The philosophical literature on scientific explanation contains a striking diversity of accounts. I use novel empirical methods to address this fragmentation and assess the importance and generality of explanation in science. My evidence base is a set of 781 articles from one year of the journal Science, and I begin by applying text mining techniques to discover patterns in the usage of “explain” and other words of philosophical interest. I then use random sampling from the data set to develop and (...) test a classification scheme for scientific explanation. My results show that explanation and inference to the best explanation are ubiquitous in science, that they occur across a wide range of scientific disciplines, and that they are a goal of scientific practise. These explanations and inferences to the best explanation come in a diversity forms, which at least partially justifies the fragmentation of philosophical accounts. I draw two methodological lessons: first that text mining can enhance traditional conceptual analysis by establishing facts about word usage; and second that random sampling of cases can increase our confidence that a philosophical account applies in general. These empirical techniques supplement traditional philosophical methods. (shrink)

Machamer, Darden, and Craver's account of the nature and role of mechanisms in the special sciences has been very influential. Unfortunately, a confusing array of ontic, epistemic, and pragmatic distinctions is required to individuate their mechanisms, mechanism schemata, and mechanism sketches. I diagnose this as a conflation of token-level causal relations with type-level relations. I propose instead that a mechanism is an abstraction that relates entity types and activity types on the model of a directed graph. Mechanisms have an ontic (...) status distinct from the causal chains of token entities and token activities that instantiate them. (shrink)

Scientific explanation is an important goal of scientific practise. Philosophers have proposed a striking diversity of seemingly incompatible accounts of explanation, from deductive-nomological to statistical relevance, unification, pragmatic, causal-mechanical, mechanistic, causal intervention, asymptotic, and model-based accounts. In this dissertation I apply two novel methods to reexamine our evidence about scientific explanation in practise and thereby address the fragmentation of philosophical accounts. I start by collecting a data set of 781 articles from one year of the journal Science. Using automated text (...) mining techniques I measure the frequency and distribution of several groups of philosophically interesting words, such as "explain", "cause", "evidence", "theory", "law", "mechanism", and "model". I show that "explain" words are much more common in scientific writing than in other genres, occurring in roughly half of all articles, and that their use is very often qualified or negated. These results about the use of words complement traditional conceptual analysis. Next I use random samples from the data set to develop a large number of small case studies across a wide range of scientific disciplines. I use a sample of "explain" sentences to develop and defend a new general philosophical account of scientific explanation, and then test my account against a larger set of randomly sampled sentences and abstracts. Five coarse categories can classify the explanans and explananda of my cases: data, entities, kinds, models, and theories. The pair of the categories of the explanans and explanandum indicates the "form" of an explanation. The explain-relation supports counterfactual reasoning about the dependence of qualities of the explanandum on qualities of the explanans. But for each form there is a different "core relation" between explanans and explanandum that supports the explain-relation. Causation, modelling, and argument are the core relations for different forms of scientific explanation between different categories of explanans and explananda. This flexibility allows me to resolve some of the fragmentation in the philosophical literature. I provide empirical evidence to show that my general philosophical account successfully describes a wide range of scientific practise across a large number of scientific disciplines. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

This article was initially written (in 2020) for a private collection gifted to Alexander García Düttmann on the occasion of his 60th birthday. It explores themes of education and the transmission of knowledge in relation to figures of youth and extinction. Georg Trakl's poem "Abendlied" serves as the essay's centerpiece and is brought into dialogue with comments made by Levi-Strauss on a 'prima material'. Certain ecological overtones appear when an overzealous Prometheanism is contrasted with a labor of re-creation.

Fichte’s Jena Wissenschaftslehre is among the most significant products of that immensely fertile period spanning the publication of Kant’s first Critique and Hegel’s Phenomenology. Like many of Kant’s earliest disciples and critics, Fichte was preoccupied with puzzles that arose in connection with certain distinctions presupposed or drawn by Kant throughout the writings of the Critical period. Among the many distinctions developed with great care in the three Critiques, the most important for Fichte were those drawn between the various powers or (...) faculties of the human mind. Fichte came to recognize that a well-grounded philosophical science would have to account for the complex structure of human subjectivity without dividing the mind into a mere aggregate of lifeless mental faculties. As Fichte famously put it in the Grundlage, the aim of the Wissenschaftslehre is to introduce into “the whole human being that unity and connection that so many systems lack.” Despite obvious Romantic overtones, this quest for a single, unified account of the human mind amounted to the demand for a strictly scientific reconstruction of the Critical philosophy. On Fichte’s view, philosophy would be able to come forward as a rigorous science of living subjectivity, with the force and evidence of geometry, only as a closed system of propositions derived from a self-evident first principle. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Cur Deus Verba: Why the Word Became Words by Jeremy HolmesJames B. ProthroCur Deus Verba: Why the Word Became Words by Jeremy Holmes (San Francisco: Ignatius, 2021), 284 pp.This book's title plays on the incarnational analogy, and its argument begins and ends with God's purposes to draw humanity into communion with himself through revelation. In both aspects, Holmes echoes Dei Verbum (DV, §§2, 13). However, rather than pursuing (...) a revelation-historical organization or beginning with Scripture's texts to derive conclusions about its nature and purpose, the book takes a "top-down" (13) approach to bibliology. In this way, its strength is the theological framing or refraining it gives to common questions.The first three chapters culminate, he claims, in a "definition of Scripture" (11). Beginning with the Trinity and creation, Holmes argues that all things have their being by participating in the inner life (the Word) of the Father, thus reflecting him, and that the Spirit drives creatures "toward the pattern of the Son" (33). God desires creatures to be good and causes of goodness in others, patterned after and in the Son through the Spirit's impulse to return them to God. In the Incarnation, God "reconciles nature with grace" (39) and in Christ perfects these desires. In Christ, man is now "included in the life of the Trinity" (37) and an agent of revelation, reflects God perfectly, and in love sends the Spirit to return humans to God through himself. This leads to reflections on Scripture directly. "Scripture is meant to impress the interior life of the Church on each generation; put another way, it is meant to impress Christ the Head on the members of his Mystical Body" (69). This brings Holmes to the topics of inspiration and canon. In order for human texts to impress Christ on his members, to communicate the divine through human means, "God himself" must be "addressing the [End Page 393] heart of the believer" (72). He makes a case for canon by pointing to the communal nature of humans. Tradition and canon, by which truth as a common good is formulated for a society, order and inform the society regarding its purpose, history, and character. "Tradition," then, "is good for man as man" (57) even in natural society, and all the more so in the supernatural society, the Church. The "texts that embody and transmit the tradition" (63) give continuity and life to the organism that is the Church, while within that tradition these texts can function as a sort of "guide rail" and a "mirror" of its identity (67).This overall view of Scripture lends perspective to particular topics (chs. 4-12). Turning to Scripture's authorship and inspiration, Holmes emphasizes again that God means humans to be real causes of revelation as God "attaches his voice" to their writing (82, 91, and throughout). This may, in differing circumstances, involve endowing them with particular and even unusual graces, many of which God grants to others who hand on revelation (such as Augustine), but in the case of the biblical authors the ("only") difference is that God "intended" biblical texts like Luke "to sound not only Luke's voice but God's voice as well" (91). His "general account of the fact of biblical difficulties" (202), then, depicts the human "author's soul" as "like the body of an instrument, determining the overtones of everything he writes" (208). God writes the notes to be played and selects the instruments, and God "asserts what the human author asserts" (210). But the particularities of an author's soul (and upbringing, assumptions, etc.) can be seen in anything from grammatical infelicities in Paul to the author's assumptions about a geocentric solar system, the goodness of killing the Canaanites, or Qoheleth's unawareness of an afterlife. God attaches his voice to their writing, and these instruments play "only God's note" (219), but God "does not affirm or deny" the assumptions or unasserted views of the author when writing (209). Scripture's purpose is not merely to impart doctrine but to conform one to Christ, and difficult passages are inspired in part for us to... (shrink)

Competing perspectives on the nature of emotion are illustrated with latent and emergent variable models. Latent variable models draw from classical test theory, assuming that the measured indicators of emotion covary by virtue of some common executive, organizing neural circuit or network in the brain. By contrast, emergent variable models draw from a theory-driven, operational definition tradition, positing that emotions do not cause, but rather are caused by, the measured indicators of emotion, assuming no executive neural circuit or network, and (...) requiring no covariation among indicators. I suggest that the emergent variable model may be more compatible with the extant literature on the nature of emotion, especially in the age of affective neuroscience. (shrink)

Life is short, and it can be sweet. Contemplating death is looking into a mirror that allows us to see these simple facts clearly, as if for the first time. We have every reason to believe that we have but one life to live--and no good reasons to believe otherwise--and death marks the termination of each life. Examining this reality opens doors to understanding ourselves, each other, connection, love, and life itself in an entirely new way. Life in Light of (...) Death is a short exploration on the sweetness available to every person and the importance of the opportunity that living is. By looking at life as reflected by death, we can see what really matters and how best to live. (shrink)

This paper provides a critical reconstruction of J. B. Erhard's account of recognition that locates it within the context of his revolutionary natural law theory. The first three sections lay out the foundations of Erhard's position. The fourth section outlines Erhard's response to the opponents of revolution and raises a problem for it. The fifth section argues that we can resolve this problem by drawing upon Erhard's account of failures of legal recognition. The sixth and final section considers the relevance (...) of that account for contemporary legal and political theory. (shrink)

Throughout history, many Christians have existed on the margins of society; deviants and strangers in lands they call home. To survive, they have had to construct alternate identities that not only make sense of their religious experiences and beliefs but also equip them to successfully negotiate their social worlds. In Thailand, a nation where social identities are thoroughly intertwined with Buddhist religious adherence, Christians must come to terms with such a marginalized existence. By leaving Buddhism and adopting what is considered (...) a foreign faith, Christian converts become deviants to "normal" Thai identity and belonging. In response, they have discovered creative solutions for traversing this complex terrain of marginalization. This book presents a deep exploration of the phenomenon of marginalization as experienced by Thai Christian converts. In it, readers will follow participants through the heights of transformative religious experience, the lows of severe social displacement, the tensions of managing two disparate lifeworlds and two conflicting selves, and the comfort and joy of finding a new place to call home. In the end, the reader will gain deep insight into what it is like to successfully navigate a minority religious identity on the margins of society."--Publisher. (shrink)

A proven classic, this anthology stimulates readers' interest in philosophy through an innovative ldquo;sides of the argumentrdquo; presentation, representing positions on each of the fundamental philosophical principles. Each reading contains a biographical sketch of the author, with a group of further readings for those wishing to pursue issues in further depth. Using debate and argument as a vehicle, the eleventh edition ofClassic Philosophical Questionssimultaneously gives readers the fundamentals of philosophy while demonstrating that philosophy is a discourse that has spanned centuries. (...) Topics covered include knowledge, metaphysics, religion, ethics, social and political philosophy, aesthetics, and the meaning of life. This anthology offers both classic and contemporary selections that challenge readers with the basic inquiries that philosophers have discussed throughout the ages. (shrink)

David Hume, philosopher, historian, economist, librarian, and essayist, was one of the great figures of the European Enlightenment. Unlike some of his famous contemporaries, however, he was not dogmatically committed to idealised conceptions of reason, liberty, and progress. Instead, Hume was a sceptic whose arguments questioned the reach and authority of human rationality, and who put the rivalrous passions of commercial life at the centre of his theory of human -- -- itself. -- ABOUT THE SERIES: The Very Short Introductions (...) series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable. (shrink)

Psychology, philosophy and common sense -- Psychological empiricism (part A): do non-empirical psychological phenomena exist? -- Psychological empiricism (part B): a critique -- The subject matter of psychology (part A): the conscious personal self -- The subject matter of psychology (part B): differing kinds of psychic phenomena -- Locating the empirical in psychology -- Human nature and rational psychology -- Psychology, truth and personalism -- The reality and psychological significance of freedom.

This paper provides a critical reconstruction of J. B. Erhard's account of recognition that locates it within the context of his revolutionary natural law theory. The first three sections lay out the foundations of Erhard's position. The fourth section outlines Erhard's response to the opponents of revolution and raises a problem for it. The fifth section argues that we can resolve this problem by drawing upon Erhard's account of failures of legal recognition. The sixth and final section considers the relevance (...) of that account for contemporary legal and political theory. (shrink)

Medicine is facing several significant challenges as the twenty-first century unfolds, which represent barriers or limitations that threaten to cripple the advancement of medicine and its practice. One of the responses to these challenges is the emergence of systems medicine. And one of the more pertinent challenges is identifying and clarifying systems medicine's conceptual and theoretical foundations. The present book represents a sustained effort to examine this challenge and to map the terrain by which to engage it and to pursue (...) possible solutions. This conceptual and theoretical challenge in particular needs to be addressed to ensure the future success of systems medicine. To that end the book explores the conceptual and theoretical foundations of systems medicine, including the major concepts of organicism, emergence, and robustness, and contrasts these concepts to those for biomedicine, including mechanism, resultant, and homeostasis. Moreover, this challenge is critical because its resolution provides the intellectual scaffolding necessary for structuring the concepts and theories required to understand and explain more adequately or completely biological, physiological, and pathological mechanisms and processes. Importantly, with a robust conceptual and theoretical scaffolding, systems medicine must be implemented interdisciplinary not only within the medical community but also within the social and political communities, which the COVID-19 pandemic made so painfully obvious. (shrink)

This book develops an original and comprehensive theory of political liberalism. It defends bold new accounts of the nature of autonomy and individual liberty, the content of distributive justice, and the justification for the authority of the State. The theory that emerges integrates contemporary progressive and pluralistic liberalism into a broadly Aristotelian intellectual tradition. The early chapters of the book challenge the traditional conservative idea of individual liberty-the liberty to dispose of one's property as one wishes-and replace it with a (...) new one, according to which liberty is of equal value to all persons, regardless of economic position. The middle chapters present an original theory of socio-economic justice, arguing that a society in which every citizen enjoys an equal share of liberty should be the distributive goal of the State. It is argued that this goal is incompatible with the existence of large disparities in wealth and economic power, and that (contra conservative and libertarian economic arguments) such disparities are harmful to the overall health of national and global economies. The final chapters provide an original argument that the State has both a moral duty and a moral right to pursue this program of socio-economic justice (contra conservative and libertarian moral arguments), and that only the measures necessary to implement this program lie within the morally justifiable limits on the State's authority. Though primarily a political work, it spans most areas of practical philosophy-including ethical, social, and legal theory; and meta-ethics, moral psychology, and action theory. And though fundamentally a philosophical work, it incorporates research from a number of fields-including decision theory, economics, political science, and jurisprudence; primatology, neuroscience, and psychology; and history, anthropology, sociology, and ecology-and is sure to be of interest to a wide range of scholars and students. (shrink)

By highlighting relations between experimental and theoretical work, this volume explores new ways of addressing one of the central challenges in the study of language and cognition. The articles bring together work by leading scholars and younger researchers in psychology, linguistics and philosophy. An introductory chapter lays out the background on concept composition, a problem that is stimulating much new research in cognitive science. Researchers in this interdisciplinary domain aim to explain how meanings of complex expressions are derived from simple (...) lexical concepts and to show how these meanings connect to concept representations. Traditionally, much of the work on concept composition has been carried out within separate disciplines, where cognitive psychologists have concentrated on concept representations, and linguists and philosophers have focused on the meaning and use of logical operators. This volume demonstrates an important change in this situation, where convergence points between these three disciplines in cognitive science are emerging and are leading to new findings and theoretical insights. This book is open access under a CC BY license. (shrink)

An historical survey of Thomas Kuhn's 1962 The Structure of Scientific Revolutions, charting the development of this influential work throughout Kuhn's career and exploring the continuing impact of Kuhn on the philosophy of science.

To approach the many challenges involved in the notion of engineering concepts, it is important to have a clear idea of the starting point – the concepts that people use in their everyday lives, in conversations and in expressing beliefs, desires, intentions and so forth. The first Section of this chapter introduces evidence that I have accumulated over the last many years concerning the flexibility, context-dependence, and vagueness of such common concepts. The concept engineer needs to understand the structure of (...) the “raw material” with which she is working. In Section 2, I summarise some results concerning the amount of individual variation that exists within a single relatively homogenous population of individuals, both in what examples are considered most typical of a category, and in what properties are considered most central to a category (Hampton & Passanisi, 2016). The demonstration of a significant degree of reliable variation in responses to these questions, that is stable over time, illustrates the potential for conceptual engineering interventions to affect individuals’ concepts. Concepts are rarely fixed or uniformly understood in the same way. I then discuss the different ways in which concepts track the world, and I speculate about how different conceptual domains are governed by different criteria of validity or acceptability. This reflection will lead to Section 3 in which I summarise some results from recent research (Thorne, Quilty-Dunn, Smortchova, Shea, & Hampton, 2021), investigating for the first time how people view the value of different familiar concepts. Knowing how people appraise concepts will be a key to developing ideas for improving the reliability and validity of the concepts that they commonly use. A final section contains some (largely speculative) discussion about the implications of work in psychology of concepts for the project of conceptual engineering. (shrink)

This essay explores how human rights norms—particularly the body of law that forbids discrimination on grounds of racial or ethnic origin—can be deployed to combat the worst effects of citizenship denial and ill-treatment of non-citizens.

Examines key narratives animating the techno-progressive rhetoric of the human enhancement movement, arguing that enhancement and transhumanist discourse performs distinctly mythic functions. They cast a vision of a technological future involving enhanced posthumans, immortality, human merger with machines and space colonization.

A detailed account of certain traits of intellectual character—the epistemic virtues—and of their relation to the responsibility for one's beliefs.

What big questions and large‐scale narratives give coherence to the history of science? From the late 1970s onward, the field has been transformed through a stress on practice and fresh perspectives from gender studies, the sociology of knowledge, and work on a greatly expanded range of practitioners and cultures. Yet these developments, although long overdue and clearly beneficial, have been accompanied by fragmentation and loss of direction. This essay suggests that the narrative frameworks used by historians of science need to (...) come to terms with diversity by understanding science as a form of communication. The centrality of processes of movement, translation, and transmission is already emerging in studies of topics ranging from ethnographic encounters to the history of reading. Not only does this approach offer opportunities for crossing boundaries of nation, period, and discipline that are all too easily taken for granted; it also has the potential for creating a more effective dialogue with other historians and the wider public. (shrink)

What big questions and large‐scale narratives give coherence to the history of science? From the late 1970s onward, the field has been transformed through a stress on practice and fresh perspectives from gender studies, the sociology of knowledge, and work on a greatly expanded range of practitioners and cultures. Yet these developments, although long overdue and clearly beneficial, have been accompanied by fragmentation and loss of direction. This essay suggests that the narrative frameworks used by historians of science need to (...) come to terms with diversity by understanding science as a form of communication. The centrality of processes of movement, translation, and transmission is already emerging in studies of topics ranging from ethnographic encounters to the history of reading. Not only does this approach offer opportunities for crossing boundaries of nation, period, and discipline that are all too easily taken for granted; it also has the potential for creating a more effective dialogue with other historians and the wider public. (shrink)

It is now—at least loosely—acknowledged that most health and clinical outcomes are influenced by different interacting causes. Surprisingly, medical research studies are nearly universally designed to study—usually in a binary way—the effect of a single cause. Recent experiences during the coronavirus disease 2019 pandemic brought to the forefront that most of our challenges in medicine and healthcare deal with systemic, that is, interdependent and interconnected problems. Understanding these problems defy simplistic dichotomous research methodologies. These insights demand a shift in our (...) thinking from ‘cause and effect’ to ‘causes and effects’ since this transcends the classical way of Cartesian reductionist thinking. We require a shift to a ‘causes and effects’ frame so we can choose the research methodology that reflects the relationships between variables of interest—one-to-one, one-to-many, many-to-one or many-to-many. One-to-one (or cause and effect) relationships are amenable to the traditional randomized control trial design, while all others require systemic designs to understand ‘causes and effects’. Researchers urgently need to re-evaluate their science models and embrace research designs that allow an exploration of the clinically obvious multiple ‘causes and effects’ on health and disease. Clinical examples highlight the application of various systemic research methodologies and demonstrate how ‘causes and effects’ explain the heterogeneity of clinical outcomes. This shift in scientific thinking will allow us to find the necessary personalized or precise clinical interventions that address the underlying reasons for the variability of clinical outcomes and will contribute to greater health equity. (shrink)