Adding logic to the toolbox of molecular biology

Abstract

The aim of this paper is to argue that logic can play an important role in the “toolbox” of molecular biology. We show how biochemical pathways, i.e., transitions from a molecular aggregate to another molecular aggregate, can be viewed as deductive processes. In particular, our logical approach to molecular biology — developed in the form of a natural deduction system — is centered on the notion of Curry-Howard isomorphism, a cornerstone in nineteenth-century proof-theory

MitopatHs: A new logically-framed tool for visualizing multiple mitochondrial pathways

“…Last, since the Z-interaction operator ∗ is binary, it cannot immediately express a direct bind event of more than two proteins without resorting to coupling them into sub-complexes. Moreover, the molecule bindings expressed in MitopatHs overcome the commutativity and associativity properties of the logical operator ∗, thus it is not possible to rely here on the automated theorem prover available for Zsyntax ( Boniolo et al., 2015 ) to automatically infer whether a given complex is reachable from a given set of proteins through a (chain of) mitochondrial pathway.…”

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.…”

Molecular Biology Meets Logic: Context-Sensitiveness in Focus

“…processes (Boniolo et al 2010(Boniolo et al , 2013(Boniolo et al , 2015 and, more in general, to deal with extra-logical information Pulcini 2016, 2017;Sestini and Crafa 2018). According to this pathway-as-deduction paradigm, aggregates of molecules are interpreted as logical types (formulas) and biochemical pathways/processes are formally shaped as logical deductions, i.e., chains or trees of inferences performed according to the rules of a logical system.…”

“…In spite of the still persisting misunderstandings about the role of logic in biology among a number of philosophers of biology and biomedicine, a decade ago some of us put forward Zsyntax, a multifaceted project concerning a logical language for molecular biology and originally designed to deal with text mining (Boniolo et al 2010). Zsyntax was later developed and refined so as to cover also crucial aspects such as non-monotonicity, resource awareness, and automated deduction (Boniolo et al 2013;D'Agostino et al 2014;Boniolo et al 2015;Sestini and Crafa 2018). The whole project relies on a a simple but intriguing idea: representing biochemical types as logical formulae and, consequently, molecular processes as formal derivations.…”