Charles Darwin worried that the fossil record looked strangely abrupt, with complex animals appearing in a geological instant instead of gradually unfolding over deep time. A new idea about how evolution’s internal “clock” might have ticked faster in the distant past offers a way to reconcile that apparent jump with slow, continuous change. If the biological stopwatch that governs genetic change once ran hot, then the gaps that troubled Darwin could be a mirage created by time itself.
Rather than rewriting natural selection, this emerging view reframes how I think about the tempo of early animal evolution. It suggests that the ancestors of today’s complex creatures had far more time to diversify than the rocks alone imply, and that their genes may have been racing ahead long before their bodies left clear traces in stone.
Darwin’s fossil headache and the mystery of missing ancestors
When Darwin published “On the Origin of Species,” he knew he had a problem: the oldest obvious animal fossils seemed to appear suddenly, without the long chain of intermediate forms his theory predicted. The Cambrian layers were full of shells, trilobites and other complex body plans, but the deeper rocks that should have held their simpler forebears looked stubbornly empty. Darwin treated this as a serious objection, arguing that the geological record was incomplete rather than that evolution had somehow leapt forward in a single creative burst.
More than a century later, that tension still shapes debates about early animal life. The fossil record has filled in around the edges, yet the first clearly complex animals still seem to arrive in a relatively tight window, while molecular studies often point to much older origins. The new “speeding clock” idea does not deny Darwin’s gradualism, it tries to explain why the rocks and the genes tell slightly different stories about when complex animals truly began.
How the molecular clock became evolution’s timekeeper
To understand why a fast-running clock matters, I first have to explain what that clock is. The molecular clock is the idea that changes in DNA accumulate at a roughly steady rate over long periods, so counting those changes can reveal how long ago two lineages split. In the words of Jan, as set out in the book Tree of Life, the method relies on the steady drip of mutations that build up in genes generation after generation.
In practice, researchers compare DNA sequences from living species, tally the differences and then translate those differences into time using an assumed rate of change. When the clock is well calibrated, it can reveal branching events that left no fossils at all, which is why it has been so influential in reconstructing the early history of animals. Yet if the rate of change was not constant in the deep past, then the clock can mislead, making ancient splits look younger or older than they really were.
Jan’s speeding clock: a hotter tempo in early animal evolution
The fresh twist comes from Jan’s argument that the molecular clock itself may have ticked faster during the dawn of animal life. Instead of assuming a single, steady rate, Jan suggests that early animals could have had genes that changed more rapidly, then slowed as lineages stabilized. In this view, the ancestors of complex animals had a long, largely invisible prehistory in which their DNA was evolving quickly, even though their bodies left few durable traces in the sediment.
According to Jan, that faster tempo would mean there was ample time for the ancestor of complex animals to evolve, unhurriedly splitting into new lineages long before any of them acquired hard parts that fossilize well. The new idea is that a speeding clock allowed early animals to diversify genetically in the shadows, before finally leaving a fossil record that looks abrupt only because the earlier stages are missing. That scenario, laid out in detail in a recent analysis of Darwin’s dilemma, turns the apparent jump in complexity into a sampling problem rather than a challenge to evolutionary theory.
Faster genes, faster faces: why appearance can outrun the rocks
If genes were changing more quickly, then outward appearance could have shifted rapidly too. Jan argues that faster changing genes would have allowed animals’ bodies, from their symmetry to their sensory organs, to transform in relatively short bursts of geological time. That does not mean evolution was instantaneous, only that the visible traits that define major groups could have crystallized over spans that look compressed when we read them off the rock record alone.
This is where the idea becomes particularly helpful for Darwin’s old headache. A rapid phase of genetic change would let animal lineages experiment with new body plans and ecologies before any of them left abundant fossils, then appear suddenly in the strata once they acquired shells, skeletons or other hard tissues. In that sense, the speeding clock is actually rather helpful to Darwin, because it preserves his gradual, branching tree of life while explaining why the fossils seem to show a series of leaps. The link between faster genes and faster visible change is central to Jan’s case, as laid out in a detailed discussion of Faster molecular change.
Why scientists disagree on when animals truly began
Even with better clocks, there is still no consensus on the exact timing of animal origins. Today, scientists are in disagreement over whether the first animals emerged close to the time of the earliest clear fossils or whether they stretch back tens of millions of years earlier. Some molecular studies place the roots of animal life around 570 million years ago, while others hint at even deeper origins that would push the story further into the Precambrian darkness.
Jan’s proposal does not magically resolve those disputes, but it reframes them. If the molecular clock ran faster in the earliest animals, then dates that once seemed wildly old might be more compatible with the fossil record than they first appeared. Instead of forcing a choice between “late and sudden” or “early and invisible,” a variable clock allows for a long, cryptic prelude followed by a visible flourish, which is exactly what the rocks and genes together seem to suggest.
Re-reading the Cambrian “explosion” through a new lens
Viewed through this lens, the famous Cambrian “explosion” starts to look less like a singular event and more like the moment when an already diverse cast finally stepped into the spotlight. If early animals had been evolving in soft-bodied, fragile forms for a long time, then the sudden appearance of shells and skeletons would naturally create the illusion of an evolutionary big bang. The speeding clock idea gives that narrative a mechanistic backbone, by tying the hidden prelude to a period of rapid genetic experimentation.
For Darwin, the abruptness of the Cambrian record was a source of unease, one he attributed to missing rocks and undiscovered fossils. With Jan’s framework, I can reinterpret that same pattern as the visible tip of a much older iceberg, whose submerged bulk is encoded in DNA rather than stone. The fossils still matter, but they are no longer the sole arbiters of timing, and their gaps become clues to how the evolutionary clock itself has changed.
What a variable clock means for evolution beyond animals
If the molecular clock can speed up and slow down, the implications reach far beyond the first animals. Other major transitions, from the rise of land plants to the diversification of flowering species, might also have unfolded under shifting tempos of genetic change. A period of rapid mutation could precede a burst of ecological innovation, followed by a slowdown as successful forms become entrenched, leaving a fossil record that looks punctuated even if the underlying process was continuous.
For me, that possibility underscores why calibrating the clock carefully is so important. It is not enough to assume a single rate and read deep time off a genetic stopwatch. Instead, researchers have to treat the clock as an evolving trait in its own right, shaped by population sizes, life histories and environmental pressures. Jan’s work on a speeding clock at the dawn of animal life is one prominent example of that shift in thinking, and it invites similar scrutiny of other chapters in the history of life.
Why Darwin’s worry still matters in the age of genomics
Darwin’s anxiety about missing fossils might seem quaint in an era of genome sequencing and high-resolution imaging, but it remains surprisingly relevant. The core issue he wrestled with was how to reconcile a theory of gradual change with evidence that often looks patchy and abrupt. The modern twist is that the gaps are no longer only in the rocks, they are also in our understanding of how fast evolution can run under different conditions.
By proposing that the evolutionary clock itself once ticked faster, Jan is not discarding Darwin’s insights, but extending them into the molecular age. The idea that the tree of life has deep, unseen roots fits comfortably with Darwin’s vision, even if the tools used to trace those roots would have been unimaginable in his time. In that sense, a clock that once ran hot does more than explain a few awkward gaps, it helps knit together fossils and genomes into a single, coherent story of life’s early unfolding.
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