Molecular Biology Meets Logic: Context-Sensitiveness in Focus

Abstract

Some real life processes, including molecular ones, are context-sensitive, in the sense that their outcome depends on side conditions that are most of the times difficult, or impossible, to express fully in advance. In this paper, we survey and discuss a logical account of context-sensitiveness in molecular processes, based on a kind of non-classical logic. This account also allows us to revisit the relationship between logic and philosophy of science (and philosophy of biology, in particular).

DNA Tandem Repeats as Iterable Objects to Count Cell Divisions: A Computational Model

“…Indeed, the hypothesis that tandem repeats might work as genomic counters came up years ago [55]: telomere shortening, a much debated and controversial subject (telomeres, the ends of linear chromosomes, are made up of TRs) had been suspected to work as a "replicometer" [56]; telomere shortening occurs during cell division and has been associated with the replicative capacity of cells, in the sense that its shortening could limit the remaining number of divisions, causing cell senescence [57]. The computational model "Lineages" tests a different method to count cell divisions: no losses of material (telomere shortening is a consequence of rough nucleotide depletions), rather precise, intrinsic, and autonomous molecular mechanisms capable of running over TRs, using, as said, the same Boolean logic-algebra that governs algorithms [46] [47] [48] [49]. To count cell divisions, ordered natural numbers are not necessary for cells: different lengths of satDNA se-quences [58] [59], selected during evolution to satisfy the iterative needs of the species, are enough to count different amounts of iterations.…”

Control flow in active inference systems

“…Bowties introduce semantic ambiguities that must be resolved by context. Each incoming signal has its own governing semantics, but the relevant context can depend on boundary conditions which can be exceedingly difficult (if not impossible) to predetermine (see e.g., [163,164] for general discussions of the history and semantic depth of this problem). As pointed out in [22], a context change x → y is semantically problematic if for a fixed set {o i } of observations, the conditional probability distributions P(o i |x) and P(o i |y) are well defined, but the joint distribution P(o i |x ∨ y) is not [106].…”

The logic of explanation in molecular biology: historical-processual and logical-procedural aspects

“…9 Zsyntax has been elaborated to represent types of biological processeswhich can be as long as needed by the analysis at stakeas logical theorems, by taking into account context-sensitivity as well. Initially it was thought especially to deal with text mining (see Boniolo et al, 2010), then improved in certain aspects concerning non-monotonicity (see Boniolo et al, 2013Boniolo et al, , 2015Boniolo et al, , 2021, and finally expanded and provided with an automated theorem prover (see Sestini & Crafa, 2018). Now, given such developments, it is meant as the core of a research program arguing for the place logic should have as the formal counterpart (and representation) of what occurs at the empirical level in molecular biology.…”

“…With respect to ii), it is worth stressing that Zsyntax allows us not only to adequately represent molecular transitions, which can be expressed by empirical generalizations, but also to capture a further crucial aspect of real molecular processes, that is, their being dependent on the context: the EVFs are context-sensitive empirical generalisations, that is, they are valid given a range of specified circumstances. Far from being a marginal aspect, context-sensitivity is central, since all biochemical reactions and biochemical processes always occur in a specific molecular environment (see Boniolo et al, 2021). Zsyntax is able to grasp this feature, for example through the Z-modus ponens, showing that the validity of the empirical generalizations (the EVFs) depends on the particular molecular contextual conditions (given by Δand S) that realize the environment in which the latter take place.…”

“…Features of complex systems and biological organization are largely investigated by means of computational tools, that are simply not the object of this paper. Nevertheless, coming to feedback processes (more generally to control processes) and networks biology, it is to note that very recently some papers have been published exactly on these aspects showing how Zsyntax is able to capture them too (see Boniolo et al, 2021;Boniolo & Lanfrancone, 2016). In sum, the adequacy of the proposal put forward in this paper is to be measured with respect to the exact job that Zsyntax is called to play here.…”