This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...) terms of the Zsyntax language allows us to represent causal interactions by taking into account their context-sensitivity, and amounts to partly reviving the spirit of the so-called received view of explanation – which aimed to capture scientific explanatory accounts in terms of their logical structure and their appealing to nomological relations. Such a partial revival is pursued by invoking here non-classical deductions and empirical generalisations, which are called to provide the epistemic norms to explain the behavior of molecular pathways. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

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).

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.

Biological modalities (e.g., biological possibility, necessity and counterfactuality) play an important explanatory role in biological practice. However, biological modalities lack truth conditions and the inferential relationship between biological and other modalities is unclear. This thesis addresses these problems, first, by improving upon Daniel Dennett's Library of Mendel. Second, a family of modal logics is introduced. In the simplest model, states are interpreted as codons, the binary relation is interpreted as single substitution mutation and the valuation induces a partition of blocks (...) of codons that code for some amino acid. In addition, the proposed framework allows for a grading of biological possibility and captures various competing notions of biological possibility. Applications include a model checker and a lawless Lewis-style semantics for biological counterfactuals. In short, this thesis lays the groundwork for a theory of biological modalities. (shrink)

The complexity of intracellular molecular pathways can be simplified by the use of Network Biology that breaks down the intricacy of biological processes into components and interactions among them. In the paper we show that any complex interactome, that is, a biological network representing protein-protein, protein-DNA and DNA-RNA interactions, can be decomposed into a conjunction of logical theorems expressed in terms of Zsyntax, a formal language which allows representing biological pathways. This result, illustrated with the case study of melanoma network, (...) opens the possibility for a computable model of the cell expressed in a logical language and shows how a formal way of intending philosophy can be useful to cope with the complexity of the biological world. (shrink)