In recent years, particularly in the emerging field of biosemiotics, it has been proposed that semiotics – the study of signification processes – could bring a paradigmatic shift in our scientific conception of life, and consequently in scientific biology in general and beyond. Most if not all semiotic notions, however, derive from studies in logic and linguistics, and a naturalistic, encompassing theory of semiosis that applies to the whole biological realm is still largely lacking. Today, much controversy still exists even about the precise nature of semiosis as well as whether there is only one type of semiosis, or rather that qualitatively different types of semiosis characterize the different levels of life on earth. The goal of this proposal is to help resolve some of these controversies by working out a scientific theory of semiosis from an evolutionary cybernetic perspective, and to apply it to some of the remaining puzzles in evolutionary theory such as the origin of organic codes and the occurrence of major transitions in macroevolution.