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.

通常动物的繁衍生息需要动物的活动与周围可预测活动同步。因此，生物功能的时间与节律也就理所应当必须与昼夜交替、潮涨潮落、月圆月缺和四季更迭这样的周期性事件保持大体一致。动物的活动与这些周期之间的关系，特别是与昼夜交替之间的关系，引起人们浓厚的兴趣，而且因为大量的工作都是在其基础之上完成的而意义重大，从而也延伸出了一个特别的研究领域：生物钟学。通常意义上讲，动物活动的经常性转变——例如，睡觉、喂食、活动、繁殖、新陈代谢以及产生酶和荷尔蒙，都与环境的节律同步。但是关键问题在于，动物的作息时间是否受制于外界环境，比如日出日落，又或者是依赖于他们自身独立的生物节律。生物学家普遍认为，所有真核生物（包括除病毒和某些藻类之外的所有生物）都有内部的生物钟。通过将生物与外界的周期性现象完全隔离，生物学家们发现生物的确有生物钟。例如，一种叫脉孢菌的细菌在航天飞机中与一切地球时间线索隔离的情况下，所有生物日常活动周期可以持续一个礼拜左右。在没有外界信号的时候生物也能延续生物节律，这说明生物是具有生物钟的。 将小龙虾置于黑暗环境中，即使持续四五个月，它们的复眼也仍然继续按昼夜交替时间来调节视野。人们发现，马蹄蟹可以在黑暗中连续待一年依然能保持连续的大脑周期活动，这与他们的眼睛适应日常交替的强光光与弱光的周期一致。如同大多数失去外界线索的日循环动物一样，马蹄蟹在这种无光的情况下时长也不一定是准确的24小时。这种和一天的循环周期很接近但不完全同步的循环叫做生理节奏。不同的马蹄蟹生理节奏也不一样，在22.2小时到25.5小时之间浮动。有的动物可以将其特有的准确循环时间维持很多天。的确，稳定性是生物钟最重要的特性之一，即使生物所处环境的诸多要素发生显著变化，例如温度可能会对生物活性产生很大影响。通常外部循环发生突变以后，生物钟持续性就会出现进一步的证据，如科研或者横跨东西快速的长途旅行通常，动物日常的周期循环活动仍然会继续并不会发生什么改变。但与此同时，生物活动又因为新环境的外部循环而产生变化。外界时间信号与内部固有的时间表不同步时出现的迷乱的症状，比如飞行时差综合症，我们会因此持续几天活数周,直到某些信号改变之后，比如日照和黑暗循环需要重新设定生物钟并同步到新环境的日常节律之。 动物需要日出等自然界的周期信号来保持24小时的循环周期。这样的外部信号不仅可以通过当地白昼的特性调节动物的日常节律，而且还保证生物钟循环周期接近地球自转周期——因为这些活动日复一日。但是尽管与生物钟周期同步，动物的时钟仍然延续着它遗传上区别于外部的循环周期，接近24小时但不完全一致。在没有外部信号时，不同的收集方式和这种内在的调节机制作用下的生物活动保持着继续，比如潮汐，就与太阳日有关系。这一趋势在许多动物和生物活动中被广泛研究，从孵化的果蝇卵到松鼠的滚轮跑都有涉及。光在调节生物钟里占主导位置。甚至在持续黑暗环境下仅15分钟的强光照射也会改变动物的生理节律。通常来讲，内部节律会紧随环境循环的步伐。举个例子，如果一个家鸽以太阳作为其导航飞行，那么它的生物钟就必须严格遵守日出日落的循环周期。