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4 Probing RNA Structure, Function, and History by Comparative Analysis

Norman R. Pace, Brian C. Thomas, Carl R. Woese


Life on this planet is a profusion of incredibly complex systems. From the biologist’s perspective it is indeed fortunate that all these systems have sprung from a common ancestor. They have by their nature retained traces of their ancestries, and so are similar—homologous—to a greater or lesser extent. The science of biology has been built from its beginning upon cataloging similarities and differences among different living systems (and various states of the same system), the method that has become known as comparative analysis. It is only through this simple and sometimes tedious approach that biologists could begin to understand the complexity with which they are confronted, could begin to distinguish the important elements from the unimportant, and so reduce living systems to a set of understandable essentials. It is also through such comparisons, through measuring similarity and difference in degree and kind, that biologists have come to learn the genealogical relationships among all organisms.

Despite its compelling utility, comparative analysis has not been a commonly used tool in molecular biology. This is not because comparative analysis is without value at the molecular level: The secondary structures of the ribosomal RNAs, major accomplishments of modern molecular biology, are tribute to the comparative approach (Woese et al. 1980; Noller et al. 1981). The molecular biologist’s aversion to comparative analysis would seem to lie in the molecular paradigm itself. Molecular biology arose from chemistry and physics. The entities with which these sciences deal, atoms and their relatively simple chemical combinations, do...

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