3-D scans reveal secrets of extinct creatures

New modeling paired with X-ray scanning exposes every angle of hard-to-extract fossils

reconstruction of an arachnid

VIRTUALLY THERE  On a paleontologist’s computer screen, this arachnid moves as it did 410 million years ago.

R. Garwood and J. Dunlop/Journal of Paleontology 2014

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All Rachel Racicot wanted to do was look at a fossil. As a paleontology graduate student at San Diego State University, Racicot had scheduled some time with a local hospital’s CT scanner. She was going to examine a 3-million-year-old porpoise jaw.

But when the day came to slide the fossil into the scanner, the hospital put her on hold. A stabbing victim needed the CT machine. Paleontology would have to wait.

For Racicot and her colleagues, such temporary setbacks are a small price to pay. In the last few years, cutting-edge CT scans and other novel techniques have dramatically altered how paleontologists visualize and study ancient life. Detailed images provided by the improved technologies are allowing researchers to build digital three-dimensional reconstructions of prehistoric plants and animals like never before.

This field is called virtual paleontology. It has become much more than a source for nifty images of cool fossils; it reveals fundamental new insights about past life.

Synchrotron scans of a fossil from China’s Doushantuo formation (top) yield a 3-D image (bottom) showing three nuclei, indicating the fossil is not from an animal or embryo, but a protist. T. Huldtgren et al/Science 2011

Once Racicot finally snared the scanner for her fossil, the resulting images revealed a porpoise unlike any known today. Elsewhere, scientists using animation software have digitally reactivated an ancient predatory arachnid that walked the planet hundreds of millions of years ago. Other teams have used three-dimensional CT scans to explore extraordinary detail preserved in fossilized plant seeds, allowing scientists to reconstruct new histories of how plant groups evolved and spread over time.  

“We’re now getting down to resolutions that no one ever imagined,” says paleon­tologist Imran Rahman of the University of Bristol in England. “Sometimes we know much more about the fossils than about the living animals they are related to.”

 Rahman and colleagues reviewed the field’s promise in June in Trends in Ecology & Evolution.

Paleontologists have been trying to build 3-D visualizations of fossils since the early 20th century,  when William Sollas of the University of Oxford perfected a technique for grinding through a fossil sequentially. Sollas would grind away for a fraction of a millimeter, then stop and photograph the exposed fossil in exquisite detail. By repeating this process time and again — sometimes through hundreds of layers — Sollas eventually built a slice-by-slice encyclopedia of a given fossil, which he could then reconstruct as a 3-D wax model.

In 1904, William Sollas devised a method of grinding through a fossil layer by layer (top) to build up a 3-D wax reconstruction, such as the model of the vertebrate Palaeospondylus (below). J. Cunningham et al/Trends in Ecology & Evolution 2014

But his method destroyed the fossil and took a lot of time. By the 1980s, paleontologists had taken to zapping fossils in machines such as CT scanners, which send X-rays through an object to build up a three-dimensional picture of what’s hidden inside. In recent years, that technology has improved enough for scientists to extract tantalizing information about fossils.

In most cases, an ordinary CT scanner will do. Researchers typically take a rock to their local hospital or university CT laboratory and adjust the settings until the X-rays penetrate at just the right energies to reveal the form encased in the rock. In more complicated cases, such as when the fossil and the rock surrounding it look stubbornly similar, the scientists might take the rock to a more sophisticated machine.

Virtual dissection

Paleontologist John Cunningham, also at the University of Bristol, regularly packs up his most precious fossils and flies with them to the Swiss Light Source in Villigen, Switzerland. That machine is a synchrotron, which accelerates electrons to nearly the speed of light. The accelerated electrons emit radiation including X-rays, which are usually used to explore questions in physics, materials science and chemistry. Unlike CT scanners, which use X-rays over a range of wavelengths, synchrotrons can produce X-rays of a single wavelength. That level of control allows scientists to manipulate the scan far more
precisely and coax out detail from even the most stubborn structures hidden within rock.

Cunningham has used the Swiss synchrotron to explore some of paleontology’s most controversial fossils: millimeter-sized blobs in 570-million-year-old rocks from the Doushantuo formation in southern China. Some scientists think the blobs represent embryos of some of the oldest known animals in the fossil record, which if true would be an astonishing witness to the earliest evolution of animals. But nobody could see past the surface.

Using the super-sharp insight of the synchrotron X-rays, Cunningham’s team virtually dissected the blobs, revealing structures within. Those structures, some as small as a thousandth of a millimeter across, may be the nuclei of ancient cells. If so, they show that the fossil creatures had been developing differently than would be expected from early animals, and probably belong instead to a group known as protists.

Even an ancient fossil as fragile as a daddy longlegs can be visualized in exquisite detail. R. Garwood, National Museum of Natural History, France

The work, reported in 2011 in Science, underscored the power of synchrotron imaging for studying complicated fossils. Cunningham is now looking at slightly younger fossils, embryos from about 542 million years ago — just after a diversity of animals spilled forth in the evolutionary burst known as the Cambrian explosion. The synchrotron images reveal details about how the embryos developed: One of them “might look like a worm curled up and about to hatch, or something with spines around its mouth,” Cunningham says. By piecing together different fossils that represent the various stages as these embryos developed, he and his colleagues are building a more complete picture of how early animals might have been related to one another.

Rahman has been using CT scans to work out the digestive systems of ancient echinoderms, a group of marine animals including starfish and sea urchins. Searching the literature, he found mostly century-old information on the digestive systems of a modern group of echinoderms. That drove him to start scanning as many echinoderms as possible, to try to build up a database of information on how the modern and ancient groups might relate to one another.

Rahman’s scans revealed the first known digestive tract in ancient echinoderms. It looks remarkably similar to the guts of modern echinoderms. “Instead of this idea of things starting out simple and becoming incredibly complex, almost from the very beginning of the appearance of these different organisms, they have been rather complex,” he says.

Ancient versus modern life

Sometimes the scans show more than just never-before-seen details: They help paleontologists reconstruct major evolutionary changes from the past. Rahman’s scans revealed that the earliest echinoderms had a body plan that was bilaterally symmetrical, where one side mirrors the other. Modern echino­derms, such as the five-pointed starfish, are fivefold symmetric. If their ancestors displayed a twofold symmetry, Rahman says, the creatures must have undergone some significant changes in body design over the last half-billion years. “You can see that in the fossil record,” he says.

Larger than life The ancient arachnid Eophrynus pops into virtual reality when its fossil (left) is given dimension in a computer reconstruction (middle) and printed on a 3-D printer (right). I. Rahman <iet al/Evo. Edu. Outreach 2012; I. rahman et al/Evo. Edu. Outreach 2012; I. Rahman

Such insights wouldn’t have been possible without the exceptional detail coming from computer scans. The discoveries are more than just pretty pictures — they divulge fundamental differences between ancient and modern life, allowing biologists to better understand how organisms evolved.

“In the past paleontologists may have been guilty of coming up with ideas that we weren’t really able to test,” Rahman says. “With these new modeling and imaging approaches, we can go about testing some of these hypotheses and try to unlock the secrets of the history of life.”

Russell Garwood is taking this challenge to the extreme. A paleontologist at the University of Manchester in England, Garwood specializes in arthropods, the invertebrate animals that thrived on land well before creatures with a spine ever crawled out of the sea. He has studied fossils from the Rhynie Chert, a famous rock formation from northern Scotland. Silica-rich water from a hot spring infiltrated an ancient terrestrial ecosystem there and then mineralized, preserving plants and animals in extraordinary detail.

A computer-generated reconstruction of a creature called a trigonotarbid, an extinct arachnid, scuttles along in this video. The creature lived 410 million years ago in what is now Scotland. Russell Garwood, a paleontologist at the University of Manchester, reconstructed the animal’s movement by studying slices of a fossil and putting the data into animation software.

Russell Garwood; adapted by Ashley Yeager

Garwood chose a 410-million-year-old fossil of a creature called a trigonotarbid, which despite being just a couple of millimeters long was one of the first predators to ever stalk on land. Garwood didn’t use X-rays to probe the fossil, because it is so similar to the rock encasing it that even synchrotron beams can’t tease it out. Instead, he used old-school techniques, studying thin sections of rock containing the fossil to develop 3-D maps. He transferred his maps of the animal’s leg fragments to computer-graphics software similar to that used to animate movie characters.

“Each joint within the leg has only the range of motion available to it that we think the original creature had,” Garwood says. “You can then work out how we think it walked.” He calculated the creature’s center of mass and then compared its possible motion to living arachnids.

The result: an extinct arachnid, resurrected and walking around on Garwood’s computer screen. His calculations suggest that it moved pretty much like modern spiders and could scuttle relatively fast. Its mouth parts — including a filtering plate where it might have pre-digested food — indicate that it fed on other animals, so “we can say they were probably running down their prey,” Garwood says. This tiny terror adds to the understanding of what the ancient Rhynie Chert landscape looked like and how its inhabitants interacted.

“The more work like this we do, the more complete picture we have of the fossil record,” Garwood says. For instance, he and his colleagues have figured out something new about a 305-million-year-old daddy longlegs. The fossil was preserved within an iron-rich mineral called siderite, which often precipitates out around dying organisms in coal-rich rocks. The animal becomes entombed in siderite and, after its body rots away, leaves behind a hole reflecting its shape.

Garwood and colleagues used a CT scanner to obtain exquisite detail on the daddy longlegs fossil. They discovered a pair of structures on its side, which they argue might be a second pair of eyes. Modern daddy longlegs have only one pair of eyes, but spiders have multiple pairs aimed in different directions. The ancient daddy longlegs could have had eyes on both its front and its sides before losing the side pair in evolutionary history, the team wrote in May in Current Biology.

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An aquatic lifestyle

Computer scans and reconstructions are helpful not only for probing tiny animals, but also for shedding light on bigger creatures. For instance, Racicot uses 3-D scans to explore the evolution of whales, dolphins and porpoises. Unlike most marine animals, whales once lived on land and moved into the sea starting about 50 million years ago. Somewhere along the way, dolphins and porpoises also evolved the ability to use echolocation to find their way around the deep. That meant major evolutionary changes to their skulls.

“Their heads are just really weird,” says Racicot, who is now with Howard University in Washington, D.C. “They committed totally to an aquatic lifestyle.” For example, the noses of toothed whales moved from the fronts of their faces to the top of the skull to form a blowhole. They also developed a lump of specialized fat tissue atop the head, known as the melon, which helps the animals focus and direct sound to bounce off nearby fish.

PECULIAR PORPOISE Computerized scans of a now-extinct porpoise called Semirostrum reveal the sensory organs (middle, red) embedded in its unusually long lower jaw. The animal may have used the organs to sense prey as it rooted through seafloor sediments. R. Racicot et al/Current Biology 2014

Three-dimensional fossil scans help expose those differences as the animals evolved, Racicot says. “If you scan it, then you basically have a copy of it forever, and you can reconstruct things like the brain, the little holes and areas that are important in different ways.”

In San Diego, she finally managed to scan the skull and other parts of a 3-million-year-old porpoise that had been unearthed at a construction site. Ever since the fossil’s discovery in 1990, paleon­tologists had noticed the animal’s odd protruding lower jaw.

The CT scans allowed Racicot to see that the sensory canals in the porpoise’s jaw extended the entire length of the bone. The only modern animals that have this sort of structure are skimmer birds and a kind of fish known as a halfbeak, she says. Both of those feed by using sensory canals in their jaws to sense nearby prey and then snap down their dinner as they skim above or through the water. Similarly, the extinct porpoise may have used its pointy chin to root through the soft sand on the seafloor, sensing the vibration of small animals and then eating them. In the March 31 Current Biology, Racicot and her colleagues dubbed the animal Semirostrum, since the upper part of its jaw, or rostrum, is so much shorter than its elongated lower part.

It’s not clear when or why Semirostrum eventually went extinct, although changing sea levels may have played a role by shrinking the animals’ available habitat. Modern porpoises also find their food in seafloor sediment, but they don’t have the extra sensory organs in their jaws that Semirostrum appears to have had millions of years ago. “It’s pretty obvious that this animal was extremely specialized compared to any of the modern porpoises that we see,” Racicot says.

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Botanical surprises

The same is true for many ancient plants revealed through 3-D computer scanning. Paleobotanists have long used microscopes to devise detailed pictures of the surface of plant fossils. But X-rays can penetrate inside to expose crucial structures such as the stamen or pollen-bearing organ. In a comparison of different flowers from the Cretaceous period, from 145 million to 66 million years ago, paleobotanist Else Marie Friis of the Swedish Museum of Natural History in Stockholm and her colleagues described a range of botanical surprises. For one, X-ray scans revealed that a single fragmentary fossil from western Portugal was actually the oldest known flower from the group that today includes water lilies. And scans of rare Swedish flower bud fossils confirm that they had an unusual number of stamens hidden inside, Friis’ team reports in the July Journal of Paleontology.

Seeds of discovery A grain-of-paradise (Aframomum melegueta) seed (photographed, at left) is scanned and made into a 3-D volume rendering on the computer (middle). At right is a single digital slice through the seed. Botanists use these images to explore the evolutionary relationships among plants. S. Smith/University of Michigan
Selena Smith, a paleobotanist at the University of Michigan in Ann Arbor, uses X-ray imaging to explore the evolutionary history of banana and ginger plants from the order Zingiberales through their fossilized seeds. “Seeds have an amazing amount of information in them, even more than flowers for some groups,” she says. How the seed coating is put together, which parts are thicker than others and how many cells and layers are in different parts of different seeds are the kind of details that help botanists trace the relationships among various plants.

Smith has been studying a part of the seed called an operculum, a little lid through which a germinating plant must push to escape the seed. The shape of the operculum varies dramatically among the banana and ginger plants, helping Smith place the seeds in their proper places on the evolutionary tree. Surprisingly, she says, botanists know relatively little about modern banana and ginger seeds, so she is scanning many of them as well.

As scanning technologies and computer software get more sophisticated, 3-D reconstructions will probably gain in popularity among paleontologists. Some are already copying fossils using 3-D printers so that they can touch specimens they once only dreamed of handling. Rahman says the applications he has seen are striking.

“The technology has been taken in directions no one really anticipated.”

A member of an extinct group of arachnids called the trigonotarbids. This fossil is 312 million years old and 23 mm long. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
This is a 305-million-year-old juvenile insect that is 21 mm long and bears lots of spines — probably defensive adaptation. Russell Garwood, National Museum of Natural History, France
A 305-million-year-old, 6.5-mm-long fossil harvestman, shown with the legs removed. Russell Garwood, National Museum of Natural History, France
The same spiny insect nymph (juvenile) as seen earlier, shown from the front. Russell Garwood, National Museum of Natural History, France
The spiny nymph from above. Russell Garwood, National Museum of Natural History, France
The spiny nymph from above. Russell Garwood, National Museum of Natural History, France
A 312-million-year-old arachnid, that’s 17 mm in length and a member of an extinct order called the phalangiotarbids. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
A member of another extinct arachnid order called the Haptopoda. The 312-million-year-old fossil is 12.4 mm long. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
A 305-million-year-old insect nymph, this one probably a young cockroach-like species, 21mm long. Russell Garwood, National Museum of Natural History, France
The same harvestmen shown previously, this time with legs. Russell Garwood, National Museum of Natural History, France
The upper side of the trigonotarbid arachnid shown in the first image. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
A 312-million-year-old scorpion, 30 mm long, that is probably lying somewhere close to the origin of all living scorpions. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
A 305-million-year-old harvestman with defensive spines and incompletely preserved legs. Its body is 9.28 mm long. Russell Garwood, National Museum of Natural History, France
A 312-million-year-old creepy-crawly 15 mm in length, whose closest living relative remains unclear. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
An extinct millipede, 312 million years in age, and 35 mm long. Russell Garwood, © The Trustees of the Natural History Museum, London. All rights reserved 2014
Another extinct trigonotarbid arachnid, 312 million years old and 25 mm long, with lots of defensive spines. Russell Garwood, Lapworth Museum, Birmingham

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