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Calibrating a simulation is a crucial step for certain kinds of simulation modeling, and it results in a simulation that is epistemically different from its pre- or uncalibrated counterpart. This article discusses how simulation model builders mitigate uncertainty about model parameters that are necessary for modeling through calibration and argues that the simulation outcomes after calibration are physically meaningful and relevant. When evaluating the epistemic status of computer simulations, comparisons between computer simulations and traditional experiments need to consider this important (...) |
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. In this paper I present two ways in which climate modelers use general circulation models for exploratory purposes. The complexity of Earth’s climate system makes it difficult to predict precisely how lower-order climate dynamics will interact over time to drive higher-order dynamics. The same issues arise for complex models built to simulate climate behavior like the Community Earth Systems Model. I argue that as a result of system complexity, climate modelers use general circulation models to perform model dynamic exploration (...) |
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Ian Hacking’s Representing and Intervening is often credited as being one of the first works to focus on the role of experimentation in philosophy of science, catalyzing a movement which is sometimes called the “philosophy of experiment” or “new experimentalism”. In the 1980s, a number of other movements and scholars also began focusing on the role of experimentation and instruments in science. Philosophical study of experimentation has thus seemed to be an invention of the 1980s whose central figure is Hacking. (...) |
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In his famous article “The Unreasonable Effectiveness of Mathematics in the Natural Sciences” Eugen Wigner argues for a unique tie between mathematics and physics, invoking even religious language: “The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve”. The possible existence of such a unique match between mathematics and physics has been extensively discussed by philosophers and historians of mathematics. Whatever the merits (...) |
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This book addresses key conceptual issues relating to the modern scientific and engineering use of computer simulations. It analyses a broad set of questions, from the nature of computer simulations to their epistemological power, including the many scientific, social and ethics implications of using computer simulations. The book is written in an easily accessible narrative, one that weaves together philosophical questions and scientific technicalities. It will thus appeal equally to all academic scientists, engineers, and researchers in industry interested in questions (...) |
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Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) |
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This article aims to develop a new account of scientific explanation for computer simulations. To this end, two questions are answered: what is the explanatory relation for computer simulations? And what kind of epistemic gain should be expected? For several reasons tailored to the benefits and needs of computer simulations, these questions are better answered within the unificationist model of scientific explanation. Unlike previous efforts in the literature, I submit that the explanatory relation is between the simulation model and the (...) |
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Building computational models of engineered exemplars, or prototypes, is a common practice in the bioengineering sciences. Computational models in this domain are often built in a patchwork fashion, drawing on data and bits of theory from many different domains, and in tandem with actual physical models, as the key objective is to engineer these prototypes of natural phenomena. Interestingly, such patchy model building, often combined with visualizations, whose format is open to a wide range of choice, leads to the discovery (...) |
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Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the contemporary philosophical debate (...) |
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Where should computer simulations be located on the ‘usual methodological map’ which distinguishes experiment from theory? Specifically, do simulations ultimately qualify as experiments or as thought experiments? Ever since Galison raised that question, a passionate debate has developed, pushing many issues to the forefront of discussions concerning the epistemology and methodology of computer simulation. This review article illuminates the positions in that debate, evaluates the discourse and gives an outlook on questions that have not yet been addressed. |
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In this paper I argue that the appropriate analogy for “understanding what makes simulation results reliable” in global climate modeling is not with scientific experimentation or measurement, but—at least in the case of the use of global climate models for policy development—with the applications of science in applied design problems. The prospects for using this analogy to argue for the quantitative reliability of GCMs are assessed and compared with other potential strategies. |
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I discuss here the definition of computer simulations, and more specifically the views of Humphreys, who considers that an object is simulated when a computer provides a solution to a computational model, which in turn represents the object of interest. I argue that Humphreys's concepts are not able to analyse fully successfully a case of contemporary simulation in physics, which is more complex than the examples considered so far in the philosophical literature. I therefore modify Humphreys's definition of simulation. I (...) |
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It is often claimed that scientists can obtain new knowledge about nature by running computer simulations. How is this possible? I answer this question by arguing that computer simulations are arguments. This view parallels Norton’s argument view about thought experiments. I show that computer simulations can be reconstructed as arguments that fully capture the epistemic power of the simulations. Assuming the extended mind hypothesis, I furthermore argue that running the computer simulation is to execute the reconstructing argument. I discuss some (...) |
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Experimental activity is traditionally identified with testing the empirical implications or numerical simulations of models against data. In critical reaction to the ‘tribunal view’ on experiments, this essay will show the constructive contribution of experimental activity to the processes of modeling and simulating. Based on the analysis of a case in fluid mechanics, it will focus specifically on two aspects. The first is the controversial specification of the conditions in which the data are to be obtained. The second is conceptual (...) |
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There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and "high-throughput" instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order (...) |
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Deep neural networks have become increasingly successful in applications from biology to cosmology to social science. Trained DNNs, moreover, correspond to models that ideally allow the prediction of new phenomena. Building in part on the literature on ‘eXplainable AI’, I here argue that these models are instrumental in a sense that makes them non-explanatory, and that their automated generation is opaque in a unique way. This combination implies the possibility of an unprecedented gap between discovery and explanation: When unsupervised models (...) |
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Computer simulations have conventionally been understood to be either extensions of formal methods such as mathematical models or as special cases of empirical practices such as experiments. Here, I argue that computer simulations are best understood as instruments. Understanding them as such can better elucidate their actual role as well as their potential epistemic standing in relation to science and other scientific methods, practices and devices. |
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Model organisms are a living form of scientific models. Despite the widespread use of model organisms in scientific research, the actual representational relationship between model organisms and their target species is often poorly characterized in the context of cross-species research. Many model organisms do not represent the target species adequately, let alone accurately. This is partly due to the complex and emergent life phenomena in the organism, and partly due to the fact that a model organism is always taken to (...) |
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In this paper, we show that reproducibility is a severe problem that concerns simulation models. The reproducibility problem challenges the concept of numerical solution and hence the conception of what a simulation actually does. We provide an expanded picture of simulation that makes visible those steps of simulation modeling that are numerically relevant, but often escape notice in accounts of simulation. Examining these steps and analyzing a number of pertinent examples, we argue that numerical solutions are importantly different from usual (...) |
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The considerations set out in the paper are intended to suggest that in practical contexts predictive power does not play the outstanding roles sometimes accredited to it in an epistemic framework. Rather, predictive power is part of a network of other merits and achievements. Predictive power needs to be judged differently according to the specific conditions that apply. First, predictions need to be part of an explanatory framework if they are supposed to guide actions reliably. Second, in scientific expertise, the (...) |
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Computer simulations are nowadays often directly involved in the generation of experimental results. Given this dependency of experiments on computer simulations, that of simulations on models, and that of the models on free parameters, how do researchers establish trust in their experimental results? Using high-energy physics (HEP) as a case study, I will identify three different types of robustness that I call conceptual, methodological, and parametric robustness, and show how they can sanction this trust. However, as I will also show, (...) |
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Even though the philosophy of simulation is intended as a comprehensive reflection about the practice of computer simulation in contemporary science, its output has been disproportionately shaped by research on equation-based simulation in the physical and climate sciences. Hence, the particularities of alternative practices of computer simulation in other scientific domains are not sufficiently accounted for in the current philosophy of simulation literature. This article centres on agent-based social simulation, a relatively established type of simulation in the social sciences, to (...) |
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An overview of the German philosophy of science community is given for the years 1992–2012, based on a survey in which 159 philosophers of science in Germany participated. To this end, the institutional background of the German philosophy of science community is examined in terms of journals, centers, and associations. Furthermore, a qualitative description and a quantitative analysis of our survey results are presented. Quantitative estimates are given for: (a) academic positions, (b) research foci, (c) philosophers’ of science most important (...) |
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In this paper I study the activity of mathematical problem-solving in scientific practice, focussing on enquiries in mathematical social science. I identify three salient phases of mathematical problem-solving and adopt them as a reference frame to investigate aspects of applications that have not yet received extensive attention in the philosophical literature. |
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In philosophical studies regarding mathematical models of dynamical systems, instability due to sensitive dependence on initial conditions, on the one side, and instability due to sensitive dependence on model structure, on the other, have by now been extensively discussed. Yet there is a third kind of instability, which by contrast has thus far been rather overlooked, that is also a challenge for model predictions about dynamical systems. This is the numerical instability due to the employment of numerical methods involving a (...) |
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The paper discusses modelling uncertainties in climate models and how they can be addressed based on physical principles as well as based on how the models perform in light of empirical data. We ar... |
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Verification and validation of computer codes and models used in simulations are two aspects of the scientific practice of high importance that recently have been discussed widely by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to the model’s relation to the real world and its intended use. Because complex simulations are generally opaque to a practitioner, the Duhem problem can (...) |
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Both thought experiments and simulation experiments apparently belong to the family of experiments, though they are somewhat special members because they work without intervention into the natural world. Instead they explore hypothetical worlds. For this reason many have wondered whether referring to them as “experiments” is justified at all. While most authors are concerned with only one type of “imagined” experiment – either simulation or thought experiment – the present chapter hopes to gain new insight by considering what the two (...) |
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As climate policy decisions are decisions under uncertainty, being based on a range of future climate change scenarios, it becomes a crucial question how to set up this scenario range. Failing to comply with the precautionary principle, the scenario methodology widely used in the Third Assessment Report of the International Panel on Climate Change (IPCC) seems to violate international environmental law, in particular a provision of the United Nations Framework Convention on Climate Change. To place climate policy advice on a (...) |
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Experiments are commonly thought to have epistemic privilege over simulations. Two ideas underpin this belief: first, experiments generate greater inferential power than simulations, and second, simulations cannot surprise us the way experiments can. In this article I argue that neither of these claims is true of experiments versus simulations in general. We should give up the common practice of resting in-principle judgments about the epistemic value of cases of scientific inquiry on whether we classify those cases as experiments or simulations, (...) |
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Paul Thagard has recently argued that thought experiments are dangerous and misleading when we try to use them as evidence for claims. This paper refutes his skepticism. Building on Thagard’s own work in cognitive science, I suggest that Thagard has much that is positive to say about how thought experiments work. My last section presents some new directions for research on the intersection between thought experiments and cognitive science. |
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In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...) |
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Making sense of why something succeeded or failed is central to scientific practice: it provides an interpretation of what happened, i.e. an hypothesized explanation for the results, that informs scientists’ deliberations over their next steps. In philosophy, the realism debate has dominated the project of making sense of scientists’ success and failure claims, restricting its focus to whether truth or reliability best explain science’s most secure successes. Our aim, in contrast, will be to expand and advance the practice-oriented project sketched (...) |
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We claim that adjustable parameters play a crucial role in building and applying simulation models. We analyze that role and illustrate our findings using examples from equations of state in thermodynamics. In building simulation models, two types of experiments, namely, simulation and classical experiments, interact in a feedback loop, in which model parameters are adjusted. A critical discussion of how adjustable parameters function shows that they are boon and bane of simulation. They help to enlarge the scope of simulation far (...) |
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Along three measurements at the Large Hadron Collider (LHC), a high energy particle accelerator, we analyze procedures and consequences of exploratory experimentation (EE). While all of these measurements fulfill the requirements of EE: probing new parameter spaces, being void of a target theory and applying a broad range of experimental methods, we identify epistemic differences and suggest a classification of EE. We distinguish classes of EE according to their respective goals: the exploration where an established global theory cannot provide the (...) |
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Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state (...) |
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The present paper introduces "ontomimetic simulation" and argues that this class of models has enabled the investigation of hypotheses about complex systems in new ways that have epistemological relevance. Ontomimetic simulation can be differentiated from other types of modeling by its reliance on causal similarity in addition to representation. Phenomena are modeled not directly but via mimesis of the ontology (i.e. the "underlying physics", microlevel etc.) of systems and a subsequent animation of the resulting model ontology as a dynamical system. (...) |
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Numerical simulations have come to be widely used in scientific work. Like experiments, simulations generate large quantities of numbers that require analysis and constant concern with uncertainty and error. How do simulationists convince themselves, and others, about the credibility of output? The present analysis reconstructs the perspectives related to performing numerical simulations, in general, and the situations in which simulationists deal with uncertain output, in particular. Starting from a distinction between idealized and realistic simulations, the paper presents the principal methods (...) |
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Computational modeling is one of the primary approaches to constructing protein–protein interfaces in the laboratory. The algorithm-driven computational protein design has been successfully applied to the construction of functional proteins with improved binding affinity and increased thermostability. It is intriguing how a computational protein modeling approach can construct and shape the reality of new functional proteins from scratch. I articulate an account of abstraction and exploration-driven strategies in this computational endeavor. I aim to show that how a computational modelling approach, (...) |
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