Scientific development influences philosophical thought, and vice versa. If philosophy is to be of any use to the production, evaluation or application of biochemical knowledge, biochemistry will have to explicate its needs. This paper concentrates on the need for a philosophical analysis of methodological challenges in biochemistry, above all the problematic relation between in vitro experiments and the desire for in vivo knowledge. This problem receives much attention within biochemistry, but the focus is on practical detail. It is discussed how (...) a theoretical analysis can go beyond a naïve understanding of scientific success and failure in such cases. Several examples are presented to elucidate this issue, including the methodological implications of the precautionary principle, the possible interplay between theoretical methodology of biochemistry and the science studies, and the methodological complexities related to experimental protocol standardisation and use of instruments and kits. (shrink)

Scientific practices have been changed by the increasing use of computer simulations. A central question for philosophers is how to characterize computer simulations. In this paper, we address this question by analyzing simulations in biochemistry. We propose that simulations have been used in biochemistry long before computers arrived. Simulation can be described as a surrogate relationship between models. Moreover, a simulative aspect is implicit in the classical dichotomy between in vivo–in vitro conditions. Based on a discussion about how to characterize (...) a simulative aspect in this dichotomy, we will argue that an adequate understanding of computer simulations in biochemistry requires a previous understanding of simulations in experimental contexts. (shrink)

This paper investigates the interface between philosophy and biochemistry. While it is problematic to justify the application of a particular philosophical model to biochemistry, it seems to be even more difficult to develop a special “Philosophy for Biochemistry”. Alternatively, philosophy can be used in biochemistry based on an alternative approach that involves an interdependent iteration process at a philosophical and (bio)chemical level (“Exeter Method”). This useful iteration method supplements more abstract approaches at the interface between philosophy and natural sciences, and (...) serves the biochemical community to systematically locate logical inconsistencies that arise from more theoretical aspects of the scientific process. Initial cycles of this iteration process identify the in vitro–in vivo problem as a central epistemological difficulty in biochemical research. While previous attempts have generated ad hoc rules to mend the gap between chemistry, biochemistry and biology in order to justify in vitro experimentation, this paper concludes that in vitro experimentation is heavily based on chemistry and cannot derive definite statements about biological processes. It can, however, generate results that will influence the direction of future biological research. The consequence is that the relationship between in vitro and in vivo experimentation is more of a psychological or social one than of a logical nature. Apart from highlighting these inconsistencies in biochemical thinking (“problem awareness”), the Exeter Method demands an improvement of biochemical terminology that contains separate and unequivocally defined terms for in vitro and in vivo systems. (shrink)

In this paper we use some ideas of Hertz and Duhem to propose a new concept of representation that overcomes the dichotomy between representation and intervention. It is based on the category-theoretical notion of adjoint situations and is used to explain the relation between empirical facts and theoretical laws in a new way.