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Scientists long believed that two nerve clusters in the human hypothalamus, called suprachiasmatic nuclei (SCNs), were what controlled our circadian rhythms. Those rhythms are the biological cycles that recur approximately every 24 hours in synchronization with the cycle of sunlight and darkness caused by Earth's rotation. Studies have demonstrated that in some animals, the SCNs control daily fluctuations in blood pressure, body temperature, activity level, and alertness, as well as the nighttime release of the sleep-promoting agent melatonin. Furthermore , cells in the human retina dedicated to transmitting information about light level to the SCNs have recently been discovered.

Four critical genes governing circadian cycles have been found to be active in every tissue, however, not just the SCNs, of flies, mice, and humans. In addition, when laboratory rats that usually ate at will were fed only once a day, peak activity of a clock gene in their livers shifted by 12 hours, whereas the same clock gene in the SCNs remained synchronized with light cycles. While scientists do not dispute the role of the SCNs in controlling core functions such as the regulation of body temperature and blood pressure, scientists now believe that circadian clocks in other organs and tissues may respond to external cues other than light – including temperature changes – that recur regularly every 24 hours.