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)

In this book Daniel Wegner offers a novel understanding of the relation of consciousness, the will, and our intentional and voluntary actions. Wegner claims that our experience and common sense view according to which we can influence our behavior roughly the way we experience that we do it is an illusion.

We often think about the alternatives to a decision that has been made. Thinking in this way is known as counterfactual thinking, that is, thinking about what could have been had an alternative dec...

Supporters of open borders sometimes argue that the state has no pro tanto right to restrict immigration, because such a right would also entail a right to exclude existing citizens for whatever reasons justify excluding immigrants. These arguments can be defeated by suggesting that people have a right to stay put. I present a new form of the exclusion argument against closed borders which escapes this “right to stay put” reply. I do this by describing a kind of exclusion that (...) has not been discussed in depth, which I call “territorial exclusion.” Territorial exclusion is the process according to which the group that wishes to exclude current citizens secedes from the territory in which those citizens reside. I argue that the wrongness of territorial exclusion explains why there is no pro tanto right for a state to exclude immigrants, because otherwise there would be a pro tanto right for the state to kick people out by seceding from the territory they inhabit. Because kicking people out like this is typically wrong, borders cannot be closed. (shrink)

I defend the cosmopolitan instrumentalist theory of secession, according to which a group has a right to secede only if this would promote cosmopolitan justice. I argue that the theory is preferable to other theories of secession because it is an entailment of cosmopolitanism, which is independently attractive, and because, unlike other theories of secession, it allows us to give the answers we want to give in cases like secession of the rich or secession that would make things worse for (...) minorities. I defend the view against the objections that it allows for colonialism and annexation, that it is not a distinct theory, and that it is impractical. (shrink)

Wittgenstein famously remarks that ‘the meaning of a word is its use’ (PI §43). Whether or not one views this as gesturing at a ‘theory’ of meaning, or instead as aiming primarily at dissuading us from certain misconceptions of language that are a source of puzzlement, it is clear that Wittgenstein held that for certain purposes the meaning of an expression could profitably be characterised as its use. Throughout his later writings, however, Wittgenstein’s appeal to the notion of use pulls (...) in two directions. In several places, Wittgenstein seems to connect the notion of an expression’s meaning with that of use in the sense of usage or practice. More specifically, he suggests that for an expression to possess meaning is for there to be a practice of employing it according to certain rules. ‘That’, he tells us, ‘is why there exists a correspondence between the concepts “rule” and “meaning”’ (OC §62; cf. PG 68; PO 51; RFM VI §28; VW 103). Indeed, Wittgenstein goes so far as to say, ‘The rule-governed nature of our languages permeates our life’ (RC §303). Call the view that the meaning of an expression is determined by a general principle governing its use, rulism. (shrink)

Majority rule is often regarded as an important democratic principle. But modern democracies divide voters into districts. So if the majority should rule, which majority should rule? Should it be the popular majority, or an electoral majority (i.e., either the majority of voters in the majority of districts, or the majority of voters in districts that contain the majority of the population)? I argue that majority rule requires rule by the popular majority. This view is not novel and may seem (...) obvious. But it is rarely defended, and often rejected. I defend it by arguing that this view about which majority should rule is best supported by the arguments for why the majority should rule, and best avoids the arbitrary and perverse verdicts of rule by electoral majorities. I close by considering the significant practical implications of the view. The Electoral College is often criticized on the basis that the winner of the popular vote doesn’t always win the election. But all district-based democracies have this feature, so all district-based democracies must be reformed if they are to satisfy the principle of majority rule. (shrink)

As a strategy for exploring the relationship between understanding and knowledge, we consider whether epistemic luck – which is typically thought to undermine knowledge – undermines understanding. Questions about the etiology of understanding have also been at the heart of recent theoretical debates within epistemology. Kvanvig (2003) put forward the argument that there could be lucky understanding and produced an example that he deemed persuasive. Grimm (2006) responded with a case that, he argued, demonstrated that there could not be lucky (...) understanding. In this paper, we empirically examine how participants' patterns of understanding attributions line up with the predictions of Kvanvig and Grimm. We argue that the data challenge Kvanvig's position. People do not differentiate between knowing-why and understanding-why on the basis of proper etiology: attributions of knowledge and understanding involve comparable (and minimal) roles for epistemic luck. We thus posit that folk knowledge and understanding are etiologically symmetrical. (shrink)

According to an influential recent view, S is propositionally justified in believing p iff S is in no position to know that S is in no position to know p. I argue that this view faces compelling counterexamples.

I argue that there is a tension between two of the most distinctive theses of Sven Rosenkranz’s Justification as Ignorance: the central thesis concerning justification, according to which an agent has propositional justification to believe p iff they are in no position to know that they are in no position to know p and the desire to avoid logical omniscience by imposing only “realistic” idealizations on epistemic agents.

Ludwig Wittgenstein's notoriously elusive later writings are dominated by remarks on language. However, while the textual analysis of Wittgenstein's writings is presently a booming industry, the tendency is to focus narrowly on exegetical matters with little attention to their bearing on philosophy at large. Moreover, one finds in contemporary philosophy of language various ideas with a distinctively Wittgensteinian ring to them but whose pedigree is uncertain. This volume brings together distinguished Wittgenstein scholars and renowned philosophers of language in order to (...) examine just what Wittgenstein has to say about language and to assess its significance for current philosophy. The topics discussed include the connection between the meaning of a word and its use, the bearing the context of utterance has on how words are to be understood, the role of rules in the employment of language and whether Wittgenstein's reflections on these issues encourage sceptical or relativist thoughts."--BOOK JACKET. (shrink)

When policymakers craft rules for use by the general public, they must take into account the ways in which their rules are likely to be misapplied. Should contractualists and rule consequentialists do the same when they search for rules whose general acceptance would be non-rejectable or ideal? I argue that these theorists face a dilemma. If they ignore the possibility of misapplication, they end up with an unrealistic view that rejects rules designed to protect us from others’ mistakes. On the (...) other hand, if they take misapplication into account, they end up rejecting rules that appeal to what really matters morally in favor of easier-to-apply proxies for these rules. This leaves them unable to say why certain wrong acts are wrong, which in turn may lead them to mistaken verdicts about moral worth and wronging. I show how this misapplication dilemma applies to standard contractualist and rule consequentialist theories, but also suggest how it might generalize to other two-level theories, including those designed to avoid the ideal world objection. (shrink)

Daniel Whistler argues that Hemsterhuis' philosophy matters and that its exclusion from the canon of modern philosophy has been unjust. This is not just because of its influence on later thinkers, but is primarily because Hemsterhuis' philosophy contains a rich assemblage of ideas and philosophical practices.

A large and growing body of research in computational psychiatry draws on Bayesian modelling to illuminate the dysfunctions and aberrations that underlie psychiatric disorders. After identifying the chief attractions of this research programme, we argue that its typical focus on abstract, domain-general inferential processes is likely to obscure many of the distinctive ways in which the human mind can break down and malfunction. We illustrate this by appeal to psychosis and the social phenomenology of delusions.

Plato's dialogues frequently criticize traditional Greek myth, yet Plato also integrates myth with his writing. Daniel S. Werner confronts this paradox through an in-depth analysis of the Phaedrus, Plato's most mythical dialogue. Werner argues that the myths of the Phaedrus serve several complex functions: they bring nonphilosophers into the philosophical life; they offer a starting point for philosophical inquiry; they unify the dialogue as a literary and dramatic whole; they draw attention to the limits of language and the limits (...) of knowledge; and they allow Plato to co-opt cultural authority as a way of defining and legitimating the practice of philosophy. Platonic myth, as a species of traditional tale, is thus both distinct from philosophical dialectic and similar to it. Ultimately, the most powerful effect of Platonic myth is the way in which it leads readers to participate in Plato's dialogues and to engage in a process of self-examination. (shrink)

In recent years, an old challenge to informed consent has been rediscovered: the challenge of ignorance. Several authors argue that due to the presence of irreducible ignorance in certain treatments, giving informed consent to these treatments is not possible. The present paper examines in what ways ignorance is believed to prevent informed consent and which treatments are affected by that. At this, it becomes clear that if the challenge of ignorance truly holds, it poses a major problem to informed consent. (...) The paper argues, however, that from both an empirical and a theoretical point of view, it is not convincing that ignorance prevents informed consent. Still, it seems important that the presence of irreducible ignorance is openly discussed during the informed consent process. (shrink)

Having concepts is a distinctive sort of cognitive capacity. One thing that conceptual thought requires is obeying the Generality Constraint: concepts ought to be freely recombinable with other concepts to form novel thoughts, independent of what they are concepts of. Having concepts, then, constrains cognitive architecture in interesting ways. In recent years, spurred on by the rise of evolutionary psychology, massively modular models of the mind have gained prominence. I argue that these architectures are incapable of satisfying the Generality Constraint, (...) and hence incapable of underpinning conceptual thought. I develop this argument with respect to two well-articulated proposals, due to Dan Sperber and Peter Carruthers. Neither proposal gives us a satisfactory explanation of Generality within the confines of a genuinely modular architecture. Massively modular minds may display considerable behavioral and cognitive flexibility, but not humanlike conceptualized thought. (shrink)

I argue that an act can be wrong _because_ it wrongs a particular person. I then show how this thesis serves as a constraint on moral theories, using Kantian ethics as a case study.

Having concepts is a distinctive sort of cognitive capacity. One thing that conceptual thought requires is obeying the Generality Constraint: concepts ought to be freely recombinable with other concepts to form novel thoughts, independent of what they are concepts of. Having concepts, then, constrains cognitive architecture in interesting ways. In recent years, spurred on by the rise of evolutionary psychology, massively modular models of the mind have gained prominence. I argue that these architectures are incapable of satisfying the Generality Constraint, (...) and hence incapable of underpinning conceptual thought. I develop this argument with respect to two well-articulated proposals, due to Dan Sperber and Peter Carruthers. Neither proposal gives us a satisfactory explanation of Generality within the confines of a genuinely modular architecture. Massively modular minds may display considerable behavioral and cognitive flexibility, but not humanlike conceptualized thought. (shrink)

At the climax of Ender's Game, we see Ender exhausted and at wit's end. Sorting out the mess of who is actually responsible for what is difficult–we feel conflicted about the whole thing, just as Ender does. In this chapter, Aristotle helps us make sense of responsibility and voluntary action and considers whether a person can be responsible for something that he or she did not cause. It looks at why we should care about whether a fictional character is responsible (...) and consider an alternative notion of responsibility that explains Ender's post‐xenocide actions as Speaker for the Dead. The chapter first establishes what moral responsibility is and then contrasts moral responsibility with causal responsibility. He is not to blame for the destruction of the buggers, he does what he can to try to make things right. (shrink)

Though the 'medieval' is often deployed as a stigmatic symbol of all that is retrograde, against modernity, and barbaric, the medieval is increasingly being sought as a bedrock of tradition, heritage, and identity, especially by writers and politicians on the far right. Both characterisations- the medieval as violent other and the medieval as vital foundation- are mined and studied in this book. It examines contemporary political uses of the Middle Ages to ask why the medieval continues to play such a (...) prominent role in the political and historical imagination today." -- Back cover. (shrink)

This chapter explores the notion of territory in the works of both Gilles Deleuze and Martin Heidegger. It examines whether race and its minor theatre want a dwelling place and investigates whether there is a political potential within the body without organs which offers a resistance to the homely conception of dwelling. It provides a contextualisation of this future theatre in the Deleuzo-Guattarian project of minor literature as a whole and questions the practicality of the schizo-stroll and the BWO. It (...) also discusses the notion of Heideggerian deterritorialisation. (shrink)

Lovejoy (1873-1962) was America's foremost historian of ideas, a major participant in the philosophical debates of the twentieth century, and a prominent advocate of academic freedom. The product of an emotionally unsettled childhood and an evangelical father, Lovejoy reacted against his father by postulating the certainty of self-sufficient reason. He believed that only the principles of reason could order the world and so make our universe intelligible. Originally published in 1980. A UNC Press Enduring Edition -- UNC Press Enduring Editions (...) use the latest in digital technology to make available again books from our distinguished backlist that were previously out of print. These editions are published unaltered from the original, and are presented in affordable paperback formats, bringing readers both historical and cultural value. (shrink)

Modern Jewish Philosophy and the Politics of Divine Violence Is commitment to God compatible with modern citizenship? In this book, Daniel H. Weiss provides new readings of four modern Jewish philosophers - Moses Mendelssohn, Hermann Cohen, Franz Rosenzweig, and Walter Benjamin - in light of classical rabbinic accounts of God's sovereignty, divine and human violence, and the embodied human being as the image of God. He demonstrates how classical rabbinic literature is relevant to contemporary political and philosophical debates. Weiss (...) brings to light striking political aspects of the writings of the modern Jewish philosophers, who have often been understood as non-political. In addition, he shows how the four modern thinkers are more radical and more shaped by Jewish tradition than has previously been thought. Taken as a whole, Weiss' book argues for a fundamental rethinking of the relationship between Judaism and politics, the history of Jewish thought, and the ethical and political dynamics of the broader Western philosophical tradition. (shrink)

Public philosophy distinguishes itself from other philosophical undertakings by either addressing public problems, i.e. those with broad social consequence, or doing the work of philosophy in a public setting beyond the confines of a purely academic environment. The ironic and darkly absurd character of the defining features of civilization and progress – realities Indigenous Peoples have confronted with devastating consequences for centuries – is the way in which both generate tremendous unhappiness and destruction. The living historical character of our cultures (...) is captured in the power plus place equals personality axiom that Deloria formulated. The modus operandi of Indigenous solutions not only addresses the “know‐how” but the moral “should we” dimensions of proposed solutions. Most of humankind talks about resources because the worldview guiding the powerful economic and political interests thinks in those terms about our relatives. (shrink)