Abstract
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 (epigenetics, proteomics, etc.) and philosophy (process 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.
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Notes
For more information see (Stein 2004) who described enzymes as a particular example of proteins from this dynamic perspecitve.
(In the original, “non è semplicemente un oggetto, bensì è un oggetto che significa qualcosa per un altro Oggetto”)
There is another possible understanding of referentiality in molecules. It might be argued that molecules represent the actual state of the environment. In this way the self-reference could be avoided at the level of molecules. Nevertheless, from a functional viewpoint, the “referents” of proteins are not states of the environment in general, but are states of environment with a direct relation to a proteinic function. Thus, although molecules in general can be comprehended as having a direct reference (state of environment), proteins and substrates in particular are rather self-referential signs.
The term “ostension” in a semiotic background has been a matter of inetrest to the Czech semiotic school, with mainly Ivo Osolsobě working on this notion. Osolsobě defines ostensive signs as things standing for themselves (Osolsobě 2002).
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Acknowledgements
This paper was supported by an internal research grant of Faculty of Arts, Palacký University in Olomouc (2019-2021), project number FPVC2019/03. I declare no conflict of interest.
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Lacková, Ľ. Towards a Processual Approach in Protein Studies. Biosemiotics 12, 469–480 (2019). https://doi.org/10.1007/s12304-019-09370-y
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DOI: https://doi.org/10.1007/s12304-019-09370-y