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Taphonomy is the study of how organisms are preserved in the fossil record (the term is derived from the Greek word taphos, which means grave). Taphonomists seek to understand how an organism died and what happened to its body before and during burial. They also try to determine what factors may have contributed to unequal representation of certain groups in the fossil record due to differences in their rates of preservation.

One of the challenges taphonomists are often presented with is the interpretation of fossilized broken bones. The scientists must determine if the damage occurred while the animal was alive, after it died, or even after the bone was buried. If the bone broke while the animal was alive, there may be new growth showing that the injury was healing. Bones broken after the animal died will not show any signs of healing. Unfortunately, it is sometimes difficult to determine whether the damage occurred before burial, perhaps by gnawing or trampling, or afterwards.

The study of preservation processes is central to taphonomy. There is much to be learned from the nature of a fossil's preservation, but if a fossil is not well preserved, then there will be little evidence to study.

Rapid burial is crucial to good preservation. One reason is that buried remains are much less likely to be disturbed by scavengers or swept away by rivers. Scavengers pull skeletons apart, scatter bones, and eat some parts preferentially to others. Rivers transport animal and plant remains far from the site of death. Indeed, most organisms are not buried where they die, but are first shuffled around either in part or in whole. This movement may be small, as in the sinking of a fish to the bottom of a lake, or extensive, as when an animal's body floats hundreds of miles in ocean currents. A second reason is that burial, especially in fine-grained muds, may slow down bacterial decay so tissues are better preserved.

Of the organisms that eventually become fossilized, few are preserved intact. This is due to differences in the ability of various parts to resist decay. On the one hand, teeth and bones are very hard, and fossilized specimens are relatively common. On the other, it is quite a find indeed to recover a fossilized heart or other soft part. Since soft parts nearly always decay, even if deeply buried, their pattern can only be preserved if minerals such as carbonate, pyrite, or phosphate replace the soft tissues. Such tissues will not decay if the organism happens to be buried in a sterile environment such as amber or a peat bog.

The hard parts of an organism are held together by soft parts, and when these decay, the organism's anatomy often becomes jumbled and scattered. This may make it difficult to determine what type of organism a part came from, and sometimes different parts of the same organism are accidentally classified as different species. A case in point is Anomalocaris canadensis. Until intact specimens of this prehistoric animal were found, the body was thought to be a sea cucumber, the mouth a jellyfish, and the feeding appendages shrimp-like creatures. By helping to solve puzzles like this, taphonomists increase our understanding of the fossil record.

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