Bending Molecules or Bending the Rules? The Application of Theoretical Models in Fragrance Chemistry Ann-Sophie Barwich Konrad Lorenz Institute for Evolution and Cognition Research What does it take for a scientific model to represent? Models, as an integral part of scientific practice, are historically and contextually bound in their application. Practice-oriented debates in recent philosophy of science have emphasised how models can be said to act as representations in practice, e.g., as “mediators” between theory and data. However, the questions that remain open are: what exactly is it that is represented by a scientific model, and in which sense can we speak of a representation? I argue that the proper object of representation in scientific practice is not a model as such but, rather, the entire experimental system in which a model is an active part. The implication of my claim is a strongly historicized perspective on the capacity models to represent: the capacity of a model to represent must be judged against the individual life of an experimental system. In support of my argument, I turn to modelling issues in fragrance chemistry regarding the molecular basis of odors. Explanations of irregularities in the pursuit of so-called structure-odor relations provide an interesting example to analyze the modelling strategies that inform the notion of chemical similarity. 1. The Proper Object of Representation in Modelling Practices What does it take for a scientific model to represent? Scientificmodels have received a great deal of attention in recent philosophical literature. Following Morgan and Morrison’s account of “Models as Mediators” I want to thank the KLI Institute for funding this work. I am grateful to John Dupré, Sabina Leonelli, Hasok Chang, Werner Callebaut, Michael Morrison, Luca Turin two anonymous reviewers and the editors for comments on earlier drafts of this paper. In par- ticular, I am indebted to Stuart Firestein and his many drawings of molecules and receptor sequences until the pub ran out of paper napkins. Perspectives on Science 2015, vol. 23, no. 4 ©2015 by The Massachusetts Institute of Technology doi:10.1162/POSC_a_00183 443 Downloaded from http://www.mitpressjournals.org/doi/pdf/10.1162/POSC_a_00183 by guest on 30 September 2021 444 Bending Molecules or Bending Rules? (1999), analysis of how models represent has changed from questioning what properties of models can be said to correlate with the world to asking how models are used to relate to an intended target-system. This turn to a practice-oriented approach of understanding models was a response to a general philosophical problem that attends the empirical application of scientific representations such as models. This problem is twofold. Models, on the one hand, are often said to make false claims about the world, i.e., assumptions not literally realized in the physical systems they are supposed to represent. On the other hand, models have often been shown to lack forms of resemblance to the physical system they are used to address. These issues can be summarized in the following question: Under what particular conditions do we take models as a representation of the empirical phe- nomena they aim to explain? (Bailer-Jones 2009, p. 177). Given the vast variety of what counts as a model in scientific practice, ranging from material models such as moulages in earlier medical practice to computer simulations of chemical ligand-binding today, no common- ality in terms of what kind of things models are was found. Analyzing various forms of mediation for linking theoretical assumptions to obser- vations, models have been more and more defined by what they do, i.e., how they facilitate access to phenomena we try to understand. Such activity-based approaches often focus on the notion of agency attributed to the modeller and that underlie the construction process (Knuuttila 2005). For instance, abstraction, rather than a property of a representation, is considered to be an intentional activity of the modeller that becomes manifested in a model and its application (Leonelli 2008). The application of a model is defined by its capacity to generate inferences about an in- tended target-system and to act as a vehicle for reasoning (Suárez 2004). In line with this understanding of an epistemic (i.e., knowledge-making) activity of models, further arguments have been provided that emphasize the need to view models in the specific contexts within which they are applied (Morgan 2011), and to analyze modelling practices through their multiple relations of competing with, coordinating and complementing each other (Barwich 2013). Emphasis on the contextuality in the application of models, in turn, resonated with awareness of a certain degree of historicity inherent in modelling. In order to judge the adequacy of inferences generated from a model, these inferences must be situated in and analyzed against the theoretical background in which they are introduced (Musgrave 1974; Worrall 2012). The resulting degree of circularity of evidence construction can be seen to form an epistemic system of “self-vindication” (Hacking 1992). Especially within laboratory sciences, i.e., those sciences whose study of phenomena require techniques to isolate and interfere with materials that Downloaded from http://www.mitpressjournals.org/doi/pdf/10.1162/POSC_a_00183 by guest on 30 September 2021 Perspectives on Science 445 rarely appear observable in a pure state, any theoretical explanation is judged against an organized system of types of analysis, techniques, instruments and specifically chosen research materials. This contextual environment— what Hacking calls “apparatus” (1992) and Rheinberger refers to as an “experimental system” (1997)—constitutes a relatively stable yet sufficiently dynamic background against which explanations drawn from models are evaluated. With respect to this contextuality and historicity in their application, a practice-oriented notion of models addresses how these can be said to rep- resent in scientific practice. Nonetheless, given this emphasis on a model’s interaction with other elements in a model context, rather than its relation or correlation to the target-system, the question remains: what exactly is it that is being represented by a scientific model, and in what sense do we have a representation? To answer this question, I turn to contemporary modelling issues in fragrance chemistry regarding the molecular basis of odors. Research in fragrance chemistry concerns the design of new odorants (odoriferous mol- ecules) from descriptions of molecular parameters. Until today, however, any rule linking the structure of molecules to their odor faces significant exceptions and remains far from law-like (Sell 2006). In the course of this paper, I will analyze the explanation of irregular data in the pursuit of structure-odor relations (SORs). Central to these explanations are a variety of models and instrumental techniques developed throughout the twen- tieth century. In recounting the strategies involved in creating new mole- cules and building models to select and interpret molecular parameters, I draw particular attention to the increasing involvement of model-based inferences coming from outside the laboratory practice of fragrance chem- istry. These models are part of a wider discourse surrounding the molecular basis of smell within molecular biology. By outlining the conceptual devel- opment underlying the central notion of chemical similarity, I will argue for a historicized perspective on the representational capacity of models in scientific practice. The claim I put forward is that the proper object of representation in scientific practice is not a model as such but, rather, the entire experimental system within which a model is embedded. This implies that model-based inferences cannot simply be judged against a general theoretical background that produces the data for their validation. Whether a model represents, rather, needs to be judged against the indi- vidual life of an active experimental system in which it employs a productive role. As some experimental systems, despite being fundamentally inter- twined in their application of a theoretical model, exhibit different stages of theoretical development, some models thus represent in one context but cease to do so in another. Downloaded from http://www.mitpressjournals.org/doi/pdf/10.1162/POSC_a_00183 by guest on 30 September 2021 446 Bending Molecules or Bending Rules? 2. Contemporary Issues in Fragrance Chemistry Odor perceptions are caused by a variety of chemicals that are processed in the olfactory bulb. When we perceive smells we recognize particular fea- tures of the volatile molecules that carry them. But which are the causally relevant features? Investigations into the molecular basis of olfaction are mainly located within two domains: fragrance chemistry and molecular biology. Linking smell to molecular features, research in fragrance chemis- try focuses on regularities between the structure of molecules and their odor quality, leading to the development of rules for SORs (Rossiter 1996; Chastrette 1997). Studies in molecular biology, seeking for insight in the activity patterns of the interaction between odorants and olfactory receptors (ORs), concern the understanding of receptor activation patterns (Peterlin et al. 2008). Although fairly autonomous, both domains act under the shared working hypothesis that the key feature underlying the molec- ular perception mechanism, determining receptor