Jumping Genes Are Not Fitting the Darwinian Narrative

The closer you look at transposable
elements (TEs), the less they resemble
debris, and the more they resemble design

 

Jumping Genes and the Tree of Life
When data opens a door, and modern science rushes to shut it

by John D. Wise, PhD

1. When the Door Opens – WONDER

Wonder in the genome

Increasingly over the last decade, new scientific data uncover and open a door no one expected to exist.

Current Biology, “Robust termite phylogenies built using transposable element composition and insertion events,” November 5, 2025. This is the journal article.

This time, that door stands in the genome of termites: intricate little architects whose bodies hide thousands of mobile DNA sequences known as transposable elements (TEs) or “jumping genes.” This study sequenced 45 termite species and 2 cockroaches, tracking the presence and absence of more than 38,000 TE families across their genomes.

To the researchers’ wonder, the pattern of TE insertions produced a clear phylogenetic signal, one that in some places even outperformed standard gene-based approaches. Mobile bits of DNA — the very emblem of movement, novelty, and openness — were suddenly signposts in a branching lineage.

But something else stirs here, beneath the data.

When you realize that nearly half of the human genome is built from the ‘relics’ of these “jumping genes,” something shifts. An unexpected space opens behind our current map of the world — a structure larger on the inside of the genome than on its “outside.”

It feels, for a moment, like standing before a wardrobe door — the kind you’re warned never to shut behind you. What might lie on the other side? Only what our limited experience would lead us to expect, or something more?

In this case, the door opened is the ability to sequence genomes, The wonders we’ve discovered since that door opened routinely defy secular scientific expectations. What this article and so many others like it reveal is a genome that is not a static library but a living, breathing landscape.

A note from the researchers themselves

“Jumping Genes Help Resolve the Tree of Life,” Astrobiology, November 12, 2025. As first author Cong Liu of Okinawa Institute of Science and Technology (OIST) explains, transposons were long overlooked simply because the tools to see them weren’t ready:

“Until recent advances in sequencing technologies and bioinformatics annotation, transposon characterization at the genome level was difficult. Phylogenetics has tended to focus on conserved genes, such as those encoding proteins …. These usually only change slowly over time, so are good for examining changes over evolutionary timescales.”

But this stability becomes a liability when species diverge quickly (as seems to be the trend in most recent research):

“In such cases, transposons may provide helpful information on species divergence, given their active movement across the genome.”

In other words, what once looked like noise (junk DNA) turns out to be signal — and a surprisingly crisp one.

2. When the Door Narrows – METHOD

From openness to data; from mobility to metric

But science cannot operate on wonder. It can only operate on what wonder leaves behind. This is the poverty of science. Powerful, yes, but also limited.

So the termite researchers narrow the opening. They take the mobility of transposons — their freedom to jump, land, copy, multiply — and turn it into data points. An insertion becomes a marker; a marker becomes a branch; a branch becomes a position on the Tree of Life.

This is not a flaw in the method; it is how the method works. Yet the narrowing is unmistakable:

• The openness of the genome becomes a matrix of checkmarks.
• The fluidity becomes structure.
• The movement becomes a map.
• The living dynamism becomes a filing system.

The door, once wide, now stands only slightly ajar — open just enough to admit the data, but not enough to admit where the data might lead. It is the kind of careful opening adults approve of (and adventurous children resent): the fresh air of discovery without the risk of stepping outside the room.

Still … something lingers.

The closer you look at TEs, the less they resemble debris, and the more they resemble design: regulatory enhancers, chromatin organizers, contributors to neural development. Even the so-called “domesticated” elements — TE sequences essential for immune diversity or placental formation — pose a quiet question:

Are these tamed wanderers from evolutionary history? Or are they misunderstood tools?

(The Octopus Clue)

Live Science, “Octopuses may be so terrifyingly smart because they share humans’ genes for intelligence,” November 14, 2022

Termites are not the only place this architecture appears. In octopuses — creatures famous for their fluid intelligence — researchers have found active LINE transposons[1] in the brain’s learning centers, the same TE family involved in human neural development. These mobile elements activate in the octopus’s vertical lobe, a region associated with memory.

When the scientists took a closer look at octopus jumping genes that could freely copy and paste around the genome, they discovered transposons from the LINE family. This element was active in the octopus’s vertical lobe — a brain section in octopuses that is critical for learning and is functionally analogous to the human hippocampus.

Mobility, it seems, is woven even into the circuitry of thought — a regulated flexibility, not a parasitic accident.

Although the OIST researchers did not describe their results as “surprising,” the clarity of the TE-based signal carries the unmistakable note of scientific wonder — the sense that a familiar genomic landscape has quietly opened into a deeper world just beyond the lab coats.

The room from which the wardrobe opens is starting to look too small.

3. When the Door Closes – NARRATIVE

There is a pattern at work here — one we will call moving forward the compulsion to closure: discovery opens the conceptual space; method narrows it; interpretation rushes to seal it.

Science must do this to operate, but when the rhythm becomes reflexive, the closing gesture can harden into dogma, and each new doorway becomes a guarded threshold, lest somehow an uninvited presence might sneak through it.

For these transposons, mobility becomes lineage; novelty becomes ancestry; coherence becomes another brick in the structure the system expects to see.

And here — right here — is where the theory-script reasserts itself.

In the press releases and interviews for this study, the familiar evolutionary narrative confidently steps forward and shuts the door with a familiar click:

• TEs were accidents.
• They were genomic parasites.
• Hosts suppressed them.
• A few lucky ones were “co-opted.”
• Their insertions trace unguided descent.

Conclusion: The Phylogenetic Tree stands tall, its branches reaffirmed. Evolution has triumphed.

The genetic mobility, so jarring at first, is quickly assimilated into the only story the system allows: life building itself from below, structure emerging from chaos. And the wardrobe door closes — not because the world behind it isn’t real, but because what it implies must be kept from entering the room.

The data is welcome, but what the data suggest must stay outside. Like TEs themselves, discovery must be “domesticated.”

But … though you might hold the door against it, Reality is not so easily tamed.

Eliot’s warning

TS Eliot described divine revelation as “the hint half-guessed, the gift half-understood.”

This is precisely the tension here. Transposons offer a hint — a glimpse of deeper coherence — but for the evolutionary scientists the gift will only be ‘half-received.’

The more the genome opens outward — into mobility, novelty, regulation, coherence — the more urgently the narrative moves to slam the door.

“Human kind cannot bear very much reality.”

4. Another Open Door – ALTERNATIVE

But if we pause and resist the reflex to close the door, if we simply look at the data as they are … a world waits where:

• Mobility coexists with order.
• Novelty occurs within boundaries.
• Regulation governs flexibility.
• TEs behave less like accidents and more like modules.
• Epigenetics orchestrates activation with exquisite precision.
• Half the genome’s “junk” turns out to be purposeful architecture.

In that world, the wardrobe leads outward, not inward; the genome becomes a system built for adaptability, not a battlefield of parasites, and TE patterns look like variation within created kinds, not proof of a single unguided tree.

This is not imposing a narrative; it is refusing to shut the door prematurely.

Because the truth is this: the data themselves neither prove nor require the evolutionary storyline. They show mobility, regulation, structure and relationships. But where the data point — upward or downward, chaos or design — comes from the teller, not the text.

And the deeper world refuses to vanish just because one confines himself to the spare room. Edmund is no innocent — but he is already aligned, by a choice he barely knew he was making, with the reigning climate of his world, powerful enough to make the larger reality seem … “inconvenient.”

So when he waves off Lucy’s truthful report as mere childish fancy, the betrayal is deliberate, but its impulse is inherited. Her truth remains; and his attempt to tame it into something manageable only reveals the deeper fear behind that closed door and those holding the keys.[2]

Conclusion

The termite study, the octopus findings, the regulatory discoveries — all point to a genome far richer than the evolutionary story used to explain it. Transposons are not debris. They are movement within order, freedom within form, openness disciplined by constraint.

The new data hold open the door. The question is no longer whether we will walk through it … but whether we will continue to allow evolutionary science to be the force that reaches back and shuts it.

Footnotes

[1] LINE stands for Long Interspersed Nuclear Element, a class of retrotransposons that copies itself through an RNA intermediate and reinserts new copies back into the genome. In humans, LINE-1 (L1) elements make up roughly 17% of the genome, and although most copies are inactive, a small number remain capable of “jumping.” These active LINEs are involved in neuronal development, early embryogenesis, and the creation of genetic diversity within tissues. Their presence in octopus learning centers — and in human neural progenitor cells — suggests a regulated flexibility built into the genome rather than random parasitism.

[2] Hopefully the extended metaphor is not lost. Like Edmund, most scientists didn’t really choose their allegiances. They inherit them. They can envision no other explanation, defaulting to evolution by simple acquiescence. And when their career depends upon it, no matter what the evidence may proclaim, refusing Turkish Delight for bread and water is no simple decision.

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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.