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After studying this chapter, the student should be able to:

  • Understand how circadian rhythms are ubiquitous throughout all life and in virtually all cells in most species.

  • Know how circadian rhythms are derived from intrinsic clock mechanisms.

  • Understand how light sensed by some cells within an organism synchronizes the circadian rhythms of the entire organism.

  • Understand the difference between synchronization and entrainment of circadian clocks.

  • Understand how circadian rhythms work in terms of sleep/activity epochs.

  • Understand the molecular basis of intrinsic circadian rhythms and its robustness with respect to temperature and other perturbations.

  • Recount the role of the suprachiasmatic nucleus (SCN) and retinal output in circadian rhythms.

  • Be aware of the importance of vasoactive intestinal polypeptide (VIP) in circadian rhythms.

  • Understand how the SCN influences the rest of the body’s circadian rhythms.

  • Understand dysfunctions in circadian rhythms such as seasonal affective disorder and sleep problems.


The result of billions of years of evolution, the innate biological clock is a nearly ubiquitous feature of life on Earth. The conservation of its basic function—the maintenance of a stable relationship between the organism’s internal physiologic processes and the environmental light cycle—across such a wide swath of species speaks volumes about its importance. This timekeeping mechanism is not simply a response to changing light, but rather an innate clock that responds slowly and predictably to changes in the architecture of daily light cycles. Behaviorally, this clock allows organisms to predict daily changes in the environment and to react accordingly. Physiologically, the clock serves as a master regulator of many processes, providing a temporal pattern for internal organization and output. In humans and other mammals, the master circadian clock is located in the suprachiasmatic nuclei of the hypothalamus—a pair of densely packed nuclei receiving direct light input from specialized cells in the retina and other indirect timing and physiologic information from a slew of other areas in the nervous system and body. In this chapter, we will explore the basic properties of circadian and seasonal rhythms, the more complex molecular constituents of the clock, and finally, their impact on human health.


At the formation of the solar system, the planetary nursery in the accretion disk had a natural motion, orbiting our nascent Sun and serving as the birthplace of dozens of planetoids colliding with each other like a game of cosmic pinball. These planetoids had a natural rotation parallel with the orbit of the accretion disk, but these planetary rotations tended to vary wildly as their axes wobbled in space or they slowed until they were tidally locked with their star. For Earth, the planet’s rotation was cemented and stabilized approximately 4.4 billion years ago when a Mars-sized planetoid named Theia crashed into it and formed our moon. The Moon stabilized Earth’s axis, slightly off perpendicular to the planet’s orbit around the Sun. The Moon also gave us tides ...

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