English: The master circadian clock in the human brain.

Circadian systems need to be considered in relation to three differing levels of organization of information and operation. First is the way in which the physical environment communicates (or ‘Inputs’) key information, particularly related to differentiation of night from day, to the internal ‘master’ clock (located in the brain’s suprachiasmatic nucleus (SCN)). Second are the ‘Intrinsic’ brain factors, consisting of the master clock and its linked regulatory systems (notably secretion of melatonin from the pineal gland). These contribute to sleep onset, sleep architecture, sleep-wake cycles and other central nervous system (CNS)-dependent behavioral changes. Third is the way in which the circadian system coordinates all other hormonal, metabolic, immune, thermoregulatory, autonomic nervous and other physiological processes to optimize the relationships between behavior and body functions (that is, the ‘Outputs’).

At the cellular level, almost all individual cells and, hence, organ systems have their own intrinsic clocks. As these cellular (for example, fibroblasts, fat cells, muscles) and organ-based (for example, liver, pancreas, gut) clocks run to intrinsically different period lengths, the differing physiological systems need to be aligned in coherent patterns. Fundamentally, the master circadian clock permits the organism to align key behavioral and intrinsic physiological rhythms optimally to the external 24-hour light–dark cycle.