Bioinformatics and biological reality

Many bioinformaticians seem to shy away from believing that we can have knowledge about a mind-independent biological reality. This paper attempts to show that this tendency is neither well-founded nor harmless. Even though most bioinformaticians work only with terms and concepts, they cannot altogether disregard the question whether these terms and concepts have any real referents. The paper consists of three parts. Part I clarifies three different positions in the philosophy of science with which it would be good for the philosophical outlook of bioinformaticians to become familiar, and it defends one of them, Karl Popper's epistemological realism. Part II discusses a distinction which is necessary for epistemological realism and is of practical importance for bioinformatics, the distinction between the use and mention of terms and concepts. Part III, finally, contains some brief concluding words about realism, both in general and in relation to bioinformatics.