WE AIM HERE to outline a theory of evidence for use. More specifically we lay foundations for a guide for the use of evidence in predicting policy effectiveness in situ, a more comprehensive guide than current standard offerings, such as the Maryland rules in criminology, the weight of evidence scheme of the International Agency for Research on Cancer (IARC), or the US ‘What Works Clearinghouse’. The guide itself is meant to be well-grounded but at the same time to give practicable (...) advice, that is, advice that can be used by policy-makers not expert in the natural and social sciences, assuming they are well-intentioned and have a reasonable but limited amount of time and resources available for searching out evidence and deliberating. (shrink)

The claims of randomized controlled trials to be the gold standard rest on the fact that the ideal RCT is a deductive method: if the assumptions of the test are met, a positive result implies the appropriate causal conclusion. This is a feature that RCTs share with a variety of other methods, which thus have equal claim to being a gold standard. This article describes some of these other deductive methods and also some useful non-deductive methods, including the hypothetico-deductive method. (...) It argues that with all deductive methods, the benefit that the conclusions follow deductively in the ideal case comes with a great cost: narrowness of scope. This is an instance of the familiar trade-off between internal and external validity. RCTs have high internal validity but the formal methodology puts severe constraints on the assumptions a target population must meet to justify exporting a conclusion from the test population to the target. The article reviews one such set of assumptions to show the kind of knowledge required. The overall conclusion is that to draw causal inferences about a target population, which method is best depends case-by-case on what background knowledge we have or can come to obtain. There is no gold standard. (shrink)

In the last few decades, philosophy of science has increasingly focused on multilevel models and causal mechanistic explanations to account for complex biological phenomena. On the one hand, biological and biomedical works make extensive use of mechanistic concepts; on the other hand, philosophers have analyzed an increasing range of examples taken from different domains in the life sciences to test—support or criticize—the adequacy of mechanistic accounts. The article highlights some challenges in the elaboration of mechanistic explanations with a focus on (...) cancer research and neuropsychiatry. It jointly considers fields, which are usually dealt with separately, and keeps a close eye on scientific practice. The article has a twofold aim. First, it shows that identification of the explananda is a key issue when looking at dynamic processes and their implications in medical research and clinical practice. Second, it discusses the relevance of organizational accounts of mechanisms, and questions whether thorough self-sustaining mechanistic explanations can actually be provided when addressing cancer and psychiatric diseases. While acknowledging the merits of the wide ongoing debate on mechanistic models, the article challenges the mechanistic approach to explanation by discussing, in particular, explanatory and conceptual terms in the light of stances from medical cases. (shrink)

Monte Carlo simulations arrive at their results by introducing randomness, sometimes derived from a physical randomizing device. Nonetheless, we argue, they open no new epistemic channels beyond that already employed by traditional simulations: the inference by ordinary argumentation of conclusions from assumptions built into the simulations. We show that Monte Carlo simulations cannot produce knowledge other than by inference, and that they resemble other computer simulations in the manner in which they derive their conclusions. Simple examples of Monte Carlo simulations (...) are analysed to identify the underlying inferences. (shrink)

We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not require material manipulation. We also (...) suggest that material manipulation, although still present in in the practice of data mining, fulfill a different epistemic role. (shrink)

Computer simulations are an exciting tool that plays important roles in many scientific disciplines. This has attracted the attention of a number of philosophers of science. The main tenor in this literature is that computer simulations not only constitute interesting and powerful new science, but that they also raise a host of new philosophical issues. The protagonists in this debate claim no less than that simulations call into question our philosophical understanding of scientific ontology, the epistemology and semantics of models (...) and theories, and the relation between experimentation and theorising, and submit that simulations demand a fundamentally new philosophy of science in many respects. The aim of this paper is to critically evaluate these claims. Our conclusion will be sober. We argue that these claims are overblown and that simulations, far from demanding a new metaphysics, epistemology, semantics and methodology, raise few if any new philosophical problems. The philosophical problems that do come up in connection with simulations are not specific to simulations and most of them are variants of problems that have been discussed in other contexts before. (shrink)

The final work of a distinguished physicist, this remarkable volume examines the emotive significance of time, the time order of mechanics, the time direction of thermodynamics and microstatistics, the time direction of macrostatistics, and the time of quantum physics. Coherent discussions include accounts of analytic methods of scientific philosophy in the investigation of probability, quantum mechanics, the theory of relativity, and causality. "[Reichenbach’s] best by a good deal."—Physics Today. 1971 ed.

It is surely obvious that medicine, like any other rational activity, must be based on evidence. The interest is in the details: how exactly are the general principles of the logic of evidence to be applied in medicine? Focussing on the development, and current claims of the ‘Evidence-Based Medicine’ movement, this article raises a number of difficulties with the rationales that have been supplied in particular for the ‘evidence hierarchy’ and for the very special role within that hierarchy of randomized (...) controlled trials (and meta-analyses of the results of randomized controlled trials). The point is not at all to question the application of a scientific approach to evidence in medicine, but, on the contrary, to indicate a number of areas where philosophers of science can contribute to a proper implementation of exactly that scientific-evidential approach. (shrink)

Simulations (both digital and analog) and experiments share many features. But what essential features distinguish them? I discuss two proposals in the literature. On one proposal, experiments investigate nature directly, while simulations merely investigate models. On another proposal, simulations differ from experiments in that simulationists manipulate objects that bear only a formal (rather than material) similarity to the targets of their investigations. Both of these proposals are rejected. I argue that simulations fundamentally differ from experiments with regard to the background (...) knowledge that is invoked to argue for the “external validity” of the investigation. (shrink)

This paper develops a probabilistic reconstruction of the No Miracles Argument in the debate between scientific realists and anti-realists. The goal of the paper is to clarify and to sharpen the NMA by means of a probabilistic formalization. In particular, we demonstrate that the persuasive force of the NMA depends on the particular disciplinary context where it is applied, and the stability of theories in that discipline. Assessments and critiques of "the" NMA, without reference to a particular context, are misleading (...) and should be relinquished. This result has repercussions for recent anti-realist arguments, such as the claim that the NMA commits the base rate fallacy. It also helps to explain the persistent disagreement between realists and anti-realists. (shrink)

The philosophical theory of scientific explanation proposed here involves a radically new treatment of causality that accords with the pervasively statistical character of contemporary science. Wesley C. Salmon describes three fundamental conceptions of scientific explanation--the epistemic, modal, and ontic. He argues that the prevailing view is untenable and that the modal conception is scientifically out-dated. Significantly revising aspects of his earlier work, he defends a causal/mechanical theory that is a version of the ontic conception. Professor Salmon's theory furnishes a robust (...) argument for scientific realism akin to the argument that convinced twentieth-century physical scientists of the existence of atoms and molecules. To do justice to such notions as irreducibly statistical laws and statistical explanation, he offers a novel account of physical randomness. The transition from the "reviewed view" of scientific explanation to the causal/mechanical model requires fundamental rethinking of basic explanatory concepts. (shrink)

This paper discusses several distinct process theories of causality offered in recent years by Phil Dowe and me. It addresses problems concerning the explication of causal process, causal interaction, and causal transmission, whether given in terms of transmission of marks, transmission of invariant or conserved quantities, or mere possession of conserved quantities. Renouncing the mark-transmission and invariant quantity criteria, I accept a conserved quantity theory similar to Dowe's--differing basically with respect to causal transmission. This paper also responds to several fundamental (...) constructive criticisms contained in Christopher Hitchcock's discussion of both the mark-transmission and the conserved quantity theories. (shrink)

In Making Sense of Life , Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive (...) science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (shrink)

In Making Sense of Life, Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive science. (...) I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (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)

A number of recent discussions comparing computer simulation and traditional experimentation have focused on the significance of “materiality.” I challenge several claims emerging from this work and suggest that computer simulation studies are material experiments in a straightforward sense. After discussing some of the implications of this material status for the epistemology of computer simulation, I consider the extent to which materiality (in a particular sense) is important when it comes to making justified inferences about target systems on the basis (...) of experimental results. (shrink)

The problem of collecting, analyzing and evaluating evidence on adverse drug reactions (ADRs) is an example of the more general class of epistemological problems related to scientific inference and prediction, as well as a central problem of the health-care practice. Philosophical discussions have critically analysed the methodological pitfalls and epistemological implications of evidence assessment in medicine, however they have mainly focused on evidence of treatment efficacy. Most of this work is devoted to statistical methods of causal inference with a special (...) attention to the privileged role assigned to randomized controlled trials in Evidence Based Medicine. Regardless of whether the RCT’s privilege holds for efficacy assessment, it is nevertheless important to make a distinction between causal inference of intended and unintended effects, in that the unknowns at stake are heterogonous in the two contexts. This point has been emphasized by epidemiologists in the last decade. Their main focus is methodological, and regards the fact that bias and confounding do not affect studies on intended and unintended effects in the same way. However, deeper concerns ground the intuition for such a distinction; these are related to the constraints which we impose on evidence and their epistemological justification. My thesis is that such constraints ought to be understood to be different in the case of evidence for risk vs. benefit assessment. I present the recent debate on the causal association between acetaminophen and asthma in order to illustrate the point at issue. (shrink)

Philosophical discussions have critically analysed the methodological pitfalls and epistemological implications of evidence assessment in medicine, however they have mainly focused on evidence of treatment efficacy. Most of this work is devoted to statistical methods of causal inference with a special attention to the privileged role assigned to randomized controlled trials (RCTs) in evidence based medicine. Regardless of whether the RCT’s privilege holds for efficacy assessment, it is nevertheless important to make a distinction between causal inference of intended and unintended (...) effects, in that the unknowns at stake are heterogonous in the two contexts. However, although “lower level” evidence is increasingly acknowledged to be a valid source of information contributory to assessing the risk profile of medications on theoretical or empirical grounds, current practices have difficulty in assigning a precise epistemic status to this kind of evidence because they are more or less implicitly parasitic on the (statistical) methods developed to test drug efficacy. My thesis is that (1) “lower level” evidence is justified on distinct grounds and at different conditions depending on the different epistemologies which one wishes to endorse, in that each impose different constraints on the methods we adopt to collect and evaluate evidence; (2) such constraints ought to be understood to be different in the case of evidence for risk versus benefit assessment for a series of reasons which I will illustrate on the basis of the recent debate on the causal association between acetaminophen (a.k.a. paracetamol) and asthma. (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)

Counterfactuals is David Lewis' forceful presentation of and sustained argument for a particular view about propositions which express contrary to fact conditionals, including his famous defense of realism about possible worlds and his theory of laws of nature.

Philosophical discussions on causal inference in medicine are stuck in dyadic camps, each defending one kind of evidence or method rather than another as best support for causal hypotheses. Whereas Evidence Based Medicine advocates the use of Randomised Controlled Trials and systematic reviews of RCTs as gold standard, philosophers of science emphasise the importance of mechanisms and their distinctive informational contribution to causal inference and assessment. Some have suggested the adoption of a pluralistic approach to causal inference, and an inductive (...) rather than hypothetico-deductive inferential paradigm. However, these proposals deliver no clear guidelines about how such plurality of evidence sources should jointly justify hypotheses of causal associations. We here develop such guidelines by first giving a philosophical analysis of the underpinnings of Hill’s viewpoints on causality. We then put forward an evidence-amalgamation framework adopting a Bayesian net approach to model causal inference in pharmacology for the assessment of harms. Our framework accommodates a number of intuitions already expressed in the literature concerning the EBM vs. pluralist debate on causal inference, evidence hierarchies, causal holism, relevance, and reliability. (shrink)

Judea Pearl has been at the forefront of research in the burgeoning field of causal modeling, and Causality is the culmination of his work over the last dozen or so years. For philosophers of science with a serious interest in causal modeling, Causality is simply mandatory reading. Chapter 2, in particular, addresses many of the issues familiar from works such as Causation, Prediction and Search by Peter Spirtes, Clark Glymour, and Richard Scheines. But philosophers with a more general interest in (...) causation will also profit from reading Pearl’s book, especially the material in chapters 7, 9, and 10, which is self-contained and less technical than other parts of the book. The present review is aimed primarily at readers of the second type. (shrink)

Computer simulations are an exciting tool that plays important roles in many scientific disciplines. This has attracted the attention of a number of philosophers of science. The main tenor in this literature is that computer simulations not only constitute interesting and powerful new science , but that they also raise a host of new philosophical issues. The protagonists in this debate claim no less than that simulations call into question our philosophical understanding of scientific ontology, the epistemology and semantics of (...) models and theories, and the relation between experimentation and theorising, and submit that simulations demand a fundamentally new philosophy of science in many respects. The aim of this paper is to critically evaluate these claims. Our conclusion will be sober. We argue that these claims are overblown and that simulations, far from demanding a new metaphysics, epistemology, semantics and methodology, raise few if any new philosophical problems. The philosophical problems that do come up in connection with simulations are not specific to simulations and most of them are variants of problems that have been discussed in other contexts before. (shrink)

Computer simulations are an exciting tool that plays important roles in many scientific disciplines. This has attracted the attention of a number of philosophers of science. The main tenor in this literature is that computer simulations not only constitute interesting and powerful new science, but that they also raise a host of new philosophical issues. The protagonists in this debate claim no less than that simulations call into question our philosophical understanding of scientific ontology, the epistemology and semantics of models (...) and theories, and the relation between experimentation and theorising, and submit that simulations demand a fundamentally new philosophy of science in many respects. The aim of this paper is to critically evaluate these claims. Our conclusion will be sober. We argue that these claims are overblown and that simulations, far from demanding a new metaphysics, epistemology, semantics and methodology, raise few if any new philosophical problems. The philosophical problems that do come up in connection with simulations are not specific to simulations and most of them are variants of problems that have been discussed in other contexts before. (shrink)

This paper examines Wesley Salmon's "process" theory of causality, arguing in particular that there are four areas of inadequacy. These are that the theory is circular, that it is too vague at a crucial point, that statistical forks do not serve their intended purpose, and that Salmon has not adequately demonstrated that the theory avoids Hume's strictures about "hidden powers". A new theory is suggested, based on "conserved quantities", which fulfills Salmon's broad objectives, and which avoids the problems discussed.

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.

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.

This book, published in 2000, is a clear account of causation based firmly in contemporary science. Dowe discusses in a systematic way, a positive account of causation: the conserved quantities account of causal processes which he has been developing over the last ten years. The book describes causal processes and interactions in terms of conserved quantities: a causal process is the worldline of an object which possesses a conserved quantity, and a causal interaction involves the exchange of conserved quantities. Further, (...) things that are properly called cause and effect are appropriately connected by a set of causal processes and interactions. The distinction between cause and effect is explained in terms of a version of the fork theory: the direction of a certain kind of ordered pattern of events in the world. This particular version has the virtue that it allows for the possibility of backwards causation, and therefore time travel. (shrink)

The claims of RCTs to be the gold standard rest on the fact that the ideal RCT is a deductive method: if the assumptions of the test are met, a positive result implies the appropriate causal conclusion. This is a feature that RCTs share with a variety of other methods, which thus have equal claim to being a gold standard. This paper describes some of these other deductive methods and also some useful non-deductive methods, including the hypothetico-deductive method. It argues (...) that with all deductive methods, the benefit that the conclusions follow deductively in the ideal case comes with a great cost: narrowness of scope. This is an instance of the familiar trade-off between internal and external validity. RCTs have high internal validity but the formal methodology puts severe constraints on the assumptions a target population must meet to justify exporting a conclusion from the test population to the target. The paper reviews one such set of assumptions to show the kind of knowledge required. The overall conclusion is that to draw causal inferences about a target population, which method is best depends case-by-case on what background knowledge we have or can come to obtain. There is no gold standard. (shrink)

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)