Methods

Molecular Fossils. In the classical terms of paleobiology, there is no fossil record of the most ancient forms of life or the molecules from which they were made. However, just as mineralized bones, shells, or cell walls tell us about the evolution of modern cellular organisms, contemporary biological molecules provide clues regarding the evolution of the earliest forms of life. In order to discuss precellular evolution in terms that are most accessible to a wide variety of disciplines, we use the phrase "molecular fossil" to describe the molecules that are central to this analysis. A molecular fossil is any molecule whose contemporary structure or function provides a clue to its evolutionary history. Molecular fossils are not to be confused with fossil molecules (DNA preserved in amber), or "living fossils" (slowly evolving species such as the coelacanth), or the physical fossils of cells and multicellular organisms that constitute the raw data for tracing more recent evolution. A molecular fossil is, of necessity, an abstraction rather than a tangible object: it records, embodies, and reflects ancient evolution but is not itself ancient.

Many Interesting Macromolecules Are Social and Are Therefore Constrained to Coevolve. There would be no such thing as a molecular fossil if evolution inevitably erased its own footsteps. But many biological macromolecules are social—they interact with other macromolecules. These interactions constrain the evolution of any individual molecule as well as the ensemble of other molecules with which it interacts. As diagrammed in Figure 2, a social macromolecule can change only in ways that preserve its ability to interact with its important partners. A change in any partner that alters one of these interactions will be tolerated only if all other partners change accordingly. Coevolution of this kind is possible for a molecule that interacts with one or a few different partners but becomes more difficult as the size of the ensemble

Figure 2 Social macromolecules. Evolution of a solitary macromolecule is almost unconstrained as long as it remains functional. The larger the interacting ensemble of macromolecules, the more difficult it is for any one of them to change.



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