Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

In this volume, leading philosophers of psychiatry examine psychiatric classification systems, including the Diagnostic and Statistical Manual of Mental Disorders, asking whether current systems are sufficient for effective diagnosis, treatment, and research. Doing so, they take up the question of whether mental disorders are natural kinds, grounded in something in the outside world. Psychiatric categories based on natural kinds should group phenomena in such a way that they are subject to the same type of causal explanations and respond similarly to (...) the same type of causal interventions. When these categories do not evince such groupings, there is reason to revise existing classifications. The contributors all question current psychiatric classifications systems and the assumptions on which they are based. They differ, however, as to why and to what extent the categories are inadequate and how to address the problem. Topics discussed include taxometric methods for identifying natural kinds, the error and bias inherent in DSM categories, and the complexities involved in classifying such specific mental disorders as "oppositional defiance disorder" and pathological gambling. -/- Contributors George Graham, Nick Haslam, Allan Horwitz, Harold Kincaid, Dominic Murphy, Jeffrey Poland, Nancy Nyquist Potter, Don Ross, Dan Stein, Jacqueline Sullivan, Serife Tekin, Peter Zachar. (shrink)

This paper considers two reasons that might support Russell’s choice of a ramified-type theory over a simple-type theory. The first reason is the existence of purported paradoxes that can be formulated in any simple-type language, including an argument that Russell considered in 1903. These arguments depend on certain converse-compositional principles. When we take account of Russell’s doctrine that a propositional function is not a constituent of its values, these principles turn out to be too implausible to make these arguments troubling. (...) The second reason is conditional on a substitutional interpretation of quantification over types other than that of individuals. This reason stands up to investigation: a simple-type language will not sustain such an interpretation, but a ramified-type language will. And there is evidence that Russell was tacitly inclined towards such an interpretation. A strong construal of that interpretation opens a way to make sense of Russell’s simultaneous repudiation of propositions and his willingness to quantify over them. But that way runs into trouble with Russell’s commitment to the finitude of human understanding. (shrink)

I argue that most counterfactuals are false.

Bayesianism is our leading theory of uncertainty. Epistemology is defined as the theory of knowledge. So “Bayesian Epistemology” may sound like an oxymoron. Bayesianism, after all, studies the properties and dynamics of degrees of belief, understood to be probabilities. Traditional epistemology, on the other hand, places the singularly non-probabilistic notion of knowledge at centre stage, and to the extent that it traffics in belief, that notion does not come in degrees. So how can there be a Bayesian epistemology?

Logicism is, roughly speaking, the doctrine that mathematics is fancy logic. So getting clear about the nature of logic is a necessary step in an assessment of logicism. Logic is the study of logical concepts, how they are expressed in languages, their semantic values, and the relationships between these things and the rest of our concepts, linguistic expressions, and their semantic values. A logical concept is what can be expressed by a logical constant in a language. So the question “What (...) is logic?” drives us to the question “What is a logical constant?” Though what follows contains some argument, limitations of space constrain me in large part to express my Credo on this topic with the broad brush of bold assertion and some promissory gestures. (shrink)

There have long been calls from industry for guidance in implementing strategies for sustainable development. The Circular Economy represents the most recent attempt to conceptualize the integration of economic activity and environmental wellbeing in a sustainable way. This set of ideas has been adopted by China as the basis of their economic development, escalating the concept in minds of western policymakers and NGOs. This paper traces the conceptualisations and origins of the Circular Economy, tracing its meanings, and exploring its antecedents (...) in economics and ecology, and discusses how the Circular Economy has been operationalized in business and policy. The paper finds that while the Circular Economy places emphasis on the redesign of processes and cycling of materials, which may contribute to more sustainable business models, it also encapsulates tensions and limitations. These include an absence of the social dimension inherent in sustainable development that limits its ethical dimensions, and some unintended consequences. This leads us to propose a revised definition of the Circular Economy as “an economic model wherein planning, resourcing, procurement, production and reprocessing are designed and managed, as both process and output, to maximize ecosystem functioning and human well-being”. (shrink)

Contrary to economics or history, for example, there does not exist an organized field dedicated to the philosophy of political science. Given that the philosophical issues raised by political science research are just as pressing and vibrant as those raised in these more organized fields, fostering a field that labels itself Philosophy of Political Science (PoPS) is important. PoPS is advanced here as a fruitful meeting place where both philosophers and practicing political scientists contribute and discuss—with philosophical discussions that are (...) close to and informed by actual developments in political science, making philosophy of science continuous with the sciences in line with contemporary naturalist philosophy of science. The topics scrutinized in the different chapters of the Handbook will figure prominently in PoPS, as we lay out in this chapter. (shrink)

This paper has three aims: to define autonomism clearly and charitably, to offer a positive argument in its favour, and to defend a larger view about what is at stake in the debate between autonomism and its critics. Autonomism is here understood as the claim that a valuer does not make an error in failing to bring her moral and aesthetic judgements together, unless she herself values doing so. The paper goes on to argue that reason does not require the (...) valuer to make coherent her aesthetic and moral evaluations. Finally, the paper shows that the denial of autonomism has realist commitments that autonomism does not have, and concludes that issues of value realism and irrealism are relevant to the debates about autonomism in ways that have not hitherto been recognized. (shrink)

Discourse carries thin commitment to objects of a certain sort iff it says or implies that there are such objects. It carries a thick commitment to such objects iff an account of what determines truth-values for its sentences say or implies that there are such objects. This paper presents two model-theoretic semantics for mathematical discourse, one reflecting thick commitment to mathematical objects, the other reflecting only a thin commitment to them. According to the latter view, for example, the semantic role (...) of number-words is not designation but rather the encoding of cardinality-quantifiers. I also present some reasons for preferring this view. (shrink)

Immoralists hold that in at least some cases, moral fl aws in artworks can increase their aesthetic value. They deny what I call the valence constraint: the view that any effect that an artwork’s moral value has on its aesthetic merit must have the same valence. The immoralist offers three arguments against the valence constraint. In this paper I argue that these arguments fail, and that this failure reveals something deep and interesting about the relationship between cognitive and moral value. (...) In the fi nal section I offer a positive argument for the valence constraint. (shrink)

This paper and its sequel “look under the hood” of the usual sorts of proof-theoretic systems for certain well-known intuitionistic and classical propositional modal logics. Section 1 is preliminary. Of most importance: a marked formula will be the result of prefixing a formula in a propositional modal language with a step-marker, for this paper either 0 or 1. Think of 1 as indicating the taking of “one step away from 0.” Deductions will be constructed using marked formulas. Section 2 presents (...) the model-theoretic concepts, based on those in [7], that guide the rest of this paper. Section 3 presents Natural Deduction systems IK and CK, formalizations of intuitionistic and classical one-step versions of K. In these systems, occurrences of step-markers allow deductions to display deductive structure that is covered over in familiar “no step” proof-theoretic systems for such logics. Box and Diamond are governed by Introduction and Elimination rules; the familiar K rule and Necessitation are derived (i.e. admissible) rules. CK will be the result of adding the 0-version of the Rule of Excluded Middle to the rules which generate IK. Note: IK is the result of merely dropping that rule from those generating CK, without addition of further rules or axioms (as was needed in [7]). These proof-theoretic systems yield intuitionistic and classical consequence relations by the obvious definition. Section 4 provides some examples of what can be deduced in IK. Section 5 defines some proof-theoretic concepts that are used in Section 6 to prove the soundness of the consequence relation for IK (relative to the class of models defined in Section 2.) Section 7 proves its completeness (relative to that class). Section 8 extends these results to the consequence relation for CK. (Looking ahead: Part 2 will investigate one-step proof-theoretic systems formalizing intuitionistic and classical one-step versions of some familiar logics stronger than K.). (shrink)

So-called “traditional epistemology” and “Bayesian epistemology” share a word, but it may often seem that the enterprises hardly share a subject matter. They differ in their central concepts. They differ in their main concerns. They differ in their main theoretical moves. And they often differ in their methodology. However, in the last decade or so, there have been a number of attempts to build bridges between the two epistemologies. Indeed, many would say that there is just one branch of philosophy (...) here—epistemology. There is a common subject matter after all. In this paper, we begin by playing the role of a “bad cop,” emphasizing many apparent points of disconnection, and even conflict, between the approaches to epistemology. We then switch role, playing a “good cop” who insists that the approaches are engaged in common projects after all. We look at various ways in which the gaps between them have been bridged, and we consider the prospects for bridging them further. We conclude that this is an exciting time for epistemology, as the two traditions can learn, and have started learning, from each other. (shrink)

Human social intelligence comprises a wide range of complex cognitive and affective processes that appear to be selectively impaired in autistic spectrum disorders. The study of these neuro- developmental disorders and the study of canonical social intelligence have advanced rapidly over the last twenty years by investigating the two together. Specifically, studies of autism have provided important insights into the nature of ‘theory of mind’ abilities, their normal development and underlying neural systems. At the same time, the idea of impaired (...) development of the neurocognitive mechanisms underlying ‘theory of mind’ has shed new light on the nature of autistic disorders. This general approach is not restricted to the study of impairments but extends to mapping areas of social intelligence that are spared in autism. Here we investigate basic moral judgment and find that it appears to be substantially intact in children with autism who are severely impaired in ‘theory of mind’. At the same time, we extend studies of moral reasoning in normal development by way of a new control task, the ‘cry baby’ task. Cry baby scenarios, in which the distress of the victim is ‘unreasonable’ or ‘unjustified,’ do not elicit moral condemnation from normally developing preschoolers or from children with autism. Judgments of moral transgressions in which the victim displays distress are therefore not likely the result of a simple automatic reaction to the distress and more likely involve moral reasoning. Mapping the cognitive co-morbidity patterns of disordered development should encompass both impairments and sparings because both will be needed to make sense of the neural and genetic levels. (shrink)

Ancient Chinese and Greek thinkers alike were preoccupied with the moral value of music; they distinguished between good and bad music by looking at the music’s effect on moral character. The idea can be understood in terms of two closely related questions. Does music have the power to affect the ethical character of either listener or performer? If it does, is it better as music for doing so? I argue that an affirmative answers to both questions are more plausible than (...) it might seem at first. (shrink)

A comprehensive introduction to the ways in which meaning is conveyed in language. Alan Cruse covers semantic matters, but also deals with topics that are usually considered to fall under pragmatics. A major aim is to highlight the richness and subtlety of meaning phenomena, rather than to expound any particular theory.

Biomedical science has been remarkably successful in explaining illness by categorizing diseases and then by identifying localizable lesions such as a virus and neoplasm in the body that cause those diseases. Not surprisingly, researchers have aspired to apply this powerful paradigm to addiction. So, for example, in a review of the neuroscience of addiction literature, Hyman and Malenka (2001, p. 695) acknowledge a general consensus among addiction researchers that “[a]ddiction can appropriately be considered as a chronic medical illness.” Like other (...) diseases, “Once addiction has taken hold, it tends to follow a chronic course.” (Koob and La Moal 2006, p. ?). Working from this perspective, much effort has gone into characterizing the symptomology of addiction and the brain changes that underlie them. Evidence for involvement of dopamine transmission changes in the ventral tegmental area (VTA) and nucleus accumbens (NAc) have received the greatest attention. Kauer and Malenka (2007, p. 844) put it well: “drugs of abuse can co-opt synaptic plasticity mechanisms in brain circuits involved in reinforcement and reward processing”. Our goal in this chapter to provide an explicit description of the assumptions of medical models, the different forms they may take, and the challenges they face in providing explanations with solid evidence of addiction. <br>. (shrink)

A model-theoretic approach to the semantics of set-theoretic discourse.

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct (...) facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

Aesthetic internalism claims a link between judgement and motivation: aesthetic judgements bring with them motivations to act in characteristic ways. Critics object that there is a difference between merely liking something and judging it to be aesthetically good, and that it is our likings, not our aesthetic judgements, that motivate us. This paper develops a version of aesthetic internalism that can respond to this criticism. Wholehearted aesthetic judgements are characterized by stability, attention, and motivation. Making such judgements is an important (...) part of a good life, and so at least some aesthetic judgements are motivating. So we have reason to think that this version of aesthetic internalism is true. This paper defends wholehearted aesthetic internalism against objections, and assesses an argument from aesthetic internalism to aesthetic non-cognitivism. While wholehearted aesthetic internalism can only offer qualified support to non-cognitivism, it nonetheless offers a number of fruitful avenues for further work. (shrink)

Where $\underline{a}$ is a Turing degree and ξ is an ordinal $ , the result of performing ξ jumps on $\underline{a},\underline{a}^{(\xi)}$ , is defined set-theoretically, using Jensen's fine-structure results. This operation appears to be the natural extension through $(\aleph_1)^{L^\underline{a}}$ of the ordinary jump operations. We describe this operation in more degree-theoretic terms, examine how much of it could be defined in degree-theoretic terms and compare it to the single jump operation.

The topic of this essay is how non-realistic novels challenge our philosophical understanding of the moral significance of literature. I consider just one case: Joseph Heller’s Catch-22. I argue that standard philosophical views, based as they are on realistic models of literature, fail to capture the moral significance of this work. I show that Catch-22 succeeds morally because of the ways it resists using standard realistic techniques, and suggest that philosophical discussion of ethics and literature must be pluralistic if it (...) is to include all morally salient literature, and not just novels in the “Great Tradition” and their ilk. (shrink)

Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...) outstanding moral obligations. It is engaged scholarship because it required building relationships with affected persons and taking responsibility for his institution’s legacy, as well as transforming Wilson’s own outlook along the way. It is socially relevant philosophy and history of science because it brings to light issues that remain salient today, especially how eugenic themes are ubiquitous in societal discourse and evinced in everyday decisions. It is interdisciplinary because to accomplish this type of analysis requires intellectual gymnastics that range over diverse domains of research: from standpoint theory and disability studies to oral history and governmental policy; from the evolutionary biology of prosociality and variation to conceptual questions about the categorization of human traits and types. (shrink)

Compares and contrasts Open Theism with Theological Determinism, Molinism, and Process Theism.

In this article we revisit the concept of a profession. Definitions of the concept are readily encountered in the literature on professions and we have collected a sample of such definitions. From this sample we distil frequently occurring elements and ask whether a synthesis of these elements adequately explains the concept. We find that bringing the most frequently occurring elements together does not adequately address the reason that society differentiates professions from other occupations or activities -- why there is a (...) concept of ‘profession’ at all. We suggest an alternative approach that attempts to make sense of the concept at a more general level. This more philosophical approach employs analytical tools from Julius Kovesi, Patricia Hanna and Bernard Harrison to address the question of what is the point of the concept. (shrink)

I prove that the Boolean Prime Ideal Theorem is equivalent, under some weak set-theoretic assumptions, to what I will call the Cut-for-Formulas to Cut-for-Sets Theorem: for a set F and a binary relation |- on Power(F), if |- is finitary, monotonic, and satisfies cut for formulas, then it also satisfies cut for sets. I deduce the CF/CS Theorem from the Ultrafilter Theorem twice; each proof uses a different order-theoretic variant of the Tukey- Teichmüller Lemma. I then discuss relationships between various (...) cut-conditions in the absence of finitariness or of monotonicity. (shrink)

Morality is often thought of as non-rational or sub-rational. In Moral Notions, first published in 1967, Julius Kovesi argues that the rationality of morality is built into the way we construct moral concepts. In showing this he also resolves the old Humean conundrum of the relation between 'facts' and 'values'. And he puts forward a method of reasoning that might make 'applied ethics' (at present largely a hodge-podge of opinions) into a constructive discipline. Kovesi's general theory of concepts - important (...) in its own right - is indebted to his interpretation of Plato, and his three papers on Plato, first published here, explain this debt. This new edition of Moral Notions also includes a foreward by Philippa Foot, a biography of the author, and a substantial afterword in which the editors, Robert Ewin and Alan Tapper, explain the signficance of Kovesi's work. (shrink)

Divers presents a set of de re modal truths which, he claims, are inconvenient for Lewisean modal realism. We argue that there is no inconvenience for Lewis.

I explore the claim that “fictive imagining” – imagining what it is like to be a character – can be morally dangerous. In particular, I consider the controversy over William Styron’s imagining the revolutionary protagonist in his Confessions of Nat Turner. I employ Ted Cohen’s model of fictive imagining to argue, following a generally Kantian line of thought, that fictive imagining can be dangerous if one has the wrong motives. After considering several possible motives, I argue that only internally directed (...) motives can satisfy the moral concern. Finally, I suggest that when one has the right motives, fictive imagining is morally praiseworthy since it improves one’s ability to imagine the lives of others. (shrink)

Part 1 [Hodes, 2021] “looked under the hood” of the familiar versions of the classical propositional modal logic K and its intuitionistic counterpart. This paper continues that project, addressing some familiar classical strengthenings of K and GL), and their intuitionistic counterparts. Section 9 associates two intuitionistic one-step proof-theoretic systems to each of the just mentioned intuitionistic logics, this by adding for each a new rule to those which generated IK in Part 1. For the systems associated with the intuitionistic counterparts (...) of D and T, these rules are “pure one-step”: their schematic formulations does not use □ or ♢. For the systems associated with the intuitionistic counterparts of K4, etc., these rules meet these conditions: neither □ nor ♢ is iterated; none use both □ and ♢. The join of the two systems associated with each of these familiar logics is the full one-step system for that intuitionistic logic. And further “blended” intuitionistic systems arise from joining these systems in various ways. Adding the 0-version of Excluded Middle to their intuitionistic counterparts yields the one-step systems corresponding to the familiar classical logics. Each proof-theoretic system defines a consequence relation in the obvious way. Section 10 examines inclusions between these consequence relations. Section 11 associates each of the above consequence relations with an appropriate class of models, and proves them sound with respect to their appropriate class. This allows proofs of some failures of inclusion between consequence relations. Section 12 proves that the each consequence relation is complete or weakly complete, that relative to its appropriate class of models. The Appendix presents three further results about some of the intuitionistic consequence relations discussed in the body of the paper. For Keywords, see Part 1. (shrink)

I argue that metaphysical views of material objects should be understood as 'packages', rather than individual claims, where the other parts of the package include how the theory addresses 'recalcitant data', and that when the packages meet certain general desiderata - which all of the currently competing views *can* meet - there is nothing in the world that could make one of the theories true as opposed to any of the others.

Hume's contributions to discussions on causality and necessary connection are significant and influential. Yet they remain a source of ongoing debate among philosophers. The analysis in my book is an attempt to dissipate some of the perplexities that surround these issues. The arguments here support what I call a subjectivist interpretation of Hume's views on necessary connection. My central thesis is the suggestion that Hume identifies necessary connection or power with a specific psychological dispositon of the mind "to carry our (...) thought from one object to another". In addition to explaining and exploring this thesis, I critically investigate Hume's arguments for his powerful epistemological paradigm. (shrink)

Proof uses forcing on perfect trees for 2-quantifier sentences in the language of arithmetic. The result extends to exact pairs for the hyperarithmetic degrees.

This article tackles the sole surviving ancient commentary on what was perhaps the second most important Platonic work, with special interest for the manner in which the ancients tackled the setting of Plato's dialogues, Socratic ignorance, Socratic eros, the central myth-like Palinode, and the question of oral as against written teaching.

Christopher Columbus Langdell has not only damaged the study of law with his three follies: his legal formalism, his redacted appellate case method, and his notion that legal practice taints the professor of law. His three follies have also impaired character development critical for legal actors. This Article focuses on four such critical character traits and virtues impaired by Langdell: (i) imagination, (ii) empathy, (ii) balance, and (iv) integrity. -/- This Article also calls out potential character issues with two professor (...) types inspired by Langdell: (v) the hazing professor who confuses intellectual rigor with intense discomfort and who uses the redacted appellate case method to inflict such discomfort at the expense of better pedagogy, and (vi) the professor without substantial practice experience who is substantially paid to teach what she has never practiced. -/- Agreeing with C.S. Pierce that the best argument is a cable rather than a chain, I end by weaving in a Langdell villanelle. I hope such a cable can help lift Langdell and his follies from legal education and the world. (shrink)

Cyclist Lance Armstrong cheated his way to seven Tour de France . Such cheating is wrong because it harms society. To explain how that harm affects all of us, I use Aristotle's ideas of virtue ethics to argue that Armstrong, despite his charitable work, is not a virtuous person. Virtue is to some extent determined by society, so we need to be clear that Armstrong is not a person to emulate. A society which does not clearly disapprove of vice is (...) less than it might otherwise be because a good society is one that encourages virtue in its citizens. (shrink)