Your thesis focuses on protein-based methods for identifying ancient human fossils. What are the links between chemistry and human evolution ?
When you excavate an archaeological site, you find lots of different things. We then have to determine what they are. In the case of bones, the main challenge is to identify them. I work with bones dating from the Pleistocene, a geological period that stretches from 2.58 million years ago to 11 700 years ago. More specifically, I'm working on skeletal remains dating from - 45 000 to - 35 000 years ago. These are highly fragmented bones, making it difficult to identify them by their morphology : are they from an animal ? a human ? We can answer these questions using molecular methods.
There aren't many laboratories that can do this kind of analysis. So we receive archaeological remains from all over Europe. The bones may come from Germany, Italy, Portugal... We use different methods to identify them, but the objective is always the same : to extract proteomic material and compare it with an online database to identify it. We try to be as minimally invasive as possible and as accurate as possible.
Your method involves using proteins to carry out such work..
I've been working for a long time on ancient DNA analysis, which to date is the most widely recognized method for analyzing archaeological bone material. Despite its advantages, it has certain limitations, as DNA generally degrades faster than proteins over the centuries. When we find a bone fragment, the DNA molecules are also fragmented. If we're lucky, we only have a few micrograms of DNA to work with. Sometimes, there's nothing left. We need to develop methods that are mainly suitable for degraded proteins, i.e. proteins that are highly destroyed, and for very small quantities of them. I opted for protein extraction because it allows us to go further back in time.
How does it work ?
In the method we're trying to improve with my thesis supervisor, Prof. Jean-Jacques Hublin, there are two stages. First, we have to extract the proteins. This takes around three days for two hundred bone samples. Then, we carry out a spectrometric and computer analysis. This only takes a day. This analysis gives us the protein sequence. Based on this analysis, we can assign species by comparison with an online database. This is taxonomic identification, which can take from a week to a month depending on the number of specimens analyzed. One of the advantages of this method is its relative speed.
Do you take a very broad view of the history of mankind, or rather a chemist's view, closer to the process of fossil identification ?
I'd say chemistry is the tool, and understanding human evolution is the answer. My first curiosity concerned science and chemistry. I was fascinated by the challenge of extracting as much precise information as possible from degraded materials. My discipline accompanies the progress of science and our understanding of human history. Although my point of view is primarily that of chemistry, it's always stimulating to see how it influences our knowledge of evolution.
How does it feel to hold a human bone fossil in your hand ?
When I started out, I only worked with human DNA. At first, of course, I had mixed feelings about bone remains. But with time, you get used to it and know how to handle it. It really is a unique feeling to think that such small fragments of bone from organisms that have been dead for millennia could be of use to mankind. I think the most shocking thing for me was when we had children, and I could tell just by the size of the bone. Again, I tried to focus on the benefits of this analysis.
What difficulties do you encounter ?
There are two main difficulties in my work. The first, and most important, is the quality and quantity of fossil materials. These are not inexhaustible materials, which is a real challenge for us. When you find a Neanderthal bone, you are of course very careful about how you treat it and how much you use for your analyses. The major argument in favor of our technique is that we only use 5 mg of the bone. We try to have a minimal impact. The other point of difficulty concerns the accuracy of the database we use for species identification. In this database, certain proteomes, i.e. all the proteins in a cell, may not be available, particularly for extinct species such as woolly rhinoceroses and mammoths.
Do you have a memory that would have been the starting point for your interest in your discipline ?
In Greece, we have the Foundation for Research and Technology. It has a laboratory dedicated to ancient DNA, which is linked to the University of Crete where I studied. A few years ago, they organized a science festival. My friends and I went there to see the exhibits and their type of research. I discovered this ancient DNA laboratory which interested me, and I got in touch with people working there. I contacted Prof. Kafetzopoulos and did my undergraduate thesis there. That's how I discovered that this field existed and that chemistry could be useful in it. With a background in chemistry, you can work in every conceivable field, even those you'd never thought of. For me, it's an added challenge to work with highly degraded bones and develop appropriate methods for analyzing this type of material.
You travel to different countries for your studies, have you noticed any differences in the way you work ?
I started my studies in Greece, where I'm from, and then worked in Denmark, Germany, the Netherlands and now France. There are always differences, depending on the material and issues involved in each project. But each one is just as fascinating to me. What's more, working with different people from a wide range of disciplinary backgrounds has enabled me to see the distinct but complementary perspectives of our research.
Would you say that your research has changed your perception of our species ?
One of the questions we ask ourselves is when and why our direct ancestors left Africa, and what their behavior was like. The past holds many mysteries, and it's by solving them that we can understand the present and imagine the future. This can be very disappointing at times, but it can also be unique. It can provide answers we didn't even know existed. I think that's the great thing about science. You can sometimes sense it, but you never know what's going to come next, and that's sometimes surprising.
Dorothea Mylopotamitaki is a doctoral student in the Paleoanthropology team at the Collège de France's Centre interdisciplinaire de recherche en biologie, under the supervision of Prof. Jean-Jacques Hublin, Paleoanthropology Chair, and Dr. Frido Welker (University of Copenhagen). Her thesis is entitled " MS/MS-Based Bone CHIP Species Identification ".
Photos © Patrick Imbert
Interview by Aurèle Méthivier
