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Survival and successful reproduction usually require the activities of animals to be coordinated with predictable events around them. Consequently, the timing and rhythms of biological functions must closely match periodic events like the solar day, the tides, the lunar cycle, and the seasons. The relations between animal activity and these periods, particularly for the daily rhythms, have been of such interest and importance that a huge amount of work has been done on them and the special research field of chronobiology has emerged. Normally, the constantly changing levels of an animal's activity—sleeping, feeding, moving, reproducing, metabolizing, and producing enzymes and hormones, for example—are well coordinated with environmental rhythms, but the key question is whether the animal's schedule is driven by external cues, such as sunrise or sunset, or is instead dependent somehow on internal timers that themselves generate the observed biological rhythms. Almost universally, biologists accept the idea that all eukaryotes (a category that includes most organisms except bacteria and certain algae) have internal clocks. By isolating organisms completely from external periodic cues, biologists learned that organisms have internal clocks. For instance, apparently normal daily periods of biological activity were maintained for about a week by the fungus Neurospora when it was intentionally isolated from all geophysical timing cues while orbiting in a space shuttle. The continuation of biological rhythms in an organism without external cues attests to its having an internal clock.

When crayfish are kept continuously in the dark, even for four to five months, their compound eyes continue to adjust on a daily schedule for daytime and nighttime vision. Horseshoe crabs kept in the dark continuously for a year were found to maintain a persistent rhythm of brain activity that similarly adapts their eyes on a daily schedule for bright or for weak light. Like almost all daily cycles of animals deprived of environmental cues, those measured for the horseshoe crabs in these conditions were not exactly 24 hours. Such a rhythm whose period is approximately—but not exactly—a day is called circadian. For different individual horseshoe crabs, the circadian period ranged from 22.2 to 25.5 hours. A particular animal typically maintains its own characteristic cycle duration with great precision for many days. Indeed, stability of the biological clock's period is one of its major features, even when the organism's environment is subjected to considerable changes in factors, such as temperature, that would be expected to affect biological activity strongly. Further evidence for persistent internal rhythms appears when the usual external cycles are shifted—either experimentally or by rapid east-west travel over great distances. Typically, the animal's daily internally generated cycle of activity continues without change. As a result, its activities are shifted relative to the external cycle of the new environment. The disorienting effects of this mismatch between external time cues and internal schedules may persist, like our jet lag, for several days or weeks until certain cues such as the daylight/darkness cycle reset the organism's clock to synchronize with the daily rhythm of the new environment.

Animals need natural periodic signals like sunrise to maintain a cycle whose period is precisely 24 hours. Such an external cue not only coordinates an animal's daily rhythms with particular features of the local solar day but also—because it normally does so day after day-seems to keep the internal clock's period close to that of Earth's rotation. Yet despite this synchronization of the period of the internal cycle, the animal's timer itself continues to have its own genetically built-in period close to, but different from, 24 hours. Without the external cue, the difference accumulates and so the internally regulated activities of the biological day drift continuously, like the tides, in relation to the solar day. This drift has been studied extensively in many animals and in biological activities ranging from the hatching of fruit fly eggs to wheel running by squirrels. Light has a predominating influence in setting the clock. Even a fifteen-minute burst of light in otherwise sustained darkness can reset an animal's circadian rhythm. Normally, internal rhythms are kept in step by regular environmental cycles. For instance, if a homing pigeon is to navigate with its Sun compass, its clock must be properly set by cues provided by the daylight/darkness cycle.

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