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 (...) of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo’s description of simulations as “compromises” and “glue”, they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades. (shrink)

Mechanistic explanation has an impressive track record of advancing our understanding of complex, hierarchically organized physical systems, particularly biological and neural systems. But not every complex system can be understood mechanistically. Psychological capacities are often understood by providing cognitive models of the systems that underlie them. I argue that these models, while superficially similar to mechanistic models, in fact have a substantially more complex relation to the real underlying system. They are typically constructed using a range of techniques for abstracting (...) the functional properties of the system, which may not coincide with its mechanistic organization. I describe these techniques and show that despite being non-mechanistic, these cognitive models can satisfy the normative constraints on good explanations. (shrink)

In the 1960s, theoretical biologist Richard Levins criticised modellers in his own discipline of population biology for pursuing the “brute force” strategy of building hyper-realistic models. Instead of exclusively chasing complexity, Levins advocated for the use of multiple different kinds of complementary models, including much simpler ones. In this paper, I argue that the epistemic challenges Levins attributed to the brute force strategy still apply to state-of-the-art climate models today: they have big appetites for unattainable data, they are limited by (...) computational tractability, and they are incomprehensible to the human modeller. Along the lines Levins described, this uncertainty generates a trade-off between realistic, precise models with predictive power and simple, highly idealised models that facilitate understanding. In addition to building ensembles of highly complex dynamical models, climate modellers can address model uncertainty by comparing models of different types, such as dynamical and data-driven models, and by systematically comparing models at different levels of what climate modellers call the model hierarchy. Despite its age, Levins’ paper remains incredibly insightful and should be considered an important entry into the philosophy of computational modelling. (shrink)

The aim of this paper is to show that science, understood as pure research, ought not to be affected by non-epistemic values and thus to defend the traditional ideal of value-free science. First, we will trace the distinction between science and technology, arguing that science should be identified with pure research and that any non-epistemic concern should be di­rected toward technology and technological research. Second, we will examine different kinds of values and the roles they can play in scientific research (...) to argue that science understood as pure research is mostly and in any case ought to be value-free. Third, we will consider and dismiss some widespread arguments that aim to defend, especially at a normative level, the inevitable value-ladenness of science. Finally, we will briefly return to the connections among science, technology, and values. (shrink)

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 (...) represent a broad range of diverse organisms. More often than not, model organisms are taken as a reference point for an extrapolation to be made to the unknown characteristics of other species. I propose to view model organisms as analogue simulators which represent the emergent phenomenon in the context of cross-species research. A model organism represents a wide range of species by simulating their molecular microstates which underlie various emergent phenomena. I show that although model organisms represent the target species inadequately at many levels of complexity, they have epistemic values as a simulator in virtue of which the emergent phenomenon can be modeled dynamically, a virtue that is hardly attainable by non-dynamic models. (shrink)

It is assumed that scientific models contain no superfluous model elements in scientific representation. A representational model is constructed with all the model elements serving the representational purpose. The received view has it that there are no redundant model elements which are non-representational. Contrary to this received view, I argue that there exist some non-representational model elements which are essential in scientific representation. I call them representation-supporting model elements in virtue of the fact that they play the role to support (...) the representational role of representational model elements. Representation-supporting model elements, which have a characteristic of dependability, are not to be eliminated in the process of modeling although they are playing second fiddle to representational model elements in scientific representation. (shrink)

The philosophy of measurement studies the conceptual, ontological, epistemic, and technological conditions that make measurement possible and reliable. A new wave of philosophical scholarship has emerged in the last decade that emphasizes the material and historical dimensions of measurement and the relationships between measurement and theoretical modeling. This essay surveys these developments and contrasts them with earlier work on the semantics of quantity terms and the representational character of measurement. The conclusions highlight four characteristics of the emerging research program in (...) philosophy of measurement: it is epistemological, coherentist, practice oriented, and model based. (shrink)

In this paper, we argue for the centrality of prediction in the use of computational models in science. We focus on the consequences of the irreversibility of computational models and on the conditional or ceteris paribus, nature of the kinds of their predictions. By irreversibility, we mean the fact that computational models can generally arrive at the same state via many possible sequences of previous states. Thus, while in the natural world, it is generally assumed that physical states have a (...) unique history, representations of those states in a computational model will usually be compatible with more than one possible history in the model. We describe some of the challenges involved in prediction and retrodiction in computational models while arguing that prediction is an essential feature of non-arbitrary decision making. Furthermore, we contend that the non-predictive virtues of computational models are dependent to a significant degree on the predictive success of the models in question. (shrink)

We address some of the epistemological challenges highlighted by the Critical Data Studies literature by reference to some of the key debates in the philosophy of science concerning computational modeling and simulation. We provide a brief overview of these debates focusing particularly on what Paul Humphreys calls epistemic opacity. We argue that debates in Critical Data Studies and philosophy of science have neglected the problem of error management and error detection. This is an especially important feature of the epistemology of (...) Big Data. In “Error” section we explain the main characteristics of error detection and correction along with the relationship between error and path complexity in software. In this section we provide an overview of conventional statistical methods for error detection and review their limitations when faced with the high degree of conditionality inherent to modern software systems. (shrink)

What does it mean to trust the results of a computer simulation? This paper argues that trust in simulations should be grounded in empirical evidence, good engineering practice, and established theoretical principles. Without these constraints, computer simulation risks becoming little more than speculation. We argue against two prominent positions in the epistemology of computer simulation and defend a conservative view that emphasizes the difference between the norms governing scientific investigation and those governing ordinary epistemic practices.

This article argues in favour of an inferential role for fictions in scientific modelling. The argument proceeds by means of a detailed case study, namely models of the internal structure of stars in stellar astrophysics. The main assumptions in such models are described, and it is argued that they are best understood as useful fictions. The role that conditionals play in these models is explained, and it is argued that fictional assumptions play an important role as either background or antecedent (...) conditions. I then expand on the argument for the compatibility of fictions and scientific realism. I argue that realism and antirealism plausibly offer correspondingly different accounts of the semantics of these fictional conditionals. (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)

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 (...) by Arthur Fine in his work on the Natural Ontological Attitude. An important obstacle to articulating a positive program, we suggest, has been overlooking how scientists adopt standardized rules and procedures in order to define and operationalize meanings for success and failure relative to their situated goals. To help fill this gap, we introduce two new ideas, design specifications and track records, and show how they advance our ability to make sense of scientific modeling practices while maintaining a deflationary stance toward the realism debate. (shrink)

This article critically examines a recent philosophical debate on the role of values in climate change forecasts, such as those found in assessment reports of the Intergovernmental Panel on Climate Change. On one side, several philosophers insist that the argument from inductive risk, as developed by Rudner and Douglas among others, applies to this case. AIR aims to show that ethical value judgments should influence decisions about what is sufficient evidence for accepting scientific hypotheses that have implications for policy issues. (...) Advocates of extending AIR to climate science claim that values are deeply... (shrink)

This paper combines naturalized metaphysics and a philosophical reflection on a recently evolving interdisciplinary branch of quantum chemistry, ab initio molecular dynamics. Bridging the gaps among chemistry, physics, and computer science, this cutting-edge research field explores the structure and dynamics of complex molecular many-body systems through computer simulations. These simulations are allegedly crafted solely by the laws of fundamental physics, and are explicitly designed to capture nature as closely as possible. The models and algorithms employed, however, involve many approximations and (...) significant degrees of idealization of their target systems. Therefore, for philosophers of science the pivotal question of whether relying only on the fundamental laws of physics supports a reductionist or realist stance arises. One conceivable answer to this question is that the irreducible approximations and idealizations support rather anti-realist positions. After reviewing an influential attitude in the philosophy of computer simulations and the debate concerning scientific realism, I offer a fair interpretation of such ab initio modelling in quantum chemistry within a naturalistic metaphysical framework that gives rise to a specific type of ontic structural realism. (shrink)

Experimentation represents today a ‘hot’ topic in computing. If experiments made with the support of computers, such as computer simulations, have received increasing attention from philosophers of science and technology, questions such as “what does it mean to do experiments in computer science and engineering and what are their benefits?” emerged only recently as central in the debate over the disciplinary status of the discipline. In this work we aim at showing, also by means of paradigmatic examples, how the traditional (...) notion of controlled experiment should be revised to take into account a part of the experimental practice in computing along the lines of experimentation as exploration. Taking inspiration from the discussion on exploratory experimentation in the philosophy of science—experimentation that is not theory-driven—we advance the idea of explorative experiments that, although not new, can contribute to enlarge the debate about the nature and role of experimental methods in computing. In order to further refine this concept we recast explorative experiments as socio-technical experiments, that test new technologies in their socio-technical contexts. We suggest that, when experiments are explorative, control should be intended in a posteriori form, in opposition to the a priori form that usually takes place in traditional experimental contexts. (shrink)

Computational modeling should play a central role in philosophy. In this introduction to our topical collection, we propose a small topology of computational modeling in philosophy in general, and show how the various contributions to our topical collection fit into this overall picture. On this basis, we describe some of the ways in which computational models from other disciplines have found their way into philosophy, and how the principles one found here still underlie current trends in the field. Moreover, we (...) argue that philosophers contribute to computational modeling not only by building their own models, but also by thinking about the various applications of the method in philosophy and the sciences. In this context, we note that models in philosophy are usually simple, while models in the sciences are often more complex and empirically grounded. Bridging certain methodological gaps that arise from this discrepancy may prove to be challenging and fruitful for the further development of computational modeling in philosophy and beyond. (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.

Naturalism in the philosophy of science has proceeded differently than the familiar forms of meta-philosophical naturalism in other sub-fields, taking its cues from “science as we know it” (Cartwright in The Dappled World, Oxford University Press, Oxford, 1999, p. 1) rather than from a philosophical conception of “the Scientific Image.” Its primary focus is scientific practice, and its philosophical analyses are complementary and accountable to empirical studies of scientific work. I argue that naturalistic philosophy of science is nevertheless criterial for (...) other versions of meta-philosophical naturalism; relying on a conflicting conception of scientific understanding would constitute a “first philosophy” imposed on the sciences. Moreover, naturalistic philosophy of science provides the basis for a “radically” naturalistic alternative to the familiar forms of orthodox or liberal naturalism. Goodman, Sellars and Hempel had previously challenged empiricist scruples against causal connections or nomological necessity by arguing that scientific concepts already had modal import. The radical naturalism I defend similarly challenges meta-philosophical naturalists’ conception of the Scientific Image as anormative, and instead shows how the normativity of scientific understanding in practice is a scientifically intelligible natural phenomenon. This account then provides a basis for naturalistic reflection on how other practices and normative concerns fit together with the best scientific understanding of human ways of life. (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)

Both ecologists and statistical physicists use a variety of highly idealized models to study active matter and self-organizing critical phenomena. In this paper, I show how universality classes play a crucial role in justifying the application of highly idealized ‘minimal’ models to explain and understand the critical behaviors of active matter systems across a wide range of scales and scientific fields. Appealing to universality enables us to see why the same minimal models can be used to explain and understand behaviors (...) across these different systems despite drastic differences in the causes and mechanisms responsible for the behaviors of interest. After analyzing these cases in detail, I argue that accounts that focus on identifying common causes or mechanisms in order to explain patterns are unable to accommodate these cases. In contrast, I argue that the justification for using these minimal models is that they are within the same universality class as real systems whose causes and mechanisms are known to be different. I also use these cases to identify several different kinds of explanatory autonomy that have important implications for how scientists ought to approach the modeling of multiscale phenomena. (shrink)

In a previous article, I argued that some recent philosophical work on the use of fictions in science is, while illuminating about some aspects of current scientific practice, unduly limited to cases of well-established fictions. In other words, this earlier work contended, a philosophical account of scientific fictions can do more than merely describe scientific practices, but can aid in the resolution of disputes about the proper interpretation of scientific theories and the epistemic status of some scientific models. In the (...) present paper, I expand upon the variational account of fictions and idealizations... (shrink)

The epistemology of computer simulations has become a mainstream topic in the philosophy of technology. Within this large area, significant differences hold between the various types of models and simulation technologies. Agent-based and multi-agent systems simulations introduce a specific constraint on the types of agents and systems modelled. We argue that such difference is crucial and that simulation for the artificial sciences requires the formulation of its own specific epistemological principles. We present a minimally committed epistemology which relies on the (...) methodological principles of the Philosophy of Information and requires weak assumptions on the usability of the simulation and the controllability of the model. We use these principles to provide a new definition of simulation for the context of interest. (shrink)

Usually within the context of computer simulations in quantum chemistry practices, there is a distinction between ab initio and semi-empirical methods. Related to this, a controversy within the scientific and philosophical communities came about regarding the superiority of the ab initio methods due to their theoretical rigor. In this article we re-evaluate the condition of the semi-empirical simulations in this area of research. We examine some of the aspects of this debate that have been considered in philosophy and provide additional (...) elements to the analysis. (shrink)

This article presents the evolution of philosophical and methodological considerations concerning empiricism in computer/computing science. In this study, we trace the most important current events in the history of reflection on computing. The forerunners of Artificial Intelligence H.A. Simon and A. Newell in their paper Computer Science As Empirical Inquiry started these considerations. Later the concept of empirical computer science was developed by S.S. Shapiro, P. Wegner, A.H. Eden and P.J. Denning. They showed various empirical aspects of computing. This led (...) to a view of the science of computing - the science of general scope. Some interesting contemporary ways towards a generalized perspective on computations were also shown. (shrink)

We begin by distinguishing computationalism from a number of other theses that are sometimes conflated with it. We also distinguish between several important kinds of computation: computation in a generic sense, digital computation, and analog computation. Then, we defend a weak version of computationalism—neural processes are computations in the generic sense. After that, we reject on empirical grounds the common assimilation of neural computation to either analog or digital computation, concluding that neural computation is sui generis. Analog computation requires continuous (...) signals; digital computation requires strings of digits. But current neuroscientific evidence indicates that typical neural signals, such as spike trains, are graded like continuous signals but are constituted by discrete functional elements (spikes); thus, typical neural signals are neither continuous signals nor strings of digits. It follows that neural computation is sui generis. Finally, we highlight three important consequences of a proper understanding of neural computation for the theory of cognition. First, understanding neural computation requires a specially designed mathematical theory (or theories) rather than the mathematical theories of analog or digital computation. Second, several popular views about neural computation turn out to be incorrect. Third, computational theories of cognition that rely on non-neural notions of computation ought to be replaced or reinterpreted in terms of neural computation. (shrink)

Making sense of modeling: beyond representation Content Type Journal Article Category Original paper in Philosophy of Science Pages 335-352 DOI 10.1007/s13194-011-0032-8 Authors Isabelle Peschard, Philosophy Department, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912 Journal Volume Volume 1 Journal Issue Volume 1, Number 3.

Frigg and Reiss (2009) argue that philosophical problems in simulation bear enough resemblance to recognized issues in the philosophy of modeling that they only pose challenges analogous to those found in standard analytic models used to represent natural systems. They suggest that there are no new philosophical problems in computer simulation modeling beyond those found in traditional mathematical modeling. Winsberg (2009) has countered that there appear to be genuinely new epistemological problems in simulation modeling because the knowledge obtained from them (...) is ‘downward, motley, and autonomous.’ Here I draw out some specific ways that these epistemological problems are manifest in complex ecological simulation, especially in agent-based models. These models contain novel features that were impossible to anticipate prior to the computer revolution, and continue to present difficulties and challenges of both a practical and philosophical nature (Humphreys 2002). (shrink)

By the end of the twentieth century, many prominent cosmologists were fascinated by the questions why is the universe the way it is, and why does the universe appear to be just right for life to emerge.1 Indeed, the shift to posing questions beginning with why rather than what or how is a relatively recent development in modern cosmology. This paper begins by looking at the emergence of why questions in cosmological discourse by tracing affiliated anthropic reasoning and fine-tuning arguments (...) in cosmology. I also consider recent suggestions that the laws of physics may themselves evolve. In response to the why questions, this paper then examines the proliferation of multiverse discourse in the late twentieth... (shrink)

Philosophers continue to debate both the actual and the ideal roles of values in science. Recently, Eric Winsberg has offered a novel, model-based challenge to those who argue that the internal workings of science can and should be kept free from the influence of social values. He contends that model-based assignments of probability to hypotheses about future climate change are unavoidably influenced by social values. I raise two objections to Winsberg’s argument, neither of which can wholly undermine its conclusion but (...) each of which suggests that his argument exaggerates the influence of social values on estimates of uncertainty in climate prediction. I then show how a more traditional challenge to the value-free ideal seems tailor-made for the climate context. (shrink)

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, (...) per se. To the extent that either methodology puts researchers in a privileged epistemic position, this is context sensitive. (shrink)

Can computer simulation results be evidence for hypotheses about real-world systems and phenomena? If so, what sort of evidence? Can we gain genuinely new knowledge of the world via simulation? I argue that evidence from computer simulation is aptly characterized as higher-order evidence: it is evidence that other evidence regarding a hypothesis about the world has been collected. Insofar as particular epistemic agents do not have this other evidence, it is possible that they will gain genuinely new knowledge of the (...) world via simulation. I illustrate with examples inspired by uses of simulation in meteorology and astrophysics. (shrink)

If the twentieth century was the age of the world picture taken as a photograph of the Whole Earth from outer space, today’s observations of the planet are produced by means of computer simulation. Pandemic models are of paramount sociological interest in this respect, since modelling contagion is closely intertwined with modelling the material connectivities of social life. By envisioning the global dynamics of disease transmission, pandemic simulations enact the relationscapes of a transnational world. This article seeks to analyse such (...) an enactment: It asks how simulation methods can establish a particular relation to the social from within the social. To provide an answer to this question, and adopting Niklas Luhmann’s theory of world society, pandemic simulations are described as modes of global self-observation that can be specified factually, socially, spatially and temporally. They instantiate a ‘doubling of reality’ designed to apprehend the potential future threat of disease transmission along the pathways marked by global infrastructures. They constitute scopic regimes that virtually synthesize a global situation of universal communicability in order to turn the world into an object of political intervention. (shrink)

This essay presents a model-theoretic account of dispositional properties, according to which dispositions are not ordinary properties of real entities; dispositions capture the behavior of abstract, idealized models. This account has several payoffs. First, it saves the simple conditional analysis of dispositions. Second, it preserves the general connection between dispositions and regularities, despite the fact that some dispositions are not grounded in actual regularities. Finally, it brings together the analysis and the explanation of dispositions under a unified framework.

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)

It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins, ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models, and representations of protein (...) structure is one of integrative pluralism. Our defence appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science. 1. Introduction2. Partiality of Representation3. Protein Functional Complexity4. Modelling Protein Structure4.1 Integrating ab initio and experimental models4.2 Integrating multiple experimental models5. Conclusion. (shrink)

‘Mapping accounts’ of applied mathematics hold that the application of mathematics in physical science is best understood in terms of ‘mappings’ between mathematical structures and physical structures. In this paper, I suggest that mapping accounts rely on the assumption that the mathematics relevant to any application of mathematics in empirical science can be captured in an appropriate mathematical structure. If we are interested in assessing the plausibility of mapping accounts, we must ask ourselves: how plausible is this assumption as a (...) working hypothesis about applied mathematics? In order to do so, we examine the role played by mathematics in the multiscalar modelling of sea ice melting behaviour and examine whether we can indeed capture the mathematics involved in the kind of mathematical structure employed by the mapping account. Along the way, we note that the cases of applied mathematics that appear in discussions of mapping accounts almost exclusively involve the employment of a single clearly circumscribed mathematical field or domain. While the core assumption of mapping accounts may appear plausible in such situations, we ultimately suggest that the mapping account is not able to handle the important added complexities involved in our sea ice case study. In particular, the notion of mathematical structure around which such accounts are framed does not seem to be able to capture the way in which some applications of mathematics require that very different pieces of mathematics be related to one another on the basis of both mathematical and empirical information. (shrink)

According to standard accounts of mathematical representations of physical phenomena, positing structure-preserving mappings between a physical target system and the structure picked out by a mathematical theory is essential to such representations. In this paper, I argue that these accounts fail to give a satisfactory explanation of scientific representations that make use of inconsistent mathematical theories and present an alternative, robustly inferential account of mathematical representation that provides not just a better explanation of applications of inconsistent mathematics, but also a (...) compelling explanation of mathematical representations of physical phenomena in general. 1Inconsistent Mathematics and the Problem of Representation2The Early Calculus3Mapping Accounts and the Early Calculus3.1Partial structures3.2Inconsistent structures3.3Related total consistent structures4A Robustly Inferential Account of the Early Calculus in Applications 4.1The robustly inferential conception of mathematical representation4.2The robustly inferential conception and inconsistent mathematics4.3The robustly inferential conception and mapping accounts5Beyond Inconsistent Mathematics. (shrink)

Modeling and computer simulations, we claim, should be considered core philosophical methods. More precisely, we will defend two theses. First, philosophers should use simulations for many of the same reasons we currently use thought experiments. In fact, simulations are superior to thought experiments in achieving some philosophical goals. Second, devising and coding computational models instill good philosophical habits of mind. Throughout the paper, we respond to the often implicit objection that computer modeling is “not philosophical.”.

In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is guided (...) by an interventionist conception of causal structure. While doubts have been raised about the applicability of this notion of causality to complex biological systems, it is here seen to be an adequate guide to inquiry. (shrink)

At least since Kuhn’s Structure, philosophers have studied the influence of social factors in science’s pursuit of truth and knowledge. More recently, formal models and computer simulations have allowed philosophers of science and social epistemologists to dig deeper into the detailed dynamics of scientific research and experimentation, and to develop very seemingly realistic models of the social organization of science. These models purport to be predictive of the optimal allocations of factors, such as diversity of methods used in science, size (...) of groups, and communication channels among researchers. In this paper we argue that the current research faces an empirical challenge. The challenge is to connect simulation models with data. We present possible scenarios about how the challenge may unfold. (shrink)

How climate models came to gain and exercise epistemic authority has been a key concern of recent climate change historiography. Using newly released archival materials and recently conducted interviews with key actors, we reconstruct negotiations between UK climate scientists and policymakers which led to the opening of the Hadley Centre for Climate Prediction and Research in 1990. We historicize earlier arguments about the unique institutional culture of the Hadley Centre, and link this culture to broader characteristics of UK regulatory practice (...) and environmental politics. A product of a particular time and place, the Hadley Centre was shaped not just by scientific ambition, but by a Conservative governmental preference for ‘sound science’ and high evidential standards in environmental policymaking. Civil servants sought a prediction programme which would appeal to such sensibilities, with transient and regional climate simulation techniques seemingly offering both scientific prestige and persuasive power. Beyond the national level, we also offer new insights into the early role of the Intergovernmental Panel on Climate Change and an evolving international political context in the shaping of scientific practices and institutions. (shrink)

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 (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

In an attempt to determine the epistemic status of computer simulation results, philosophers of science have recently explored the similarities and differences between computer simulations and experiments. One question that arises is whether and, if so, when, simulation results constitute novel empirical data. It is often supposed that computer simulation results could never be empirical or novel because simulations never interact with their targets, and cannot go beyond their programming. This paper argues against this position by examining whether, and under (...) what conditions, the features of empiricality and novelty could be displayed by computer simulation data. I show that, to the extent that certain familiar measurement results have these features, so can some computer simulation results. (shrink)

Climate change assessments rely upon scenarios of socioeconomic developments to conceptualize alternative outcomes for global greenhouse gas emissions. These are used in conjunction with climate models to make projections of future climate. Specifically, the estimations of greenhouse gas emissions based on socioeconomic scenarios constrain climate models in their outcomes of temperatures, precipitation, etc. Traditionally, the fundamental logic of the socioeconomic scenarios—that is, the logic that makes them plausible—is developed and prioritized using methods that are very subjective. This introduces a fundamental (...) challenge for climate change assessment: The veracity of projections of future climate currently rests on subjective ground. We elaborate on these subjective aspects of scenarios in climate change research. We then consider an alternative method for developing scenarios, a systems dynamics approach called ‘Cross-Impact Balance’ (CIB) analysis. We discuss notions of ‘objective’ and ‘objectivity’ as criteria for distinguishing appropriate scenario methods for climate change research. We distinguish seven distinct meanings of ‘objective,’ and demonstrate that CIB analysis is more objective than traditional subjective approaches. However, we also consider criticisms concerning which of the seven meanings of ‘objective’ are appropriate for scenario work. Finally, we arrive at conclusions regarding which meanings of ‘objective’ and ‘objectivity’ are relevant for climate change research. Because scientific assessments uncover knowledge relevant to the responses of a real, independently existing climate system, this requires scenario methodologies employed in such studies to also uphold the seven meanings of ‘objective’ and ‘objectivity.’. (shrink)

This paper proposes an account of scientific data that makes sense of recent debates on data-driven and ‘big data’ research, while also building on the history of data production and use particularly within biology. In this view, ‘data’ is a relational category applied to research outputs that are taken, at specific moments of inquiry, to provide evidence for knowledge claims of interest to the researchers involved. They do not have truth-value in and of themselves, nor can they be seen as (...) straightforward representations of given phenomena. Rather, they are fungible objects defined by their portability and prospective usefulness as evidence. (shrink)

Over the course of the twentieth century, hydraulic engineering has come to rely primarily on the use of computational models. Disco and van den Ende hint towards the reasons for widespread adoption of computational models by pointing out that such models fulfill a crucial role as management tools in Dutch water management, and meet a more general desire to quantify water-related phenomena. The successful application of computational models implies blackboxing : “[w]hen a machine runs efficiently … one need focus only (...) on its inputs and outputs and not on its internal complexity. Thus, paradoxically, the more science and technology succeed, the more opaque and obscure they become”.. (shrink)

Idealizing conditions are scapegoats for scientific hypotheses, too often blamed for falsehood better attributed to less obvious sources. But while the tendency to blame idealizations is common among both philosophers of science and scientists themselves, the blame is misplaced. Attention to the nature of idealizing conditions, the content of idealized hypotheses, and scientists’ attitudes toward those hypotheses shows that idealizing conditions are blameless when hypotheses misrepresent. These conditions help to determine the content of idealized hypotheses, and they do so in (...) a way that prevents those hypotheses from being false by virtue of their constituent idealizations. (shrink)