A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (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)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

It is common to hear talk of the aim of belief and to find philosophers appealing to that aim for numerous explanatory purposes. What belief 's aim explains depends, of course, on what that aim is. Many hold that it is somehow related to truth, but there are various ways in which one might specify belief 's aim using the notion of truth. In this article, by considering whether they can account for belief 's standard of correctness and the epistemic (...) norms governing belief, I argue against certain prominent specifications of belief 's aim given in terms of truth, and advance a neglected alternative. (shrink)

The _Physics_ is a foundational work of western philosophy, and the crucial one for understanding Aristotle's views on matter, form, essence, causation, movement, space, and time. This richly annotated, scrupulously accurate, and consistent translation makes it available to a contemporary English reader as no other does—in part because it fits together seamlessly with other closely associated works in the New Hackett Aristotle series, such as the _Metaphysics_, _De Anima_, and forthcoming _De Caelo_ and _On Coming to Be and Passing Away_. (...) Eventually the series will include all of Aristotle's works. Sequentially numbered endnotes provide the information most needed at each juncture, while a detailed Index of Terms indicates places where focused discussion of key notions occurs. An illuminating general Introduction describes the book that lies ahead, explaining what sort of work it is and what sorts of evidence it relies on. (shrink)

Infallibilism is the view that a belief cannot be at once warranted and false. In this essay we assess three nonpartisan arguments for infallibilism, arguments that do not depend on a prior commitment to some substantive theory of warrant. Three premises, one from each argument, are most significant: if a belief can be at once warranted and false, then the Gettier Problem cannot be solved; if a belief can be at once warranted and false, then its warrant can be transferred (...) to an accidentally true belief; if a belief can be at once warranted and false, then it can be warranted and accidentally true. We argue that each of these is either false or no more plausible than its denial. Along the way, we offer a solution to the Gettier Problem that is compatible with fallibilism. (shrink)

" Qualia " is an unfamiliar term for something that could not be more familiar to each of us: the ways things seem to us. As is so often the case with philosophical jargon, it is easier to give examples than to give a definition of the term. Look at a glass of milk at sunset; the way it looks to you--the particular, personal, subjective visual quality of the glass of milk is the quale of your visual experience at the (...) moment. The way the milk tastes to you then is another, gustatory quale, and how it sounds to you as you swallow is an auditory quale; These various "properties of conscious experience" are prime examples of qualia. Nothing, it seems, could you know more intimately than your own qualia ; let the entire universe be some vast illusion, some mere figment of Descartes' evil demon, and yet what the figment is made of will be the qualia of your hallucinatory experiences. Descartes claimed to doubt everything that could be doubted, but he never doubted that his conscious experiences had qualia, the properties by which he knew or apprehended them. (shrink)

The social sciences playa variety of multifaceted roles in the policymaking process. So varied are these roles, indeed, that it is futile to talk in the singular about the use of social science in policymaking, as if there were one constant relationship between two fixed and stable entities. Instead, to address this issue sensibly one must talk in the plural about uses of dif ferent modes of social scientific inquiry for different kinds of policies under various circumstances. In some cases, (...) the influence of social scientific research is direct and tangible, and the connection between the find ings and the policy is easy to see. In other cases, perhaps most, its influence is indirect-one small piece in a larger mosaic of politics, bargaining, and compromise. Occasionally the findings of social scientific studies are explicitly drawn upon by policymakers in the formation, implementation, or evaluation of particular policies. More often, the categories and theoretical models of social science provide a general background orientation within which policymakers concep tualize problems and frame policy options. At times, the in fluence of social scientific work is cognitive and informational in nature; in other instances, policymakers use social science primarily for symbolic and political purposes in order to le gitimate preestablished goals and strategies. Nonetheless, amid this diversity and variety, troubling general questions persistently arise. (shrink)

1. Happiness, then and now -- Happiness, eudaimonia, and practical reasoning -- Happiness as eudaimonia -- Happiness and virtuous activity -- New directions from old debates -- 2. Happiness then: the sufficiency debate -- Aristotle's case against the sufficiency thesis -- 3. Happiness now: rethinking the self -- Socrates' case for the sufficiency thesis -- Epictetus and the stoic self -- The Stoics' case for the sufficiency thesis -- The embodied conception of the self -- The embodied conception and psychological (...) well-being -- The Stoics' case against the embodied conception. (shrink)

Sometimes it takes years of debate for philosophers to discover what it is they really disagree about. Sometimes they talk past each other in long series of books and articles, never guessing at the root disagreement that divides them. But occasionally a day comes when something happens to coax the cat out of the bag. "Aha!" one philosopher exclaims to another, "so that's why you've been disagreeing with me, misunderstanding me, resisting my conclusions, puzzling me all these years!".

Schober et al. describe two studies on how survey interview respondents misunderstand interview questions. After answering a survey, participants are given standardized definitions of the questions they have just answered. Even apparently simple questions such as “Have you smoked more than 100 cigarettes?” are interpreted very differently by participants. Moreover, clarifying the meaning of the definitions with the interviewer does not always help resolve the miscommunication.

Sometimes, learning about the origins of a belief can make it irrational to continue to hold that belief—a phenomenon we call ‘genealogical defeat’. According to explanationist accounts, genealogical defeat occurs when one learns that there is no appropriate explanatory connection between one’s belief and the truth. Flatfooted versions of explanationism have been widely and rightly rejected on the grounds that they would disallow beliefs about the future and other inductively-formed beliefs. After motivating the need for some explanationist account, we raise (...) some problems for recent versions of explanationism. Learning from their failures, we then produce and defend a more resilient explanationism. (shrink)

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...) of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. (shrink)

Realists about possible worlds typically identify possible worlds with abstract objects, such as propositions or properties. However, they face a significant objection due to Lewis (1986), to the effect that there is no way to explain how possible worlds-as-abstract objects represent possibilities. In this paper, I describe a response to this objection on behalf of realists. The response is to identify possible worlds with propositions, but to deny that propositions are abstract objects, or indeed objects at all. Instead, I argue (...) that realists should follow Prior (1971) and others in treating higher-order quantification (e.g. quantification into predicate or sentence position) as a genuine form of quantification in its own right, and so in particular, not to be analysed in terms of first-order quantification over abstract objects. I argue that from this ‘higher-orderist’ perspective, there is a relatively straightforward answer to the question of how possible worlds-as-propositions succeed in representing possibilities. (shrink)

Realists about possible worlds typically identify possible worlds with abstract objects, such as propositions or properties. However, they face a significant objection due to Lewis (1986), to the effect that there is no way to explain how possible worlds-as-abstract objects represent possibilities. In this paper, I describe a response to this objection on behalf of realists. The response is to identify possible worlds with propositions, but to deny that propositions are abstract objects, or indeed objects at all. Instead, I argue (...) that realists should follow Prior (1971) and others in treating higher-order quantification (e.g. quantification into predicate or sentence position) as a genuine form of quantification in its own right, and so in particular, not to be analysed in terms of first-order quantification over abstract objects. I argue that from this ‘higher-orderist’ perspective, there is a relatively straightforward answer to the question of how possible worlds-as-propositions succeed in representing possibilities. (shrink)

In this groundbreaking book, Daniel D. Novotny explores one of the most controversial topics of Suarez's philosophy: "beings of reason." Beings of reason are impossible intentional objects, such as blindness and square-circle.

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

This paper explores various subtleties in our ordinary thought and talk about normative reasons—subtleties which, if taken seriously, have various upshots, both substantive and methodological. I focus on two subtleties in particular. The first concerns the use of reason (in its normative sense) as both a count noun and as a mass noun, and the second concerns the context-sensitivity of normative reasons-claims. The more carefully we look at the language of reasons, I argue, the clearer its limitations and liabilities become. (...) The cumulative upshot is that although talk of reasons is intelligible and useful for the purposes of communication, we should be wary of placing much weight on it when engaging in substantive normative inquiry. By way of illustration, I consider some potential pitfalls of taking our talk of reasons too seriously, explaining how careful attention to the language of reasons undermines the main argument for moral particularism, Mark Schroeder’s recent defense of Humeanism about practical reasons, and the “reasons-first” program in metanormativity. (shrink)

The Jewish Philosophy Reader is the first comprehensive anthology of classic writings on Jewish philosophy from the Bible to postmodernism. The Reader is clearly divided into four separate parts: Foundations and First Principles, Medieval and Renaissance Jewish Philosophy, Modern Jewish Thought, and Contemporary Jewish Philosophy. Each part is clearly introduced by the editors. The readings featured are representative writings of each era listed above and are from the following major thinkers: Abrabanel, Baeck, Bergman, Borowitz, Buber, Cohen, Crescas, Fackenheim, Geiger, Gersonides, (...) Goodman, Graetz, Halevi, Hartman, Heschel, Hess, Hirsch, Ibn Ezra, Ibn Gabirol, Ibn Paquda, Kellner, Kook, Krochmal, Leibowitz, Levinas, Maimonides, Maybaum, Mendelssohn, Novak, Philo, Plaskow, Rosenzweig, Saadia, Scholem, Seeskin, Soloveitchik, Spinoza, Strauss, Wolf, Zunz. (shrink)

Both new and seasoned psychotherapists wrestle with the relationship between psychological distress and inequality across race, class, gender, and sexuality. How does one address this organically in psychotherapy? What role does it play in therapeutic action? Who brings it up, the therapist or the patient? Daniel José Gaztambide addresses these questions by offering a rigorous decolonial approach that rethinks theory and technique from the ground up, providing an accessible, evidence-informed reintroduction to psychoanalytic practice. He re-examines foundational thinkers from three (...) traditions—Freudian, relational-interpersonal, and Lacanian—through the lens of revolutionary psychiatrist Frantz Fanon, and offers a detailed analysis of Fanon’s psychoanalytic practice. Drawing on rich yet grounded discussions of theory and research, Gaztambide presents a clinical model that facilitates exploration of the social in the clinical space in a manner intimately related to the patient’s presenting problem. In doing so, this book demonstrates that clinicians no longer have to choose between attending to the personal, interpersonal, or sociopolitical. It is a guide to therapeutic action “on the couch,” which envisions political action “off the couch” and in the streets. Decolonizing Psychoanalytic Technique provides a comprehensive, practice-oriented and compelling guide for students, practitioners, and scholars of critical, multicultural and decolonial approaches to psychotherapy. (shrink)

This exceptional anthology immerses students in such powerful ideas that they will find themselves not just reading about, but actually participating in, the kind of philosophical thinking that can change the way they look at their lives and the world around them. Now in a new edition, The Experience of Philosophy features eighty-five readings that challenge students' thinking about God, freedom, reality, nothingness, death, and their own identities. Provocative and accessible, these selections have been carefully chosen for their ability to (...) draw students out of an ordinary frame of reference into exciting new territory. Although the editors include many classic sources from philosophers such as Plato, Descartes, Locke, and Kant, the emphasis is on contemporary writings. Articles by Derek Parfit, Bertrand Russell, and others help students see philosophy's links to literature, the natural sciences, and the physical and social sciences. The sixth edition features twelve new essays--by Augustine, Alvin Plantinga and Daniel Kolak, Georges Rey, Fred Dretske, David Reisman, Paul Teller, Clea F. Rees, Padmasiri de Silva, Daniel Kolak, Karl Marx, Anand Chandavarkar, and Vincent Hendricks--as well as more text boxes offering excerpts from other relevant works. The Experience of Philosophy, Sixth Edition, integrates helpful pedagogical aids including section introductions, a brief introduction to each selection, biographical information on each author, and questions before and after each reading to reinforce main ideas and promote thinking. Further readings after each selection direct students to additional material on related issues. Ideal for introductory philosophy courses, The Experience of Philosophy, Sixth Edition, encourages students to "do" philosophy, rather than just read about its history. (shrink)

We are bombarded with more information each day than our brains can process especially in election season. It's raining bad data, half-truths, and even outright lies. Daniel J. Levitin shows how to recognize misleading announcements, statistics, graphs, and written reports revealing the ways lying weasels can use them.

The problem known as Buridan’s Ass says that a hungry donkey equipoised between two identical bales of hay will starve to death. Indecision kills the ass. Some philosophers worry about human analogs. Computer scientists since the 1960s have known about the computer versions of such cases. From what Leslie Lamport calls ‘Buridan’s Principle’—a discrete decision based on a continuous range of input-values cannot be made in a bounded time—it follows that the possibilities for human analogs of Buridan’s Ass are far (...) more wide-ranging and securely provable than has been acknowledged in philosophy. We are never necessarily decisive. This is mathematically provable. I explore four consequences: first, increased interest of the literature’s solutions to Buridan’s Ass; second, a new asymmetry between responsibility for omissions and responsibility for actions; third, clarification of the standard account of akrasia; and, fourth, clarification of the role of credences in normative decision-theory. (shrink)

In Lukács: Praxis and the Absolute, Daniel Andrés López reassembles Lukács’s philosophy of praxis on a Hegelian basis, as a conceptual-historical totality, both defending him and proposing an unprecedented, immanent critique that raises problems for Marxian philosophy as a whole.