Rediscoveries are not rare in biology. A recent example is the re-birth of the "fluctuation fit" concept developed by F. B. Straub and G. Szabolcsi in the sixties of the last century, under various names, the most popular of which is the "conformational selection". This theory offers an alternative to the "induced fit" concept by Koshland for the interpretation of the mechanism of protein—ligand interactions. A central question is whether the ligand induces a conformational change (as described by the induced (...) fit model) or rather selects and stabilizes a complementary conformation from a pre-existing equilibrium of various states of the protein (according to the fluctuation fit/conformational selection model). Straub and Szabolcsi’s role and the factors hindering the spread of the fluctuation fit theory are discussed in the context of the history of the Hungarian biology in the 1950s and 1960s. (shrink)

The description of how individual models in families of models are related to each other is crucial for the general philosophical understanding of model-based scientific practice. We focus on the Capital Asset Pricing Models (CAPM) family, a cornerstone in financial economics, to provide a descriptive analysis of model relations within a family. We introduce the concepts of theoretical and empirical complementarity to characterise model relations. Our complementarity analysis of model relations has two types of payoff. Specifically regarding the CAPM, our (...) analysis reveals why this model family, which has been empirically contested, has yet remained popular and important: the different models that have been added over time have made new empirically and theoretically complementary contributions to the model family. More generally, our analysis reveals the dynamic character of model-based scientific practice. Characterising relations between models as theoretically and/or empirically complementary yields three hitherto underappreciated lessons: (i) actual modelling purposes are not always primarily epistemic, (ii) a model's individual import is relative, not absolute, and (iii) there is an important interplay between theory and data models. Faithfully characterising scientific modelling in this way facilitates subsequent analysis of models' epistemic import. (shrink)

It is assumed that scientific models contain no superfluous model elements in scientific representation. A representational model is constructed with all the model elements serving the representational purpose. The received view has it that there are no redundant model elements which are non-representational. Contrary to this received view, I argue that there exist some non-representational model elements which are essential in scientific representation. I call them representation-supporting model elements in virtue of the fact that they play the role to support (...) the representational role of representational model elements. Representation-supporting model elements, which have a characteristic of dependability, are not to be eliminated in the process of modeling although they are playing second fiddle to representational model elements in scientific representation. (shrink)

Conceptual constructive models are a type of scientific model that can be used to construct or reshape the target phenomenon conceptually. Though it has received scant attention from the philosophers, it raises an intriguing issue of how a conceptual constructive model can construct the target phenomenon in a conceptual way. Proponents of the conception of conceptual constructive models are not being explicit about the application of the constructive force of a model in the target construction. It is far from clear (...) that how a conceptual constructive model exerts its constructive force on the constructed phenomenon of interest. Consequently, the function and the epistemic status of a conceptual constructive model are dubious at best. Making use of the conception of abstraction-as-aggregation, I argue that a conceptual constructive model can be used to construct the phenomenon of interest conceptually via a two-step process of abstraction: (1) abstracting away the lower-level details; and (2) aggregating the relevant information into a higher-level composite element. I contend that this process of abstraction, which is not playing the representational role as in a typical representational model, confers the constructive force on a model. (shrink)

Generative models have been proposed as a new type of non-representational scientific models recently. A generative model is characterized with the capacity of producing new models on the basis of the existing one. The current accounts do not explain sufficiently the mechanism of the generative capacity of a generative model. I attempt to accomplish this task in this paper. I outline two antecedent accounts of generative models. I point out that both types of generative models function to generate new homogenous (...) models in the sense that the latter is a straightforward derivative of the former, both of which share many similar features. Unfortunately, both accounts are implicit about the generative capacity of generative models. Using a case study, I articulate that a two-staged process of abstraction and idealization in modeling may contribute to the generative capacity of a scientific model. I also demonstrate that this two-staged process may go beyond the capacity of generating new homogenous models to generating new heterogeneous models. (shrink)

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated with biological mechanisms: the former (...) is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects. (shrink)

Callender and Cohen have proposed to apply a “Gricean strategy” to the constitution problem of scientific representation, taking inspiration from Grice’s reduction of linguistic meaning to mental states. They suggest that scientific representation can be reduced to stipulation by epistemic agents. This account has been criticised for not making a distinction between symbolic and epistemic representation and not taking into account the communal aspects of scientific representation. I argue that these criticisms would not apply if Grice’s actual strategy were properly (...) employed. I present Grice’s account of linguistic meaning and transpose his actual strategy and method to epistemic representation. This results in a reduction of epistemic representation to mental states that does not fall prey to the same criticisms. The main novelty of the resulting account is a distinction between contextual representational use and general representational status, which I address using the notion of indexicality. (shrink)

It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins, ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models, and representations of protein (...) structure is one of integrative pluralism. Our defence appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science. 1. Introduction2. Partiality of Representation3. Protein Functional Complexity4. Modelling Protein Structure4.1 Integrating ab initio and experimental models4.2 Integrating multiple experimental models5. Conclusion. (shrink)

ABSTRACT It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins, ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models, and representations of (...) protein structure is one of integrative pluralism. Our defence appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science. _1._ Introduction _2._ Partiality of Representation _3._ Protein Functional Complexity _4._ Modelling Protein Structure _4.1_ Integrating ab initio and experimental models _4.2_ Integrating multiple experimental models _5._ Conclusion. (shrink)

Our concern is in explaining how and why models give us useful knowledge. We argue that if we are to understand how models function in the actual scientific practice the representational approach to models proves either misleading or too minimal. We propose turning from the representational approach to the artefactual, which implies also a new unit of analysis: the activity of modelling. Modelling, we suggest, could be approached as a specific practice in which concrete artefacts, i.e., models, are constructed with (...) the help of specific representational means and used in various ways, for example, for the purposes of scientific reasoning, theory construction and design of experiments and other artefacts. Furthermore, in this activity of modelling the model construction is intertwined with the construction of new phenomena, theoretical principles and new scientific concepts. We will illustrate these claims by studying the construction of the ideal heat engine by Sadi Carnot. (shrink)

The recent discussion on scientific representation has focused on models and their relationship to the real world. It has been assumed that models give us knowledge because they represent their supposed real target systems. However, here agreement among philosophers of science has tended to end as they have presented widely different views on how representation should be understood. I will argue that the traditional representational approach is too limiting as regards the epistemic value of modelling given the focus on the (...) relationship between a single model and its supposed target system, and the neglect of the actual representational means with which scientists construct models. I therefore suggest an alternative account of models as epistemic tools. This amounts to regarding them as concrete artefacts that are built by specific representational means and are constrained by their design in such a way that they facilitate the study of certain scientific questions, and learning from them by means of construction and manipulation. (shrink)

The concepts of adaptation and fitness have such an appeal that they have been used in other scientific domains, including the social sciences. One particular aspect of this theory transfer concerns the so-called fitness landscape models. At first sight, fitness landscapes visualize how an agent, of any kind, relates to its environment, how its position is conditional because of the mutual interaction with other agents, and the potential routes towards improved fitness. The allure of fitness landscapes is first and foremost (...) that it represents a complex story about adaptation and fitness in one coherent image. Different accounts of fitness landscapes in different domains in the social sciences suggest that the properties and functions of fitness landscapes are attributed rather freely. These differences are testimony of the model’s versatility. At the same time, one will notice that the different approaches can also create ambiguity about the exact meaning and role of fitness landscapes in the social sciences. This article presents an extensive literature survey of the diverging interpretations and uses of fitness landscapes in the social sciences and discusses the implications in terms of how these models inform scientific inquiry. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

Science provides us with representations of atoms, elementary particles, polymers, populations, genetic trees, economies, rational decisions, aeroplanes, earthquakes, forest fires, irrigation systems, and the world’s climate. It's through these representations that we learn about the world. This entry explores various different accounts of scientific representation, with a particular focus on how scientific models represent their target systems. As philosophers of science are increasingly acknowledging the importance, if not the primacy, of scientific models as representational units of science, it's important to (...) stress that how they represent plays a fundamental role in how we are to answer other questions in the philosophy of science. This entry begins by disentangling ‘the’ problem of scientific representation, before critically evaluating the current options available in the literature. (shrink)

Scientific models are important, if not the sole, units of science. This thesis addresses the following question: in virtue of what do scientific models represent their target systems? In Part i I motivate the question, and lay out some important desiderata that any successful answer must meet. This provides a novel conceptual framework in which to think about the question of scientific representation. I then argue against Callender and Cohen’s attempt to diffuse the question. In Part ii I investigate the (...) ideas that scientific models are ‘similar’, or structurally morphic, to their target systems. I argue that these approaches are misguided, and that at best these relationships concern the accuracy of a pre-existing representational relationship. I also pay particular attention to the sense in which target systems can be appropriately taken to exhibit a ‘structure’, and van Fraassen’s recent argument concerning the pragmatic equivalence between representing phenomena and data. My next target is the idea that models should not be seen as objects in their own right, but rather what look like descriptions of them are actually direct descriptions of target systems, albeit not ones that should be understood literally. I argue that these approaches fail to do justice to the practice of scientific modelling. Finally I turn to the idea that how models represent is grounded, in some sense, in their inferential capacity. I compare this approach to anti-representationalism in the philosophy of language and argue that analogous issues arise in the context of scientific representation. Part iii contains my positive proposal. I provide an account of scientific representation based on Goodman and Elgin’s notion of representation-as. The result is a highly conventional account which is the appropriate level of generality to capture all of its instances, whilst remaining informative about the notion. I illustrate it with reference to the Phillips-Newlyn machine, models of proteins, and the Lotka-Volterra model of predator-prey systems. These examples demonstrate how the account must be understood, and how it sheds light on our understanding of how models are used. I finally demonstrate how the account meets the desiderata laid out at the beginning of the thesis, and outline its implications for further questions from the philosophy of science; not limited to issues surrounding the applicability of mathematics, idealisation, and what it takes for a model to be ‘true’. (shrink)

The central question of this thesis is how one can learn about particular targets by using models of those targets. A widespread assumption is that models have to be representative models in order to foster knowledge about targets. Thus the thesis begins by examining the concept of representation from an epistemic point of view and supports an account of representation that does not distinguish between representation simpliciter and adequate representation. Representation, understood in the sense of a representative model, is regarded (...) as a success term. That is, a representative model is one relatum in a relation of adequate representation (Chapter 2). When a representative model represents a target, it allows users of this model to learn something about the target. It is argued that a representative model has this epistemic function because it shares relevant features with the target. This presupposes a similarity view of representation. Similarity views of representation face serious objections, which will be rebutted (Chapter 3). One way of spelling out a similarity view of representation is to defend an indirect view of representation. In this thesis, which does not argue for an indirect view, it is assumed that the indirect view is a good option, if not the best, for articulating the similarity view. It is demonstrated how such an indirect view can be expanded to account for cases of technological modeling. A case study in bioengineering is used to show that the indirect view of representation must acknowledge a distinction between two directions of fit in relations between vehicles and targets. In this context the notion of design is interpreted as a relation between a vehicle and a target, thereby connecting ideas from philosophy of science with ideas from philosophy of technology (Chapter 4). Fictionalist accounts of models are intended to tackle the issue of the ontology of models. In this thesis, however, two prominent fictionalist accounts are discussed from an epistemological point of view in light of the central question regarding how one can learn about targets by using models. This question is addressed from the standpoint of Waltonian fictionalism. The result of the discussion is that the two discussed Waltonian fictionalist accounts cannot sufficiently answer the question. These accounts are criticized for their inability to deliver a satisfactory epistemology of representation (Chapter 5). Although Waltonian fictionalism is criticized, the present thesis also shows that the foundational theory of Waltonian fictionalism, the theory of make-believe can nevertheless be used to account for the distinction between projections and predictions that is made by the Intergovernmental Panel on Climate Change (Chapter 6). (shrink)