Diagenesis part 1: Words

Spectroscopy has been used to get a handle on diagenesis, and many different techniques have been developed to assess diagenetic alteration of fossils. Despite the range of options, and partially because of it, a tendency has arisen to treat spectroscopic instruments as “black boxes” that produce diagenetic conclusions. Or, otherwise put, when all you have is a hammer, every problem looks like a nail. You can imagine how bad this might be when you build a skyscraper using nothing but nails…

Part of the problem is semantics. Diagenesis refers to chemical and physical changes that occur during burial. Diagenetic alteration of fossils therefore refers to changes in the chemistry or structure of a fossil once it has been buried. This is basically an open book, and you can pretty much expect every fossil to have been diagenetically altered. Got no collagen? Altered. Increased your fluoride? Altered. Slightly warped? Altered. This is where we have to get a bit picky, and ask whether diagenetic alteration of a fossil has been significant. Significant diagenetic alteration is when a chemical or physical parameter you wish to measure is distinct (statistically distinguishable) from the original, biogenic composition. So, a fossil can be diagenetically altered, and they almost all are, and you might not care less. On occasion though, diagenetic alteration can be a real [bother], with significant changes to the chemistry of the bone actually obscuring any biological information.

A second issue lies in perspective. There appears to be two schools of thought regarding the priority of diagenesis. One approach is to carefully select the fossil to be studied, to carefully select a region of that fossil, to eliminate as much interference from that sample as possible, and then physically or chemically measure the sample. As all possible care has been taken and a sound methodology has been followed, the results can then be interpreted as a biogenic signal. Take the measurement of carbon and oxygen isotopes from apatite carbonate, for example. You select a fossil tooth with clean, thick enamel, you sample only the enamel, and you treat the sample for secondary carbonates: interpretations about diet and environment can then be made from the measured isotopic compositions. Any evidence for diagenetic alteration is left to compete with biological explanations for the dataset.  This is akin to logical positivism.

The second approach is to follow the same methodology as the first, but instead of assuming that your careful sampling and preparation has netted biological values, you simply assume that you are measuring a completely altered sample. This might seem like fatalism, but bear with me. The burden of proof is now on you to disprove your assumption, and in so doing, find empirical reasons why your samples reflect biology and not diagenesis. Here instead we are working with critical rationalism.

This will bring us back to spectroscopy, and how it has been used to identify alteration.

#Archive: Red blooded killer

Two spectroscopic techniques helped identify heme from a Tyrannosaurus rex bone

Fourteen years ago Mary Schweitzer and colleagues published a paper in PNAS with the title “Heme compounds in dinosaur trabecular bone”. This was a huge step forward in the study of ancient organic tissues. The paper described a meticulous study, and the abstract opened with “Six independent lines of evidence point to the existence of heme-containing compounds and/or hemoglobin breakdown products in extracts of trabecular tissues of the large theropod dinosaur Tyrannosaurus rex”. One of those techniques was Raman spectroscopy, and another was UV/Visible spectroscopy.

The UV-Vis spectra of tissue extracts exhibited a distinct band at around 405 nm, “…consistent with the absorbance characteristic of the Soret band of hemoglobin and other heme proteins…”. Likewise, Raman spectra of the tissue extract exhibited a set of “marker” bands in the 1300 to 1600 cm^-1 region that could be linked to similar bands in modern day hemoglobin. Hence, both spectroscopic techniques were used to “fingerprint” hemoglobin from a 70 million year old fossil. Isn’t spectroscopy wonderful?

Schweitzer MH et al. 1997. Heme compounds in dinosaur trabecular bone. Proceedings of theNationalAcademyof Sciences of theUnited States of America. 94: 6291-6296.

Image compiled from Wikimedia Commons

#Recent news: Chemical images of Archaeopteryx

Chemical mapping has revealed the remnants of feathers preserved in this specimen of Archaeopteryx

Synchrotron rapid scanning X-ray fluorescence has given the world more than just an impressive acronym. In fact, SRS-XRF has been used to describe hidden feather traces and bone chemistry in a specimen of Archaeopteryx. SRS-XRF is a chemical mapping technique that applies the basic approach of XRF (see X-ray fluorescence below) to points spaced 100 μm apart, allowing elemental maps to be made at a staggering rate of one square centimetre every 30 seconds. Uwe Bergmann and colleages reported their SRS-XRF maps of Archaeopteryx last year, where they show a phosphorus distribution that picks out all of the bone, as well as shafts of feathers. Zinc was shown almost exclusively associated with the bone, and may reflect the original diet of Archaeopteryx. This study is a great step forward in visualising otherwise unseen fossil evidence.

Bergmann U, Morton RW, Manning PL, Sellers WI, Farrar S, Huntley KG, Wogelius RA, Larson P. 2010. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1001569107

Image from Wikipedia