In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

It has been argued that Plato sought to make his rulers invulnerable to any kind of wrongdoing. In this paper we argue that this (humanly impossible) claim misunderstand the ways in which Plato shapes his state precisely in order to make the rulers safe from what could corrupt them.

In this book review, I discuss Smith’s new interpretation of Socrates' epistemology of virtue, according to which (a) Socratic virtue knowledge is craft knowledge (knowing how to live well), and such knowledge comes in degrees; and (b) Socrates has a certain degree of virtue knowledge, and one does not have to be an inerrant expert to have any virtue knowledge at all. I argue that Smith succeeds in presenting Socratic philosophy in a new light, while also pointing to (...) remaining questions about his account of virtue—specifically, about what exactly the craft of virtue is and how we can practice it and thereby improve ourselves. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, (...) Henry Stapp. (shrink)

Scholars have argued that Plato's decision to include women in the ruling class was either intended as a joke, or else was forced on him by other political commitments. In tis paper, I argue that the arguments he offers for including women in positions of power can and should be taken as sincere.

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

This chapter takes a critical look at universities from the perspective of the neopragmatist philosophy of education outlined by Richard Rorty. The chapter begins with a discussion of Rorty’s view of the ends that educational institutions properly serve in a liberal democracy. It then considers the kind of culture that Rorty takes to be conducive to those ends and the kind that is antithetical to them. Rorty sometimes characterizes the latter as a culture of ‘egotism’. After describing the main aspects (...) of such a culture, the chapter uses it as an interpretive key for understanding the ‘dark side’ of the contemporary university. Our thesis is that within a Rortyan, neo-pragmatist philosophy of higher education, the ends that universities are meant to serve in a liberal democracy are vulnerable to frustration and corruption by a culture of egotism. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

In this paper, I argue that the two versions of divided line create problems that cannot be solved — with or without the hypothesis that the objects belonging to the level of διάνοια on the divided line are intermediates. I also argue that the discussion of arithmetic and calculation does not fit Aristotle’s attribution of intermediates to Plato and provides no support for the claim that Plato had such intermediates in mind when he talked about διάνοια in the Republic. The (...) upshot of my argument is negative: even if Aristotle’s report about Plato and intermediates is correct, there is no evidence for such objects provided in the passages I review from the Republic. If they are to be found in Plato, it will have to be elsewhere that they are found. (shrink)

This is the first book-length philosophical study of Husserl’s transcendental phenomenology and Freud’s theory of the unconscious. The book investigates the possibility for Husserl’s transcendental phenomenology to clarify Freud’s concept of the unconscious with a focus on the theory of repression as its centre. Repression is the unconscious activity of pushing something away from consciousness, while making sure that it remains active as something foreign within us. How this is possible is the main problem addressed in the work. Unlike previous (...) literature (including Ricœur, Merleau-Ponty and Derrida) this book makes full use of the resources of genetic phenomenology and passivity in the attempt to clarify the Freudian unconscious. The central argument developed is that the structure of the lebendige Gegenwart as the core of Husserl’s theory of passivity consists of preliminary forms of bodily kinaesthesia, feelings and drives in a constantly ongoing process where repression occurs as a necessary part of all constitution. The clarification of Freudian repression thus takes place by showing how it presupposes a broad conception of consciousness such as that presented by Husserl’s genetic phenomenology. By arguing that “repression” is central to any philosophical account of subjectivity, this book takes on the most distinct challenge to philosophy posed by Freud. (shrink)

I suggest that the post-Hegelian tradition presents us with three contrasting normative models of work. According to the first model, the core norms of work are those of means-ends rationality. In this model, the modern world of work is constitutively a matter of deploying the most effective means to bring about given ends. The rational kernel of modern work, the core norm that has shaped its development, is on this view instrumental reason, and this very same normative core, in the (...) shape of advanced technology and more efficient, time-saving production, can help to liberate it. The second model, by contrast, takes the core norms of work to be internal to working activity. Rather than work gaining its normativity from something external to it, from ends to which the work is a contingent means, on this second view the core norms of work are expressions of values or meanings that are immanent to working practices themselves. The expressive model of work regards the actual world of work to be constituted historically by work-specific norms, norms which working subjects themselves have invoked and mobilised around in the course of their struggles for emancipation. According to the third model, the core norms of work have to do neither with instrumental rationality nor authentic self-expression. Rather they concern norms that relate either to individual achievement or contribution through work (in the form of esteem) or to the conditions that must in place for individuals to participate in the exchange of services by which market societies reproduce themselves (in the form of mutual respect). (shrink)

This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...) to which the introduction of an UBI would meet these criteria is then examined, with a focus on the social role that stands to be most affected by an UBI, namely that of the worker-earner. It is argued that while an UBI is likely to be only partially effective as an instrument of specifically social freedom, its main justification lies not here, but in securing a basis for the subjective freedom that social freedom presupposes. (shrink)

I begin by picking up on Brandom’s suggestion that expressivism follows American pragmatism in seeking to advance the cause of the Enlightenment. This provides us with a first point of contrast with Taylor’s understanding of expressivism, since Taylor takes expressivism to be inseparably bound up with the Romantic critique of the Enlightenment and as fundamentally opposed to Enlightenment naturalism. I then distinguish two features of what we ordinarily mean by the term ‘expression’, one of which provides an intuitive basis for (...) understanding Brandom’s expressivist program, the other of which provides an interpretive key for understanding Taylor’s version of expressivism. After looking briefly at the main tenets of Taylor’s expressivism, I conclude by considering its relation to Romanticism on the one hand, and to Brandom’s expressivist renewal of the Enlightenment project on the other. (shrink)

An analysis of how the sphere of work can be considered to instantiate norms of recognition, even when those norms give rise to paradoxes and ideologies surrounding how work ought to be done and the goods at stake in it.

What is the fundamental purpose that justifies the existence of the modern university? The answer proposed in this essay is the promotion of social freedom. The essay begins by distinguishing social freedom from negative freedom and reflective freedom along the lines proposed by other theorists of social freedom, such as Frederick Neuhouser and Axel Honneth. After noting the need for a more developed account of the university than has so far been provided by these other theorists, the essay analyses the (...) various dimensions in which universities have, at their best, promoted social freedom. The essay then explains why it is through the promotion of social, as distinct from negative or reflective freedom, that universities fulfil their purpose. It concludes with some reflections on how this understanding of the purpose of the university fits an “immanent” model of social criticism. (shrink)

The aim of this article is to situate Arendt’s account of labour as a critical response to humanisms of labour, or put otherwise, to situate it as an anti-humanism of labour. It compares Arendt’s account of labour with that of the most prominent humanist theorist of labour at the time of the composition of The Human Condition: Georges Friedmann. Arendt’s and Friedmann’s accounts of labour are compared specifically with respect to the range of capacities, social relations, and possibilities of fulfilment (...) at stake in the activity of labour. The comparison provides a previously unexplored context for understanding Arendt’s account of labour and her distinction between labour and work. The relevance of Arendt’s and Friedmann’s theories of labour for the contemporary debate about the meaning of work in an age of automation is also briefly discussed. (shrink)

In this text I would like to show two things. Firstly, that the so-called “timelessness” of the Freudian unconscious can be elucidated through an interpretation of the concept of Nachträglichkeit, and showing thereby that there is indeed a temporality specific to the workings of the unconscious. Freud’s analysis of early psychic trauma related to sexual phenomena pointed to a serious complication for all believers in the immediate transparency of consciousness. For the “wound” itself was constituted over time, and the possibility (...) of coming to understand the trauma (thereby achieving a certain freedom from its repercussions) was again only possible after the event had passed. The Nachträglichkeit involved in the psychoanalytical understanding of sexual trauma thus hinges on a threefold temporal process at work in subjective life. Secondly, I wish to show that Husserl, in his analyses of time and intersubjectivity, delivered the materials with which a phenomenological clarification of Nachträglichkeit can be given. Since Nachträglichkeit is essentially tied to the structure of repression (and thus the very constitution of the unconscious), what I am suggesting is a prolegomenon to a phenomenological clarification of Freudian repression. This clearly suggests the need for further investigations into the phenomenology of sexual life. (shrink)

Although the contrast between ‘economy’ and culture’ that structures the Fraser-Honneth debate derives ultimately from Weber, it has a more proximate ancestry in Habermas’ work. I begin by glancing back at Habermas’ formulation, not just because its background role in shaping the current debate has not been properly acknowledged (though I believe that is the case), but because Fraser and Honneth’s original responses to it provide a nice segue into their current positions. After briefly reviewing what those responses were, I (...) then offer a critical analysis of the conceptions of economy and culture they now propose. (shrink)

Even though Husserl’s thinking has received a remarkable amount of attention over the last decades, the full extent of many of its central aspects still remains surprisingly unknown. It is in particular the development of genetic phenomenology that is at stake here, as it plunges ever deeper into “originary constitution” ferreting out the structural relations between inner time-consciousness, affectivity and intersubjectivity, while at the same time never giving up static phenomenology and a certain prioritizing of Cartesian subjectivity. In the following (...) I would like to point to a reading of Husserl’s philosophy of time and subjectivity that is based on material that was never examined by Derrida. A general problem for interpreting this theme is that Husserl never succeeded in presenting a systematic overview of a phenomenological “transcendental aesthetics”. As a consequence, the co-originality and mutual interdependence of the constitution of space and time, of originary spacing as flesh (Urleib) and originary temporization (Urzeitigung), which first enables a comprehensive grasp of the originary processes in the living streaming present, has remained virtually unknown. In order to reach these themes, the interaction between the radicalized and the universal reductions has to be outlined. (shrink)

A summary of the main features of a 'recognition-theoretic' research program in the social sciences and a brief account of how it promises to advance on rival research programs in the social sciences.

The essay reflects on Gadamer’s ambiguous legacy for the philosophy of work. On the one hand, there are times when Gadamer reproduces the problematic distinction between language and labor which short-circuits the very idea of a hermeneutics of work. This is particularly evident in Gadamer’s reflections on technique and craftsmanship in the central sections of Truth and Method, as well as in his descriptions of the “art” of dialogue and the tasks of hermeneutics that separate them emphatically them from the (...) sphere of “making.” I raise some questions about the adequacy of the distinction Gadamer draws between techne and phronesis that structures this account. I argue here that Gadamer’s characterization of the learning process involved in the mastery of a technique, as well as his conception of the instrumentality and monologicality of technical knowledge, is difficult to sustain, especially in view of recent research in the psychology and anthropology of work. I then go on to point out that elsewhere in his oeuvre Gadamer himself is critical of the conception of work that emerges through the lens of the techne / phronesis distinction. Indeed, on these occasions he hints at a conception of work that points beyond the Arendt / Habermas conception towards a critical hermeneutics of working life. This alternative approach to work is particularly apparent in Gadamer’s appropriation of Hegel’s dialectic, in his understanding of play, and in some of his later diagnostic reflections on the spirit of the age. In section four, I offer some suggestions for explaining how the tensions evident in Gadamer’s approach to work came about. Here I am interested in what prevented Gadamer from embracing whole-heartedly the project of a hermeneutics of work that he himself helped to lay the foundations for. I conclude with some brief remarks on why we should seek to build upon these foundations and renew the project of a critical hermeneutics of work today. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...) show how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato's dialogues by date, more general challenges to historicist interpretations of Plato's dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

This synthesis of 5 prominent conflict management paradigms uses power differential as the single most contributing variable to their process and outcome of conflict. Efforts of scholars to integrate or synthesize conflict paradigms have been unsuccessful or clumsy by the scholars’ own assessments. The 5 selected paradigms represent an interdisciplinary set of normative and descriptive paradigms from different social contexts and intellectual frameworks. The 5 share the common traits of rival goals, three levels of socially constructed power differential, and outcomes (...) relative to the total value of the rival goal. An inverse relationship between power differential and the total value of conflict outcomes is supported by all 5 paradigms and empirical data. Explanatory metatheory is the methodology used for synthesis. An increase in power differential results in a decrease in total value of the rival goal. Power differential is constructed using Max Weber’s ideal-type method. The power differentials are abstracted from the paradigms themselves. Empirical work form secondary sources and case studies complete the analysis. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (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)

In this book I show that science suffers from a damaging but rarely noticed methodological disease, which I call rationalistic neurosis. It is not just the natural sciences which suffer from this condition. The contagion has spread to the social sciences, to philosophy, to the humanities more generally, and to education. The whole academic enterprise, indeed, suffers from versions of the disease. It has extraordinarily damaging long-term consequences. For it has the effect of preventing us from developing traditions and institutions (...) of learning rationally devoted to helping us learn how to make progress towards a wiser, more civilized world. On our fragile earth, overcrowded, fraught with injustice, inequality and conflict, menaced by unprecedented and terrifying technological and industrial means for change and destruction, we urgently need to acquire a little more wisdom and civilization if we are to avoid repeating horrors of the kind suffered by so many during the 20th century (and already suffered by many in the first few years of the 21st century). We can ill afford to have in our hands instruments of learning botched and bungled from the standpoint of helping us learn how to live more wisely. It may seem scarcely credible that something as important as our institutions of learning can suffer from wholesale, structural defects. Why has this not been noticed before? Why have not armies of scientists and scholars appreciated the point and, long ago, put the matter right? The answer will emerge as my argument unfolds. I will show that one of the most damaging features of rationalistic neurosis is that it has built-in methodological and institutional mechanisms which effectively conceal that anything is wrong. But there is also an immediately obvious reason: specialization, and the resulting fragmentation of academia, has resulted in a situation in which hardly anyone takes responsibility for the overall ideals, the overall aims and methods, of academic inquiry. Academics, these days, are specialists, furiously trying to keep abreast of developments in their own specialist fields. They have no time, and no inducement, to lift their eyes from their particular disciplines, and look at the whole endeavour. Science has long been under attack, at least since the Romantic movement. Blake objected to “Single vision & Newton’s sleep” and declared that “Art is the Tree of Life... Science is the Tree of Death”. Keats lamented that science will “clip an Angel’s wings” and “unweave a rainbow”. Whereas the Enlightenment had valued science and reason as tools for the liberation of humanity, Romanticism found science and reason oppressive and destructive, and instead valued art, imagination, inspiration, individual genius, emotional and motivational honesty rather than careful attention to objective fact. Much subsequent opposition to science stems from, or echoes, the Romantic opposition of Blake, Wordsworth, Keats and many others. There is the movement Isaiah Berlin has described as the “Counter-Enlightenment” (Berlin, 1979, ch. 1). There is existentialism, with its denunciation of the tyranny of reason, its passionate affirmation of the value and centrality of irrationality in human life, from Dostoevsky, Kierkegaard and Nietzsche to Heidegger and Sartre (see, for example, Barrett, 1962). There is the attack on Enlightenment ideals concerning science and reason undertaken by the Frankfurt school, by postmodernists and others, from Horkheimer and Adorno to Lyotard, Foucault, Habermas, Derrida, MacIntyre and Rorty (see Gascardi, 1999). The soul-destroying consequences of valuing science and reason too highly is a persistent theme in literature: it is to be found in the works of writers such as D.H. Lawrence, Doris Lessing, Max Frisch, Y. Zamyatin. There is persistent opposition to modern science and technology, and to scientific rationality, often associated with the Romantic wing of the green movement, and given expression in such popular books as Marcuse’s One Dimensional Man, Roszak’s Where the Wasteland Ends, Berman’s The Reenchantment of the World and Appleyard’s Understanding the Present. There is the feminist critique of science and conceptions of science: see, for example, Fox Keller (1984) and Harding (1986). And there are the corrosive implications of the so-called “strong programme” in the sociology of knowledge, and of the work of social constructivist historians of science, which depict scientific knowledge as a belief system alongside many other such conflicting systems, having no more right to claim to constitute knowledge of the truth than these rivals, the scientific view of the world being no more than an elaborate myth, a social construct (see Barnes and Bloor, 1981; Bloor, 1991; Barnes, Bloor and Henry, 1996; Shapin and Schaffer, 1985; Shapin, 1994; Pickering, 1984; Latour, 1987). This latter literature has provoked a counter-attack by scientists, historians and philosophers of science seeking to defend science and traditional conceptions of scientific rationality: see Gross and Levitt (1994), Gross, Levitt and Lewis (1996), and Koertge (1998). This debate between critics and defenders of science came abruptly to public attention with the publication of Alan Sokal’s brilliant hoax article ‘Transgressing the boundaries’ in a special issue of the cultural studies journal Social Text in 1996 entitled Science Wars: see Sokal and Bricmont (1998). What does this book have to contribute, given the above avalanche of criticism of science? The criticisms of science developed in this book are diametrically opposed to the above, in so far as the above criticisms oppose scientific rationality, seek to diminish or restrict its influence, or hold that it is unattainable. My central point is that we suffer, not from too much scientific rationality, but from not enough. What is generally taken to constitute scientific rationality is actually nothing of the kind. It is rationalistic neurosis, a characteristic, influential and damaging kind of irrationality masquerading as rationality. Science is damaged by being trapped within a widely upheld but severely defective philosophy of science; free science from this defective philosophy, provide it with a more intellectually rigorous philosophy, and it will flourish in both intellectual and humanitarian terms. And more generally, as we shall see, academic inquiry as a whole is damaged by being trapped within an intellectually defective philosophy of inquiry; free it from this defective philosophy, from its rationalistic neurosis, and it will flourish in intellectual and human terms. It is not reason that is damaging, but defective pretensions to reason — rationalistic neurosis —masquerading as reason. Thus what I seek to do here is the exact opposite of what all those who oppose science and scientific rationality do. I shall argue that Reason, the authentic article, arrived at by generalizing the progress-achieving methods of science, can have profoundly liberating and enriching consequences for all worthwhile, problematic aspects of life, and thus deserves to enter into every aspect of life. The bare bones of the argument of this book can be stated quite simply like this. Science cannot proceed without making the substantial metaphysical assumption that the universe is physically comprehensible (to some extent at least). But this conflicts with the orthodox view that in science everything is assessed impartially with respect to evidence, nothing being permanently assumed independently of evidence. So the metaphysical assumption of comprehensibility is repressed. Science pretends that no such assumption is made. But this damages science. For the assumption is substantial, influential and highly problematic. It needs to be made explicit within science so that it can be critically scrutinized, so that alternatives can be developed and considered. Pretending the assumption is not being made undermines the intellectual rigour of science, its intellectual value and success. And it does not stop there. For science also makes value assumptions. Quite properly, science is concerned to discover that which is of value. New factual knowledge devoid of all value (whether intellectual or practical) does not contribute to science. But the orthodox view of science holds that values have no place within science. As in the case of metaphysics, here too, science pretends that values have no role to play within the intellectual domain of science. And this damages science. For values are, if anything, even more influential and problematic than metaphysics (in influencing the direction of research). Here too, values need to be made explicit within science so that they can be scrutinized, so that alternatives can be developed and assessed. Pretending that values play no role within the intellectual domain damages science; both the intellectual and the practical aspects of science are adversely affected. Science fails to pursue those avenues of research that lie in the best interests of humanity. And it goes further. Science is pursued in a social, cultural, economic and political context. It is a part of various social, economic and political projects which seek to achieve diverse human objectives. But the idea that science is an integral part of humanitarian or political enterprises with political ends clashes, once again, with the official view of science that the aim of science is to improve factual knowledge. The political objectives of science are repressed. And, once again, this damages science. For, of course, the political objectives of science, like all our political objectives, are profoundly problematic. These need to be made explicit so that they can be scrutinized, so that alternatives can be developed and considered. The pretence that science does not have this political dimension once again undermines the intellectual rigour of science, and its human value. It lays science open to becoming a part of economic, corporate and political enterprises that are not in the best interests of humanity. The upshot of the line of argument just indicated is that we need to bring about a revolution in the aims and methods of science, and of academic inquiry more generally. Natural science needs to change; its relationship with the rest of academic inquiry, with social inquiry and the humanities, needs to change; and most importantly and dramatically, academic inquiry as a whole needs to change. The basic task of the academic enterprise needs to become to help humanity learn how to tackle its problems of living in more cooperatively rational ways than at present. We need to put the intellectual tasks of articulating our problems of living, and proposing and critically assessing possible solutions, possible and actual actions, at the heart of academic inquiry. The basic task needs to be to help humanity learn a bit more wisdom – wisdom being the capacity to realize what is of value in life, for oneself and others, wisdom including knowledge and technological know-how, but much else besides. Natural science, despite its flaws, has massively increased our knowledge and technological know-how. This in turn has led to a massive and sometimes terrifying increase in our power to act. Often this unprecedented power to act is used for human good, as in medicine or agriculture. But it is also used to cause harm, whether unintentionally (initially at least) as when industrialization and modern agriculture lead to global warming, destruction of natural habitats and rapid extinction of species, or intentionally, as when the technology of war is used by governments and terrorists to maim and kill. Before the advent of modern science, when we lacked the means to do too much damage to ourselves and the planet, lack of wisdom did not matter too much. Now, with our unprecedented powers to act, bequeathed to us by science, lack of wisdom has become a menace. This is the crisis behind all the other current global crises: science without wisdom. In these circumstances, to continue to pursue knowledge and technological know-how dissociated from a more fundamental quest for wisdom can only deepen the crisis. As a matter of urgency, we need to free science and academia of their neuroses; we need to bring about a revolution in the academic enterprise so that the basic aim becomes to promote wisdom by intellectual and educational means. At present science and the humanities betray both reason and humanity. The argument of this book, which I have just summarized, begins with a discussion of the philosophical and methodological problems that beset theoretical physics. At once, many of those who are concerned about moral, political and environmental issues that plague our world today, will feel impatient. What have the methodological problems of theoretical physics to do with third world poverty, war and the threat of war, pollution, extinction of species, the menace of conventional, chemical, biological and nuclear armaments? I can only plead with such a reader: patience. The root cause of the sickness of our times does indeed lie, I claim, with a methodological sickness of natural science or, even more specifically, of physical science. What makes the modern world so utterly different from all previous ages is our possession of modern science and technology. This is the instrument that has changed the conditions of human life almost beyond all recognition, and put unprecedented, and sometimes terrifying, powers into our hands. One should not dismiss out of hand the suggestion that a part of our problem may lie with this instrument, this engine, of rapid change. We see, here, too, the way in which intellectual specialization, referred to above, has effectively concealed from view the nature and extent of the problem that confronts us. The argument that I shall develop in what follows begins with physics, with problems concerning the aims and methods of physics. But it then leaps to social science, to philosophy, to the humanities, to education, to psychotherapy, and to politics: in the end there is scarcely an aspect of modern life that is not touched and, potentially, affected by the argument. How many academic experts are prepared to follow, to take seriously, an argument that ranges so recklessly across such a wide range of academic disciplines? How many non-academic non-experts? But just this is what the argument and message of this book requires. I hope that the reader will endure with patience the somewhat esoteric discussion concerning the aims and methods of physics pursued in chapter one. This may not seem to have anything much to do with the urgent problems of our times, but it does. This is in part how the intellectual disaster I seek to expose in this book conceals itself from view: it buries itself in the obscure, recondite field of the philosophy of physics. Those who devote their lives to the philosophy of physics are, by and large, too myopic to see how their specialized field of study has anything to do with the great and dreadful humanitarian problems and disasters of our age; and those who are above all concerned with these humanitarian disasters have no time at all for abstruse issues concerning the aims and methods of physics. And so the connection is never made. As it happens, the methodological neurosis of physics, with which we begin in chapter one, is actually a quite simple matter to grasp. It does not require any real knowledge of physics to understand. Indeed, physicists and philosophers of physics are much more likely to find the argument difficult to follow than are non-experts. We non-scientists can stand back and see the whole wood; scientists, trained to think in terms of the current orthodox conception of science, trapped in the thickets of research, will find this much harder to do. In an attempt to take this peculiar circumstance into account, I have arranged the exposition as follows. In chapter one I give a simple exposition of the case for declaring natural science to suffer from what I call "rationalistic neurosis"; this avoids all technicalities, and goes straight to the heart of the matter. In the appendix I tackle a host of more technical objections that may be made to the elementary argument of chapter one. So, those experts in the fields of the philosophy of physics and philosophy of science who find the argument of chapter one naïve and unconvincing, should consult the appendix before tossing the book away in disgust. I write in the hope that there will be a few who will not dismiss out of hand the suggestion that the question of how we are to go about learning how to live in wiser and more civilized ways might have something to learn from scientific learning, and will take the trouble to pursue the line of argument traced out in this book. I write in the hope that these few will grasp just how desperate our situation is, how urgent the need to change the status quo, and will do everything in their power to alert others to the need to heal the methodological sickness from which our institutions and traditions of learning at present suffer. To begin with, we need a campaigning organization, modelled perhaps on "Friends of the Earth", which might be called something like "Friends of Wisdom". (shrink)

In the Nintendo game Animal Crossing: New Horizons, players move to an uninhabited island and quickly become instrumental to the naming, aesthetic development, and biodiversity of the island. In some ways, the game can foster a love for and curiosity about nature. In other ways, the game reinforces harmful colonialist values and attitudes that are ultimately an obstacle to conservation in the real world. Here I critique the game values relevant to conservation, both the values that benefit and the values (...) that hinder conservation. I discuss possibilities for a future version of the game that reinforces values better aligned with conservation. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Socrates' attitude towards falsehood is quite puzzling in the Republic. Although Socrates is clearly committed to truth, at several points he discusses the benefits of falsehood. This occurs most notably in Book 3 with the "noble lie" (414d-415c) and most disturbingly in Book 5 with the "rigged sexual lottery" (459d-460c). This raises the question: What kinds of falsehoods does Socrates think are beneficial, and what kinds of falsehoods does he think are harmful? And more broadly: What can this tell us (...) about the relationship between ethics and epistemology? The key to answering these questions lies in an obscure and paradoxical passage in Book II; at 382a-d Socrates distinguishes between "true falsehoods" and "impure lies." True falsehoods are always bad, but impure lies are sometimes beneficial. Despite Socrates' insistence that he is not saying anything deep, his distinction is far from straightforward. Nevertheless, in order to determine why some falsehoods are beneficial and why some are always harmful, we must understand what exactly true falsehoods are and how they differ from impure lies. In this paper, I argue that true falsehoods are a restricted class of false beliefs about ethics; they are false beliefs about how one should live and what one should pursue. I refer to these beliefs as "normative commitments." False normative commitments are always pernicious because they create and sustain psychological disharmony. Unlike true falsehoods, impure lies can be about anything. Nevertheless, they are only beneficial when they help produce and sustain true normative commitments. I argue that the upshot of this is that practical concerns have a kind of primacy over theoretical concerns. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)