The bad news for creationism continues unabated. Scientists led by Professor Timothy G. Bromage of the Department of Molecular Pathobiology at New York University College of Dentistry have developed a technique that opens an entirely new window onto the deep past. By analysing metabolites preserved in fossilised bones, the researchers are able to extract detailed biological and environmental information from animals that lived between 1.3 and 3 million years ago.
The team have published their findings in Nature, describing a method that pushes palaeobiology well beyond traditional morphology-based reconstruction.
The significance of this technique lies in its ability to reconstruct ancient environments with remarkable precision. From the chemical signatures locked within fossil bone, researchers can infer temperature, soil conditions, rainfall patterns, vegetation, and even the presence of parasites. The resulting picture is one of ecosystems changing over time, with animals adapting in step with shifting environments — exactly what evolutionary theory predicts, and wholly incompatible with the childish notion of magical creation a few thousand years ago or a recent biological reset caused by a genocidal flood.
How Fossil Chemistry Reveals Ancient Lives and Landscapes. What Are Metabolites?A news release from New York University explains the research and its wider significance for palaeobiology.
Metabolites are small molecules produced by normal biological processes. They include compounds involved in digestion, energy use, immune responses, and interactions with parasites and microbes. Unlike DNA or proteins, which are fragile and degrade relatively quickly, some metabolites — or their chemically altered remnants — are remarkably robust.
Crucially, metabolites reflect how an organism actually lived: what it ate, the stresses it experienced, the diseases it carried, and the environment it inhabited. In modern biology they are widely used to diagnose illness or reconstruct diet. What is new is their application to deep time.
How Can Chemical Signals Survive for Millions of Years?
Fossilisation is not a simple process of organic material being destroyed and replaced. Bone, in particular, creates a stable microenvironment. Its mineral matrix, rich in hydroxyapatite, can bind organic molecules and shield them from complete decay. In some cases, metabolites become chemically altered yet still retain diagnostic structures that modern analytical techniques can identify.
Using advanced mass spectrometry, scientists can detect these molecular traces at extremely low concentrations. What survives is not intact tissue, but a chemically readable record — rather like smoke residues revealing the existence and nature of a long-extinguished fire.
This directly undermines the common claim that “nothing organic can last millions of years”. The chemistry shows otherwise.
What This Reveals That Fossil Bones Alone Cannot
Traditional palaeontology relies largely on morphology: the size, shape, and structure of bones and teeth. That tells us what an animal looked like. Metabolite analysis tells us how it lived.
From fossil chemistry, researchers can infer:
- Dietary patterns and nutritional stress
- Seasonal or long-term environmental change
- Soil chemistry and vegetation types
- Parasite infections and physiological stress
In other words, fossils are no longer silent stones. They carry biochemical evidence of ecosystems, climates, and life histories that cannot be read from anatomy alone.
Together, these chemical signatures build a picture of animals embedded in changing environments over deep time — precisely what evolutionary theory predicts, and exactly what sudden creation or global catastrophe models fail to explain.
Metabolic Analyses of Animal Fossils Helps Scientists Reconstruct Million-Year-Old Environments
Thanks to molecules trapped in ancient animal bones, fossils tell stories about disease, diet, and climate
For the first time, scientists have analyzed metabolism-related molecules from the fossilized bones of animals that lived 1.3 to 3 million years ago, revealing insights about both the animals and their environments.
The metabolic clues about the animals’ health and diets enabled researchers to paint a picture of their living conditions, including the temperature, soil, rainfall, and vegetation. Their findings, published in Nature, reveal warmer and wetter conditions across these environments compared to today.
Studying metabolites—the molecules produced and used in digestion and other chemical processes in the body—can provide information about health and disease, as well as external factors like diet and environmental exposures. While metabolomic research is increasingly used in studying human diseases and drugs, few scientists have explored its use in understanding the prehistoric world. Instead, they largely focus on DNA in fossils, which is primarily used for establishing genetic relationships.
I’ve always had an interest in metabolism, including the metabolic rate of bone, and wanted to know if it would be possible to apply metabolomics to fossils to study early life. It turns out that bone, including fossilized bone, is filled with metabolites.
Professor Timothy Bromage, lead author
College of Dentistry
New York University
New York, USA.
Measuring metabolites
In recent years, paleontologists learned that collagen—the protein that provides structure to bones, skin, and connective tissues—can be preserved in ancient bones, including those of dinosaurs.
I thought, if collagen is preserved in a fossil bone, then maybe other biomolecules are protected in the bone microenvironment as well.
Professor Timothy Bromage.
The surfaces of bones are spongy and surrounded by capillary networks, exchanging oxygen and nutrients between the bloodstream and bones. Bromage suspected that, during the process of bone formation, metabolites carried in the bloodstream enter and become trapped in tiny niches in bone.
To test this idea, the researchers employed mass spectrometry, an analytical technique that converts molecules into ions, to see if they could extract metabolites from bone. Using present-day mouse bones, they identified nearly 2,200 metabolites for analysis. The technology also analyzed proteins to detect collagen in some bone samples.
Antelope bone fragment in rock from the 3-million-year-old early human site, Makapansgaat (South Africa).
A polarized light image of fossilized antelope bone showing intact collagen (scale: 1 mm across)
Credit: Timothy Bromage and Bin Hu, NYU Dentistry
The researchers then turned to animal fossils from 1.3 million to 3 million years ago, collected for prior paleontological research at sites in Tanzania, Malawi, and South Africa where early humans lived. Focusing on species with living counterparts near these sites today, they used the same analytical methods on fossilized bone fragments from rodents (mouse, ground squirrel, gerbil), as well as an antelope, pig, and elephant.
The analyses yielded thousands of metabolites, many of which were shared with modern-day animals.
The stories fossils tell
Many of the metabolites the researchers found in the fossilized bones represent normal biological functions, including the metabolism of amino acids, carbohydrates, and vitamins and minerals. Several pointed to genes associated with estrogen, suggesting that some of the animals were female.
Other metabolites revealed the animals’ response to disease. Notably, in the bone of a 1.8-million-year-old ground squirrel from the Olduvai Gorge in Tanzania, the researchers found evidence that the squirrel was infected with a parasitic disease known as sleeping sickness in humans, caused by the Trypanosoma brucei parasite and transmitted by the tsetse fly.
What we discovered in the bone of the squirrel is a metabolite that is unique to the biology of that parasite, which releases the metabolite into the bloodstream of its host. We also saw the squirrel’s metabolomic anti-inflammatory response, presumably due to the parasite.
Professor Timothy Bromage.
The researchers could also deduce what plants the animals ate. While data on plant metabolites are much more limited than those documented in human and animal health, they identified the metabolites of several regionally specific plants, including forms of aloe and asparagus.What that means is that, in the case of the squirrel, it nibbled on aloe and took those metabolites into its own bloodstream. Because the environmental conditions of aloe are very specific, we now know more about the temperature, rainfall, soil conditions, and tree canopy, essentially reconstructing the squirrel’s environment. We can build a story around each of the animals.
Professor Timothy Bromage.
The reconstructed environments corroborate what other research has found about these settings millions of years ago—for instance, that the Olduvai Gorge Bed in Tanzania was freshwater woodland and grassland, while the Olduvai Gorge Upper Bed was dry woodlands and marsh. Across all of the sites studied, the conditions in which the animals lived were wetter and warmer than the regions are today.
Olduvai Gorge, an important archaeological site in northern Tanzania.Credit: Friedemann Schrenk, Goethe University and Senckenberg Research Institute and Natural History Museum
Using metabolic analyses to study fossils may enable us to reconstruct the environment of the prehistoric world with a new level of detail, as though we were field ecologists in a natural environment today.
Professor Timothy Bromage.
Additional study authors include Bin Hu, Sher Poudel, Sasan Rabieh, and Shoshana Yakar of NYU College of Dentistry; Thomas Neubert, Christopher Lawrence de Jesus, and Hediye Erdjument-Bromage of NYU Grossman School of Medicine; and collaborators from the National Museum of Natural History (France), Senkenberg Research Institute and Natural History Museum (Germany), Goethe University (Germany), McGill University (Canada), Hessisches Landesmuseum Darmstadt (Germany), Rutgers University (US), Eurofins Lancaster Laboratories (US), and Université de Bordeaux (France.) The research was supported by The Leakey Foundation, with additional support for the technology used in the analyses by the National Institutes of Health (1S10 OD026989-01, S10 OD023659, and S10 RR027990).
Publication:
This work represents yet another line of evidence that creationism has no credible way to absorb. It does not merely rely on radiometric dating, stratigraphy, or evolutionary inference — all of which creationists habitually attempt to dismiss — but on the internal chemical records preserved within fossil bones themselves. These records independently encode ecological continuity, environmental change, and biological response over spans of time that simply do not exist in any creationist chronology.
Most damaging of all is the internal consistency of the picture that emerges. The metabolic signatures recovered from these fossils align with what geology, palaeoclimatology, ecology, and evolutionary biology have been saying for decades. They show animals responding to shifting climates, changing vegetation, and long-term environmental pressures in ways that make sense only in a deep-time framework. There is no sign of a recent global catastrophe, no chemical scrambling of ecosystems, and no trace of the kind of biological reset demanded by flood mythology.
Creationism depends on the hope that gaps in knowledge might yet provide room to manoeuvre. But advances like this do the opposite: they close gaps. They add independent, converging evidence that does not rely on bones alone, or dates alone, or assumptions about ancestry, but on the direct chemical residues of ancient life itself. Each new technique tightens the net, leaving less and less space for supernatural explanations to hide.
Far from rescuing creationism, discoveries like this underline its central problem: it is not merely contradicted by one branch of science, but by all of them simultaneously. Fossil chemistry now joins anatomy, genetics, geology, climatology, and archaeology in telling the same story — one of a dynamic, ancient, evolving biosphere that bears no resemblance whatsoever to the simplistic myths of magical creation a few thousand years ago.
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