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)

It is argued that a number of important, and seemingly disparate, types of representation are species of a single relation, here called structural representation, that can be described in detail and studied in a way that is of considerable philosophical interest. A structural representation depends on the existence of a common structure between a representation and that which it represents, and it is important because it allows us to reason directly about the representation in order to draw conclusions about the (...) phenomenon that it depicts. The present goal is to give a general and precise account of structural representation, then to use that account to illuminate several problems of current philosophical interest — including some that do not initially seem to involve representation at all. In particular, it is argued that ontological reductions (like that of the natural numbers to sets), compositional accounts of semantics, several important sorts of mental representation, and (perhaps) possible worlds semantics for intensional logics are all species of structural representation and are fruitfully studied in the framework developed here. (shrink)

Starting with some illustrative examples, I develop a systematic account of a specific type of experimentation--an experimentation which is not, as in the "standard view", driven by specific theories. It is typically practiced in periods in which no theory or--even more fundamentally--no conceptual framework is readily available. I call it exploratory experimentation and I explicate its systematic guidelines. From the historical examples I argue furthermore that exploratory experimentation may have an immense, but hitherto widely neglected, epistemic significance.

This paper proposes an outline for a typology of the different forms that scientific objects can take in the life sciences. The first section discusses preparations (or specimens)—a form of scientific object that accompanied the development of modern biology in different guises from the seventeenth century to the present: as anatomical–morphological specimens, as microscopic cuts, and as biochemical preparations. In the second section, the characteristics of models in biology are discussed. They became prominent from the end of the nineteenth century (...) onwards. Some remarks on the role of simulations—characterising the life sciences of the turn from the twentieth to the twenty-first century—conclude the paper. -/- . (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)

The paper presents an argument for treating certain types of computer simulation as having the same epistemic status as experimental measurement. While this may seem a rather counterintuitive view it becomes less so when one looks carefully at the role that models play in experimental activity, particularly measurement. I begin by discussing how models function as “measuring instruments” and go on to examine the ways in which simulation can be said to constitute an experimental activity. By focussing on the connections (...) between models and their various functions, simulation and experiment one can begin to see similarities in the practices associated with each type of activity. Establishing the connections between simulation and particular types of modelling strategies and highlighting the ways in which those strategies are essential features of experimentation allows us to clarify the contexts in which we can legitimately call computer simulation a form of experimental measurement. (shrink)

The goal of this article is to address the problem of inconsistent models and the challenge it poses for perspectivism. I analyze the argument, draw attention to some hidden premises behind it, and deflate them. Then I introduce the notion of perspectival models as a distinctive class of modeling practices whose primary function is exploratory. I illustrate perspectival modeling with two examples taken from contemporary high-energy physics at the Large Hadron Collider at the European Organization for Nuclear Research, which are (...) designed to show how a plurality of seemingly incompatible models is methodologically crucial to advance the realist quest in cutting-edge areas of scientific inquiry. (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)

The recent discussion of fictional models has focused on imagination, implicitly considering fictions as something nonconcrete. We present two cases from synthetic biology that can be viewed as concrete fictions. Both minimal cells and alternative genetic systems are modal in nature: they, as well as their abstract cousins, can be used to study unactualized possibilia. We approach these synthetic constructs through Vaihinger’s notion of a semi-fiction and Goodman’s notion of semifactuality. Our study highlights the relative existence of such concrete fictions. (...) Before their realizations neither minimal cells nor alternative genetic systems were any well-defined objects, and the subsequent experimental work has given more content to these originally schematic imaginings. But it is as yet unclear whether individual members of these heterogeneous groups of somewhat functional synthetic constructs will eventually turn out to be fully realizable, remain only partially realizable, or prove outright impossible. (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)

One striking feature of the contemporary modelling practice is its interdisciplinary nature. The same equation forms, and mathematical and computational methods, are used across different disciplines, as well as within the same discipline. Are there, then, differences between intra- and interdisciplinary transfer, and can the comparison between the two provide more insight on the challenges of interdisciplinary theoretical work? We will study the development and various uses of the Ising model within physics, contrasting them to its applications to socio-economic systems. (...) While the renormalization group methods justify the transfer of the Ising model within physics – by ascribing them to the same universality class – its application to socio-economic phenomena has no such theoretical grounding. As a result, the insights gained by modelling socio-economic phenomena by the Ising model may remain limited. (shrink)

This paper distinguishes between causal isolation robustness analysis and independent determination robustness analysis and suggests that the triangulation of the results of different epistemic means or activities serves different functions in them. Circadian clock research is presented as a case of causal isolation robustness analysis: in this field researchers made use of the notion of robustness to isolate the assumed mechanism behind the circadian rhythm. However, in contrast to the earlier philosophical case studies on causal isolation robustness analysis (Weisberg and (...) Reisman in Philos Sci 75:106–131, 2008 ; Kuorikoski et al. in Br J Philos Sci 61:541–567, 2010 ), robustness analysis in the circadian clock research did not remain in the level of mathematical modeling, but it combined it with experimentation on model organisms and a new type of model, a synthetic model. (shrink)

The epistemic value of models has traditionally been approached from a representational perspective. This paper argues that the artifactual approach evades the problem of accounting for representation and better accommodates the modal dimension of modeling. From an artifactual perspective, models are viewed as erotetic vehicles constrained by their construction and available representational tools. The modal dimension of modeling is approached through two case studies. The first portrays mathematical modeling in economics, while the other discusses the modeling practice of synthetic biology, (...) which exploits and combines models in various modes and media. Neither model intends to represent any actual target system. Rather, they are constructed to study possible mechanisms through the construction of a model system with built-in dependencies. (shrink)

This paper presents an artifactual approach to models that also addresses their fictional features. It discusses first the imaginary accounts of models and fiction that set model descriptions apart from imagined-objects, concentrating on the latter :251–268, 2010; Frigg and Nguyen in The Monist 99:225–242, 2016; Godfrey-Smith in Biol Philos 21:725–740, 2006; Philos Stud 143:101–116, 2009). While the imaginary approaches accommodate surrogative reasoning as an important characteristic of scientific modeling, they simultaneously raise difficult questions concerning how the imagined entities are related (...) to actual representational tools, and coordinated among different scientists, and with real-world phenomena. The artifactual account focuses, in contrast, on the culturally established external representational tools that enable, embody, and extend scientific imagination and reasoning. While there are commonalities between models and fictions, it is argued that the focus should be on the fictional uses of models rather than considering models as fictions. (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)

Whereas computer simulations involve no direct physical interaction between the machine they are run on and the physical systems they are used to investigate, they are often used as experiments and yield data about these systems. It is commonly argued that they do so because they are implemented on physical machines. We claim that physicality is not necessary for their representational and predictive capacities and that the explanation of why computer simulations generate desired information about their target system is only (...) to be found in the detailed analysis of their semantic levels. We provide such an analysis and we determine the actual consequences of physical implementation for simulations. (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)

The mathematical theory of communication.

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)

This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.

This paper is intended to sketch the definition of a methodological tool -- the notion of a format of representation -- for the study of scientific theorising. One of its main assumption is that a philosophical study of theorising needs to pay attention to other types of units of analysis than the traditional ones, namely, theories and models approached in a logical and structural way, since scientific reasoning is always led on concrete representational devices and depends upon their specific properties. (...) The notion of a format is intended to characterise the differences between various types of representational devices, in terms of the inferences they enable cognitive agents to draw. (shrink)

This paper argues that a significant focus in computational organic chemistry, alongside the construction and deployment of models, is the “deconstruction” of computational models. This practice has arisen in response to difficulties and controversies resulting from the use of plural methods and computational models to study organic reaction mechanisms. Diagnostic controllability is the capacity of cognitive agents to gain epistemic access to grey-boxed computational models, to identify and explain the impact of specific idealizations on results, and to demonstrate the applicability (...) of computational methods to target systems. (shrink)