Some traces of hidden codes

Recent results in comparative genetics reveal processes of neutral evolution that are reminiscent of neutral codon substitutions, although they operate on novel kinds of sequences and molecular structures. This suggests that in addition to the genetic code, previously unrecognized "degenerate" codes might govern molecular interactions at other levels of biological information. If they exist, such multiple degenerate codes cannot be accounted for by the two concepts usually placed at the heart of molecular biology, i.e. molecular cascades and gene networks. This article reports on some representative examples of putative degenerate codes involving three fundamental levels of biological regulation, i.e. transcription, post-transcriptional regulation and signal transduction. From these examples we suggest that degenerate codes are organized hierarchically and that the concept of neutral evolution can be generalized to all kinds of molecular interactions. In addition, a case of functional evolution is interpreted as the emergence of novel, possibly degenerate codes. Comparative genetics and molecular embryology will be instrumental in testing the existence of multiple degenerate codes and hence, in unraveling the causes of evolution.