According to the sixteenth-century philosopher René Descartes, the pineal gland was the location of the soul. Descartes' first step in his philosophy was to deconstruct everything he knew in order to start from the very beginning. Applying this idea to the human body, he recognised that every part of the brain has a function except for the pineal gland, which was then apparently vestigial. Thus he believed that the organ must be where the soul resides.

And according to health fanatics, the pineal gland is a magical organ that will allow for restful sleep, banish jetlag and wrinkles and increase fertility.

In reality, the organ regulates circadian rhythms through communication with the eye. This is where the idea of being a "third eye" originates. It's also why blind people may sometimes go through long periods without sleep or develop otherwise irregular sleeping patterns. In less-developed vertebrates the pineal gland is structured much like an eye, which suggests that the gland may have been evolution's first attempt at sight. The pineal gland controls sleepiness by stimulating and preventing the release of a hormone called melatonin, when it receives signals from the suprachiasmatic nucleus in the hypothalamus. Light information passes from the retinas to the nucleus, which then sends impulses via the pineal nerve to the gland. The pineal gland then either prevents the "retinal clock" from producing melatonin or causes it to produce more, depending on the light information sent.

Melatonin is currently being studied in an attempt to de-mystify this "vestigial" gland. So far, tests on animals have shown that the hormone inhibits growth of some tumours, and a study on blind women highlighted the link between high melatonin levels and few cases of breast cancer. It has also been suggested that very high levels of melatonin may be a cause of depression, specifically SAD (Seasonal Affective Disorder). Supporters of this idea say that the pineal gland in affected people is in imbalance, and releases too much melatonin in the darker months.

Melatonin may also be effective against disorders such as Paget's Disease, hypertension, epilepsy and sexual dysfunction. A theory claiming that the hormone inhibits sexual development has risen from the fact that the pineal gland produces low levels of melatonin until puberty. Melatonin levels begin to decrease again as the body ages and its pineal gland calcifies, so the hormone may also play a role in delaying the ageing process.

The pineal gland in reptiles and some mammals and amphibians (for example, treefrogs and lizards) does not need to interact with the eye, as it sits fairly close to the skin and so can detect light changes independently. It also controls hibernation periods. As well as monitoring light levels, the pineal gland may also play a part in navigation. It is believed that in birds the gland acts as a navigational centre, which detects magnetic fields around the head and aligns and balances the body. Magnetic material has not yet been found in the human pineal, but researchers believe that the theory satisfactorily explains how the blind are able to navigate.