🧪 This new method allows us to redraw life from several million years ago

The architecture of fossilized bones possesses a chemical memory. Researchers have indeed identified molecular traces within them linked to the daily lives of animals that disappeared several million years ago. This discovery reveals a new method for tracing the health and diet of animals, as well as the climate of the world in which they lived.

Until now, the study of fossils largely relied on the morphological analysis of skeletons, or in some cases on the analysis of DNA fragments. An international team, however, has worked on a radically different approach: the analysis of the metabolome. This refers to the complete set of molecules produced by the internal functioning of an organism.


Their work, published in Nature, demonstrates that these biochemical signatures preserved in bone structure can survive on timescales well exceeding a million years and reveal previously unknown information. While DNA allows us to trace family trees, metabolites can represent how the organism functioned during its life.

The Biochemical Black Box of Bone

Contrary to its solid appearance, bone is a dynamic and vascularized tissue. Its dense network of micro-channels, which initially serves blood irrigation and nutrient exchange, ultimately acts as a natural trap. During bone growth, metabolites circulating in the blood (residues from digestive, hormonal, or immune processes) can infiltrate and lodge in this microporous matrix, which offers remarkable protection against degradation.

A team of researchers was able to verify this hypothesis by analyzing mouse bones using mass spectrometry, a technique capable of identifying molecules by their weight. The analysis revealed the presence of nearly 2200 metabolites, which validated the principle. The scientists then applied this same method to fossils of animals (rodents, antelope, elephant) from major sites for human evolution in southern and eastern Africa, dating from 1.3 to 3 million years ago.

The analysis revealed a large quantity of molecules linked to normal biological functions, such as amino acid or vitamin metabolism. The presence of certain specific markers even made it possible to determine that some fossil individuals were females. This preservation therefore offers a biochemical snapshot of the animal's physiological state at the time of its death, information that was previously inaccessible.

Stories of Disease and Environment

The study took an unexpected step by identifying an infectious pathology in a squirrel bone dating back 1.8 million years. The researchers indeed succeeded in isolating a metabolite specific to the parasite Trypanosoma brucei, the agent of sleeping sickness transmitted by the tsetse fly. They also detected the chemical signature of the host animal's inflammatory response. This is one of the oldest direct pieces of evidence of an infectious disease preserved in fossil remains.

The discovery of plant-origin metabolites also delivered equally valuable secrets about vanished landscapes. The chemistry of the squirrel bone contained traces of aloe, a plant with strict ecological requirements regarding temperature, precipitation, and sunlight. The presence of these molecules not only indicates the animal's diet but allows for deducing the climatic conditions of its habitat with remarkable precision.

These environmental reconstructions, deduced from fossil biochemistry, corroborate existing geological data. Thanks to this information, a representation of ancient eastern Africa, warmer and considerably more humid than today, with landscapes of light forests, grasslands, and marshy areas, is gradually taking shape. Each fossil thus becomes a rich data point for mapping past ecosystems.

To go further: What is Metabolomics?

Metabolomics is the science that studies the complete set of small molecules, called metabolites, present in an organism at a given moment. These molecules are the final or intermediate products of the countless chemical reactions that sustain life, such as the transformation of food into energy or the synthesis of hormones. Their profile, the metabolome, is a unique and dynamic fingerprint.

Unlike the genome, which is stable and inherited, the metabolome reflects the constant interaction between genes and the environment. It changes in response to diet, stress, illness, or exposure to toxins. In modern medicine, the analysis of the metabolome is thus used for early diagnosis or understanding the mechanisms of certain pathologies.

Its application to archaeology and paleontology, as in this study, is recent and bold. It involves searching for these ephemeral biochemical signatures in ancient materials. Their detection proves that they can fossilize under favorable conditions, thus allowing us to obtain information about the physiology and living conditions of now-extinct organisms.