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
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
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
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.
Is this water-clock mechanism a relaxation
The water-driven clock shown in schematic here does NOT use a relaxation oscillator, but is
conceptually more like an hourglass.
Credit 30 Click to watch the video
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.
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.