Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...) considerably richer than those suggested by a nomological framework. Second, the fact that mechanisms involve organized systems of component parts and operations provides direction to both the discovery and testing of mechanistic explanations. Finally, models of mechanisms are developed for specific exemplars and are not represented in terms of universally quantified statements. Generalization involves investigating both the similarity of new exemplars to those already studied and the variations between them. (shrink)

Taking scientific practice as its starting point, this book charts the complex territory of models used in science. It examines what scientific models are and what their function is. Reliance on models is pervasive in science, and scientists often need to construct models in order to explain or predict anything of interest at all. The diversity of kinds of models one finds in science – ranging from toy models and scale models to theoretical and mathematical models – has attracted attention (...) not only from scientists, but also from philosophers, sociologists, and historians of science. This has given rise to a wide variety of case studies that look at the different uses to which models have been put in specific scientific contexts. By exploring current debates on the use and building of models via cutting-edge examples drawn from physics and biology, the book provides broad insight into the methodology of modelling in the natural sciences. It pairs specific arguments with introductory material relating to the ontology and the function of models, and provides some historical context to the debates as well as a sketch of general positions in the philosophy of scientific models in the process. (shrink)

Diagrams have distinctive characteristics that make them an effective medium for communicating research findings, but they are even more impressive as tools for scientific reasoning. Focusing on circadian rhythm research in biology to explore these roles, we examine diagrammatic formats that have been devised to identify and illuminate circadian phenomena and to develop and modify mechanistic explanations of these phenomena.

In this paper, I defend the view that there are many scientific images that have a serious epistemic role in science but this role is not adequately accounted for by the going view of representation and its attendant theoretical commitments. The relevant view of representation is Laura Perini’s account of representation for scientific images. I draw on Adina Roskies’ work on scientific images as well as work on models in science to support my conclusion.

Recent philosophy of science has seen a number of attempts to understand scientific models by looking to theories of fiction. In previous work, I have offered an account of models that draws on Kendall Walton’s ‘make-believe’ theory of art. According to this account, models function as ‘props’ in games of make-believe, like children’s dolls or toy trucks. In this paper, I assess the make-believe view through an empirical study of molecular models. I suggest that the view gains support when we (...) look at the way that these models are used and the attitude that users take towards them. Users’ interaction with molecular models suggests that they do imagine the models to be molecules, in much the same way that children imagine a doll to be a baby. Furthermore, I argue, users of molecular models imagine themselves viewing and manipulating molecules, just as children playing with a doll might imagine themselves looking at a baby or feeding it. Recognising this ‘participation’ in modelling, I suggest, points towards a new account of how models are used to learn about the world, and helps us to understand the value that scientists sometimes place on three-dimensional, physical models over other forms of representation. (shrink)

Scientists typically use a variety of representations, including different kinds of figures, to present and defend hypotheses. In order to understand the justification of scientific hypotheses, it is essential to understand how visual representations contribute to scientific arguments. Since the logical understanding of arguments involves the truth or falsity of the representations involved, visual representations must have the capacity to bear truth in order to be genuine components of arguments. By drawing on Goodman's analysis of symbol systems, and on Tarski's (...) work on truth, I show that the figures used in science meet this criterion. (shrink)

. . . Unlike Dewey, he has provided detailed incisive argumentation, and has shown just where the dogmas and dualisms break down." -- Richard Rorty, The Yale Review.

The paper studies various functions of Berzelian formulas in European organic chemistry prior to the mid-nineteenth century from a semiotic, historical and epistemological perspective. I argue that chemists applied Berzelian formulas as productive ‘paper tools’ for creating a chemical order in the ‘jungle’ of organic chemistry. Beginning in the late 1820s, chemists applied chemical formulas to build models of the binary constitution of organic compounds in analogy to inorganic compounds. Based on these formula models, they constructed new classifications of organic (...) substances. They further applied Berzelian formulas in a twofold way to experimentally investigate organic chemical reactions: as tools which supplemented laboratory tools and as tools for constructing interpretive models of organic reactions. The scrutiny of chemists' performances with chemical formulas on paper also reveals a dialectic which contributed considerably to the formation of the new experimental culture of synthetic carbon chemistry that emerged between the late 1820s and the early 1840s. In an unintended and unforeseen way, the tools reacted back on the goals of their users and contributed to conceptual development and a shift of scientific objects and practices which transcended the originally intended chemical order. (shrink)

A general account of modeling in physics is proposed. Modeling is shown to involve three components: denotation, demonstration, and interpretation. Elements of the physical world are denoted by elements of the model; the model possesses an internal dynamic that allows us to demonstrate theoretical conclusions; these in turn need to be interpreted if we are to make predictions. The DDI account can be readily extended in ways that correspond to different aspects of scientific practice.

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)

Models are of central importance in many scientific contexts. The centrality of models such as inflationary models in cosmology, general-circulation models of the global climate, the double-helix model of DNA, evolutionary models in biology, agent-based models in the social sciences, and general-equilibrium models of markets in their respective domains is a case in point (the Other Internet Resources section at the end of this entry contains links to online resources that discuss these models). Scientists spend significant amounts of time building, (...) testing, comparing, and revising models, and much journal space is dedicated to interpreting and discussing the implications of models. In short, models are one of the principal instruments of modern science. (shrink)

Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic (...) representation is especially well suited for a particular kind of explanation common in molecular biology and biochemistry: namely, functional analysis, in which a capacity of the system is explained in terms of capacities of its component parts. (shrink)

In the early nineteenth century, chemistry emerged in Europe as a truly experimental discipline. What set this process in motion, and how did it evolve? Experimentalization in chemistry was driven by a seemingly innocuous tool: the sign system of chemical formulas invented by the Swedish chemist Jacob Berzelius. By tracing the history of this “paper tool,” the author reveals how chemistry quickly lost its orientation to natural history and became a major productive force in industrial society. These formulas were not (...) merely a convenient shorthand, but productive tools for creating order amid the chaos of early nineteenth-century organic chemistry. With these formulas, chemists could create a multifaceted world on paper, which they then correlated with experiments and the traces produced in test tubes and flasks. The author’s semiotic approach to the formulas allows her to show in detail how their particular semantic and representational qualities made them especially useful as paper tools for productive application. (shrink)

The present paper argues that ‘mature mathematical formalisms’ play a central role in achieving representation via scientific models. A close discussion of two contemporary accounts of how mathematical models apply—the DDI account (according to which representation depends on the successful interplay of denotation, demonstration and interpretation) and the ‘matching model’ account—reveals shortcomings of each, which, it is argued, suggests that scientific representation may be ineliminably heterogeneous in character. In order to achieve a degree of unification that is compatible with successful (...) representation, scientists often rely on the existence of a ‘mature mathematical formalism’, where the latter refers to a—mathematically formulated and physically interpreted—notational system of locally applicable rules that derive from (but need not be reducible to) fundamental theory. As mathematical formalisms undergo a process of elaboration, enrichment, and entrenchment, they come to embody theoretical, ontological, and methodological commitments and assumptions. Since these are enshrined in the formalism itself, they are no longer readily obvious to either the novice or the proficient user. At the same time as formalisms constrain what may be represented, they also function as inferential and interpretative resources. (shrink)

This volume showcases the best of recent research in the philosophy of science. A compilation of papers presented at the EPSA 13, it explores a broad distribution of topics such as causation, truthlikeness, scientific representation, gender-specific medicine, laws of nature, science funding and the wisdom of crowds. Papers are organised into headings which form the structure of the book. Readers will find that it covers several major fields within the philosophy of science, from general philosophy of science to the more (...) specific philosophy of physics, philosophy of chemistry, philosophy of the life sciences, philosophy of psychology, and philosophy of the social sciences and humanities, amongst others. This volume provides an excellent overview of the state of the art in the philosophy of science, as practiced in different European countries and beyond. ​It will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to explore the latest work on the themes explored. (shrink)

Recent work on the role of models in science has revealed a great many kinds of models performing many different roles. In this paper I suggest that one can find much unity among all this diversity by thinking of many models as being components of distributed cognitive systems. I begin by distinguishing the relevant notion of a distributed cognitive system and then give examples of different kinds of models that can be thought of as functioning as components of such systems. (...) These include both physical and abstract models. After considering several objections, I conclude by locating distributed cognition within larger movements in contemporary cognitive science. (shrink)

This article reconsiders the theoretical role of the genetic code. By drawing on published and unpublished sources from the 1950s, I analyse how the code metaphor was actually employed by the scientists who first promoted its use. The analysis shows that the term ‘code’ picked out mechanism sketches, consisting of more or less detailed descriptions of ordinary molecular components, processes, and structural properties of the mechanism of protein synthesis. The sketches provided how-possibly explanations for the ordering of amino acids by (...) nucleic acids. I argue that employing the code metaphor was justified in virtue of its descriptive-denotational and explanatory roles, and because it highlighted a similarity with conventional codes that was particularly salient at the time. 1 Introduction2 Coding Schemes in the 1950s2.1 The research problem: Determining amino acid sequences2.2 The solution: Mapping schemes or ‘codes’3 The Code Metaphor Played Descriptive and Explanatory Roles4 Theness of Codes and the Expendability of the Code Metaphor5 The Role of Arbitrariness6 Conclusions. (shrink)

Organic chemists have been able to develop a robust, theoretical understanding of the phenomena they study; however, the primary theoretical devices employed in this field are not mathematical equations or laws, as is the case in most other physical sciences. Instead it is diagrams, and in particular structural formulas and potential energy diagrams, that carry the explanatory weight in the discipline. To understand how this is so, it is necessary to investigate both the nature of the diagrams employed in organic (...) chemistry and how these diagrams are used in the explanations of the discipline. I will begin this paper by characterizing some of the major ways that structural formulas used in organic chemistry. Next I will present a model of the explanations in organic chemistry and describe how both structural formulas and potential energy diagrams contribute to these explanations. This will be followed by several examples that support my abstract account of the role of diagrams in the explanations of organic chemistry. In particular, I will consider both the appeal to ‘hyperconjugation’ in the explanation of alkene stability and how the idea of ‘ring strain’ was developed to explain the relative stability of cyclic compounds. (shrink)

This volume showcases the best of recent research in the philosophy of science. A compilation of papers presented at the EPSA 13, it explores a broad distribution of topics such as causation, truthlikeness, scientific representation, gender-specific medicine, laws of nature, science funding and the wisdom of crowds. Papers are organised into headings which form the structure of the book. Readers will find that it covers several major fields within the philosophy of science, from general philosophy of science to the more (...) specific philosophy of physics, philosophy of chemistry, philosophy of the life sciences, philosophy of psychology, and philosophy of the social sciences and humanities, amongst others. This volume provides an excellent overview of the state of the art in the philosophy of science, as practiced in different European countries and beyond. ​It will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to explore the latest work on the themes explored. (shrink)

One way visual representations might function in scientific reasoning is to convey content that is true or false, analogous to making a claim. An alternative way that visual representations might function is as an object that may make statements true or false, but is not itself true or false, analogous to a scientific model. In this paper I evaluate the most recent and extended defense of this latter position and show that the case study involved does not in fact support (...) the view that the diagrams discussed function as truth-makers rather than truth bearers. (shrink)

This paper evaluates a general argument for the conclusion that visual representations in science must play the role of truth bearers if they are to figure as legitimate contributors to scientific arguments and explanations. The argument is found to be unsound. An alternative approach to assessing the role of visual representations in science is exemplified by an examination of the role of structural formulas in organic chemistry. Structural formulas are found not to play the role of truth bearers; nonetheless, they (...) contribute to the arguments and explanations of organic chemistry. An early success of conformational analysis is presented in order to illustrate the role of structural formulas in the discourse of organic chemistry. *Received January 2007; revised July 2009. †To contact the author, please write to: Department of Philosophy and Religious Studies, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028; e‐mail: [email protected]. (shrink)

Philosophers have recently paid more attention to the physical aspects of scientific models. The attention is motivated by the prospect that a model’s physical features strongly affect its use and that this suggests re-thinking modelling in terms of extended or distributed cognition. This paper investigates two ways in which physical features of scientific models affect their use and it asks whether modelling is an instance of extended cognition. I approach these topics with a historical case study, in which scientists kept (...) records not only of their findings, but also of some the mental operations that generated the findings. The case study shows how scientists can employ a physical model as an external information store, which allows alternating between mental manipulations, recording the outcome externally, and then feeding the outcome back into subsequent mental manipulations. The case study also demonstrates that a models’ physical nature allows replacing explicit reasoning with visuospatial manipulations. I argue, furthermore, that physical modelling does not need to exemplify a strong kind of extended cognition, the sort for which external features are mereological parts of cognition. It can exemplify a weaker kind, instead. (shrink)