The story of Hayy Ibn Yaqzan takes place on an equatorial island uninhabited by human beings. There Hayy is found alone as an infant. Philosophers were of the opinion that he was born spontaneously when the mixture of elements reached an equilibrium state, making it possible for this mixture to receive a human soul from the divine world. Traditionalists believed that he was the son of a woman who chose to keep her marriage to her relative, Yaqzan, secret from her brother who ruled a neighbouring island and did not find any man qualified to marry his sister. After breastfeeding Hayy well, she put him in a box and threw it into the waters, which took him to the uninhabited island. A deer who had just lost her son and was still experiencing the feelings of motherhood heard Hayy's cries. She suckled him, protected him from harmful things and took care of him until she died when he was seven years of age. By then he had learned to imitate other animals in speech, and he covered parts of his body with leaves after noticing that those animal parts are covered with hair or feathers. The deer's death transformed Hayy's life from one of dependency to one of exploration and discovery. In an effort to find out the reason for the deer's death, a reason which he could not locate by observing her appearance, he dissected her with sharp stones and dry reeds. Noticing that every bodily organ has a proper function and that the left cavity of her heart was empty, he concluded that the source of life must have been in this cavity, and must have abandoned it. He reflected on the nature of this vital thing, its link to the body, its source, the place to which it has departed, the manner of its departure and so on. He realized that it was not the body but this vital entity that was the deer and the source of its actions. With this realization he lost interest in the deer's body, which he then viewed as a mere instrument. While he could not decipher the nature of this vital thing, he observed that the shape of all deer was similar to that of his mother. From this he concluded that all deer were managed by something similar to the vital thing that managed his mother's life. After his discovery of life, he came across a fire. He noticed that, contrary to other natural objects, which move downward, fire moves upward. This indicated to him that the essence of fire is other than that of natural things. He continued to investigate other parts of nature: animal organs, their arrangement, number, size and position, as well as the qualities that animals, plants and inanimate things have in common and those that are proper to each of them. Through continued reasoning he grasped the concepts of matter and form, cause and effect, unity and multiplicity, as well as other general concepts concerning the earth and the heavens. Concluding that the universe is one in spite of its multiple objects, he moved on to consider whether it is created or eternal. Through highly sophisticated reasoning, he found that neither the idea of creation nor that of eternity is immune to objection. Though he could not rationally decide whether the universe is created or eternal, he concluded that it must have a cause on which it remains dependent and that this cause or necessary being is non-physical and above it in essence, even if not in time. He also concluded that the thing in him which knew this cause must also be non-physical. The more detached this non-physical thing in him was from sensory perceptions, the clearer was its vision of this cause, a vision that gave the highest joy. Even though sensations obstructed this vision, he felt obliged to imitate animals by experiencing sensations to preserve his animal soul, which would enable him to imitate the heavenly bodies. Imitating the heavenly bodies by doing things like circular movement provided him with continuous but impure vision, for attention in this type of imitation is still paid to the self.
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