This circadian rhythm controls alertness, sleep, hormone production,body temperature and organ function. The clock is not an organ; it could be called an organ system or a body-wide synchronization of oscillators that exist at a cellular level.
The relationship between core body temperature and waking/sleeping times plays out this circadian rhythm. When the body temperature is dropping, it is easier to get to sleep. When it rises, we tend to wake up. That is why it is easier to sleep in cool rooms.
We live on a clock, whether we want to or not. Not a man-made clock necessarily, but a natural clock that even our Stone Age ancestors followed. The rhythms of our days are at least partly biological. Physiological functions as well as social and cultural events occur in cycles. Even in our modern technological world these cycles are important and measurable differences in abilities are everyday tasks (cognitive and physical) depend on the time of day and where the body is within its cycles.
It is important that we be aware of our rhythms and the rhythms of others. How cranky or amiable people are can depend on where they are in the cycle. Job performance varies depending on where people are on the cycle, and such dangerous matters as drowsy driving are of informed by circadian rhythms.
The body’s physiological processes differ considerably in how sensitive they are to circadian rhythms. Some respond more to circadian clock changes and others more to the sleep-wake process. A variety of mechanisms in the body keep it all together, and external cues from the environment entrain the body to the larger world. The most important external cue is daylight, and temperature, smells (moreso in some animals than humans), and food intake tell the body where it is on the timeline. Man-made, cultural cues are important, too. These include work and school times, television and radio programs, and the activity of friends and family. Sometimes man-made clocks clash with the body’s natural clock and this can result in circadian rhythm sleep disorders.
The processes for keeping it altogether are manifold and a triumph of evolution. It is a combination of a top-down control with feedback and checks and balance from various organ systems. The brain, as might be expected, is in more-or-less control. In particular, an area of the brain called the suprachiasmatic nucleus functions as a master clock, although the control is not as tight as it is in say, the master clock of a computer system.
The SCN is a system of smaller oscillators. The individual SCN neurons can move in different periods (time cycles) in the laboratory – outside the body. But when the neurons are bundled together in the brain they oscillate together. The communication and syncing between the neurons is not due to neurotransmitters but to electrical potential. The overall cycle of the SCN is therefore an emergent property – an agreement among the various neurons that work together.
Daylight and darkness provide external cues to the body and sync the circadian cycle to Nature. The mechanism for this synchronization involves light hitting the eye and sending a signal to the SCN. Detailed study has found the rods and cones in the retina are only tangentially involved in this process. The most important anatomical features are neurons in the retina called ganglion cells that directly communicate to the SCN. The pigments melanopsin and cryptochrome appear to be involved in the ganglion cells and their response to light, although the process is not fully understood.
Now, what happens in the rest of the body? Every human cell appears to have some oscillation, some circadian activity. But left alone, they drift. When studies in laboratory glassware, cells lose their rhythm. One thing the body does on a system-wide basis is coordinate cycles. The SCN functions as the master clock and physiological systems tie things together. These systems include nerves as well as chemicals like cortisol and melatonin. Different parts of the body respond and react in their own ways and not all systems adjust or entrain as well as others. For instance, the liver is slow to adjust. Scientists found kidney cells have a clock of 24.5 hours and cornea cells have one of 21.5 hours This partially explains the vague feelings of disruption people feel when they change time zones – each organ is adjusting one its own terms.
There is feedback from the rest of the body to the brain pacemaker. This can also be in the form of nervous signals or hormone release. Referred to as "peripheral circadian oscillators", these subsystems in the body outside the brain run on their own but are influenced by and influence the master clock. Circadian cycles are quite complex.