Genes Tell No Tales About Language Evolution

The better we understand the machinery
of life, the more intricate it becomes –
and the more the evolutionary narrative
begins to look like a theoretical jury-rigging

Ancient DNA, Modern Storytelling

by John D. Wise, PhD

Ancient DNA shared with Neanderthals may explain human language (ScienceDaily, 12 June 2026). Researchers from University of Iowa Health Care examined a class of non-coding DNA elements called Human Accelerated Quantitative Enhancer Regions (HAQERs), regulatory sequences that influence gene expression in the brain.

By correlating variation in these enhancers with differences in present-day language ability, the team argues that some of the genetic architecture underlying language predates the divergence of modern humans and Neanderthals.

“What we’re seeing is how a very small part of the genome can have an outsized influence, not just on who we were as a species, but on who we are as individuals,” Michaelson [one of the authors of the journal article] says, noting that HAQERs represent less than a tenth of a percent of the genome but drive roughly 200 times more impact on language ability than any other genomic region.

The study does not identify a “gene for language,” nor does it uncover a new biological mechanism.

HAQERs are a subclass of already known regulatory DNA, enhancers that help control when and where genes are expressed. These DNA elements do not code for proteins; they function by modulating the activity of other genes, often at a distance. Over the past two decades, such regions have moved from the margins of genomics to the center, as the old notion of “junk DNA” has given way to the far more intricate picture of genome-wide regulation.

That picture has only grown more complex and integrated with the rise of the “4D genome.” DNA is not a linear string but a folded, dynamic structure. Enhancers like HAQERs exert their effects through spatial proximity, looping across the genome to contact target genes, and their activity depends on timing, cell type, and developmental context. In such a system, causation is distributed and non-local.

From 4D Reality to 1D Statistics

What is new in this study is not the existence of these elements, but the statistical association drawn between their variation and language performance in living populations. From this, the authors infer deep evolutionary continuity, projecting present-day correlations back into an ancestral narrative spanning millions of years.

This brings us to the journal paper itself:

Ancient regulatory evolution shapes individual language abilities in present-day humans, (Science Advances, Lucas G. Casten, et al., 22 April 2026).

The authors draw this deep time inference with a brand new statistical method, pioneered specifically by these scientists for this paper. It is called an Evolutionary Stratified Polygenic Score (ES-PGS):

To investigate the genetic origins of language ability, we developed an ES-PGS approach that systematically examines how genetic variants from different evolutionary periods contribute to traits.

In essence, ES-PGS is a statistical tool that aggregates many small genetic correlations with a trait, in this case, language-related performance, and then groups those correlations according to when the underlying DNA variants are thought to have arisen/emerged in evolutionary history. By comparing genomes across species and fitting them to a phylogenetic model, the method assigns variants to different “time layers,” some stretching back tens of millions of years.

This procedure does not directly observe evolutionary events.

It begins with present-day genetic variation and, using a model of evolutionary relationships and assumed timelines, it infers when particular variants likely emerged.

The resulting “history” is thus reconstructed through the assumptions built into the model itself.

The Neanderthal Paradox

The Neanderthal comparison sharpens the difficulty. Some of these regulatory elements are shared with Neanderthals (“ancient DNA”), and in certain cases the Neanderthal-associated variants appear just as prominent, if not more so. This complicates the standard secular narrative in which language is a uniquely modern human achievement assembled through incremental genetic change. If similar regulatory architecture is present in Neanderthals, then either they possessed comparable language capacities, or these elements do not explain language in the first place.

The Hardware Metaphor and the Myth of Linear Progress

A further complication follows. Regulatory systems are not linear. More enhancers, or stronger enhancer signals, do not translate straightforwardly into more advanced traits. Yet the authors rely heavily on a linear framework to explain the divergence between language and general cognition. As Michaelson puts it,

“This HAQERs aspect, a sliver of the genome, has remained relatively constant, even as other aspects have been going up and up and up to make modern humans smarter and smarter. We can say humans at least had the ‘hardware’ for language earlier than what we previously thought.”

Treating regulatory complexity as a simple ladder, where some traits remain static while others go “up and up,” imports assumptions that the 4D biology itself does not justify. In a system where function depends on spatial configuration and developmental timing, sequence alone cannot function as a historical record in the way the method requires.

This friction becomes explicit when the researchers attempt to explain why these crucial language switches abruptly stopped evolving across deep time while the rest of the genome supposedly marched onward.

“We think that early humans maxed out this pathway to developing the kind of brain that could be a vessel for language, and they hit that ceiling pretty early on and then remained stable, while other aspects of genetics that improve brain development for higher intelligence … continued to evolve,” Michaelson says.

Incidentally, it is worth noticing that this language of “maxing out” and “ceiling” imports a teleological structure into what is presented as an undirected process.

Conclusion: History by Model

The data do support a modest conclusion: certain regulatory DNA variants are correlated with language-related traits in modern humans. The larger claim, that these findings illuminate the evolutionary origin of language and/or validate evolutionary history, goes well beyond what the evidence can securely establish. In a genome where true biological function depends on 4D spatial configuration and precise developmental timing, a statistical model built on linear sequence variation alone cannot bear the explanatory weight being placed on it.

In essence, we are presented again with the ever-present circularity and self-reinforcement of evolutionary reasoning. ES-PGS partitions present-day genetic correlations according to an assumed evolutionary timeline, and then reports the results as evidence of that timeline. As in our Sweet Potato genome article, we can expect many more such stories to follow, now that this narrative-dependent technology (ES-PGS) provides a standardized blueprint for manufacturing the very historical evidence it assumes.

The better we understand the machinery of life, the more intricate it becomes – and the more this evolutionary narrative begins to look like a theoretical jury-rigging, straining to reduce a dynamic, 4D reality into a flat, linear history that biology itself does not tell.

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John Wise received his PhD in philosophy from the University of CA, Irvine in 2004. His dissertation was titled Sartre’s Phenomenological Ontology and the German Idealist Tradition. His area of specialization is 19th to early 20th century continental philosophy.

He tells the story of his 25-year odyssey from atheism to Christianity in the book, Through the Looking Glass: The Imploding of an Atheist Professor’s Worldview (available on Amazon). Since his return to Christ, his research interests include developing a Christian (YEC) philosophy of science and the integration of all human knowledge with God’s word.

He has taught philosophy for the University of CA, Irvine, East Stroudsburg University of PA, Grand Canyon University, American Intercontinental University, and Ashford University. He currently teaches online for the University of Arizona, Global Campus, and is a member of the Heterodox Academy. He and his wife Jenny are known online as The Christian Atheist with a podcast of that name, in addition to a YouTube channel: John and Jenny Wise.