Laser tech cracks code of 'Rosetta Stone' fossils, yielding fresh early life clues

A new study combines the latest imaging techniques with advanced data analysis and machine learning to uncover a never-before-seen preservation of 400 million-year-old fossils.
Sade Agard
A small piece of Rhynie fossil plant with fossil fungi colonising the ends, viewed through a microscope.
A small piece of Rhynie fossil plant with fossil fungi colonising the ends, viewed through a microscope.

Loron et al. 

  • The Rhynie chert, discovered in Aberdeenshire, Scotland, offers a remarkable glimpse into life during the Early Devonian period.
  • A new study combines the latest non-destructive imaging with data analysis, exposing the molecular fingerprint of these ancient fossils.
  • The findings reveal never-before-seen preservation of the fossils, helping to resolve more stranger organisms. 

In the heart of Aberdeenshire, Scotland, near the tranquil village of Rhynie, lies a world-renowned fossil ecosystem that has captivated scientists since its discovery in 1912. 

Preserved within the impenetrable embrace of chert, a hardened rock composed of silica, the Rhynie chert offers a window into the past, hailing from the ancient Early Devonian period, approximately 407 million years ago (ma). This remarkable geological treasure holds a crucial role in unraveling the mysteries of life on Earth. 

Now, armed with cutting-edge non-destructive imaging techniques, advanced data analysis, and the power of machine learning, a team of researchers has embarked on a groundbreaking exploration of the fossil collections held by National Museums Scotland, as well as the Universities of Aberdeen and Oxford. 

Through their innovative approach, scientists from the University of Edinburgh have unveiled unprecedented insights into the Rhynie chert that could revolutionize our understanding of even the most poorly preserved samples. 

Curious to delve further into the impact of this research on our understanding of the ancient world, Interesting Engineering (IE) connected with Dr. Corentin Loron, one of the study's lead authors.

The Rhynie chert: a 'Rosetta Stone' of the fossil world

"The fossils studied here are specimens of plants, fungi (the kingdom that includes mushrooms, yeasts, and molds), bacteria, and animals from the ca. 400 million years old Rhynie chert, a fossil site in Aberdeenshire, Scotland, long known for its exceptional abundance of fossils," Loron described to IE

She explained that the fossils are encased within a silica matrix—a very hard mineral—which has ensured that they are "pristinely preserved" both morphologically and, as her study has revealed, molecularly, too.

"The Rhynie chert assemblage is a crucial one for the study of how life evolved on the continents because it contains a lot of the early unambiguous examples of some biological lineages," she said. 

In this way, she explained, the Rhynie chert assemblage qualifies as a strong positive control for the study of molecular signals in fossils because the signal can be compared to the organism it corresponds to.

"In a sense, it provides a key to understanding more cryptic or ambiguous signals within the assemblage or earlier in time, just as the Rosetta stone allowed for the hieroglyphs," she clarified. 

FTIR spectroscopy yields never-before-seen preservation

The fossils were analyzed using FTIR spectroscopy, which stands for Fourier Transform InfraRed. "In this technique, the samples are shot with an infrared laser which, going through the fossil material, will excite the bonds between atoms," Loron explained. 

Laser tech cracks code of 'Rosetta Stone' fossils, yielding fresh early life clues
An example of an FTIR spectrometer: This one is fitted with an attenuated total reflectance (ATR) attachment.

In simpler terms, FTIR spectroscopy uses light to identify the molecules in a sample; it helps scientists understand what the sample is made of.

It works by shining infrared light onto a sample and measuring the wavelengths of light absorbed by the molecules within the sample. 

Each molecule type has a unique absorption pattern, like a fingerprint, which the instrument can detect. The instrument records the intensity of the absorbed light at various wavelengths and converts it into a spectrum. 

"These bonds are going to vibrate at different frequencies according to their type (e.g., a bond between two carbon atoms, or between a carbon and an oxygen) and chemical functional group," Loron told IE

"The result will be a spectrum showing the chemical composition of our material that we can exploit to reconstruct and understand its molecular structure," she added. In other words, by comparing this spectrum to known spectra of different molecules, scientists can identify the presence of specific compounds or analyze the chemical structure of a substance. 

"One approach that we used to analyze these spectra is a machine learning approach, which is simply a supervised statistical approach," she said. 

"For example, we teach the machine to differentiate the spectrum of a fossil X from the spectrum of a fossil Y by indicating this is X and this is Y (the training). Then, we test it by asking how it would classify another unlabelled dataset."

She revealed that in their research, the machine successfully distinguished between fossil eukaryotes (including fungi, plants, and animals) and prokaryotes (bacteria).

Machine learning unravels the identity of mysterious organisms

Notably, this approach was then employed to identify previously puzzling organisms within the Rhynie ecosystem, including two specimens of a mysterious tubular organism known as a "nematophyte." 

Laser tech cracks code of 'Rosetta Stone' fossils, yielding fresh early life clues
Photomicrographs of representative Rhynie chert organisms. Figure f is a nematophyte.

These peculiar life forms, discovered in Devonian (419 ma) and later Silurian (443 ma) sediments, exhibit characteristics of both algae and fungi, making their classification challenging. However, the recent findings suggest they are unlikely to belong to either lichens or fungi.

"Nematophytes represent a "basket" group that includes several fossils for which the biological affinity is unclear. They might have part of a plant, bacteria, or fungi, for example," Loron explained. 

"The specimens we studied in our work possess a molecular fingerprint lacking the features that characterize fungal fingerprints, hence our conclusion that they were most probably representing something closer to plants in terms of molecular composition."

She asserted that while this is an important finding for scientists studying the Rhynie chert, its significance extends beyond that. Above all, it confirms the effectiveness of their approach when analyzing fossils with uncertain biological origins, here and in other locations.

"We have shown how a quick, non-invasive method can be used to discriminate between different lifeforms," emphasized co-lead author Dr. Sean McMahon from the School of Physics and Astronomy and School of GeoSciences, University of Edinburgh in an earlier press release

Molecular fingerprint confirms the resilience of fossils over time

Loron also unveiled that the most surprising finding during this research was the outcomes of the statistical analyses.

"It is impressive to see that despite the age, the fossilization process, and the overwhelming influence of the minerals on the signal recorded with our instrument, the fossils still retained a molecular fingerprint of their past composition that can be picked up and studied," she said. 

In this context, perhaps it's safe to say that the molecular information within the fossils has survived the test of time, offering a unique glimpse into the past.

When asked about what inspired the team to undertake this study, Dr. Loron's response was crystal clear: 

"Our team's motivation is to understand how life has evolved on Earth, first from unicellular form toward multicellular—but also later—how life has emerged from the oceans to continents."

"Studying early life forms not only provides wonderful insights into our own biological heritage but also gives us keys to understanding how the process of life can emerge and thrive on Earth but also potentially elsewhere in our universe," she emphasized. 

She acknowledged that similar to many paleontological studies, the team faces limitations in their interpretations due to the significant transformations the fossils have undergone compared to their original, living organisms.

Cracking the molecular code of Earth's earliest complex life

"Because DNA cannot preserve in fossils that old, we can only base our conclusions on recalcitrant morphological and molecular features, which can limit and bias conclusions," she said. 

That said, she also reasoned these biases could be overcome by understanding the geological context in which the fossils have formed. 

"Next steps, in addition to continuing our investigations of this wonderful fossil site, will be to expand our approach to older assemblages, for example, in the Precambrian, the period anterior to 540 million years, to crack the molecular code of the earliest traces of complex life on Earth," Loron concluded. 

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