The Internal Clock

The internal clock is of utmost importance for our body. It regulates almost all physiological functions   [KrMe13, S.4, 55, 68, 128]:

  • Activation of genes and proteins

  • Cognitive and physical performance

  • Time windows, in which sleeping is effective

  • Blood pressure and pulse frequency

  • Hormonal balance, including melatonin and cortisol

  • Metabolism

  • Digestion

  • Urine production

  • Cell division

  • Immune system activity

  • Body temperature

  • Detoxification of the body

But what is the internal clock?

In our body, every organ, every tissue, every cell works 24 hours a day - but not the same way at all times of the day. They have a rhythm, their own daily routine [KrMe13, S.10, 46, 55].

This even persists when individual cells are removed from the body and observed in an artificial environment. However, their work cycle is not exactly, but rather approximately, 24 hours long [KrMe13, S.48]. Therefore, it is called "circadian rhythm" (circa: approximately, dian: Latin dies = day) [KrMe13, S.4]


However, it would be detrimental if every piece of tissue in the body worked according to its own internal clock without aligning with one another. After all, all biochemical processes have to intertwine in a coordinated way for our body to function.

This task of coordinating the various countless body clocks is the responsibility of the SCN (Suprachiasmatic Nucleus) in the hypothalamus of our brain [KrMe13, S.5]. Consisting of 10,000 to 15,000 neurons [KrMe13, S.104] it forms the control center of our internal (circadian) clocks. Via neural signals, hormone expression and regulation of body temperature it synchronizes, like a conductor in the orchestra, all other body clocks in the periphery (peripheral clocks) [KrMe13, S.5]. As a result, the peripheral clocks are slightly delayed compared to the central clock [KrMe13, S.132].

The SCN also ensures that our internal clock works in a 24-hour cycle so it can fit exactly in an Earth day. This is done by coupling its own rhythm to the day-night light change, which is caused by the Earth's rotation [KrMe13, S.69]. The needed light information is collected by the retina and transmitted via the optic nerve. For that reason, light is called the zeitgeber (from German, “time administrator”) for the internal clock [KrMe13, S.13, Roen19]

If one or more internal clocks or the internal and the external clock (time of the day) are misaligned to one another, this is known as circadian misalignment [Vett20]. This has negative effects on health [KrMe13, S.35].

The discrepancy of the internal clock and the social time is caused by travel jetlag or social jetlag [WDMR06]. While travel jetlag is a temporary effect, which disappears, when the internal clock adapts to the light conditions of the destination, social jetlag is chronic in many cases. The misalignment of the various internal clocks is believed to be the cause of the jetlag-related physical discomfort [RPZW19].

This is how the internal clock is set

As mentioned before, the internal clock is entrained by light signals, which are transmitted from the retina to the SCN by the optic nerve [KrMe13, S.13].


Without the external zeitgeber light, meaning under constant light conditions, the internal clock would tick with its own internal period [Czei99, ESTC15]. Therefore, completely blind people are not able to synchronize with the 24-hour rhythm of the day [Alle19]. The average internal cycle of the human internal clock lasts approximately 24.2 hours [Czei99, ESTC15]

In the process of setting the internal clock, the sun-induced light-dark change plays a decisive role, even in our modern society with electric light. This is concluded from the fact that the natural average wake-up time (without external constraint) delays within a time zone from east to west almost exactly four minutes per longitude. This corresponds to the east-west motion of the sun [RoKM07]. There are also seasonal effects. In winter, most people's inner clocks are usually later than in summer [HBWC18, HBWH14, HNST18, KJMR07].

Contrary to widespread opinion, the setting of the internal clock through social times is not possible, or only indirectly possible through the associated changes in light conditions [RoDM03]. Also, contrary to some literature, the external temperature is not a timer for the internal clock in mammals [BuYT10]. In fact, the SCN regulates peripheral body clocks via the body temperature, especially those of the red blood cells [KrMe13, S.9f]. If external temperature did indeed regulate the internal clock, that would result in total disarray of the body’s biochemical processes.

The synchronization process with light is a complex interplay of many cellular mechanisms. Therefore, it shows, much like other body characteristics, a genetic variance. The internal clock of different individuals synchronizes differently with the light-dark change, some earlier others later, which results in various Chronotypes [Roen19].


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