Research is unveiling layers of complexity in the systems that allow plants, animals and humans to keep time. Here are some recent developments.
In “Nature’s Intricate Clockwork” in Science July 13, Brian R. Crane of Cornell marveled at “tiny clocks in your cells” that try to keep you on schedule despite your late-night study binges or attempts to get up earlier. “Over the past decade, remarkable progress has been made in elucidating the molecular genetics of these single-cell oscillators,” he writes. “More recently, structural biology has begun to contribute a detailed picture of our clock components.” The ghost of William Paley studying components of a watch found on a heath rises at the sound of statements like this. (Emphasis added in all quotations.)
Crane was commenting on work by Huang et al., in the same issue of Science. (see our June 5 article). They identified two proteins that are part of the “autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete.” The proteins form a complex that “controls the expression of numerous genes, including those that code for the oscillator proteins of the clock itself.” These proteins, CLOCK and BMAL1, are “made up of two domains that are found throughout biology, serving a range of functions.” Moreover, they contain numerous interfaces to other proteins. Speaking of a particular association with PAS proteins, Crane made this Paley-supporting analogy:

Thus, it is tempting to think that the clock mechanism is partly based on exchanges between PAS domains, binding and releasing each other, like the interlocking teeth of a watch gear.

Clock Calibration
The biological-clock literature often uses the word “mechanism” but rarely mentions “evolution.” One example is in another paper in Science from July 12 that begins, “The circadian clock is an intrinsic time-keeping mechanism that controls the daily rhythms of numerous physiological processes, such as sleep/wake behavior, body temperature, hormone secretion, and metabolism.” In that paper, Hirota et al. identify a small molecule that binds to a cryptochrome — another component of the biological clock. This small molecule works to stabilize the clock from perturbations and is implicated with glucose production, offering insight into disorders as diverse as sleep disorders and diabetes.
Gene Transcription by the Clock
“Transcription runs like clockwork” is the headline of a press release from the Howard Hughes Medical Institute. The core discovery of the HHMI team is that “the function of the enzyme that transcribes genes so that they can be made into proteins — RNA polymerase — varies according to the circadian cycle.” It actually pauses for a few hours each day, the team of Joseph S. Takahashi found:

“What we ended up discovering was that RNA polymerase II initiation is circadian on a genome-wide level,” says Takahashi. “Along with the global regulation of RNA polymerase II and transcription, we also found a global regulation of chromatin state by the circadian clock. Histone proteins that are critical for maintaining the integrity of DNA were also modified extensively on a circadian basis across the genome.“

Healthy Clocks
Disrupting normal biological rhythms can take a toll on health, Science Daily reports, putting the human body at risk of heart disease, stroke, chronic inflammation, cancer, obesity and diabetes. Swedish researchers found that disruption of normal circadian rhythms in zebra fish inhibited normal growth of blood vessels. It also affected the expression of genes that regulate the circadian clock. This story shows how important the clock is to many physiological systems.
Brain Clock
The biological clock is also implicated in metabolism, as we all can attest by hunger cycles. A news release from the University of Illinois at Urbana-Champaign reveals an intriguing bit of brain science:

The rhythm of life is driven by the cycles of day and night, and most organisms carry in their cells a common, (roughly) 24-hour beat. In animals, this rhythm emerges from a tiny brain structure called the suprachiasmatic nucleus (SCN) in the hypothalamus. Take it out of the brain and keep it alive in a lab dish and this “brain clock” will keep on ticking, ramping up or gearing down production of certain proteins at specific times of the day, day after day.

Imagine finding that while walking upon a heath. The team found a form of chemical energy, known as redox reactions, involved in the SCN. “These redox reactions, the researchers found, oscillate on a 24-hour cycle in the brain clock, and literally open and close channels of communication in brain cells.” Since redox involves the transfer of electrons, it might be reasonable to say our brains run on an electrical clock. See Science on August 17 for the original paper and count the instances of the word “evolution” (hint: it’s an integer less than 1).
Electrical Clock
Speaking of electricity, Current Biology published a paper August 30 with the title, “Electrical Activity Can Impose Time of Day on the Circadian Transcriptome of Pacemaker Neurons.” The conclusion: “The electrical state of a clock neuron can impose time of day to its transcriptional program. We propose that this acts as an internal zeitgeber to add robustness and precision to circadian behavioral rhythms.”
Watching the Clock
How does one read a clock with no hands? There’s a new way, as scientists reported in the Proceedings of the National Academy of Sciences on August 28 (see the summary at PhysOrg): watch the rise and fall of two metabolites in the blood. “The team based their research on an idea by botanist Carolus Linnaeus, who suggested that a bio or flower clock could be made by observing the opening and closing times of different types of flowers and planting them amongst one another.” With the blood metabolite method, scientists estimated the correct time within 3 hours — a start at least. Science Magazine News was impressed.
Subsidiary Clocks
The biological clock can be reset by temperature, PhysOrg reports, based on work at the University of Geneva. “The master clock also controls coordination signals that are sent to subsidiary oscillators,” the article notes. Body temperature is one of the resetting cues. To learn how it worked, researchers subjected cells to temperature cycles and monitored transcription of genes. They identified a protein named CIRP that follows even 1-degree changes in temperature. “This system functions a bit like that of a clockwork: temperature variations induce a rhythmic production of CIRP, which in turn reinforces cyclic activation of circadian oscillator genes.” New Scientist said this suggests that CIRP is another component essential to our biological clock.
Plant Clocks
Plants need to keep time, too. Current Biology on August 21 spoke of the “Complexity in the Wiring and Regulation of Plant Circadian Networks.” It’s complex, all right: the authors describe “Interconnected Transcriptional Circuits in the Clock Network,” including the “core oscillator loop.” They describe “Molecular Interactions and Complex Formation Underlying Oscillator Function” including RNA-based regulation and post-translational modifications. Then there’s “Rhythmic Chromatin Regulation” and “Interconnected Outputs from the Oscillator.” The paper uses the word “mechanism” 27 times.
Clocks and Design
So much clockwork, so little evolution. For a theory that’s supposed to make sense of everything in biology, you would expect evolution to be mentioned everywhere, but the only paper using the word, surprisingly, was this last one on how complex the plant clock is. The key paragraph assumes evolution is capable of producing all these complex systems, merely out of need:

As a result of the earth’s rotation on its axis, most organisms live in environments that oscillate with a period of approximately 24 hours. The circadian clock is an intrinsic and entrainable timekeeping mechanism that has evolved in organisms, allowing them to adapt to periodic environmental fluctuations such as light and temperature. Being a self-sustaining mechanism, the clock is able to buffer against both subtle and extreme changes, and persists in the absence of environmental cues, which also contribute to setting the phase of the clock. Anticipating these cyclic changes confers an adaptive advantage since organisms are better able to coordinate important physiological and developmental processes to occur at optimal times during the day, thus improving fitness.

While adaptation and fitness are surely good things for a plant to have, the paragraph says nothing about how an unguided, purposeless process of mutation and natural selection could produce “interconnected transcriptional circuits,” to say nothing of all the other parts that work together in all their interrelated complexity. The authors speculate that this or that part were “likely added” during plant evolution and then expanded upon by genome duplication events, but most of the rest of their mentions of evolution emphasize how conserved the parts are across the living world: an “an evolutionarily conserved protein complex” here, “an evolutionarily conserved serine/threonine protein kinase” there, a “few evolutionarily conserved molecular components” over yonder. Conservation is not evolution; it is how the complexity that’s already there is maintained!
Whether biological or artificial, clocks are irreducibly complex systems that are calibrated, regulated, and maintained. Our uniform experience with mechanisms of that sort is that intelligence — and only intelligence — is capable of producing them.
The silence on the part of these scientists and reporters when it comes to evolution suggests, at least, that evolutionary theory is useless for research into biological clocks, and by extension, any biological mechanism of comparable functional complexity and interrelatedness. Since the idea of “mechanisms” was on these authors’ minds to begin with, we can conclude that design thinking is a powerful motivation to explore nature’s complex, interrelated designs.