Could proteins found in dinosaur fossils come from microbes?

As analytic techniques improve, chemists can discover more and more about the prehistoric animals that lived on Earth before us. But some scientists sparked some controversy in the past decade after they reported discovering proteins preserved in the fossilized bones of dinosaurs.

An international team of researchers now suggests another source of the biological material found in these fossils. The proteins, they say, aren’t dinosaur in origin, but microbial. And a fossil they dug up has a distinct microbiome all of its own (eLife 2019, DOI: 10.7554/eLife.46205).

The work “once again demonstrates how bone’s ‘open-system’ behavior warrants extra caution when assessing the authenticity of ancient molecules,” says Beatrice Demarchi, of the University of Turin, who was not involved in the new work.

Evan T. Saitta at the Field Museum of Natural History in Chicago has a background in examining how soft tissues like connective tissue, feathers, and scales get preserved during fossilization. To study the process, he uses a mix of geochemistry and more traditional paleontology, subjecting biological materials to high temperatures and pressures to simulate how the fossils of soft tissues could form. Because of this background, Saitta became skeptical of the claims of discovering preserved dinosaur proteins. For example, he found that the protein keratin in feathers breaks down into pyrolysis products under fossilization conditions.

In 2007, Mary H. Schweitzer at North Carolina State University reported finding collagen in preserved dinosaur bones, and then ten years later Robert R. Reisz at the University of Toronto independently made similar claims, but with a much older dinosaur fossil. Schweitzer and colleagues detected the proteins by first dissolving their dinosaur bones in weak acid before using protein-binding antibodies and mass spectroscopy to look for dino proteins. Meanwhile, Reisz’s team used nondestructive microscopy techniques to examine organic material in their fossilized bones.

Saitta wanted to look at fossilized dinosaur bones with a battery of tests, such as variable pressure scanning electron microscopy, pyrolysis-gas chromatography-mass spectrometry, and radiocarbon accelerator mass spectrometry, that he thought were more reliable than some of the techniques used by other researchers. Those other methods, he says, can be overly sensitive and not specific enough for identifying dinosaur proteins.

Saitta went to the appropriately named Dinosaur Provincial Park in Alberta and dug up bones from a horned dinosaur called Centrosaurus. He didn’t find any indication of dinosaur collagen protein. Instead, Saitta found more recent organic molecules that he attributed to microbes growing in the fossilized bones. He thinks that the fossilized bones provide favorable habitats for microbes under soil.

However, Schweitzer and Reisz still stand by their findings.

“I’m pretty confident in my data,” Schweitzer says. She’s been aware of Saitta’s paper since he uploaded a preprint to BioRxiv last year. She points out that her data came from multiple fossils, so the findings weren’t some fluke artifact. These new findings are another part of a debate that is playing out in the literature and can sometimes feel personal, Schweitzer admits, adding she’s worried that some criticisms of her rather than her work could ultimately hurt the field by dismissing valid results without enough evidence to justify it.

Schweitzer has continued with her research on studying biomolecules in fossils and coauthored a recent review article (Proteomics J. 2019, DOI: 10.1002/pmic.201800251) that proposes criteria for assessing the presence of endogenous biomolecules in ancient fossil remains, as well as appropriate controls and validation techniques.

Reisz also continues to support the claim that dinosaur fossils can contain fragments of original dinosaur proteins. He points out that everyone in the field acknowledges that microbes exist in these fossils. After all, microbes are everywhere. He also argues that the new findings from Saitta’s team do not adequately address all of Reisz’s findings, such as the fact that the proteins he found were in specific structures in fossilized bone where scientists would expect to find those proteins.

For Matthew Collins, an expert in ancient proteins at the University of Copenhagen, the value of the Saitta’s work is that it “attempts to comprehensively report what is present in dinosaur bone.” But he says both sides of this ongoing debate have merit. As Schweitzer herself concludes, ultimately the science will win out.