Biosemiotics—a discipline in the process of becoming established as a new research enterprise—faces a double task. On the one hand it must carry out the theoretical and experimental investigation of an enormous range of semiotic phenomena relating organisms to their internal components and to other organisms (e.g., signal transduction, replication, codes, etc.). On the other hand, it must achieve a philosophical re-conceptualization and generalization of theoretical biology in light of the essential role played by semiotic notions in biological explanation and (...) modeling. This paper attempts to contribute to the second task by tracing some aspects of the historical evolution of explanatory models in biology. In so doing, a parallel can be drawn between the present status of biosemiotics and that of physics during the early decades of the last century. By following the career of the concept instrument (organon) in Aristotelian science, we revisit historical stages of the antithetical (but often complementary) roles of mechanical and teleological forms of explanation. The impact of the introduction of the organic codes in biology is seen to be somewhat analogous to that of the introduction of the quantum of action in physics. Faced with intractable empirical facts, physicists combined experimental results and bold philosophical speculation to create quantum physics—a wider, deeper framework that accommodates the new facts through a wholesale reformulation of the classical ideas. Essential to this development was the articulation of the epistemic functions of instruments, which was absent from classical physics. Similarly, the consideration of the role of instruments in biology may lead to a synthesis of Aristotelian and Kantian intuitions within a wider framework capable of joining now separate perspectives, such as Jablonka’s four-fold view of inheritance information, Barbieri’s theory of artifactual copymakers and codemakers, and recently developed models of causation based on the idea of manipulative interventions. (shrink)