Two great, opposing concepts of the history of the Earth and life dominated thought throughout the Middle Ages. The first was the Biblical account of creation: the world and its life were formed by God a few thousand years before the present. The second was the philosophy of Aristotle and his commentators: the world, and the animals and plants living on it, were eternal, uncreated, and unchanging. Much of the intellectual history of the later Middle Ages revolved around the attempt to integrate and synthesize these two worldviews.
Neither of these two cosmogonies permitted anything like modern evolutionary theory, which postulates an old -- but not eternal -- world, in which organismal lineages arise, change, and go extinct. Nevertheless, various scholars suggested that God might have created the universe by allowing it to evolve acording to natural laws. St. Augustine of Hippo (354- 430) was one of these, writing that God had created the universe as nebulous matter, within which lay "primal seeds", or rationes seminales. These "seeds" grew and developed into the universe and its life forms, guided by the natural laws that God had laid down. Yet investigation and debate about such matters was not encouraged in the early Middle Ages; Augustine himself wrote, "Seek not to understand that you may believe, but believe that you may understand."
Several Islamic writers arrived at concepts that resemble evolution; Othman Amr al-Jahiz (died 869) and Abu-l-Hasan 'Ali al-Masudi (died 956) proposed an evolution "from mineral to plant, from plant to animal, and from animal to man". al-Masudi was exiled from Baghdad, possibly for advocating ideas like these.
The Great Flood, described in the book of Genesis, was used by many medieval and Renaissance Christian writers as an explanation for how fossils came to be (modern-day "scientific creationists" are still hanging on to it). The early Christian writer Tertullian (c. 155 - c. 222 C.E.) wrote: "Yes, and the whole earth was changed once, being covered by all the waters. To this day, sea conchs and tritons' shells are found as strangers on the mountains, desiring to prove to Plato that the heights have once flowed with water." Much later, a thirteenth-century Italian monk, Ristoro d'Arezzo, wrote:
For we have picked up and excavated near the top of a very high mountain, quantities of shells of those fishes which we call cockles or mussels, similar to those which painters use to hold their colors. And in that place they are found mixed with sand, and with round stones among them, both large and small, as if they came from rivers; and this is a sign that that mountain was made by the Deluge.
The diluvial hypothesis became popular in the 17th and 18th centuries, as pious scientists struggled to relate their observations to the Biblical account of creation. The English scientist John Woodward (1665-1728) was perhaps the greatest exponent of the Flood as the creator of fossils. In the words of an admirer, Woodward's book, An Essay toward a Natural History of the Earth, "Vindicates, supports and maintains the Mosaick Account of things, as exactly agreeable to the Phaenomena of Nature." Woodward held that the Flood had dissolved every rock and picked up every living thing into "one common confused Mass," which eventually settled down. The heavier rock particles and fossils sank first, with the lighter particles coming later.
Woodward's enthusiastic follower, the Swiss Johann Scheuchzer (1672- 1733), found fossil tree cones and argued that, since the cones were "tender, young, vernal", the Flood happened in May. He also described a partial skeleton from Oeningen, Germany, as "the bony skeleton of one of those infamous men whose sins brought upon the world the dire misfortune of the deluge." Scheuchzer named the skeleton Homo diluvii testis ("head of a Flood man"). Unfortunately for Scheuchzer's reputation, in 1811 Georges Cuvier examined the skeleton and showed that it was the remains of a giant salamander. The fossil salamander was named Andrias scheuchzeri in Scheuchzer's dubious honor.
In hindsight, the flood theorists actually had gotten one thing right which not everyone else agreed with: fossils were the remains of once-living organisms. There were equally popular theories which stated that fossils were not and never had been living organisms. Some theorized that they were "sports of nature" -- nothing more than unusually shaped rocks. Others, working in the tradition of Aristotle, held that fossils grew inside the Earth, due to some fertile power or "hidden virtue" within the Earth; or that they formed when particles that carried the "form" of an animal or plant landed in rocky matter. In either case, the result was a piece of earthly matter that had the form of an animal or plant. An influential proponent of this view was the Moslem physician Abu 'Ali al-Husayn ibn Abdallah ibn Sina, known in the West as Avicenna (980-1037). Avicenna's writings represented a great advance on previous medical theory. However, his skepticism about alchemy -- the attempts to transmute lesser metals into gold -- led him to believe that bones could not turn to stone. Instead, he thought, a "shaping force" or vis plastica within the Earth had formed stone into the shapes of bones. Avicenna's writings on medicine, translated into Latin, became the standard medical texts in universities all through Europe from the twelfth through the seventeenth centuries.
The debate over the origin of fossils carried on all through the Renaissance and afterwards. Although great scientists like Leonardo da Vinci and John Ray devoted time and effort to solving the problem, the question was not firmly resolved everywhere until about the year 1700.