Using light to describe the ancient world

Archive for January, 2011


I have just found out that I will be presenting a talk at NIR2011 in Cape Town (13-20 May). NIR2011 is an international conference that will showcase all of the latest research in the field of near infrared spectroscopy, including unusual applications like fossils.  I am going to be talking about Near infrared spectroscopy of fossil antelope bone from South Africa. Find out more from the conference website (, or you can email Professor Marena Manley ( or Ms Deidre Cloete ( for more information, including registration details.

Near infrared spectroscopy of fossil antelope bone from South Africa

Daniel B. Thomas­, Cushla M. McGoverin and Anusuya Chinsamy­

Introduction: Raw materials for constructing bone are supplied by food, water and air, and are ultimately sourced from the external environment. Bone chemistry consequently records the living environment of an animal, and such information may persist after death and into the fossil record. Chemical alteration of bone during burial (diagenesis) may erase the life history signals from fossil bone, however, severely reducing the analytical utility of fossil material. We have used NIR spectroscopy to screen fossil bone for signs of diagenetic alteration.

Materials and methods: Fossil antelope bone from the Western Cape of South Africa was studied using two instruments: 1) large sample volume (bulk) measurements were collected using a Spectrum IdentiCheck FT-NIR, and 2) low sample volume (hyperspectral, chemical imaging) measurements were collected using a sisuChema short wave infrared imaging system.

Results and discussion: Bulk NIR spectroscopy indicated that secondary minerals had been deposited within the fossil bone. Fossils from different sites could be distinguished by secondary mineralogy, where bone from coastal Swartklip 1 featured calcium carbonate (calcite), and inland Elandsfontein Main exhibited clay mineral infill. Hyperspectral NIR spectroscopy allowed the distribution of secondary minerals to be mapped. Both clay and calcite were concentrated in cancellous spaces, as the residue of deeply infiltrating pore water. Water is the primary agent of diagenetic alteration, and NIR data indicated that the fossil antelope bones had been saturated.

Conclusions: NIR spectroscopy provided evidence for ancient pore water movement through fossil antelope bone. Different secondary minerals had accumulated inside bones from different sites, and informed of different palaeoenvironments. We found NIR spectroscopy to be a useful tool when screening fossil bone for evidence of diagenetic alteration.

Novelty statement: NIR data collected from fossil antelope bone provided evidence for ancient pore water suffusion. NIR represents a new, non-destructive tool for studying bone diagenesis.

Summary statement: Large and small sample volume near infrared spectroscopic data were collected from fossil antelope bone. Fossils from different sites were distinguished by secondary mineral deposits, which were found concentrated in cancellous spaces. Secondary minerals represent residues of ancient pore waters that would have suffused the fossil bones.


#Recent news: Snap frozen

The skin of Ötzi the Iceman is in excellent condition according to Raman spectroscopy. Image from Wikipedia (details below).

Ötzi the Iceman was a man of distinction during the Copper Age; a possible village chief. He may have been powerful, but Ötzi was mortal, and was likely felled by a flint arrowhead. Buried in the Ötztal Alps, Ötzi was preserved for 5300 years and discovered in 1991. Ötzi has since been exhumed and has provided a window into European culture and civilisation during the Copper Age. A recent study by Janko and colleagues (2010) examined Ötzi using Atomic force microscopy and Raman spectroscopy. Raman spectra of skin gave remarkable results: the collagen in Ötzi’s 5300 year old skin is completely intact. Collagen in living animals is made by twisting chains of smaller molecules around each other to form a helix. Collagen rapidly degrades after death (geologically speaking), and the helix unwinds and the chains break apart. Raman spectroscopy showed that Ötzi’s collagen retains its helical conformation – Ötzi was snap frozen, which is why he is still with us today.

Janko M, Zink A, Gigler AM, Heckl WM, Stark RW (2010) Nanostructure and mechanics of mummified type I collagen from the 5300-year-old Tyrolean Iceman. Proceedings of the Royal Society B: Biological Sciences. doi:10.1098/rspb.2010.0377

Image: Iceman

#Recent news: Martian fossils

Possible Martian fossil… but not if Raman spectroscopy has anything to say about it . Image from Nasa (details below).

The search for extra terrestrial life is not all peering through telescopes looking for someone peering back – it also involves looking for alien fossils. It was during this noble quest that astrobiologists (=space paleontologists) became incredibly excited when they studied the surface of a Martian meteorite found in Allan Hills, Antarctica (meteorite ALH84001). David McKay and colleagues (1996) reported possible organic structures in ALH84001, a gift from our celestial neighbour. Debate ensued, and Raman spectroscopy was eventually called in to help clarify whether ALH84001 showed signs of life. Steele and colleagues (2007) analysed regions of the meteorite that contained carbonate, an anion mineralised in both sea shells and volcanoes. The variation in carbonate chemistry within ALH84001, as indicated by Raman Spectroscopy, was consistent with carbonate minerals in one million year old volcanic rocks from Svalbard. This meant that the Martian meteorite structures could have been made by simple rock-melting, and didn’t have to have an alien fossil explanation. Way to ruin a party, Raman spectroscopy.

McKay DS, Gibson Jr EK, Thomas-Keprta KL, Vali H, Romanek CS, Clemett SJ, Chillier XDF, Maechling CR, Zare RN (1996) Search for past life on Mars: possible relic biogenic activity in Martian meteorite ALH84001. Science 273:924-930.

Steele A, Fries MD, Amundsen HEF, Mysen BO, Fogel ML, Schweizer M, Boctor NZ (2007) Comprehensive imaging and Raman spectroscopy of carbonate globules from Martian meteorite ALH 84001 and a terrestrial analogue from Svalbard. Meteoritics and Planetary Science 42:1549-1566.

Image: ALH84001

Infrared light

Please allow me to very briefly introduce near infrared light. Everything you see is reflecting visible light, and you see different colours because the reflected light has different wavelengths. The light that your eyes detect can be described as a wave radiating out from the surface you are looking at. Imagine a perfectly flat pond, and imagine yourself dropping a pebble into the middle of that pond. The pebble causes ripples to move from the place where you dropped the stone, towards the edge of the pond. Now, let the ripples travel for a few seconds… and stop. Hold your pond as a mental photograph. You should see a set of ripples, forming rings around each other on the surface of the pond. The distance between each ring is a wavelength.

This is an example for how light works. Light is reflecting off of everything you look at, in ripples, and the wavelengths of these ripples are between 380 nm and 700 nm (nanometre). A nanometre is a millionth of a millimetre – so the light ripples are really close together. Blue light has a wavelength of 380 nm, and red light has a wavelength of 700 nm. Wavelengths higher than 700 nm are known as infrared light. “Infra” means “below”, and infrared is actually less energetic than red light.Infrared light is incredibly important to spectroscopy, and we will get to this in due time. One thing I do want to show is the infrared light in our daily lives. Many remote controls send signals using infrared light. We can’t see infrared, but some digital cameras can. Below are two images of a remote, and in one of them a button is being pressed. The camera that I used to take these photos has detected the normally “invisible” infrared light as a shade of pink. Please try this at home.

Infrared light from a remote can be seen using a digital camera

X-ray fluorescence spectroscopy

Handheld x-ray fluorescence spectrometer analysing a fossil antelope horn

X-ray fluorescence (XRF) spectroscopy is a venerable technique that has been applied to countless rocks, but very few fossils. Traditional XRF is destructive, and fossils are precious, but the information provided is incredibly valuable – x-ray fluorescence spectroscopy tells us about the elemental makeup of a sample. X-rays are high energy photons with wavelengths far too short for our eyes to detect. X-rays energise atoms wherever they meet them, boosting the energy of orbiting electrons. The effect is only temporary though, and the bolstered electrons eventually find themselves at unsustainable heights. The electrons shed their newfound energy to return to their original places within the atom. Energy is shed from an electron in the form of an x-ray, and the released x-rays have energies characteristic of the atom they are released from. The goal of XRF spectroscopy (or Energy Dispersive Spectroscopy; EDS) is to collect the x-rays released from atoms, because they can be used to identify the element they have come from.

A new form of XRF spectroscopy has become available very, very recently. Instead of destroying a specimen and analysing it in a lab, samples can be analysed using a handheld device. Looking like pieces from a futuristic arsenal, handheld XRF spectrometers are ideal for describing elemental compositions of fossils because… they are completely non-destructive!

Raman Spectroscopy

Apatite crystal irradiated by a laser for Raman Spectroscopy

The first technique I want to introduce is one of the latest spectroscopic technologies used to study fossils. Raman Spectroscopy involves shining (irradiating) a sample with a very gentle laser and measuring the light that is scattered away. I discussed scattering below, but here we need to be a bit more technical. Laser light is a stream of photons with a single, specific wavelength (energy). The light from your green laser pointer probably has a wavelength of 532 nm. When a photon from a laser encounters a sample it may be reflected, absorbed or scattered (see The Light Fantastic). On very rare occasions, the light will undergo a special type of scattering called inelastic scattering: the photon will cause molecular-level movement in the sample. There are costs to everything, however, and the movement might drain a small amount of energy from the interacting photon. Occasionally, the movement will bolster the photon, and it will actually be more energetic after the interaction. The photons are then scattered away after the energy changes. The goal of Raman spectroscopy is to collect these inelastically scattered photons, because the small changes in energy are directly related to the type of molecu

lar-level movement they helped sponsor. Molecular movement (vibrations) are highly specific, and only certain types of molecule can perform certain vibrations. What is more, the exact structural arrangement of molecules controls the amount of energy taken from, or donated to, inelastically scattered photons. The net result is that Raman Spectroscopy can be used to explore the chemistry and physical structure of a substance. The best part, Raman Spectroscopy is completely non-destructive.

The Light Fantastic

Light from the setting sun is reflected from the glass and absorbed by the wine. The sun would soon set, but scattered light from beyond the horizon would allow us to see the wine glass for a while longer.

Spectroscopy is a science built on three key interactions between light and matter. Light is interacting with all of the matter you can see through the process of Reflection. Light from a source, possibly the sun, reflects from your shirt, and is detected by your eye. Not all of the light survives the encounter though – your shirt greedily traps some of the light in the process of Absorption. Sunlight is made up of a mixture of photons with different energies. Different photons have different wavelengths, which we see as different colours when they are separated apart, but appear as white light when all mixed together. White light adopts colour when it interacts with a pigment; some light is absorbed by the pigment and removed from the white light mixture. When you look at your shirt, the colour you see is the result of absorbed photons and reflected light. What you may not notice while looking at your shirt, but you can test, is the process of Scattering. Try this: sit in a room without the lights on, on an overcast day, with the curtains or blinds pulled. The first thing you will notice is all of the little points of light coming into the room – the corners of the curtains, light from under the door. The second thing you will notice is that you can see the objects in the room, even though they are not being directly lit. This is because light coming into the room is being scattered off all of the surfaces. Consider scattering a sort of recycled reflection (scattering is also known as diffuse reflection).

So there you have it – three interactions between matter and light that form a basis for studying the ancient world. I would highly recommend the Wikipedia pages on Reflection, Absorption and Scattering for more details.


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