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)
This essay criticizes the proposal recently defended by a number of prominent economists that welfare economics be redirected away from the satisfaction of people's preferences and toward making people happy instead. Although information about happiness may sometimes be of use, the notion of happiness is sufficiently ambiguous and the objections to identifying welfare with happiness are sufficiently serious that welfare economists are better off using preference satisfaction as a measure of welfare. The essay also examines and criticizes the position associated (...) with Daniel Kahneman and a number of co-authors that takes welfare to be ‘objective happiness’ – that is, the sum of momentary pleasures. (shrink)
In this book, Daniel Hutto and Erik Myin promote the cause of a radically enactive, embodied approach to cognition that holds that some kinds of minds -- basic minds -- are neither best explained by processes involving the manipulation of ...
Distinguished contributors take up eminent scholar Daniel R. Schwarz’s reading of modern fiction and poetry as mediating between human desire and human action. The essayists follow Schwarz’s advice, “always the text, always historicize,” thus making this book relevant to current debates about the relationships between literature, ethics, aesthetics, and historical contexts.
The tenuous claims of cost-benefit analysis to guide policy so as to promote welfare turn on measuring welfare by preference satisfaction and taking willingness-to-pay to indicate preferences. Yet it is obvious that people's preferences are not always self-interested and that false beliefs may lead people to prefer what is worse for them even when people are self-interested. So welfare is not preference satisfaction, and hence it appears that cost-benefit analysis and welfare economics in general rely on a mistaken theory of (...) well-being. This essay explores the difficulties, criticizes standard defences of welfare economics, and then offers a new partial defence that maintains that welfare economics is independent of any philosophical theory of well-being. Welfare economics requires nothing more than an evidential connection between preference and welfare: in circumstances in which people are concerned with their own interests and reasonably good judges of what will serve their interests, their preferences will be reliable indicators of what is good for them. (shrink)
Physicalism, the thesis that everything is physical, is one of the most controversial problems in philosophy. Its adherents argue that there is no more important doctrine in philosophy, whilst its opponents claim that its role is greatly exaggerated. In this superb introduction to the problem Daniel Stoljar focuses on three fundamental questions: the interpretation, truth and philosophical significance of physicalism. In answering these questions he covers the following key topics: -/- (i)A brief history of physicalism and its definitions, (ii)what (...) a physical property is and how physicalism meets challenges from empirical sciences, (iii)'Hempel’s dilemma’ and the relationship between physicalism and physics, (iv)physicalism and key debates in metaphysics and philosophy of mind, such as supervenience, identity and conceivability, and (v)physicalism and causality. -/- Additional features include chapter summaries, annotated further reading and a glossary of technical terms, making Physicalism ideal for those coming to the problem for the first time. (shrink)
This essay attempts to distinguish the pressing issues for economists and economic methodologists concerning realism in economics from those issues that are of comparatively slight importance. In particular I shall argue that issues concerning the goals of science are of considerable interest in economics, unlike issues concerning the evidence for claims about unobservables, which have comparatively little relevance. In making this argument, this essay raises doubts about the two programs in contemporary economic methodology that raise the banner of realism. In (...) particular I argue that the banner makes it more difficult to relate the concerns of those who wave it to those of other methodologists. Although this essay argues that many of the debates in this century between scientific realists and their opponents are not relevant to economics, it does not attack scientific realism, and it does not urge economists or economic methodologists to reject it. (shrink)
Established wisdom in cognitive science holds that the everyday folk psychological abilities of humans -- our capacity to understand intentional actions performed for reasons -- are inherited from our evolutionary forebears. In _Folk Psychological Narratives_, Daniel Hutto challenges this view and argues for the sociocultural basis of this familiar ability. He makes a detailed case for the idea that the way we make sense of intentional actions essentially involves the construction of narratives about particular persons. Moreover he argues that (...) children acquire this practical skill only by being exposed to and engaging in a distinctive kind of narrative practice. Hutto calls this developmental proposal the narrative practice hypothesis. Its core claim is that direct encounters with stories about persons who act for reasons supply children with both the basic structure of folk psychology and the norm-governed possibilities for wielding it in practice. In making a strong case for the as yet underexamined idea that our understanding of reasons may be socioculturally grounded, Hutto not only advances and explicates the claims of the NPH, but he also challenges certain widely held assumptions. In this way, _Folk Psychological Narratives_ both clears conceptual space around the dominant approaches for an alternative and offers a groundbreaking proposal. (shrink)
People can be disgusted by the concrete and by the abstract -- by an object they find physically repellent or by an ideology or value system they find morally abhorrent. Different things will disgust different people, depending on individual sensibilities or cultural backgrounds. In _Yuck!_, Daniel Kelly investigates the character and evolution of disgust, with an emphasis on understanding the role this emotion has come to play in our social and moral lives. Disgust has recently been riding a swell (...) of scholarly attention, especially from those in the cognitive sciences and those in the humanities in the midst of the "affective turn." Kelly proposes a cognitive model that can accommodate what we now know about disgust. He offers a new account of the evolution of disgust that builds on the model and argues that expressions of disgust are part of a sophisticated but largely automatic signaling system that humans use to transmit information about what to avoid in the local environment. He shows that many of the puzzling features of moral repugnance tinged with disgust are by-products of the imperfect fit between a cognitive system that evolved to protect against poisons and parasites and the social and moral issues on which it has been brought to bear. Kelly's account of this emotion provides a powerful argument against invoking disgust in the service of moral justification. (shrink)
Physicalism is the thesis that everything is physical, or as contemporary philosophers sometimes put it, that everything supervenes on, or is necessitated by, the physical. The thesis is usually intended as a metaphysical thesis, parallel to the thesis attributed to the ancient Greek philosopher Thales, that everything is water, or the idealism of the 18th Century philosopher Berkeley, that everything is mental. The general idea is that the nature of the actual world (i.e. the universe and everything in it) conforms (...) to a certain condition, the condition of being physical. Of course, physicalists don't deny that the world might contain many items that at first glance don't seem physical — items of a biological, or psychological, or moral, or social nature. But they insist nevertheless that at the end of the day such items are either physical or supervene on the physical. (shrink)
Many libertarians believe that self-ownership is a separate matter from ownership of extra-personal property. “No-proviso” libertarians hold that property ownership should be free of any “fair share” constraints, on the grounds that the inability of the very poor to control property leaves their self-ownership intact. By contrast, left-libertarians hold that while no one need compensate others for owning himself, still property owners must compensate others for owning extra-personal property. What would a “self” have to be for these claims to be (...) true? I argue that both of these camps must conceive of the boundaries of the self as including one's body but no part of the extra-personal world. However, other libertarians draw those boundaries differently, so that self-ownership cannot be separated from the right to control extra-personal property after all. In that case, property ownership must be subject to a fair share constraint, but that constraint does not require appropriators to pay compensation. This view, which I call “right libertarianism,” differs importantly from the other types primarily in its conception of the self, which I argue is independently more plausible. (shrink)
In Happiness for Humans , Daniel C. Russell takes a fresh look at happiness from a practical perspective: the perspective of someone trying to solve the wonderful problem of how to give himself a good life. From this perspective, "happiness" is the name of a solution to that problem for practical deliberation. Russell's approach to happiness falls within a tradition that reaches back to ancient Greek and Roman philosophers--a tradition now called "eudaimonism." Beginning with Aristotle's seminal discussion of the (...) role of happiness in practical reasoning, Russell asks what sort of good happiness would have to be in order to play the role in our practical economies that it actually does play. Looking at happiness from this perspective, Russell argues that happiness is a life of activity, with three main features: it is acting for the sake of ends we can live for, and living for them wisely; it is fulfilling for us, both as humans and as unique individuals; and it is inextricable from our connections with the particular persons, pursuits, and places that make us who we are. By returning to this ancient perspective on happiness, Russell finds new directions for contemporary thought about the good lives we want for ourselves. (shrink)
In his new book, eminent psychologist - Daniel Stern, explores the hitherto neglected topic of 'vitality'. Truly a tour de force from a brilliant clinician and scientist, Forms of Vitality is a profound and absorbing book - one that will be essential reading for psychologists, psychotherapists, and those in the creative arts.
Dan Haybron presents an illuminating examination of well-being, drawing on important recent work in the science of happiness. He shows that we are remarkably prone to error in judgements of our own personal welfare, and suggests that we should rethink traditional assumptions about the good life and the good society.
Moral debunking arguments are meant to show that, by realist lights, moral beliefs are not explained by moral facts, which in turn is meant to show that they lack some significant counterfactual connection to the moral facts (e.g., safety, sensitivity, reliability). The dominant, “minimalist” response to the arguments—sometimes defended under the heading of “third-factors” or “pre-established harmonies”—involves affirming that moral beliefs enjoy the relevant counterfactual connection while granting that these beliefs are not explained by the moral facts. We show that (...) the minimalist gambit rests on a controversial thesis about epistemic priority: that explanatory concessions derive their epistemic import from what they reveal about counterfactual connections. We then challenge this epistemic priority thesis, which undermines the minimalist response to debunking arguments (in ethics and elsewhere). (shrink)
We review the current state of play in the game of naturalizing content and analyse reasons why each of the main proposals, when taken in isolation, is unsatisfactory. Our diagnosis is that if there is to be progress two fundamental changes are necessary. First, the point of the game needs to be reconceived in terms of explaining the natural origins of content. Second, the pivotal assumption that intentionality is always and everywhere contentful must be abandoned. Reviving and updating Haugeland’s baseball (...) analogy in the light of these changes, we propose ways of redirecting the efforts of players on each base of his intentionality All-Star team, enabling them to start functioning effectively as a team. Only then is it likely that they will finally get their innings and maybe, just maybe, even win the game. (shrink)
The psychological condition of happiness is normally considered a paradigm subjective good, and is closely associated with subjectivist accounts of well-being. This article argues that the value of happiness is best accounted for by a non-subjectivist approach to welfare: a eudaimonistic account that grounds well-being in the fulfillment of our natures, specifically in self-fulfillment. And self-fulfillment consists partly in authentic happiness. A major reason for this is that happiness, conceived in terms of emotional state, bears a special relationship to the (...) self. These arguments also point to a more sentimentalist approach to well-being than one finds in most contemporary accounts, particularly among Aristotelian forms of eudaimonism. (shrink)
This paper presents and defends an argument that the continuum hypothesis is false, based on considerations about objective chance and an old theorem due to Banach and Kuratowski. More specifically, I argue that the probabilistic inductive methods standardly used in science presuppose that every proposition about the outcome of a chancy process has a certain chance between 0 and 1. I also argue in favour of the standard view that chances are countably additive. Since it is possible to randomly pick (...) out a point on a continuum, for instance using a roulette wheel or by flipping a countable infinity of fair coins, it follows, given the axioms of ZFC, that there are many different cardinalities between countable infinity and the cardinality of the continuum. (shrink)
Danielle Macbeth offers a new account of mathematical practice as a mode of inquiry into objective truth, and argues that understanding the nature of mathematical practice provides us with the resources to develop a radically new conception of ourselves and our capacity for knowledge of objective truth.
The primary units of meaning in the use and comprehension of language are speech acts of the type called illocutionary acts. In Foundations of Illocutionary Logic John Searle and Daniel Vanderveken presented the first formalized logic of a general theory of speech acts. In Meaning and Speech Acts Daniel Vanderveken further develops the logic of speech acts and the logic of propositions to construct a general semantic theory of natural languages. Volume I, Principles of Language Use, explains the (...) general principles that connect meaning, reason, thought and speech acts in the semantic structure of language. It presupposes no detailed knowledge of logical formalism, and will be accessible to a large readership of students and scholars from philosophy, lingustics, cognitive psychology and computer science. Volume II, Formal Semantics of Success and Satisfaction uses the resources of philosophical and mathematical logics to develop a formalization of the laws of the semantic theory advanced in Volume I. It will be of interest to theoretical linguists and those involved in mathematical logic and artificial intelligence. (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)
Contingent negative existentials give rise to a notorious paradox. I formulate a version in terms of metaphysical grounding: nonexistence can't be fundamental, but nothing can ground it. I then argue for a new kind of solution, expanding on work by Kit Fine. The key idea is that negative existentials are contingently zero-grounded – that is to say, they are grounded, but not by anything, and only in the right conditions. If this is correct, it follows that grounding cannot be an (...) internal relation, and that no complete account of reality can be purely fundamental. (shrink)
A lot of good philosophy is done in the armchair, but is nevertheless a posteriori. This paper clarifies and then defends that claim. Among the a posteriori activities done in the armchair are assembling and evaluating commonplaces; formulating theoretical alternatives; and integrating well-known past a posteriori discoveries. The activity that receives the most discussion, however, is the application of theoretical virtues to choose philosophical theories: the paper argues that much of this is properly seen as a posteriori.
This Handbook maps a central terrain of philosophy, and provides the definitive guide to it. An illustrious team of philosophers explore the concept of a reason to do or believe something, in order to determine what these reasons are and how they work. And they investigate the nature of 'normative' claims about what we ought to do or believe.