A paper recently published in Nature details the application of a new field known as palaeometabolomics to reconstruct ancient African environments and track how they changed over time.
Modern medicine can learn a great deal about our health and lifestyle from a blood test, because blood contains traces of metabolites derived from the food we eat, as well as indicators of liver and kidney function and how effectively metabolic waste is disposed of.
But what if we could perform blood tests on archaic animals and human ancestors? Over time, this could tell us not only what they ate, but how their diets changed, which in turn reveals changes in rainfall, temperature, vegetation cover — forest versus savannah — and the species that were hunted and consumed.
Mass Spectrometry — how scientists identify molecules from deep time. Mass spectrometry is one of the most powerful analytical techniques in modern science, allowing researchers to identify and quantify molecules with extraordinary precision — even when only trace amounts are present.Creationists, who are wedded by dogma to a 6,000–10,000-year timeframe for the entire history of life on Earth, are often baffled by the idea of recovering biochemical information from fossilised bones that are millions of years old. As usual, this misunderstanding is likely to be exploited. They will misrepresent the science, claim that “blood” has been recovered intact, insist that the fossils must therefore be young, and declare this to be “proof” of a young Earth. All of this rests on a failure to understand what bone is, how it forms, and what has actually been recovered from fossils.
In simple terms, the process works by converting molecules into electrically charged particles (ions) and then sorting them according to their mass and electrical charge. Because every molecule has a characteristic mass, this produces a distinctive “fingerprint” that allows it to be identified unambiguously.
In palaeometabolomics, metabolites extracted from fossil bone are first carefully isolated and purified to eliminate modern contamination. These molecules are then ionised — often using gentle techniques such as electrospray ionisation — so that they fragment as little as possible. The ions are accelerated through an electric or magnetic field, and their flight time or trajectory is measured. Lighter ions move differently from heavier ones, allowing the instrument to determine their mass-to-charge ratios with extreme accuracy.
The resulting mass spectrum is a plot showing the relative abundance of ions at different mass-to-charge values. This spectrum can be compared with extensive reference libraries containing millions of known molecular signatures. Even complex mixtures can be disentangled, and closely related molecules distinguished from one another.
Crucially, mass spectrometry does not “see” blood, tissues, or cells. It detects stable chemical structures that can survive long after biological material itself has decayed. The technique is routinely used in archaeology, forensic science, environmental monitoring, and planetary science — including the analysis of organic compounds in meteorites and Martian samples — so its application to fossil bone is a natural extension, not an extraordinary claim.
What makes palaeometabolomics particularly powerful is that metabolites reflect real biological processes: diet, physiology, stress, and environment. When these chemical signals are found in fossils whose geological ages are independently constrained by stratigraphy and radiometric dating, they add yet another, entirely independent line of evidence for deep time and evolutionary change — and one that creationist narratives have no coherent way to accommodate.
Bone is built by specialised cells called osteoblasts, which lay down a matrix that later becomes mineralised as crystals of calcium phosphate are deposited. Blood is supplied through a network of tiny capillaries forming the Haversian canal system. As bone forms, microscopic spaces — only a few microns in diameter — remain within the mineral matrix. These spaces are large enough for small molecules from the blood to diffuse into, but far too small for bacteria to enter.
The result is that trace metabolites become trapped within the bone as it mineralises and eventually fossilises. What is extracted is not blood itself, but the chemical remnants of metabolites that were present in the bloodstream at the time of death. Using sophisticated chemical extraction techniques and mass spectrometry, these molecules can be identified and analysed. This is the essence of palaeometabolomics, and it is already yielding a remarkable amount of information about life in deep prehistory.
For anyone who understands how science works — and how independent lines of evidence converge on a single, coherent account of the past — it will come as no surprise that biochemical data, palaeontology, geology, climatology, and evolutionary biology all tell the same story. Evidence produced by the same historical processes is internally consistent and mutually reinforcing.
It will also come as no surprise that none of this evidence supports the creation myths of Bronze Age storytellers, grounded as they were in ignorance, guesswork, and evidence-free cultural assumptions borrowed from neighbouring societies and bent to justify land claims, power, land theft, and genocide.
This new science is described for a general audience in an article in The Conversation by Timothy G. Bromage, lead author of the paper in Nature. His article is reproduced here under a Creative Commons licence and reformatted for stylistic consistency.
Life in fossil bones: what we can learn from tiny traces of ancient blood chemicals
Antelope bone fragment in rock from the 3-million-year-old early human site, Makapansgaat (South Africa). Its bone marrow cavity is filled with a white carbonate-rich precipitate.
Credit: Timothy Bromage and Bin Hu,
NYU College of Dentistry
NYU College of Dentistry
For more specific information, another kind of blood test looks at the tiny traces of chemical processes taking place at tissue, organ, and even cellular levels. This fine-scale kind of test, metabolomics, studies metabolites – the by-products of metabolism (the body’s way of producing energy and recycling chemicals).
You’d never think this kind of test could be done for animals that lived millions of years ago. But what was very recently science fiction is now reality: it’s called “palaeometabolomics”.
Why would anyone want to know about the metabolites of long-dead creatures?
Metabolites are a way for scientists like me (a biological anthropologist) to learn more about the health, diet, environment and evolution of those creatures – including early humans.
What makes this possible is the way bones are formed: by special cells secreting a soft matrix – mainly collagen – that later crystallises and hardens into a porous material.
Metabolites in the blood that leak from blood vessels during bone formation are so tiny that they become trapped inside the bone matrix (the material that makes up bone) as it hardens. The spaces where they are trapped are so small (nanometre in scale) that bacteria and fungi, which are much bigger, can’t always get in there. Not even in a million years. And because bone mineral structures at these fine scales contain minute traces of water, metabolites are preserved there in fossils.
Studying the metabolites in animal fossils has given us a new way to discover more about the environment at sites where early humans evolved.
My colleagues and I looked at rodent fossils from Olduvai Gorge in Tanzania (about 1.8 million to 1.7 million years old); elephant tooth fossil material from the Chiwondo Beds in Malawi (2.4 million years old); and an antelope bone fossil from Makapansgat in South Africa (about 3 million years old). Fossils of ancient relatives of humans (species of Australopithecus, Paranthropus, and early Homo) have also been found at these sites.
For 100 years, scientists have devised methods for reconstructing the environment that early humans lived in and adapted to. Until now, these methods depended mainly upon geological clues and the kinds of animal and plant fossils found at a site. Now, by performing palaeometabolomics – especially by analysing the chemical traces left in animal bones by the plants that the animals ate – we have established a “molecular ecological” approach for describing ancient habitats.
This new method can add very specific information to other kinds of reconstructions. The metabolites allow us to describe soil pH, minimum and maximum rainfall and temperature, the type of tree cover, and elevations above sea level of plants.
We also made a surprising finding about the relationship between soil and living things.
How to give a fossil a blood test
To perform palaeometabolomics, we established a method to dissolve bits of bone no larger than a pea in a tube containing weak acid. The acid is strong enough to slowly pass the mineral into a solution, but weak enough not to degrade the metabolites. This take several days. We then let the large proteins sink to the bottom of the tube and spin it at high speed in a centrifuge, which leaves the smallest and lightest molecules at the top. We inject the metabolite “soup” into a mass spectrometer, a piece of equipment designed to measure the weights of all small molecule compounds, and refer these to a library of known masses. That’s how we identify the metabolites.
The ones generated within the body – “endogenous” metabolites – offer clues about the health and well-being of an animal. That’s interesting enough, but it’s not the full picture.
All living organisms produce metabolites, including plants. Plants also have metabolisms reflecting their physiological adaptations to the environment. If an animal eats a plant, metabolites of that plant circulate through the animal’s bloodstream and are also trapped at developing bone surfaces. These are called “exogenous” metabolites, and they tell us about the diet of the animal.
What was just interesting now becomes remarkable, because if we can identify the plant that a metabolite came from, we should also be able to reconstruct the environment the plant was adapted to.
What the body says about the bigger picture
The endogenous metabolites we identified from our fossils depict a variety of normal mammalian biological functions and disease states. The exogenous metabolites provide evidence of the environment in the distant past.
For instance, some of our fossil samples had a metabolite derived from the parasite that causes sleeping sickness in humans after a bite from an infected tsetse fly. Wild animals are tsetse fly reservoirs for the parasite. Tsetse flies have very specific environmental conditions, so that helped our reconstructions.
We also identified plant metabolites which implied that the Tanzanian and South African sites were wetter than they are now. Minimum temperatures were warmer, and the landscape contained more forest shade. It seems to have been a mixed, seasonally dry and wet tropical habitat. The reconstructed conditions of the Malawi site indicate a wetter environment, also with wet and dry seasons.
Reading the soil
There was one particularly interesting surprise.
Going into this study, we assumed that metabolites from ancient soils surrounding the fossils – known as palaeosols – should be considered contaminants and be disregarded from our analyses. But when we analysed metabolites of modern animals of the same fossil species living near the sites, whose bones never touched the soil, we found that both the modern and fossil animals shared large percentages of the palaeosol metabolites.
This means that the palaeosol reflects the lives of all the organisms living there. Once plants and animals live on that soil, their metabolites become a part of the soil matrix. The animals and the soil are completely connected by shared metabolites, which represent the flow of materials that sustain the habitat. They are not contaminants to be disregarded.
Our biomolecular approach – using metabolites from fossil bones and teeth as a way to reconstruct ancient environments – is a new one. It might one day make it possible to describe past habitats as precisely as we can describe modern ones.
Timothy G. Bromage, Professor, New York UniversityThis article is republished from The Conversation under a Creative Commons license. Read the original article.
As so often, what creationists will seize upon is not what the research actually shows, but a caricature of it. No blood has been recovered, no cells have survived for millions of years, and no laws of chemistry have been suspended. What palaeometabolomics recovers are stable molecular fragments — metabolites — that were trapped within the mineral structure of bone as it formed, protected from biological decay by their physical isolation and later by fossilisation. To describe this as “soft tissue” is simply false, and to pretend otherwise is to rely on deliberate misrepresentation rather than evidence.
This is not a new pattern. Creationists have been making the same claims for decades whenever proteins, pigments, or other molecular remnants are detected in fossils. Each time, the explanation is the same and well understood: chemistry does not abruptly cease to exist after death, and some molecular structures are far more stable than creationist rhetoric allows. None of these discoveries challenges radiometric dating, stratigraphy, or the geological timescale; all of them are entirely consistent with it.
What palaeometabolomics adds is yet another independent line of evidence — one that connects biology, chemistry, geology, and climate science into a single, coherent picture of life in deep time. When metabolites extracted from fossil bones align with known shifts in African climate, vegetation, and faunal turnover, they reinforce what the fossil record, isotopic studies, sedimentology, and evolutionary theory have been telling us for over a century.
For creationism, this is yet another problem with no solution. A young-Earth narrative cannot accommodate molecular signals that track environmental change across millions of years, nor can it explain why independent methods converge on the same history of life and climate. Science, by contrast, does exactly what it is supposed to do: it predicts, tests, corrects, and integrates evidence into an ever more detailed and internally consistent account of the past — one that continues to grow stronger the more closely it is examined.
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