This paper provides a restatement and defense of the data/ phenomena distinction introduced by Jim Bogen and me several decades ago (e.g., Bogen and Woodward, The Philosophical Review, 303–352, 1988). Additional motivation for the distinction is introduced, ideas surrounding the distinction are clarified, and an attempt is made to respond to several criticisms.

In this paper, I discuss the discovery of the DNA structure by Francis Crick and James Watson, which has provoked a large historical literature but has yet not found entry into philosophical debates. I want to redress this imbalance. In contrast to the available historical literature, a strong emphasis will be placed upon analysing the roles played by theory, model, and evidence and the relationship between them. In particular, I am going to discuss not only Crick and Watson's well-known model (...) and Franklin's x-ray diffraction pictures (the evidence) but also the less well known theory of helical diffraction, which was absolutely crucial to Crick and Watson's discovery. The insights into this groundbreaking historical episode will have consequences for the ‘new’ received view of scientific models and their function and relationship to theory and world. The received view, dominated by works by Cartwright and Morgan and Morrison ([1999]), rather than trying to put forth a ‘theory of models’, is interested in questions to do with (i) the function of models in scientific practice and (ii) the construction of models. In regard to (i), the received view locates the model (as an idealized, simplified version of the real system under investigation) between theory and the world and sees the model as allowing the application of the former to the latter. As to (ii) Cartwright has argued for a phenomenologically driven view and Morgan and Morrison ([1999]) for the ‘autonomy’ of models in the construction process: models are determined neither by theory nor by the world. The present case study of the discovery of the DNA structure strongly challenges both (i) and (ii). In contrast to claim (i) of the received view, it was not Crick and Watson's model but rather the helical diffraction theory which served a mediating purpose between the model and the x-ray diffraction pictures. In particular, Cartwright's take on (ii) is refuted by a comparison of Franklin's bottom-up approach with Crick and Watson's top-down approach in constructing the model. The former led to difficulties, which only a strong confidence in the structure incorporated in the model could circumvent. How to Get to the Structure 1.1 X-ray diffraction and its synthesis 1.2 Model building and Pauling's panache 1.3 The structure of proteins 1.3.1 A failed inference to the best explanation 1.3.2 The misleading 5.1 Å spot in proteins and how to get rid of it 1.3.3 Derived predictions from Pauling's alpha-helix of protein molecules The CCV Theory of Helical X-Ray Diffraction 2.1 The role of the CCV theory in the discovery of the DNA structure Killing the Helix 3.1 Appreciating all evidence—in vain Conclusion Epilogue: Chargaff's Ratios CiteULike Connotea Del.icio.us What's this? (shrink)

This essay attempts to provide additional motivation for the data/phenomena framework advocated in Bogen and Woodward, “Saving the Phenomena”.

In recent years, the use of historical cases in philosophy of science has become a proper topic of reflection. In this article I will contribute to this research by means of a discussion of one very famous example of case-based philosophy of science, namely the debate on the London & London model of superconductivity between Cartwright, Suárez and Shomar on the one hand, and French, Ladyman, Bueno and Da Costa on the other. This debate has been going on for years, (...) without any satisfactory resolution. I will argue here that this is because both sides impose on the historical case a particular philosophical conception of scientific representation that does not do justice to the historical facts. Both sides assume, more specifically, that the case concerns the discovery of a representational connection between a given experimental insight – the Meissner effect – and the diamagnetic meaning of London and London’s new equations of superconductivity. I will show, however, that at the time of the Londons’ publication, neither the experimental insight nor the meaning of the new equations was established: both were open for discussion and they were stabilized only later. On the basis of this historical discussion, I will then propose an alternative approach to the case study: the case should not be seen as a site of confrontation between pre-existing philosophical accounts, but rather as a way to historically elaborate and develop philosophical concepts. I will then show how approaching the historical episode in this way suggests an alternative approach to the philosophical study of representation, according to which it involves the establishment, over time, of a stable connection between constellations of different elements that, through discussion and engagement with alternative views and approaches, come to constitute phenomenon and meaning. (shrink)

Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the contemporary philosophical debate (...) on the scientific value of simulations, as we demonstrate its ability to form a scientific explanation of natural phenomena and to generate new emergent behaviors, making possible a prediction or hypothesis about the equivalent real-life phenomena. (shrink)

Some twenty years ago, Bogen and Woodward challenged one of the fundamental assumptions of the received view, namely the theory-observation dichotomy and argued for the introduction of the further category of scientific phenomena. The latter, Bogen and Woodward stressed, are usually unobservable and inferred from what is indeed observable, namely scientific data. Crucially, Bogen and Woodward claimed that theories predict and explain phenomena, but not data. But then, of course, the thesis of theory-ladenness, which has it that our observations are (...) influenced by the theories we hold, cannot apply. On the basis of two case studies, I want to show that this consequence of Bogen and Woodward’s account is rather unrealistic. More importantly, I also object against Bogen and Woodward’s view that the reliability of data, which constitutes the precondition for data-to-phenomena inferences, can be secured without the theory one seeks to test. The case studies I revisit have figured heavily in the publications of Bogen and Woodward and others: the discovery of weak neutral currents and the discovery of the zebra pattern of magnetic anomalies. I show that, in the latter case, data can be ignored if they appear to be irrelevant from a particular theoretical perspective (TLI) and that, in the former case, the tested theory can be critical for the assessment of the reliability of the data (TLA). I argue that both TLI and TLA are much stronger senses of theory-ladenness than the classical thesis and that neither TLI nor TLA can be accommodated within Bogen and Woodward’s account. (shrink)

Three decades ago, James Bogen and James Woodward argued against the possibility and usefulness of scientific explanations of data. They developed a picture of scientific reasoning where stable phenomena were identified via data without much input from theory. Rather than explain data, theories ‘save the phenomena’. In contrast, I argue that there are good reasons to explain data, and the practice of science reveals attempts to do so. I demonstrate that algorithms employed to address inverse problems in remote-sensing applications should (...) be understood as attempts to identify phenomena by explaining the data. Thus, this paper furthers understanding of data-to-phenomena reasoning in science, and demonstrates theory may play a more central role in phenomena identification than previously recognized. (shrink)

Taking Bogen and Woodward's discussion of data and phenomena as his starting point, McAllister presents a challenge to scientific realism. I discuss this challenge and offer a suggestion for how the scientific realist could respond to both its epistemic and ontological aspects. In so doing, I urge that the scientific realist should not reject ontological pluralism from the start, but should seek to explore versions of scientific realism that leave open the possibility of certain kinds of pluralist ontology. I investigate (...) the available options and use a law-constitutive approach to offer a strategy for the scientific realist who is open-minded about ontological pluralism. (shrink)