Hayy Ibn Yaqzān argues for the compatibility of natural science and theology by depicting how Hayy is able to deduce the existence of God described in the same way as in Islamic doctrine, entirely through the use of observation of the natural world and reasoning. The premise of the text, that Hayy is a boy who grows up entirely without human contact on a remote equatorial island, allows the author to argue for the validity of the Islamic faith by indicating that it is the natural and rational conclusion of any intelligent human who carefully observes the world.

The tale begins by describing how Hayy gained knowledge of the material world, showing him developing a scientific process because of his interest in anatomy and medicine. After the death of the deer who raised him, Hayy begins to study how the body works in order to understand why she died. He first dissects his mother and then “he followed this up by dissecting and vivisecting many animals, constantly learning and improving the quality of his mind until he had reached the level of the finest natural scientists” (117). By suggesting that Hayy first had to become an exemplary natural scientist before he became a spiritual philosopher, Ibn Tufayl suggests that the two viewpoints are harmonious and actively complementary.