Chemistry helps shine a light on a paleontological mystery

Chemistry has played a central role in answering a long-standing question in the field of paleontology: What were the colours of long-extinct, fossilized creatures? Until recently, colour in fossils had been almost impossible to determine because pigments were thought to degrade. Relying on a combination of techniques in chemistry and physics, paleontologists revealed the complete pigmentation pattern of a fossilized bird for the first time with their publication of their findings on the Science Express website in June 2011.

The team that performed the research demonstrates the utility of a cross-disciplinary approach, combining the knowledge and skills of experts from around the world. The international team was led by Phil Manning, a paleontologist; Uwe Bergmann, a physicist; and Roy Wogelius, a geochemist. Their work was performed at the SLAC National Accelerator Laboratory in Menlo Park, California, using the Stanford Synchrotron Radiation Lightsource. Using a new technique to map chemical ‘ghosts’, the researchers were able to chemically map the beautifully preserved feathers in the fossilized remains of the primitive birds Confuciusornis sanctus and Gansus yumenensis, both from over 100 million years ago.

This experiment applied a technique known as Synchrotron Rapid Scanning X-ray Fluorescence, a method of analysis that involves measuring the presence, distribution and concentration of elements by bombarding a surface with extremely intense X-rays. As the X-rays strike the fossil, the electrons surrounding the nucleus are knocked from the inner electronic shell. An electron from an outer shell 'falls-back' into the place of the lost electron, but in doing so generates a distinctive secondary X-ray emission. This secondary emission is measured using a sensitive detector as each element has its own distinctive emission energy. The chemistry of fossils is determined on an element-by-element level. This technique is astoundingly sensitive because of the high intensity and high energy X-rays from the synchrotron light source.

The study allowed the researchers to paint a monochrome picture of the ancient bird. A blue jay feather, squid, and fossil fish with feather are shown in optical images (top) and X-ray images (bottom) showing the distribution of copper (red). Copper in the dark parts of the feathers, the fish eye, and the squid ink sack indicates the presence of melanin pigmentation.

The researchers used this technique to find traces of different elements that may have been crucial to life; according to the researchers, the presence of trace metals such as copper can indicate the presence of eumelanin, a pigment that provides dark colouring in hair, eyes, and feathers of almost all animals. The copper structures bound to the melanin take certain forms that are distinct from other traces of copper found in the fossil, and the X-rays were sufficiently intense to find these specific copper structures. These traces of elements were then analyzed to identify density and distribution patterns over the entirety of the fossil. This allowed the scientists to discover the patterns of dark and light based on the differing copper concentrations. The researchers confirmed their hypothesis by using the same technique to create chemical pigmentation maps using the remains of extant species.

Prior to this study, scientists had relied on electron microscopes to scan fossils for the different melanosome structures in which melanin pigments are synthesized; however, the technique requires damaging the fossil in order to obtain a sample, and the small size of the samples makes learning about the overall distribution of the pigments impossible. In contrast, this new technique of using synchrotron X-rays to identify trace metals can work in fossils long after the melanosome structures themselves have degraded and can map the entirety of the fossil without doing any damage to it.

The results of the research have several important implications for the field of paleontology. Learning more about the colouring of extinct species will improve hypotheses about their behaviour in terms of communication and breeding habits as well as improve the understanding of their environment by suggesting possible camouflage uses. The discovery will also help paleontologists learn more about the biochemistry of fossilized animals. In addition, Manning notes that being able to chemically map the pigmentation of extinct animals can “[shed] light on the evolution of colour pigments in modern species.” According to Wogelius, the experiment also has uses beyond paleontology: “We may also be able to use this research to improve our ability to sequester toxic materials such as radioactive waste and to devise new strategies for stabilizing man-made organic compounds.”

This technique is useful for identifying the dark and light patterns of pigmentation, but not the actual colours, which still leaves plenty to the imagination and a lot of reasons for continuing the use of chemistry in an inter-disciplinary approach to improve our understanding of the prehistoric past. In the meantime, as Manning states, “The potential for this technique to gently unpick the chemistry of long extinct species is quite breathtaking.”

Further information

The original report can be found on the Science Express website, but requires either a subscription or purchase of the article for access to it beyond the summary. However, the press release from SLAC can be read for free on the SLAC website with accompanying photos and videos.

If you’re interested in quickly learning more about synchrotron radiation, Symmetry online magazine’s “Explain it in 60 Seconds” feature has an article at

For a first-hand account of the experiment, you can check out blog entries from Dr. Phil Manning, one of the researchers involved.

Thanks to Dr. Phil Manning for his helpful advice with regards to the explanation of Synchrotron Rapid Scanning X-ray Fluorescence.