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The concept of a homunculus (Latin for "little man", plural "homunculi"; the diminutive of homo, "human being") is often used to illustrate the functioning of a system. In the scientific sense of an unknowable prime actor, it can be viewed as an entity or agent.

“Preformationism,” a theory of heredity, claimed either the egg or the sperm (exactly which was a contentious issue) contained a complete preformed individual called a homunculus. Development was therefore a matter of enlarging this into a fully formed being. In the days of preformationism, genetic disease was variously interpreted: sometimes as a manifestation of the wrath of God or the mischief of demons and devils; sometimes as evidence of either an excess of or a deficit of the father's “seed”; sometimes as the result of “wicked thoughts” on the part of the mother during pregnancy. On the premise that fetal malformation can result when a pregnant mother's desires are thwarted, Napoleon passed a law permitting expectant mothers to shoplift.

The term appears to have been first used by the alchemist Paracelsus. He once claimed that he had created a false human being that he referred to as the homunculus. The creature was to have stood no more than 12 inches (300 mm) tall, and did the work usually associated with a golem. However, after a short time, the homunculus turned on its creator and ran away. The recipe consisted of a bag of bones, semen, skin fragments and hair from any animal, of which the chimeric homunculus would be a hybrid. This was to be laid in the ground surrounded by horse manure for forty days, at which point the embryo would form.

In Carl Jung's studies of Alchemy, he believed the first record of a homunculus in alchemical literature appeared in the Visions of Zosimos, written in the third century AD, although the actual word "homunculus" was never used. In the visions, Zosimos mentions encountering a man who impales him with a sword, and then undergoes "unendurable torment," his eyes become blood, he spews forth his flesh, and changes into "the opposite of himself, into a mutilated anthroparion, and he tore his flesh with his own teeth, and sank into himself," which is a rather grotesque personification of the ouroboros, the dragon that bites its own tail, which represents the dyophysite nature in alchemy: the balance of two principles. Zosimos later encounters several other homunculi, named as the Brazen Man, the Leaden Man, and so forth. Commonly, the homunculi "submit themselves to unendurable torment" and undergo alchemical transformation. Zosimos made no mention of actually creating an artificial human, but rather used the concept of personifying inanimate metals to further explore alchemy.

There are also variants cited by other alchemists. One such variant involved the use of the mandrake. Popular belief held that this plant grew where semen ejaculated by hanged men (during the last convulsive spasms before death) fell to the ground, and its roots vaguely resemble a human form to varying degrees. The root was to be picked before dawn on a Friday morning by a black dog, then washed and "fed" with milk and honey and, in some prescriptions, blood, whereupon it would fully develop into a miniature human which would guard and protect its owner. Yet a third method, cited by Dr. David Christianus at the University of Giessen during the 18th century, was to take an egg laid by a black hen, poke a tiny hole through the shell, replace a bean-sized portion of the white with human semen, seal the opening with virgin parchment, and bury the egg in dung on the first day of the March lunar cycle. A miniature humanoid would emerge from the egg after thirty days, which would help and protect its creator in return for a steady diet of lavender seeds and earthworms.

The term homunculus was later used in the discussion of conception and birth. In 1694, Nicolas Hartsoeker discovered "animalcules" in the semen of humans and other animals. This was the beginning of spermists' theory, who held the belief that the sperm was in fact a "little man" (homunculus) that was placed inside a woman for growth into a child. This seemed to them to neatly explain many of the mysteries of conception. It was later pointed out that if the sperm was a homunculus, identical in all but size to an adult, then the homunculus may have sperm of its own. This led to a reductio ad absurdum, with a chain of homunculi "all the way down". This was not necessarily considered by spermists a fatal objection however, as it neatly explained how it was that "in Adam" all had sinned: the whole of humanity was already contained in his loins. The spermists' theory also failed to explain why children tend to resemble their mothers as well as their fathers, though some spermists believed that the growing homunculus assimilated maternal characteristics from the womb environment in which they grew.

The homunculus is also commonly used to describe the distorted human figure drawn to reflect the relative space our body parts occupy on the somatosensory cortex (sensory homunculus) and the motor cortex (motor homunculus). The lips, hands, feet and sex organs have more sensory neurons than other parts of the body, so the homunculus has correspondingly distortedly large lips, hands, feet, and genitals. Well known in the field of neurology, this is also commonly called 'the little man inside the brain.'