Theory testing in experimental biology: the chemiosmotic mechanism of ATP synthesis
Introduction
Traditional philosophy of science has construed research essentially as a process of inventing and testing theories (for example, Popper, 1959). Today, this view is widely rejected. For example, ‘New Experimentalists’ such as Hacking (1983) have argued that a considerable part of experimental practice is independent of high-level theories. Similarly, historians of biology have given accounts of episodes in the history of experimental disciplines such as genetics (for example, Kohler, 1994) or molecular biology (Rheinberger, 1997) which focus on experimental systems and research tools rather than experimental tests of theories. These accounts have greatly enriched our understanding of the complexity of experimental practice. However, it is worth examining whether the methodology of theory testing is, indeed, totally irrelevant to understanding the nature of experimental biology. What about famous ‘crucial experiments’, such as the Meselson-Stahl experiment establishing the semi-conservative replication of DNA (Judson, 1979, pp. 188–92), or Tonegawa's final demonstration of the clonal selection mechanism generating antibody diversity (Podolsky & Tauber, 1998)? Were these not experimental tests of theories or hypothetical mechanisms? I would like to maintain that they were, and that a complete understanding of experimental biology requires a study of the methodological principles underlying experimental theory testing.
In order to support this thesis, I examine a case from the history of biochemistry known as the oxidative phosphorylation controversy (ca. 1961–1977). This controversy involved two alternative theories on how mitochondria convert the energy derived from respiration into biologically useful energy (ATP). In Section 2, I introduce these two theories and some other basic features of the ox-phos controversy. Then I turn to the experimental debates which went on in the 1960s and '70s and which eventually led to a resolution of the controversy (Section 3). In Section 4, I take a methodological viewpoint and argue that one of the crucial pieces of evidence responsible for the closure of the controversy can be reconstructed as an argument from error in the sense of Mayo (1996). Next, I examine the same episode from the experimental systems perspective (Section 5). Finally, I conclude that both the methodological and experimental systems perspectives are necessary in order to account for the dynamics of this controversy.
Section snippets
The oxidative phosphorylation controversy
For more than a decade (ca. 1961–1977), biochemists argued over the fundamental mechanism by which cells generate biologically useful energy in the form of adenosine triphosphate (ATP) from the aerobic oxidation of organic compounds. One important set of components responsible for this process was described at a considerable level of detail in the 1940s and '50s: the ‘respiratory chain’, a set of enzyme complexes located in the inner membrane of mitochondria which transfer electrons derived
Protons: movers or moved?
The chemiosmotic theory started to bother a community of scientists immersed in hypothetical chemical intermediates in the mid-1960s.2 Mitchell had
Methodological considerations
The account of some of the experimental work given in the last section raises a puzzle. On the one hand, it seems clear that Mitchell's hypothesis enjoyed a considerable amount of experimental support in the 1960s, especially the acid bath experiment, Mitchell's data on proton translocation (Section 3.1), and the successful prediction that uncouplers increase the proton conductance of biological membranes (Section 3.2). I have argued that the fact that many of Mitchell's opponents did
The experimental systems perspective
According to Rheinberger (1997, p. 28), experimental systems are the ‘smallest integral working units of research’. He further characterizes them as ‘systems of manipulation designed to give unknown answers to questions that the experimenters themselves are not yet able clearly to ask’. In Rheinberger's account, the dynamics of experimental disciplines is largely ‘driven from behind’ by the intrinsic capacities of experimental systems, and not by the evaluation of theories or theoretical
Conclusions
I conclude that only a combination of the New Experimentalist approach with a methodological analysis provides a full explanation of the dynamics of a complex episode in the history of experimental biology such as the one presented here. The New Experimentalist's story is needed because the experiments that biologists do at any given time are not simply derived from a theory in conjunction with methodological principles.
Acknowledgements
I am indebted to Douglas Allchin, Gottfried Schatz and audiences at the Max-Planck-Institute for the History of Science (Berlin) and the University of Minnesota Center for Philosophy of Science and Studies of Science and Technology Program for stimulating discussions of the ox-phos story. I also wish to thank Hanne Andersen, Jay Aronson, Paul Hoyningen-Huene, Eric Oberheim and an anonymous referee for helpful comments on various drafts of this essay.
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2021, Advances in Microbial PhysiologyCitation Excerpt :Protons can simply be moved along the surface of the bacteriorhodopsin sheets (Heberle, 2000; Heberle, Riesle, Thiedemann, Oesterhelt, & Dencher, 1994; Mulkidjanian, Heberle, & Cherepanov, 2006). It has been widely argued that the ability to effect energy coupling by a purified ATP synthase co-located in a membrane that also contains bacteriorhodopsin (Racker & Stoeckenius, 1974) was a critical experiment that somehow ‘proved’ the veracity of the chemiosmotic coupling hypothesis (Allchin, 1996; Morange, 2007; Weber, 2002). Nicholls and Ferguson (2013) phrase it thus: ‘An important point about this experiment is that the ATP synthase and the bacteriorhodopsin originate from such disparate sources; it is inconceivable that the coupling between them occurred through any other mechanism than a proton circuit.’
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