, when Hendrik Poinar joined our lab. Hendrik was a jovial Californian and the son of George Poinar, then a professor at Berkeley and a well-respected expert on amber and the creatures found in it. Hendrik had published some of the amber DNA sequences with Raul Cano, and his father had access to the best amber in the world. Hendrik came to Munich and went to work in our new clean room. But he could not repeat what had been done in San Luis Obisco. In fact, as long as his blank extracts were clean, he got no DNA sequences at all out of the amber—regardless of whether he tried insects or plants. I grew more and more skeptical, and I was in good company. (58)

Those blank extracts were important not just to test for bacteria in the samples but to check for human cells as well. Indeed, one of the special challenges of isolating Neanderthal DNA is that it looks so much like the DNA of the anatomically modern humans handling the samples and the sequencing machines.

A high percentage of the dust that accumulates in houses is made up of our sloughed off skin cells. And Polymerase Chain Reaction (PCR), the technique Pääbo’s team was using to increase the amount of target DNA, relies on a powerful amplification process which uses rapid heating and cooling to split double helix strands up the middle before fitting synthetic chemicals along each side like an amino acid zipper, resulting in exponential replication. The result is that each fragment of a genome gets blown up, and it becomes impossible to tell what percentage of the specimen’s DNA it originally represented. Researchers then try to fit the fragments end-to-end based on repeating overlaps until they have an entire strand. If there’s a great deal of similarity between the individual you’re trying to sequence and the individual whose cells have contaminated the sample, you simply have no way to know whether you’re splicing together fragments of each individual’s genome. Much of the early work Pääbo did was with extinct mammals like giant ground sloths which were easier to disentangle from humans. These early studies were what led to the development of practices like running blank extracts, which would later help his team ensure that their supposed Neanderthal DNA wasn’t really from modern human dust.

Despite all the claims of million-year-old DNA being publicized, Pääbo and his team eventually had to rein in their frustration and stop “playing the PCR police” (61) if they ever wanted to show their techniques could be applied to an ancient species of human. One of the major events in Pääbo’s life that would make this huge accomplishment a reality was the founding of the Max Planck Institute for Evolutionary Anthropology in 1997. As celebrated as the Max Planck Society is today, though, the idea of an institute devoted to scientific anthropology in Germany at the time had to overcome some resistance arising out of fears that history might repeat itself. Pääbo explains,

As do many contemporary German institutions, the MPS had a predecessor before the war. Its name was the Kaiser Wilhelm Society, and it was founded in 1911. The Kaiser Wilhelm Society had built up and supported institutes around eminent scientists such as Otto Hahn, Albert Einstein, Max Planck, and Werner Heisenberg, scientific giants active at a time when Germany was a scientifically dominant nation. That era came to an abrupt end when Hitler rose to power and the Nazis ousted many of the best scientists because they were Jewish. Although formally independent of the government, the Kaiser Wilhelm Society became part of the German war machine—doing, for example, weapons research. This was not surprising. Even worse was that through its Institute for Anthropology, Human Heredity, and Eugenics the Kaiser Wilhelm Society was actively involved in racial science and the crimes that grew out of that. In that institute, based in Berlin, people like Josef Mengele were scientific assistants while performing on inmates at Auschwitz death camp, many of them children. (81-2)

Even without such direct historical connections, many scholars still automatically leap from any mention of anthropology or genetics to dubious efforts to give the imprimatur of science to racial hierarchies and clear the way for atrocities like eugenic culling or sterilizations, even though no scientist in any field would have truck with such ideas and policies after the lessons of the past century.

            Pääbo not only believed that anthropological science could be conducted without repeating the atrocities of the past; he insisted that allowing history to rule real science out of bounds would effectively defeat the purpose of the entire endeavor of establishing an organization for the study of human origins. Called on as a consultant to help steer a course for the institute he was simultaneously being recruited to work for, Pääbo recalls responding to the administrators’ historical concerns,

Perhaps it was easier for me as a non-German born well after the war to have a relaxed attitude toward this. I felt that more than fifty years after the war, Germany could not allow itself to be inhibited in its scientific endeavors by its past crimes. We should neither forget history nor fail to learn from it, but we should also not be afraid to go forward. I think I even said that fifty years after his death, Hitler should not be allowed to dictate what we could or could not do. I stressed that in my opinion any new institute devoted to anthropology should not be a place where one philosophized about human history. It should do empirical science. Scientists who were to work there should collect real hard facts about human history and test their ideas against them. (82-3)

As it turned out, Pääbo wasn’t alone in his convictions, and his vision of what the institute should be and how it should operate came to fruition with the construction of the research facility in Leipzig.

            Faced with Pääbo’s passionate enthusiasm, some may worry that he’s one of those mad scientists we know about from movies and books, willing to push ahead with his obsessions regardless of the moral implications or the societal impacts. But in fact Pääbo goes a long way toward showing that the popular conception of the socially oblivious scientist who calculates but can’t think, and who solves puzzles but is baffled by human emotions is not just a caricature but a malicious fiction. For instance, even amid the excitement of his team’s discovery that humans reproduced with Neanderthals, Pääbo was keenly aware that his results revealed stark genetic differences between Africans, who have no Neanderthal DNA, and non-Africans, most of whose genomes are between one and four percent Neanderthal. He writes,

When we had come this far in our analyses, I began to worry about what the social implications of our findings might be. Of course, scientists need to communicate the truth to the public, but I feel that they should do so in ways that minimize the chance for it to be misused. This is especially the case when it comes to human history and human genetic variation, when we need to ask ourselves: Do our findings feed into prejudices that exist in society? Can our findings be misrepresented to serve racists’ purposes? Can they be deliberately or unintentionally misused in some other way? (199-200)

In light of the Neanderthal’s own caricature—hunched, brutish, dimwitted—their contribution to non-Africans’ genetic makeup may actually seem like more of a drawback than a basis for any claims of superiority. The trouble would come, however, if some of these genes turned out to confer adaptive advantages that made their persistence in our lineage more likely. There are already some indications, for instance, that Neanderthal-human hybrids had more robust immune responses to certain diseases. And the potential for further discoveries along these lines is limitless.

            Neanderthal Man explores the personal and political dimensions of a major scientific undertaking, but it’s Pääbo’s remembrances of what it was like to work with the other members of his team that bring us closest to the essence of what science is—or at least what it can be. At several points along the team’s journey, they were faced with a series of setbacks and technical challenges that threatened to sink the entire endeavor. Pääbo describes what it was like when during one critical juncture where things looked especially dire everyone brought their heads together in weekly meetings to try to come up with solutions and assign tasks:

To me, these meetings were absorbing social and intellectual experiences: graduate students and postdocs know that their careers depend on the results they achieve and the papers they publish, so there is always a certain amount of jockeying for opportunity to do the key experiments and to avoid doing those that may serve the group’s aim but will probably not result in prominent authorship on an important publication. I had become used to the idea that budding scientists were largely driven by self-interest, and I recognized that my function was to strike a balance between what was good for someone’s career and what was necessary for a project, weighing individual abilities in this regard. As the Neanderthal crisis loomed over the group, however, I was amazed to see how readily the self-centered dynamic gave way to a more group-centered one. The group was functioning as a unit, with everyone eagerly volunteering for thankless and laborious chores that would advance the project regardless of whether such chores would bring any personal glory. There was a strong sense of common purpose in what all felt was a historic endeavor. I felt we had the perfect team. In my more sentimental moments, I felt love for each and every person around the table. This made the feeling that we’d achieved no progress all the more bitter. (146-7)

Those “more sentimental moments” of Pääbo’s occur quite frequently, and he just as frequently describes his colleagues, and even his rivals, in a way that reveals his fondness and admiration for them. Unlike James Watson, who in The Double Helix, his memoir of how he and Francis Crick discovered the underlying structure of DNA, often comes across as nasty and condescending, Pääbo reveals himself to be bighearted, almost to a fault.

            Alongside the passion and the drive, we see Pääbo again and again pausing to reflect with childlike wonder at the dizzying advancement of technology and the incredible privilege of being able to carry on such a transformative tradition of discovery and human progress. He shows at once the humility of recognizing his own limitations and the restless curiosity that propels him onward in spite of them. He writes,

My twenty-five years in molecular biology had essentially been a continuous technical revolution. I had seen DNA sequencing machines come on the market that rendered into an overnight task the toils that took me days and weeks as a graduate student. I had seen cumbersome cloning of DNA in bacteria be replaced by the PCR, which in hours achieved what had earlier taken weeks or months to do. Perhaps that was what had led me to think that within a year or two we would be able to sequence three thousand times more DNA than what we had presented in the proof-of-principle paper in Nature. Then again, why wouldn’t the technological revolution continue? I had learned over the years that unless a person was very, very smart, breakthroughs were best sought when coupled to big improvements in technologies. But that didn’t mean we were simply prisoners awaiting rescue by the next technical revolution. (143)

Like the other members of his team, and like so many other giants in the history of science, Pääbo demonstrates an important and rare mix of seemingly contradictory traits: a capacity for dogged, often mind-numbing meticulousness and a proclivity toward boundless flights of imagination.

Denisovan Finger Bone
What has been the impact of Pääbo and his team’s accomplishments so far? Their methods have already been applied to the remains of a 400,000-year-old human ancestor, led to the discovery of completely new species of hominin known as Denisovans (based on a tiny finger bone), and are helping settle a longstanding debate about the peopling of the Americas. The out-of-Africa hypothesis is, for now, the clear victor over the multiregionalist hypothesis, but of course the single origin theory has become more complicated. Many paleoanthropologists are now talking about what Pääbo calls the “Leaky replacement” model (248). Aside from filling in some of the many gaps in the chronology of humankind’s origins and migrations—or rather fitting together more pieces in the vast mosaic of our species’ history—every new genome helps us to triangulate possible functions for specific genes. As Pääbo explains, “The dirty little secret of genomics is that we still know next to nothing about how a genome translates into the particularities of a living and breathing individual” (208). But knowing the particulars of how human genomes differ from chimp genomes, and how both differ from the genomes of Neanderthals, or Denisovans, or any number of living or extinct species of primates, gives us clues about how those differences contribute to making each of us who and what we are. The Neanderthal genome is not an end-point but rather a link in a chain of discoveries. Nonetheless, we owe Svante Pääbo a debt of gratitude for helping us to appreciate what all went into the forging of this particular, particularly extraordinary link.