The pineal gland is a secretory gland in the brain midline that is responsible for the release of melatonin. The pineal gland of some amphibians are sensitive to light and helps entrain their circadian rhythms to light. The skulls over the pineal is usually thin for these amphibians. Therefore, rather than taking in daylight through the eyes, they detect it through their skull.

Pineal gland and circadian rhythm

During the genetic dissection of Drosophila melanogaster fruit flies, it was shown that certain genes such as per could affect their circadian cycles. Mammals have one or more versions of these genes. These genes contribute to a molecular clock, regulating each other so that their protein products fluctuate in an approximately 24 hour cycle. The cells in the SCN create two proteins: Clock and Cycle (Drosophila)/Bmal1 (mammals). These two proteins bind to create a dimer. The dimer binds to the cell's DNA and creates two other genes: Per and Cry. These Per and Cry proteins create a dimer as well which inhibits the activity of the Clock and Cycle genes. The Per and Cry proteins break down eventually, which causes the inhibition on the Clock and Cycle genes to disappear. This cycle takes about 24 hours, which creates a molecular circadian cycle within the SCN cells. Each SCN neuron uses this method to keep time and communicate with each other through electrical synapses. The same molecular clock exists in almost every cell in the body, and they all operate as long as the SCN is functioning, which shows that the SCN is the center for molecular rhythm.
- Entrainment of molecular circadian rhythm

Molecular levels of circadian rhythm

Axons from light-sensitive neurons in the retina carry information about how much light is present to the suprachiasmatic nucleus (SCN), allowing the brain's internal clock to stay synchronized with the outside world.

Retinal Light Input to the SCN

A small subregion of the hypothalamus, the suprachiasmatic nucleus (SCN) is in charge of serving as the biological clock. Damage to the SCN affects circadian rhythms relating to drinking and locomotion. Transplant experiments by Ralph et al. showed that when nonmutant hamsters with damage to the SCN were placed in conditions with a constant level of light, their circadian rhythms were gone. However, after these hamsters received SCN transplants from fetal hamsters, the hamsters started showing free-running activity again.

- Pineal gland
- Retinohypothalamic pathway
- Molecular levels of circadian rhythm

University of Rochester

When animals continue to maintain their own cycle even when they aren't provided external cues about time of day, it is called free-running. The cycle during free-running is not exactly 24 hours. 
- changes in circadian rhythm
- hypothalamus 

Free running

Breedlove, S. & Watson, N. (2017). Behavioral neuroscience, eighth edition. Oxford University Press.

Behavioral Neuroscience 8th Edition

Normally, internal clocks are dependent on light. Therefore, if a free-running animal is exposed to constant periods of light and dark, their circadian rhythm can be shifted. For example, a free-running hamster exposed to set periods of light and dark can adjust the hamster's cycle to do its wheel running in the dark period instead of the light period. The change in the circadian rhythm is called a phase shift and the process of synchronizing the rhythm to the environmental stimulus is called entrainment. Zeitgebers are any cues that animals use to synchronize their rhythm with the environment, and it is usually the light-dark cycle. Usually, the zeitgeber entrains circadian rhythms, which causes a phase shift.

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