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The pineal gland (also called the pineal body, epiphysis cerebri, or epiphysis) is a small endocrine gland in the brain. It produces melatonin, a hormone that may weakly modulate wake/sleep patterns.  It is shaped like a tiny pine cone, and is located near the center of the brain, between the two hemispheres, tucked in a groove where the two rounded thalamic bodies join.
The pineal gland is a reddish-gray body about the size of a pea (8 mm in humans), located just rostro-dorsal to the superior colliculus and behind and beneath the stria medullaris, between the laterally positioned thalamic bodies. It is part of the epithalamus.
Structure and composition
The pineal gland consists mainly of pinealocytes, but four other cell types have been identified.
The pineal gland receives a sympathetic innervation from the superior cervical ganglion. However, a parasympathetic innervation from the sphenopalatine and otic ganglia is also present. Further, some nerve fibers penetrate into the pineal gland via the pineal stalk (central innervation). Finally, neurons in the trigeminal ganglion innervates the gland with nerve fibers containing the neuropeptide, PACAP. Human follicles contain a variable quantity of gritty material, called corpora arenacea (or "acervuli", or "brain sand"). Chemical analysis shows that they are composed of calcium phosphate, calcium carbonate, magnesium phosphate, and ammonium phosphate. . Recently, calcite deposits have been described as well .
In lower vertebrates
Pinealocytes in lower vertebrate animals have a strong resemblance to the photoreceptor cells of the eye. Some evolutionary biologists believe that the vertebrate pineal cells share a common evolutionary ancestor with retinal cells.
In humans and other mammals, this function is served by the retinohypothalamic system that sets the rhythm within the suprachiasmatic nucleus. Cultural and social interactions produce exposures to artificial light that influence the setting of the suprachiasmatic clock. Evidence for a role for opsin-related light-sensing compounds in the skin of mammals is presently controversial. Research suggests that the pineal gland may serve a magnetoreceptive function in some animals. 
Some early vertebrate fossil skulls have a pineal foramen. This corroborates with the physiology of the modern lamprey, tuatara, and some other vertebrates.
The pineal gland was originally believed to be a "vestigial remnant" of a larger organ (much as the appendix is thought to be a vestigial digestive organ). Aaron Lerner and colleagues at Yale University discovered that melatonin, the most potent compound then known to lighten frog skin, was present in the highest concentrations in the pineal . Melatonin is a derivative of the amino acid tryptophan, which also has other functions in the central nervous system. The production of melatonin by the pineal gland is stimulated by darkness and inhibited by light.  The retina detects the light, and directly signals and entrains the suprachiasmatic nucleus (SCN). Fibers project from the SCN to the paraventricular nuclei (PVN), which relay the circadian signals to the spinal cord and out via the sympathetic system to superior cervical ganglia (SCG), and from there into the pineal gland. The function(s) of melatonin in humans is not clear.
The pineal gland is large in children, but shrinks at puberty. It appears to play a major role in sexual development, hibernation in animals, metabolism, and seasonal breeding. The abundant melatonin levels in children is believed to inhibit sexual development, and pineal tumors have been linked with precocious puberty. When puberty arrives, melatonin production is reduced. Calcification of the pineal gland is typical in adults.
Pineal cytostructure seems to have evolutionary similarities to the retinal cells of chordates.  Modern birds and reptiles have been found to express the phototransducing pigment melanopsin in the pineal gland. Avian pineal glands are believed to act like the suprachiasmatic nucleus in mammals. 
Studies suggest that in rodents the pineal gland may influence the actions of recreational drugs, such as cocaine,  and antidepressants, such as fluoxetine (Prozac), and contribute to regulation of neuronal vulnerability.
Mythologies, Cultures and Philosophies
The secretory activity of the pineal gland has only relatively recently become understood. Historically, its location deep in the brain suggested to philosophers that it possessed particular importance. This combination led to its being a "mystery" gland with myth, superstition and metaphysical theories surrounding its perceived function.
René Descartes, who dedicated much time to the study of the pineal gland, called it the "seat of the soul" . He believed that is was the point of connection between the intellect and the body. This was in part because of his belief that it is unique in the anatomy of the human brain in being a structure not duplicated on the right and left sides. This observation is not true, however; under a microscope one finds the pineal gland is divided into two fine hemispheres. Another theory was that the pineal operated as a valve releasing fluids, thus the position taken during deep thought, with the head slightly down meeting the hand, was an allowance for the opening of these 'valves'.
The pineal gland is occasionally associated with the sixth chakra (also called Ajna or the third eye chakra in yoga) or sometimes the Seventh (Crown) chakra. It is believed by some to be a dormant organ that can be awakened to enable telepathic communication.
The relevance of the pineal gland to Discordianism, an idiosyncratic religion with roots in California psychedelic culture whose doctrines display great fondness for paradox, is great if not well understood.
Writers such as Alice Bailey, considered an early proponent of the new age movement, use the pineal-eye as a key element in their spiritual world-view...(see Alice Bailey: "A Treatise on White Magic")
The notion of a 'pineal-eye' is also crucial to the philosophy of the seminal French writer Georges Bataille, which is analyzed at length by literary scholar Denis Hollier in his study Against Architecture. 
"But the head has a hole in it. The pineal eye, the organ of not-knowing, is the undoing of science. If science thought up man, the pineal eye unthinks him, spends him extravagantly, makes him loose the reserve in which, at the summit, from his head position, he was guarding himself."
In this work Hollier discusses how Bataille uses the concept of a 'pineal-eye' as a reference to a blind-spot in Western rationality.
"When I carefully seek out, in deepest anguish, some strange absurdity, an eye opens at the top, in the middle of my skull. This eye opening up onto the sun in all its glory, to contemplate it in its nakedness, privately, is not the work of my reason: it is a cry escaping from me. For at the moment when the flash blinds me I am the splintering brilliance of a shattered life, and this life - agony and vertigo - opening up onto an infinite void, bursts and exhausts itself all at once in this void."
intermediate/middle/tuberal/pituitary: infundibulum • median eminence • arcuate nucleus • Ventromedial nucleus • Dorsomedial hypothalamic nucleus • Tuber cinereum, Pituitary gland (Anterior pituitary, Posterior pituitary)
posterior/lateral: posterior nucleus • Mammillary body • Lateral nucleus
other: Medial forebrain bundle
|Subthalamus||Subthalamic nucleus • Zona incerta • Thalamic fasciculus • Lenticular fasciculus|
|Thalamus/nuclei||Ventral nuclear group (VA/VL, VP/VPM/VPL) • MD • AN • LNG (Pulvinar) • Intralaminar nucleus (Centromedian nucleus) • Midline nuclear group • Thalamic reticular nucleus • Metathalamus (MG, LG) • Interthalamic adhesion|
|Third ventricle||recesses: (Optic recess, Infundibular recess, Suprapineal recess, Pineal recess) • Hypothalamic sulcus|
|Other||Interventricular foramina • Optic chiasm • Subfornical organ • Mammillothalamic tract|