Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (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)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Deep brain stimulation has been of considerable interest to bioethicists, in large part because of the effects that the intervention can occasionally have on central features of the recipient’s personality. These effects raise questions regarding the philosophical concept of authenticity. In this article, we expand on our earlier work on the concept of authenticity in the context of deep brain stimulation by developing a diachronic, value-based account of authenticity. Our account draws on both existentialist and essentialist approaches to authenticity, and (...) Laura Waddell Ekstrom’s coherentist approach to personal autonomy. In developing our account, we respond to Sven Nyholm and Elizabeth O’Neill’s synchronic approach to authenticity, and explain how the diachronic approach we defend can have practical utility, contrary to Alexandre Erler and Tony Hope’s criticism of autonomy-based approaches to authenticity. Having drawn a distinction between the authenticity of an individual’s traits and the authenticity of that person’s values, we consider how our conception of authenticity applies to the context of anorexia nervosa in comparison to other prominent accounts of authenticity. We conclude with some reflections on the prudential value of authenticity, and by highlighting how the language of authenticity can be invoked to justify covert forms of paternalism that run contrary to the value of individuality that seems to be at the heart of authenticity. (shrink)

“Bioconservatives” in the human enhancement debate endorse the conservative claim that we should reject the use of biotechnologies that enhance natural human capacities. However, they often ground their objections to enhancement with contestable claims about human nature that are also in tension with other common tenets of conservatism. We argue that bioconservatives could raise a more plausible objection to enhancement by invoking a strain of conservative thought developed by G.A. Cohen. Although Cohen’s conservatism is not sufficient to fully revive the (...) bioconservative objection, we argue that it can be supplemented by an account of reasonable partiality for humanity in a way that provides further support to the bioconservative position in a manner congruous with broader conservatism. We propose that the idea of partiality to humanity can buttress the bioconservative objection into its strongest possible form. However, we conclude by arguing that, even in this form, the objection cannot do all the work that bioconservatives expect of it. (shrink)

Three professors reflect on the experience of creating a learning community of 22 students by linking courses in Literature and Ethics. The project demonstrates practical strategies for incorporating feminist scholarship and pedagogy into the core curriculum and for integrating core courses from diverse disciplines.

Religious traditions can be sources of values and attitudes supporting the liberal polity in ways that political theorizing and conceptions of public reason often fail to recognize. moreover, religious traditions can give support through the ways reason is crucial to their self-understanding. one understanding of Judaism is examined as an example. Also, the particularism of traditions can encourage commitment to universally valid values and ideals. reason’s role in Judaism and other religious traditions makes possible constructive interaction between those traditions and (...) between religious and secular thought. exclusion of religiously grounded considerations from the discourse and deliberations of liberal polities can be counterproductively illiberal. (shrink)

If science relates only to the objectifiable, how can it relate to consciousness? I.

In Faith and Humility, Jonathan Kvanvig argues for an account of two virtues that balance, or provide correction for, the other: faith and humility. Faith is the disposition to act in service of an ideal, a disposition that remains despite difficulties or setbacks. One can, however, pursue distorted ideals or pursue them in the wrong way—with unquestioning zeal, for example. Humility, which helps to correct this extreme, is the disposition to attend to the value of one’s aims and the (...) extent of one’s contribution toward accomplishing them. To establish these accounts, Kvanvig first argues for a method that directs his arguments, and he then develops the accounts as he articulates and responds to alternative views. In what follows, instead of summarizing the book chapter by chapter, I provide a summary of Kvanvig’s positions and his arguments for them as they are eventually developed throughout the book. (shrink)

The recovery of ancient skepticism in the sixteenth century had broad consequences in various intellectual domains, including fictional discourse. In the following centuries several authors echoed skeptical philosophical discourse and made literary use of skepticism. Jonathan Swift (1667-1745) is inserted in the hall of the modern writers who echoed and assimilated the skeptical tradition. Satires as A Tale of a Tub (1704), The Battle of Books (1704) and Gulliver's Travels (1726) are framed with marks of skepticism. Thus, my purpose (...) is to present a study on the incorporation of skeptical aspects and arguments in Swift's fictional and satirical discourse. I will try to show that Swift assimilates and uses artifices of skeptical discourse, and therefore, given his relation and knowledge of this tradition, has a place in the history of skeptical thinking. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona (...) fide boundaries yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find (...) in the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto. (shrink)

The 18th-century American philosopher Jonathan Edwards argues that nothing endures through time. I analyze his argument, paying particular attention to a central principle it relies on, namely that “nothing can exert itself, or operate, when and where it is not existing”. I also consider what I supposed to follow from the conclusion that nothing endures. Edwards is sometimes read as the first four-dimensionalist. I argue that this is wrong. Edwards does not conclude that things persist by having different temporal (...) parts; he concludes that nothing persists. (shrink)

Commentary on Crowe's metaethics and his theory of law as a goodness-fixing kind.

In this paper we investigate composition models of incarnation, according to which Christ is a compound of qualitatively and numerically different constituents. We focus on three-part models, according to which Christ is composed of a divine mind, a human mind, and a human body. We consider four possible relational structures that the three components could form. We argue that a ‘hierarchy of natures’ model, in which the human mind and body are united to each other in the normal way, and (...) in which they are jointly related to the divine mind by the relation of co-action, is the most metaphysically plausible model. Finally, we consider the problem of how Christ can be a single person even when his components may be considered persons. We argue that an Aristotelian metaphysics, according to which identity is a matter of function, offers a plausible solution: Christ's components may acquire a radically new identity through being parts of the whole, which enables them to be reidentified as parts, not persons. (shrink)

Our generation is turning to mentoring as an instrument of God to repair the ruin of our personal losses.

Public reason as a political ideal aims to reconcile reasonable disagreement; however, is public reason itself the object of reasonable disagreement? Jonathan Quong, David Estlund, Andrew Lister, and some other philosophers maintain that public reason is beyond reasonable disagreement. I argue this view is untenable. In addition, I consider briefly whether or not two main versions of the public reason principle, namely, the consensus version and the convergence version, need to satisfy their own requirements. My discussion has several important (...) implications for the debate on public reason. (shrink)

The topic of this article is the ontology of practical reasons. We draw a critical comparison between two views. According to the first, practical reasons are states of affairs; according to the second, they are propositions. We first isolate and spell out in detail certain objections to the second view that can be found only in embryonic form in the literature – in particular, in the work of Jonathan Dancy. Next, we sketch possible ways in which one might respond (...) to each one of these objections. A careful evaluation of these complaints and responses, we argue, shows that the first view is not as obviously compelling as it is thought by Dancy. Indeed, it turns out that the view that practical reasons are propositions is by no means unworkable and in fact, at least under certain assumptions, explicit considerations can be made in favour of a propositional construal of reasons. (shrink)

Debates between political liberals and liberal perfectionists have been reinvigorated by Jonathan Quong’s Liberalism Without Perfection. In this paper I argue that certain forms of perfectionism can rebut or evade Quong’s three central objections – that perfectionism is manipulative, paternalistic, and illegitimate. I then argue that perfectionists can defend an ‘internal conception’ of perfectionism, parallel in structure to Quong’s ’internal conception’ of political liberalism, but with a different conception of the justificatory constituency. None of Quong’s arguments show that his (...) view should be preferred to this perfectionist internal conception. It can thus equally claim to achieve ‘justification to all reasonable citizens’. (shrink)

Even among those who find lethal defense against non-responsible threats, innocent aggressors, or justified aggressors justified even in one to one cases, there is a debate as to what the best explanation of this permissibility is. The contenders in this debate are the liability account, which holds that the non-responsible or justified human targets of the defensive measures are liable to attack, and the justified infringement account, which claims that the targets retain their right not to be attacked but may (...) be attacked anyway, even in one to one situations. Given that we normally think that rights are trumps, this latter claim is counter-intuitive and rather surprising, and therefore in need of justification and explanation. So far only Jonathan Quong has actually tried to provide an explanation; however, I will argue that his explanation fails and that Quong’s own account of liability is misguided. I then address Helen Frowe’s critique of the liability account. She makes the important concession that the tactical bomber has to compensate his victims, but she tries to block the conclusion that he must therefore be liable. I will demonstrate that her attempt to explain away liability fails once that concession is made. (shrink)

This review confirms Herman’s work as a praiseworthy contribution to East-West and comparative philosophical literature. Due credit is given to Herman for providing English readers with access to Buber’s commentary on, a personal translation of, the Chuang-Tzu; Herman’s insight into the later influence of I and Thou on Buber’s understanding of Chuang-Tzu and Taoism is also appropriately commended. In latter half of this review, constructive criticisms of Herman’s work are put forward, such as formatting inconsistencies, a tendency toward verbosity and (...) jargon, and a neglect of seemingly important hermeneutical issues. Such issues, seemingly substantive but neglected by Herman, are the influence of Buber’s prior familiarity with Hasidic teachings on his encounter with Chuang-Tzu, as well as the prevalence of Hasidic and Taoist thought in Buber’s conception of good and evil. (shrink)

This paper evaluates Jonathan Quong’s attempt to defend a version of political liberalism from the asymmetry objection. I object that Quong’s defence relies on a premise that has not been adequately supported and does not look as if it can be given adequate support.

For Berkeley, minds are not Cartesian spiritual substances because they cannot be said to exist (even if only conceptually) abstracted from their activities. Similarly, Berkeley's notion of mind differs from Locke's in that, for Berkeley, minds are not abstract substrata in which ideas inhere. Instead, Berkeley redefines what it means for the mind to be a substance in a way consistent with the Stoic logic of 17th century Ramists on which Leibniz and Jonathan Edwards draw. This view of mind, (...) I conclude, is definitely not the bundle theory that some critics have portrayed it as being. (shrink)

In a widely read essay, “For the Law, Neuroscience Changes Nothing and Everything,” Joshua Greene and Jonathan Cohen argue that the advance of neuroscience will result in the widespread rejection of free will, and with it – of retributivism. They go on to propose that consequentialist reforms are in order, and they predict such reforms will take place. We agree that retributivism should be rejected, and we too are optimistic that rejected it will be. But we don’t think that (...) such a development will have much to do with neuroscience – it won’t, because neuroscience is unlikely to show that we have no free will. We have two main aims in this paper. The first is to rebut various aspects of the case against free will. The second is to examine the case for consequentialist reforms. We take Greene and Cohen’s essay as a hobbyhorse, but our criticisms are applicable to neurodeterministic anti-free-willism in general. We first suggest that Greene and Cohen take proponents of free will to be committed to an untenable homuncular account of agency. But proponents of free will can dispense with such a commitment. In fact, we argue, it is Greene and Cohen who work with an overly simple account of free will. We sketch a more nuanced conception. We then turn to the proposal for consequentialist reforms. We argue that retributivism will fall out of favor not as a consequence of neuroscience-driven rejection of free will, but rather, as a result of a familiar feature of moral progress – the expanding circle of concern. In short, retributivism can and must die, but neuroscience will not kill it – humanity will. (shrink)

Berkeley's immaterialism has more in common with views developed by Henry More, the mathematician Joseph Raphson, John Toland, and Jonathan Edwards than those of thinkers with whom he is commonly associated (e.g., Malebranche and Locke). The key for recognizing their similarities lies in appreciating how they understand St. Paul's remark that in God "we live and move and have our being" as an invitation to think to God as the space of discourse in which minds and ideas are identified. (...) This way of speaking about God, adapted by Karl Barth and Paul Tillich, opens up new ways to think about the relation between God and finite minds. (shrink)

According to Jonathan Kvanvig, the practice of taking back one’s assertion when finding out that one has been mistaken or gettiered fails to speak in favour of a knowledge norm of assertion. To support this claim, he introduces a distinction between taking back the content of the assertion, and taking back the speech act itself. This paper argues that Kvanvig’s distinction does not successfully face close speech-act-theoretic scrutiny. Furthermore, I offer an alternative diagnosis of the target cases sourced in (...) the normativity of action. (shrink)

In a recent paper, Jonathan Quong tries to offer further support for “the proposition that there are sometimes agent-relative prerogatives to harm nonliable persons.” In this brief paper, I will demonstrate that Quong’s argument implicitly relies on the premise that the violinist in Thomson’s famous example has a right not to be unplugged. Yet, first, Quong provides no argument in support of this premise; and second, the premise is clearly wrong. Moreover, throughout his paper Quong just question-beggingly and without (...) argument assumes that one cannot lose rights in other ways than by one’s own responsible action. I conclude that Quong has failed to provide further support for his thesis. (shrink)

The article begins with Jonathan Dancy’s attempt to refute the Humean Theory of Motivation. It first spells out Dancy’s argument for his alternative position, the view he labels ‘Pure Cognitivism’, according to which what motivate are always beliefs, never desires. The article next argues that Dancy’s argument for his position is flawed. On the one hand, it is not true that desire always comes with motivation in the agent; on the other, even if this was the case, it would (...) still not follow that desire is identical with the state of being motivated. When this negative work is done, the article turns to some positive, albeit admittedly tentative remarks about what sort of cognitivist theory of motivation one should endorse. The aim at this point is not to present a brand new theory, but rather to sketch an alternative that stems from what Dancy himself says and is in line with many of his endorsed commitments in other areas. In this way, by moving beyond Pure Cognitivism, the paper sketches a different, but still ‘Dancyesque’ theory of motivation. (shrink)

Instead of focusing on the Malebranche-Edwards connection regarding occasionalism as if minds are distinct from the ideas they have, I focus on how finite minds are particular expressions of God's will that there be the distinctions by which ideas are identified and differentiated. This avoids problems, created in the accounts of Fiering, Lee, and especially Crisp, about the inherently idealist character of Edwards' occasionalism.

Jonathan Lowe has argued that a particular variation on C.I. Lewis' notion of strict implication avoids the paradoxes of strict implication. We show that Lowe's notion of implication does not achieve this aim, and offer a general argument to demonstrate that no other variation on Lewis' notion of constantly strict implication describes the logical behaviour of natural-language conditionals in a satisfactory way.

Jonathan Quong proposes the following “Stringency Principle” for proportionality in self-defense: “If a wrongful attacker threatens to violate a right with stringency level X, then the level of defensive force it is proportionate to impose on the attacker is equivalent to X.” I adduce a counter-example that shows that this principle is wrong. Furthermore, Quong assumes that what determines the stringency of a person’s right is exclusively the amount of force that one would have to avert from someone else (...) in order to have a necessity justification for one’s transgressing the right in order to avert said force. Yet, Quong provides no argument as to why, first, the stringency of a right should be measured exclusively with reference to permissible rights-infringement; and second, he provides no explanation as to why the permissibility of the rights-infringement should be established with reference to “someone else,” namely with reference to an “innocent person,” instead of with reference to the person against whom the right in question is actually being held: the aggressor. I argue that the latter option is certainly the more plausible one, but so amended the stringency principle will be unable to adjudicate any substantive questions about proportionality in self-defense. In particular, Quong’s account cannot “explain” – contrary to what Quong claims – the allegedly intuitive judgment that one must not kill in defense of property or in order to avoid minor injuries. (shrink)

The Emotions chapter (XXV) in James' Principles of Psychology traverses the entire range of experienced emotions from the “coarser” and more instinctual to the “subtler” emotions intimately involved in cognitive, moral, and aesthetic aspects of life. But Principles limits himself to an account of emotional consciousness and so there are few direct discussions in the text of Principles about what later came to be called moral psychology, and fewer about anything resembling philosophical ethics. Still, James’ short section on the subtler (...) emotions, when read in connection with his later philosophical writings, still provides insight on James’ views about how human emotion colors our moral psychology and agency. The paper tries to articulate how James' somatic account of emotion adds significantly to contemporary discussions at the borders of moral psychology and philosophy: discussions over the foreground/background distinction, emotional temperament, emotional learning, moral imagination, and selfhood and narrativity. The final section focuses on the neo-Jamesian character of "new sentimentalist" moral psychologists. Among the substantial connections I discuss between James and 1) between Jonathan Haidt’s “social intuitionism” and 2) Jesse Prinz’s "emotionism" are the critiques that they each share of the pretensions of hard universalist ethical theories. (shrink)

Joanna Mary Firth and Jonathan Quong argue that both an instrumental account of liability to defensive harm, according to which an aggressor can only be liable to defensive harms that are necessary to avert the threat he poses, and a purely noninstrumental account which completely jettisons the necessity condition, lead to very counterintuitive implications. To remedy this situation, they offer a “pluralist” account and base it on a distinction between “agency rights” and a “humanitarian right.” I argue, first, that (...) this distinction is spurious; second, that the conclusions they draw from this distinction do not cohere with its premises; third, that even if one granted the distinction, Firth’s and Quong’s implicit premise that you can forfeit your agency rights but not your “humanitarian right” is unwarranted; fourth, that their attempt to mitigate the counterintuitive implications of their own account in the Rape case relies on mistaken ad-hoc assumptions; fifth, that even if they were successful in somewhat mitigating said counterintuitive implications, they would still not be able to entirely avoid them; and sixth, that even in the unlikely case that none of these previous five critical points are correct, Firth and Quong still fail to establish that aggressors can be liable to unnecessary defensive harm since they fail to establish that unnecessary harm can ever be defensive in the first place. (shrink)

This article is a joint critical notice of Sean McKeever and Michael Ridge's book Principled Ethics and Jonathan Dancy's book Ethics Without Principles.

This paper criticizes an influential argument from Thomas Nagel’s THE POSSIBILTIY OF ALTRUISM, an argument that plays a foundational role in the philosophies of (at least) Philippa Foot, John McDowell and Jonathan Dancy. Nagel purports to prove that a person can be can be motivated to perform X by the belief that X is likely to bring about Y, without a causally active or biffy desire for Y. If Cullity and Gaut are to be believed (ETHICS AND PRACTICAL REASONING) (...) this is widely regarded within the practical reasoning industry as an established fact. My thesis is a simple one. Nagel’s argument is an abject failure and the philosophies that are founded on it are built upon sand. There is a little bit of rather amateurish X-Phi at the end, but I don’t want readers to get too excited about this as it is essentially icing on the cake. This paper is not primarily an exercise in Experimental Philosophy but in Baby Logic, and it’s central thesis is a logical one, namely that Nagel (to put the point politely) fails to prove his thesis. (shrink)

I hope to show that, although belief is subject to two quite robust forms of agency, "believing at will" is impossible; one cannot believe in the way one ordinarily acts. Further, the same is true of intention: although intention is subject to two quite robust forms of agency, the features of belief that render believing less than voluntary are present for intention, as well. It turns out, perhaps surprisingly, that you can no more intend at will than believe at will.

This paper argues for a methodological point that bears on a relatively long-standing debate concerning collective beliefs in the sense elaborated by Margaret Gilbert: are they cases of belief or rather of acceptance? It is argued that epistemological accounts and distinctions developed in individual epistemology on the basis of considering the individual case are not necessarily applicable to the collective case or, more generally, uncritically to be adopted in collective epistemology.