Saturday, 29 October 2016

Imaging Life on Earth...

Archaeopteryx from the Late Jurassic of Southern Germany.
Since the dawn of time, our species has recorded images of life on Earth. Whether it be the beautiful cave paintings that captured our world over 17,000 years ago to the brush-strokes of Rembrandt, they share our species desire to capture the world around us. The origin and evolution of our own species has been preceded by billions of years of evolution that is complemented by a rich and diverse record of life on this planet. While there were no artists to record on canvas this rich tapestry of life through time, rare circumstances arose that would preserve the remains of life as fossils. Most have considered fossil remains as mere echoes of their former biological selves, but some fossil do preserve astoundingly high fidelity structures of both hard (e.g. bone, shell) and soft tissues (e.g. feathers, skin).

Fossils provide us with the evidence that narrates the story of decent with modification that is the evolution of life on Earth. Unravelling genomes and reconstructing molecular phylogenies can now precisely measure the evolutionary distance between organisms in the tapestry of extant species. The DNA that defines life is a fragile molecule, unable to resist even the gentlest ravages of geological time. The molecule of life is recovered from rare samples no older than 1 million years old, and then only in exceptional circumstances. The proteome might be the next logical focus, as proteins are more robust and might leave tantalizing evidence for the very building blocks of life. Here the frustration is also evident to those who study such ancient molecules, as anything older than 10 million years is rare. Is there another way that we can unpick the biological codec concealed within fossil remains?

However, the fossil remains that litter deep time are not so easy to characterize, but have the potential to constrain much of what we know record about the evolution of life on Earth.

The very atoms that construct biological materials can and do survive deep time, this is evident by the breakdown products of organic remains that drive our hydrocarbon-based economy. There is good reason that hydrocarbons are often termed ‘fossil fuel’. It is therefore strange that there is such amazement at the survival of organic remains within discrete biological structures, otherwise known as fossils.  Recent work has shown there are biomarkers that can be identified, mapped and quantified in both extant and extinct organisms (plants and animals). Such biomarkers are powerful tools when unlocking the puzzle of organismal biology, physiology and the very biosynthetic pathways that built, regulated and drove the evolution of life. The advent of synchrotron-based imaging techniques are now allowing us to piece together the complex relationships between trace-metals, rare earth elements that help study tissue types that comprise life, both past and present. The fragile paradigm that fossils merely represent shadows of past life is now being challenged, not with the promise of DNA or intact proteins, but from the fundamental building blocks of everything, elements. The chemistry of life is now helping reveal hitherto unseen 'chemical ghosts' by shining some of the brightest light in the universe upon fossils.

Synchrotron-Rapid Scanning X-Ray Fluorescence Map of Archaeopteryx scanned at beam line 6-2 at SSRL

Fossils are indeed partially composed of chemistry that directly links them to the organisms from which the fossils remains came. They really cannot be considered minerals (a solid naturally occurring inorganic substance), but are truly ‘geobiological’ composites of both inorganic and organic molecules that were constructed through biological and post-burial processes that preserve the fossil through deep time. The alteration that occurs to the biological tissue through subsequent mineralization rarely overprints the organic composition of an organism completely. Our team at the College of Charleston, University of Manchester and also at the Stanford Synchrotron Radiation Lightsource (Stanford University, USA) have been chemically mapping fossils (above) using multiple imaging techniques to elucidate these geobiological composites we commonly know as fossils.

The carbon cycle is remarkably efficient at recycling organic material, but under certain preservational circumstances, some of the chemical building blocks of an organism make it through this taphonomic (literally "burial laws") filter. In exceptionally preserved fossils, it is possible that remnants of structural proteins and associated organic molecules survive and can be mapped to help resolve original biological structures. The potential for new techniques to compositionally or spatially resolve such ‘chemical fossils’ is being realized with the recognition of elemental and organic residues that once comprised living tissue. Until the advent of techniques sensitive enough to resolve trace amounts of organic compounds and organically bound elements, it was difficult to untangle potential material transfer from microbes, geochemical fluids and the contamination from sampling and/or conservation techniques applied to a sample. However, the advent of synchrotron-based imaging and infrared spectroscopy has revolutionized sample analysis, enabling high-resolution scans that spatially resolve reaction aureoles, precipitates, etc. The suite of de novo techniques available to paleontology is completely changing our understanding of what constitutes a ‘fossil’.

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