Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the (...) relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this talk is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupre has recently noted that there exists a ‘General Problem of Biological Individuality’ which relates to the issue of how one divides ‘massively integrated and interconnected’ systems into discrete components. In response Dupre advocates a form of ‘Promiscuous Realism’ that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupre and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology. (shrink)

Computer simulations are an exciting tool that plays important roles in many scientific disciplines. This has attracted the attention of a number of philosophers of science. The main tenor in this literature is that computer simulations not only constitute interesting and powerful new science , but that they also raise a host of new philosophical issues. The protagonists in this debate claim no less than that simulations call into question our philosophical understanding of scientific ontology, the epistemology and semantics of (...) models and theories, and the relation between experimentation and theorising, and submit that simulations demand a fundamentally new philosophy of science in many respects. The aim of this paper is to critically evaluate these claims. Our conclusion will be sober. We argue that these claims are overblown and that simulations, far from demanding a new metaphysics, epistemology, semantics and methodology, raise few if any new philosophical problems. The philosophical problems that do come up in connection with simulations are not specific to simulations and most of them are variants of problems that have been discussed in other contexts before. (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)

It's uncontroversial that notions of idealization and approximation are central to understanding computer simulations and their rationale. What's not so clear is what exactly these notions come to. Two distinct forms of approximation will be distinguished and their features contrasted with those of idealizations. These distinctions will be refined and closely tied to computer simulations by means of Scott-Strachey denotational programming semantics. The use of this sort of semantics also provides a convenient format for argumentation in favor of several theses (...) I shall propose concerning the role computer implemented approximations and idealizations play in fixing what the acceptance of an underlying scientific theory is or should be. (shrink)

Scientific discourse is rife with passages that appear to be ordinary descriptions of systems of interest in a particular discipline. Equally, the pages of textbooks and journals are filled with discussions of the properties and the behavior of those systems. Students of mechanics investigate at length the dynamical properties of a system consisting of two or three spinning spheres with homogenous mass distributions gravitationally interacting only with each other. Population biologists study the evolution of one species procreating at a constant (...) rate in an isolated ecosystem. And when studying the exchange of goods, economists consider a situation in which there are only two goods, two perfectly rational agents, no restrictions on available information, no transaction costs, no money, and dealings are done immediately. Their surface structure notwithstanding, no competent scientist would mistake descriptions of such systems as descriptions of an actual system: we know very well that there are no such systems. These descriptions are descriptions of a model-system, and scientists use model-systems to represent parts or aspects of the world they are interested in. Following common practice, I refer to those parts or aspects as target-systems. What are we to make of this? Is discourse about such models merely a picturesque and ultimately dispensable façon de parler? This was the view of some early twentieth century philosophers. Duhem (1906) famously guarded against confusing model building with scientific theorizing and argued that model building has no real place in science, beyond a minor heuristic role. The aim of science was, instead, to construct theories, with theories understood as classificatory or representative structures systematically presented and formulated in precise symbolic.. (shrink)

Using an example of a computer simulation of the convective structure of a red giant star, this paper argues that simulation is a rich inferential process, and not simply a "number crunching" technique. The scientific practice of simulation, moreover, poses some interesting and challenging epistemological and methodological issues for the philosophy of science. I will also argue that these challenges would be best addressed by a philosophy of science that places less emphasis on the representational capacity of theories (and ascribes (...) that capacity instead to models) and more emphasis on the role of theory in guiding (rather than determining) the construction of models. (shrink)

As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them by microscopic (...) imaging, the different styles of reasoning involved, and the various theoretical, methodological, and axiological differences. I conclude by arguing that, except for the probe microscopes that are used, there is very little in common between the two cases. At the nanoscale, physics and molecular biology seem to meet in a non-unified way. (shrink)

Using an example of a computer simulation of the convective structure of a red giant star, this paper argues that simulation is a rich inferential process, and not simply a “number crunching” technique. The scientific practice of simulation, moreover, poses some interesting and challenging epistemological and methodological issues for the philosophy of science. I will also argue that these challenges would be best addressed by a philosophy of science that places less emphasis on the representational capacity of theories and more (...) emphasis on the role of theory in guiding the construction of models. (shrink)

Physics matters less than we once thought to the making of Mendel. But it matters more than we tend to recognize to the making of Mendelism. This paper charts the variety of ways in which diverse kinds of physics impinged upon the Galtonian tradition which formed Mendelism’s matrix. The work of three Galtonians in particular is considered: Francis Galton himself, W. F. R. Weldon and William Bateson. One aim is to suggest that tracking influence from physics can bring into focus (...) important but now little-remembered flexibilities in the Galtonian tradition. Another is to show by example why generalizations about what happens when ‘physics’ meets ‘biology’ require caution. Even for a single research tradition in Britain in the decades around 1900, these categories were large, containing multitudes. (shrink)

In Making Sense of Life , Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive (...) science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (shrink)

In its most common use, the term ‘model’ refers to a simplified and stylised version of the socalled target system, the part or aspect of the world that we are interested in. For instance, in order to determine the orbit of a planet moving around the sun we model the planet and the sun as perfect homogenous spheres that gravitationally interact with each other but nothing else in the universe, and then apply Newtonian mechanics to this system, which reveals that (...) the planet moves on an elliptical orbit. Views diverge about what sort of entity such a model is. Those focussing on the formal aspects of models regard them either as equations or settheoretical structures, while those opposed to such an approach take them to be descriptions or abstract (yet non-mathematical) entities. A further question concerns the relation of models and theories. In some cases models can be derived from theory simply by specifying the relevant determinables in a theory’s general equations. But many models cannot be obtained from theory in this straightforward way, and some even involve assumptions that contradict the fundamental theory. The relation of models to their respective target systems is equally complex and fraught with controversy. Two influential proposals take the relation between a model and its target to be isomorphism or similarity, respectively. This, however, has been criticised as too restrictive as many models do not seem to fit this mould. (shrink)