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The Clock Metaphor

The views expressed are those of the author and are not necessarily those of Scientific American.


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Originally published on June 30, 2009.

Chad Orzel wrote a neat history of (or should we say ‘evolution of’) clocks, as in “timekeeping instruments”. He points out the biological clocks are “…sort of messy application, from the standpoint of physics…” and he is right – for us biologists, messier the better. We wallow in mess, cherish ambiguity and relish complexity. Anyway, he is talking about real clocks – things made by people to keep time. And he starts with a simple definition of what a clock is:

In order to really discuss the physics of timekeeping, you need to strip the idea of a clock down to the absolute bare essentials. At its core, a clock really has only one defining characteristic: A clock is a thing that ticks.

OK, I’m using a fairly broad definition of “tick,” here, but if you’ll grant that leeway, “ticking” is the essential property of clocks. In this context, “ticking” just refers to some regular, repetitive behavior that takes place in a periodic fashion.

This reminds me that a “biological clock” is a metaphor. A useful metaphor, but a metaphor nonetheless (and just like metaphors of cellular machinery are taken literally by Creationists, they have been known on occasion to talk about circadian clocks as if they had real wheels and cogs and gears!).

I want to stress that the clock metaphor has been very useful for the study of biological rhythms. Without Pittendrigh’s insight that cycles in nature can be modeled with the math of physical oscillators, we would be probably decades behind (unless someone else of authority in the field at the time had the same insight back then) in our understanding of the underlying biology. Just check how useful it was in the entire conceptualization of entrainment and photoperiodism. The Phase-Response Curve, based on the math of physical oscillators, is the Number One tool in the chronobiological repertoire.

But, just as most people in the field take the clock metaphor for granted and without much thinking, there have been a few people who questioned its utility for some areas of research. For instance, for the study of biological rhythms in nature within an ecological and evolutionary context, Jim Enright proposed a metaphor of an audio-tape set on continuous play (Enright, J.T. (1975). The circadian tape recorder and its entrainment. In Physiological Adaptation to the Environment (ed. F.J.Vernberg), pp. 465-476. Intext Educational Publishers, Ney York.). Only a dozen or so publications since then took him seriously and tried to apply this concept. Today, in the age of CDs and iPods, who even remembers audio tapes?

While fully utilizing the utility of the clock metaphor and applying it myself in my own work, I was always cautious about it. Aware that it is a metaphor, I always wondered if it constrains the way we think about the biological process and if we may miss important insights by not thinking in terms of other possible metaphors.

While far from mature, my thinking is that different metaphors apply best to different areas of research and different questions. While the clock metaphor is great for understanding the entrainment of the circadian system (including whole organism, tissues and individual cells) and photoperiodism, and Enright’s endless tape (or some modern substitute) may be useful for ecological studies (including temporal learning and memory), other angles of study may require other concepts.

For instance, I think that the study of what goes inside the cell can benefit from a different metaphor. Studying the molecular basis of circadian rhythms may best be done by utilizing a Rube-Goldberg Machine metaphor: event A triggers event B which starts process C which results in event D….and so on until the event Z causes the event A to happen again. If that last step is missing, it is not a circadian rhythm – it is more akin to an hourglass clock in which something outside of the system needs to start the process all over again.

For studying the outputs, i.e., how the circadian system orchestrates timing of all the other processes in the body, the metaphor may have to fit the organism. An ON-OFF switch is the best metaphorical description of the clock system in (Cyano)bacteria, where there are only two states of the system: the day state and the night state.

For something a little bit more eukaryotic, a relay may be a better metaphor (more than two, but not too many states). The metaphor of a camshaft in car engines that times the opening and closing of cylinders would be fine for fungi and plants and perhaps some invertebrates.

But I had a hard time coming up with a decent metaphor that could apply to complex animals, like us. So far, the best I could come up with is the barrel of a Player Piano. Many little knobs on its surface determine when each note will be played. If you make the barrel rotate slowly and the song lasts 24 hours, then outputs from circadian pacemakers are knobs and the target organs (and peripheral oscillators in them) are those long prongs that make music. Can you think of a better metaphor?

Related reading:

Basics: Biological Clock
Circadian clock without DNA–History and the power of metaphor
A Pacemaker Is A Network
Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)
Seasonal Affective Disorder – The Basics
Sun Time is the Real Time
Lesson of the Day: Circadian Clocks are HARD to shift!
Lithium, Circadian Clocks and Bipolar Disorder
Are Zombies nocturnal?
Diversity of insect circadian clocks – the story of the Monarch butterfly
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
The Mighty Ant-Lion
City Of Light: Insomniac Urban Animals
Spring Forward, Fall Back – should you watch out tomorrow morning?



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  1. 1. Bonnie Nordby 11:20 pm 12/15/2011

    What popped out for me was the start of a question and perhaps the beginning of an answer. Is creation (all that is) circadian in nature? A-Z and back again? It seems pleasing to think so. It certainly seems better than the hour glass metaphor. Creator standing outside creation and having to reboot the whole thing when time runs out. Can time run out? Then I start to think of my very light knowledge of indian philosophy and the intricacies of the twin pairs of creator, sustainer and destroyer dieties and how the whole is woven in that dance of balance between pairs of opposites. It will take some time to fully explore that question. Hopefully time will not run out.

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