This paper argues that the difference between contemporary software intensive scientific practice and more traditional non-software intensive varieties results from the characteristically high conditionality of software. We explain why the path complexity of programs with high conditionality imposes limits on standard error correction techniques and why this matters. While it is possible, in general, to characterize the error distribution in inquiry that does not involve high conditionality, we cannot characterize the error distribution in inquiry that depends on software. Software intensive (...) science presents distinctive error and uncertainty modalities that pose new challenges for the epistemology of science. (shrink)

My aim in this paper is to articulate an account of scientific modeling that reconciles pluralism about modeling with a modest form of scientific realism. The central claim of this approach is that the models of a given physical phenomenon can present different aspects of the phenomenon. This allows us, in certain special circumstances, to be confident that we are capturing genuine features of the world, even when our modeling occurs independently of a wholly theoretical motivation. This framework is illustrated (...) using a recent debate from meteorology. (shrink)

This article is an introduction to the Synthese Special Issue, Philosophy of Epidemiology. The overall goals of the issue are to revisit the state of philosophy of epidemiology and to provide a forum for new voices, approaches, and perspectives in the philosophy of epidemiology literature. The introduction begins by drawing on Geoffrey Rose’s work on how to conceptualize and design interventions for populations, rather than individuals. It then goes on to highlight some themes that emerged in the articles that make (...) up the issue: philosophy of epidemiology and epidemiological theory—what they are and what they ought to be, pluralism in measurement and causal attribution, epistemic and non-epistemic values in disputes epidemiological practices, decentering philosophy of epidemiology’s Eurocentrism, letting pragmatism guide uses of big data in epidemiology, and revisiting the lessons of classic texts in epidemiological causal inference. The introduction concludes with comments on a philosophy of epidemiology debate we see on, regarding the politics of philosophy of epidemiology. (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)

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

What do biologists want? If, unlike their counterparts in physics, biologists are generally wary of a grand, overarching theory, at what kinds of explanation do biologists aim? A history of the diverse and changing nature of biological explanation in a particularly charged field, "Making Sense of Life" draws our attention to the temporal, disciplinary, and cultural components of what biologists mean, and what they understand, when they propose to explain life.

one takes to be the most salient, any pair could be judged more similar to each other than to the third. Goodman uses this second problem to showthat there can be no context-free similarity metric, either in the trivial case or in a scientifically ...

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

Computer simulations have conventionally been understood to be either extensions of formal methods such as mathematical models or as special cases of empirical practices such as experiments. Here, I argue that computer simulations are best understood as instruments. Understanding them as such can better elucidate their actual role as well as their potential epistemic standing in relation to science and other scientific methods, practices and devices.

Diane Vaughan’s analysis of the causes of the Challenger accident suggests ways to apply science and technology studies to the teaching of engineering ethics. By sensitizing future engineers to the ongoing construction of risk during mundane engineering practice, we can better prepare them to address issues of public health, safety, and welfare before they require heroic intervention. Understanding the importance of precedents, incremental change, and fallible engineering judgment in engineering design may help them anticipate potential threats to public safety arising (...) from routine aspects of workplace culture. We suggest modifications of both detailed case studies on engineering disasters and hypothetical, ethical dilemmas employed in engineering ethics classes. Investigating the sociotechnical aspects of engineering practice can improve the initial recognition of ethical problems in real-world settings and provide an understanding of the role of workplace organization and culture in facilitating or impeding remedial action. (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)

Models are of central importance in many scientific contexts. The roles the MIT bag model of the nucleon, the billiard ball model of a gas, the Bohr model of the atom, the Gaussian-chain model of a polymer, the Lorenz model of the atmosphere, the Lotka- Volterra model of predator-prey interaction, agent-based and evolutionary models of social interaction, or general equilibrium models of markets play in their respective domains are cases in point.

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (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.

How can we be certain that software is reliable? Is there any method that can verify the correctness of software for all cases of interest? Computer scientists and software engineers have informally assumed that there is no fully general solution to the verification problem. In this paper, we survey approaches to the problem of software verification and offer a new proof for why there can be no general solution.

The book examines issues related to the way modeling and simulation enable us to reconstruct aspects of the world we are investigating. It also investigates the processes by which we extract concrete knowledge from those reconstructions and how that knowledge is legitimated.

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Software-intensive systems are ubiquitous in the industrialized world. The reliability of software has implications for how we understand scientific knowledge produced using software-intensive systems and for our understanding of the ethical and political status of technology. The reliability of a software system is largely determined by the distribution of errors and by the consequences of those errors in the usage of that system. We select a taxonomy of software error types from the literature on empirically observed software errors and compare (...) that taxonomy to Giuseppe Primiero’s Minds and Machines 24: 249–273, (2014) taxonomy of error in information systems. Because Primiero’s taxonomy is articulated in terms of a coherent, explicit model of computation and is more fine-grained than the empirical taxonomy we select, we might expect Primiero’s taxonomy to provide insights into how to reduce the frequency of software error better than the empirical taxonomy. Whether using one software error taxonomy can help to reduce the frequency of software errors better than another taxonomy is ultimately an empirical question. (shrink)

How can we be certain that software is reliable? Is there any method that can verify the correctness of software for all cases of interest? Computer scientists and software engineers have informally assumed that there is no fully general solution to the verification problem. In this paper, we survey approaches to the problem of software verification and offer a new proof for why there can be no general solution.