Seemingly Ordinary Fossils May Be Hiding Some Major Clues to the Past

Monday, November 30, 2020

Detail of a partially decalcified Allosaurus bone fossil at Yale Peabody Museum. (Photo: Jasmina Wiemann)

Paleontologists are lucky to find complete sets of fossilised bones. Sometimes, they get even luckier, finding preserved impressions of delicate features like feathers. Beyond those clues, though, most of the biology of extinct species — their DNA, internal organs, and unique chemistry — has been totally destroyed by the many millions of years that separate us. Except, what if it hasn’t? Some scientists now claim they can tease much more complex biological information out of apparently mundane fossils, including things that most paleontologists don’t expect to survive over millions of years, such as skin and eggshell.

Molecular paleobiologist Jasmina Wiemann has been on the forefront of this exciting research since 2018, co-authoring papers that reveal elements of fossils that cannot be immediately seen with our eyes but can be detected through a series of complex chemical and statistical analyses. Her recent paper, published this summer with Jason Crawford and Derek Briggs, builds upon other, similar research from the past two years. She and her co-authors claim they can determine the chemical signatures of skin, bone, teeth, and eggshell. Even better, they can train anyone else in the field within approximately 20 minutes to find these ancient traces using their techniques. It’s an opportunity they hope will be widely used within museum collections the world over.

Consider that most museums only display a small percentage of the fossils they have in their collection. Those fossils chosen for display are either partially complete skeletons or fossils that are readily recognisable to the general public. What remains in many collections’ storage rooms are shelves upon shelves of the rest: the less-flashy fossils that nonetheless offer insight into ancient life. What if they all could be tested for hidden biomarkers?

Fossilised dinosaur cells, blood vessel, and bone matrix. (Image: Jasmina Wiemann)

It takes a specific set of circumstances for something to survive thousands of years, much less millions. And if it does become fossilised, think about the incredible pressure and heat it undergoes over eons. While it’s remarkable that bones and other hard tissues survive, it is currently assumed that less hardy structures, such as cells, blood vessels, skin, and their molecular building blocks, will not, especially after hundreds of millions of years.

Biomolecules — the chemical building blocks for which these scientists search — are the molecules that make up all animal tissues: proteins, lipids, and sugars. The specific fossilisation products of biomolecules indicate to which kind of animal a fossil tissue once belonged, if it was biomineralised, and exactly what type of tissue it represents.

“Until now, it was assumed that biological signals preserved in modern biomolecules were lost during fossilisation,” explained Wiemann in a phone interview. “Our study represents the very first exploration of original biosignatures in complex, fossil organic matter. Contrary to previous targeted analyses, we wanted to objectively explore if there are any signals preserved and what they can actually tell us about a fossil organism.”

In other words, rather than search for a specific molecule on one particular fossil, they wanted to determine what molecules — if any — were on the sample set of fossils they explored. What they consistently discovered was that traces of certain ancient molecules survived, chemically altered but still distinct. The team could identify different types of molecular fossils, and they could interpret their biological meaning.

“When we published our first paper on molecular preservation in 2018, we found evidence not only of the fossilised products of lipids, as previously reported, but also of the fossilisation products of proteins and sugars,” Wiemann said. “This was a surprise to the field, and a very bold claim back then, especially because many previous case studies on fossil organic matter were affected by sample contamination. Now, two years later, our results have been reproduced multiple times by different laboratories, adding independent support to the fossilisation potential of biomolecules through chemical transformation.”

Wiemann brings a different perspective to paleontology. At the age of 15, she won a scholarship in Germany to study chemistry, which enabled her to complete degrees in geosciences and evolutionary biology before attending Yale University, where she is currently a PhD candidate. In the past two years, she has discovered egg colour in dinosaurs, contributed to research offering further evidence that the Tully Monster (Tullimonstrum) is a vertebrate, and helped reveal evidence that soft-shelled eggs evolved in dinosaurs before calcified eggshells. Translating the ancient chemical properties associated with those fossils was her role. As she explained, “I develop molecular proxies for all kinds of evolutionary topics to unlock information otherwise inaccessible to paleontologists.”

Wiemann was one of 16 students chosen to present research for the Romer Prize at this year’s annual meeting of the Society of Vertebrate Paleontologists. Her presentation, titled “Fossil Biomolecules Reveal the Physiology and Paleobiology of Extinct Amniotes,” described the method she has developed using Raman spectroscopy to ascertain fossil biomolecules and how this can be applied to greater understanding of extinct animals in deep time. While her talk didn’t win, “the committee was definitely impressed by the quality of her work,” wrote Kenneth Angielczyk, chair of the Romer Prize Committee, in an email to Gizmodo.

“A background in chemistry provides you with a different approach to complex problems: Molecules are invisible to the naked eye, so it often takes a certain degree of creativity and transfer of knowledge from related sciences to fully understand how reactions operate,” Wiemann said.

The field of paleontology has been around for over 200 years, and, in that time, we’ve grown from simply finding bones and determining what they are to learning how those animals died, what they ate, what diseases they had, studying tissues within the bone, tracing genetics, and learning more about the subtle aspects of evolution. Each generation has built upon the work of those that came before it. And every now and then, there are substantial leaps in our understanding — technology and insights that take our breath away.

Magnified image of the extracellular matrix from an Allosaurus fragilis vertebra. The originally collagenous matrix fibres are preserved, and osteocytes (bone cells) with filipodia are dark and infilled. (Image: Wiemann et al/Nature Communications 2018)

The assertion that proteins, lipids, and sugars may indeed survive beyond the estimated 3.8 million years currently accepted by science — and that this research can be applied to any fossil in any collection — is astounding. The implications of what we might learn could change the face of paleontology. This is particularly the case for fossils that are incomplete or that don’t preserve the telltale forms that tell us about the kind of species it might have been.

Consider the controversial, 300-million-year-old Tully Monster fossil: a unique-looking organism that has prompted debate since it was formally described in 1966. Traces of soft tissues discovered through the chemical analysis of Victoria McCoy, Wiemann, and their co-authors match those of vertebrate tissues, adding further proof to the indication it was a jawless, soft-bodied vertebrate rather than an invertebrate. And while the collection of Protoceratops fossil embryos discovered in Mongolia contain no visible eggshells, the work of Mark Norell, Wiemann, and colleagues provides evidence that they were once encased in soft-shelled eggs. These structures, reduced now to microscopic traces, wouldn’t be known without such scientific and technological progress.

Paleontologist Jingmai O’Connor is delighted by the research that illuminated the soft-shelled fossil eggs. She refers to the most recent paper by Wiemann and colleagues as a “methods paper” — a description of how this research was accomplished and how others might be able to replicate it.

“This is an example of the kind of exciting information that can be extracted with these methods,” O’Connor wrote in an email to Gizmodo, referencing the soft-shelled eggs unseen to our eyes. “This discovery is huge and makes so many oddities suddenly make sense (why eggshells are so different between different dinosaur lineages and why certain lineages have no known eggs in the fossil record). Here she [and her team are] expanding it to a great range of fossil tissues and showing that there is a detectable phylogenetic signal in the biomolecular residues.”

“There are many things in their papers that I find quite intriguing and that I think are really worth wrestling with,” Evan Saitta, research associate at the Field Museum in Chicago, said by phone. “I think it brings the debate up to a much higher level.”

With bold new claims, however, comes scepticism.

The biggest controversies surrounding this work are that it challenges three long-standing scientific premises: one, that ancient tissues are largely not expected to survive fossilisation; two, that the oxidative environments from which the fossils studied by Wiemann originated are not necessarily conducive to preservation; and three, that the chances of microbial contamination (or “biofilm”) on any fossil is high, therefore making contamination unavoidable.

“What’s radical about this model is that they’re suggesting organic preservation in highly oxidised environments, because those are the environments that promote this sort of chemistry,” Saitta said. “This is quite a departure, not only from what we understand in geology, where we tend to associate high organic content with low oxygen, but also in terms of bioarchaeology and the chemistry of much more recent bones. What we know from that work is that there is a breakdown and depletion of the original organic material in the bone, and, simultaneously, an increase in contamination from the surrounding environment over time.”

In other words, we often look to environments with low oxygen content as ideal locations for fossil preservation. Oxygen-rich environments are generally associated with decay. But that is not what Wiemann and colleagues are suggesting in this paper, offering a window into new possible worlds of geological preservation.

For other paleontologists, there are concerns that only one technology — Raman microspectroscopy — was used to determine the biomolecules. To be clear, Raman spectroscopy is incredibly complex on its own. The method was developed by physicist Chandrasekhara Venkata Raman in 1928, for which he won the Nobel Prize in 1930. In the most basic terms, a laser excites the molecules on the surface of any type of sample such that they vibrate and produce scattered light. Chemical bonds alter that light in ways that enable scientists to interpret what they are.

Paleontologist and professor at North Carolina State University Mary Schweitzer has recently started using Raman technology in her studies. She, too, has made bold claims in paleontology, including being the first to discover evidence of blood vessels and soft tissues in dinosaur fossils.

“Raman is a good method to detect functional groups or the presence of amide bonds, which are indeed consistent with proteins,” she wrote in an email. “But amide bonds may also be found in glues, consolidants (commonly applied in the field during recovery), biofilm, embedding medium if the fossil has been sectioned, and many other compounds, or as the result of normal lab contamination.”

Using Raman spectroscopy alone, she said, is not enough to determine whether complex organic chemical compounds from an extinct creature — original biomolecules including proteins — are indeed present.

Professor of physics Hans Hallen, also at NC State University and Schweitzer’s collaborator, has been working with Raman spectroscopy since the 1990s. He said his biggest concern is that “it looks like they’re subtracting out some of the real Raman signal with their adaptive baseline technique,” he said in a phone interview. Put another way, “they’re going to be underestimating the Raman signal because they subtracted part of it as baseline.”

“If I was to summarise, I’d say that this is a new approach to doing very hard science,” Hallen said. “But no matter what technique you use, it’s going to be hard. Raman is a good technique, but it’s not without its issues.”

One common concern was that other techniques, such as chromatography, mass spectrometry, and resonance Raman, were not also employed to confirm biosignals of ancient molecules. Chromatography and mass spectrometry, however, both require the destruction of the fossil to obtain information. And “there are only a few setups in the world that can use tunable deep-UV excitation for resonance Raman,” said Hallen, who added, “I happen to have one of them.”

Most universities, by contrast, do have access to standard Raman spectroscopy, and it is a non-destructive method. That accessibility and the preservation of the fossils themselves were important to Wiemann and her co-authors.

Moreover, Wiemann countered, concern with relying solely on Raman spectroscopy had already been addressed in a paper she and her colleagues published a year ago. Were this technology a new process, questions about its efficacy might be warranted. But it’s a method that has been used extensively in multiple fields since the 1970s.

Other labs, she explained in an email, have successfully used Raman spectroscopy to find biomolecules and have confirmed them using other methods. She cites recent papers offering evidence of possible blood vessels found in a T. rex fossil, evidence of tail feathers in a theropod fossil discovered in China, and one that suggests these chemical traces may indeed survive the intense pressures fossils undergo over millions of years.

Regarding concerns of contamination, Wiemann and her team specifically tested for the similarity of molecular signatures in fossil soft tissues and polyacrylamide glues in their most recent studies, demonstrating that fossil organic matter — at least in the analysed specimens — is not the result of contamination.

“The problem is, very few people can truly understand her work,” O’Connor wrote. “I know from Jasmina’s perspective, this is simple chemistry, and us paleo people just don’t have a good enough understanding of chemistry to comment or to criticise (and it must be frustrating for her to deal with us!).”

Paleontologists who would be more apt to understand this level of science are organic geochemists. One such organic geochemist, Gordon Love, a professor of Earth sciences at UC Riverside, has been studying ancient lipids that make up part of the structures in living cells. The study of these lipids, he explained, is not new. The search for ancient lipid biomarkers has been employed by the oil and gas industry for at least four decades — a way to find the rocks that produce the natural gas and oil used for fuel.

One aspect of this research that surprised Love was the preservation differences between the fossils examined and the rock in which they were found, specifically in the over 500-million-year-old examples from the Burgess Shale. He wonders how much phylogenetic information — clues that point to the evolutionary history of a species — can be determined by ancient molecules derived from proteins in fossils of that age but said he is eager to see what further research will bring.

“I do not think the support for a phylogenetic signature in the data is particularly strong relative to the biomineral signature,” Saitta said, referring to the ability to use Wiemann’s technique to determine what species belong where on the family tree. “But if the phylogenetic signature is genuine, that would actually be, in my opinion, really, really strong evidence that a lot of these organics are from the original fossil.”

“I like their approach and think it has merits, because precious samples are not destroyed by the analyses undertaken,” wrote organic geochemist of paleontology Professor Kliti Grice of Curtin University. “However, this is only one approach — I think their data could be complimented and by using molecular geochemistry on some samples carried out in parallel, as there is an untapped archive of molecular information, especially in fossils that are exceptionally well preserved in concretions.”

That Wiemann and her collaborators might be able to unlock secrets within fossils and be able to train others to do so offers incredible potential for our understanding of life on this planet.

“I hope that in the future,” Wiemann said, “scientists interested in animal relationships, the evolution of physiological innovations, and animal tissue types will explore molecular biosignatures to complement anatomical insights from fossils. Molecular data have the potential to provide completely new perspectives on the history of life, and might be the key to go beyond the current limitations of the fossil record.”

An easily taught, cost-effective, non-destructive technique that could potentially offer new insight into species millions of years old? It’s like getting a key to the biggest library: a wealth of untapped information. It could, both literally and figuratively, flesh out ancient beings, and it has the potential to breathe fresh energy into museum collections the world over.