Using light to describe the ancient world

Archive for the ‘Diagenesis’ Category

#Smithsonian intern coauthors scientific article

Charlotte Doney during her undergraduate internship at the Museum Conservation Institute. Charlotte is shown here sitting in front of an FT-Raman spectrometer in Dr. Odile Madden's Modern Materials lab. Photo source:

Charlotte Doney during her undergraduate internship at the Museum Conservation Institute. Charlotte is sitting in front of an FT-Raman spectrometer in Dr. Odile Madden’s Modern Materials lab. Photo source.

My colleagues at the Smithsonian Institution and I have recently published an article that explores the preservation of old collagen. I think this is a great methods paper that could lead on to some really interesting applications, and I will get to the details of the article in a little bit. First though, I want to highlight one of the most fun aspects of this paper – a good chunk of the work was done by Charlotte Doney, an undergraduate intern from George Washington University.

In 2012, Dr. Christine France successfully attracted funding for undergraduate students to take up research projects in the Museum Conservation Institute. This Institute is housed within the Smithsonian Institution’s Museum Support Center, in Suitland, Maryland. Charlotte Doney was interested in working with Dr. France and Dr. Odile Madden on a project these senior researchers had discussed some years prior – can Raman spectroscopy tell us if collagen in an ancient bone is well preserved? Charlotte was interested in both the challenge and answer.

Raman spectroscopy provides chemical information about a sample, and in the case of an old bone, is useful for studying both the collagen and the bone mineral. Furthermore, the isotopic compositions of carbon and nitrogen in collagen can tell us about the lifestyle of the person or animal the bone is from. Raman spectroscopy doesn’t report on the isotopic composition of collagen – this is the job of a mass spectrometer. Instead, Raman spectroscopy gives us an idea about how much collagen is present in the bone. As collagen degrades, the isotopic composition becomes less meaningful about the original lifestyle of the person or animal. As collagen degrades, there is less and less of it left in the bone, and we can detect this with Raman spectroscopy. Charlotte collected Raman spectra from bones that had known isotopic compositions.

I was working in Dr. Madden’s lab at the time and had the privilege of training Charlotte to collect Raman spectra, and then later I analysed the data and we each cowrote the now published manuscript.

During my time at the University of Otago and the University of Cape Town I hadn’t worked alongside undergraduate interns, so this was one of the new experiences I encountered at the Smithsonian. I had undertaken (and later, worked with) summer studentships at the University of Otago, and looking back there are many similarities. A dedicated research project, a short and fixed time frame, an opportunity to work with professional researchers. I can’t value these experiences highly enough, and if the student is particularly motivated, like Charlotte, then the work can be recognised as a formal publication. How good is that!

France, C. A. M., Thomas, D. B., Doney, C. R. and Madden, O. 2014. FT-Raman spectroscopy as a method for screening collagen diagenesis in bone. Journal of Archaeological Science 42: 346–355


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.

Spectroscopy of fossil bone 2: Infrared Splitting Factor

Calculating the infrared crystallinity index, modified from Shemesh (1990).

Infrared spectroscopy is probably the second most commonly used spectroscopic technique applied to fossils. Infrared spectroscopy, or mid-infrared spectroscopy if you want to be picky, is fairly simple in principal: a range of infrared wavelengths are directed at a sample, and the wavelengths that are NOT absorbed are collated at a detector. Hence, an infrared spectrum tells you about the wavelengths that are absorbed by your sample, where specific wavelengths are absorbed by specific vibrational modes (see #Spectroscopy of fossil bone Part 1). In other words, an infrared spectrum gives you the molecular components in your sample: it’s a chemical fingerprint.

Focussing in on an individual band within an infrared spectrum can give you even more chemical data. The position of a band can tell you about the average chemical environment that a vibrational mode occurs in, and the width of a band tells you about the variation across the chemical environments. For example, the phosphate molecule has a vibrational mode where all of the oxygens stretch away from the central phosphorus in sync (=symmetric stretch). If this phosphate is in a mineral lattice, then it will be surrounded by neighbouring ions. Minerals are made up of repeated unit cells, so we have lots of phosphate in the mineral lattice, all eager to symmetrically stretch. If the ions surrounding phosphate are all the same, and the phosphate is in the same lattice site throughout the mineral, then the symmetric stretch will occur within a consistent environment. If you substitute half of the surrounding ions with a different type of ion, then you will change the chemical environment surrounding some of the phosphate. Symmetric stretching will now occur in multiple environments, which we can interpret from the position and width of spectral bands.

This is how infrared spectroscopy is applied to fossils. Infrared spectroscopy makes good use of non-degenerate vibrational modes. We describe a vibrational mode by the type of movement it makes, but there is room for interpretation. Consider the antisymmetric bending of phosphate (see #Spectroscopy of fossil bone Part 1). Phosphate is an anion with a central phosphorus atom bound to four oxygen atoms. During an antisymmetric bend, two of the oxygen atoms are pulled in one direction, while the other two are pulled in another. The chemical environments encountered by each oxygen pair during an antisymmetric bend might differ, and then change again during the next bend. Think of the bending oxygens as feelers that are probing their chemical environment. The chemical environment encountered during an antisymmetric bend will affect the position and width of that vibrational mode, and each stretching geometry of the vibrational mode is recorded as a band on an infrared spectrum. This means that the set of spectral bands produced by the antisymmetric bending of phosphate within bone mineral can tell you about the chemical structure of fossil bone. The variation between the antisymmetic bending bands will be smallest when the mineral has a homogeneous chemical composition, with variation being larger when the mineral is more chemically variable. Shemesh (1990) developed a crystallinity index (CIFTIR) from the antisymmetric bending bands: higher CIFTIR values indicate a more homogenous crystal lattice. Natural bone mineral straight from the animal is chemically heterogeneous and has CIFTIR values less than 3.8. Bone is chemically altered during burial however, and the heterogeneous chemistry is replaced with a standardised, geologically robust chemistry. Hence, altered bone has a high CIFTIR value (Shemesh 1990). The crystallinity index developed by Shemesh (1990) has seen wide use, and is also referred to as the Infrared Splitting Factor of fossil bone.

Shemesh, A. 1990. Crystallinity and diagenesis of sedimentary apatites. Geochimica et Cosmichimica Acta 54: 2433–2438.

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