Refuting Creationism - Microbes That Create Life From Non-Life

Mud volcano

Fig. 9: Schematic of microbial succession and biogeochemical processes in serpentinite mud at the Mariana forearc.
This schematic depicts lipid biomarker transitions from pelagic sediment communities to extremophiles adapted to high pH and redox conditions in serpentinite mud. The Mariana forearc biosphere is fueled by alkaline serpentinization fluids enriched in H₂, CH₄, DIC, and organic acids, sustaining specialized microbial communities. Lipid and stable carbon isotope data reveal a shift from relict methanogenic archaea, likely engaged in hydrogenotrophic methanogenesis, to a later ANME-SRB community mediating anaerobic oxidation of methane (AOM). Changes in substrate availability likely drove this transition. Distinct lipid signatures, including unsaturated diethers, acyclic GDGTs, and ether-based glycolipids, highlight adaptations to pH stress, phosphate limitation, and fluctuating redox conditions. The presence of in-situ branched GDGTs suggests previously uncharacterized bacterial communities persisting in these ultra-oligotrophic conditions. The Mariana forearc serpentinite biosphere, shaped by episodic fluid flow and substrate shifts, provides insights into deep-sea subsurface habitability. DIC = dissolved inorganic carbon, ANME anaerobic methanotrophic archaea, SRB sulfate-reducing bacteria, AOM anaerobic oxidation of methane, GDGT glycerol dialkyl glycerol tetraether.

Kumawat, P., Albers, E., Bach, W. et al. (2025).

Fats provide clues to life at its limits in the deep sea

Researchers at MARUM – Bremen University’s Centre for Marine Environmental Sciences – have made a discovery, just published open access in the journal Communications Earth & Environment, which, properly understood, should make depressing reading for creationists.

They have found living organisms both on and within the ocean floor, surviving in conditions where normal life would be impossible. These microorganisms inhabit mud volcanoes with a pH of 14, metabolising hydrogen and carbon to form methane by drawing energy from minerals in the surrounding rock. In other words, they live entirely without oxygen and with almost no organic matter, synthesising all they need from inorganic sources.

Informed creationists will recognise that these organisms directly refute their frequent assertion that life cannot arise from non-life — because producing life from non-life is precisely what these microorganisms are doing.

This also contradicts the biblical claim that all living things were created for the benefit of humans, since there is no conceivable way these organisms could serve any human purpose. Of course, to be fair, the authors of the Bible were completely ignorant of microorganisms, deep-ocean mud volcanoes, and chemosynthetic metabolism. They could only attempt to explain the larger creatures that lived in the limited region around their homes in the Canaanite hills.

And, as any informed creationist should also understand, these are exactly the sort of extreme conditions that biologists believe may have fostered the emergence of the earliest living organisms during the origin of life on Earth — once again undermining any claim that abiogenesis is impossible.

Background^ Chemosynthetic Extremophiles. Chemosynthetic extremophiles are microorganisms that survive in environments too hostile for most known life. Instead of relying on sunlight for energy (as photosynthetic organisms do), they extract energy from chemical reactions involving inorganic compounds such as hydrogen, methane, ammonia, or sulphides.

These organisms thrive in extreme conditions — high pressure, intense heat or cold, high salinity, or extreme acidity or alkalinity — where oxygen and organic nutrients are scarce or absent. They are commonly found around deep-sea hydrothermal vents, cold seeps, and mud volcanoes, as well as in acidic mines and alkaline lakes.

Chemosynthesis typically involves oxidising inorganic molecules (e.g. hydrogen sulphide, hydrogen, or iron) to obtain energy, which is then used to convert carbon dioxide or methane into organic compounds. This allows entire ecosystems — such as those around black smokers on the ocean floor — to exist entirely independent of sunlight.

These extremophiles are of major interest to biologists and astrobiologists because they demonstrate that life can originate and persist in conditions once thought uninhabitable. Their existence supports hypotheses that early life on Earth, and potentially elsewhere in the universe, may have begun in similar environments where energy was derived chemically rather than from sunlight.

The research is explained in a Universität Bremen news item.

Fats provide clues to life at its limits in the deep sea

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Researchers use lipid biomarkers to reveal survival strategies in extreme ecosystems

Diverse life forms exist on and within the ocean floor. These primarily consist of microbes, tiny organisms that can cope with extreme environmental conditions. These include high pressures and salinities, as well as extreme pH values and a limited supply of nutrients. A team of researchers has now been able to detect microbial life in two newly discovered mud volcanoes with very high pH values. Their findings have been published in the professional journal Communications Earth & Environment.

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Blue serpentinite mud from a newly discovered mud volcano in a gravity core. The samples have been studied by a team in order to decipher the survival strategies of microorganisms.

Photo: SO292/2 Expedition Science Party

In their study, first author Palash Kumawat of the Geosciences Department at the University of Bremen and his colleagues used lipid biomarker analyses to decipher the survival strategies of the microbes in this harsh ecosystem. The high pH value of 12 here is especially challenging for deep-sea life; This is one of the highest known value so far in ecosystems. In order to detect life at all, the researchers had to resort to special methods of trace analysis. In this situation, the detection of DNA can be ineffectual where there is a low number of living cells.

But we were able to detect fats. With the help of these biomarkers we were able to obtain insights into the survival strategies of methane- and sulfate-metabolizing microbes in this extreme environment.

Palash Kumawat, first author
Faculty of Geosciences
University of Bremen
Bremen, Germany.

Microbial communities metabolize carbon in the deep sea and thereby contribute to the global carbon cycle. However, the communities that the team describe in the publication draws its energy from minerals within rocks and gases such as carbon dioxide and hydrogen to produce methane, for example, an important greenhouse gas. These processes initially take place independently of the ocean above. The lipids also provide clues to the age of the microorganisms. If the cellular biomolecules are intact, they represent a living or recently dead community. If they are not intact, they are geomolecules, which means that they are fossil communities from the past. According to Kumawat, the combination of isotopes and the lipid biomarkers indicates that multiple microbial communities now live in this inhospitable habitat and have lived there in the past.

This distinction helps us when working in areas with extremely low biomass and nutrient deficiency.

Palash Kumawat.

Dr. Florence Schubotz, organic geochemist at MARUM – Center for Marine Environmental Sciences at the University of Bremen and co-author of the study, adds:

What is fascinating about these findings is that life under these extreme conditions, such as high pH and low organic carbon concentrations is even possible. Until now, the presence of methane-producing microorganisms in this system has been presumed, but could not be directly confirmed. Furthermore, it is simply exciting to obtain insights into such a microbial habitat because we suspect that primordial life could have originated at precisely such sites.

Dr. Florence Schubotz, co-author
MARUM – Center for Marine Environmental Sciences
University of Bremen
Bremen, Germany.

The samples for the study come from a sediment core that was retrieved by the Research Vessel Sonne in 2022 during Expedition SO 292/2. Not only were the scientists able to discover the previously unknown mud volcanoes of the Mariana forearc during this cruise, but also to sample them.
The samples were obtained as part of the Cluster of Excellence “The Ocean Floor – Earth's Uncharted Interface.” Palash Kumawat and his colleagues are now planning to cultivate organisms in an incubator to find out more about their nutrient preferences in inhospitable environments.

Publication:

Kumawat, P., Albers, E., Bach, W. et al.
Biomarker evidence of a serpentinite chemosynthetic biosphere at the Mariana forearc. Commun Earth Environ 6, 659 (2025). https://doi.org/10.1038/s43247-025-02667-6

Abstract
Present-day serpentinization systems, such as that at the Mariana forearc, are prominent sources of reduced volatiles, including molecular hydrogen (H₂) and methane (CH₄), and are considered analogs for chemosynthetic ecosystems on early Earth. However, seepage of serpentinization fluids through mud volcanoes at the Mariana forearc seafloor is defined by high pH, and nutrient scarcity, creating challenging conditions for microbial life. We present geochemical and lipid biomarker evidence for a subsurface biosphere shaped by episodic substrate availability, highlighting microbial persistence across steep geochemical gradients within serpentinite mud. Light stable carbon isotope compositions from diagnostic lipids reveal a temporal shift from hydrogenotrophic methanogenesis to sulfate-dependent anaerobic methane oxidation. Membrane adaptations, including unsaturated diether, acyclic and branched tetraether, and ether-based isoprenoidal and non-isoprenoidal glycosidic lipids, reflect microbial strategies for coping with this extreme environment. Our findings establish the Mariana forearc as a unique serpentinite-hosted biosphere, where life operates at the fringes of habitability.

Introduction
The subseafloor biosphere is estimated to harbor up to 15% of the global biomass¹. Recent advances in deep biosphere research have improved our understanding of the distribution and diversity of microbial life in the rocky oceanic crust, especially around hydrothermal vents^2,3. This subseafloor biosphere has to adapt to limited carbon and nutrient availability, accompanied by harsh environmental conditions such as high temperature and pressure, elevated salinity, and/or extreme pH levels⁴. Serpentinization of mantle rocks by seawater can generate high levels of H₂^5,6 that, in turn, drives the abiotic reduction of carbon to form CH₄ and other organic compounds⁷, which can be oxidized by chemosynthetic organisms^8,9,10, forming the foundation for a serpentinite biosphere¹¹. The type locality for such a serpentinite biosphere is the Lost City hydrothermal vent field near the Mid-Atlantic Ridge, where hydrothermal fluids fuel microbial communities in active and inactive vent structures¹². Methanogenic archaea there are found in active brucite-calcite vents, whereas older carbonate chimneys host a syntropic consortium of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that perform the anaerobic oxidation of methane (AOM)^13,14.

The process of serpentinization takes place in a range of geotectonic settings, including rifted continental margins, mid-oceanic ridges, transform faults, and convergent margins. Among the latter, the forearc of the Mariana subduction system is of particular interest because it provides access to serpentinization products from within an active subduction zone. There, dewatering of the subducting Pacific Plate leads to serpentinization of the mantle wedge of the overriding Philippine Sea Plate. Faults reaching 10–25 km deep into the forearc allow serpentinite, together with fluids derived from the subducting slab, to buoyantly rise and form large ‘serpentinite mud volcanoes’ on the seafloor^15,16 (Fig. 1a, c). Fluids venting from the mud volcanoes are cold (<3.5 °C), hyperalkaline (pH up to 12.6), and enriched in H₂ and CH₄ (both up to ~1 mM)^17,18 and slab-derived sulfate (SO₄²⁻; up to 28 mM)¹⁹. These fluids are also enriched in short-chain organic acids like acetate (0.04 mM) and formate (0.1 mM), contributing ~20–30% of the dissolved organic carbon (DOC)²⁰, and in methanol (0.03 mM)^20,21. The δ¹³C of CH₄ (−37‰ to 2‰), acetate (−8‰), formate (4.8‰) and methanol (2.3‰) point to their abiotic formation^17,21. While these serpentinization fluids sustain chemosynthetic life at the seafloor^22,23, the functioning and extent of the chemosynthetic microbial biosphere below the seafloor remains largely unknown. Cell counts in the serpentinite mud are variable, but overall low (101 to 106 cells cm−3)^20,24, presumably because of the high pH and intermittent fluid seepage^13,16. Extremophilic archaea are believed to perform AOM as inferred from the detection of phospholipid-derived diphytanyl diethers and reduced sulfur species in the formation fluids18. Metabolic transcripts for denitrification and AOM were interpreted as evidence for nitrate-dependent AOM within the serpentinite mud volcanoes²⁴. Although AOM is considered thermodynamically favorable here^19,25, direct evidence for AOM and its associated microorganisms is still lacking. Methanogenesis is a common metabolic strategy in serpentinization systems¹³, but since CH₄ formation at the Mariana forearc is dominantly abiotic, the extent of microbial methanogenesis remains uncharacterized.

Fig. 1: Study area and geological context of serpentinite mud volcanism in the Mariana subduction system.

a Bathymetry map of the Mariana subduction system showing the incoming Pacific Plate, the overriding Philippine Sea Plate, the Mariana Trench, and a subset of the known serpentinite mud volcanoes on the forearc seafloor. Stars mark the locations of the Pacman and Subetbia mud volcanoes investigated in this study. Bathymetry from GEBCO Compilation Group¹²⁵. b Bathymetry map showing the Pacman mud volcano and the location of gravity core GeoB24917-1 retrieved during expedition SO292/2. Bathymetric data collected during expedition SO292/2²⁶. c Schematic of serpentinite mud volcano formation, following serpentinization of the mantle wedge by slab-derived fluids, formation of H₂ and CH₄, and the rise of serpentinite mud and fluids through deep-seated faults towards the seafloor.

This study documents AOM coupled to sulfate reduction as a key metabolic process in the Mariana forearc, indicating the importance of methane cycling for the indigenous microbial community. Our findings also provide evidence of relict methanogenesis in the serpentinite mud, where its temporal distribution is possibly controlled by variable substrate availability. We present a comprehensive lipid biomarker and isotopic record from the Pacman and Subetbia mud volcanoes, providing insights into the habitability and survival strategies of extremophilic chemosynthetic life in this serpentinite biosphere.

Kumawat, P., Albers, E., Bach, W. et al.
Biomarker evidence of a serpentinite chemosynthetic biosphere at the Mariana forearc. Commun Earth Environ 6, 659 (2025). https://doi.org/10.1038/s43247-025-02667-6

Copyright: © 2025 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Creationists often insist that “life cannot come from non-life,” claiming that the origin of life through natural processes — abiogenesis — is impossible. Yet these microorganisms thriving deep beneath the ocean floor undermine that argument completely. They demonstrate that life does not require sunlight, oxygen, or organic nutrients. Instead, it can sustain itself entirely through chemical reactions involving inorganic matter, precisely the kind of chemistry that would have been available on the early Earth long before photosynthesis or complex ecosystems evolved.

These microbes survive by harnessing energy from the oxidation of minerals and gases such as hydrogen and carbon, producing methane as a by-product. In doing so, they show that biological systems can indeed emerge and persist using nothing more than inorganic chemistry and environmental energy sources. If life can continue this way today — in conditions strikingly similar to those thought to exist on the early Earth — then it is perfectly reasonable to infer that the same processes could once have given rise to life itself.

Creationists’ claim that life from non-life violates natural law is based on a false analogy with modern life, which relies on pre-existing organic systems. But these extremophiles illustrate that the boundary between “non-living” chemistry and “living” biochemistry is not a rigid wall — it is a continuum. The metabolic reactions that sustain these organisms are direct chemical extensions of the mineral and geochemical reactions occurring in their surroundings. Life in such places does not appear magically; it emerges naturally from the physical and chemical conditions of its environment.

Far from being a problem for evolutionary science, discoveries like this one strengthen the case for a natural origin of life. They show that even today, the chemistry of life and the chemistry of rocks remain intimately connected. To deny that such chemistry could, under the right conditions, cross the threshold into life is to deny the very evidence creationists claim to seek — evidence that life can, and demonstrably does, arise from the non-living world through the workings of natural law.

Sadly, the same creationists who continue to parrot the 'no life from non-life' fallacy won't have understood a word of that and will continue to make proven false claims.

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Refuting Creationism - Diverging Sloth Genomes - Just As The TOE Predicts

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[right caption]

Deforested genomes: scientists find signs of environmental degradation in the genomes of the endangered Maned Sloths - Leibniz Institute for Zoo and Wildlife Research

The discovery fits seamlessly within the framework of Darwinian evolution. Two once-connected populations became isolated and exposed to different ecological conditions, followed their own evolutionary paths. Over time, their genomes accumulated distinct mutations reflecting adaptation, genetic drift, and local environmental pressures. The result is two clearly defined species whose divergence can be explained entirely by natural processes acting over generations — a textbook demonstration of evolution in action.

Yet this same process now drives both species along a far more perilous trajectory. As their habitats continue to shrink and fragment, their populations are losing genetic diversity and becoming increasingly inbred. Evolution has no foresight or purpose; it cannot plan for the future or reverse the consequences of environmental destruction. The very mechanism that once diversified life on Earth can, under relentless human pressure, just as readily lead to extinction.

There is no sign of “intelligent design” in this grim reality — only the blind, natural workings of selection, drift, and chance operating within a degraded environment. If a designer were guiding life towards some higher purpose, it would hardly produce a situation where its own creations are being driven to extinction by the ecological collapse of their habitats. The plight of the maned sloths stands as a vivid reminder that life’s diversity, beauty, and tragedy arise not from supernatural intent, but from the impersonal and unyielding logic of evolution.

As world leaders prepare for COP30 in Brazil, the message from the maned sloths’ genomes could not be clearer: conservation must be guided by evolutionary science and ecological understanding, not by comforting myths of divine oversight. Only by recognising the true, natural processes that shape life can we hope to protect what remains of it.

Refuting Creationism - Another of Those 'Living Fossils' For Creationists To Misrepresent

Adult marine shell-boring spionid polychaete.

Vasily Radishevsky/
Far Eastern Branch of the Russian Academy of Sciences

Spionid traces on fossilized bivalve shells.

Javier Ortega-Hernandez/Harvard University.

Half-billion-year-old parasite still threatens shellfish | UCR News | UC Riverside

It’s Coelacanth time for creationist disinformers again.

Hilariously, I’ve known creationists claim that the 'fact' that coelacanths haven’t changed for 200 million years somehow proves the “evilutionists” are wrong and that Earth is only 6,000–10,000 years old. How they managed to examine the genome of a 200-million-year-old fossil remains a mystery, but DNA appears to play no part in a creationist’s definition of evolution.

So, for an alternative fallacious argument, here’s an even older fossil that’s still around today, apparently in much the same form as it was almost half a billion years ago. It’s a parasitic worm that attacks oysters. The details have just been published in the journal iScience by scientists led by University of California, Riverside palaeobiologist Karma Nanglu, with colleagues from Harvard.

The parasitic, soft-bodied bristle worm belongs to a group called the spionids. It’s common in today’s oceans and feeds on the shells of mussels and oysters, leaving a characteristic question mark-shaped track in their shells. Their parasitism doesn’t kill the shellfish but probably shortens their lifespan.

Refuting Creationism - 300,000 Years Of Stone Technology In Africa - Over 2 Million Years Before 'Creation Week'

Fig. 1: Map of Turkana Basin with the Namorotukunan Archeological Site and timeline of currently known events in the Plio-Pleistocene.

a Geographical context of the Koobi Fora Formation (red stripes), the paleontological collection area 40 (green square), and the location of the site of Namorotukunan (black dot); [map produced Natural Earth and NOAAA ETOPO 202295]; b Stratigraphic context of the Koobi Fora Formation highlighting members and key volcanic ash marker levels, yellow bars refer to the age of archeological horizons (tephrostratigraphy after McDougall et al.⁹⁶); c A chronology of key Plio-Pleistocene hominins from the East African Rift System (EARS)^11,74,97,98 d A chronology and key localities associated with hominin lithic technology^3,6,12 (images of Nyayanga provided by E. Finestone; images of Lomekwi and BD1 based on 3D models; artifact images are for representation and not to scale) and the investigations at Namorotukunan: red arrows represent the artifact levels in the archeological excavations (photos DRB), and colored circles (lettered A-G) represent geologic sections investigated to develop a synthetic stratigraphic column (presented in Figs. 2 and 3).

Braun, D.R., Palcu Rolier, D.V., Advokaat, E.L. et al (2025)

Stone Tools Through Generations: 300,000 Years of Human Technology | Media Relations | The George Washington University

The story of our origins is written in the ground of Africa. It is real, tangible, and objective — a record that doesn’t rely on belief or interpretation, but on physical evidence left behind by our ancient ancestors. A fresh chapter of that record has just been described in a new open-access paper in Nature Communications, authored by an international team of palaeoanthropologists led by Professor David R. Braun of the Center for the Advanced Study of Human Paleobiology at George Washington University, and the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

By comparison, the origins narrative found in Genesis reflects the worldview and assumptions of people who believed the Earth was small, flat, and covered by a solid dome. It is astonishing that, even today, some treat that ancient cosmology as a more reliable account of human history than the rich and expanding fossil and archaeological record in Africa. Yet such individuals continue to seek influence over policy, law, morality, and social institutions, grounding their authority not in evidence, but in pre-scientific tradition — a worldview formed long before the wheel, let alone modern science.

Refuting Creationism - Evolution By LOSS of Genetic Information

Dysdera tilosensis

Credit: Marc Domènech and Pedro Oromí

Dysdera catalonica

Dysdera tilosensis

Fotografies: Marc Domènech and Pedro Oromí

Deciphering the mechanisms of genome size evolution - Current events - University of Barcelona

For years, creationists have confidently assured anyone who’ll listen that evolution can’t possibly work, because losing genetic material is always disastrous — rather like claiming a book can’t be edited without collapsing into meaningless gibberish. Yet nature has an unhelpful habit of ignoring such pronouncements and getting on with things regardless. And now, a tiny spider living quietly in the Canary Islands has delivered another inconvenient data point: it’s been shedding DNA at a remarkable rate, and doing perfectly well in the process.

Researchers led by Julio Rozas and Sara Guirao, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) at the University of Barcelona, have shown that a spider endemic to the Canary Islands has lost almost half its genome in only a few million years.

The spider, Dysdera tilosensis, is a close relative of the mainland species D. catalonica and the familiar British woodlouse-hunter, D. crocata, yet is morphologically almost identical to both.

The findings have been published in the journal Molecular Biology & Evolution.

This discovery runs counter to a general pattern in evolutionary biology, in which adaptation to oceanic island environments often involves increases in genome size. Rather than undermining evolution, this unexpected result enriches the scientific debate over how and why genome size changes during evolution.

It also raises awkward questions for creationist dogma. Why would an intelligent designer equip spiders with almost twice as much genetic material as they actually need? And how would one distinguish such closely related species or show a transition from one to the other in the fossil record, if genome size — the key difference — leaves no trace in fossils?

How Science Works - Expanding Our Knowledge of Coelacanth Evolution.

Reconstruction of a large mawsoniid coelacanth from the British Rhaetian.

Artist credit: Daniel Phillips

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Coelacanth, Latimeria chalumnae

Fraser, Michael D.; Henderson, Bruce A.S., et al (2020). CC BY 4.0, Link

Ancient fish was hiding in plain sight hundreds of years after its believed extinction, study shows - Taylor & Francis Newsroom

A recent re-examination of museum coelacanth fossils has shown that there was more than one taxon in the Late Triassic and that, where we believed there were just four specimens, there are actually more than fifty. These fossils were hiding in plain sight, mis-identified for decades in collections across Britain. This significantly expands the known diversity of coelacanths at that time and neatly illustrates how science continually refines and improves its understanding as new evidence and careful re-analysis emerge.

Coelacanths have long been a favourite talking-point for creationists, who seized on the 1938 discovery of living Latimeria — a lineage once known only from the fossil record and thought extinct — as supposed proof that evolution had somehow stalled. Because the modern species still carries the name “coelacanth”, they leap to the assumption that the fish has remained unchanged for over 200 million years, and therefore evolution must be false. I have even seen creationists claim that if coelacanths have “not evolved” in all that time, the Earth must therefore be only a few thousand years old. It’s an extraordinary logical contortion — and one born of misunderstanding both biology and evidence.

In reality, the modern coelacanth is not the same species as the ancient Triassic forms, nor is evolutionary change required to be dramatic or constant for every lineage. Species can remain broadly similar when their ecological niche remains stable — a concept perfectly consistent with evolutionary theory. What this study demonstrates, once again, is the iterative, self-correcting nature of science: questions are never closed, evidence is always open to re-examination, and conclusions adapt as new data emerges.

Refuting Creationism - Ancient Teeth Show Mixed Origins Of A Transitional Hominin - 2 Million Years Before 'Creation Week'

Paranthropus robustus

Parathropus robustus (Artist's impression)

Bary Davies, RCA

New clues from 2 million-year-old tooth enamel tell us more about an ancient relative of humans

Human evolution isn’t a tidy staircase; it’s a branching, tangled tree full of transitional forms. And now, cutting-edge protein analysis from two-million-year-old teeth has revealed that Paranthropus robustus — one of our distant cousins — carried mixed ancestry, adding powerful new evidence to the evolutionary story creationists work so hard to deny.

If there is anything guaranteed to send a creationist into a fit of denial — desperately trying to redefine basic terms such as “transitional”, “species”, and “evolution”, and, as a last resort, claiming palaeontologists must have faked the evidence — it is the discovery of a transitional species in human evolutionary history.

But the hominin fossil record, like the evolutionary record for most living species, is absolutely packed with transitional forms. In fact, there are so many in human palaeontology that it can be difficult to single out one that is clearly more ‘transitional’ than the rest, because they form a fairly smooth continuum from the australopiths through to the genus Homo, just as we would expect of a slow process unfolding over tens of thousands or millions of years.

However, one species, Paranthropus robustus, stands out for its mosaic of features consistent with a lineage intermediate between the common ancestor of chimpanzees and hominins and the australopiths that followed.

And this mosaic has now been expanded to include genetic-level evidence, thanks to advances in palaeoproteomics. Proteins can persist far longer than DNA, yet they retain a direct correspondence to DNA via RNA, which encodes their amino-acid sequences. Once ancient proteins have been recovered and analysed, researchers can work backwards to reconstruct the RNA, and therefore the DNA, that produced them.

Using proteins extracted from the tooth enamel of four P. robustus fossils, researchers led by the University of Copenhagen have shown that these individuals themselves had mixed ancestry — indicating interbreeding with contemporaneous relatives, just as we now know happened among later hominin species, and almost certainly among the australopiths too.

The findings of the team were published in Science in May 2025, and are the subject of a recent article in The Conversation by three of the team.

Published: July 9, 2025 3.00pm BST

New clues from 2 million-year-old tooth enamel tell us more about an ancient relative of humans

Proteins were taken from the enamel of this Paranthropus robustus’ tooth.

By Ditsong National Museum of Natural History - Own work, CC BY-SA 4.0, Link

Palesa P. Madupe, University of Copenhagen; Claire Koenig, University of Copenhagen, and Ioannis Patramanis, University of Copenhagen

For nearly a century, scientists have been puzzling over fossils from a strange and robust-looking distant relative of early humans: Paranthropus robustus. It walked upright, and was built for heavy chewing with relatively massive jaws, and huge teeth with thick dental enamel. It’s thought to have lived between 2.25 million and 1.7 million years ago.

Humans today have a diverse array of hominin distant relatives and ancestors from millions of years ago. The South African fossil record ranges from early hominins such as Australopithecus prometheus, A. africanus (Taung child), A. sediba and P. robustus, to early members of the genus Homo (H. erectus/ergaster, H. habilis), to later hominins such as H. naledi and Homo sapiens (humans).

Fossils show how these early relatives evolved from as far back as A. africanus, 3.67 million years ago. They also document milestones in evolution, including the transition to walking on two legs, tool making and increased brain development. Ultimately, our species – Homo sapiens – appeared in South Africa 153,000 years ago.

Palaeontology: a way of reaching into the past to build lessons for the present

Fossils of P. robustus were first discovered in South Africa in 1938. But crucial questions remained. How much variation was there within the species? Were the size differences related to sex, or did they reflect the presence of multiple species? How was P. robustus related to the other hominins and early Homo? And what, genetically, made it distinct?

Until now, answers to these questions have been elusive. As a team of African and European molecular science, chemistry and palaeoanthropology researchers, we wanted to find answers but we couldn’t use ancient DNA to help us. Ancient DNA has been a game-changer in studying later hominins like Neanderthals and Denisovans but it doesn’t survive well in Africa’s climate because of its simple structure.

We experienced a breakthrough when we decided to use palaeoproteomics – the analysis of ancient proteins. We extracted these from the enamel of the 2-million-year-old teeth of four P. robustus fossils from Swartkrans Cave in South Africa’s Cradle of Humankind.

World's oldest _Homo sapiens_ footprint identified on South Africa's Cape south coast

Luckily, proteins that are millions of years old preserve well because they stick to teeth and bones and are not affected by the warm weather. One of these proteins tells us the biological sex of the fossils. This is how we found that two of the individuals were male and two were female.

These findings open a new window into human evolution – one that could reshape how we interpret diversity in our early ancestors by providing some of the oldest human genetic data from Africa. From there, we can understand more about the relationships between the individuals and potentially even whether the fossils come from different species.

More than one kind of Paranthropus?

The protein sequences also revealed other subtle but potentially significant genetic differences. One standout difference was found in a gene which makes enamelin, a critical enamel-forming protein. We found that two of the individuals shared an amino acid with modern and early humans, chimpanzees and gorillas. The other two had an amino acid that among African great apes is, so far, unique to Paranthropus.

What’s even more interesting is that one of the individuals had both the distinct amino acids. This is the first documented time we can show heterozygosity (a state of having two different versions of a gene) in proteins that are 2 million years old.

When studying proteins, specific mutations are thought to indicate different species. We were quite surprised to discover that what we initially thought was a mutation unique to Paranthropus robustus was actually variable within that group – some individuals had it while others did not. Again, this was the first time anyone had observed a protein mutation in ancient proteins (these mutations are usually observed in ancient DNA).

When did our ancestors start to eat meat regularly? Fossilised teeth get us closer to the answer

We realised that instead of seeing a single, variable species, we might be looking at a complex evolutionary puzzle of individuals with different ancestries. This shows that combining analyses of morphology (the study of the form and structure of organisms) and the study of ancient proteins, we can create a clearer evolutionary picture of the relationships among these early hominin individuals.

However, to confirm that P. robustus fossils have different ancestry, we will need to take samples of tooth enamel protein from more of their teeth. To do this, we plan to sustainably sample more P. robustus from other sites in South Africa where they’ve been found.

Preserving Africa’s fossil heritage

Our team was careful to balance scientific innovation with the need to protect irreplaceable heritage. Fossils were sampled minimally, and all work followed South African regulations. We also involved local laboratories in the analysis. Many of the authors were from the African continent. They were instrumental in guiding the research agenda and approach from the early stages of the project.

Doing this kind of high-end science on African fossils in Africa is an important step towards transformation and decolonisation of palaeontology. It builds local capacity and ensures that discoveries benefit the regions from which the fossils come.

Africa's rich fossil finds should get the air time they deserve

By combining data on molecules and morphology, our study offers a blueprint for future research – one that could clarify whether early hominins were more or less diverse than we’ve known.

For now, the Paranthropus puzzle just got a little more complex – and a lot more exciting. As palaeoproteomic techniques improve and more fossils are analysed, we can expect more surprises from our ancient relatives.

(Jesper V. Olsen, Rebecca R. Ackermann and Enrico Cappellini were also the principal investigators on this project.)

Palesa P. Madupe, Postdoctoral Researcher, University of Copenhagen; Claire Koenig, Post doc researcher, University of Copenhagen, and Ioannis Patramanis, Postdoctoral Researcher, University of Copenhagen

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Published by The Conversation.
Open access. (CC BY 4.0)

Abstract
Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern Africa with no genetic evidence reported so far. In this work, we describe the mass spectrometric sequencing of enamel peptides from four ~2 million–year-old dental specimens attributed morphologically to P. robustus from the site of Swartkrans in South Africa. The identification of AMELY-specific peptides enabled us to assign two specimens to male individuals, whereas semiquantitative mass spectrometric data analysis attributed the other two to females. A single amino acid polymorphism and the enamel-dentine junction shape variation indicated potential subgroups present within southern African Paranthropus. This study demonstrates how palaeoproteomics can help distinguish sexual dimorphism from other sources of variation in African Early Pleistocene hominins.

Palesa P. Madupe et al.
Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus.
Science 388, 969-973 (2025). DOI: 10.1126/science.adt9539

© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Once again, the evidence aligns from every direction: anatomy, geology, developmental biology, genetics, and now ancient proteins all tell the same story. Human evolution is a messy, branching, experimentally rich process — and *Paranthropus robustus* sits right where we would expect a transitional form to sit, complete with the genetic fingerprints of interbreeding and divergence.

Creationists often demand “transitional forms” as though evolution should be obliged to produce museum-ready half-and-half creatures on command. Yet when the fossil record delivers precisely what any honest inquirer would recognise as transitional, the response is denial, distortion, and conspiracy theories about forged fossils. It is not evidence they lack; it is the willingness to accept it.

Science advances not by clinging to comforting myths, but by following data wherever it leads. And as our tools improve — from classical morphology to whole-genome sequencing and now ancient protein reconstruction — the picture of human origins becomes richer, more detailed, and entirely consistent with evolution by natural processes. The real story of our species is far more fascinating than any manufactured pseudoscience: we are the product of deep time, branching ancestries, and countless experiments in survival — a lineage written in bone and now, quite literally, in protein.