Paul Boyer shared a Nobel Prize in 1997 for his work on the mechanism of ATP synthase. His earlier work, though (which contributed indirectly to his triumph), included major errors, both experimental and theoretical. Two benchmark cases offer insight into how scientists err and how they deal with error. Boyer's work also parallels and illustrates the emergence of bioenergetics in the second half of the twentieth century, rivaling achievements in evolution and molecular biology.

The term philosophy of chemistry is here construed broadly to include some publications from the history of chemistry and chemical education. Of course this initial selection of material has inevitably been biased by the interests of the author. This bibliography supersedes that of van Brakel and Vermeeren (1981), although no attempt has been made to include every single one of their entries, especially in languages other than English. Also, readers interested particularly in articles in German may wish to consult the (...) bibliography by Dittus and Mayer which also contains some material not included here (Dittus and Mayer, 1992). The aim is to maintain an up-to-date version of this bibliography and to publish a revised version in due course. Suggestions for further inclusions should be sent to the author. (shrink)

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)

We investigate the context of discovery of two significant achievements of twentieth century biochemistry: the chemiosmotic mechanism of oxidative phosphorylation and the dark reaction of photosynthesis. The pursuit of these problems involved discovery strategies such as the transfer, recombination and reversal of previous causal and mechanistic knowledge in biochemistry. We study the operation and scope of these strategies by careful historical analysis, reaching a number of systematic conclusions: even basic strategies can illuminate “hard cases” of scientific discovery that go far (...) beyond simple extrapolation or analogy; the causal–mechanistic approach to discovery permits a middle course between the extremes of a completely substrate-neutral and a completely domain-specific view of scientific discovery; the existing literature on mechanism discovery underemphasizes the role of combinatorial approaches in defining and exploring search spaces of possible problem solutions; there is a subtle interplay between a fine-grained mechanistic and a more coarse-grained causal level of analysis, and both are needed to make discovery processes intelligible. (shrink)

There is an ongoing methodological debate in philosophy of science concerning the use of case studies as evidence for and/or against theories about science. In this paper, I aim to make a contribution to this debate by taking an empirical approach. I present the results of a systematic survey of the PhilSci-Archive, which suggest that a sizeable proportion of papers in philosophy of science contain appeals to case studies, as indicated by the occurrence of the indicator words “case study” and/or (...) “case studies.” These results are confirmed by data mined from the JSTOR database on research articles published in leading journals in the field: Philosophy of Science, the British Journal for the Philosophy of Science (BJPS), and the Journal for General Philosophy of Science (JGPS), as well as the Proceedings of the Biennial Meeting of the Philosophy of Science Association (PSA). The data also show upward trends in appeals to case studies in articles published in Philosophy of Science, the BJPS, and the JGPS. The empirical work I have done for this paper provides philosophers of science who are wary of the use of case studies as evidence for and/or against theories about science with a way to do philosophy of science that is informed by data rather than case studies. (shrink)

: Errors in science range along a spectrum from those relatively local to the phenomenon (usually easily remedied in the laboratory) to those more conceptually derived (involving theory or cultural factors, sometimes quite long-term). One may classify error types broadly as material, observational, conceptual or discoursive. This framework bridges philosophical and sociological perspectives, offering a basis for interfield discourse. A repertoire of error types also supports error analytics, a program for deepening reliability through strategies for regulating and probing error.

In the 1950s–60s biochemists searched intensively for a series of high-energy molecules in the cell. Although we now believe that these molecules do not exist, biochemists claimed to have isolated or identified them on at least sixteen occasions. The episode parallels the familiar eighteenth-century case of phlogiston, in illustrating how error is not simply the loss of facts but, instead, must be actively constructed. In addition, the debates surrounding each case demonstrate how revolutionary-scale disagreement is sometimes resolved by differentiating or (...) partitioning empirical domains, rather than by replacement of one theory by another. (shrink)