In humans, mammals, fish, insects, and very many other organisms, the 'Core Clock' which regulates variations in body functions is set to (approximately) 24 hours. This is the so-called Circadian Rhythm. - which in many organisms, is synchronised via daylight.
The clock is regulated via a brain area known as the Suprachiasmatic nucleus (SCN). Neurons in the SCN fire action potentials in a 24-hour rhythm. At mid-day, the firing rate reaches a maximum, and, during the night, it falls again.
Although the SCN has been extensively studied, and the majority of its internal processes are now well understood, fundamental questions still remain. Notably, how the gene expression cycle connects to the SCN's neural firing, and how the neurons in the SCN remain in synch.
[…] whereas the core circadian oscillatory mechanism was obscure only a decade ago, we now have a standard model for the innermost clockworks. Much remains to be determined. What are the requirements for being part of the core mechanistic loop? Because cellular redox state can influence Clock:Bmal1 DNA binding and is likely influenced by clock-controlled phenomena such as electrical activity, is redox potential in or out of the loop? The cell biology of core clock components, particularly regulation of their nuclear export and entry, remains poorly understood. We also do not understand why clock mechanisms have retained (at least) two interconnected loops. What advantages does this confer over a single-loop system? As more detail of the innermost clock’s working is discerned, a major challenge to the field has become stepping back out of the loops and determining how these core oscillations are translated into a temporal program for the whole organism.“
Source : CircadianRhythms:In the Loop at Last Science 6 June 2003 Vol. 300
For examples of current research on the core circadian clock, see the publications of the Partch Lab (archived) at the University of California Santa Cruz, Teams at the lab have recently managed to create an 'in vitrio' simulation of the the bio-clock of some bacteria (ref.) , which involves just 3 proteins, forming a biochemical 'oscillator.'
The intimate coupling between oscillator and input-output components blurs their distinction, although the extent to which this coupling can be generalized to eukaryotic clocks remains an open question.”
Source : Science Vol. 374, No. 6564
In addition to the 'daily' clock, many organisms - from bacteria to mammals - also have a 'yearly' clock known as the Circannual Rhythm.
For example, many mammals moult their fur at certain times of year, or go into hibernation. Various experiments, in which mammals and birds have been kept in artificial indoor environments (i.e. without access to changes in sunlight and temperature etc) have shown that they can still maintain their annual cycle.
The implication is that the organisms have an internal ' clock' of some kind which runs over long timescales of a year or more.
The location of the physical circannual timer in organisms and how it works are almost entirely unknown.
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