Paley’s Watch all over Again!

Paley’s Watch Found in Bacteria   10/31/2008    
Oct 31, 2008 — A clock with cogs, gears and ratchets that keeps accurate time – what more could William Paley wish for?  The 18th century natural theologian used the illustration of stumbling upon a watch in a heath as an example of reasoning from design to a Designer – as from watch to watchmaker.  Skeptics like David Hume challenged such reasoning of the natural theologians as a mere argument from analogy: living things are very different from mechanical machines, he argued.  One can only wonder how their debate would unfold with the discovery of a ticking watch inside one of the simplest forms of life.
    Scientists have long wondered how living things keep time.  We are all aware of our own natural cycles throughout the day.  Organisms without eyes and ears, though, like bacteria, also keep time with diurnal cycles.  How do they do it?  The secret has only been coming to light in the last few years (see 05/17/2005)  Johnson, Egli and Stewart wrote a review article in Science this week that describes what is currently known about the circadian clock present in cyanobacteria.1  They could not help but use mechanical terms for this biological machinery.  It began right in their opening paragraph:

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression.  Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction.  The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC.  These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation.  The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally.  This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo.  The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

“Conformational change” is jargon for bending, springing, unfolding and other kinds of motion that take place as the proteins operate.  Proteins are therefore the “moving parts” of the clock.
    Later, they spoke of “cogs and gears” in the “clockwork mechanism” evident in the Kai-ABC proteins.  Each protein, in turn, is made up of multiple parts, composed of hundreds of amino acids.  KaiC, for instance, is a barrel mechanism with two donut-shaped rings, each made of six toothed parts that make it look like a gear wheel.  The clock runs on ATP energy pellets.  It accumulates hydrogen bonds through phosphorylation events that force it to “tick” like a ratchet in one direction.  It keeps an accurate 24-hour cycle, releasing its energy for the next round in conjunction with feedback loops from the nucleus and cytoplasm.  These, in turn, affect what genes are expressed by the transcribers in the nucleus and translators in the ribosomes.
   In his description of the clock posted last April on Reasons to Believe, Dr. Fazale Rana described how the KaiA and KaiB parts interact with KaiC like a rotor and wing nut.  He made the same connection to Paley.  Describing this as a “biochemical watch on a heath,” he showed how it refutes David Hume’s criticism of natural theology.  The discovery of molecular machines like the circadian clock have revitalized the watchmaker argument for the existence of God, he said.
    The Science article pointed out that several questions remain.  How is the clock robust against temperature fluctuations?  Does the eukaryotic clock, which employs very different molecular systems, operate on similar design principles?  They referred to evolution twice, but only in a very indistinct, indirect way:

The benefit of a clockwork that is imperturbable even when buffeted by the massive intracellular changes of cell division could have provided an evolutionary driving force for convergent circadian clock mechanisms among diverse organisms.
    We now recognize KaiABC as a dynamically oscillating nanomachine that has evolved to precess unidirectionally and robustly. 

These sentences, however, merely assume that evolution produced the machines in the first place.  Since the clocks are present in some of the simplest forms of life, it would seem a grand challenge to believe that a blind, directionless process stumbled upon all this interacting, mechanical system by chance.  Incidentally, they pointed out that each cell has 10,000 KaiC proteins.  If it is difficult to imagine getting one clock by chance, imagine getting 10,000 that tick together. “The challenges ahead,” they ended, “are to delve deeper into the molecular nature of its temperature compensation … and to discover if the clocks in our own cells have attributes that are similar to those of bacteria.”


1.  Johnson, Egli and Stewart, “Structural Insights into a Circadian Oscillator,” Science, 31 October 2008: Vol. 322. no. 5902, pp. 697-701, DOI: 10.1126/science.1150451.

Oh, for the sight of David Hume and Charles Darwin being confronted with a ticking clock inside a “simple” cell.  We can get an idea of their reaction, though, by looking at the fact that the three authors of this review, after having described an intricate mechanism of oscillators, ratchets and feedback loops, attributed it all to evolution.  The many biochemists aware of these and other exquisite molecular machines follow suit.  In spite of overpowering evidence for design, their minds are made up: they will follow Charlie to the bitter end and die with him rather than acknowledge design.
    The Apostle Paul said in Romans 1 that the evidence for God and His attributes is clearly seen in creation, so that men are without excuse.  Each generation has evidence of sufficient clarity for its knowledge base.  For the Romans and Egyptians, the diurnal cycles of the sun, moon and stars have been more than sufficient to remove their excuses for unbelief and mistaken belief.  For today’s scientists, the diurnal cycles of nanoscopic protein clocks throughout life is more than sufficient.  The true challenge ahead is not just to delve deeper into the molecular nature of the design we already see, but to hold it up for display and preach the implications, so that it takes effect in the human mind – as Paul said, “casting down imaginations, and every high thing that exalts itself against the knowledge of God” (II Corinthians 10:5; cf. 01/17/2007).
Next headline on:  Cell BiologyAmazing Facts

  A swarm of bee stories abuzz with design, from 10/27/2006.

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