The introduction to the volume and the overview of the idea of naturalizing the mind.

I distinguish three theses associated with the new mechanistic philosophy – concerning causation, explanation and scientific methodology. Advocates of each thesis are identified and relationships among them are outlined. I then look at some recent work on natural selection and mechanisms. There, attention to different kinds of New Mechanism significantly affects of what is at stake.

After a decade of intense debate about mechanisms, there is still no consensus characterization. In this paper we argue for a characterization that applies widely to mechanisms across the sciences. We examine and defend our disagreements with the major current contenders for characterizations of mechanisms. Ultimately, we indicate that the major contenders can all sign up to our characterization.

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I (...) argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. (shrink)

In this article, I introduce the notion of horizon for scientific practice (HSP), representing limits or boundaries within which scientists ply their trade, to facilitate analysis of scientific discovery and progress. The notion includes not only constraints that delimit scientific practice, e.g. of bringing experimentation to a temporary conclusion, but also possibilities that open up scientific practice to additional scientific discovery and to further scientific progress. Importantly, it represents scientific practice as a dynamic and developmental integration of activities to investigate (...) and analyze the natural world. I use the discovery of the clotting factor, thrombin, and the experiments conducted by the Johns Hopkins physiologist, William Howell, on the enzymatic nature of thrombin to illustrate the notion of HSP. In a concluding section, I compare the notion of HSP to other notions for scientific practice proposed in the history and philosophy of science literature. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...) Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases (‘the tetranucleotide hypothesis’); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of these (...) cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts. (shrink)

Philosophy strives to give us a firmer hold on our concepts. But what about their hold on us? Why place ourselves under the sway of a concept and grant it the authority to shape our thought and conduct? Another conceptualization would carry different implications. What makes one way of thinking better than another? This book develops a framework for concept appraisal. Its guiding idea is that to question the authority of concepts is to ask for reasons of a special kind: (...) reasons for concept use, which tell us which concepts to adopt, adhere to, or abandon, thereby shoring up—or undercutting—the reasons for action and belief that guide our deliberations. Traditionally, reasons for concept use have been sought either in timeless rational foundations or in concepts’ inherent virtues, such as precision and consistency. Against this, the book advances two main claims: that we find reasons for concept use in the conceptual needs we discover when we critically distance ourselves from a concept by viewing it from the autoethnographic stance; and that sometimes, concepts that conflict, or exhibit other vices such as vagueness or superficiality, are just what we need. By considering not what concepts are absolutely best, but what concepts we now need, we can reconcile ourselves to the contingency of our concepts, determine the proper place of efforts to tidy up thought, and adjudicate between competing conceptions of things—even things as contested as liberty or free will. A needs-based approach separates helpful clarification from hobbling tidy-mindedness, and authoritative definition from conceptual gerrymandering. (shrink)

The type-level abstraction is a formal way to represent molecular structures in biological practice. Graphical representations of molecular structures of biological objects are also used to identify functional processes of things. This paper will reveal that category theory is a formal mathematical language not only to visualize molecular structures of biological objects as type-level abstraction formally but also to understand how to infer biological functions from the molecular structures of biological objects. Category theory is a toolkit to understand biological knowledge (...) at the type-level formally, not individual token-level, as well as typical heuristic strategies in molecular biology. (shrink)

Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids are (...) incorporated into growing protein chains. Independently from and concomitantly with Crick’s hypothesis, Mahlon Hoagland and Paul Zamecnik conducted experiments with no guiding theory that culminated in discoveries of the actual adaptors, transfer RNA (tRNA) molecules, and their amino acids charging enzymes. This paper traces the parallel histories of Crick’s adaptor hypothesis and of the experimental discovery of tRNA and compares their relative impacts on the scientific community. Remarkably, despite the brilliance of Crick’s confirmed prognostication, it had marginal impact on practicing scientists. Conversely, Hoagland and Zamecnik’s experimental discoveries and their evidence-based model of protein synthesis had immediate and enduring impact. I discuss possible explanations for the different impacts of the theoretical prediction and experimental identifications of the same entities. (shrink)

This article addresses the contributions of the literature on the new mechanistic philosophy of science for the scientific practice of model building in ecology. This is reflected in a one-to-one interdisciplinary collaboration between an ecologist and a philosopher of science during science-in-the-making. We argue that the identification, reconstruction and understanding of mechanisms is context-sensitive, and for this case study mechanistic modeling did not present a normative role but a heuristic one. We expect our study to provides useful epistemic tools for (...) the improvement of empirically-riven work in the debates about mechanistic explanation of ecological phenomena. (shrink)

An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM argue that applying Woodward’s account to this philosophical problem conflates causation and constitution, thus rendering the account incoherent. These criticisms, we (...) argue, arise from failing to distinguish the semantic, epistemic, and metaphysical aspects of the problem of constitutive relevance. In distinguishing these aspects of the problem and responding to these critics accordingly, we amend MM into a refined epistemic criterion, the “matched interlevel experiments” account. Further, we explain how this epistemological thesis is grounded in the plausible metaphysical thesis that constitutive relevance is causal betweenness. (shrink)

One of the defining features of the classical gene was its position. In molecular genetics, positions are defined instead as nucleotide numbers and there is no clear correspondence with its classical counterpart. However, the classical gene position did not simply disappear with the development of the molecular approach, but survived in the lab associated to different genetic practices. The survival of classical gene position would illustrate Waters’ view about the practical persistence of the genetic approach beyond reductionism and anti-reductionist claims. (...) We show instead that at the level of laboratory practices there are also reductive processes, operating through the rise and fall of different techniques. Molecular markers made the concept of classical gene position practically dispensable, leading us to rethink whether it had any causal role or was just a mere heuristic. (shrink)

I propose a dynamic causal approach to characterizing the notion of a mechanism. Levy and Bechtel, among others, have pointed out several critical limitations of the new mechanical philosophy, and pointed in a new direction to extend this philosophy. Nevertheless, they have not fully fleshed out what that extended philosophy would look like. Based on a closer look at neuroscientific practice, I propose that a mechanism is a dynamic causal system that involves various components interacting, typically nonlinearly, with one another (...) to produce a phenomenon of interest. (shrink)

A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively (...) parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Philosophers of science and medicine now aspire to provide useful, socially relevant accounts of mechanism. Existing accounts have forged the path by attending to mechanisms in historical context, scientific practice, the special sciences, and policy. Yet, their primary focus has been on more proximate issues related to therapeutic effectiveness. To take the next step toward social relevance, we must investigate the challenges facing researchers, clinicians, and policy makers involving values and social context. Accordingly, we learn valuable lessons about the connections (...) between mechanistic processes and more fundamental reasons for medical interventions, particularly moral, ethical, religious, and political concerns about health, agency, and power. This paper uses debates over the controversial morning-after pill to gain insight into the deeper reasons for the production and use of mechanistic knowledge throughout biomedical research, clinical practice, and governmental regulation. To practice socially relevant philosophy of science, I argue that we need to account for mechanistic knowledge beyond immediate effectiveness, such as how it can also provide moral guidance, aid ethical categorization in the clinic, and function as a political instrument. Such insights have implications for medical epistemology, including the value-laden dimensions of mechanistic reasoning and the “epistemic friction” of values. Furthermore, there are broader impacts for teaching research ethics and understanding the role of science advisors as political advocates. (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

Psychological construction represents an important new approach to psychological phenomena, one that has the promise to help us reconceptualize the mind both as a behavioral and as a biological system. It has so far been developed in the greatest detail for emotion, but it has important implications for how researchers approach other mental phenomena such as reasoning, memory, and language use. Its key contention is that phenomena that are characterized in (folk) psychological vocabulary are not themselves basic features of the (...) mind, but are constructed from more basic psychological operations. The framework of mechanistic explanation, currently under development in philosophy of science, can provide a useful perspective on the psychological construction approach. A central insight of the mechanistic account of explanation is that biological and psychological phenomena result from mechanisms in which component parts and operations do not individually exhibit the phenomena of interest but function together in an orchestrated and sometimes in a complex dynamical manner to generate it. While at times acknowledging the compatibility of the mechanist approach with constructionist approach (Lindquist, Wager, Kober, Bliss-Moreau, & Barrett, 2012), proponents of the constructionist approach have at other times pitched their approach as anti-mechanist. For example, Barrett (2009) claims that the psychological constructionist approach rejects machines as the primary metaphor for understanding the mind, instead favoring a recipe metaphor; constructionism also purportedly rejects the “mechanistic” picture of causation, which it portrays as linear or sequential in nature (see also Barrett, Wilson-Mendenhall, & Barsalou, in press). While some mechanistic accounts do fit this description, we will see that the mechanisms generating phenomena can be complex and dynamic, producing phenomena far less stereotypic and more adaptive than people often associate with machines. Our goal, however, is not just to render constructionism and mechanism compatible. Philosophers of science have been examining the nature of mechanistic explanation in biology with the goal of gaining new insights into the operation of science. We will identify some of the places where the mechanistic account can shed new light on the constructionist project. (shrink)

It is often claimed that the greatest value of the Bayesian framework in cognitive science consists in its unifying power. Several Bayesian cognitive scientists assume that unification is obviously linked to explanatory power. But this link is not obvious, as unification in science is a heterogeneous notion, which may have little to do with explanation. While a crucial feature of most adequate explanations in cognitive science is that they reveal aspects of the causal mechanism that produces the phenomenon to be (...) explained, the kind of unification afforded by the Bayesian framework to cognitive science does not necessarily reveal aspects of a mechanism. Bayesian unification, nonetheless, can place fruitful constraints on causal–mechanical explanation. 1 Introduction2 What a Great Many Phenomena Bayesian Decision Theory Can Model3 The Case of Information Integration4 How Do Bayesian Models Unify?5 Bayesian Unification: What Constraints Are There on Mechanistic Explanation?5.1 Unification constrains mechanism discovery5.2 Unification constrains the identification of relevant mechanistic factors5.3 Unification constrains confirmation of competitive mechanistic models6 ConclusionAppendix. (shrink)

Evidence-based medicine (EBM) makes use of explicit procedures for grading evidence for causal claims. Normally, these procedures categorise evidence of correlation produced by statistical trials as better evidence for a causal claim than evidence of mechanisms produced by other methods. We argue, in contrast, that evidence of mechanisms needs to be viewed as complementary to, rather than inferior to, evidence of correlation. In this paper we first set out the case for treating evidence of mechanisms alongside evidence of correlation in (...) explicit protocols for evaluating evidence. Next we provide case studies which exemplify the ways in which evidence of mechanisms complements evidence of correlation in practice. Finally, we put forward some general considerations as to how the two sorts of evidence can be more closely integrated by EBM. (shrink)

Work on analogy has been done from a number of disciplinary perspectives throughout the history of Western thought. This work is a multidisciplinary guide to theorizing about analogy. It contains 1,406 references, primarily to journal articles and monographs, and primarily to English language material. classical through to contemporary sources are included. The work is classified into eight different sections (with a number of subsections). A brief introduction to each section is provided. Keywords and key expressions of importance to research on (...) analogy are discussed in the introductory material. Electronic resources for conducting research on analogy are listed as well. (shrink)

A shared problem across the sciences is to make sense of correlational data coming from observations and/or from experiments. Arguably, this means establishing when correlations are causal and when they are not. This is an old problem in philosophy. This paper, narrowing down the scope to quantitative causal analysis in social science, reformulates the problem in terms of the validity of statistical models. Two strategies to make sense of correlational data are presented: first, a 'structural strategy', the goal of which (...) is to model and test causal structures that explain correlational data; second, a 'manipulationist or interventionist strategy', that hinges upon the notion of invariance under intervention. It is argued that while the former can offer a solution the latter cannot. (shrink)

What is the relationship between pain and the body? I claim that pain is best explained as a type of personal experience and the bodily response during pain is best explained in terms of a type of mechanical neurophysiologic operation. I apply the radical philosophy of identity theory from philosophy of mind to the relationship between the personal experience of pain and specific neurophysiologic mechanism and argue that the relationship between them is best explained as one of type identity. Specifically, (...) pain is a specific type of personal experience identical to a specific type of allostatic stress response comprised of interdependent nervous, endocrine and immune mechanical operations. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

Contrary to common views that philosophy is extraneous to cognitive science, this paper argues that philosophy has a crucial role to play in cognitive science with respect to generality and normativity. General questions include the nature of theories and explanations, the role of computer simulation in cognitive theorizing, and the relations among the different fields of cognitive science. Normative questions include whether human thinking should be Bayesian, whether decision making should maximize expected utility, and how norms should be established. These (...) kinds of general and normative questions make philosophical reflection an important part of progress in cognitive science. Philosophy operates best, however, not with a priori reasoning or conceptual analysis, but rather with empirically informed reflection on a wide range of findings in cognitive science. (shrink)

This paper reviews Rosenberg’s and McShea’s textbook in philosophy of biology, entitled Philosophy of Biology. A Contemporary Introduction. I insist on the excellent quality of this textbook, then I turn to more critical comments, which deal mainly with what philosophy of biology is, and what it should be.

I offer an explication of the notion of computer, grounded in the practices of computability theorists and computer scientists. I begin by explaining what distinguishes computers from calculators. Then, I offer a systematic taxonomy of kinds of computer, including hard-wired versus programmable, general-purpose versus special-purpose, analog versus digital, and serial versus parallel, giving explicit criteria for each kind. My account is mechanistic: which class a system belongs in, and which functions are computable by which system, depends on the system's mechanistic (...) properties. Finally, I briefly illustrate how my account sheds light on some issues in the history and philosophy of computing as well as the philosophy of mind. (shrink)

Thought experiments play a role in science and in some central parts of contemporary philosophy. They used to play a larger role in philosophy of science, but have been largely abandoned as part of the field’s “practice turn”. This chapter discusses possible roles for thought experimentation within a practice-oriented philosophy of science. Some of these roles are uncontroversial, such as exemplification and aiding discovery. A more controversial role is the reliance on thought experiments to justify philosophical claims. It is proposed (...) that if we adopt an underlying empiricist view of concepts, then thought experiments can be seen as affording us contact with scientific practice, despite their seemingly a priori character. The advantages and drawbacks of thought experiments are discussed via comparison with case studies, on the one, and simulations on the other hand. The chapter closes with some remarks on how to combine thought experiments with other methods. (shrink)

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn’s terminology, this (...) discovery of a major biological entity was made during a ‘normal science’ project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese’s project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies. (shrink)

Scientific communities as social groupings and the role that such communities play in scientific change and the production of scientific knowledge is currently under debate. I examine theory change as a complex social interaction among individual scientists and the scientific community, and argue that individuals will be motivated to adopt a more radical or innovative attitude when confronted with striking similarities between model systems and a more robust understanding of specialised vocabulary. Two case studies from the biological sciences, Barbara McClintock (...) and Stanley Prusiner, help motivate the idea that sharing of models and specialised vocabulary fill the gap between discovery and scientific change by promoting the dispersal of important information throughout the scientific community. (shrink)

Current research in molecular epidemiology uses biomarkers to model the different disease phases from environmental exposure, to early clinical changes, to development of disease. The hope is to get a better understanding of the causal impact of a number of pollutants and chemicals on several diseases, including cancer and allergies. In a recent paper Russo and Williamson address the question of what evidential elements enter the conceptualisation and modelling stages of this type of biomarkers research. Recent research in causality has (...) examined Ned Hall’s distinction between two concepts of causality: production and dependence. In another recent paper, Illari examined the relatively under-explored production approach to causality, arguing that at least one job of an account of causal production is to illuminate our inferential practices concerning causal linking. Illari argued that an informational account solves existing problems with traditional accounts. This paper follows up this previous work by investigating the nature of the causal links established in biomarkers research. We argue that traditional accounts of productive causality are unable to provide a sensible account of the nature of the causal link in biomarkers research, while an informational account is very promising. (shrink)

In this paper, we examine what is to be said in defence of Machamer, Darden and Craver’s (MDC) controversial dualism about activities and entities (Machamer, Darden and Craver’s in Philos Sci 67:1–25, 2000). We explain why we believe the notion of an activity to be a novel, valuable one, and set about clearing away some initial objections that can lead to its being brushed aside unexamined. We argue that substantive debate about ontology can only be effective when desiderata for an (...) ontology are explicitly articulated. We distinguish three such desiderata. The first is a more permissive descriptive ontology of science, the second a more reductive ontology prioritising understanding, and the third a more reductive ontology prioritising minimalism. We compare MDC’s entities-activities ontology to its closest rival, the entities-capacities ontology, and argue that the entities-activities ontology does better on all three desiderata. (shrink)

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...) models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

In this paper, we compare the mechanisms of protein synthesis and natural selection. We identify three core elements of mechanistic explanation: functional individuation, hierarchical nestedness or decomposition, and organization. These are now well understood elements of mechanistic explanation in fields such as protein synthesis, and widely accepted in the mechanisms literature. But Skipper and Millstein have argued that natural selection is neither decomposable nor organized. This would mean that much of the current mechanisms literature does not apply to the mechanism (...) of natural selection.We take each element of mechanistic explanation in turn. Having appreciated the importance of functional individuation, we show how decomposition and organization should be better understood in these terms. We thereby show that mechanistic explanation by protein synthesis and natural selection are more closely analogous than they appear—both possess all three of these core elements of a mechanism widely recognized in the mechanisms literature. (shrink)

The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.

The US Food and Drug Administration (FDA) is fraught with controversies over the role of values and politics in regulatory science, especially with drugs in the realm of reproductive health. Philosophers and science studies scholars have investigated the ways in which social context shapes medical knowledge through value judgments, and feminist scholars and activists have criticized sexism and injustice in reproductive medicine. Nonetheless, there has been no systematic study of values and gender norms in FDA drug regulation. I focus on (...) three questions about values in regulatory science. First, how have societal values and gender norms shaped the way that the FDA regulates drugs in the realm of reproductive health, specifically with drug labels? Second, what are the ethical, epistemic, and social consequences of these influences on regulation for women and other marginalized groups? Third, which societal values and gender norms ought to influence drug regulation about reproductive health, and how ought this happen? Integrating philosophical analysis with historical archival research and in-depth interviews, I conduct three case studies of drug labeling about reproductive health: (1) the “drug fact” about the mechanism of the morning-after pill; (2) the package inserts for patients about the health risks of oral contraceptives; and (3) the special physician labels made for prescribing drugs to pregnant women. I identify three challenges for the FDA and suggest ways to reduce the influence of sexist values and facilitate feminist alternatives. First, across these cases, I have found that there are many ways in which other concerns in reproductive medicine (such as zygotic life, fetal health, and population control) have devalued women’s health. Second, both knowledge and ignorance xvi about their reproductive health have contributed to women’s oppression, especially poor women and women of color. Finally, by avoiding the epistemic dimensions of ethics, powerful, mostly male parties in medicine (such as doctors, pharmaceutical companies, and religious institutions) have misused “informed consent,” “religious freedom,” and “paternalism” for unethical purposes. For improvement, I suggest extracting sexist values and gender norms from regulatory science that cause epistemic injustices, and I point to success stories for reforming sexism with feminism at the FDA. (shrink)

A striking characteristic of the highly successful techniques in molecular biology is that they are derived from natural systems. RNA interference, for example, utilises a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other examples include restriction enzymes, the polymerase chain reaction, green fluorescent protein and CRISPR-Cas. I propose that biologists exploit natural molecular mechanisms for their effectors’ activity and biological specificity. I also show that the developmental trajectory of novel techniques in molecular biology, such as RNAi, is (...) four characteristic phases. The first phase is discovery of a biological phenomenon, typically as curiosity driven research. The second is identification of the mechanism’s trigger, the effector and biological specificity. The third is the application of the technique. The final phase is the maturation and refinement of the molecular biology technique. The development of new molecular biology techniques from nature is crucial for biological research. These techniques transform scientific knowledge and generate new knowledge. (shrink)

This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...) themes discussed. (shrink)

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)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

Cognitive science is an interdisciplinary research endeavor focusing on human cognitive phenomena such as memory, language use, and reasoning. It emerged in the second half of the 20th century and is charting new directions at the beginning of the 21st century. This chapter begins by identifying the disciplines that contribute to cognitive science and reviewing the history of the interdisciplinary engagements that characterize it. The second section examines the role that mechanistic explanation plays in cognitive science, while the third focuses (...) on the importance of mental representations in specifically cognitive explanations. The fourth section considers the interdisciplinary nature of cognitive science and explores how multiple disciplines can contribute to explanations that exceed what any single discipline might accomplish. The conclusion sketches some recent developments in cognitive science and their implications for philosophers. (shrink)

Some biological processes move from step to step in a way that cannot be completely understood solely in terms of causes and correlations. This paper develops a notion of mechanistic information that can be used to explain the continuities of such processes. We compare them to processes that do not involve information. We compare our conception of mechanistic information to some familiar notions including Crick’s idea of genetic information, Shannon-Weaver information, and Millikan’s biosemantic information.

Malware has been around since the 1980s and is a large and expensive security concern today, constantly growing over the past years. As our social, professional and financial lives become more digitalised, they present larger and more profitable targets for malware. The problem of classifying and preventing malware is therefore urgent, and it is complicated by the existence of several specific approaches. In this paper, we use an existing malware taxonomy to formulate a general, language independent functional description of malware (...) as transformers between states of the host system and described by a trust relation with its components. This description is then further generalised in terms of mechanisms, thereby contributing to a general understanding of malware. The aim is to use the latter in order to present an improved classification method for malware. (shrink)

This paper explores multiple experimental interventions in molecular biology. By “multiple,” we mean that molecular biologists often use different modes of experimental interventions in a series of experiments for one and the same subject. In performing such a series of experiment, scientists may use different modes of interventions to realize plural goals such as testing given hypotheses and exploring novel phenomena. In order to illustrate this claim, we develop a framework of multiple modes of experimental interventions to analyze a series (...) of experiments for a single subject. Our argument begins with a brief characterization of Craver and Darden’s taxonomy of experiments, because the taxonomy they have made implies various modes of interventions. We propose to extract two interventional directions and two interventional effects from their taxonomy as the basis of classification. The vertical or inter-level direction means that an intervention is performed between different levels of organization and the horizontal or inter-stage direction means that an intervention is performed between different stages of a mechanism. Interventions may produce an excitatory or an inhibitory effect. As a consequence, we can classify modes of interventions according to different directions and effects. We illustrate our claims by doing a case study of the PaJaMo experiment, which is a series of experiments for a single subject. The final goal in this paper is to provide a taxonomy of characteristics of experimentation in which the PaJaMo experiment is adequately located. (shrink)