Icons of ID: Paley’s watch

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We’re all familiar with the use of William Paley’s famous watch analogy as an indicator of design. But did you know that cyanobacteria have their own watches? In the 9/4/99 issue of Science, an article appears entitled “New Timepiece Has a Familiar Riing,” written by Marcia Barinaga. The article even has a nice picture of cyanobacteria, with a caption that some might enjoy:

Thus starts a posting titled “Finding a watch in the ocean” by an intelligent design proponent on biological clocks.

These biological clocks, also known as ‘circadian clock’ have all the attributes of ‘design’, they seem to be complex and specified (clock, feedback loop, oscillator). So what do we know about these circadian clocks?

Before I address the issue of specification and complexity I would like to explain what are ‘circadian rhythms’.

Circadian Clocks

Circadian rhythms refer to clock like patterns with match closely a 24 hour period. The word Circadian is a combination of the word circa (approximately) and dian (day) and means “with about a 24hr length”.

Circadian rhythms are cycles in the behavior, the neuronal functions, the metabolism or the biochemistry of an organism. Examples of Circadian rhythms can be found throughout the animal and plant world. Since light entrainment seems to be found in almost all organisms, a likely hypothesis is that the Circadian clock evolved first in photosynthesis. The earliest report which looked at Circadian rhythms was presented by Jean Jacques d’Ortous de Mairan in 1729 to the Acad�mie Royale des Sciences de Paris. He had noticed how his heliotrope plants (heliotrope: Following the sun) would open and close its leaves even when left in the dark. This meant that the plant was not responding to the cycle of solar light but rather to an internal clock. The term Circadian was coined by Franz Halberg, M.D., of the University of Minnesota one of the world’s foremost specialists in chronobiology.

Typically a Circadian clock consists of an endogenous oscillator and a zeitgeber (time keeper), an external signal which resets or synchronizes the clock. This resetting of the clock is also referred to as entrainment. Circadian clocks can be shown to infer an advantage onto the organism. These advantages come in at least two forms. The first form is the advantage of following the daily rhythms found in nature. (phase locking) For instance plants which shut down their leaves at night. In other words this advantage saves resources, reduces and waste. The second advantage is in the form of being able to predict cycles (the actual clock). For example in plants, genes which encode an enzyme which creates an UV protection (sunburn) can be shown to peak just before sun-rise.

Circadian rythms can be found in almost all organisms. A comparisson among the animal world seems to indicate that there is little conservation of the various components involved. In other words, these clocks have arisen multiple times. But the clocks do share some common features such as a positive and negative transcriptional and translational feedback loops or the presence of a common protein domain (PAS) in the critical clock components. The Circadian clocks seem to be resistant to mutations, in other words few single mutations will destroy the clock function. The Circadian rhythms are temperature independent. In some organisms light was the factor in turning on various processes (plants), in other organisms it was ‘flight from light’ which led light sensitive processes to occur at night. And while light is a common zeitgeber, other external stimuli can play this role as well. The output of these Circadian clocks are the input to the regulation of other genes or other clocks/oscillators.

Fitness effects

The following observations are important from a Darwinian perspective:

  • There is a variability in circadian periods within a species Allows for instance for adaptation at different lattitudes.
  • Genetic mutations affect period and/or amplitude Rather than single mutations leading to the clock falling apart, many mutations have been shown to lead to variation in the period/amplitude of the clock signal
  • Circadian clocks have fitness effect The closer the period to match the external clock, the higher the fitness

It is widely believed from an evolutionary perspective that circadian clocks improve survival by facilitating adaptation to the environment.(2) More specifically, circadian regulation enables a predictive control to achieve the maximum efficiency in metabolism, whereas passive response to environment signals would be reactive. In unicellular cyanobacteria, the circadian clock could precisely regulate photosynthetic genes to be active during day and genes involved in nitrogen fixation to be active at night. However, the merit of circadian control is not always so obvious. In many species, clock mutants (including arrhythmic mutants) survive as well as wild-type organisms, at least in laboratory conditions. This casts doubt upon the adaptive significance of the circadian clock. Enhanced fitness of wild-type cyanobacteria has been demonstrated by competition experiments, however.(24) In these studies, wild-type and period mutants were cultured in the same test tube, so that the two strains competed against each other for their growth under exactly the same conditions. The results clearly indicated that the strain with the period most similar to that of the external light/dark cycles was most successful. Similar results have been obtained in the studies of the lifespan of Drosophila clock mutants.(25)

The circadian clock of cyanobacteriaTakao Kondo and Masahiro Ishiura Review article BioEssays 22:10-15, 2000.

Now it’s time to explore the issue of Complex Specified Information and Irreducible completiy.


In order to establish whether or not the information of the system is complex need to look at the probabilities involved. For this we need to understand the lengths of the genes involved. For cyanobacteria, three genes from a single gene complex appear to be necessary. KaiA, kaiB and KaiC. Although variable in length the kaiA gene varies from 450-900 bp, kaiB genes are typically 300 bp long up to 850 bp and kaiC genes are the longest with lengts varying from 700 to 1500 bp.


Circadian clock (oscillator, clock) Entrainment mechanism (reset, synchronization) Predictor (fitness advantage) Phase locking

Irreducibly complex

A good example of an Irreducibly Complex system was proposed by various ID proponents. I will show that the evolution Circadian rhythm shows how such an IC can evolve after all. Paul Gross’s article Intelligent Design and that Vast Right-wing Conspiracy mentioned the Circadian Rhythm as a good example of an IC system.

But there are in the scientific literature – and have been for sixty years – considerations and examples of the evolution such systems as Behe identifies, structures and processes that have demonstrably evolved from simpler precursors, less complex and sometimes with different functions than those of the contemporary structure or reaction pathway. (See, for a beautiful current example, “Origin and evolution of circadian clock genes in prokaryotes,” by Volodymyr Dvornyk and others, in Proceedings of the National Academy of Sciences, 100 (5): 2495-2500, 2003).

I decided to do some research and found various ID proponents making similar claims. Such as Here, and here.

On a related note, it looks like the clock of cyanobacteria may be irreducibly complex in that it requries kaiABC: Inactivation of any single kai gene abolished these rhythms and reduced kaiBC-promoter activity.Science. 1998 Sep 4;281(5382):1519-23.

The idea that the clock is irreducibly complex is supported in the literature. In addition to the above mentioned Science article:

Comprehensive study of the kaiABC cluster expression in Synechococcus sp. PCC7942 showed that all three kai genes are essential for circadian rhythmicity, and inactivation of any of them completely abolishes it (2).

From: Expression of a Gene Cluster kaiABC as a Circadian Feedback Process in Cyanobacteria

… to be continued soon …

Watch how the Paley Watch comes back to haunt ID


I assume you are working toward the point, but I think that the whole “irreducible complexity” argument suffers from a major logical flaw, which is the notion that if you can break the machine by removing a part, then the parts themselves must be useless. Evolution is full of examples of jerry-rigged (sp?) machines that are not robust in the sense of irreducibility, but the parts themselves (or homologs) may have other roles. One only needs to think of the many overlapping signaling pathways based on phosphorylation/dephosphorylation, and recall that this is also one way that energy is transferred and stored, to recognize that closely related molecules can serve wildly different functions.

An additional point specific to Synechococcus and other bacterial systems. Most, if not all, bacterial cells contain “back-up” systems that allow them to live under various conditions. For example, many phototrophs (photosynthetic bacteria, like the Cyanos) can use organic carbon or even inorganic redox reactions for energy. It may even turn out that photosynthesis is a late comer to this organisms metabolism (a good deal of research indicates that Cyanobacterial fossils, stromatolites, date back far earlier than the time when photosynthesis is likely to have begun), and thus the mechanisms regulating it may be more fragile.

Finally, I don’t really think that Science paper is a good argument for IC, because knockouts are pretty standard fare, and what they really demonstrate is the present interdependency of the genes in the pathway. It may be that significant alterations could be made to the genes without wrecking the system, just not total ko of the gene. I could go on and on, but I think I’ll stop.…

You may be correct that IC suffers from a major logical flaw but what I am doing is applying ID proponents’ claims about this system being IC and their methods how to infer ICness to show how an apparantly IC system could have evolved. A bonus is that this IC system is about ‘watches’, somewhat ironic given Paley’s argument about a watch in a desert… I agree that IC is likely a flawed concept but what better way than to take a claimed IC system and show how it could have evolved

Well, I didn’t really expect you to be defending it!!! I will be interested to read your arguments. I certainly won’t quibble with your tactics (I don’t really have the patience for it myself, but kudos to all of you!), although in my real world job type thing I expect this stuff will come up, so I keep an eye on it. Cheers

The Circadian clock is fascinating to me as it involves some of my interests such as non-linear feedback, instabilities etc. The Circadian clock with its delayed feedback seems to be quite fascinating to study and model. Understanding how such a system may have evolved is already fascinating enough. Having the system be an IC system is just icing on the cake. I am NOT an expert in biology so I am likely to make plenty of mistakes but I have been reading many a paper on the Circadian clock and its functioning, evolution etc are quite well understood although over time more and more fine tuning is needed. The simple 3 gene system which stops working when one of the three genes is disabled, combined with its unique specification (Paley’s watch so to speak) makes it an interesting topic to me. That it also serves to rebut one of the many flawed claims of ID is just ‘icing’.

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This page contains a single entry by PvM published on July 7, 2004 9:00 PM.

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