Genes Tell Time with Help from ‘Junk’ DNA
We don’t sense time as an
external arrival. We inhabit it
as an internal necessity.
The Clock We Cannot Imagine Away
by John D. Wise, PhD
A recent essay in Aeon, “The clock in our genes: The biologist Victoria Foe discovered a timing device in ‘junk’ DNA that could unlock the evolution of complex life,” 24 March 2026, tells the story (and it is well worth reading) of developmental biologist Victoria Foe, whose work presses against one of the most persistent assumptions in modern biology: that DNA is primarily information, a code to be read with lots of “useless stuff” all around it. Foe’s work suggests something far more physical, and far more interesting:
… the recognition that genes operate within complex regulatory networks did little to dislodge the deeper assumption that biological meaning resides primarily in information coded in DNA sequences. Foe’s work presses against that assumption. Genes are not only messages but material entities embedded in time, subject to interruption, constraint and decay. [emphasis added]
Genes are not just messages.
RNA’s are not just messengers.
If a short gene takes five minutes to be copied, its RNA will appear on the scene swiftly and in copious amounts.… A longer gene unit … will be finished only by the very end. If a gene is extra-long, its transcription will be halted midway…. Once the cell has split in two, the clock resets.
In her studies of embryonic development, Foe observed that gene length directly affects when proteins are produced. The result is not merely variation in output, but variation in time.
Gene length, she argues, functions as a molecular clock, regulating when developmental processes occur. As the Aeon essay notes:
A gene’s length determines its transcription time. This means that a cell’s genes are not just a collection of instructions; they are a collection of timers. [emphasis added]
The choreography of life, from cell division to tissue formation, depends not just on what genes say, but on how long they take to say it.
Transcription is not the transmission of a signal; it is the physical traversing of a distance. Length is duration. In Foe’s world, the cell doesn’t ‘calculate’ time; it ‘endures’ it.
This is not a metaphor.
It is a real constraint.
Time is not something the organism observes.
It is something the organism obeys.
And here, a curious tension emerges.
As Jo Marchant recently put it:
Time is elusive in other ways, too. We have no sensory organs for detecting it, nor any dedicated brain areas for tracking it. Our experience of time can vary hugely… we can easily be fooled about how much time has elapsed.
The observation is fair, but as we’ve seen, the inference drawn from it – that time is subjective – is not.
Time is not localized because it is not a signal.
Time is an objective condition.
We are told, increasingly, that time and reality are not features of the world, but constructs of experience, that time is a bookkeeping device, a way of organizing events rather than something that exists independently of us.
We are reminded that biology offers no dedicated organ for time, as it does for sight or sound.
Reality Check: These arguments miss the point entirely. We do not have a ‘time organ’ for the same reason a fish does not have a ‘wetness organ.’ We don’t sense time as an external arrival; we inhabit it as an internal necessity. To the embryo, time isn’t a ‘bookkeeping device’ – it is the narrow gate through which every protein must pass or perish.
Vision can be assigned to an eye because light arrives. Sound can be assigned to an ear because vibrations propagate. But time does not arrive.[1]
It orders.
We don’t “sense” time, we live within it. This is why biology does not build a “time organ.” Instead, it builds systems that depend on time’s reality:
Transcription requires duration.
Cell division interrupts processes in a sequence.
Development unfolds in ordered stages that cannot be rearranged without consequence.
Remove time from the world, and biological systems aren’t “misinterpreted.”
They simply fail.
And so we arrive at an unexpected irony.
While some areas of physics and philosophy suggest that time may be a feature of consciousness, biology continues to operate as though time is a real structuring feature of the world, one that organisms must measure, accommodate, and survive within.
Victoria Foe herself is an unlikely witness to this tension. Deeply committed to evolutionary biology, she frames her work within that tradition. And yet her discoveries point not to abstraction, but to embodiment, constraint, fragility, and order.
Life does not behave as though time is optional or a “bookkeeping device.” It behaves as though time is a gift.
During the first two hours of the embryo’s life, its nuclei divide in lockstep. Soon, that unity breaks: distinct rhythms of division set in, with groups of cells falling into their own tempos as the embryo begins laying the foundation for different parts of the body to develop. The timing and locations of these dividing groups, Foe realised, were highly predictable.
For all our theorizing, Creation keeps its own counsel.
It builds, divides, repairs, and unfolds –
not according to what we imagine or experience,
but according to what IS.
“And God said, ‘Let there be…’ and it was so.”
We can “lose track of time.”
Biology cannot.
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.