“Probably Peirce’s best-known works are the first two articles in a series of six that originally were collectively entitled Illustrations of the Logic of Science and published in Popular Science Monthly from November 1877 through August 1878. The first is entitled ‘The Fixation of Belief’ and the second is entitled ‘How to Make Our Ideas Clear.’ In the first of these papers Peirce defended, in a manner consistent with not accepting naive realism, the superiority of the scientific method over other (...) methods of overcoming doubt and ‘fixing belief.’” — Robert Burch, “Charles Sanders Peirce,” entry in the Stanford Encyclopedia of Philosophy (2021 revision) -/- “Pragmatist epistemologies often explore how we can carry out inquiries in a self-controlled and fruitful way. (Where much analytic epistemology centres around the concept of knowledge, considered as an idealised end-point of human thought, pragmatist epistemology centres around the concept of inquiry, considered as the process of knowledge-seeking and how we can improve it.) So pragmatists often provide rich accounts of the capacities or virtues that we must possess in order to inquire well, and the rules or guiding principles that we should adopt. A canonical account is Peirce’s classic early paper ‘The Fixation of Belief‘. Here Peirce states that inquiry is a struggle to replace doubt with “settled belief“, and that the only method of inquiry that can make sense of the fact that at least some of us are disturbed by inconsistent beliefs, and will subsequently reflect upon which methods of fixing belief are correct is the Method of Science, which draws on the Pragmatic Maxim described above. This contrasts with three other methods of fixing belief: i) refusing to consider evidence contrary to one’s favored beliefs (the Method of Tenacity), ii) accepting an institution’s dictates (the Method of Authority), iii) developing the most rationally coherent or elegant-seeming belief-set (the A Priori Method).“ — Catherine Legg, “Pragmatism,” entry in the Stanford Encyclopedia of Philosophy (2021 revision). (shrink)

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. (shrink)

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)