Biochemistry Research Group
The Biochemistry Research Group leverages biochemical and isotopic techniques to characterize and understand the past. Our research themes range from tracking the trade of aromatics and characterizing the diet of past fauna and hominins to reconstructing past climates and understanding the role of domesticated animals in the development of early complex societies. To answer these research questions, we detect various biomolecules from archaeological and environmental materials:
- Lipid residues in archaeological pottery and determining their carbon stable isotope ratios.
- Secondary metabolites such as terpenes and alkaloids in archaeological artefacts.
- Faecal biomarkers from soil and lake biogeochemical records.
- Carbon and nitrogen stable isotope ratios of single amino acids from both ancient and modern samples.
These analyses are possible thanks to our wet chemistry facilities including a clean laboratory and instrumentation such as a Gas Chromatography Mass Spectrometer (Agilent 8890), a liquid chromatography system with a triple quad mass spectrometer (Shimadzu LCMS 8050), and a Gas Chromatography Combustion Isotope Ratio Mass Spectrometer (elementar isoprime visION System). We collaborate with the Stable Isotope and Archaeoinformatics groups to obtain radiocarbon ages, bulk isotope values, and infrared spectra of bones and organic residues. To answer archaeological questions with the large volumes of data generated in our lab, we apply univariate and multivariate statistical analyses. We use R programming for statistical computing and data visualization.
Biomolecular data can be a rich source of information about the past when coupled with other lines of evidence. For this reason, we also gather information about the matrix and provenience in which the samples were found, and their association with other archaeological samples and sources of information. Archaeological contextual information is also important for establishing age chronologies and assessing the degree biochemical records may have undergone degradation.
To help us improving interpretations of biochemical data from ancient samples, we produce data from controlled laboratory studies to understand how biomolecules are degraded and synthesized under different environmental conditions. We also engage in studies of modern biota to generate baseline data and comprehend how organisms respond to rapid environmental change.
Globalizing Scents and Spices: Tracking the trade of aromatics through biomolecular archaeology
Project leader: Barbara Huber
Long-distance trade of commodities played a major role in forming political structures and transferring socio-cultural practices among the major centres of ancient civilization in the Old World. Some of the most high-value products that moved along ancient trade routes, were not substantive, calorie-laden foods, but resins, powders, extracts, and obscure dried plant components that nonetheless packed substantial flavour and aroma. Not only did these substances possess the ability to transform cuisines and to scent people and spaces, they also often played significant roles in economic, cultural, medicinal and ritual contexts.
This project aims to investigate the global dimensions of the dispersal of these so-called spices throughout Asia and East Africa. This includes not only the spread of goods, but also the transfer of socio-cultural practices associated with their use. To trace these often “invisible” substances in the archaeological record, Barbara seeks to study organic remains of them by using biochemical and biomolecular approaches. These draw on chromatography, mass spectrometry, and bioinformatics to recover and analyze rare molecules (secondary metabolites, lipids and proteins) preserved within ancient ‘scent archives’. These archives can be archaeological artefacts, such as incense burners, perfume flasks, cooking pots or storage vessels found at different sites along ancient trade routes. Other features such as dental calculus on teeth, mummified remains, or floor surfaces can also function as archives. The most important property of such scent archives is that they contain the remains of aromatic substances used in the past that can be sampled, analysed and identified. Through this approach, the individual aromatics can be pinpointed at places of origin, at the different stops of the trade routes and at destinations, allowing not only to reconstruct ancient trade, exchange systems distribution ranges of these goods, but also to study past networks and connectivity.
Exploring funerary and embalming rituals in ancient Egypt through metabolic profiling
Project leader: Barbara Huber
Ancient Egyptian mummification involved a cocktail of plant mixtures, colloquially referred to as embalming fluids, specifically used to preserve the body as well as human organs for the afterlife. The embalming rituals were practiced throughout most of Egyptian history and continued through the Roman period, making them a characteristic feature of Egyptian funerary archaeology. However, the ingredients used in this process remain poorly identified and historian and archaeologists have widely discussed their identities.
In this study, we integrate complementary approaches in metabolomic profiling and lipid residue analysis to shed light on the identity of the ingredients used during mummification. Furthermore, practices involved in body treatment and preparing the deceased for the afterlife, which are reported in ancient texts, can be complemented by the actual substances and remedies used to preserve these organs.
Understanding the role of domesticated animals in the development of early complex societies in Northwestern South Asia
Project leader: Kalyan Sekhar Chakraborty
The Secondary Products Revolution model argues that the human exploitation of secondary animal products (milk, wool, and traction) was one of the crucial factors behind the development of complex societies during the Holocene. This research aims to test this model in the context of South Asia, one of the most populous parts of the world today. This project aims to understand human-animal interactions in this part of the world and how they may have shaped the social, political, and economic aspects of the Indus Civilization, the earliest civilization of South Asia. This research aims to investigate how animals were raised, how they were exchanged, and how they were consumed, and then contextualize it with the archaeological observation of cultural, political, and social changes.
It is now well established that animal herding and utilization of domesticated animals for both dietary and non-dietary purposes were crucial for the Indus people. However, the role of pastoralism and increased consumption of secondary animal products in the development and expansion of this civilization is still understudied. In this project, using δ 13C of carbonate, δ 13C fingerprinting of amino acids, and Sr isotope ratios of animal and human remains and δ 13CFA of ceramic residues, we aim to investigate the intensification of herding practices and the intensification of the consumption of primary and secondary animal products during pre-Indus, Indus, and post-Indus periods. The majority of the settlements under study are already dated; however, as part of this project, all of these settlements will be dated using AMS and Bayesian statistics, to develop a secure radiometric chronology.
The Archaeological and Ecological Applications of Faecal Biomarker Analysis
Project leader: Yiming Wang
Human impact on the planet is often associated with European colonialism and the Industrial Revolution, but a too narrow focus on these recent changes overlooks how humans have transformed ecosystems in the past, especially in relation to our history of domesticating animals and cultivating the land. Searching for major thresholds of human impacts on earth systems in the past has been hindered by a lack of suitable markers of anthropogenic change that can be applied globally. This project seeks to develop a method in which to extract and measure human and animal faecal from archaeological and natural sediment accumulations to understand shifts in human presence and environmental impacts.
Faecal biomarker profiles specific to humans and different animals are being increasingly used to determine the presence of different taxa and their palaeodemography through time. Faeces contain unique biochemical tracers that may preserve for millennia under favourable conditions.
However, to gain better understanding of preservation processes, faecal biomarker transport, and landscape level variation in faecal accumulation it is essential to develop modern baselines for specific geographical, climatic, and anthropological contexts. Much of this baseline work is yet to be done in an anthropological context meaning that interpretations of such proxies in the archaeological record remain tentative. We are currently developing innovative baseline studies in a variety of climatic settings, in close collaboration with a number of diverse local communities, in order to determine how faecal biomarkers are preserved and presented across modern anthropogenic, particularly pastoral, landscapes.
In tandem, we are also beginning to initiate a series of projects that investigate the demographics of wild and domesticated animals in response to human hunting and domestication using faecal biomarkers (bile acids and stanols) recovered from well-dated sediments. We will be applying these methodologies in areas where active archaeological research is being undertaken by the Department of Archaeology, and where we have solid existing contextual knowledge in relation to the presence of hunter-gatherers, pastoralists, and farmers in different regions through time. However, we will also expand our scope based on sample availability and the regional and temporal interests of members of the Department at any given time.
Impacts of Climate Change and Resource Stress on Arctic Ecosystems
Project leader: Thomas Larsen
Climate change is having obvious and severe impacts in the Polar Regions. The Arctic is currently warming at more than double the rate of other parts of the globe, causing unprecedented change to the region’s ocean environment. The Arctic Ocean’s ecosystem is especially sensitive to warming because of its reliance on sea ice, from the algae that grow on its underside to large predatory mammals that hunt and live on its surface. In addition, top predators in Arctic ecosystems are increasingly affected by exposure to organic contaminants from anthropogenic sources.
The project LOMVIA, which is jointly supported by Germany’s Federal Ministry of Education and Research (BMBF) and the UK’s Natural Environment Research Council (NERC), studies the effect of climate change and exposure to organic contaminants on two congeneric seabird species breeding in Iceland. Iceland is a key region for understanding anthropogenic impacts in Arctic regions because it hosts both temperate and arctic species that are under threat by the increasingly changeable environment and exposure to contaminants. By employing biochemical methods and telemetry, the study compares the foraging areas and the food base of the true arctic Brünnich’s guillemot (Uria lomvia) and the boreal/temperate Common guillemot (Uria aalge) to test 1) whether interspecies competition for food resources are exacerbating the effect of climate change, and 2) whether the seabirds’ wintering strategies affect accumulation of ‘forever’ chemicals such as perfluoroalkyl substances (PFASs).
Studying the Effects of Catastrophic Events on Marine Biogeochemical and Ecological Processes
Project leader: Yiming Wang
Extreme events caused by global change are increasingly affecting the ocean’s biogeochemical cycling and ecosystem functioning. However, our current understanding of how biogeochemical disruptions affect trophodynamics is limited because of the inherent challenges of studying food web responses to rapid habitat disturbances. In this project, we seized a unique opportunity to understand how specialists and generalists in a hydrothermal vent area respond and adapt to drastic biogeochemical disruptions. In 2016, the shallow hydrothermal vents at Kueishantao (KST) Island in East China Sea were hit by the two consecutive extreme events, an earthquake and a typhoon, causing a near vent shutdown for two years.
By using multiple geochemical tracers, we aim to study for the first-time temporal variability of the vent system, its responses to large geophysical and meteorological perturbations, and the effects on local biogeochemical and ecological processes. Also, we also use stable isotope (d13C, d 15N, d 34S) as well as compound specific isotope ratios of individual amino acids to understand the benthic food web shifts after the extreme disturbances. The KST catastrophic events are analogous to man-made perturbations on coastal and deep-sea ecosystems, e.g., by industry discharges, mineral mining, or seabed dredging. Hence, quantifying their impact on marine ecosystems might shed light on the management of such anthropogenic perturbations.
Palaeoclimate & Palaeoceanography
Paleoclimate and Environment Changes in Tropic Monsoon Regions
Project leader: Yiming Wang
Addressing and anticipating future tropical monsoon changes under continuing global warming is of critical importance for the food security and socioeconomic well-being of 40% of the world’s population. Despite the far-reaching consequences, predicting tropical monsoon behaviour under climate warming scenarios remains a key challenge for both global and regional climate models. This knowledge gap limits our understanding of the extent to which ISM intensity responds to rapidly changing climatic factors—such as rising sea surface temperature (SST), elevated atmospheric greenhouse gas (GHG) concentrations, changing vegetation cover, and decreasing ice sheets and sea ice cover—and their interactive dynamics in a warming climate.
We use compound specific stable isotope analyses of terrestrial biomarkers, namely leaf wax n-alkanes from marine sediments, to reconstruct changes in monsoon rainfall and vegetation in East Africa and South Asia. In addition, we also employ a suite of inorganic and organic proxies, which include foraminifera Mg/Ca ratio and d18O, and alkenone unsaturation index UK’37 to reconstruct past oceanographic conditions (e.g. sea surface temperature and salinity changes) in Indian Ocean, which exert important influence on the adjacent continental hydroclimate. Besides generating new climate records, we have also collaborated with climate modelers to gain deeper understanding of mechanism controlling climatic and oceanographic conditions. These paleoclimate reconstructions also provide regional climatic and environmental context for the information relating to demography and human social changes.
Past Resource Use
Human History on the Island of Madagascar
Project leader: Sean Hixon
Madagascar, a large island sitting off the southeastern coast of the African continent, is a critical location for exploring past human migrations, adaptations to climate change, and anthropogenic influences on the environment. Today, the country faces some of the most severe threats in terms of species extinctions, habitat degradation, and economic stability anywhere in the world.
While much is still unclear, it now seems that humans arrived to Madagascar from various places in the past, with early arrivals from Africa being joined by seafaring populations with links as far off as southeast Asia. This diverse history of occupation has resulted in a rich linguistic and cultural heritage, as well as the arrival of different forms of land use and species.
This project uses combinations of field research (e.g., survey, excavation, sediment coring, and modern plant and animal specimen collection) and laboratory analysis (e.g., microfossil inventories and chemical analyses of plants and bones) to investigate human history on the island of Madagascar, including the following longstanding.
- When did humans arrive on Madagascar? How did different pulses of arrival vary in terms of their material culture and economic strategies?
- What forms of land use and which species did different groups of humans bring with them?
- How did different human groups, from hunter-gatherers to herders, from village dweller to town residents, respond to climate changes documented over the course of the Holocene?
- How did different human groups, in turn, impact the environments of Madagascar? How have these activities left legacies for communities living in the region today?
The project ties together a diversity of laboratories within the Department of Archaeology and beyond and involves close cooperation with Malagasy collaborators in the context of fieldwork and policy implications.
Stable Isotope Ratios of Amino Acids as Proxies for Trophic Position and Dietary Sources
Project leader: Thomas Larsen
Understanding the diets of hominids and fauna, and the environments in which they lived, has long been a goal of paleoanthropological and archaeological research. While conventional methods such as examination of past plant and animal remains, and bulk stable isotope analysis of archaeological tissue remains have yielded important insights into past diets, the dietary interpretations associated with these methods are sometimes uncertain. These uncertainties can in part be overcome with stable isotope analysis of single amino acids, the building blocks of proteins. Research has shown that their carbon and nitrogen stable isotope ratios can inform of trophic level and dietary sources independent of environmental conditions. Amino acids are valuable dietary markers because each of them has unique metabolic functions and properties. The multitude of data derived from amino acids can therefore be placed into statistical models to explore new resolution of food sources.
While the strengths of applying stable isotope ratios of amino acids for palaeodietary reconstruction are compelling, we are cognisant of the methodological challenges and interpretive knowledge gaps associated with this method. For this reason, our group takes an active interest in understanding how factors such as food preparation, digestive and metabolic processes, and diet quality affect isotope ratios of amino acids. We are also committed to making the method less cost prohibitive and improve data comparability across labs. To learn more about these topics, read our recently published guide on how best to use stable isotope ratios of amino acids: https://doi.org/10.1093/biosci/biac028