Sharing the Bones

Duke researchers bring digital tools to the Stone Age findings of the Rising Star cave expedition
Writer: 
December 11, 2015

Streaked with ancient limestone dust, the scientist hovering near Steve Churchill’s worktable waited to see his reaction to the fossil she’d surgically removed from its eons-old resting place eighty meters below ground. Crammed in the tent’s open window, a camera crew from National Geographic gathered more footage. Researchers came in and out, sidestepping the tangle of cables and lab equipment. Two bloggers tapped away on their laptops. Already the team had stowed nearly a hundred bones and fragments of an extinct human ancestor in the vault, but which one was still anyone’s guess. Every new specimen was a clue, a possibility.

Churchill’s glasses slid down his nose as he scrutinized the hominid fossil under the task light. He was certain of one thing: They had more than a couple of individuals. Maybe many more. How did they all get there? The paleoanthropologists in South Africa were as stumped as the armchair science buffs following the tweets and posts in real-time. As quickly as the Rising Star cave was giving up its secrets, it was adding to its mystery—one that easily could take Churchill and a generation of his Duke students their whole careers to solve.

In a profession in which the number of fossils available for study is dwarfed by the number of human paleontologists clambering to study them, even a lunch bag of hominid bone fragments constitutes a wild success. The Rising Star Expedition in November 2013 changed all that in more ways than one: Not only is it the largest cache of hominid fossils ever found on the African continent, but it also pulled back the tent flaps on the whole process, setting a new standard for open-access science. And by uploading the fossil data to Duke’s own 3D data archive, MorphoSource, the team has upended the secretive and exclusionary way our human ancestry is studied and shared.

Paleoanthropologists have long been a cagey and territorial bunch, notorious for keeping their discoveries close to the proverbial safari vest for fear a colleague might scoop them. “It’s a little bit like a Mafia thing,” says Churchill in describing how scholars typically treat their precious finds—and each other. “People who have exclusive access to the fossils have got a lot of power, because other people know if they do anything to upset them, they’re never going to see that fossil. People play the game because the reward to some degree is access.”

Churchill and his expedition partner in Johannesburg, Lee Berger, are advocating for a more democratic model of scholarship, one in which fossils are shared, not hoarded, and collaboration is considered essential. “To me the open-access aspect of this is as exciting as the science,” says Churchill. Inclusivity always has been a part of his teaching and research: He’s welcomed undergraduates on field expeditions and offered his Ph.D. candidates plum billing on important publications. But putting newly discovered human ancestor fossil data on an open-access website is taking that practice to the extreme.

“The idea is to change the game for everyone,” says Doug Boyer, assistant professor of evolutionary anthropology at Duke and the creator of MorphoSource. Through his website, scientists can share information on fossils in a new way, and anyone with an account can download a fossil and print out a replica on a 3D printer. “Instead of working with a hundred specimens per study, you could be working with 500 or 1,000. People will feel more willing and more obligated to share when they’ve benefited themselves from other people sharing.”

But sharing is not a virtue that comes naturally to the stone-and-bone set. Churchill, a world-renowned expert on Neanderthals and their gnarly weaponry, is not surprised that open science is attracting slings and arrows. No one expects evolution to be easy, least of all those who study it.

On the morning of October 2, 2013, Churchill arrived at his BioSci office intent on hunkering down with the book he was writing on Neanderthals. He was still on sabbatical and determined to make headway on the manuscript. Nonetheless, when he checked his e-mail, he found a worthy distraction: pictures of a lower jaw lodged in cave sediment next to a tape measure sent by his good pal Berger, a research professor in the Evolutionary Studies Institute at the University of the Witwatersrand, Johannesburg (nicknamed Wits).

Judging the wear patterns on the teeth, Churchill thought it might be a robust Australopith (a more ape-like hominid) called Paranthropus. A terrific discovery, because only bits and pieces of the species had been found, and a new collection could be a Rosetta Stone of sorts. What intrigued him even more, though, was the evidence of buried fossils—maybe even a skull—studding the ground in the photos. A flurry of e-mails between the two men followed, and by the end of the day, Churchill had agreed to join Berger for a week in November to bring up the bones of the Rising Star cave system.

Churchill’s partnership with the charismatic and ruddy-faced Berger, who can work an Indiana Jones fedora just as well as his optimal camera angles, goes back more than twenty years. “He does not lack for serotonin, or confidence,” says Churchill, a tall, fit fifty-six, who plays the reserved, thoughtful straight man to Berger’s showman. “But he has the most generous spirit you’ll ever meet.”

They met in 1994, then two green Ph.D.s, at a conference at Berkeley. Berger, his pockets full of fossil casts, told Churchill about some sites in South Africa’s Free State that had fossils from the time period Churchill was interested in. Churchill had done fieldwork in Israel and throughout Europe and knew that established teams in those areas made it nearly impossible for young upstarts to get a foothold. What he needed was an unencumbered corner of the map and a partner to explore it with.

The next day, he spotted Berger across the book room and thought, “Well, no guts, no glory,” and marched up to him. “I said, ‘You know those sites you were talking about last night? Well, let’s excavate them together. I’ll raise the money. I’ll take care of logistics. I’ll bring the crew, and we’ll publish everything together.’ ”

The following summer they were in South Africa, nosing around the caves where predators dragged hapless hominids and the clumsy ones fell to their deaths.

“What’s really funny is that Lee had found most of the money and did most of the organizing,” says Churchill. “I didn’t really hold up my end of the deal.” Lucky for him they were well-suited to work together—not only because of the yin and yang of their personalities, but also because they shared, even as early-career scientists, a desire to change the standard practices of the profession. They made a pact: to take a “reasonable” amount of time to publish on anything they found, and after that anybody with credentials could see the casts and originals—even their worst enemies.

Churchill struck on a field model to support their research. From 1999 to 2007, he ran Duke in South Africa, a six-week, two course-credit program for between six and twenty students who often got more adventure than they bargained for. (Once Churchill, Berger, and their Duke charges narrowly escaped being trampled by a nursery herd of mother elephants and their young.) The partnership paid off in 2008 when they made a major discovery with the other two members of their team, Darryl de Ruiter and Peter Schmid in the Cradle of Humankind, a fossil dreamscape roughly 200 miles from Johannesburg. At the time, five known hominid species, including our own, had called the area home.

In a de-roofed cave in Malapa, not far from Rising Star, they recovered two partial skeletons of a previously unknown species they named Austalopthicus sediba. It was the most complete hominid assemblage since Lucy, the famous Australopithecus afarensis found in Ethiopia in 1974 and named after the trippy Beatles song. True to their promise, the team members published in two years, shared their fossils widely, and invited younger scientists to work on the prestigious announcement papers.

Five years later, in November 2013, Berger got the band back together at Rising Star—and what he had planned this time would up the ante once more.

While Churchill puzzled over the curious mandibles and phalanges coming out the cave, Doug Boyer prepared to quietly launch his own fossil project, MorphoSource. The idea for a digital archive that could store and share three-dimensional data on natural objects—from fossils and weird beetles to large mammals— was something he’d been working on since 2009 as a graduate student. When he came to Duke in 2012 to teach, he brought the bare-bones idea with him, and the university funded the development.

“The idea stuck with me because it seemed so practical,” he says. “It’s a way to provide more access and at the same time help museums protect their valuable collections.” Digital 3D images can be found on other Web archives, of course, but Boyer says the quality and terms of use vary too much to be useful on a large scale. The images often are incompatible with other data sets, and the websites don’t have special features to protect privacy, facilitate collaboration, or track how and when the digital specimens are used.

The genius of MorphoSource is that it can do and be so many different things at once: personal locker, virtual museum, searchable database, intellectual-property manager. Scanned and uploaded specimens can be downloaded or viewed among a select group or as a solo project, in a highly controlled environment. Data usage is tracked, and after publication, private data can be opened to all. A peer-review option is built into the system, too. The clean design is simple to navigate, and anyone—even a middle-school student—with an account can participate, but scientists and curators are able to select the level of access they give to their specimens.

Above all, Boyer says the platform must protect the authenticity of the fossils and scientific data, and to do that the interests of the institutions that house the real specimens must be respected. “Museums are the stewards of physical collections,” he says. “We can’t lose the connection between the digital data and the original specimen or we lose the integrity of the system.”

The scholarly applications are endless: Boyer and his crack team of undergraduates, grad students, and postdocs are digitizing and uploading the Lemur Center’s remarkable collection of 32,000 early-primate fossils, including an extinct gorilla- sized, lemur-like creature. And there’s discussion of a partnership with the American Museum of Natural History.

But in the fall of 2013, Boyer was keeping long hours in his plain and narrow BioSci office, working out the last glitches. Directly below him was Churchill’s darkened lab, stocked with sepia-tinted long bones and skulls, where most semesters students can be heard gasping and laughing as they shoot arrowheads into ballistics gel. “The cosmic coincidence,” says Boyer, “is that his specimens were discovered about the same time the site became available.”

Out on the veld, Churchill didn’t know the powerful tool he had waiting for him on campus. Nor did Boyer know what his senior faculty adviser had unearthed in South Africa. Each had a project that would transform the other’s work.

A few days after Berger e-mailed Churchill those first photos of the jawbone, he posted an eye-catching want-ad on Facebook. He needed anthropologists with excavation experience, but also, “The person must be skinny and preferably small. They must not be claustrophobic, they must be fit, and they should have some caving experience,” it read.

One reason the expedition would be so challenging was the structure of the cave system itself. The fossils were located at the end of an obstacle course of cramped tunnels and climbs ending in a vertical chute, about eight inches wide and thirty- nine feet long, that drops into the final small chamber. Air moves more slowly underground, and the oxygen and CO2 levels inside had to be monitored closely. The cables for electricity and communications snaking through the route would need to be maintained. The survey equipment used in typical excavations was too bulky to fit through the passageways, so a techy grad student at Wits co-opted a hand-held 3D scanner to record the position of every fossil.

And everyone going into and out of the cave would have to watch each step: The fossils themselves were very fragile, because they were buried in sediment, not the usual concrete matrix, and therefore not as heavily mineralized.

The potential for danger was constant— on one of Churchill’s first days, the CO2 levels spiked, and the cavers were evacuated. Days later a violent lightning storm blew down tents and cut off all communication with the cavers.

Marina Elliott, then still finishing her Ph.D. in archaeology in British Columbia, was one of fifty-seven people who answered the ad, and fitting all the qualifications, she was awarded one of the six cave-excavator positions. Berger told her he had sent his two teenage children along the route into the chamber first, because, she recalls him saying, “If one of you had been injured, there’s no way I could stand in front of your parents and say I had not been prepared to send my own children in there.”

Elliott was more concerned about doing good work than getting hurt. “At the time I still felt very much like a student in awe of all these big guns who turned up,” she says. Down in the chamber, she would hear the disembodied voices of Churchill and the other senior scientists as she recorded data and dug out fossils. “They were watching us on the monitors above ground, and [through microphones] we could hear their ‘Ooos’ and ‘ahhs.’ ”

But the mood in the communications tent would turn somber as the cavers, their fossil cases packed with invaluable specimens, disappeared into the nightmarish chimney chute, scrabbled down an incline called Dragon’s Back, belly-crawled through the narrow tunnel, and climbed step by careful step toward the shaft of light where they began. The cases went to Berger and then the science tent, and the caver—dirty, sweaty, jittery, and by then very hungry—usually followed to see what the senior scientists thought of the fossils.

Elliott remembers when they brought up a piece of cranium. The scientists gathered around the specimen whispering, and the tent went quiet as everyone strained to eavesdrop. Finally, news of the genus—“Unequivocally Homo!”—and Elliott says everyone broke into cheers. There was so much excitement and anticipation in the moment, Elliott says, “they probably could have said anything, and we would have cheered.”

The reaction might well have been relief, too. The professional stakes—mounting a $2.5 million expedition chronicled in real-time over social media—could not have been higher for the scientists. But Elliott remembers Churchill as the calm, steadying force of the group. “He doesn’t jump into every conversation. Lee would be describing something in true Lee fashion, quite boisterous, and then there would be a lull, and that’s when Steve would add something that clarified it. And it was always right on the mark.”

At night they sat around the campfire with guitars and beers and big stories of dangers in the field. In the wee hours, cavers might stir from their tent to Skype with grade-school students. Elliott Skyped from inside a cave chamber with a school in Hawaii. “The kids were agog,” she says. “People can’t get enough of human origins, and scientists may have dropped the ball in not getting people more engaged. There’s the sexy stuff, the adventure and danger, but really what people want is the science.”

Above ground and half a continent away, Chris Walker Ph.D. ’15, then one of Churchill’s most promising Ph.D. students, was holed up in a hostel in Ethiopia, struggling to collect the final data he needed for his dissertation. In Europe, the twenty-seven-year-old hit roadblock after roadblock. Tanzania and Ethiopia brought more government paperwork, more rejections to his requests, and worse, the maddening silence of no reply at all from the Western scientists who controlled the fossils he needed to see.

“It’s a tough system to navigate as an early-career scientist,” says Walker. “It’s very cliquey. Even if you need, say, a day or two with fossils in Ethiopia, you have to book ten or twelve days because you never know what problems you’ll run into. When I was there, I wasn’t allowed to get measurements on fossils I needed that had been announced and described.”

Luminaries like Churchill find themselves defeated by the system, too. There’s a certain Homo erectus skull Churchill wants to study for comparison and, “even though ten papers have come out on it, we still can’t see it,” he says. “And probably that will be the situation for my lifetime.”

The discouragement can prove too much for students. Walker wondered if he could succeed in such a dysfunctional profession—paranoia was rampant, grants have a 2 percent acceptance rate, and protocols are slow to change. While in Ethiopia, he says, he “questioned whether I wanted to stay in academia at all.” But, as if by kismet, he flipped on the TV just in time to hear a BBC report mention a familiar name. The newscaster was talking about Lee Berger and the impressive team he’d gathered at a cave about thirty miles from Johannesburg called Rising Star.

In Walker’s second year at Duke studying evolutionary anthropology, Churchill had invited him to work on sediba’s post-cranial skeleton analysis—everything below the neck, Churchill’s specialty—and in 2010, he accompanied his professor to the Wits campus to see the original sediba fossils on display. The city was hosting the World Cup, and vuvuzelas blared long into the night. Now he could picture them—Berger, Churchill, de Ruiter, and John Hawks— their infectious optimism, and all the young scientists like himself, swarming the place, itching for a piece of the action. He’d planned to go to South Africa after Ethiopia— he couldn’t believe his luck.

By the time he arrived in December, the high-tech camp that housed a core group of forty or so cavers, scientists, and support staff was long gone, and the fossils transported to a temporary holding room at Wits. The crew from National Geographic had weeks of footage to edit, and the bloggers’ posts were getting hits. Churchill was back in Durham—on sabbatical with his book—but Berger, still bone-drunk and happy to share with a trusted young colleague, brought out a box that contained a special specimen.

Walker opened it. “I knew instantly that it was like nothing I’d ever seen before,” he says of the immature tibia. After showing him more fossils, Berger invited him to apply to the month-long workshop that he, Churchill, and the other senior scientists would be leading in May to put as many highly trained eyeballs on the more than 1,550 specimens, all skeletal remains from as many as fifteen individuals, young to old.

“These fossils speak to the history of every person alive today,” says Walker. When he got back to Duke, he was fired up once again. He met with Churchill and told him, “This thing is weird. I don’t know what it is, but it’s weirder than I ever thought.” Churchill had left the site halfway through the expedition to get back to his writing and hadn’t seen all the material Berger had showed Walker at Wits. It would be a long five months before the workshop, but then they would have access to the treasure trove.

“If it weren’t for Steve, Lee, and the workshop, I probably would have abandoned the profession altogether,” says Walker, who is now a researcher and instructor at North Carolina State University’s College of Veterinary Medicine. “Rising Star brought me back.”

In May, Walker arrived in Johannesburg to join caver Marina Elliott and the other early-career scientists Berger had invited to the workshop. With this new batch of bones to study, he decided to scrap his dissertation plan—an exhilarating and terrifying move—and start anew with the Rising Star fossils. Wits set up a special study space—a veritable Rising Star War Room—complete with a fossil vault, lab equipment, microscopes, laptops, and everything else the team of researchers would need to begin deciphering the mysteries of that bleak chamber.

The fossil assemblage included nearly every type of bone—jaws, ribs, teeth, five partial skulls, pelvises, a nearly complete set of bones for a foot, another for a hand, and a third for an inner ear. Some of the junior scientists on the sediba team five years earlier were now leading small groups on this project. Churchill gathered all the leaders of the various post-cranial skeleton teams—the foot group, the pelvis team, the upper-limb folks, etc.—at a coffee shop to ask them what they were seeing. “And it was like drinking from a fire house,” he says. “This was the first opportunity they had to hear a coherent picture of what was starting to emerge. They’re telling me so much, and this creature is making no sense.”

Night after night, discussions would continue at the hotel where everyone was staying, or spill into the local pub. Elliott, currently a postdoc research fellow at Wits, proved herself as adept at analysis as she was at spelunking, but admits she was no match for Churchill at the pool table. “I don’t know if Steve misspent his youth playing pool or what, but he was certainly better than me,” she says.

Their hominid took shape quickly: Standing less than five-feet tall, she is bipedal with arched feet good for striding long distances, but with curved toes that indicate she can climb trees like earlier primates. Her shortened arms and longer legs are similar to Homo erectus, but her brain is too small to fit that species, says Churchill. The combination of traits and characteristics—some from more ape-like creatures and others more closely resembling modern humans—convinced the team that they indeed had discovered a new species.

Berger named her Homo naledi, after the word for “star” in the South African language of Sesotho. Now the team had to figure out how to make her widely accessible once they were ready to publish. MorphoSource had been launched softly and safely into the world, but Boyer was so busy tweaking things, adding new features as fresh data were uploaded, that he hadn’t talked to Churchill about it in great detail. Then one afternoon when the two were meeting as faculty mentor and protégé to discuss what Boyer would be teaching, the conversation turned to their own research. For the first time, both men saw the potential, and Churchill suggested they meet with Berger.

The next month the three of them gathered around Boyer’s computer monitor as he zoomed in on the 3D image of a prized Venezuelan primate fossil. He rotated it, flipped it over, and demonstrated the site’s other whistles and bells. Berger slapped his hands on the desk, recalls Boyer, and said, “You’ve already built the site I was looking for! It’ll take two phone calls—to your vice provost and my vice chancellor— and we’re done!”

It took a bit more than that. A memorandum of understanding was drawn up for both Wits and Duke to sign. In it, Boyer said, they had to make clear that the project would promote scholarship for South African students and protect the value of the university’s fossil collection. “Africa has suffered from first-world countries usurping scholarship and scientific objects,” says Boyer. “We had to reassure them that they wouldn’t be cut out of the loop.”

On September 10, 2015, two years after the expedition—and 10,000 person- hours of work later—Homo naledi was introduced to the world with maximum limelight. The announcement paper, published in the open-source science journal elife, listed forty-eight co-authors. Eighty-six specimens were up on MorphoSource for scientists and teachers to download that day. At the same time, PBS streamed a two-hour documentary on the expedition, a Nova and National Geographic joint production, and aired it on television six days later. Finally, Berger and Churchill had proven it is possible to liberate paleoanthropology from its notoriously creaky and cranky roots.

“There are middle-school teachers out there who have a better cast collection of naledi than I do,” says Churchill, sitting at a shady table outside Twinnies, a coffee shop in Duke’s Pratt School of Engineering, two years, nearly to the day, after that fateful e-mail from Berger. “And probably that’s how it should be.” Indeed, his former student Walker has printed out several casts for local schools to use.

Churchill is trying to settle back into campus life after the media whirlwind, but now he has critics to deal with, too. Media darling naledi has not been embraced by everyone: Some colleagues at other universities have questioned whether the group published too fast—the fossils haven’t been dated yet, and Churchill estimates thousands remain in the cave system. Others have cast doubt on the accuracy of the species identification.

“As with any science, people are going to bring different perspectives to it, and they’re going to see the evidence differently,” he says. “The beauty is that if you want to prove us wrong, we’ll do everything in our power to help you. You can print casts of the fossils. We’ll arrange for the cavers to take you into the cave.”

But a plane ticket to South African isn’t always necessary when you can examine fossils on a computer screen. Boyer says one of naledi’s most vocal critics has downloaded thirteen of her bones.

No matter what the next analysis brings, the Rising Star team already has brought to life the vision Berger and Churchill shook hands on twenty years ago. And in that way, Homo naledi is the missing link—between the old methodologies and the new. Now, somewhere in South Africa or North Carolina, a sixth-grader running her finger over a warm, fresh-from-the-classroom-printer fossil cast, knows the naledi mystery exists and that she may spend her life in wonder looking for the answer, too.

  • Louise Flynn is the associate editor at Duke Magazine.