Although biological mechanisms do not work with the accuracy or stability of modern clocks, a sense of time and its rhythm is built into the functioning of the human body. Our heart, with its beating pulse, is the clock-like internal rhythm of which we are most aware. In his discovery of the law of the pendulum, which turned out to have the most profound effect on all later time—measuring devices, Galileo used—if legend can be believed—his own pulse beat as the test. There are, however, other biological timekeepers that play important roles in our lives. These inner clocks are generally very regular, but they can also be "reset" and will fall in step with a shifted rhythm. Even after we take a long flight across the Atlantic or Pacific, our lack of synchronization with the local time slowly disappears. The technical term, introduced in 1959, for the internal timer that keeps track of this 24-hour periodicity and retains it even in the absence of external cues is the circadian system (from the Latin circa for "about" or "approximately" and dies for "day"). Though known to biologists for over 200 years, biological clocks have been the subject of intensive research during the last half century.

The first human physiological variables that scientists observed to be governed by a circadian rhythm were pulse rate and body temperature. Even if a person rests in bed and fasts, his or her deep-body temperature will vary by almost one degree centigrade between its low in the early morning hours and a high late in the afternoon. More than 100 additional physiological and psychological variables are also subject to diurnal periodicities. For example, the speed with which children can do computations varies by about 10 percent between its slowest value in the early morning to a high before noon, dropping to a nadir in the early afternoon, rising again to a peak at about 6 o'clock and then falling off in the evening. This pattern was first measured in 1907 and replicated a half century later.

The extremely controversial question that arose immediately was to what extent this human circadian rhythm was an autonomous mechanism rather than a simple response to external signals, such as changes in the level of light, the times of meals, or social interactions with our surroundings. It has not been easy to find the answer, but careful laboratory experiments have led to the definite conclusion that our body contains an autonomous timekeeper. Individuals who volunteered to be kept in artificial isolation with no time cues of any kind also helped find the answer. In 1962 a French researcher spent two months in a cold cave, 375 feet underground in the Alps. The Frenchman called his aboveground supporters by telephone whenever he ate, went to sleep, and woke, and he recorded in detail his thoughts and impressions of the passage of time. He and all such explorers found themselves subject to definite internal time signals. It turned out, however, that the measured period of their bodily variables (all of which were consistent with one another), as well as their subjective impression of the time of day and their periods of sleep and waking, was slightly longer than 25 hours. By the time they emerged from their prolonged isolation, their internal timer was many hours out of phase with the external 24-hour clock.

Today, the autonomy of biological clocks is a well-established fact. Though running at a steady rate, our internal clock is "slow" by about an hour per day, but since it is continually automatically reset by cycles of light and dark, under normal circumstances the loss of time is not cumulative, our internal clock is entrained with the rhyme of the Sun.