This Innovative Device Allows South American Paleontologists to Share Fossils With the World

In October 2021, New York University computer scientist Claudio Silva found himself in the basement of a paleontology museum in remote northeastern Brazil. He’d just visited a dig site in the nearby Araripe Basin, one of the most fossil-rich regions in the world—a journey that required a flight on a tiny, four-seater aircraft. Now, he was surrounded by the bounty of that basin in the Plácido Cidade Nuvens Museum of Paleontology (known by the Portuguese abbreviation MPPCN). A labyrinth of floor-to-ceiling metal shelving units was stacked high with piles of the most beautiful fossils he’d ever seen—fish, insects, sea urchins, turtles, pterosaurs.

Months earlier, at home amid the Covid-19 pandemic, Silva had read an article in the paper that opened up his world. The story mentioned an incredibly rare pterosaur fossil, the most complete ever found, that was seized in a police raid on a smuggling ring at a Brazilian port along with 3,000 other specimens. What stood out to him was where the fossils had been extracted—the Araripe Basin in the Santana do Cariri region, near his hometown. Silva is an expert on graphics visualization and geometry processing, not dinosaur bones. But fresh off a project developing software to scan preserved fish specimens, he felt confident he could help digitize MPPCN’s collection.

But now, surrounded by mountains of fossils, his promise to digitize all 11,000 specimens in the museum’s collection suddenly felt incredibly daunting. Silva would not admit defeat, though. In two short years he resolved to be back, with a device of his own creation that could revolutionize paleontology in South America while making the field more equitable. The innovative scanner he built has the potential to open up fossil digitization to resource-poor but fossil-rich museums across the global south.

The fossils of the Araripe Basin

The quality of the fossils found at Araripe—often with intact stomach contents, gill parasites, plants, bacteria and fungi—impresses even the most seasoned paleontologists. “The Araripe Basin has a unique feature: the exceptional preservation of its fossils,” says Álamo Saraiva, a paleontologist at the Regional University of Cariri, Brazil’s top paleontological research facility, and curator at MPPCN. “Here, soft parts can be found preserved, as if the specimens had been frozen, though everything is petrified.” The quality and sheer number of fossils make reconstructing the Cretaceous period food web and answering big paleo-ecology questions about changes in entire ecosystems over time possible.

But despite the scientific wealth of its collections, MPPCN, like rural paleontology museums across South America, lacks the funding, staff and technology required to safely store and study its scientifically valuable fossil collection. The facility’s remoteness also makes it challenging for international paleontologists and even researchers based elsewhere in Brazil to access. While vast collections sit in basements like this one, inaccessible to the larger paleontology community, those big questions about prehistoric ecosystems go unanswered. Digitizing the museum’s specimens, as has already been done with many collections in the global north, would open a wealth of Araripe Basin fossil data to scientists worldwide.

What’s more, the Araripe Basin’s abundant fossils have long made the region a target for smugglers, who fill demand for fossils from both paleontologists and collectors in wealthier nations. “The Araripe Basin is the largest site for illegal fossil trafficking in the world, and this crime has been depleting Brazil’s scientific and cultural heritage,” says Saraiva.

Present day fossil trafficking is an outgrowth of paleontology’s long colonial history in countries like Brazil. “The First World has really had a predatory relationship with these areas,” says Silva. “Scientists from around the world would go to these areas and start their own excavations without proper authorization and then smuggle things out.” Brazil is currently in repatriation talks with Germany, France, the United States and the United Kingdom to get fossils returned.

Saraiva hopes that scanning the Araripe Basin’s fossils and making them available to the world will reduce international demand for trafficked fossils. “This is a good bet to ensure that foreign researchers don’t need to resort to trafficking to obtain the form of a species,” he says. Plus, once a fossil’s form is scanned, it can’t be completely lost to science: Even if it’s stolen or otherwise lost or damaged (in transport to another facility, for example), a virtual backup exists. “The form is what is used for description, whether it is made of calcite, limonite or plastic resin produced by a 3D printer,” Saraiva says. He also plans to make MPPCN’s fossil database available to the Brazil Federal Police, to help them better identify fossils in their fight to stop trafficking.

Scanning for a solution

Since the 1990s, paleontologists have used CT scanners and other commercial technologies to digitize, model and upload fossils to massive online databases like Morphosource. Fossil databases have revolutionized the scale of questions paleontologists can ask about ancient ecosystems. But the global south has largely been left behind, because existing scanners are incredibly expensive, are difficult to move to and operate in remote areas, and require expertise to run and maintain. And transporting fragile fossils great distances to urban centers with scanning capabilities is expensive and risky.

After his visit to MPPCN, it quickly became clear to Silva that an existing commercial scanner wouldn’t be the solution here. “Given the number of the fossils and the remoteness of the area, that equipment would not be appropriate,” he says. It would take far too long to scan the vast fossil collection with a low-throughput CT scanner—not to mention the cost or difficulty of transporting one to the rural museum. Other commercial scanners, which use 3D cameras or structured light, rely on controlled lab conditions and were also out of the price range. “So, we decided: Let’s back up a bit and figure out the right way to do this so it’s scalable and works for these communities that are more resource-hungry.”

Back in New York, Silva and his team went into problem-solving mode—they needed to create a new scanner that could quickly and cheaply digitize thousands of fossils at high resolution. Plus, it had to be portable enough to move between rural museums over rough roads and simple enough for museum staff to operate without much training or on-hand technicians. And the scanner had to be able to operate without onsite computers for image processing, which aren’t always available at rural museums.

They called the device they came up with PaleoScan. It consists of a high-quality camera mounted to a frame that moves on two axes to take thousands of individual raw photos of a fossil under controlled light conditions. The whole setup is operated by a microcontroller and a touchscreen. After capturing photos, it immediately sends the raw images off to the cloud for processing offsite. The software Silva’s team developed then calibrates and stitches together all the photos into a 3D model of the fossil.

With PaleoScan ready to go, Silva asked Akinobu Watanabe, a paleontologist at the New York Institute of Technology who works with digitized fossils, how the scanner’s images compared to those of existing technologies—was it good enough for science? Watanabe was impressed by PaleoScan’s resolution and what its widespread use could mean for paleontology in the global south. “Empowering resource-poor museums and institutions to scan their own fossils and provide virtual versions of those fossils to the rest of the world, I think, would really help the scientific community, but also the institutions themselves,” he says. “I think it’s a game changer.”

As promised, two years later, in July 2023, Silva returned to Brazil to set up PaleoScan at MPPCN. He was greeted by an excited Saraiva and Naiara Cipriano, a visiting researcher at the museum. “Claudio traveled from New York to the city of Santana do Cariri with these large wooden boxes of considerable weight,” Cipriano says, “which made me think that those who have the will can truly make it happen.”

Over the next week, they assembled the prototype and began testing a variety of specimens. A year on, several hundred fossils have been digitized. The museum is in the process of applying for federal grant funding to support scanning the rest of the collection at a quicker rate. “As a user of PaleoScan, I can attest that it is a simple and efficient device,” says Cipriani. “The preliminary results we are obtaining are truly remarkable.”

The future of PaleoScan

Museums in Chile and Mexico have already expressed interest in PaleoScan, Silva says. Jeanette Pirlo, a paleontologist at California State University Stanislaus not affiliated with the project, is also excited about the device. She uses virtual and 3D-printed fossils based on scans in her own teaching and outreach, as her university lacks the funding and fossil collection that major research institutions enjoy. She also has a collaborator who works with rural museums in Colombia that she says would benefit from a cheap scanner—if PaleoScan was adapted to scan in true 3D. (The fossils in the Araripe Basin are mostly flat, so the current model only moves the camera in two dimensions.) Silva says that’s a future goal. “Having access to something like PaleoScan, where with a very quick turnaround, you can create these 3D models, is really powerful,” Pirlo says.

To Gerhard Weber, one of the founders of virtual paleoanthropology and head of a micro-CT lab at the University of Vienna, PaleoScan isn’t necessarily the game changer X-ray scanning was. As an optical scanner, it can’t penetrate into fossils, which is necessary for studying the very few known hominid teeth and skull specimens his field has to work with. But Weber says he sees the value of PaleoScan for paleontology. Researchers in the field have collected thousands of undigitized specimens, and any type of scan would be an improvement over none. Still, the bigger challenge, he says, is making sure the digitized data is accessible.

“If I’m a fish researcher, and I see oh, wow, they have 500 scans, I want to get them: What are the regulations?” he says. “PaleoScan is just providing the technology, but it then really depends on the politics and the strategy of the museums, how they handle it.”

At MPPCN at least, that openness shouldn’t be a problem. The museum is pursuing a grant from the Brazilian state research funding agency, known as FUNCAP, to support digitizing the full collection. At that point, “this material will be made democratically available to interested parties,” says Saraiva. He hopes once the collection is uploaded to online databases, the fossil scans will promote more international collaborations with Brazilian researchers. “Knowledge should be universalized,” he says. “To me, this is the purpose of doing science. Science for only a few hinders humanity and hardens the hearts of men.”

Christian Elliott | READ MORE

Christian Elliott is a science and environmental journalist based in Illinois. He has a master's degree in science journalism from Northwestern University in Chicago.