Abstract The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify
everything that was wrongheaded, misguided, and just plain wrong with early twentieth …

System biology provides the basis to understand the behavioral properties of complex
biological organisms at different levels of abstraction. Traditionally, analysing systems …

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 …

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, ie, transitions from a molecular …

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 …

In this paper, which is part of the Zsyntax project outlined in Boniolo et al.(2010)[2], we
provide a proof-theoretical setting for the study of context-sensitive interactions by means of …

In this article, two issues regarding mechanisms are discussed. The first concerns the
relationships between “mechanism description” and “mechanism explanation.” It is …

We introduce a logic for knowledge representation and reasoning on protein-protein
interactions. Modulo a theory, formulas describe protein structures and dynamic changes …

This thesis addresses the issue of “Executable Knowledge Representation” in the context of
molecular biology. We introduce the foundation of a logical framework, termed iota, whose …

Recent progress in nanotechnology and optical imaging offers promising features to
develop effective drugs to cure chronic diseases, such as cancer and malaria. However …