Oscillation

Across the tree of life, from bacteria to humans, clocks use oscillating levels of proteins in feedback loops to keep time. Perhaps more amazing, fruit flies and mice — separated by nearly 700 million years of evolution — share the very same timekeeping proteins.
— "First Runner Up: A Remarkable Year for Clocks," Science, 1998.

The term biological clock has been in use for almost half a century, but the precise nature of the analogy has proven elusive for most of that time. A mechanical clock relies on gears, pulleys, weights, and springs. What makes the biological clock tick? How is the clock able to keep time in the absence of environmental cues? Can the clock's function be understood in specific molecular terms?

In seeking a physical model to explain biological timekeeping, scientists hypothesized that the biological clock was a chemically based oscillating system — one that alternates between two extreme states in a regular rhythm in much the same way that a clock-driven pendulum alternates between two extreme physical positions. The system has an input (primarily in the form of light signals), various outputs (chemically controlled cycles), and one or more core mechanisms. These core oscillators operate at the cellular level and rely on molecular feedback loops.



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Pendulum Oscillators.
Galileo discovered the principles of pendulums, and subsequent clockmakers used his discoveries to produce the first reliable mechanical clocks. This late 19th century gravity-driven pendulum was used by exploring expeditions to test gravitational forces at various locations.


Click to watch the video

Relaxation Oscillators.
The pipette washer is a device used to wash laboratory pipettes. It uses an influx of water and a siphoning action that empties or relaxes (see film footage). This basic water-in/water-out mechanism exemplifies a type of oscillator, known as a relaxation oscillator, that was initially appealing as a model for biological oscillators.


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Is this water-clock mechanism a relaxation oscillator? The water-driven clock shown in schematic here does NOT use a relaxation oscillator, but is conceptually more like an hourglass.


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A Chemical Oscillator.
Boris Belousov and Anatol Zhabotinsky are credited with this chemical reaction, which bears their names. When first presented for publication in 1951, the initial paper describing the reaction was rejected as being "quite impossible."

The basic oscillation in this chemically oscillating system is between two different valence states of iron — ferrous (FE2+) and ferric (FE3+). The difference between the two states is made made visible by the presence of a chemical indicator, which turns either red or blue depending on which valence state predominates at any given moment. The oscillation results from two alternating chemical reactions. The first reaction (labeled I) is the autocatalytic oxidation by bromate, by which ferrous ions become ferric ions. The autocatalyst (labeled X) is of uncertain chemical composition. The second reaction (labeled II) is the reduction of ferric ions by malonic acid, which produces bromide ion, which in turn inhibits reaction I. As the ferric ions decrease, so does the bromide ion — and the reaction begins all over again.


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Making K'nexions — A Mechanical Model of Feedback Loops.
This entertaining motor-driven device illustrates the concept of period regulation and feedback loops. The balls (numbered 1–4) follow four distinct pathways, which cycle in a regular and predictable pattern. Each time a ball follows a pathway, it closes a gate — thus causing the next ball to follow a different pathway. The four pathways are grouped, two and two. If this machine were to run continually at an even pace, the period of oscillation would be the time it takes four consecutive balls to complete the cycle. This time period would be a constant.

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