When one considers the many ways by which organisms are completely destroyed after death, it is remarkable that fossils are as common as they are. Attack by scavengers and bacteria, chemical decay, and destruction by erosion and other geologic agencies make the odds against preservation very high. However, the chances of escaping complete destruction are vastly improved if the organism happens to have a mineralized skeleton and dies in a place where it can be quickly buried by sediment. Both of these conditions are often found on the ocean floors, where shelled invertebrates (organisms without spines) flourish and are covered by the continuous rain of sedimentary particles. Although most fossils are found in marine sedimentary rocks, they also are found in terrestrial deposits left by streams and lakes. On occasion, animals and plants have been preserved after becoming immersed in tar or quicksand, trapped in ice or lava flows, or engulfed by rapid falls of volcanic ash.

The term "fossil" often implies petrifaction, literally a transformation into stone. After the death of an organism, the soft tissue is ordinarily consumed by scavengers and bacteria. The empty shell of a snail or clam may be left behind, and if it is sufficiently durable and resistant to dissolution, it may remain basically unchanged for a long period of time. Indeed, unaltered shells of marine invertebrates are known from deposits over 100 million years old. In many marine creatures, however, the skeleton is composed of a mineral variety of calcium carbonate called aragonite. Although aragonite has the same composition as the more familiar mineral known as calcite, it has a different crystal form, is relatively unstable, and in time changes to the more stable calcite.

Many other processes may alter the shell of a clam or snail and enhance its chances for preservation. Water containing dissolved silica, calcium carbonate, or iron may circulate through the enclosing sediment and be deposited in cavities such as marrow cavities and canals in bone once occupied by blood vessels and nerves. In such cases, the original composition of the bone or shell remains, but the fossil is made harder and more durable. This addition of a chemically precipitated substance into pore spaces is termed "permineralization."

Petrifaction may also involve a simultaneous exchange of the original substance of a dead plant or animal with mineral matter of a different composition. This process is termed " replacement" because solutions have dissolved the original material and replaced it with an equal volume of the new substance. Replacement can be a marvelously precise process, so that details of shell ornamentation, tree rings in wood, and delicate structures in bone are accurately preserved.

Another type of fossilization, known as carbonization, occurs when soft tissues are preserved as thin films of carbon. Leaves and tissue of soft-bodied organisms such as jellyfish or worms may accumulate, become buried and compressed, and lose their volatile constituents. The carbon often remains behind as a blackened silhouette.

Although it is certainly true that the possession of hard parts enhances the prospect of preservation, organisms having soft tissues and organs are also occasionally preserved. Insects and even small invertebrates have been found preserved in the hardened resins of conifers and certain other trees. X-ray examination of thin slabs of rock sometimes reveals the ghostly outlines of tentacles, digestive tracts, and visual organs of a variety of marine creatures. Soft parts, including skin, hair, and viscera of ice age mammoths, have been preserved in frozen soil or in the oozing tar of oil seeps.

The probability that actual remains of soft tissue will be preserved is improved if the organism dies in an environment of rapid deposition and oxygen deprivation. Under such conditions, the destructive effects of bacteria are diminished. The Middle Eocene Messel Shale (from about 48 million years ago) of Germany accumulated in such an environment. The shale was deposited in an oxygen-deficient lake where lethal gases sometimes bubbled up and killed animals. Their remains accumulated on the floor of the lake and were then covered by clay and silt. Among the superbly preserved Messel fossils are insects with iridescent exoskeletons (hard outer coverings), frogs with skin and blood vessels intact, and even entire small mammals with preserved fur and soft tissue.