A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by (...) drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable—a research programme that is perhaps taken to its most extreme form in systems biology’s sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to ‘dirty, unruly living systems’. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. (shrink)

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...) models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

Western philosophers have traditionally concentrated on theory as the means for expressing knowledge about a variety of phenomena. This absorbing book challenges this fundamental notion by showing how objects themselves, specifically scientific instruments, can express knowledge. As he considers numerous intriguing examples, Davis Baird gives us the tools to "read" the material products of science and technology and to understand their place in culture. Making a provocative and original challenge to our conception of knowledge itself, _Thing Knowledge _demands that we (...) take a new look at theories of science and technology, knowledge, progress, and change. Baird considers a wide range of instruments, including Faraday's first electric motor, eighteenth-century mechanical models of the solar system, the cyclotron, various instruments developed by analytical chemists between 1930 and 1960, spectrometers, and more. (shrink)

A theory of analogy must describe how the meaning of an analogy is derived from the meanings of its parts. In the structure‐mapping theory, the interpretation rules are characterized as implicit rules for mapping knowledge about a base domain into a target domain. Two important features of the theory are (a) the rules depend only on syntactic properties of the knowledge representation, and not on the specific content of the domains; and (b) the theoretical framework allows analogies to be distinguished (...) cleanly from literal similarity statements, applications of abstractions, and other kinds of comparisons.Two mapping principles are described: (a) Relations between objects, rather than attributes of objects, are mapped from base to target; and (b) The particular relations mapped are determined by systematicity, as defined by the existence of higher‐order relations. (shrink)

Scientific representation is a currently booming topic, both in analytical philosophy and in history and philosophy of science. The analytical inquiry attempts to come to terms with the relation between theory and world; while historians and philosophers of science aim to develop an account of the practice of model building in the sciences. This article provides a review of recent work within both traditions, and ultimately argues for a practice-based account of the means employed by scientists to effectively achieve representation (...) in the modelling sciences. (shrink)

The logical empiricists held that an analogical hypothesis does not gain any acceptability from the analogy on which it is founded. On this view, the acceptability of a hypothesis cannot be discounted by criticizing the foundational analogy. Yet scientists commonly appear to level exactly this sort of criticism. If scientists are able to discount the acceptability of analogical hypotheses in this way, then the logical empiricist view is mistaken. I analyze four forms of analogy counterargument, disanalogy, misanalogy, counteranalogy, and false (...) analogy, with examples from the debate over the asteroid impact hypothesis. These counterarguments do address the acceptability of analogical hypotheses, indicating that analogies can confer acceptability, confirmation notwithstanding. 1 Introduction 2 The asteroid impact hypothesis 3 Analogy counterarguments 3.1 Disanalogy 3.2 Misanalogy 3.3 Counteranalogy 3.4 False analogy 4 Acceptability 5 Conclusions. (shrink)

Mary Hesse's well-known work on models and analogies gives models a creative role to play in science, which rests on developing certain analogical properties considered neutral between the two fields. Case study material from Irving Fisher's work (The Purchasing Power of Money, 1911), in which he used analogies to construct models of monetary relations and the monetary system, highlights certain omissions in Hesse's account. The analysis points to the importance of taking account of the negative properties in the analogies and (...) to certain differences between "ready-made" analogies (models of systems based on existing analogical structures) and "designed" analogies (models built up from separate analogical features). (shrink)

This article shows how the MISS account of models—as isolations and surrogate systems—accommodates and elaborates Sugden’s account of models as credible worlds and Hausman’s account of models as explorations. Theoretical models typically isolate by means of idealization, and they are representatives of some target system, which prompts issues of resemblance between the two to arise. Models as representations are constrained both ontologically (by their targets) and pragmatically (by the purposes and audiences of the modeller), and these relations are coordinated by (...) a model commentary. Surrogate models are often about single mechanisms. They are distinguishable from substitute models, which are examined without any concern about their connections with the target. Models as credible worlds are surrogate models that are believed to provide access to their targets on account of their credibility (of which a few senses are distinguished). (shrink)

This article shows how the MISS account of models—as isolations and surrogate systems—accommodates and elaborates Sugden’s account of models as credible worlds and Hausman’s account of models as explorations. Theoretical models typically isolate by means of idealization, and they are representatives of some target system, which prompts issues of resemblance between the two to arise. Models as representations are constrained both ontologically (by their targets) and pragmatically (by the purposes and audiences of the modeller), and these relations are coordinated by (...) a model commentary. Surrogate models are often about single mechanisms. They are distinguishable from substitute models, which are examined without any concern about their connections with the target. Models as credible worlds are surrogate models that are believed to provide access to their targets on account of their credibility (of which a few senses are distinguished). (shrink)

The question is discussed how noise gained a functional meaning in the context of biology. According to the common view, noise is considered a disturbance or perturbation. I analyze how this understanding changed and what kind of developments during the last 10 years contributed to the emergence of a new understanding of noise. Results gained during a field study in a synthetic biology laboratory show that the emergence of this new research discipline—its highly interdisciplinary character, its new technologies and novel (...) modeling strategies—provided essential impulses, which led to the observed change in the concept of noise. The laboratory study is combined with a historical analysis, which explores the general question as to how concepts travel between disciplines and, specifically, how noise was transferred from engineering and physics into biology. In the past, scientists, such as Lotka and Goodwin, tried to introduce a statistical mechanics into biology and discussed the problem of “unfitting” concepts. The change in the meaning of the concept can be interpreted as a way of making it fit to the novel context in which it is applied. (shrink)

Representation has been one of the main themes in the recent discussion of models. Several authors have argued for a pragmatic approach to representation that takes users and their interpretations into account. It appears to me, however, that this emphasis on representation places excessive limitations on our view of models and their epistemic value. Models should rather be thought of as epistemic artifacts through which we gain knowledge in diverse ways. Approaching models this way stresses their materiality and media-specificity. Focusing (...) on models as multi-functional artifacts loosens them from any pre-established and fixed representational relationships and leads me to argue for a two-fold approach to representation. (shrink)

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as (...) a kind of material recomposition strategy also points beyond the mechanistic paradigm. (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)

Computational methods such as computer simulations, Monte Carlo methods, and agent-based modeling have become the dominant techniques in many areas of science. Extending Ourselves contains the first systematic philosophical account of these new methods, and how they require a different approach to scientific method. Paul Humphreys draws a parallel between the ways in which such computational methods have enhanced our abilities to mathematically model the world, and the more familiar ways in which scientific instruments have expanded our access to the (...) empirical world. This expansion forms the basis for a new kind of empiricism, better suited to the needs of science than the older anthropocentric forms of empiricism. Human abilities are no longer the ultimate standard of epistemological correctness.Humphreys also includes arguments for the primacy of properties rather than objects, the need to consider technological constraints when appraising scientific methods, and a detailed account of how the path from computational template to scientific application is constructed. This last feature allows us to hold a form of selective realism in which anti-realist arguments based on formal reconstructions of theories can be avoided. One important consequence of the rise of computational methods is that the traditional organization of the sciences is being replaced by an organization founded on computational templates.Extending Ourselves will be of interest to philosophers of science, epistemologists, and to anyone interested in the role played by computers in modern science. (shrink)

I argue for an intentional conception of representation in science that requires bringing scientific agents and their intentions into the picture. So the formula is: Agents (1) intend; (2) to use model, M; (3) to represent a part of the world, W; (4) for some purpose, P. This conception legitimates using similarity as the basic relationship between models and the world. Moreover, since just about anything can be used to represent anything else, there can be no unified ontology of models. (...) This whole approach is further supported by a brief exposition of some recent work in cognitive, or usage-based, linguistics. Finally, with all the above as background, I criticize the recently much discussed idea that claims involving scientific models are really fictions. (shrink)

The semantic, or model-theoretic, approach to theories has recently come under criticism on two fronts: (i) it is claimed that it cannot account for the wide diversity of models employed in scientific practice—a claim which has led some to propose a “deflationary” account of models; (ii) it is further contended that the sense of “model” used by the approach differs from that given in model theory. Our aim in the present work is to articulate a possible response to these claims, (...) drawing on recent developments within the semantic approach itself. Thus, the first is answered by utilizing the notion of a “partial structure”, first introduced in this context by da Costa and French in 1990. The second claim is undermined by consideration of van Fraassen's understanding of “model” which corresponds well with that evinced by modem mathematicians. This latter discussion, in particular, has an impact on the continuing debate regarding the relative merits of the semantic and syntactic views and the developments presented here can be taken to provide further support to the former. (shrink)

Scientists have used models for hundreds of years as a means of describing phenomena and as a basis for further analogy. In Scientific Models in Philosophy of Science, Daniela Bailer-Jones assembles an original and comprehensive philosophical analysis of how models have been used and interpreted in both historical and contemporary contexts. Bailer-Jones delineates the many forms models can take (ranging from equations to animals; from physical objects to theoretical constructs), and how they are put to use. She examines early mechanical (...) models employed by nineteenth-century physicists such as Kelvin and Maxwell, describes their roots in the mathematical principles of Newton and others, and compares them to contemporary mechanistic approaches. Bailer-Jones then views the use of analogy in the late nineteenth century as a means of understanding models and to link different branches of science. She reveals how analogies can also be models themselves, or can help to create them. The first half of the twentieth century saw little mention of models in the literature of logical empiricism. Focusing primarily on theory, logical empiricists believed that models were of temporary importance, flawed, and awaiting correction. The later contesting of logical empiricism, particularly the hypothetico-deductive account of theories, by philosophers such as Mary Hesse, sparked a renewed interest in the importance of models during the 1950s that continues to this day. Bailer-Jones analyzes subsequent propositions of: models as metaphors; Kuhn's concept of a paradigm; the Semantic View of theories; and the case study approaches of Cartwright and Morrison, among others. She then engages current debates on topics such as phenomena versus data, the distinctions between models and theories, the concepts of representation and realism, and the discerning of falsities in models. (shrink)

Scientific representation is a booming field nowadays within the philosophy of science, with many papers published regularly on the topic every year, and several yearly conferences and workshops held on related topics. Historically, the topic originates in two different strands in 20th-century philosophy of science. One strand begins in the 1950s, with philosophical interest in the nature of scientific theories. As the received or “syntactic” view gave way to a “semantic” or “structural” conception, representation progressively gained the center stage. Yet, (...) there is another, older, strand that links representation to fin de siècle modeling debates, particularly in the emerging Bildtheorie of Boltzmann and Hertz, and to the ensuing discussion among philosophers thereafter. Both strands feed into present-day philosophical work on scientific representation. There are a number of different orthogonal questions that philosophers ask regarding representation. One set of questions concerns the nature of the representational relation between theories or models, on the one hand, and the real-world systems they purportedly represent. Such questions lie at the more metaphysical and abstract end of the spectrum—and they are often addressed with the abstract tools of the analytical metaphysician. They constitute what we may refer to as the “analytical inquiry” into representation. On the other hand there are questions regarding the use that scientists put some representations to in practice—these are questions that are best addressed by means of some of the favorite tools of the philosopher of science, including descriptive analysis, illustration by means of case studies, induction, exemplification, inference from practice, etc., and are best referred to as the “practical inquiry” into representation. The notion of representation invoked in such inquiries may be “deflationary” or “substantive”—depending on whether it construes representation as a primitive notion, or as susceptible to further reduction or analysis in terms of something else. (shrink)