September 9, 2011 | David F. Coppedge

Are Biological Clocks Like Paley’s Watch?

What is a clock made of?  We think of springs, gears and moving parts made out of metal.  But a clock could, in theory, be designed with almost any material.  There are water clocks, sundials, and electromagnetic oscillators that all function to tell time.  What difference does it make if the parts are made of liquids, laser beams, or plastic?  What if a clock was made of biological material—would it be any less a device for keeping time?  Would it surprise you that such clocks exist in your body and in every living thing?

In living things, biological clocks are given the name circadian systems.  They help organisms from bacteria to humans adjust to day-night (diurnal) cycles or other natural rhythms like seasons.  They control metabolic levels, feeding, reproduction and most other biological functions.  As scientists peer into the mechanisms behind circadian systems, they are finding remarkable similarities to man-made clocks.  One PhysOrg article was entitled, “Finding mechanism behind bacteria's biological clock” – i.e., “how these biological clocks work at the level of biochemical mechanism.” Scientists at the University of California at Merced uncovered one clever mechanism: “One of the proteins, in the course of a 24-hour cycle, shifts from being squishy to hard and then back to squishy. The changes lead to all three proteins connecting and disconnecting.”  So it’s not just the connections proteins make with each other because of their shapes, but also their flexibility.  The article ended by saying these discoveries are changing the way researchers look at biological clocks.  “It’s now believed the proteins are more involved than previous [sic] thought.”

PhysOrg also reported last month that scientists at Tel Aviv University are studying the biological clocks in zebrafish for clues to help humans.  A gene called Period2, “also present in humans,” responds to light and helps calibrate the clock.  It has a region called Light Responsive Model, they said.  “Within this region” (of the gene), they said, “there are short genetic sequences called Ebox, which mediate clock activity, and Dbox, which confer light-driven expression.”  The interplay between these sequences is responsible for synchronization of the circadian system.  Remarkably, “In these fish cells, the human LRM behaved in exactly the same way, activating Period2 when exposed to light — and unveiling a fascinating connection between humans and the two-inch-long fish,” even though, according to evolution, fish and mammals have been separated by many millions of years.

Once we understand biological clocks in fish, we might learn how to fine-tune our own internal clocks.  Malfunctions in circadian systems in humans can cause depression, insomnia and other problems.  In Medical Xpress, a subheading reads, “Researchers at Brigham and Women's Hospital (BWH) have demonstrated that the circadian system, the body’s internal clock, regulates human platelet function and causes a peak in platelet activation corresponding to the known morning peak in adverse cardiovascular events.”  In another paper in Current Biology, scientists uncovered a protein called Nocturnin that regulates the biological clock in our gut.  Authors Gimbel and Floyd said, “What mechanisms control circadian rhythms in the gastrointestinal tract and how does this impact nutrient metabolism? The deadenylase and leucine zipper protein Nocturnin is now shown to play a central role.”  Studies like this can help us understand and correct for the effects of jet lag. Our health and sanity depend on our internal timepieces being properly calibrated.

Bacteria have ways of synchronizing their clocks, too.  Science Daily reported on work at UC San Diego that used glowing proteins to let the scientists see how the cells do it.  The article used machine language to describe the mechanism: “Within each bacterium, the genetic machinery responsible for the biological clock oscillations was tied to green fluorescent protein, which caused the bacteria to periodically fluoresce.”

Plants have biological clocks.  In Current Biology,1 a summary of a paper by Hubbard and Webb reads, “Plants are more sensitive to light in the day than at night due to the circadian clock. The protein that acts downstream from the clock to modulate blue light signalling in stomata comes as a surprise; it is FT, which is thought to be the long-distance regulator of flowering.”

Like man-made machines, biological clocks apparently need to be oiled.  A commentary in PNAS was titled, “Dynamic fluctuations lubricate the circadian clock.”2  These are not random fluctuations, though.  Another PNAS paper described oscillators in the clocks: “Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in Synechococcus.”3  The word oscillator brings to mind the mechanisms in the back of a pocket watch or the back-and-forth motion of a pendulum clock; except in the case of the bacterium, three circadian proteins, KaiA, KaiB, and KaiC oscillate in the levels of their expression, keeping time with the sun (see our entries from 9/15/2004, 5/17/2005, and especially 10/31/2008, where these proteins were described by scientists as having cogs and gears).

Like man-made clocks, circadian clocks can tinkered with by humans.  An article on Science Daily was titled, “Manipulating Plants’ Circadian Clock May Make All-Season Crops Possible.”  Describing how a Yale team is identifying plants’ “morning genes” and “evening genes,” the article stated, “The circadian clock is the internal timekeeper found in almost all organisms that helps synchronize biological processes with day and night.”

One environment where a clock would seem unnecessary would be in the perpetual darkness of a cave.  Remarkably, though, scientists detected circadian rhythms still partially functional in blind cave fish.  In PLoS Biology, Cavallari et al. discovered that the clock still worked, but was not calibrated by light, as with surface-living organisms.4  Science Daily and Live Science both commented on this unusual finding.  And in the same issue of PLoS Biology, Robin Mejia commented,5

Whether it’s a jay that starts its day at first light, an ice worm that burrows into a glacier when the sun comes out, or a bat that heads out to feed at dusk, virtually all animals follow a daily pattern of activity. While the need for this kind of pattern, called the circadian rhythm, is not fully understood, it is remarkably conserved across species, and disruptions to an animal’s circadian cycle produce stress.

In 1804, in his book Natural Theology, William Paley famously made an inference to design from the idea of finding a watch on a heath, examining its parts, and observing that it functioned as a timepiece.  Critics of his design inference have focused on the differences between mechanical watches (which we can see being manufactured) and living organisms, which we cannot see being made.  Living things, furthermore, are able to reproduce themselves, indicating they have a history.  Actually, though, Paley’s design inference was based simply on the observation of seeing the watch function, whether or not he had ever seen a watch before or knew anything about who made it, how it was made, how it worked, or anything about its history. Even if he found a watch that could make copies of itself, the inference would stand – maybe even more so.  Now that we can see the actual parts of biological clocks functioning as oscillators, synchronizers and other devices common to the watches we know, Paley’s design inference seems stronger than ever.

1. Hubbard and Webb, “Circadian Rhythms: FLOWERING LOCUS T Extends Opening Hours,” Current Biology, Volume 21, Issue 16, R636-R638, 23 August 2011.

2. Commentary by Ming-Tao Pai and Charalampos Kalodimos, “Dynamic fluctuations lubricate the circadian clock,” PNAS,

3. Hosokawa et al., “Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in Synechococcus,” PNAS, published online

4. Cavallari et al., “A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception,” PLoS Biology 9(9): e1001142. doi:10.1371/journal.pbio.1001142.

5. Robin Mejia, “Cave-Dwelling Fish Provide Clues to the Circadian Cycle,” PLoS Biology 9(9): e1001141. doi:10.1371/journal.pbio.1001141.

Darwin was strongly influenced by Paley’s Watchmaker argument before he abandoned his Christian worldview.  His materialist disciples, eager to rid any Divine Artificer from science, buried Paley and said “Good riddance.”  It’s uncanny how times have changed.  The new Paleys are the leaders of the intelligent design community, who have given the argument from design new force and scholarship in works such as The Nature of Nature and Signature in the Cell.  But there’s nothing like actual clocks in living things to exhume William Paley, bring him back to life, and see him vindicated in the sequel, “Paley’s Revenge.”

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