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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: 3D printing a Homo naledi cranium. John Hawks CC-BY-NC-ND

How 3D printing fossils will change the way we look at human evolution

In September our team announced the discovery of the new species, Homo naledi. The species comes from the Dinaledi Chamber, deep within the Rising Star cave system in South Africa, where our team has uncovered more than 1500 fossil hominin specimens.

The team took the unprecedented step of releasing three-dimensional scan data for the key fossils at the same time we published their initial description. These models are available to the public from the MorphoSource site, an archive of 3D data sponsored by Duke University. Over the past two months, teachers, researchers and others around the world have downloaded the models more than 5000 times. Many of them are using 3D printers to create their own physical models of the fossils.

This move has gotten a lot of attention around the world. Human origins is a field in which the people who study fossils often seem very secretive, and many fossils are not available to other researchers. Now for the first time, people are downloading and handling fossils at the moment that they are published. People around the world are wondering, how will open access to data change the study of human origins?

Lucas Brouwers from the Dutch publication NRC Handelsblad interviewed me last month about why the Rising Star team took this open access approach. The interview was part of his article, “Voorouder komt zo uit de printer”. Brouwers kindly has allowed me to share all the questions that he wrote to me, along with the answers I wrote back. I’ve put a bit more into some of these answers before posting, because the question-and-answer was a great occasion to write about access to fossil data and how we have approached open access on the Rising Star project.

Q: An obvious question perhaps, but could you explain why the naledi-team decided to publish the 3D-files? What was your role in this decision? Was everyone on the team convinced this was a good idea from the start?

A: For many years I’ve been a vocal advocate for more open data access in paleoanthropology, so obviously I have my own perspective as a scientist and I don’t speak for everyone all the time.

Our team includes more than 60 scientists, and scientific decisions involve discussion with of a lot of people. The Dinaledi fossils are in the care of the Evolutionary Studies Institute (ESI) at the University of Witwatersrand, and most of us are associates of the University. Everything we do is shaped by the mission of the University and by South African law.

Steven Churchill was the key player in putting together a collaboration between Duke University, which hosts the MorphoSource archive, and Wits. Doug Boyer at Duke has also been tremendously helpful in facilitating our team uploading the data. The data themselves have been generated by more than a dozen of the team members, and they’ve uploaded these to MorphoSource as an archive of the work.

The move to more open access really started with Lee Berger. Lee had found the Malapa site in 2008, and assembled a team that described Australopithecus sediba from those fossil remains. He established a policy of open access to the fossils by researchers, which became a huge part of the Malapa project’s success.

So when we brought this large team of scientists to work on the anatomy of the Dinaledi fossils, Lee and the rest of us felt strongly that data generated during the project would be available to the community. We saw it as one of the most innovative things we could contribute, and it also solves two practical problems.

One of the practical challenges is the condition of the fossils. The Dinaledi fossils are very fragile and subjecting them to traditional molding would damage them. So we knew from the beginning that high-resolution 3D printing was going to be necessary to make copies of the fossils.

The other practical challenge is the collaboration among a huge team.

Providing research access to digital data is not free, and it’s not easy—somebody has to prepare those data in a form that can be useful to other scientists. You don’t want to have to do that in a different, non-standard way for every new investigator. And if the digital data are being curated by a dozen different individuals, that creates a series of bottlenecks for other people on the team who need the data. A project you could do in an afternoon suddenly takes weeks while you wait for the email chain.

The way to share data effectively across a large team is to establish an archive where the data are interoperable, in a standard format with metadata included. Once that culture of data access is in place, it becomes very easy to bring new people into the collaboration.

Q: According to your impression, how popular is 3D-printing right now amongst academics and educators? Have you had many requests for help with printing?

A: We are seeing an explosion of 3D printing. I’ve been so amazed to see thousands of people downloading these files and starting to produce prints. I showed up in Milwaukee the other day to give a lecture, carrying my bag full of fossil prints. When I got there, they had already printed up a whole set of their own! Homo naledi is everywhere—it’s like the tribbles!

We can’t do support, there are such a huge range of printers and equipment. We have heard from some people who were unable to print our surface models because the data were too high-resolution for their software or printer. One person even volunteered to make the data lower-resolution for us! Fortunately, if anyone has trouble with these, free software like MeshLab can load these files and reduce their quality to a smaller file size.

It’s been really cool to see people painting the models and customizing them, making them look like real fossils.

Q: Do you think releasing 3D-data will become common practice in anthropology? In the past, some paleoanthropologists have been very protective of ‘their’ fossils, only releasing photos and descriptions in tidbits and morsels. Do you feel this attitude is changing?

A: There is this myth that if you provide access to digital data, you are somehow losing the value of the fossils, that you should somehow make scientists pay to access the digital data. We have to learn to live in the 21st century.

The experience in South Africa at the ESI is that providing access to new fossils like Australopithecus sediba and now Homo naledi has taken the institution from a handful of scientific visitors per year up to hundreds. Access to the fossils increases scientific visits, increases scientific output, and creates long-term investment in the institutions that curate them.

I came from genetics, have done most of my research using open data archives. There is no significant research in human genetics today that does not use open access data in some way. These archives enable us to train our students on the newest research methods, and allow scientists to develop pilot data to explore hypotheses, that vastly strengthen their ability to get funding for those new ideas.

People would be surprised that many hominin fossils from other sites have been scanned lots of times, but scientists have signed agreements that prevent them from providing access to their own data. Sometimes a researcher will share data “under the table”, in violation of those agreements. That’s very negative because it means that people give data to their friends, or to people with something to trade, instead of making the data accessible to everyone. It becomes an “old boys’ network” of data.

This is one reason why we need to emphasize “access” and not “sharing”—many researchers will say, “well, I share my data”, but they’re sharing very selectively, it’s like a black market. And then new researchers come and scan the same fossils again and again. It’s such a waste of time and resources, and it’s so unnecessary.

We want to move the expectations of the field toward broader collaboration. Great ideas do not only come from one place, they take many people looking at the data.

When I think of the students who are entering paleoanthropology, they are going to be my scientific peers five, ten years from now. Why in the world would I not want them to have the best, most current data from our fieldwork? I’m struggling to understand the mindset of scientists who think that students shouldn’t see the fossils.

Screenshot from AfricanFossils.org
Screenshot of a page from the AfricanFossils.org site, showing a jawbone of the species Homo rudolfensis for viewing or download.

Q: For some museums, especially in Africa, selling high quality fossil casts to academics is one major source of income. Do think 3D-printing, in the future, will undercut this source of revenue?

A: Obviously this is a big concern for our team, because ESI has its own casting program and supplies casts internationally to many institutions.

Let’s be clear about this. Right now two of the countries that are making the most data available to the public online—South Africa and Kenya—are also the ones that are selling the most casts from their traditional casting programs. I want to draw attention not only to our own data archive, but also the AfricanFossils.org initiative from Kenya, led by Louise Leakey, and the archive of CT data from the Ditsong Museum of Natural History in South Africa. AfricanFossils.org is directed toward educational use casts, while both the Homo naledi surface models and the Ditsong CT data are research data, but both kinds of data distribution pose the same issue for traditional cast production.

What these examples show is that data access is not a zero-sum calculation. When the data are available online, many more people will have access to copies of the fossils. That drives much more interest in building collections of high-quality fossil reproductions in a broader range of institutions, including schools that never had them before.

That doesn’t mean we shouldn’t be concerned about the casting programs. We want to find ways to leverage interest into longer-term relationships for teachers and the public, so they can support the work that brings casts into South African schools, support the production of high-quality digital scans, and support new exploration.

Now I’m going to editorialize, speaking for myself only.

There are institutions that never sell casts, even to academics for research and teaching. Some countries don’t even allow casts to be exported. These institutions do not allow researchers to share digital data. “Prestige” journals permit researchers to publish without putting their data in an archive. So no one can have copies of the fossils or data from the fossils except for the original investigators.

Right now, American and European companies are selling artistic sculptures of the fossils that are curated at these institutions. Universities and schools buy those sculptural recreations, and most of them don’t even realize that these are sculptures and not based on real data. That investment doesn’t go back to the source institutions.

Try to envision NASA saying that no one can have data from the Hubble telescope, because they might make some money selling photographic prints. But then NASA doesn’t even print them! So private companies hire artists to paint space scenes, and universities buy these paintings so that students to see what distant galaxies look like.

You just can’t imagine this happening in a real science, right? But that’s what happens every day in paleoanthropology.

If “prestige” journals were to start requiring scientists to submit their digital data to an open archive, as a condition of publication, open access to data would happen overnight. How do I know this? Look at human genetics. The major countries that restrict access to digital data from fossils, right now, today, I can freely download human genetic data from all of those countries. Geneticists don’t withhold their data for years until they have published many papers—in fact large projects provide open access data before they publish their first paper.

There is no government in the world that would say that fossils are more precious than people’s blood. But the genes are in open access archives and the fossils are highly restricted.

So what’s the difference?

In human genetics everyone recognizes that open data access is necessary to have a real science. The human genetics community has developed for more than 20 years on the basis of public data archives and open data access, and journals require the deposit of data in open access archives when they publish the papers.

In paleoanthropology, we don’t publish data in open access archives, and we don’t require people to provide data when they publish.

A piece of scientific work with no data access may not be flawed, but how can we be sure? How long could a NASA contractor have hidden the flawed Hubble mirror if no one could inspect the data but their own technicians?

I want to look at all the positive benefits of open data that go beyond the science. Imagine if you tell any company—Apple, Microsoft, Google—that teachers all over the world are begging to put the company’s most innovative product in the hands of every schoolchild. That’s what South Africa is doing right now with these fossils.

Think about the long-term effects if every kid on Earth could go to school and hold the most precious objects from Ethiopia, from Kenya, Tanzania and South Africa.

Those kids are going to feel that heritage in a way that has never been possible before, and some of them are going to remember those objects, dream about visiting the place where all humankind originated. We’re talking about shaping the future, and the cost of this is just putting data online to let teachers create for themselves.

Foot printed on template
A foot of Homo naledi, ready for assembly. Photo credit: John Hawks CC-BY-NC-ND

Q: Some anthropologists I spoke to were concerned with the quality of the scans published on MorphoSource (some questioned whether they’re research-grade).

A: We don’t have the time or personnel to provide any lower quality than we are using for the research. One of the great things about a proper archive like MorphoSource is that the metadata on the scanner type and the person who did the scan can be there archived with the data. Anyone can check that out.

The surface models have higher measurement fidelity than traditional casts because silicone molds used in casting can deform, and the epoxy used to make research-grade casts will shrink. So for research purposes that involve accurate shape and measurement, the surface models are much better than traditional methods. But they do not capture surface detail nearly as well as silicone molds, so the models cannot be used for research that examines microscopic details of the bone surface.

Of course the quality of prints depend on the printer. But we use the scan models for research, and prints are mostly useful for teaching and demonstration.

Some people may be confusing surface scans with microCT, which has much higher resolution and shows internal structure, and is superior for many small objects such as teeth and hand bones. We are undertaking microCT scanning of some of the Dinaledi sample, and this will take many months of work for our team.

Q: Why have only 86 scans been released so far?

A: We worked hard before publication to release the essential scans that document the anatomy of Homo naledi, especially the holotype and paratype specimens described in our eLife paper. Those are the key specimens that we’ve described, and for most people they are the first priority for examination and printing.

More than a dozen team members have helped upload models, and they’ve also added several good examples of variation—the femora for instance provide a great record of how the Dinaledi sample varies.

As we publish descriptions of other fossils from the collection, including some of the more fragmentary specimens, we’ll be adding more. With many elements, especially small ones like teeth, ankle and hand bones, it may just make sense to wait until we have microCT data.

Q: One more question, if you permit: could you elaborate a bit more on the decision to publish in eLife? Surely could’ve been a cover article for Nature or Science? Did you want to set an example by publishing in an OA-journal?

A: We have two main considerations—we have a responsibility to our colleagues to publish the science in the best way available to us. And we have a responsibility to the people of South Africa, who have funded and supported the work, and who are guardians of the heritage that we have uncovered.

Among the senior members of the team, we have published more than 20 papers in Science and Nature, so we had been through that process many times, we knew what that would be like.

When you look at those journals just this year in paleoanthropology, you see they are publishing articles that describe only one or two specimens. We really tried but we just could not work out a way to publish Homo naledi in one of those journals with the detail to support the science and enable colleagues to understand what we have done.

On the positive side, eLife was really a pleasure to work with. They gave us all the space we needed, high-resolution photos of all the key specimens integrated with the article, and the review process was thorough and professional. The result is two papers that—–if you print them out—–total 72 pages, with 34 color figures and additional supplementary data online.

From the science side, our colleagues worldwide have given us a tremendously positive response.

From the heritage side, we have been totally blown away by the excitement people have for the open access. Some of our colleagues used to say that people aren’t really interested in reading scientific articles. We’ve shown that’s totally wrong. More than 230,000 people worldwide have viewed the scientific paper describing Homo naledi, and 81,000 have viewed the geology paper describing its context. I’ve never encountered anything like this in our field. When you provide papers with the right level of detail and rich illustrations, people will make the effort to engage with the science.

The Vice Chancellor of Wits University, Adam Habib, spoke at the announcement of Homo naledi last month, and he really said something that I think resonates widely:

We often talk about science as having no boundaries, but in our world scientific knowledge has become commodified, and too often, what should be the bequest of the world, the bequest of a common humanity, is locked up under paywalls that postgraduate students and researchers cannot get access to. So what we did when we made this discovery, was we put cameras in the cave, and we streamed it live from day one.
"We partnered with eLIFE, an open access journal, to make sure that the discovery was available to all of humanity. And what we did in that practice, is create the first elements of a common global academy….We are not simply going to be beneficiaries of open access, but we are going to be contributors to open access, to the knowledge of a common humanity."

I’ve been sharing that quote a lot, because it expresses something really central. South Africa is stepping forward to lead in the area of open access, and this is not just one team of scientists, we have tremendous support from every level of the scientific enterprise and government. Our team has gotten a lot of attention for this because people aren’t used to seeing significant new discoveries published in such an open access way. But this is the future.

Paleoanthropology is about uncovering the history that all humans share. People are curious about it, they want to encounter that history, they want to explore their origins. As scientists we have the tremendous privilege of discovery, and it gives us a responsibility to enable people to understand our common past.