Certain stages of evolution can only be reconstructed by inference from results of comparative and experimental analysis. The ultimate goal is to construct scenarios for certain critical transitions that are plausible and preferably make some predictions that were not part of the initial assumptions and that can be tested. Analysis of present-day living systems gives us strong hints that an RNA world in some form existed for a while.

Reconstruction of that world can only be partial, and should be rather based on experiments that prove certain principles. Aptamers eminently serve this purpose for the RNA world: the experimental results of their in vitro evolution can be justifiably called breathtaking. In this chapter we have addressed two key issues: how the fitness of RNA replicators is affected by mutations, and how coenzymes could have complemented the RNA world and how they, in a literary sense, could have betrayed it by paving a way out of it into the protein world. None of these issues can be taken as settled, however. Although we have put forward a detailed analysis of the function landscape of an RNA enzyme, and have used this to infer the fitness landscape of RNA replicators, many more data are needed in order to be conclusive. In a similar vein, hypotheses centered on the evolutionary role of coenzymes should be more rigorously tested. More ribozymes utilizing cofactors, including various amino acids, should be selected for. Ribozymes that charge other RNA molecules with amino acids should be analyzed to see whether codo-nic or anticodonic triplets predominate in the critical binding sites. Ultimately, some crucial steps in the takeover of ribozymes by protein enzymes need to be re-enacted in experiments and detailed models.

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