The present paper attempts to demonstrate semiotic arguments against the sequence → structure → function paradigm in protein studies. The unidirectional deterministic thinking in biological processes has been challenged by several disciplines of life sciences and philosophy. Biosemiotics comprehends living organisms as actively participating in their present and somehow creating or shaping their future, having a plurality of options for acting. Determinism and unidirectionality are in contradiction with a biosemiotic approach towards life, mostly when considering Peirce’s triadic concept of semiosis. (...) In this paper, a Peircean biosemiotic approach is applied to proteins and to the process of protein folding. Two main concepts are presented to support the arguments against the SSF paradigm in protein studies: the NonReduction Theorem and the notion of folded continuum. A processual approach is proposed as the most suitable for descriptions of proteins and their functions. (shrink)

All sciences have epistemic assumptions, a language for expressing their theories or models, and symbols that reference observables that can be measured. In most sciences the language in which their models are expressed are not the focus of their attention, although the choice of language is often crucial for the model. On the contrary, biosemiotics, by definition, cannot escape focusing on the symbol–matter relationship. Symbol systems first controlled material construction at the origin of life. At this molecular level it is (...) only in the context of open-ended evolvability that symbol–matter systems and their functions can be objectively defined. Symbols are energy-degenerate structures not determined by laws that act locally as special boundary conditions or constraints on law-based energy-dependent matter in living systems. While this partial description holds for all symbol systems, cultural languages are much too complex to be adequately described only at the molecular level. Genetic language and cultural languages have common basic requirements, but there are many significant differences in their structures and functions. (shrink)