Theory of illness causation is an important issue in all biomedical sciences, and solid etiological explanations are needed in order to develop therapeutic approaches in medicine and preventive interventions in public health. Until now, the literature about the theoretical underpinnings of illness causation research has been scarce and fragmented, and lacking a convenient summary. This interdisciplinary book provides a convenient and accessible distillation of the current status of research into this developing field, and adds a personal flavor to the discussion (...) by proposing the etiological stance as a comprehensive approach to identify modifiable causes of illness. (shrink)

In order to support health interventions, biomedical and population health researchers need to collect solid evidence. This article asks what type of evidence this should be and expands on previous work that focused on etiological explanations, or causal-mechanical explanations of why and how illness occurs. The article proposes adding predictive evidence to the explanatory evidence, in order to form a joint evidence set, or JES = [A,B,C,D], which consists of four different types of evidence: association [A], biology [B], confirmation [C], (...) and difference-making [D]. The article discusses explanatory coherence as a backbone for this proposal, suggests criteria for each type of evidence, and offers a rubric for multi-evidence mapping. (shrink)

Jonathan Y. Tsou examines and defends positions on central issues in philosophy of psychiatry. The positions defended assume a naturalistic and realist perspective and are framed against skeptical perspectives on biological psychiatry. Issues addressed include the reality of mental disorders; mechanistic and disease explanations of abnormal behavior; definitions of mental disorder; natural and artificial kinds in psychiatry; biological essentialism and the projectability of psychiatric categories; looping effects and the stability of mental disorders; psychiatric classification; and the validity of the DSM's (...) diagnostic categories. The main argument defended by Tsou is that genuine mental disorders are biological kinds with harmful effects. This argument opposes the dogma that mental disorders are necessarily diseases that result from biological dysfunction. Tsou contends that the broader ideal of biological kinds offers a more promising and empirically ascertainable naturalistic standard for assessing the reality of mental disorders and the validity of psychiatric categories. (shrink)

Multiple determination is the epistemic strategy of establishing the same result by means of multiple, independent procedures. It is an important strategy praised by both philosophers of science and practicing scientists. Despite the heavy appeal to multiple determination, little analysis has been provided regarding the specific grounds upon which its epistemic virtues rest. This article distinguishes between the various dimensions of multiple determination and shows how they can be used to evaluate the epistemic force of the strategy in particular cases. (...) Distinguishing between the various dimensions helps to resolve the disagreements regarding the relevance and epistemic import of multiple determination for scientific research. It also suggests a fruitful mode of interaction between the philosophy of science and (historical) accounts of scientific practice. (shrink)

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production (IEP). I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under (...) study; ‘intervention systems’, which are measurement/experimental systems; and new technological systems. (shrink)

In biomedical measurement, biomarkers are used to achieve reliable prediction of, and useful causal information about patient outcomes while minimizing complexity of measurement, resources, and invasiveness. A biomarker is an assayable metric that discloses the status of a biological process of interest, be it normative, pathophysiological, or in response to intervention. The greatest utility from biomarkers comes from their ability to help clinicians (and researchers) make and evaluate clinical decisions. In this paper we discuss a specific methodological use of clinical (...) biomarkers in pharmacological measurement: Some biomarkers, called ‘surrogate markers’, are used to substitute for a clinically meaningful endpoint corresponding to events and their penultimate risk factors. We confront the reliability of clinical biomarkers that are used to gather information about clinically meaningful endpoints. Our aim is to present a systematic methodology for assessing the reliability of multiple surrogate markers (and biomarkers in general). To do this we draw upon the robustness analysis literature in the philosophy of science and the empirical use of clinical biomarkers. After introducing robustness analysis we present two problems with biomarkers in relation to reliability. Next, we propose an intervention-based robustness methodology for organizing the reliability of biomarkers in general. We propose three relevant conditions for a robust methodology for biomarkers: (R1) Intervention-based demonstration of partial independence of modes: In biomarkers partial independence can be demonstrated through exogenous interventions that modify a process some number of “steps” removed from each of the markers. (R2) Comparison of diverging and converging results across biomarkers: By systematically comparing partially-independent biomarkers we can track under what conditions markers fail to converge in results, and under which conditions they successfully converge. (R3) Information within the context of theory: Through a systematic cross-comparison of the markers we can make causal conclusions as well as eliminate competing theories. We apply our robust methodology to currently developing Alzheimer’s research to show its usefulness for making causal conclusions. (shrink)

The French physicist Jean Baptiste Perrin is widely credited with providing the conclusive argument for atomism. The most well-known part of Perrin’s argument is his description of thirteen different procedures for determining Avogadro’s number (N)–the number of atoms, ions, and molecules contained in a gram-atom, gram-ion, and gram-mole of a substance, respectively. Because of its success in ending the atomism debates Perrin’s argument has been the focus of much philosophical interest. The various philosophers, however, have reached different conclusions, not only (...) about the argument’s general rationale but also the role that the multiple determination of N played in it. This paper emphasizes the historical development of Perrin’s experimental work in order to understand the role that the multiple determination of molecular magnitudes played in his argument for molecular reality. It claims that Perrin used the multiple determination strategy to put forward an exceptionally strong no-coincidence argument to argue for both the correctness of the values for the molecular magnitudes determined and the validity of the auxiliary assumptions upon which the different determinations were based. The historicist approach also allows the identification of the elements responsible for the epistemic strength of Perrin’s no-coincidence argument. (shrink)

Replicability is widely taken to ground the epistemic authority of science. However, in recent years, important published findings in the social, behavioral, and biomedical sciences have failed to replicate, suggesting that these fields are facing a “replicability crisis.” For philosophers, the crisis should not be taken as bad news but as an opportunity to do work on several fronts, including conceptual analysis, history and philosophy of science, research ethics, and social epistemology. This article introduces philosophers to these discussions. First, I (...) discuss precedents and evidence for the crisis. Second, I discuss methodological, statistical, and social-structural factors that have contributed to the crisis. Third, I focus on the philosophical issues raised by the crisis. Finally, I discuss proposed solutions and highlight the gaps that philosophers could focus on. (shrink)

Although scientific realism is the default position in the life sciences, philosophical accounts of realism are geared towards physics and run into trouble when applied to fields such as biology or neuroscience. In this paper, I formulate a new robustness-based version of entity realism, and show that it provides a plausible account of realism for the life sciences that is also continuous with scientific practice. It is based on the idea that if there are several independent ways of measuring, detecting (...) or deriving something, then we are justified in believing that it is real. I also consider several possible objections to robustness-based entity realism, discuss its relationship to ontic structural realism, and show how it has the potential to provide a novel response to the pessimistic induction argument. (shrink)

The aim of this dissertation is to comprehensively study various robustness arguments proposed in the literature from Levins to Lloyd as well as the opposition offered to them and pose enquiry into the degree of epistemic virtue that they provide to the model prediction results with respect to climate science and modeling. Another critical issue that this dissertation strives to examine is that of the actual epistemic notion that is operational when scientists and philosophers appeal to robustness. In attempting to (...) explicate this idea, the discussion turns to arguments provided by Schupbach who completely rejects probabilistic independence in favour of explanatory reasoning, Stegenga and Menon who still see some value in probabilistic independence, and Winsberg who takes applies Schupbach’s to climate science, going beyond models to involve multi-modal evidence. After an exhaustive discussion on these arguments, this dissertation attempts to provide a thorough and updated notion of robustness in climate modeling and climate science. (shrink)

Case Study research is characterized by the employment of multiple data gathering methods. In this paper, I examine the concurrent use of participant observation and qualitative interviews. The question I examine is: what is the rationale behind their combination in case study research? In the literature on case study research, the two most common reasons for using multiple methods appeal to comprehensiveness and convergent confirmation respectively. I argue that there is a third significant, yet overlooked, way to motivate the joint (...) use of participant observation and qualitative interviews: the methods may generate complementary evidence and this puts the researcher in a better position to confirm that her data manifest central epistemic values and so are suitable as basis for providing an adequate answer to her research question. I refer to this as the rationale of blended epistemic value validation. (shrink)

Experimental design is one aspect of a scientific method. A well-designed, properly conducted experiment aims to control variables in order to isolate and manipulate causal effects and thereby maximize internal validity, support causal inferences, and guarantee reliable results. Traditionally employed in the natural sciences, experimental design has become an important part of research in the social and behavioral sciences. Experimental methods are also endorsed as the most reliable guides to policy effectiveness. Through a discussion of some of the central concepts (...) associated with experimental design, including controlled variation and randomization, this chapter will provide a summary of key ethical issues that tend to arise in experimental contexts. In addition, by exploring assumptions about the nature of causation and by analyzing features of causal relationships, systems, and inferences in social contexts, this chapter will summarize the ways in which experimental design can undermine the integrity of not only social and behavioral research but policies implemented on the basis of such research. (shrink)

This paper distinguishes between two arguments based on measurement robustness and defends the epistemic value of robustness for the assessment of measurement reliability. I argue that the appeal to measurement robustness in the assessment of measurement is based on a different inferential pattern and is not exposed to the same objections as the no-coincidence argument which is commonly associated with the use of robustness to corroborate individual results. This investigation sheds light on the precise meaning of reliability that emerges from (...) measurement assessment practice. In addition, by arguing that the measurement assessment robustness argument has similar characteristics across the physical, social and behavioural sciences, I defend the idea that there is continuity in the notion of measurement reliability across sciences. (shrink)

In psychiatry, pharmacological research has played a crucial role in the formulation, revision, and refinement of neurobiological theories of psychopathology. Besides being utilized as potential treatments for various mental disorders, pharmacological drugs play an important epistemic role as experimental instruments that help scientists uncover the neurobiological underpinnings of mental disorders (Tsou, 2012). Interventions with psychiatric patients using pharmacological drugs provide researchers with information about the neurobiological causes of mental disorders that cannot be obtained in other ways. This important source of (...) evidence for the biological causes of mental disorder is often overlooked in philosophical analyses of psychiatry, especially in skeptical analyses that debase the biological aspects of psychopathology (e.g., Szasz, 1960; Scheff, 1963; Laing, 1967). In discussing pharmacological interventions as a form of evidence for the physical basis of mental disorders, this paper aims to clarify the nature, reliability, and limitations of this evidence. In addition, it illustrates the central role that pharmacological findings in applied clinical contexts play in the acquisition of neurobiological knowledge in research contexts. (shrink)

The article argues for the epistemic rationale of triangulation, namely, the use of multiple and independent sources of evidence. It claims that triangulation is to be understood as causal reasoning from data to phenomenon, and it rationalizes its epistemic value in terms of controlling for likely errors and biases of particular data-generating procedures. This perspective is employed to address objections against triangulation concerning the fallibility and scope of the inference, as well as problems of independence, incomparability, and discordance of evidence. (...) The debate on the existence of social preferences is used as an illustrative case. (shrink)

In the philosophy of science and epistemology literature, robustness analysis has become an umbrella term that refers to a variety of strategies. One of the main purposes of this paper is to argue that different strategies rely on different criteria for justifications. More specifically, I will claim that: i) robustness analysis differs from de-idealization even though the two concepts have often been conflated in the literature; ii) the comparison of different model frameworks requires different justifications than the comparison of models (...) that differ only for the assumption under test; iii) the replacement of specific assumptions with different ones can encounter specific difficulties in scientific practice. These claims will be supported by a case study in population ecology and a case study in geographical economics. (shrink)

This paper addresses philosophical issues concerning whether mental disorders are natural kinds and how the DSM should classify mental disorders. I argue that some mental disorders (e.g., schizophrenia, depression) are natural kinds in the sense that they are natural classes constituted by a set of stable biological mechanisms. I subsequently argue that a theoretical and causal approach to classification would provide a superior method for classifying natural kinds than the purely descriptive approach adopted by the DSM since DSM-III. My argument (...) suggests that the DSM should classify natural kinds in order to provide predictively useful (i.e., projectable) diagnostic categories and that a causal approach to classification would provide a more promising method for formulating valid diagnostic categories. (shrink)

This article examines a metaphilosophical issue, namely existing disagreements in philosophy of science about the significance of using multiple means of determination in scientific practice. We argue that this disagreement can, in part, be resolved by separating different questions that can be asked about the use of multiple means of determination, including the following: what can be concluded from the convergence of data or the convergence of claims about phenomena? Are the conclusions drawn from the convergence of data and of (...) statements about phenomena of special importance to the debate about realism and antirealism? Do inferences based on multiple means of determination have stronger epistemic force than inferences that are secured in other ways? Is the epistemic goal of deploying multiple means of determination well entrenched within the scientific community? Most of these questions can be discussed both in a formal and in an empirical perspective. If the differences in perspective are taken into account, some disagreements can be easily resolved. In part, however, the disagreements reflect historiographical challenges that are very difficult, if not impossible to meet. (shrink)

It is commonly argued that values “fill the logical gap” of underdetermination of theory by evidence, namely, values affect our choice between two or more theories that fit the same evidence. The underdetermination model, however, does not exhaust the roles values play in evidential reasoning. I introduce WAVE – a novel account of the logical relations between values and evidence. WAVE states that values influence evidential reasoning by adjusting evidential weights. I argue that the weight-adjusting role of values is distinct (...) from their underdetermination gap-filling role. Values adjust weights in three ways. First, values affect our trust in the testimony of others. Second, values influence the evidential thresholds required for justified epistemic judgments. Third, values influence the relative weight of a certain type of evidence within a body of multimodal discordant evidence. WAVE explains, from an epistemic perspective, rather than psychological, how smokers, for example, can find the same evidence about the dangers of smoking less persuasive than non-smokers. WAVE allows for a wider effect of values on our accepted scientific theories and beliefs than the effect for which the underdetermination model allows alone; therefore, science studies scholars must consider WAVE in their research and analysis of evidential case studies. (shrink)

I describe two traditions of philosophical accounts of evidence: one characterizes the notion in terms of signs of success, the other characterizes the notion in terms of conditions of success. The best examples of the former rely on the probability calculus, and have the virtues of generality and theoretical simplicity. The best examples of the latter describe the features of evidence which scientists appeal to in practice, which include general features of methods, such as quality and relevance, and general features (...) of evidence, such as patterns in data, concordance with other evidence, and believability of the evidence. Two infamous episodes from biomedical research help to illustrate these features. Philosophical characterization of these latter features—conditions of success—has the virtue of potential relevance to, and descriptive accuracy of, practices of experimental scientists. (shrink)

A consensus in a scientific community is often used as a resource for making informed public-policy decisions and deciding between rival expert testimonies in legal trials. This paper contains a social-epistemic analysis of the high-profile Bendectin drug controversy, which was decided in the courtroom inter alia by deference to a scientific consensus about the safety of Bendectin. Drawing on my previously developed account of knowledge-based consensus, I argue that the consensus in this case was not knowledge based, hence courts’ deference (...) to it was not epistemically justified. I draw sceptical lessons from this analysis regarding the value of scientific consensus as a desirable and reliable means of resolving scientific controversies in public life. (shrink)

Scientific consensus is widely deferred to in public debates as a social indicator of the existence of knowledge. However, it is far from clear that such deference to consensus is always justified. The existence of agreement in a community of researchers is a contingent fact, and researchers may reach a consensus for all kinds of reasons, such as fighting a common foe or sharing a common bias. Scientific consensus, by itself, does not necessarily indicate the existence of shared knowledge among (...) the members of the consensus community. I address the question of under what conditions it is likely that a consensus is in fact knowledge based. I argue that a consensus is likely to be knowledge based when knowledge is the best explanation of the consensus, and I identify three conditions—social calibration, apparent consilience of evidence, and social diversity, for knowledge being the best explanation of a consensus. (shrink)

In psychiatry, pharmacological drugs play an important experimental role in attempts to identify the neurobiological causes of mental disorders. Besides being developed in applied contexts as potential treatments for patients with mental disorders, pharmacological drugs play a crucial role in research contexts as experimental instruments that facilitate the formulation and revision of neurobiological theories of psychopathology. This paper examines the various epistemic functions that pharmacological drugs serve in the discovery, refinement, testing, and elaboration of neurobiological theories of mental disorders. I (...) articulate this thesis with reference to the history of antipsychotic drugs and the evolution of the dopamine hypothesis of schizophrenia in the second half of the twentieth century. I argue that interventions with psychiatric patients through the medium of antipsychotic drugs provide researchers with information and evidence about the neurobiological causes of schizophrenia. This analysis highlights the importance of pharmacological drugs as research tools in the generation of psychiatric knowledge and the dynamic relationship between practical and theoretical contexts in psychiatry. (shrink)

The chemical characterization of the substance responsible for the phenomenon of “transformation” of pneumococci was presented in the now famous 1944 paper by Avery, MacLeod, and McCarty. Reception of this work was mixed. Although interpreting their results as evidence that deoxyribonucleic acid (DNA) is the molecule responsible for genetic changes was, at the time, controversial, this paper has been retrospectively celebrated as providing such evidence. The mixed and changing assessment of the evidence presented in the paper was due to the (...) work’s interpretive flexibility – the evidence was interpreted in various ways, and such interpretations were justified given the neophytic state of molecular biology and methodological limitations of Avery’s transformation studies. I argue that the changing context in which the evidence presented by Avery’s group was interpreted partly explains the vicissitudes of the assessments of the evidence. Two less compelling explanations of the reception are a myth-making account and an appeal to the wartime historical context of its publication. (shrink)

This essay offers some reflections on the recent history of the disputes about the relation between history and philosophy of science (HPS) and the merits and prospects of HPS as an intellectual endeavor. As everyone knows, the issue was hotly debated in the 1960s and 1970s. That was the hey-day of the slogan "history without philosophy of science is blind, philosophy without history of science is empty" as well as of the many variations on the theme of HPS as a (...) "marriage of convenience," "intimate relation," or "marriage for the sake of reason." There was a flurry of interest in the early 1990s, as evidenced by sections in the 1992 and 1994 issues of PSA, entitled: "Do the History of Science and the Philosophy of .. (shrink)

An astonishing volume and diversity of evidence is available for many hypotheses in the biomedical and social sciences. Some of this evidence—usually from randomized controlled trials (RCTs)—is amalgamated by meta-analysis. Despite the ongoing debate regarding whether or not RCTs are the ‘gold-standard’ of evidence, it is usually meta-analysis which is considered the best source of evidence: meta-analysis is thought by many to be the platinum standard of evidence. However, I argue that meta-analysis falls far short of that standard. Different meta-analyses (...) of the same evidence can reach contradictory conclusions. Meta-analysis fails to provide objective grounds for intersubjective assessments of hypotheses because numerous decisions must be made when performing a meta-analysis which allow wide latitude for subjective idiosyncrasies to influence its outcome. I end by suggesting that an older tradition of evidence in medicine—the plurality of reasoning strategies appealed to by the epidemiologist Sir Bradford Hill—is a superior strategy for assessing a large volume and diversity of evidence. (shrink)

Amalgamating evidence of different kinds for the same hypothesis into an overall confirmation is analogous, I argue, to amalgamating individuals’ preferences into a group preference. The latter faces well-known impossibility theorems, most famously “Arrow’s Theorem”. Once the analogy between amalgamating evidence and amalgamating preferences is tight, it is obvious that amalgamating evidence might face a theorem similar to Arrow’s. I prove that this is so, and end by discussing the plausibility of the axioms required for the theorem.

One important strategy for dealing with error in our methods is triangulation, or the use multiple methods to investigate the same object. Current accounts of triangulation assume that its primary function is to provide a confirmatory boost to hypotheses beyond what confirmation of each method alone could produce. Yet, researchers often use multiple methods to examine new constructs about which they are uncertain. For example, social psychologists use multiple indirect measures to provide convergent evidence about implicit attitudes, but how to (...) characterize implicit attitudes is an open question. To make sense of triangulation under uncertainty about constructs, I suggest two changes: first, triangulation can serve multiple epistemic functions, including some that are non-confirmatory, and second, researchers should assess the epistemic risk in claims about evidence and the acceptance/rejection of hypotheses. (shrink)

This paper discusses the outstanding problem of replicability of empirical data in the context of recent work on meta-analysis, especially within the field of evidence-based medicine. Specifically, it deals with the methodological issue of how to determine the degrees of heterogeneity between different collected studies. After critically reviewing the standard measures used to quantify meta-analytical heterogeneity, we argue that they should be revised in such a way to take into account the statistical power of the individual studies. We thus propose (...) some new measures of heterogeneity. Subsequently, we apply them to re-assess concrete case-studies from clinical research, thereby showing explicitly how the relevant values of heterogeneity diverge from those obtained with the original measures. (shrink)

The use of multiple means of determination to “triangulate” on the existence and character of a common phenomenon, object, or result has had a long tradition in science but has seldom been a matter of primary focus. As with many traditions, it is traceable to Aristotle, who valued having multiple explanations of a phenomenon, and it may also be involved in his distinction between special objects of sense and common sensibles. It is implicit though not emphasized in the distinction between (...) primary and secondary qualities from Galileo onward. It is arguably one of several conceptions involved in Whewell’s method of the “consilience of inductions” (Laudan 1971) and is to be found in several places in Peirce. (From M. Brewer and B. Collins, eds., (1981); Scientific Inquiry in the Social Sciences (a festschrift for Donald T. Campbell), San Francisco: Jossey-Bass, pp. 123–162.). (shrink)

Economists reason causally. Like many other scientists, they aim at formulating justified causal claims about their object of study. This thesis contributes to our understanding of how causal reasoning proceeds in economics. By using the research on the causes of unemployment as a case study, three questions are adressed. What are the meanings of causal claims? How can a causal claim be adequately supported by evidence? How are causal beliefs affected by incoming facts? In the process of answering these semantic, (...) epistemic and dynamical questions, the richness of causal reasoning in economics is brought to the foreground. In the part on semantics, it is argued that the meaning of causal generalizations in policy-oriented economics is best captured by using the concept of ‘inferential relation’ rather than the one of ‘referential relation’. This part contributes to develop an inferentialist semantics by distinguishing among types of inferential relations. In the part on epistemology, it is argued that justification in sciences like economics often relies, and ought to rely, on evidential variety―i.e. the combination of evidence from multiple sources. An interpretation of independence among evidential sources is offered: two evidential sources are fully independent if and only if the reasons why they would be unreliable do not overlap. It is then shown that the variety-of-evidence thesis does not hold under extreme circumstances. The part on dynamics focuses on deviant-case study. A storyline is provided for what deviant-case study aims at and how it proceeds in what is characterized as an ‘eclectic science’. (shrink)

This article sketches the main features of traditional philosophical models of evidence, indicating idealizations in such models that it regards as doing more harm than good. It then proceeds to elaborate on an alternative model of evidence that is functionalist, complex, dynamic, and contextual, a view the author calls dynamic evidential functionalism (DEF). This alternative builds on insights from philosophy of scientific practice, Kuhnian philosophy of science, pragmatist epistemology, philosophy of experimentation, and functionalist philosophy of mind. Along the way, the (...) article raises concerns about the total evidence condition, requirements of certainty or incorrigibility on evidence, and accounts that restrict the type of things that can serve as evidence (to, for example, sense data, facts about particulars). DEF can also help us see the special value of novel predictions and experiments as evidence, as well as help us think about how to critically evaluate the putative evidence to determine whether it is evidence. (shrink)

Consensus conferences are social techniques which involve bringing together a group of scientific experts, and sometimes also non-experts, in order to increase the public role in science and related policy, to amalgamate diverse and often contradictory evidence for a hypothesis of interest, and to achieve scientific consensus or at least the appearance of consensus among scientists. For consensus conferences that set out to amalgamate evidence, I propose three desiderata: Inclusivity, Constraint, and Evidential Complexity. Two examples suggest that consensus conferences can (...) readily satisfy Inclusivity and Evidential Complexity, but consensus conferences do not as easily satisfy Constraint. I end by discussing the relation between social inclusivity and the three desiderata. (shrink)

It is argued in this paper that amalgamating confirmation from various sources is relevantly different from social-choice contexts, and that proving an impossibility theorem for aggregating confirmation measures directs attention to irrelevant issues.

This paper distinguishes between causal isolation robustness analysis and independent determination robustness analysis and suggests that the triangulation of the results of different epistemic means or activities serves different functions in them. Circadian clock research is presented as a case of causal isolation robustness analysis: in this field researchers made use of the notion of robustness to isolate the assumed mechanism behind the circadian rhythm. However, in contrast to the earlier philosophical case studies on causal isolation robustness analysis (Weisberg and (...) Reisman in Philos Sci 75:106–131, 2008 ; Kuorikoski et al. in Br J Philos Sci 61:541–567, 2010 ), robustness analysis in the circadian clock research did not remain in the level of mathematical modeling, but it combined it with experimentation on model organisms and a new type of model, a synthetic model. (shrink)

In the first half of this dissertation, I develop a heuristic methodology for analyzing scientific solutions to the problem of underdetermination. Heuristics are rough-and-ready procedures used by scientists to construct models, design experiments, interpret evidence, etc. But as powerful as they are, heuristics are also error-prone. Therefore, I argue that they key to prudently using a heuristic is the articulation of meta-heuristics---guidelines to the kinds of problems for which a heuristic is well- or ill-suited. Given that heuristics will introduce certain (...) errors into our scientific investigations, I emphasize the importance of a particular category of meta-heuristics involving the search for robust evidence. Robustness is understood to be the epistemic virtue bestowed by agreement amongst multiple modes of determination. The more modes we have at our disposal, and the more these confirm the same result, the more confident can we be that a result is not a mere artifact of some heuristic simplification. Through an analysis of case-studies in the philosophy of biology and clinical trials, I develop a principled method for modeling and evaluating heuristics and robustness claims in a qualitative problem space. The second half of the dissertation deploys the heuristic methodology to address ethical and epistemological issues in the science of clinical trials. To that end, I develop a network model for the problem space of clinical research, capable of representing the various kinds of experiments, epistemic relationships, and ethical justifications intrinsic to the domain. I then apply this model to ongoing research with the antibacterial agent, moxifloxacin, for the treatment of tuberculosis, tracking its development from initially successful and promising in vitro and animal studies to its disappointing and discordant performance across five human efficacy trials. Given this failure to find a robust result with moxifloxacin across animal and human studies, what should researchers now do? While my final analysis of this case does not definitively answer that question, I demonstrate how my methodology, unlike a statistical meta-analysis, helps to clarify the directions for further research. (shrink)

Robustness is often presented as a guideline for distinguishing the true or real from mere appearances or artifacts. Most of recent discussions of robustness have focused on the kind of derivational robustness analysis introduced by Levins, while the related but distinct idea of robustness as multiple accessibility, defended by Wimsatt, has received less attention. In this paper, I argue that the latter kind of robustness, when properly understood, can provide justification for ontological commitments. The idea is that we are justified (...) in believing that things studied by science are real insofar as we have robust evidence for them. I develop and analyze this idea in detail, and based on concrete examples show that it plays an important role in science. Finally, I demonstrate how robustness can be used to clarify the debate on scientific realism and to formulate new arguments. (shrink)

Policy-makers face an uncertain world. One way of getting a handle on decision-making in such an environment is to rely on evidence. Despite the recent increase in post-fact figures in politics, evidence-based policymaking takes centre stage in policy-setting institutions. Often, however, policy-makers face large volumes of evidence from different sources. Robustness analysis can, prima facie, handle this evidential diversity. Roughly, a hypothesis is supported by robust evidence if the different evidential sources are in agreement. In this thesis, I strengthen the (...) case for the use of robustness analysis in evidence-based policymaking by answering open research questions about this inference technique. First, I argue that existing taxonomies miss a fruitful category of robustness reasoning, that is predictive stability. Second, I claim that derivational robustness analysis – the investigation of whether the results of different models are in agreement – can yield interesting insights even if not the entire relevant model space is covered by available models or if the model results are only partially in agreement. Third, I claim that expert knowledge is necessary to address questions that arise when one applies measurement robustness analysis – the investigation into whether multiple means of measurement yield the same result. Finally, I argue that, in situations where evidence from different measurements is not in agreement, it can be advisable to no longer take all of the evidence into account. This can be done in a rationally defensible way by choosing the most adequate theory or model underlying parts of the evidence set. I discuss examples from climate, medical, and economic policy-making to establish my claims. (shrink)

Neuroimaging technology is the most widely used tool to study human cognition. While originally a promising tool for mapping the content of cognitive theories onto the structures of the brain, recently developed tools for the analysis, handling and sharing of data have changed the theoretical landscape of cognitive neuroscience. Even with these advancements philosophical analyses of evidence in neuroimaging remain skeptical of the promise of neuroimaging technology. These views often treat the analysis techniques used to make sense of data produced (...) in a neuroimaging experiment as one, attributing the inferential limitations of analysis pipelines to the technology as a whole. Situated against the neuroscientists own critical assessment of their methods and the limitations of those methods, this skepticism appears based on a misunderstanding of the role data analysis techniques play in neuroimaging research. My project picks up here, examining how data analysis techniques, such as pattern classification analysis, are used to assess the evidential value of neuroimaging data. The project takes the form of three papers. In the first I identify the use of multiple data analysis techniques as an important aspect of the data interpretation process that is overlooked by critics. In the second I develop an account of inferences in neuroimaging research that is sensitive to this use of data analysis techniques, arguing that interpreting neuroimaging data is a process of isolating and explaining a variety of data patterns. In the third I argue that the development and uptake of new techniques for analyzing data must be accompanied by changes in research practices and standards of evidence if they are to promote knowledge generation. My approach to this work is both traditionally philosophical, insofar as it involves reading and analyzing the work of philosophers and neuroscientists, and embedded insofar as most of the research was conducted while engaged in attending lab meetings and participating in the work of those scientists whose work is the object of my research. (shrink)

We discuss the scientific task of historical reconstruction and the problem of epistemic access. We argue that strong epistemic support for historical claims consists in the consilience of multiple independent lines of evidence, and analyze the impact hypothesis for the End-Cretaceous mass extinction to illustrate the accrual of epistemic support. Although there are elements of the impact hypothesis that enjoy strong epistemic support, the general conditions for this are strict, and help to clarify the difficulties associated with reconstructing the deep (...) past. (shrink)

There are currently serious concerns that published scientific findings often fail to be reproducible, and that some solutions may be gleaned by attending the several methodological and sociological recommendations that could be found in the literature. However, researchers would also arrive at some answers by considering the advice of the philosophy of science, particularly semantics, about theses on truth related to scientific realism. Sometimes scientists understand the correspondence thesis of truth as asserting that the next unique empirical confirmation of a (...) hypothesis suffices to attribute truth to it provisionally. Such empiricist bias is not necessarily at the core of CTT, but Mario Bunge proposed the synthetic thesis of truth, based on CTT, to explicitly avoid the bias. STT requires considering a hypothesis corroborated, both by purely empirical confirmation and external consistency or compatibility with the bulk of existing background knowledge. While a capricious understanding of CTT could be rigged to recommend the “one shot game” in hypothesis testing, STT clearly demands the use of multiple approaches, empirical as well as theoretical, and it asserts that a scientific test is effective to the extent to which it is neither purely empirical, nor viewed in isolation. Pattern consistency together with an understanding of causal relations make confirmed hypotheses robust and more reliable. The militancy of the double mechanism of hypothesis control of STT can help mitigate the reproducibility crisis. Earl Werner’s research program in community ecology is an example of the use of STT criteria, which leads to the development of reliable, cross-checked, ecological results, with high predictive capacity. (shrink)

There are currently serious concerns that published scientific findings often fail to be reproducible, and that some solutions may be gleaned by attending the several methodological and sociological recommendations that could be found in the literature. However, researchers would also arrive at some answers by considering the advice of the philosophy of science, particularly semantics, about theses on truth related to scientific realism. Sometimes scientists understand the correspondence thesis of truth as asserting that the next unique empirical confirmation of a (...) hypothesis suffices to attribute truth to it provisionally. Such empiricist bias is not necessarily at the core of CTT, but Mario Bunge proposed the synthetic thesis of truth, based on CTT, to explicitly avoid the bias. STT requires considering a hypothesis corroborated, both by purely empirical confirmation and external consistency or compatibility with the bulk of existing background knowledge. While a capricious understanding of CTT could be rigged to recommend the “one shot game” in hypothesis testing, STT clearly demands the use of multiple approaches, empirical as well as theoretical, and it asserts that a scientific test is effective to the extent to which it is neither purely empirical, nor viewed in isolation. Pattern consistency together with an understanding of causal relations make confirmed hypotheses robust and more reliable. The militancy of the double mechanism of hypothesis control of STT can help mitigate the reproducibility crisis. Earl Werner’s research program in community ecology is an example of the use of STT criteria, which leads to the development of reliable, cross-checked, ecological results, with high predictive capacity. (shrink)

This paper tells the story of G-protein coupled receptors, one of the most important scientific objects in contemporary biochemistry and molecular biology. By looking at how cell membrane receptors turned from a speculative concept into a central element in modern biochemistry over the past 40 years, we revisit the role of manipulability as a criterion for entity realism in wet-lab research. The central argument is that manipulability as a condition for reality becomes meaningful only once scientists have decided how to (...) conceptually coordinate measurable effects distinctly to a specific object. We show that a scientific entity, such as GPCRs, is assigned varying degrees of reality throughout different stages of its discovery. The criteria of its reality, we further claim, cannot be made independently of the question about how this object becomes a standard by which the reality of neighbouring elements of enquiry is evaluated. (shrink)

It is important to have an adequate model of uncertainty, since decisions must be made before the uncertainty can be resolved. For instance, flood defenses must be designed before we know the future distribution of flood events. It is standardly assumed that probability theory offers the best model of uncertain information. I think there are reasons to be sceptical of this claim. I criticise some arguments for the claim that probability theory is the only adequate model of uncertainty. In particular (...) I critique Dutch book arguments, representation theorems, and accuracy based arguments. Then I put forward my preferred model: imprecise probabilities. These are sets of probability measures. I offer several motivations for this model of uncertain belief, and suggest a number of interpretations of the framework. I also defend the model against some criticisms, including the so-called problem of dilation. I apply this framework to decision problems in the abstract. I discuss some decision rules from the literature including Levi’s E-admissibility and the more permissive rule favoured by Walley, among others. I then point towards some applications to climate decisions. My conclusions are largely negative: decision making under such severe uncertainty is inevitably difficult. I finish with a case study of scientific uncertainty. Climate modellers attempt to offer probabilistic forecasts of future climate change. There is reason to be sceptical that the model probabilities offered really do reflect the chances of future climate change, at least at regional scales and long lead times. Indeed, scientific uncertainty is multi-dimensional, and difficult to quantify. I argue that probability theory is not an adequate representation of the kinds of severe uncertainty that arise in some areas in science. I claim that this requires that we look for a better framework for modelling uncertainty. (shrink)

I argue that diversity and pluralism are valuable not just for science but for philosophy of science. Given the partiality and perspectivism of representation, pluralism preserving integration can...

Pluralism about scientific method is more-or-less accepted, but the consequences have yet to be drawn out. Scientists adopt different methods in response to different epistemic situations: depending on the system they are interested in, the resources at their disposal, and so forth. If it is right that different methods are appropriate in different situations, then mismatches between methods and situations are possible. This is most likely to occur due to method bias: when we prefer a particular kind of method, despite (...) that method clashing with evidential context or our aims. To explore these ideas, we sketch a kind of method pluralism which turns on two properties of evidence, before using agent-based models to examine the relationship between methods, epistemic situations, and bias. Based on our results, we suggest that although method bias can undermine the efficiency of a scientific community, it can also be productive through preserving a diversity of evidence. We consider circumstances where method bias could be particularly egregious, and those where it is a potential virtue, and argue that consideration of method bias reveals that community standards deserve a central place in the epistemology of science. (shrink)