Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

What’s so good about John Ames? The narrator of Marilynne Robinson’s Gilead has been much admired, but it’s far from obvious why. His life is quiet and unassuming, and has for the most part been uneventful in the extreme. In this chapter I draw on Iris Murdoch’s moral philosophy to explain the moral arc of the novel, and suggest that the novel in turn can shed light on Murdoch’s key ethical ideas. What is so notable about John Ames, I suggest, (...) is his commitment to seeing the world justly and lovingly—a commitment which for Murdoch is at the heart of virtuous agency. (shrink)

Is calculation possible without language? Or is the human ability for arithmetic dependent on the language faculty? To clarify the relation between language and arithmetic, we studied numerical cognition in speakers of Mundurukú, an Amazonian language with a very small lexicon of number words. Although the Mundurukú lack words for numbers beyond 5, they are able to compare and add large approximate numbers that are far beyond their naming range. However, they fail in exact arithmetic with numbers larger than 4 (...) or 5. Our results imply a distinction between a nonverbal system of number approximation and a language-based counting system for exact number and arithmetic. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Coronavirus disease 2019 can lead to respiratory failure. Some patients require extracorporeal membrane oxygenation support. During the current pandemic, health care resources in some cities have been overwhelmed, and doctors have faced complex decisions about resource allocation. We present a case in which a pediatric hospital caring for both children and adults seeks to establish guidelines for the use of extracorporeal membrane oxygenation if there are not enough resources to treat every patient. Experts in critical care, end-of-life care, bioethics, and (...) health policy discuss if age should guide rationing decisions. (shrink)

Taking pride in being better than others in some regard is not uncommon. In a recent paper, Christopher Morgan-Knapp argues that such pride is misguided: it ‘presents things as being some way they are not’. I argue that Morgan-Knapp's arguments do not succeed in showing that comparative pride is theoretically mistaken.

A concise review of skeptician in the Carterian model with a discussion of the reframing of the Cartesian paradigm by John McDowell in the 20th century.

What is common to all instances of friendship? Given their seemingly heterogeneous character, Phelan (2019. “Rethinking Friendship.” Inquiry) suggests that friendships are relationships that result from collaborative norm-manipulation. In this paper, I suggest that this proposal fails to account for all friendships without relying on the notion of some kind of care.

In a recent paper, Strabbing (2020) argues that forgiveness is openness to reconciliation relative to a relationship level. In this paper, we argue that the openness-to-reconciliation account of forgiveness does not constitute an improvement on the forswearing-resentment account. We argue that it does not fit well with our ordinary practices of forgiving and cannot allow for plausible cases of forgiveness without reconciliation. We also argue that the features Strabbing identifies as distinct advantages of her account are features of the forswearing-resentment (...) account as well. (shrink)

Two doxastically significant demands of friendship have been discussed in recent literature, a demand to be epistemically partial and a demand to take our friends seriously. Though less discussed than epistemic partialism, I suggest that the demand to take our friends seriously is motivated by similar cases and considerations, and can avoid key objections to epistemic partialism that have been raised. I further suggest that it does justice to what we care about in friendship, and thus is to be preferred.

‘Adams worlds’ are possible worlds that contain no creature whose life is not worth living or whose life is overall worse than in any other possible world in which it would have existed. Creating an Adams world involves no wrongdoing or unkindness towards creatures on the part of the creator. I argue that the notion of an Adams world is of little value in theodicy. Theists are not only committed to thinking that this world was created without wrongdoing or unkindness (...) but also must rule out the possibility that the world might have been better had God not existed. Nor is there much reason, independent of the availability of a satisfactory theodicy, for believing that the actual world is an Adams world. The need for a theodicy constructed along Leibnizian lines, incorporating the claim that this world is the best possible, is thus reinforced. (shrink)

In “The Best of All Possible Worlds” William E. Mann argues that some possible worlds are morally incommensurable with some others, because some choices are between incompatible alternatives that are themselves incommensurable. The best possible world must be better than, and hence commensurable with, every other world. So if anyone in the actual world ever faces a choice between incompatible alternatives that are morally incommensurable, this is not the best possible world. But it seems that some of us do, on (...) occasion, face such choices. So this is not the best possible world. (shrink)

The quantitative argument against the notion of a best possible world claims that, no matter how many worthwhile lives a world contains, another world contains more and is, other things being equal, better. Parfit’s ‘ Mere Addition Paradox ’ suggests that defenders of this argument must accept his ‘ Repugnant Conclusion ’ : that outcomes containing billions upon billions of lives barely worth living are better than outcomes containing fewer lives of higher quality. Several responses to the Paradox are discussed (...) and rejected as either inadequate or unavailable in a theistic context. The quantitative argument fails if some world is such that addition to it is not possible, i.e., if it is intensively infinite, as Liebniz claimed. If the notion of such a world is incoherent, then no world is quantitatively best and the quantitative argument succeeds, but only at the cost of embracing the Repugnant Conclusion. (shrink)

This poised and articulate volume addresses an area of pragmatist philosophy as yet relatively unexplored in pragmatism's welcome revival. Neopragmatism's preoccupation with changing philosophers' view of the relation between language (or as Rorty puts it: "vocabularies") and reality, has largely focussed their discussions on the 'metaphysics & epistemology', rather than the 'value' side of philosophy, apart from Rorty's brief flirtations with edifying Western political discourse. Yet the nature of truth in ethics has been a topic of keen discussion in recent (...) mainstream philosophy, and it's widely acknowledged that pragmatism has original and interesting things to say about truth. This book seeks to contribute in particular to discussions of objectivity in ethics which are arguably somewhat bogged down in a wealth of finely divergent terminologies and positions: prescriptivism, fictionalism, intuitionism, quasi-realism and expressivism, to name just a few. Heney organises her own discussion around a distinction between cognitivism and non-cognitivism about moral claims. (shrink)

If mourning is a proof of value, how could it be appropriate to move on when one has truly loved and valued someone? Assuming that it is appropriate to value others extremely highly – perhaps even infinitely – how could it ever make sense for one’s grief to abate? Do loss and proper mourning thus present us with a choice between living well and loving well? This paper aims to vindicate the pressing nature of these questions while arguing that we (...) do not need to choose between living well and loving well. It discusses how these questions become pressing, some empirical research seeming to imply that humans do not tend to love well at all, and finally, offers an explanation of why ceasing to mourn need not be a failure of love. In particular, we offer an account of how ceasing to mourn can be a fitting response to the object of love, as well as compatible with living well. (shrink)

The word “hacker” has an interesting double meaning: one vastly more widespread connotation of technological mischief, even criminality, and an original meaning amongst the tech savvy as a term of highest approbation. Both meanings, however, share the idea that hackers possess a superior ability to manipulate technology according to their will (and, as with God, this superior ability to exercise will is a source of both mystifying admiration and fear). This book mainly concerns itself with the former meaning. To Thomas (...) this simultaneously mystified and vilified, elusive set of individuals exemplifies “the performance of technology” xx), showing the way in which “the cultural, social and political history of the computer...is fraught with complexity and contradictions” ix). In fact, he claims that hacking is more a cultural than technological phenomenon, citing Heidegger’s, “[t]he essence of technology is not anything technological” (56). (shrink)

Remarks on naturalism--the belief that there is nothing besides the subway and its riders--and also on non-naturalism and supernaturalism, transcribed and edited from a notebook found on a subway train.

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

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)

Autorka nawiązuje do artykułu J.F. Lyotarda „A Few Words to Sing” w której filozof podejmuje się analizy utworu Sequenza III Luciano Berio napisanego i śpiewanego przez Cathy Bereberian. „A Few Words to Sing” jest przykładem podejmowania przez Lyotarda tematów muzycznych „na granicy”. W tym konkretnym przypadku autorka sugeruje, że wspomniana analiza bardzo dobrze wpisuje się w postulowane przez Lyotarda kategorie figury oraz oddania głosu [ofierze] w opozycji wobec tego co [czysto]estetyczne (resisting the aesthetic). Zainteresowania muzyczne Lyotarda, być może nie (...) tak wyeksponowane jak jego zainteresowania obrazem (choć kategorie figury i gestu okazują się łatwo przekraczać granice rodzajów sztuki) także bardzo wyraźnie wskazują na szczególny rodzaj [anty]estetyki uprawiany przez Lyotrada, gdzie udzielenie głosu ofierze staje się istotnym, jeśli nie podstawowym kryterium sztuki. (shrink)

I begin with an exposition of the two main variants of the Prosentential Theory of Truth (PT), those of Dorothy Grover et al. and Robert Brandom. Three main types of criticisms are then put forward: (1) material criticisms to the effect that (PT) does not adequately explain the linguistic data, (2) an objection to the effect that no variant of (PT) gives a properly unified account of the various occurrences of "true" in English, and, most importantly, (3) a charge (...) that the comparison with proforms is explanatorily idle. The last objection is that, given a complete semantic account of pronouns, proadjectives, antecedents, etc., together with a complete (PT), the essential semantic character of "true" could be deduced, but then, the idleness of the comparison with pronouns would be apparent. It turns out that objections (2) and (3) are related in the following way: the prosentential terminology is held to conceal the lack of unity in (PT), by describing the different data in the same terms ("proform", "antecedent", etc.). But this, I argue, is only a way of truly describing, rather than explaining, the data, these being certain relations of equivalence and consequence between sentences. I consider a language for which (PT) would be not only true, but also explanatory, but note that this language is very different from English. I end by showing that Robert Brandom's case that "is true" is not a predicate fails, and that his motivation for saying so is based on fallacious reasoning (namely, Boghossian's argument against deflationism). (shrink)

Cathy Mason (2020) argues – against my position in Phelan (2019) – that significant norm-manipulation is unnecessary for friendship. Instead, she holds that norm manipulation is a, perhaps omnipresent, causal result of the very feature I deny as necessary to friendship: mutual caring or love. Mason’s counter-examples allow for further explication of the norm-manipulation view of friendship. However, they do not constitute a compelling challenge to that view, because they do not seem to involve collaborative norm manipulation at all. (...) Instead, they are better described as cases in which people come to be subject to established cultural norms they were not previously subject to, because they voluntarily come to fall under a distinctive relationship relative to one another. (shrink)

What do we mean when we describe the history of the Caribbean as traumatic? Is it possible to use the term ‘trauma’ here in a more technical sense, or should we give it the less strict connotation of an extreme form of an event in which the past no longer stays just in the past and the future never ceases to demand something from the present? In this paper I analyze the image of the abyss, used by Édouard Glissant to (...) evoke poetically one of the beginnings of the Caribbean, as leading to a paradox on the attitude toward history: Caribbean communities have been burdened with a non-history that feels, at the same time, like too much history. I show that this image resembles the paradoxical structure of trauma developed in the works of Cathy Caruth, according to whom trauma is a paradoxical structure of experience in which the subject (or a community) is painfully possessed by an image that they have barely perceived and that is so minimal that it cannot be controlled. However, I argue, there are limits to this resemblance. I focus on the question whether the (traumatic) paradox is escapable in this region of the world, that is, whether Caribbean communities can be de-traumatized, and what are the connections of this possibility with the question, central to Glissant, of decolonization. In order to answer these questions, I analyze a central feature of the Caribbean history according to Glissant, transversality, to show in what way the paradox of history can be loosened. (shrink)

In Cathy Mason’s piece What’s Bad about Friendship with Bad People, she affirms that being friends with someone who has deep moral failings is itself corrupt. (529) Indeed her claim is true, but it is fallacious as she mistakenly ascribes the wrongfulness of such relationships to friends taking each other’s opinions seriously. But the mere consideration of unethical views is not a moral fault but a virtue and a skill. The real problem is that in befriending amoral people, we (...) by definition accept, approve of, and respect objectionable beliefs. (shrink)

This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and (...) Colin Klein identify the limitations of relying on forward and reverse inferences to cast light on the relation between cognitive functions and neural structures. There is reason to prefer Klein’s approach to that of Price and Friston’s. But Klein’s approach is neurocentric - it assumes that we ought to look solely at neural contexts to fix cognitive ontology. Using recent work on mindreading as a case study, we motivate adopting a radically different approach to cognitive ontology. Promoting the Protean Brain Hypothesis, we posit the possibility that we may need to look beyond the brain when deciding which functions are being performed in acts of cognition and in understanding how the brain contributes to such acts by adapting to circumstance. (shrink)

PHILIPPA RUTH FOOT was born on 3 October 1920, the second daughter of William Bosanquet, who had done mathematics at Cambridge and became the manager of a steelworks in Yorkshire, and Esther Cleveland, daughter of President Grover Cleveland. She was educated mainly at home in the country by governesses, and not well. She said, many years later, that, ‘unsurprisingly’, she had been left ‘extremely ignorant’, and when the last one, ‘who actually had a degree’, suggested to her that she (...) should go to Oxford, she had to work for it. She spent a year with an established Oxford entrance coach and took a correspondence course to acquire the necessary entrance Latin; the result was a place at Somerville College, where she went to read Philosophy, Politics and Economics (PPE) in 1939. (shrink)

Anselm’s ontological argument is an argument for the existence of God. This paper presents Iris Murdoch’s ontological argument for the existence of the Good. It discusses her interpretation of Anselm’s argument, her distinctive appropriation of it, as well as some of the merits of her version of the argument. In doing so, it also shows how the argument integrates some key Murdochian ideas: morality’s wide scope, the basicness of vision to morality, moral realism, and Platonism.

Many recent philosophers have been tempted by epistemic partialism. They hold that epistemic norms and those of friendship constitutively conflict. In this paper, I suggest that underpinning this claim is the assumption that friendship is not an epistemically rich state, an assumption that even opponents of epistemic partiality have not questioned. I argue that there is good reason to question this assumption, and instead regard friendship as essentially involving knowledge of the other. If we accept this account of friendship, the (...) possibility of epistemic partialism does not arise. (shrink)

Recent discussions of moral testimony have focused on the acceptability of forming beliefs on the basis of moral testimony, but there has been little acknowledgement of the limits to testimony's capacity to convey moral knowledge. In this paper I outline one such limit, drawing on Iris Murdoch's conception of private moral concepts. Such concepts, I suggest, plausibly play an important role in moral thought, and yet moral knowledge expressed in them cannot be testimonially acquired.

‘Rival creator’ arguments suggest that God must have created the best of all possible worlds. These arguments are analyzed and evaluated, and Leibniz’s position defended.

In der Korrespondenz mit Clarke ist Leibniz' Standardargument gegen die Annahme, daß Raum und Zeit absolut seien, daß Gott sich bei der Wahl des zu erschaffenden Universums gezwungen sähe, gegen das Prinzip des zureichenden Grundes zu verstoßen, wenn diese Annahme richtig wäre: Bloße Unterschiede in räumlicher und zeitlicher Hinsicht ergeben keinen Vorteilsunterschied, und da Gott nur aus Vorteilsgründen handelt, sind solche Unterschiede nicht möglich. Leibniz stellt dieses Argument als ausschließlich abhängig vom Prinzip des zureichenden Grundes dar, eine gängige Interpretation ist (...) aber, daß dies Prinzip determinierte Objekte göttlicher Wahl nur dann ergibt, wenn ein ergänzendes Prinzip von Kontingenz hinzutritt. Diese Auslegung muß falsch sein, wenn Leibniz hier authentisch bleibt, und insofern wäre doch das Prinzip des zureichenden Grundes eher als irgendein Prinzip des Besten Leibniz' Prinzip der Kontingenz. (shrink)

A graph-theoretic account of logics is explored based on the general notion of m-graph (that is, a graph where each edge can have a finite sequence of nodes as source). Signatures, interpretation structures and deduction systems are seen as m-graphs. After defining a category freely generated by a m-graph, formulas and expressions in general can be seen as morphisms. Moreover, derivations involving rule instantiation are also morphisms. Soundness and completeness theorems are proved. As a consequence of the generality of the (...) approach our results apply to very different logics encompassing, among others, substructural logics as well as logics with nondeterministic semantics, and subsume all logics endowed with an algebraic semantics. (shrink)

In a recent opinion paper, it was argued that individuals with multiple retractions or a record of academic misconduct should not serve as editors, including as editors-in-chief, on the editorial boards of scholarly or academic journals. As a first step towards appreciating how such a policy could be applied in practice, the presence of 30 individuals listed on the Retraction Watch Leaderboard on editorial boards was screened. Six cases are highlighted to gain an appreciation of the potential reputational risks that (...) journals and publishers might incur by including individuals with a tainted academic record on editorial boards. Given the reputational, legal and other risks associated with this type of assessment and decision, more formal positioning and guidance are needed by global ethics policy-related bodies such as COPE, the ICMJE, and the CSE, even more so in journals that claim to follow these organizations’ ethical guidelines. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Surprisingly little has been written about hedged assertion. Linguists often focus on semantic or syntactic theorizing about, for example, grammatical evidentials or epistemic modals, but pay far less attention to what hedging does at the level of action. By contrast, philosophers have focused extensively on normative issues regarding what epistemic position is required for proper assertion, yet they have almost exclusively considered unqualified declaratives. This essay considers the linguistic and normative issues side-by-side. We aim to bring some order and clarity (...) to thinking about hedging, so as to illuminate aspects of interest to both linguists and philosophers. In particular, we consider three broad questions. 1) The structural question: when one hedges, what is the speaker’s commitment weakened from? 2) The functional question: what is the best way to understand how a hedge weakens? And 3) the taxonomic question: are hedged assertions genuine assertions, another speech act, or what? (shrink)

Expert testimony figures in recent debates over how best to understand the norm of assertion and the domain-specific epistemic expectations placed on testifiers. Cases of experts asserting with only isolated second-hand knowledge (Lackey 2011, 2013) have been used to shed light on whether knowledge is sufficient for epistemically permissible assertion. I argue that relying on such cases of expert testimony introduces several problems concerning how we understand expert knowledge, and the sharing of such knowledge through testimony. Refinements are needed to (...) clarify exactly what principles are being tested by such cases; but once refined, such cases raise more questions than they answer. (shrink)

Recent epistemology has focused almost exclusively on propositional knowledge. This paper considers an underexplored area of epistemology, namely knowledge of persons: if propositional knowledge is a state of mind, consisting in a subject's attitude to a (true) proposition, the account developed here thinks of interpersonal knowledge as a state of minds, involving a subject's attitude to another (existing) subject. This kind of knowledge is distinct from propositional knowledge, but it exhibits a gradability characteristic of context-sensitivity, and admits of shifty thresholds. (...) It is supported by a wide range of unexplored linguistic data and intuitive cases; and it promises to illuminate debates within epistemology, philosophy of religion, and ethics. (shrink)

Some philosophers oppose recent arguments for the Knowledge Norm of Assertion by claiming that assertion, being an act much like any other, will be subject to norms governing acts generally, such as those articulated by Grice for the purpose of successful, cooperative endeavours. But in fact, Grice is a traitor to their cause; or rather, they are his dissenters, not his disciples. Drawing on Grice's unpublished papers, I show that he thought of asserting as a special linguistic act in need (...) of its own norm, and he tied his maxim of Quality to knowledge. I also develop a simple Gricean-inspired argument showing that the Quality maxim is not dependent on the Cooperative Principle. If it is not thus dependent, then the Cooperative Principle cannot be the explanation of, or source of normativity for, the Quality maxim. Thus, leveraging the insights informing the maxim of Quality actually provides the resources for a distinctive positive case that knowledge is the constitutive norm of assertion. (shrink)

Over the centuries, magicians have developed extensive knowledge about the manipulation of the human mind—knowledge that has been largely ignored by psychology. It has recently been argued that this knowledge could help improve our understanding of human cognition and consciousness. But how might this be done? And how much could it ultimately contribute to the exploration of the human mind? We propose here a framework outlining how knowledge about magic can be used to help us understand the human mind. Various (...) approaches—both old and new—are surveyed, in terms of four different levels. The first focuses on the methods in magic, using these to suggest new approaches to existing issues in psychology. The second focuses on the effects that magic can produce, such as the sense of wonder induced by seeing an apparently impossible event. Third is the consideration of magic tricks—methods and effects together—as phenomena of scientific interest in their own right. Finally, there is the organization of knowledge about magic into an informative whole, including the possibility of a science centered around the experience of wonder. (shrink)

This book examines a main theme in religious epistemology, namely, the possibility of knowledge of God. Most often philosophers consider the rationality or justification of propositional belief about God, particularly beliefs about the existence and nature of God; and they will assess the conditions under which, if there is a God, such propositional beliefs would be knowledge, particularly in light of counter-evidence or the availability of religious disagreement. This book surveys such familiar areas, then turns toward newer and less-developed terrain: (...) interpersonal epistemology, namely what it is to know another person. It then explores the prospects for understanding what it might take to know God relationally, the contours of which are significant for many theistic traditions. (shrink)