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2 Reading the Palimpsest: Contemporary Biochemical Data and the RNA World

Steven A. Benner, Mark A. Cohen, Gaston H. Gonnet, David B. Berkowitz, Kai P. Johnsson


The chemical behavior of contemporary living systems contains vestiges of the history of living chemistry on planet Earth. To read this “palimpsest” is a challenge of the first order (Benner et al. 1989). Some of the historical record has been written over by the demands of natural selection that have forced the evolution of new chemical structures to meet new biological challenges. Some has been lost in the noise arising from random events, the “neutral drift” that characterizes the structural divergence of biological molecules following the divergence of their host organisms (King and Jukes 1969; Kimura 1982). Some has undoubtedly been confused by lateral transfer of genetic information between phylogenetically distant organisms (Doolittle et al. 1990) and by “sequence convergence,” the independent emergence of polypeptide sequences that offer unique chemical solutions to particular biological problems.

Three advances of the past decade have greatly improved our ability to deconvolute the information about earlier life forms written in the biological chemistry of contemporary organisms. First, substantial progress has been made toward an integration of structural theory from chemistry and evolutionary theory from biology (Benner and Ellington 1990b). The integrated theory allows us to proceed past the classic questions in biological chemistry (what happens at a chemical level in a living system) to ask why it happens. A number of questions in biological chemistry have been addressed within the context of the integrated theory, and models are now available to understand the evolutionary status of many molecular aspects of living systems. Most of...

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