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Newly discovered traces of soft tissue provide unprecedented insights into how animals that died millions of years ago looked and lived

PETE LARSON and Phil Manning mount the dinosaur fossil on a small motorised platform inside the lead-lined chamber. The two palaeontologists make a few final adjustments, then exit the chamber and bolt it tight. At the console, geochemist Roy Wogelius flips a switch, sending a beam of X-rays sweeping over the fossil’s surface.

The scene, at the Stanford Synchrotron Radiation Lightsource in California, is reminiscent of Dr Frankenstein animating his monster. And that is essentially what Larson, Manning and Wogelius are trying to do.

Their project is one of several challenges to the conventional wisdom that when animals fossilise, all the original organic material, from the bones to the blood, is lost. Larson, of the Black Hills Institute in South Dakota, and Manning and Wogelius of the University of Manchester, UK, have already detected chemicals in a 145-million-year-old bird fossil that they believe were present in the living creature. Other groups have reported finding proteins and blood vessels inside dinosaur bones, and traces of pigments in 108-million-year-old feathers. The claims are controversial, but if true they promise to breathe new life into our understanding of ancient life.

The research could also help locate new deposits of extraordinarily well preserved fossils, says Patrick Orr of University College Dublin in Ireland – sites like the Burgess shale in Canada and Chinese feathered dinosaurs beds that have given us tremendous insights into evolution. Such deposits are usually found by accident, but the more we understand about the conditions that create them the more chance we have of discovering new ones.

First, however, researchers like Manning must convince other palaeontologists that their fossils really do preserve original material, which won’t be easy.

Palaeontologists have long studied the process of fossilisation – a field known as taphonomy – by observing the fate of dead animals and measuring what happens to the organic matter. Most of the time soft tissues are completely consumed by predators, scavengers and decay, leaving just scattered and fragmentary bones and teeth. If these fossilise they become mineralised, with all of the original material turned to rock.

Pristine preservation

Occasionally, though, nature is kind and fossilisation preserves details of an animal’s soft tissue. For example, the animals of the Burgess shale were buried rapidly in anoxic mud, allowing their soft tissues to be fossilised in amazing detail. Dinosaur “mummies” such as Dakota, a spectacularly well-preserved specimen of the duck-billed dinosaur Edmontosaurus, form when thick-skinned animals are buried quickly in fine river-bed sands, capturing impressions of the skin before the tissue decays. Impressions of feathers from Archaeopteryx were preserved in fine lime deposits on the bottom of a stagnant lagoon, and China’s celebrated feathered dinosaurs were fossilised in fine silts and layers of volcanic ash settling to the bottoms of lakes 125 million years ago.

However, even these exceptional conditions were not thought to preserve original organic material. The Chinese fossils are covered in a thin black film of carbon, but this is believed to be remains of bacteria that consumed the soft tissue before being entombed in rock. Convincing evidence of original soft tissue older than the Ice Age was lacking.

That wasn’t for lack of trying. The biggest prize was DNA, because it could reveal so much about extinct animals and their relations to living ones.

The 1993 movie Jurassic Park pumped up interest in the search for dinosaur DNA, and a year later Scott Woodward of Brigham Young University in Provo, Utah, claimed to have found dinosaur DNA in 80-million-year-old bone fragments (91av, 26 November 1994, p 12). His report in Science () made headlines across the world, but the DNA was soon found to be contamination from humans who had handled the fossil.

Technology has advanced tremendously since then. DNA has now been extracted and sequenced from mammoths, the bones of Neanderthals, and extinct cave bears. But recovering DNA from dinosaurs remains the stuff of fiction. DNA degrades much faster than proteins and other soft tissue components and nobody thinks it is possible to recover DNA that is older than about a million years.

But DNA is not the only game in town. The controversy surrounding the supposed dinosaur DNA made a lasting impression on Mary Schweitzer, who was then a graduate student at Montana State University in Bozeman. Ten years later, she reported recovering soft, flexible tissues from inside the leg bone of a 68-million-year-old Tyrannosaurus rex which she claimed were blood vessels ().

The T. rex was discovered in a remote South Dakota canyon in 2000 by a team from the Museum of the Rockies. Its femur was intact but too heavy for a helicopter to lift in one piece, so they had to break it. To everyone’s surprise the interior was hollow – fossilised bones are usually filled with minerals – so the excavation team took samples and sent them to Schweitzer for analysis. She soaked the samples in a solution to dissolve the calcium compounds in the fossil, and was surprised to be left with flexible tissue which she identified as blood vessels.

Schweitzer’s claim was met with scepticism, in part because of the immense age of the bone. “The cynics think it’s far too old,” says Derek Briggs of Yale University. Tom Kaye of the University of Washington in Seattle suggested that what she had found was a biofilm left by bacteria that had feasted on the dead animal ().

Blood from a stone

However, in 2007, Schweitzer – now at North Carolina State University – and colleagues reported that the T. rex bone also contained fragments of the protein collagen, a key component of connective tissue in animals (). That was a huge jump from the previous oldest protein found, collagen from a 600,000-year-old mastodon.

The dinosaur protein was not as well preserved, but it offered an important rebuttal to the biofilm critics. “Microbes can’t do collagen,” says Schweitzer. It must have come from the dinosaur.

She also showed that an antibody to chicken collagen reacted with the samples, which would be expected as birds are descended from dinosaurs. Further evidence comes from her colleague John Asara at Harvard Medical School, who sequenced the protein fragments and found matches to sequences of collagen taken from living species, including birds.

Collagen is an extremely durable protein but it also evolves very slowly, so sequencing its amino acid building blocks – in much the same way that DNA bases can be sequenced – is of little use if you want to identify relationships between extinct and living species. However, in 2009 Schweitzer went one better. Working with the 80-million-year-old leg of a Brachylophosaurus, her group extracted not only collagen but also haemoglobin, elastin and laminin, as well as structures that resemble blood and bone cells (). These proteins vary much more among species, so sequencing them could reveal relationships between dinosaurs and other animals.

Others have begun to report similar findings, and not just from inside bones. Manning and Wogelius have reported finding amino acids in the claw and skin of Dakota, the 66-million-year-old Edmontosaurus mummy (). Meanwhile, Orr’s former student Maria McNamara, now splitting her time between Dublin and Yale, claims to have found marrow inside the fossilised bones of 10 million-year old frogs and salamanders preserved in lake-bed deposits from Spain (). Marrow is normally among the first tissues to decay, but she found organic residues preserved in three dimensions that retained the original colour and texture of the marrow.

“The fidelity of preservation on a morphological level is remarkable, though it’s very unlikely that the biochemistry would be completely original,” says Orr. Preservation of very decay-prone soft tissues is probably more common than we realise, he adds.

As technology progresses, new techniques are being developed that can look at fossils in a whole new light, revealing details of preservation that have never been seen before. “The synchrotron is the latest thing out there,” says Briggs.

Synchrotrons generate high-energy X-rays which can blast inner-shell electrons from atoms. Outer electrons then fill the holes left behind and in the process emit radiation, the wavelength of which can be used to identify the atom that emitted it.

Larson first heard about Stanford’s synchrotron on a radio programme about a project to decipher an ancient manuscript believed to contain lost writings by Archimedes. The book was a palimpsest, written on parchment from which a previous text had been removed. The researchers were using synchrotron radiation to detect iron from the original text, in the hope they could make out the words (91av, 6 October 2007, p 43). Larson wondered what the technique could reveal about fossils, so he fixed up a test run.

The results were encouraging. “It looked like a good way to study soft tissue preservation,” he recalls. Larson showed Manning some preliminary images. “I said, my gosh, that looks impressive,” recalls Manning. So Larson invited him along to the next beam run, along with me.

That run examined part of a dinosaur mummy, a fossil lizard, a 125-million-year-old Chinese bird with feather imprints and some modern samples including a freeze-dried turtle and a duck skull. Unfortunately, the complex geometry of the dinosaur mummy made it tricky to study. Flat fossils, they found, were much more suited to the technique.

One such flat fossil that looked ripe for the synchrotron was the Thermopolis Archaeopteryx (see a photo here), the only Archaeopteryx specimen in the US, housed at the Wyoming Dinosaur Center in Thermopolis. This turned out to be ideal for the technique, and in 2009 the team published a set of stunning new views ().

Some of the X-ray images showed that the bones and feather shafts are rich in phosphorus, an important element in these parts of living birds. This suggests that the fossil preserves some original material, the team say. Nobody had expected soft-tissue chemistry to be preserved in such places, Wogelius says, and previous techniques had not been sensitive enough to reveal the phosphorus. “It’s amazing that that chemistry is preserved after 150 million years.”

That’s not all that remains. “Zinc levels in bones are not far from what we expect in modern birds,” says Wogelius. Copper, another key nutrient in modern birds, is also higher in the fossilised bones than in the surrounding rock, suggesting that nutritional balances in Archaeopteryx were similar to those in modern birds.

Other feathered fossils have revealed more surprises. When Briggs’s student looked at a 108-million-year-old fossilised bird feather under a scanning electron microscope, he noticed distinctive structures called melanosomes embedded within the feathers. These are tiny bags of the pigment melanin that colour the feathers and fur of many living birds and mammals.

In living animals the shape of the melanosome depends on the type of melanin they contain. Rice-grain shaped melanosomes about a micrometre long contain the black-brown variant eumelanin. Rounded melanosomes contain the reddish-ginger form pheomelanin. Spotting melanosomes on the ancient feather gave Vinther a peek at something long-thought unknowable: the colour of an animal that lived tens of millions of years ago.

Vinther found bands of rice-shaped melanosomes on his feather, suggesting that the bird had dark stripes (). Mike Benton of the University of Bristol, UK, and colleagues revealed similar patterning on the tail feathers of Sinosauropteryx, a small feathered dinosaur that lived in China 125 million years ago ().

This kind of insight is exactly what palaeontologists hope for. “When you look at specimens you’ve studied before with a new technique, you’ll get new information,” says Briggs.

The new techniques have not yet answered any big questions about dinosaurs: researchers like Schweitzer and Manning have devoted much of their effort to persuading sceptics that their results are real. Eventually they think they will win over the doubters and revolutionise palaeontology, but in the meantime they have the satisfaction that drives on amateur and professional fossil hunters alike. “It’s quite amazing to discover something that has never been seen before,” says Wogelius.