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)

In the international bestseller, Thinking, Fast and Slow, Daniel Kahneman, the renowned psychologist and winner of the Nobel Prize in Economics, takes us on a groundbreaking tour of the mind and explains the two systems that drive the way we think. System 1 is fast, intuitive, and emotional; System 2 is slower, more deliberative, and more logical. The impact of overconfidence on corporate strategies, the difficulties of predicting what will make us happy in the future, the profound effect of (...) cognitive biases on everything from playing the stock market to planning our next vacation—each of these can be understood only by knowing how the two systems shape our judgments and decisions. -/- Engaging the reader in a lively conversation about how we think, Kahneman reveals where we can and cannot trust our intuitions and how we can tap into the benefits of slow thinking. He offers practical and enlightening insights into how choices are made in both our business and our personal lives—and how we can use different techniques to guard against the mental glitches that often get us into trouble. Winner of the National Academy of Sciences Best Book Award and the Los Angeles Times Book Prize and selected by The New York Times Book Review as one of the ten best books of 2011, Thinking, Fast and Slow is destined to be a classic. (shrink)

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)

Examines the lived experience of social encounters drawing on phenomenological insights.

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)

Supererogatory acts—good deeds “beyond the call of duty”—are a part of moral common sense, but conceptually puzzling. I propose a unified solution to three of the most infamous puzzles: the classic Paradox of Supererogation (if it’s so good, why isn’t it just obligatory?), Horton’s All or Nothing Problem, and Kamm’s Intransitivity Paradox. I conclude that supererogation makes sense if, and only if, the grounds of rightness are multi-dimensional and comparative.

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.

" 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 rapidly increasing numbers of elderly people in our society have raised some important moral questions: How should we distribute social resources among different age groups? What does justice require from both the young and the old? In this book, Norman Daniels offers the first systematic philosophical discussion of these urgent questions, advocating what he calls a "lifespan" approach to the problem: Since, as they age, people pass through a variety of institutions, the challenge of caring for the elderly becomes (...) the prudent allocation of public resources among the various stages of people's lives. Using this philosophical approach, Daniels addresses specific public policy issues such as the allocation of medical funds, the adequacy of long-term care, current Medicare cost-containment measures, and the equitable distribution of income support over the lifespan and between generations. (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)

Supererogatory acts are those that lie “beyond the call of duty.” There are two standard ways to define this idea more precisely. Although the definitions are often seen as equivalent, I argue that they can diverge when options are infinite, or when there are cycles of better options; moreover, each definition is acceptable in only one case. I consider two ways out of this dilemma.

The potential to collect brain data more directly, with higher resolution, and in greater amounts has heightened worries about mental and brain privacy. In order to manage the risks to individuals posed by these privacy challenges, some have suggested codifying new privacy rights, including a right to “mental privacy.” In this paper, we consider these arguments and conclude that while neurotechnologies do raise significant privacy concerns, such concerns are—at least for now—no different from those raised by other well-understood data collection (...) technologies, such as gene sequencing tools and online surveillance. To better understand the privacy stakes of brain data, we suggest the use of a conceptual framework from information ethics, Helen Nissenbaum’s “contextual integrity” theory. To illustrate the importance of context, we examine neurotechnologies and the information flows they produce in three familiar contexts—healthcare and medical research, criminal justice, and consumer marketing. We argue that by emphasizing what is distinct about brain privacy issues, rather than what they share with other data privacy concerns, risks weakening broader efforts to enact more robust privacy law and policy. (shrink)

The central question in contemporary ethics is whether virtue can replace duty as the primary notion in ethical theory. The subject of intense contemporary debate in ethical theory, virtue ethics is currently enjoying an increase in interest. This is the first book to focus directly on the subject. It provides a clear, systematic introduction to the area and houses under one cover a collection of the central articles published on the debate over the past decade. The essays encompass a wide (...) range ofaspects: the difference between virtue ethics and traditional duty ethics; present arguments for and against virtue ethics; the practical implications of virtue ethics and the Aristotelian and Kantian attitudes to virtue ethics. (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)

Moral functioning is a defining feature of human personhood and human social life. Moral Psychology provides an integrative and evaluative overview of the theoretical and empirical traditions that have attempted to make sense of moral cognition, prosocial behavior, and the development of virtuous character.This is the first book to integrate a comprehensive review of the psychological literatures with allied traditions in ethics. Moral rationality and decisionmaking; the development of the sense of fairness and justice, and of prosocial dispositions; as well (...) as the notion of moral self and moral identity and their relation to issues of character and virtue are fully discussed in the rich contexts provided by psychological and philosophical paradigms. Lapsley emphasizes parenting and educational strategies for influencing moral behavior, reasoning, and character development, and charts a line of research for the “post-Kohlbergian era” in moral psychology.This book will be an invaluable text for advanced courses in moral psychology, as taught in departments of psychology, education, and philosophy. It will also prove to be a standard reference work for researchers and ethicists alike. (shrink)

Professor Little presents an introduction to the philosophy of social science with an emphasis on the central forms of explanation in social science: rational-intentional, causal, functional, structural, materialist, statistical and interpretive. The book is very strong on recent developments, particularly in its treatment of rational choice theory, microfoundations for social explanation, the idea of supervenience, functionalism, and current discussions of relativism.Of special interest is Professor Little’s insight that, like the philosophy of natural science, the philosophy of social science can profit (...) from examining actual scientific examples. Throughout the book, philosophical theory is integrated with recent empirical work on both agrarian and industrial society drawn from political science, sociology, geography, anthropology, and economics.Clearly written and well structured, this text provides the logical and conceptual tools necessary for dealing with the debates at the cutting edge of contemporary philosophy of social science. It will prove indispensible for philosophers, social scientists and their students. (shrink)

Ackn o wledgments I owe special gratitude to Professors Hugo Adam Bedau and John Rawls for many helpful discussions of the general idea and scope, ...

Public discussions of political and social issues are often characterized by deep and persistent polarization. In social psychology, it’s standard to treat belief polarization as the product of epistemic irrationality. In contrast, we argue that the persistent disagreement that grounds political and social polarization can be produced by epistemically rational agents, when those agents have limited cognitive resources. Using an agent-based model of group deliberation, we show that groups of deliberating agents using coherence-based strategies for managing their limited resources tend (...) to polarize into different subgroups. We argue that using that strategy is epistemically rational for limited agents. So even though group polarization looks like it must be the product of human irrationality, polarization can be the result of fully rational deliberation with natural human limitations. (shrink)

From an early age, humans know a surprising amount about basic physical principles, such as gravity, force, mass, and shape. We can see this in the way that young children play, and manipulate objects around them. The same behaviour has long been observed in primates - chimpanzees have been shown to possess a remarkable ability to make and use simple tools. But what does this tell us about their inner mental state - do they therefore share the same understanding to (...) that of a young child? Do they understand the simple, underlying physical principles involved? Though some people would say that they do, this book reports groundbreaking research that questions whether this really is the case. -/- Folk Physics for Apes challenges the assumptions so often made about apes. It offers us a rare glimpse into the workings of another mind, examining how apes perceive and understand the physical world - an understanding that appears to be both similar to, and yet profoundly different from our own. The book will have broad appeal to evolutionary psychologists, developmental psychologists, and those interested in the sub-disciplines of cognitive science (philosophy, anthropology). The book additionally offers for developmental psychologists some valuable new non-verbal techniques for assessing causal understanding in young children. (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.

Philosophers have found postulating possible worlds to be very useful in a number of areas, including philosophy of language and mind, logic, and metaphysics. Impossible worlds are a natural extension to this use of possible worlds, and can help resolve a number of difficulties thrown up by possible‐worlds frameworks.

A remarkable number of Nietzsche's substantive moral psychological views have been borne out by evidence from the empirical sciences. Moral judgments are products of affects on Nietzsche's view, but the latter are in turn causally dependent upon more fundamental features of the individual. Nietzsche accepts a doctrine of types. The path is short from the acceptance of the Doctrine of Types to the acceptance of epiphenomenalism, as Leiter, and more recently, Riccardi argue. This chapter explains Nietzsche's phenomenological account of willing, (...) which serves as independent motivation for the view that Nietzsche denies the causal efficacy of conscious acts of willing. It also explores that in spite of an absence of volitional freedom, self‐control can be usefully understood on a strength‐model of motivational resources. The chapter concludes with a brief discussion of how Nietzsche, without employing the contemporary methods of empirical psychology, could nonetheless be such a prescient moral psychologist. (shrink)