The ArgumentIn its reconstruction of scientific practice, philosophy of science has traditionally placed scientific theories in a central role, and has reduced the problem of mediating between theories and the world to formal considerations. Many applications of scientific theories, however, involve complex mathematical models whose constitutive equations are analytically unsolvable. The study of these applications often consists in developing representations of the underlying physics on a computer, and using the techniques of computer simulation in order to learn about the behavior (...) of these systems. In many instances, these computer simulations are not simple number-crunching techniques. They involve a complex chain of inferences that serve to transform theoretical structures into specific concrete knowledge of physical systems. In this paper I argue that this process of transformation has its own epistemology. I also argue that this kind of epistemology is unfamiliar to most philosophy of science, which has traditionally concerned itself with the justification of theories, not with their application. Finally, I urge that the nature of this epistemology suggests that the end results of some simulations do not bear a simple, straightforward relation to the theories from which they stem. (shrink)

Simulations (both digital and analog) and experiments share many features. But what essential features distinguish them? I discuss two proposals in the literature. On one proposal, experiments investigate nature directly, while simulations merely investigate models. On another proposal, simulations differ from experiments in that simulationists manipulate objects that bear only a formal (rather than material) similarity to the targets of their investigations. Both of these proposals are rejected. I argue that simulations fundamentally differ from experiments with regard to the background (...) knowledge that is invoked to argue for the “external validity” of the investigation. (shrink)

In vitro experimental approaches are of central importance to contemporary molecular and cellular biology and toxicology. However, the scientific value or impact of in vitro results depends on their relevance in vivo. In vitro effect studies address inobservable in vivo phenomena through experiments on analogous in vitro phenomena. We present a theoretical basis developed to evaluate the in vivo relevance of in vitro effect studies. As a case study, the procedure for measuring specific gene transcription in isolated cell nuclei (nuclear (...) run-off method) is analyzed It is concluded that current evidence fails to justify in vivo interpretations of nuclear run-off experiments within the framework of theoretical models of transcription, implying that quantitative in vivo interpretations are unwarranted. Qualitative interpretations of nuclear run-off experiments may be justified by inferring the best explanation, especially when significant in vitro effects follow in vivo perturbations.Elements of a general theory are proposed. It is concluded that quantitative in vivo interpretations are warranted primarily in biochemical quantitation of biomolecules, while studies on biological function should be interpreted qualitatively in terms of causal explanations. Inferences to the best explanations are strengthened through additional evidence and the creation of experimental differences (effects). (shrink)

The central claim of this paper is that computer simulation provides (though not exclusively) a qualitatively new and different methodology for the physical sciences, and that this methodology lies somewhere intermediate between traditional theoretical physical science and its empirical methods of experimentation and observation. In many cases it involves a new syntax which gradually replaces the old, and it involves theoretical model experimentation in a qualitatively new and interesting way. Scientific activity has thus reached a new milestone somewhat comparable to (...) the milestones that started the empirical approach (Galileo) and the deterministic mathematical approach to dynamics (the old syntax of Newton and Laplace). Computer simulation is consequently of considerable philosophical interest. In view of further technical developments in the near future, computer experts suggest that we are at present only at the very beginning of this new era. (shrink)

A number of recent discussions comparing computer simulation and traditional experimentation have focused on the significance of “materiality.” I challenge several claims emerging from this work and suggest that computer simulation studies are material experiments in a straightforward sense. After discussing some of the implications of this material status for the epistemology of computer simulation, I consider the extent to which materiality (in a particular sense) is important when it comes to making justified inferences about target systems on the basis (...) of experimental results. (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)

A great deal of attention has been paid by philosophers to the use of computers in the modelling of human cognitive capacities and in the construction of intelligent artifacts. This emphasis has tended to obscure the fact that most of the high-level computing power in science is deployed in what appears to be a much less exciting activity: solving equations. This apparently mundane set of applications reflects the historical origins of modem computing, in the sense that most of the early (...) computers in Britain and the U.S. were devices built to numerically attack mathematical problems that were hard, if not impossible, to solve non-numerically, especially in the areas of ballistics and fluid dynamics. The latter area was especially important for the development of atomic weapons at Los Alamos, and it is still true that a large portion of the supercomputing capacity of the United States is concentrated at weapons development laboratories such as Los Alamos and Lawrence Livermore. (shrink)

This paper examines the relationship between simulation and experiment. Many discussions of simulation, and indeed the term "numerical experiments," invoke a strong metaphor of experimentation. On the other hand, many simulations begin as attempts to apply scientific theories. This has lead many to characterize simulation as lying between theory and experiment. The aim of the paper is to try to reconcile these two points of viewto understand what methodological and epistemological features simulation has in common with experimentation, while at the (...) same time keeping a keen eye on simulation's ancestry as a form of scientific theorizing. In so doing, it seeks to apply some of the insights of recent work on the philosophy of experiment to an aspect of theorizing that is of growing philosophical interest: the construction of local models. (shrink)

Experiments (E), computer simulations (CS) and thought experiments (TE) are usually seen as playing different roles in science and as having different epistemologies. Accordingly, they are usually analyzed separately. We argue in this paper that these activities can contribute to answering the same questions by playing the same epistemic role when they are used to unfold the content of a well-described scenario. We emphasize that in such cases, these three activities can be described by means of the same conceptual framework—even (...) if each of them, because they involve different types of processes, fall under these concepts in different ways. We further illustrate our claims by presenting a threefold case study describing how a TE, a CS and an E were indeed used in the same role at different periods to answer the same questions about the possibility of a physical Maxwellian demon. We also point at fluid dynamics as another field where these activities seem to be playing the same unfolding role. We analyze the importance of unfolding as a general task of science and highlight how our description in terms of epistemic functions articulates in a noncommittal way with the epistemology of these three activities and accounts for their similarities and the existence of hybrid forms of activities. We finally emphasize that picturing these activities as functionally substitutable does not imply that they are epistemologically substitutable. (shrink)

In a famous critique, Goodman dismissed similarity as a slippery and both philosophically and scientifically useless notion. We revisit his critique in the light of important recent work on similarity in psychology and cognitive science. Specifically, we use Tversky’s influential set-theoretic account of similarity as well as Gärdenfors’s more recent resuscitation of the geometrical account to show that, while Goodman’s critique contained valuable insights, it does not warrant a dismissal of similarity.

Introduction -- Sanctioning models : theories and their scope -- Methodology for a virtual world -- A tale of two methods -- When theories shake hands -- Models of climate : values and uncertainties -- Reliability without truth -- Conclusion.