Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in for a physically (...) different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)

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, (...) we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory. (shrink)

As brightly shown by Mainzer [24], the science of complexity has many distinct origins in many disciplines. Those various origins has led to “an interdisciplinary methodology to explain the emergence of certain macroscopic phenomena via the nonlinear interactions of microscopic elements” (ibid.). This paper suggests that the parallel and strong expansion of modeling and simulation - especially after the Second World War and the subsequent development of computers - is a rationale which also can be counted as an explanation of (...) this emergence. With the benefit of hindsight, one can find three periods in the methodologies of modeling in the empirical sciences: 1st the simple modeling of the simple, 2nd the simple modeling of the complex, 3rd the complex modeling and simulation of the complex. Our main thesis is that the current spreading (since the 90’s) of complex computer simulations of systems of models (where a simulation is no more a step by step calculus of a unique logico-mathematical model) is another promising dimension of the science of complexity. Following this claim, we propose to distinguish three different types of computer simulations in the context of complex systems’ modeling. Finally, we show that these types of simulations lead to three different types of weak emergence, too. (shrink)

This paper proposes an extensionalist analysis of computer simulations (CSs). It puts the emphasis not on languages nor on models, but on symbols, on their extensions, and on their various ways of referring. It shows that chains of reference of symbols in CSs are multiple and of different kinds. As they are distinct and diverse, these chains enable different kinds of remoteness of reference and different kinds of validation for CSs. Although some methodological papers have already underlined the role of (...) these various relationships of reference in CSs and of cross-validations, this diversity is still overlooked in the epistemological literature on CSs. As a consequence, a particular outcome of this analytical view is an ability to classify existing epistemological theses on CSs according to what their authors choose to select and put at the forefront: either the extensions of symbols, or the symbol-types, or the symbol-tokens, or the internal denotational hierarchies of the CS or the reference of these hierarchies to external denotational hierarchies. Through the adoption of this extensionalist view, it also becomes possible to explain more precisely the reasons why some complete reduction of CSs to classical epistemic paradigms such as “experiment” or “theoretical argument” remains doubtful. On this last point, in particular, this paper is in agreement with what many epistemologists already have acknowledged. (shrink)

‘The problem with simulations is that they are doomed to succeed.’ So runs a common criticism of simulations—that they can be used to ‘prove’ anything and are thus of little or no scientific value. While this particular objection represents a minority view, especially among those who work with simulations in a scientific context, it raises a difficult question: what standards should we use to differentiate a simulation that fails from one that succeeds? In this paper we build on a structural (...) analysis of simulation developed in previous work to provide an evaluative account of the variety of ways in which simulations do fail. We expand the structural analysis in terms of the relationship between a simulation and its real-world target emphasizing the important role of aspects intended to correspond and also those specifically intended not to correspond to reality. The result is an outline both of the ways in which simulations can fail and the scientific importance of those various forms of failure. (shrink)

Morrison points out many similarities between the roles of simulation models and other sorts of models in science. On the basis of these similarities she claims that running a simulation is epistemologically on a par with doing a traditional experiment and that the output of a simulation therefore counts as a measurement. I agree with her premises but reject the inference. The epistemological payoff of a traditional experiment is greater (or less) confidence in the fit between a model and a (...) target system. The source of this payoff is the existence of a causal interaction with the target system. A computer experiment, which does not go beyond the simulation system itself, lacks any such interaction. So computer experiments cannot confer any additional confidence in the fit (or lack thereof) between the simulation model and the target system. (shrink)

A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) scientists integrate the cognitive, social, material, and cultural dimensions of practice. Her findings and conclusions have broad implications for researchers in philosophy, science studies, cognitive science, and interdisciplinary studies, as well as scientists, educators, policy makers, and funding agencies. In studying the epistemic practices of scientists, Nersessian pushes the boundaries of the philosophy of science and cognitive science into areas not ventured before. She recounts a decades-long, wide-ranging, and richly detailed investigation of the innovative interdisciplinary modeling practices of bioengineering researchers in four university laboratories. She argues and demonstrates that the methods of cognitive ethnography and qualitative data analysis, placed in the framework of distributed cognition, provide the tools for a philosophical analysis of how scientific discoveries arise from complex systems in which the cognitive, social, material, and cultural dimensions of problem-solving are integrated into the epistemic practices of scientists. Specifically, she looks at how interdisciplinary environments shape problem-solving. Although Nersessian’s case material is drawn from the bioengineering sciences, her analytic framework and methodological approach are directly applicable to scientific research in a broader, more general sense, as well. (shrink)

This paper explores the epistemological challenges in using computer simulations for two distinct goals: explanation via hypothesis-testing and prediction. It argues that each goal requires different strategies for justifying inferences drawn from simulation results due to different practical and conceptual constraints. The paper identifies unique and shared strategies researchers employ to increase confidence in their inferences for each goal. For explanation via hypothesis-testing, researchers need to address the underdetermination, interpretability, and attribution challenges. In prediction, the emphasis is on the model's (...) ability to generalize across multiple domains. Shared strategies researchers employ to increase confidence in inferences are empirical corroboration of theoretical assumptions and adequacy of computational operationalizations, and this paper argues that these are necessary for explanation via hypothesis-testing but not for prediction. This paper emphasizes the need for a nuanced approach to the epistemology of computer simulation, given the diverse applications of computer simulation in scientific research. Understanding these differences is crucial for both researchers and philosophers of science, as it helps develop appropriate methodologies and criteria for assessing the trustworthiness of computer simulation. (shrink)

The thesis proposes an account of the means of scientific representation focused on similarity, or more specifically, on the notion of “creative similarity”. I first distinguish between two different questions regarding the problem of representation: the question about the constituents and the question about the means of representation (following Suárez 2003; van Fraassen 2008). I argue that, although similarity is not a good candidate for constituent of representation, it can satisfactorily answer the question about the means of representation if adequately (...) characterized. To motivate this position, I dispute the main arguments offered against similarity as means of representation, namely the arguments from variety, vagueness, and misrepresentation, and contend that similarity plays a central epistemic role in practices of representing in science. The study of the role of similarity in scientific practice, I argue, requires the analysis of the uses of judgments of similarity in the construction of scientific models. I examine the cases of the Mississippi Basin Model and the San Francisco Bay Model to illustrate how judgments of similarity are directly involved in the production of epistemically fruitful models. Informed by the practical investigation developed throughout the thesis, I finally outline what I call the creative similarity account of the means of representation. The notion of “creative similarity” helps to capture the way in which similarity, as means of representation, intervenes in actual practices of representing, namely, in the form of a productive interplay of judgments of similarity and distortions (i.e. idealizations, abstractions, simplifications), which is employed by resourceful agents with the aim of understanding aspects of the natural world. (shrink)

We analyze the usage of computer simulation at the LHC and derive seven jointly necessary requirements for a simulation to be considered ’trustworthy’, such that it can be used as proxy for experiments. We show that these requirements can also be applied to systems without direct experimental access and discuss their validity for properties that have not yet been probed. While being necessary, these requirements are not sufficient. Such trustworthy simulations will be analyzed for the relative epistemic statuses of simulation (...) and material measurements, from which we argue that claims of their parity are unfounded. Instead, using credibility as a measure for epistemic status, and in view of the temporal and epistemic dependence of simulation on material measurements, we argue that the latter have a higher epistemic status than the former. We further argue that suggestions to qualify the epistemic status by ’defocussing’ on the material connection to the target system of either human or natural experiments are misleading. (shrink)

This paper examines two parallel discussions of scientific modeling which have invoked experimentation in addressing the role of models in scientific inquiry. One side discusses the experimental character of models, whereas the other focuses on their exploratory uses. Although both relate modeling to experimentation, they do so differently. The former has considered the similarities and differences between models and experiments, addressing, in particular, the epistemic value of materiality. By contrast, the focus on exploratory modeling has highlighted the various kinds of (...) exploratory functions of models in the early stages of inquiry. These two perspectives on modeling are discussed through a case study in the field of synthetic biology. The research practice in question explores biological control by making use of an ensemble of different epistemic means: mathematical models and simulations, synthetic genetic circuits and intracellular measuring devices, and finally electronic circuits. We argue that the study of exploratory modeling should trace the ways different epistemic means, in different materialities, are being combined over time. Finally, the epistemic status of such novel investigative objects as synthetic genetic circuits is evaluated, with the conclusion that they can function as both experiments and models. (shrink)

This paper argues that an important type of experiment-target inference, extrapolating causal effects, requires models to be successful. Focusing on extrapolation in Evidence-Based Policy, it is ar...

Since the discovery of dark matter in the 1980s, multiple experiments have been set up to detect dark matter particles through some other mode than gravity. Particle physicists provide detailed jus...

Although the concept of the consumer–brand relationship has undergone rapid change over the past two decades, the issue of brand addiction is still generally neglected in the literature. Based on social identity theory, the research develops a conceptual model of the influence of self-expressive brands and susceptibility to interpersonal influence on brand addiction. The results of this research demonstrate both separate and joint effects of SEBs and SUSCEP on brand addiction. In addition, harmonious brand passion and obsessive brand passion positively (...) mediate the relationships among SEB, SUSCEP, and brand addiction. The research explores the formation mechanism of brand addiction from a new perspective and has important practical implications for brand marketers concerned with finding the most effective means to enhance the consumer–brand relationship. (shrink)

Since their inception in the 1980s, complexity sciences have been described as a revolutionary new domain of research. By describing some of the practices and assumptions of its representatives, the present article shows that this field is an association of subdisciplines laying on existing disciplinary footholds. The general question guiding us here is: On what basis do complexity scientists consider their inquiry methods and results as valuable? To answer it, I describe five “epistemic argumentative regimes,” namely the ways in which (...) complexity scientists argue the credibility of their research, and five “ontological views,” that is the ways in which they interpret the material and formal causes of their study objects and models. Finally, the article proposes the term of “regime of evidence” to designate the specific combination of one ontological view with one or more epistemic argumentative regimes. (shrink)

To demarcate the limits of experimental knowledge, we probe the limits of what might be called an experiment. By appeal to examples of scientific practice from astrophysics and analogue gravity, we demonstrate that the reliability of knowledge regarding certain phenomena gained from an experiment is not circumscribed by the manipulability or accessibility of the target phenomena. Rather, the limits of experimental knowledge are set by the extent to which strategies for what we call ‘inductive triangulation’ are available: that is, the (...) validation of the mode of inductive reasoning involved in the source-target inference via appeal to one or more distinct and independent modes of inductive reasoning. When such strategies are able to partially mitigate reasonable doubt, we can take a theory regarding the phenomena to be well supported by experiment. When such strategies are able to fully mitigate reasonable doubt, we can take a theory regarding the phenomena to be established by experiment. There are good reasons to expect the next generation of analogue experiments to provide genuine knowledge of unmanipulable and inaccessible phenomena such that the relevant theories can be understood as well supported. This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’. (shrink)

The question of where, between theory and experiment, computer simulations (CSs) locate on the methodological map is one of the central questions in the epistemology of simulation (cf. Saam Journal for General Philosophy of Science, 48, 293–309, 2017). The two extremes on the map have them either be a kind of experiment in their own right (e.g. Barberousse et al. Synthese, 169, 557–574, 2009; Morgan 2002, 2003, Journal of Economic Methodology, 12(2), 317–329, 2005; Morrison Philosophical Studies, 143, 33–57, 2009; Morrison (...) 2015; Massimi and Bhimji Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics, 51, 71–81, 2015; Parker Synthese, 169, 483–496, 2009) or just an argument executed with the aid of a computer (e.g. Beisbart European Journal for Philosophy of Science, 2, 395–434, 2012; Beisbart and Norton International Studies in the Philosophy of Science, 26, 403–422, 2012). There exist multiple versions of the first kind of position, whereas the latter is rather unified. I will argue that, while many claims about the ‘experimental’ status of CSs seem unjustified, there is a variant of the first position that seems preferable. In particular I will argue that while CSs respect the logic of (deductively valid) arguments, they neither agree with their pragmatics nor their epistemology. I will then lay out in what sense CSs can fruitfully be seen as experiments, and what features set them apart from traditional experiments nonetheless. I conclude that they should be seen as surrogate experiments, i.e. experiments executed consciously on the wrong kind of system, but with an exploitable connection to the system of interest. Finally, I contrast my view with that of Beisbart (European Journal for Philosophy of Science, 8, 171–204, 2018), according to which CSs are surrogates for experiments, arguing that this introduces an arbitrary split between CSs and other kinds of simulations. (shrink)

A chronicled approach to the notion of computer simulations shows that there are two predominant interpretations in the specialized literature. According to the first interpretation, computer simulations are techniques for finding the set of solutions to a mathematical model. I call this first interpretation the problem-solving technique viewpoint. In its second interpretation, computer simulations are considered to describe patterns of behavior of a target system. I call this second interpretation the description of patterns of behavior viewpoint of computer simulations. This (...) article explores these two interpretations of computer simulations from three different angles. First, I collect a series of definitions of computer simulation from the historical record. I track back definitions to the early 1960s and show how each viewpoint shares similar interpretations of computer simulations—ultimately clustering into the two viewpoints aforementioned. This reconstruction also includes the most recent literature. Second, I unpack the philosophical assumptions behind each viewpoint, with a special emphasis on their differences. Third, I discuss the philosophical implications of each viewpoint in the context of the recent discussion on the logic of scientific explanation for computer simulations. (shrink)

Computer simulations are involved in numerous branches of modern science, and science would not be the same without them. Yet the question of how they can explain real-world processes remains an issue of considerable debate. In this context, a range of authors have highlighted the inferences back to the world that computer simulations allow us to draw. I will first characterize the precise relation between computer and target of a simulation that allows us to draw such inferences. I then argue (...) that in a range of scientifically interesting cases they are particular abductions and defend this claim by appeal to two case studies. (shrink)

A chronicled approach to the notion of computer simulations shows that there are two predominant interpretations in the specialized literature. According to the first interpretation, computer simulations are techniques for finding the set of solutions to a mathematical model. I call this first interpretation the problem-solving technique viewpoint. In its second interpretation, computer simulations are considered to describe patterns of behavior of a target system. I call this second interpretation the description of patterns of behavior viewpoint of computer simulations. This (...) article explores these two interpretations of computer simulations from three different angles. First, I collect a series of definitions of computer simulation from the historical record. I track back definitions to the early 1960s and show how each viewpoint shares similar interpretations of computer simulations—ultimately clustering into the two viewpoints aforementioned. This reconstruction also includes the most recent literature. Second, I unpack the philosophical assumptions behind each viewpoint, with a special emphasis on their differences. Third, I discuss the philosophical implications of each viewpoint in the context of the recent discussion on the logic of scientific explanation for computer simulations. (shrink)

There is a vast literature within philosophy of mind that focuses on artificial intelligence, but hardly mentions methodological questions. There is also a growing body of work in philosophy of science about modeling methodology that hardly mentions examples from cognitive science. Here these discussions are connected. Insights developed in the philosophy of science literature about the importance of idealization provide a way of understanding the neural implausibility of connectionist networks. Insights from neurocognitive science illuminate how relevant similarities between models and (...) targets are picked out, how modeling inferences are justified, and the metaphysical status of models. (shrink)

ABSTRACTExperimentation is traditionally considered a privileged means of confirmation. However, why and how experiments form a better confirmatory source relative to other strategies is unclear, and recent discussions have identified experiments with various modeling strategies on the one hand, and with ‘natural’ experiments on the other hand. We argue that experiments aiming to test theories are best understood as controlled investigations of specimens. ‘Control’ involves repeated, fine-grained causal manipulation of focal properties. This capacity generates rich knowledge of the object investigated. (...) ‘Specimenhood’ involves possessing relevant properties given the investigative target and the hypothesis in question. Specimens are thus representative members of a class of systems, to which a hypothesis refers. It is in virtue of both control and specimenhood that experiments provide powerful confirmatory evidence. This explains the distinctive power of experiments: although modelers exert extensive control, they do not exert this control over specimens; although natural experiments utilize specimens, control is diminished. (shrink)

Certain hypotheses cannot be directly confirmed for theoretical, practical, or moral reasons. For some of these hypotheses, however, there might be a workaround: confirmation based on analogical reasoning. In this paper we take up Dardashti, Hartmann, Thébault, and Winsberg’s (in press) idea of analyzing confirmation based on analogical inference Baysian style. We identify three types of confirmation by analogy and show that Dardashti et al.’s approach can cover two of them. We then highlight possible problems with their model as a (...) general approach to analogical inference and argue that these problems can be avoided by supplementing Bayesian update with Jeffrey conditionalization. (shrink)

It is often said that computer simulations generate new knowledge about the empirical world in the same way experiments do. My aim is to make sense of such a claim. I first show that the similarities between computer simulations and experiments do not allow them to generate new knowledge but invite the simulationist to interact with simulations in an experimental manner. I contend that, nevertheless, computer simulations and experiments yield new knowledge under the same epistemic circumstances, independently of any features (...) they may share. (shrink)

Au cours des dernières décennies, la philosophie des sciences est devenue la philosophie des sciences particulières. En conséquence, certaines des questions majeures de la philosophie des sciences sont adressées à la recherche en nanosciences et technologie. C’est le cas notamment des questions concernant la nature de la connaissance, le rôle de la théorie, les pratiques expérimentales et observationnelles. Ces questions habituelles suscitent des réponses inattendues, suggérant que la nanotechnoscience est un exemple non pas d’une science mais d’une technoscience.

This paper defends the naïve thesis that the method of experiment has per se an epistemic superiority over the method of computer simulation, a view that has been rejected by some philosophers writing about simulation, and whose grounds have been hard to pin down by its defenders. I further argue that this superiority does not come from the experiment’s object being materially similar to the target in the world that the investigator is trying to learn about, as both sides of (...) dispute over the epistemic superiority thesis have assumed. The superiority depends on features of the question and on a property of natural kinds that has been mistaken for material similarity. Seeing this requires holding other things equal in the comparison of the two methods, thereby exposing that, under the conditions that will be specified, the simulation is necessarily epistemically one step behind the corresponding experiment. Practical constraints like feasibility and morality mean that scientists do not often face an other-things- equal comparison when they choose between experiment and simulation. Nevertheless, I argue, awareness of this superiority and of the general distinction between experiment and simulation is important for maintaining motivation to seek answers to new questions. (shrink)

Analogue experiments have attracted interest for their potential to shed light on inaccessible domains. For instance, ‘dumb holes’ in fluids and Bose–Einstein condensates, as analogues of black holes, have been promoted as means of confirming the existence of Hawking radiation in real black holes. We compare analogue experiments with other cases of experiment and simulation in physics. We argue—contra recent claims in the philosophical literature—that analogue experiments are not capable of confirming the existence of particular phenomena in inaccessible target systems. (...) As they must assume the physical adequacy of the modelling framework used to describe the inaccessible target system, arguments to the conclusion that analogue experiments can yield confirmation for phenomena in those target systems, such as Hawking radiation in black holes, beg the question. (shrink)

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 (...) related to the general practice of computer simulations. (shrink)

This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s. -/- Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how (...) and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations. -/- . (shrink)

In this paper, we argue that, under a specific set of circumstances, designing and employing certain kinds of virtual reality (VR) experiences can be unethical. After a general discussion of simulations and their ethical context, we begin our argu-ment by distinguishing between the experiences generated by different media (text, film, computer game simulation, and VR simulation), and argue that VR experiences offer an unprecedented degree of what we call “perspectival fidelity” that prior modes of simulation lack. Additionally, we argue that (...) when VR experiences couple this perspectival fidelity with what we call “context realism,” VR experiences have the ability to produce “virtually real experiences.” We claim that virtually real experiences generate ethical issues for VR technologies that are unique to the medium. Because subjects of these experiences treat them as if they were real, a higher degree of ethical scrutiny should be applied to any VR scenario with the potential to generate virtually real experiences. To mitigate this unique moral hazard, we propose and defend what we call “The Equivalence Principle.” This principle states that “if it would be wrong to allow subjects to have a certain experience in reality, then it would be wrong to allow subjects to have that experience in a virtually real setting.” We argue that such a principle, although limited in scope, should be part of the risk analysis conducted by any Institutional Review Boards, psychologists, empirically oriented philosophers, or game designers who are using VR technology in their work. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

This paper provides the first systematic philosophical analysis of an increasingly important part of modern scientific practice: analogue quantum simulation. We introduce the distinction between `simulation' and `emulation' as applied in the context of two case studies. Based upon this distinction, and building upon ideas from the recent philosophical literature on scientific understanding, we provide a normative framework to isolate and support the goals of scientists undertaking analogue quantum simulation and emulation. We expect our framework to be useful to both (...) working scientists and philosophers of science interested in cutting-edge scientific practice. (shrink)

In 1981 Unruh proposed that fluid mechanical experiments could be used to probe key aspects of the quantum phenomenology of black holes. In particular, he claimed that an analogue to Hawking radiation could be created within a fluid mechanical `dumb hole', with the event horizon replaced by a sonic horizon. Since then an entire sub-field of `analogue gravity' has been created. In 2016 Steinhauer reported the experimental observation of quantum Hawking radiation and its entanglement in a Bose-Einstein condensate analogue black (...) hole. What can we learn from such analogue experiments? In particular, in what sense can they provide evidence of novel phenomena such as black hole Hawking radiation? (shrink)

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 (...) types of experiment share, and what they do not. A close look reveals at least one fundamental methodological difference between thought and simulation experiments: while thought experiments are a cognitive process that employs intuition, simulation experiments rest on automated iterations of formal algorithms. It will be argued that this difference has important epistemological ramifications. (shrink)

If well-designed, the results of a Randomised Clinical Trial can justify a causal claim between treatment and effect in the study population; however, additional information might be needed to carry over this result to another population. RCTs have been criticized exactly on grounds of failing to provide this sort of information Evidence, inference and enquiry. Oxford University Press, New York, 2011), as well as to black-box important details regarding the mechanisms underpinning the causal law instantiated by the RCT result. On (...) the other side, so-called In Silico Clinical Trials face the same criticisms addressed against standard modelling and simulation techniques, and cannot be equated to experiments Philosophy of molecular medicine: foundational issues in research and practice, Routledge, New York, 2017; Parker in Synthese 169:483–496, 2009; Parke in Philos Sci 81:516–536, 2014; Diez Roux in Am J Epidemiol 181:100–102, 2015 and related discussions in Frigg and Reiss in Synthese 169:593–613, 2009; Winsberg in Synthese 169:575–592, 2009; Beisbart and Norton in Int Stud Philos Sci 26:403–422, 2012). We undertake a formal analysis of both methods in order to identify their distinct contribution to causal inference in the clinical setting. Britton et al.’s study :E2098–E2105, 2013) on the impact of ion current variability on cardiac electrophysiology is used for illustrative purposes. We deduce that, by predicting variability through interpolation, ISCTs aid with problems regarding extrapolation of RCTs results, and therefore in assessing their external validity. Furthermore, ISCTs can be said to encode “thick” causal knowledge —as opposed to “thin” difference-making information inferred from RCTs. Hence, ISCTs and RCTs cannot replace one another but rather, they are complementary in that the former provide information about the determinants of variability of causal effects, while the latter can, under certain conditions, establish causality in the first place. (shrink)

This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton’s Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and (...) social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze’s reading of Plato on the relationship of ideas, copies and simulacra. (shrink)

We introduce ‘model migration’ as a species of cross-disciplinary knowledge transfer whereby the representational function of a model is radically changed to allow application to a new disciplinary context. Controversies and confusions that often derive from this phenomenon will be illustrated in the context of econophysics and phylogeographic linguistics. Migration can be usefully contrasted with concept of ‘imperialism’, that has been influentially discussed in the context of geographical economics. In particular, imperialism, unlike migration, relies upon extension of the original model (...) via an expansion of the domain of phenomena it is taken to adequately described. The success of imperialism thus requires expansion of the justificatory sanctioning of the original idealising assumptions to a new disciplinary context. Contrastingly, successful migration involves the radical representational re-interpretation of the original model, rather than its extension. Migration thus requires ‘re-sanctioning’ of new ‘counterpart idealisations’ to allow application to an entirely different class of phenomena. Whereas legitimate scientific imperialism should be based on the pursuit of some form of ontological unification, no such requirement is need to legitimate the practice of model migration. The distinction between migration and imperialism will thus be shown to have significant normative as well as descriptive value. (shrink)

This article on the epistemology of computational models stems from an analysis of the Gaïa hypothesis. It begins with James Kirchner’s criticisms of the central computational model of GH: Daisyworld. Among other things, the model has been criticized for being too abstract, describing fictional entities and trying to answer counterfactual questions. For these reasons the model has been considered not testable and therefore not legitimate in science, and in any case not very interesting since it explores non actual issues. This (...) criticism implicitly assumes that science should only be involved in the making of models that are “actual” and “specific”. I challenge both of these criticisms in this article. First by showing that although the testability—understood as the comparison of model output with empirical data—is an important procedure for explanatory models, there are plenty of models that are not testable. The fact that these are not testable has nothing to do with their being “abstract” or “what-if” but with their being predictive models. Secondly, I argue that “abstract” and “what-if” models aim at epistemic purposes distinct from those pursued by “actual and specific models”. Abstract models are used to propose how-possibly explanation or to pursue theorizing. What-if models are used to attribute causal or explanatory power to a variable of interest. The fact that they aim at different epistemic goals entails that it may not be accurate to consider the choice between different kinds of model as a “strategy“. (shrink)

I develop an account of productive surprise as an epistemic virtue of scientific investigations which does not turn on psychology alone. On my account, a scientific investigation is potentially productively surprising when results can conflict with epistemic expectations, those expectations pertain to a wide set of subjects. I argue that there are two sources of such surprise in science. One source, often identified with experiments, involves bringing our theoretical ideas in contact with new empirical observations. Another, often identified with simulations, (...) involves articulating and bringing together different parts of our knowledge. Both experiments and simulations, then, can surprise. (shrink)

Computer simulations and experiments share many important features. One way of explaining the similarities is to say that computer simulations just are experiments. This claim is quite popular in the literature. The aim of this paper is to argue against the claim and to develop an alternative explanation of why computer simulations resemble experiments. To this purpose, experiment is characterized in terms of an intervention on a system and of the observation of the reaction. Thus, if computer simulations are experiments, (...) either the computer hardware or the target system must be intervened on and observed. I argue against the first option using the non-observation argument, among others. The second option is excluded by e.g. the over-control argument, which stresses epistemological differences between experiments and simulations. To account for the similarities between experiments and computer simulations, I propose to say that computer simulations can model possible experiments and do in fact often do so. (shrink)

This paper defends the naïve thesis that the method of experiment has per se an epistemic superiority over the method of computer simulation, a view that has been rejected by some philosophers writing about simulation, and whose grounds have been hard to pin down by its defenders. I further argue that this superiority does not come from the experiment’s object being materially similar to the target in the world that the investigator is trying to learn about, as both sides of (...) dispute over the epistemic superiority thesis have assumed. The superiority depends on features of the question and on a property of natural kinds that has been mistaken for material similarity. Seeing this requires holding other things equal in the comparison of the two methods, thereby exposing that, under the conditions that will be specified, the simulation is necessarily epistemically one step behind the corresponding experiment. Practical constraints like feasibility and morality mean that scientists do not often face an other-things- equal comparison when they choose between experiment and simulation. Nevertheless, I argue, awareness of this superiority and of the general distinction between experiment and simulation is important for maintaining motivation to seek answers to new questions. (shrink)

The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling (...) pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems. (shrink)

Animal models have received particular attention as key examples of material models. In this paper, we argue that the specificities of establishing animal models—acknowledging their status as living beings and as epistemological tools—necessitate a more complex account of animal models as materialised models. This becomes particularly evident in animal-based models of diseases that only occur in humans: in these cases, the representational relation between animal model and human patient needs to be generated and validated. The first part of this paper (...) presents an account of how disease-specific animal models are established by drawing on the example of transgenic mice models for Alzheimer’s disease. We will introduce an account of validation that involves a three-fold process including from human being to experimental organism; from experimental organism to animal model; and from animal model to human patient. This process draws upon clinical relevance as much as scientific practices and results in disease-specific, yet incomplete, animal models. The second part of this paper argues that the incompleteness of models can be described in terms of multi-level abstractions. We qualify this notion by pointing to different experimental techniques and targets of modelling, which give rise to a plurality of models for a specific disease. (shrink)

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In this paper we investigate with a case study from chemistry under what conditions a simulation can serve as a surrogate for an experiment. The case-study concerns a simulation of H2-formation in outer space. We find that in this case the simulation can act as a surrogate for an experiment, because there exists comprehensive theoretical background knowledge in form of quantum mechanics about the range of phenomena to which the investigated process belongs and because any particular modelling assumptions as can (...) be justified. If these requirements are met then direct empirical validation may even be dispensable. We conjecture that this is not the case in the absence of comprehensive theoretical background knowledge. (shrink)

There is an ongoing debate on whether or to what degree computer simulations can be likened to experiments. Many philosophers are sceptical whether a strict separation between the two categories is possible and deny that the materiality of experiments makes a difference (Morrison 2009, Parker 2009, Winsberg 2010). Some also like to describe computer simulations as a “third way” between experimental and theoretical research (Rohrlich 1990, Axelrod 2003, Kueppers/Lenhard 2005). In this article I defend the view that computer simulations are (...) not experiments but that they are tools for evaluating the consequences of theories and theoretical assumptions. In order to do so the (alleged) similarities and differences between simulations and experiments are examined. It is found that three fundamental differences between simulations and experiments remain: 1) Only experiments can generate new empirical data. 2) Only Experiments can operate directly on the target system. 3) Experiments alone can be employed for testing fundamental hypotheses. As a consequence, experiments enjoy a distinct epistemic role in science that cannot completely be superseded by computer simulations. This finding in connection with a discussion of border cases such as hybrid methods that combine measurement with simulation shows that computer simulations can clearly be distinguished from empirical methods. It is important to understand that computer simulations are not experiments, because otherwise there is a danger of systematically underestimating the need for empirical validation of simulations. (shrink)

In this article we argue for the existence of ‘analogue simulation’ as a novel form of scientific inference with the potential to be confirmatory. This notion is distinct from the modes of analogical reasoning detailed in the literature, and draws inspiration from fluid dynamical ‘dumb hole’ analogues to gravitational black holes. For that case, which is considered in detail, we defend the claim that the phenomena of gravitational Hawking radiation could be confirmed in the case that its counterpart is detected (...) within experiments conducted on diverse realizations of the analogue model. A prospectus is given for further potential cases of analogue simulation in contemporary science. 1 Introduction2 Physical Background2.1 Hawking radiation in semi-classical gravity2.2 Modelling sound in fluids2.3 The acoustic analogue model of Hawking radiation3 Simulation and Analogy in Physical Theory3.1 Analogical reasoning and analogue simulation3.2 Confirmation via analogue simulation3.3 Recapitulation4 The Sound of Silence: Analogical Insights into Gravity4.1 Experimental realization of analogue models4.2 Universality and the Hawking effect4.3 Confirmation of gravitational Hawking radiation5 Prospectus. (shrink)

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.