Rosa Rubicondior: Refuting Creationism - How The Evidence Refuses To Comply With Creationist Requirements

Reconstruction of life in the Matjes River Rock Shelter, South Africa, 100,000 years ago

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Ten-thousand-year-old genomes from southern Africa change picture of human evolution – Uppsala University

The story emerging from the latest palaeogenomic research reads like a science fiction epic — only it’s real, deep, and immutably ancient. A new study published in Nature reports that prehistoric humans in southern Africa lived in virtual genetic isolation for tens of thousands of years, diverging so far from other branches of Homo sapiens that their genomes fall “outside the range of genetic variation” seen in any living people. These weren’t minor differences; the DNA of individuals who lived south of the Limpopo River for much of the last 100,000–200,000 years retains an astonishing reservoir of variation, some of which has since vanished from other populations.

This isn’t an update to a dusty side-note in human history. It’s a profound rewriting of our origin story. Instead of a simple, uniform lineage emerging neatly from a single place and time, the evidence shows a complex mosaic of populations, genomes and adaptations evolving in parallel, sometimes in long-term isolation, sometimes intermingling. What we once thought of as the “standard” range of human genetic diversity was simply a tiny slice of a much richer prehistoric past.

For those committed to a literal reading of ancient texts like the Bible, discoveries like this pose a stark challenge. The creationist narrative — anchored in a literal six-day creation a few thousand years ago, followed by the dispersion of humankind from a single family — simply cannot grapple with human populations that were genetically distinct for hundreds of millennia before any traditionally assumed timeline. And yet, even here, one predictable excuse will surface: “God planted the evidence as a test of faith.”

That response, however, collapses under the very theological claims it purports to defend. The Bible repeatedly asserts that God is truthful and incapable of deceit — that “God cannot lie” (Titus 1:2; Numbers 23:19; Hebrews 6:18). If we accept those texts at face value, it follows that the Creator would not embed misleading evidence in the earth’s deepest strata as a cosmic trap for intellect. Instead, what we see in the genetic record is precisely what natural processes — mutation, isolation, selection, drift and admixture — predict and what evolutionary theory models with remarkable fidelity.

Creationist Counter-Arguments — and Why They Fail. Whenever genetic discoveries like this appear — showing ancient human populations isolated for nearly 100,000 years and carrying variation beyond anything seen today — creationists tend to fall back on a small set of well-worn escape hatches. None of them survive contact with the evidence.

“It’s just microevolution — not real evolution.”
This is the standard retreat: accept the genetics only so long as it can be squeezed into trivial variation “within kinds.”

But this study describes *deep divergence* within Homo sapiens over tens of thousands of years, shaped by mutation, drift, selection, and long-term isolation — precisely the mechanisms of evolution operating exactly as evolutionary theory predicts. Creationists cannot accept the process while denying its cumulative consequences.

“All this variation arose after the Flood/Babel.”

Some young-Earth creationists attempt to compress all human diversity into a few centuries after Noah’s Flood or the Tower of Babel.

That is not merely implausible — it is mathematically impossible. The mutation rates required to generate such extreme genetic divergence in such a short timescale would be catastrophic, producing an unsustainable burden of harmful mutations. Population genetics simply does not permit it.

“The dating methods are wrong.”

Another reflex is to reject the timescale entirely, as though the entire scientific framework rests on one fragile assumption.

But the genetic timelines here are not based on radiometric dating alone. They arise from multiple independent lines of evidence: mutation accumulation, recombination patterns, demographic modelling, archaeological context, and comparison with other ancient genomes. To dismiss them all requires rejecting modern genetics wholesale — including the same genetics creationists rely on in medicine and ancestry testing.

“God planted the evidence as a test of faith.”

This is perhaps the most desperate argument of all: that God deliberately arranged the world to look ancient and evolved in order to mislead humanity.

Aside from being indistinguishable from deception, it directly contradicts scripture itself. The Bible explicitly states that God cannot lie (Titus 1:2), is not a man that he should deceive (Numbers 23:19), and that it is impossible for Him to lie (Hebrews 6:18).

If creationists invoke a God who fabricates false history into genomes and fossils, they are no longer defending Biblical truth — they are defending a theological trap.

“Scientists are biased against God.”

Finally, some claim the evidence is merely the product of atheistic ideology and a Satanic conspiracy paranoia.

Yet DNA has no ideology. Genetic patterns are measurable, repeatable, predictive, and independently confirmed across laboratories worldwide. The conclusions do not arise from hostility to religion, but from the stubborn fact that genomes record history — whether one likes that history or not. The conspiracy paranoia depends on the implausibility of millions of scientists, heads of research institutions, centres of higher education and publishers of scientific journals, as well as mutually hostile governments and all their staff participating, and no-one ever breaking ranks and exposing it.

In short: the creationist narrative requires reality to be wrong, evidence to be fraudulent, and God Himself to be misleading — while evolution requires only what we observe: populations change, diverge, adapt, and leave their signatures in DNA over deep time.

The study was conducted by palaeontologists and geneticists from Upsala University, Sweden with colleagues from Bloemfontein, and Johannesburg, South Africa. It is explained in a press release from Upsala University.

Ten-thousand-year-old genomes from southern Africa change picture of human evolution
In southern Africa, a group of people lived in partial isolation for hundreds of thousands of years. This is shown in a new study based on analyses of the genomes of 28 people who lived between 10,200 and 150 years ago in southern Africa. The researchers also found genetic adaptations that likely shaped Homo sapiens as a species. The study, which is the largest to date of African ancient DNA, is published in Nature.
Homo sapiens has been around for at least 300,000 years. But exactly where on the African continent our species originated has not been known. According to some theories, Homo sapiens evolved in eastern Africa and only spread southwards around 50,000 years ago. A new study by researchers at Uppsala University and the University of Johannesburg shows that this assumption is wrong.
We have long known that southern Africa was inhabited, but it was previously unclear whether these inhabitants were just predecessors of ours or whether they were Homo sapiens. We can now show that Homo sapiens have existed and evolved in southern Africa for a long time. This area has played an important role in human evolution, perhaps the most important of all.

Professor Mattias Jakobsson, lead author
Human Evolution
Department of Organismal Biology
Uppsala University
Uppsala, Sweden.

Analysed DNA from 28 individuals

The study is based on analyses of the genomes of 28 individuals who lived in southern Africa between 10,200 and 150 years ago. When the researchers compared the genomes of the Stone Age people of southern Africa with the genomes of modern and Stone Age people from all other parts of the world, they found that the Stone Age people of southern Africa had lived in isolation for a very long time.

This group seems to have been genetically separate for at least 200,000 years. It’s only relatively late, around 1,400 years ago, that we see clear traces of gene flow into this group when DNA from individuals from East Africa and West Africa begins to become visible in individuals in southern Africa.

Professor Mattias Jakobsson.

Although no new groups migrated to southern Africa earlier than about 1,400 years ago, genetic data suggest that members of the southern population migrated north during favourable climatic periods. Around 8,000 years ago, there is genetic material from the southern population in individuals in present-day Malawi, and it is possible that such expansions from the south also occurred earlier.

Tools changed, even though no new people migrated in

A large proportion of the human remains analysed have been found at the Matjes River Rock Shelter, a protective rock formation on the south coast of South Africa. The site contains five clearly defined archaeological layers representing different cultural-historical periods from around 10,000 years ago to around 1,500 years ago. Archaeological analysis shows that tools change between the layers and that each period has its own technique for making tools.

Despite this, the individuals are genetically virtually identical over the entire time period. There is no evidence of in-migration or population exchange. This differs from the picture in Europe, for example, where cultural shifts often coincide with new people moving in.

Professor Mattias Jakobsson.

Genetic changes specific to Homo sapiens

In the study, the researchers identified 79 DNA variants that alter gene function and are unique to Homo sapiens, i.e. genetic variants different from those found in Neanderthals and Denisovans, chimpanzees and gorillas. Moreover, all analysed living and prehistoric Homo sapiens carry the same variant.

The genomes of the prehistoric individuals of southern Africa are invaluable in this context, as they carry a large number of genetic variants that have been lost in other groups. One way to look at it is that the prehistoric population of southern Africa contains half of all human genetic variation, with all other groups, including people from western and eastern Africa and people outside Africa, containing the other half. Consequently, these genomes help us to see which genetic variants were really important for human evolution.

Professor Mattias Jakobsson.

Among these, there were seven genetic variants linked to kidney functions. At first sight, this surprised the researchers as they expected to mainly find genes related to the immune system and cognitive functions. Such variants were also found, but gene variants affecting kidney function were clearly over-represented.

One hypothesis is that these gene variants are linked to the unique human ability to cool the body by sweating, which requires a good ability to control fluid balance in the body. It’s possible that precisely these changes in genes that affect the morphology and function of the kidney gave our predecessors unique properties for regulating fluid balance, thereby increasing their cooling and endurance abilities – properties that Neanderthals and Denisovans lacked.

Professor Mattias Jakobsson.

In addition to these variants, the researchers found changes in genes involved in both the immune system and neuron growth, which may affect brain growth and complex cognitive functions. More than 40 per cent of these variants are associated with neurons and brain growth, suggesting a role in cognitive evolution. Several genes have been linked to attention – a mental ability that may have evolved differently in Homo sapiens compared with Neanderthals and Denisovans.

One of the most meaningful outcomes of the study is that it suggests that the complex behaviours and thinking observed in the southern African archaeological record from about 100 000 years ago originated locally, and may have subsequently trickled northward with the genes and technologies of local hunter-gatherers.

Marlize Lombard, co-corresponding author
Palaeo-Research Institute
University of Johannesburg
Johannesburg, South Africa.

Genetic material still present in modern San populations

Around 80 per cent of the genetic material is still present in modern San populations, such as the Ju/’hoansi in Namibia and Botswana, and the Karretjie people in South Africa. Thus, in contrast to previous theories, which proposed that modern-day Khoe-San peoples are descended from a widely distributed population existing across much of Africa, the results show that southern Africa’s prehistoric hunter-gatherers were isolated in the south, but nevertheless comprised a large and stable population.

What pleases me most is that these genomes give a very clear picture of the early population history of southern Africa. As we obtain more and more high-quality ancient genomes, we are now beginning, for the first time, to gain insights at a genuine population level. This gives us a much clearer basis for understanding how modern humans evolved on the African continent.

Professor Carina M. Schlebusch, co-corresponding author
Human Evolution
Department of Organismal Biology
Uppsala University
Uppsala, Sweden.

Publication:
Jakobsson, M., Bernhardsson, C., McKenna, J. et al.
Homo sapiens-specific evolution unveiled by ancient southern African genomes. Nature 650, 156–163 (2026). https://doi.org/10.1038/s41586-025-09811-4

Abstract
Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe1, but the early evolutionary process is debated^2,3,4,5,6. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25× to 7.2× genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. bp). All ancient southern Africans dated to more than 1,400 cal. bp show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans—which are likely to have evolved rapidly on the Homo sapiens branch—were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans—which are likely to have adapted rapidly on the southern African branch—were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.

Fig. 1: Archaeological sites and dates of sampled and comparative individuals.

a, All ancient African individuals from >1 ka with complete sequenced genomes (>7× coverage). The seven complete ancient genomes from southern Africa (Matjes River 1, 3 and 11, Great Brak River Cave, Cape St Francis, Springbokvlakte and Ballito Bay A) are studied in detail. The symbol shape indicates archaeological context for southern Africa (see the legend in b). The Zambezi and Limpopo rivers are highlighted in blue. b, Ancient African individuals with genomic data south of the 14th latitude. Archaeological context is given by the shape of the symbol. LSA, Later Stone Age. c, The distribution of sampled and comparative individuals across dates. Maps were created with Natural Earth in R, using vector maps from the package rnaturalearthdata.

Fig. 2: Characterization of the genomic variation in modern-day and ancient Africa.

a, PCoA of the 28 ancient southern Africans in this study (pink) and all comparative ancient individuals with genetic information across sub-Saharan Africa (modern-day individuals from southern, southeastern, eastern (E), central (C) and western (W) Africa; individual labels are shown in Extended Data Fig. 1). b, Gene flow (estimated by two different f⁴ tests) from an eastern or western African source into the ancient southern Africans, plotted against years bp and latitude south of the Equator. The vertical dotted line marks 1,300 cal. bp, when admixed individuals first appear. c, Estimated ancestry, assuming five ancestry components. The results assuming between two and ten ancestry components are provided in Extended Data Fig. 2 and Supplementary Fig. 6. d, Pairwise genetic differences visualized using a hierarchical clustering algorithm (UPGMA) among all pairs of ancient (>1 ka) high-quality genomes (>10×) from Africa and a selection of comparative high-quality ancient genomes from elsewhere (including three Neandertals and a Denisovan individual). bp, base pair. e, Genetic diversity (heterozygosity) for ancient high-quality (>10×) genomes.

Fig. 3: Graphical representation of the inferred human population history of southern Africa.

The summary of observations from the ancient genomes in this study that are shown in Figs. 1b,c and 2a–c. Individual symbols correspond to the symbols in Fig. 1b. R., river.

Jakobsson, M., Bernhardsson, C., McKenna, J. et al.
Homo sapiens-specific evolution unveiled by ancient southern African genomes. Nature 650, 156–163 (2026). https://doi.org/10.1038/s41586-025-09811-4

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)

The picture emerging from studies like this is not one of a simple, recent humanity neatly descending from a single couple a few thousand years ago, but of a rich, structured and ancient species, evolving across Africa in multiple semi-isolated populations over immense spans of time. The genomes of these southern African people are not an anomaly in need of theological rescue; they are exactly what evolutionary biology predicts when populations remain separated, accumulate mutations, adapt locally, and preserve lineages that later disappear elsewhere. Far from being an embarrassment for the theory of evolution, this is evolution doing precisely what it says on the tin.

For creationism, however, such discoveries are profoundly awkward. The Biblical narrative leaves no room for human groups diverging for 100,000 years or more, no room for deep population structure, no room for the vast prehistoric tapestry of migration, isolation and interbreeding now written indelibly into our DNA. The evidence does not merely contradict a few details of Genesis; it obliterates the entire timescale and framework on which young-Earth creationism depends.

And when the evidence becomes too stubborn to ignore, the argument sometimes retreats into desperation: perhaps God planted the evidence as a test of faith. But that is not a defence of scripture — it is an accusation against the very deity creationists claim to worship. A God who fabricates false genetic histories, who arranges the world to look ancient and evolved, would be indistinguishable from a deceiver, directly contradicting the repeated Biblical insistence that God cannot lie (Titus 1:2; Numbers 23:19; Hebrews 6:18). In trying to save a literalist reading of Genesis, they end up dismantling their own theology.

Reality, meanwhile, remains beautifully consistent. Fossils, archaeology, geology and now palaeogenomics all converge on the same conclusion: humanity is the product of deep time, shaped by natural processes, with a history far older and more intricate than any Bronze Age creation myth could possibly anticipate. Each new ancient genome does not undermine evolution — it strengthens it — and widens still further the gap between what the evidence shows and what creationists are conditioned to believe.

The genetic record is not a test of faith or a divine riddle — it is simply history, written in DNA, and it tells a story creationism cannot survive.

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