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)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

J. David Lewis and Richard L. Smith provide a history of pragmatism and Chicago sociology based on the positions of realism and nominalism. This issue is indeed the key to understanding pragmatism’s foundations in Charles Peirce’s original formulation. Lewis and Smith claim that there are two pragmatisms, a realistic one characterized by Peirce and Mead and a nominalistic one (which Lewis and Smith claim has no value) illustrated by James and Dewey. They argue that Chicago sociology, including (...) Herbert Blumer, was under the influence of the nominalistic pragmatism, and that Mead exercised little influence during his lifetime. The argument is based on an ahistorical, a priori "metatheoretical" realism-nominalism distinction that claims to be based on Peirce's discussions of realism and nominalism. Yet the authors support their understanding of realism by appealing to Mead’s discussion of “contact experience,” and claim that Peirce’s realism must be based in non-symbolic “pure resistance.” Ironically, such a view represents the main tenet of nominalism, that only individual particulars are real, and amounts to a denial of Peirce’s category of Thirdness as reducible to the “pure resistance” of Secondness. Lewis and Smith attempt to correct the subjectivist tendencies of symbolic interactionism yet would problematically replace them with an equally subjective view of what constitutes objectivity: individual reaction with an object. American Sociology and Pragmatism tends to present a monistic universe hinging on a nominalistic interpretation of realism, a single-visioned view that places more emphasis on labels than on the substance and pragmatic import of a theorist's thoughts, resulting in serious distortions pro and con. Yet it also has opened up for serious questioning the whole foundations of symbolic interactionism and Mead's place within pragmatism and Chicago sociology. Though the authors claim to be "revisionists," it seems to me that they are also "fundamentalists" in safely preserving Mead at the center of a history they claim he did not significantly influence. In my opinion the ongoing controversy will result in a broader understanding of the antecedents of contemporary symbolic interactionism, one that will call for Mead's now dominating role as the sole representative of pragmatism for many American sociologists to be reevaluated and placed within the context of the quite substantial contributions of Peirce, James, and Dewey. (shrink)

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...) they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future. (shrink)

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

A ‘lottery belief’ is a belief that a particular ticket has lost a large, fair lottery, based on nothing more than the odds against it winning. The lottery paradox brings out a tension between the idea that lottery beliefs are justified and the idea that that one can always justifiably believe the deductive consequences of things that one justifiably believes – what is sometimes called the principle of closure. Many philosophers have treated the lottery paradox as an argument against the (...) second idea – but I make a case here that it is the first idea that should be given up. As I shall show, there are a number of independent arguments for denying that lottery beliefs are justified. (shrink)

Pragmatism is the distinctive contribution of American thought to philosophy. It is a movement that attracted much attention in the early part of the twentieth-century, went into decline, and reemerged in the last part of the century. Part of the difficulty in defining pragmatism is that misconceptions of what pragmatism means have abounded since its beginning, and continue in today’s “neopragmatism.”.

My concern in this paper is with the claim that knowledge is a mental state – a claim that Williamson places front and centre in Knowledge and Its Limits. While I am not by any means convinced that the claim is false, I do think it carries certain costs that have not been widely appreciated. One source of resistance to this claim derives from internalism about the mental – the view, roughly speaking, that one’s mental states are determined by one’s (...) internal physical state. In order to know that something is the case it is not, in general, enough for one’s internal physical state to be a certain way – the wider world must also be a certain way. If we accept that knowledge is a mental state, we must give up internalism. One might think that this is no cost, since much recent work in the philosophy of mind has, in any case, converged on the view that internalism is false. This thought, though, is too quick. As I will argue here, the claim that knowledge is a mental state would take us to a view much further from internalism than anything philosophers of mind have converged upon. (shrink)

Epistemic permissivism is the view that it is possible for two people to rationally hold incompatible attitudes toward some proposition on the basis of one body of evidence. In this paper, I defend a particular version of permissivism – unacknowledged permissivism (UP) – which says that permissivism is true, but that no one can ever rationally believe that she is in a permissive case. I show that counter to what virtually all authors who have discussed UP claim, UP is an (...) attractive view: it is compatible with the intuitive motivations for permissivism and avoids a significant challenge to permissivism: the arbitrariness objection. (shrink)

This paper examines the interrelation between justice and mercy in Anselm’s prayers. Divine justice and human injustice seem to rightly cut off a human being from any assistance, grace, or reformation, since human beings has set themselves in a condition of injustice from which they cannot extricate themselves. Mercy then seems the only solution, but appears not only unjust, but also to trump divine justice, a position inconsistent with Anselm’s explicit statements. So then, how are justice and mercy rendered compatible, (...) even complementary with each other? Human beings are brought into integral roles for each other as intercessors within a divine economy of justice offering mercy within the scope of that very justice. Anselm’s rhetorically and dramatically structured prayers perform an educative as well as petitionary function in assisting the human being to locate, understand, and exert themselves within that divine economy of justice and mercy. (shrink)

In this paper, I offer reasons for thinking that two prominent sceptical arguments in the literature – the underdetermination-based sceptical argument and the closure-based sceptical argument – are less philosophically interesting than is commonly supposed. The underdetermination-based argument begs the question against a non-sceptic and can be dismissed with little fanfare. The closure-based argument, though perhaps not question-begging per se, does rest upon contentious assumptions that a non-sceptic is under no pressure to accept.

This book chapter represents one of the engagements between Catholic and Wesleyan philosophers at the 2008 Wesleyan Philosophy Society. The issue of what precisely "Wesleyan philosophy" would mean and comprise can be usefully illuminated by comparison with the positions and issues that were raised and discussed by Catholic scholars during the 1930s Christian philosophy debates in France, which included Etienne Gilson, Maurice Blondel, Jacques Maritain, and Gabriel Marcel. We also discuss how the thought on a contemporary Catholic philosopher Adriaan Peperzack, (...) specifically on affectivity, can be brought into comparison with that important theme in Wesleyan philosophy. (shrink)

Deleuze argued that a fundamental mutation in the concept of time occurred in Kant. In antiquity, the concept of time was subordinated to the concept of movement: time was a ‘measure’ of movement. In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an autonomy of its own: time becomes "the pure and empty form" of everything that moves and changes. What is essential in the theory of time is not the distinction between objective ‘clock (...) time’ (or physical time) and the subjective experience of ‘time consciousness,’ since both of them measure movements, whether the movement of extensive objects or intensive states. What is fundamental is rather the relation between time and movement, since time can only assume its own concept when it ceases to be subordinate to movement, whether that movement is objective or subjective. This article examines how Kant inverted the relation between time and movement, and how Deleuze’s own theory of time builds on Kant’s revolution and extends it further. (shrink)

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 8.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 9.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 11.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 35.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 51.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 52.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 53.

English translation of Thomas Aquinas' Commentary on the Psalms, Psalm 54.

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an account of what (...) might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs. (shrink)

This entry provides an overview of the current state of the debate between epistemic permissivists and impermissivists. Three important choice points for the permissivist are identified, and implications are discussed for plausibility of the resulting versions of permissivism.

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. (...) We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views. (shrink)

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

Certain states in the Global North have responded to refugees seeking safety on their territories through harmful practices of border violence, detention, encampment and containment that serve to prevent and deter refugee arrivals. These practices are ostensibly justified through an appeal to a right to control borders. This paper therefore assesses whether these harmful practices can indeed be morally justified by a state’s right to control borders. It analyses whether Christopher Heath Wellman’s account of a state’s right to freedom of (...) association, which represents the most restrictive account of a state’s right to control borders available in the literature, can extend to justify current harmful practices against refugees. If not, then no available justification will be able to do so, and thus contemporary harmful practices used against refugees cannot be justified by a state’s right to control borders. (shrink)

In 1976, Jo Freeman wrote an article for Ms. Magazine, entitled ‘Trashing: The Dark Side of Sisterhood’. It provoked an outpouring of letters from women relating their own experiences of trashing during the course of the second wave feminist movement—more letters than Ms. had received about any previous article. Since then, the technology has improved but the climate among feminists has not; trashing is now conducted on social media platforms like Twitter and Facebook, in front of ever-larger audiences and with (...) the magnified opportunities for destruction that these new platforms bring with them. Women already experience disproportionate harassment on social media; many feel trashing by other feminists to be much harder to accept. It’s one thing for people to hate feminists; resistance from those for whom a social justice movement represents a threat is par for the course. But it’s something else for feminists to hate each other. These are people with shared goals and a common enemy. What are the psychological mechanisms underlying this fact of life for feminist activists? Various explanations might be offered, from internalised misogyny, through volatility caused by histories of oppression, through envy and competitiveness, through ideological purity policing. Which are correct? Is the hatred that motivates trashing within feminism the same in quality and quantity, or different, from the affective dynamics inside other social movements? How does tribalism between warring feminist factions contribute to these dynamics, and to what extent is trashing underwritten by laudable moral goals (such as anti-elitism and anti-hierarchy) even when it goes too far or misfires? Can a liberation movement be successful without ideological purity policing, or is there a tension between achieving social justice outcomes and facilitating a healthy amount of disagreement and constructive criticism within a group? In this paper I’ll focus on potential explanations of the phenomena of trashing, including tribalism, power grabs, and purity policing; and the moral commitments that might lead feminists to trash each other. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

Philosophers from Plotinus to Paul Churchland have yielded to the temptation to embrace doctrines which contradict the core beliefs of common sense. Philosophical realists have on the other hand sought to counter this temptation and to vindicate those core beliefs. The remarks which follow are to be understood as a further twist of the wheel in this never-ending battle. They pertain to the core beliefs of common sense concerning the external reality that is given in everyday experience -the beliefs of (...) folk physics, as we might call them. Just as critics of Churchland et al. have argued that the folk-psychological ontology of beliefs, desires, etc. yields the best explanation we can have of the order of cognitive phenomena conceived from the perspective of first-person experience, so we shall argue that (1) the commonsensical ontology of folk physics yields the best explanation we can have of our externally directed cognitive experience and that (2) an ontology of mesoscopic things, events and processes must play a role, in particular, in our best scientific theory of human action. (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...) proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

This paper adopts the philosophical approach of Stoicism as the basis for re-examining the cognitive and ethical relationship between Homo sapiens and Neanderthals. Stoicism sets out a clear criterion for the special moral status of human beings, namely rationality. We explore to what extent Neanderthals were sufficiently rational to be considered “human”. Recent findings in the fields of palaeoanthropology and palaeogenetics show that Neanderthals possessed high-level cognitive abilities and produced viable offspring with anatomically modern humans. Our discussion offers insights for (...) reflecting on the relationship between humans and other forms of natural life and any moral obligations that result. (shrink)

We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two such subregions do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he (...) uses it to resolve a number of Zeno-like paradoxes. (shrink)

In perceptual experience we are directed towards objects in a way that establishes a real relation between a mental act and its target. In reading works of fiction we enjoy experiences which manifest certain internal similarities to such relational acts, but which lack objects. The substitution theory of art attempts to provide a reason why we seek out such experiences and the artifacts which they generate. Briefly, we seek out works of art because we enjoy the physiology and the phenomenology (...) of, for example, the experience of love or mountain climbing, and works of art serve as props for the promotion of substitutes for the corresponding genuine feelings. Art arose, or came to be separated out from other, related phenomena, through the discovery that the experience of substitute emotions can be pleasurable. (shrink)

In this essay, I evaluate four central metaethical readings of Spinoza’s moral philosophy in the literature: unqualified anti-realism, qualified anti-realism, qualified realism, and unqualified realism. More specifically, I discuss the metaethical readings of Charles Jarrett (unqualified anti-realism), Matthew Kisner (qualified anti-realism), Jon Miller (qualified realism), and Andrew Youpa (unqualified realism), each of which captures core aspects of this debate. My conclusions are that (1) Spinoza is neither an unqualified anti-realist nor an unqualified realist and (2) Spinoza’s ethical framework represents a (...) qualified synthesis of realist (naturalistic) and anti-realist (affective) features. (shrink)

To what in reality do the logically simple sentences with empirical content correspond? Two extreme positions can be distinguished in this regard: 'Great Fact' theories, such as are defended by Davidson; and trope-theories, which see such sentences being made the simply by those events or states to which the relevant main verbs correspond. A position midway between these two extremes is defended, one according to which sentences of the given sort are made tme by what are called 'dependence structures', or (...) in other words by certain complex concrete portions of reality between the parts of which relations of dependence are defined. Principles governing such dependence-structures are laid down, principles of an ontologically motivated sort which serve as basis for a topological semantics conceived as an altemative to standard set-theoretic approaches to semantics of the Tarskian sort. These principles are then used to resolve certain puzzles generated by the (semantically motivated) theory of events put forward by Davidson. (shrink)

Stephan Witasek was a student and follow of Meinong, who applied Meinong's ideas on the ontology of the non-existent to the working out of a theory of aesthetic phenomena in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows how our feelings undergo certain sorts of structural modifications when they are directed towards what does not exist. He draws a distinction between genuine mental phenomena and what he calls ‘phantasy-material’, asserting that ‘the job of the aesthetic object, whether it is (...) a work of art or a product of nature, is to excite and support the actualisation of phantasy-material in the experiencing subject’. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Report submitted by Gregory B. Sadler, Pilot Project Coordinator to Sonya Brown, WAC Activity Director, Fayetteville State University, June 28 2011. -/- A Pilot program focused on improving student performance in carrying out Close Readings in humanities-based discipline courses was developed and implemented under the auspices of Writing Across the Curriculum and Title III at Fayetteville State University in Winter and Spring 2011. Five faculty were involved in the Pilot, myself as the coordinator, and four other faculty from four (...) different disciplines as participants. -/- The central idea behind the Pilot was that by focusing on the lower-order skills which are scaffolded as components into the higher-order activity of Close Reading of texts, and redesigning courses to emphasize development of these lower-order skills, student performances in Close Readings would also be improved. This did turn out to be the case. Most of the supporting data is qualitative rather than quantitative. -/- It is recommended that similar activities be continued, but that participating faculty be required to provide much more prescriptively structured and detailed assessment data and information about their course design. (shrink)

Conventional wisdom holds that the von Neumann entropy corresponds to thermodynamic entropy, but Hemmo and Shenker (2006) have recently argued against this view by attacking von Neumann's (1955) argument. I argue that Hemmo and Shenker's arguments fail due to several misunderstandings: about statistical-mechanical and thermodynamic domains of applicability, about the nature of mixed states, and about the role of approximations in physics. As a result, their arguments fail in all cases: in the single-particle case, the finite particles case, and the (...) infinite particles case. (shrink)

Ancient philosophical schools developed and discussed perspectives and practices on the emotion of anger useful in contemporary philosophical practice with clients, groups, and organizations. This paper argues the case for incorporating these insights from four main philosophical schools (Platonist, Aristotelian, Epicurean, and Stoic) sets out eight practices drawn from these schools, and discusses how these insights can be used by philosophical practitioners with clients.

In Everettian quantum mechanics, justifications for the Born rule appeal to self-locating uncertainty or decision theory. Such justifications have focused exclusively on a pure-state Everettian multiverse, represented by a wave function. Recent works in quantum foundations suggest that it is viable to consider a mixed-state Everettian multiverse, represented by a (mixed-state) density matrix. Here, we develop the conceptual foundations for decoherence and branching in a mixed-state multiverse, and extend the standard Everettian justifications for the Born rule to this setting. This (...) extended framework provides a unification of 'classical' and 'quantum' probabilities, and additional theoretical benefits, for the Everettian picture. (shrink)