The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

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)

Behavior oftentimes allows for many possible interpretations in terms of mental states, such as goals, beliefs, desires, and intentions. Reasoning about the relation between behavior and mental states is therefore considered to be an effortful process. We argue that people use simple strategies to deal with high cognitive demands of mental state inference. To test this hypothesis, we developed a computational cognitive model, which was able to simulate previous empirical findings: In two-player games, people apply simple strategies at first. They (...) only start revising their strategies when these do not pay off. The model could simulate these findings by recursively attributing its own problem solving skills to the other player, thus increasing the complexity of its own inferences. The model was validated by means of a comparison with findings from a developmental study in which the children demonstrated similar strategic developments. (shrink)

Previous work in Game Studies has centered on several loci of investigation in seeking to understand virtual gameworlds. First, researchers have scrutinized the concept of the virtual world itself and how it relates to the idea of “the magic circle”. Second, the field has outlined various forms of experienced “presence”. Third, scholarship has noted that the boundaries between the world of everyday life and virtual worlds are porous, and that this fosters a multiplicity of identities as players identify both with (...) themselves-offline and themselves-in-game. Despite widespread agreement that these topics are targets for research, so far those working on these topics do not have mutually agreed-upon framework. Here we draw upon the work of Alfred Schutz to take up this call. We provide a phenomenological framework which can be used to describe the phenomena of interest to Game Studies, as well as open new avenues of inquiry, in a way acceptable and useful to all. This helps to distinguish the core of the field from the supplemental theoretical and critical commitments which characterize diverse approaches within the field. (shrink)

Helen Frowe (2014) depicts the following fictional case: Fran is being raped by Eric and can’t stop him with violent resistance. Nevertheless, she resists and breaks Eric’s wrist. The infliction of defensive harm on Eric is intuitively permissible, yet it runs counter to the dominant view that defensive harms must stand a reasonable chance of success. Call this the Success Condition (SC). To solve this problem, Daniel Statman (2008) contends that even if Victim’s defensive harms fail to prevent her rape, (...) they do prevent the destruction of another good, her honor, and thus SC is satisfied. Recently, Joseph Bowen (2016) has critiqued Statman’s proposal by showing that honor-based justifications for defensive harming are too permissive. In this paper, I contend that Statman’s proposal is too restrictive. First, I review Statman’s accounts of honor, dishonor, and non-honor. Second, I argue that Statman’s account requires Fran’s honor to be lost or damaged if she doesn’t resist—a highly offensive conclusion about rape victims. Third, I explain why the best alternative to this (i.e., allowing Fran’s honor to be maintained either way) satisfies SC but not the necessity condition. I conclude that we ought to reject Statman’s solution. (shrink)

In this paper, we illustrate some serious difficulties involved in conveying information about uncertain risks and securing informed consent for risky interventions in a clinical setting. We argue that in order to secure informed consent for a medical intervention, physicians often need to do more than report a bare, numerical probability value. When probabilities are given, securing informed consent generally requires communicating how probability expressions are to be interpreted and communicating something about the quality and quantity of the evidence for (...) the probabilities reported. Patients may also require guidance on how probability claims may or may not be relevant to their decisions, and physicians should be ready to help patients understand these issues. (shrink)

Alvin Plantinga theorizes the existence of a sensus divinitatis – a special cognitive faulty or mechanism dedicated to the production and non-inferential justification of theistic belief. Following Chris Tucker, we offer an evidentialist-friendly model of the sensus divinitatis whereon it produces theistic seemings that non-inferentially justify theistic belief. We suggest that the sensus divinitatis produces these seemings by tacitly grasping support relations between the content of ordinary experiences (in conjunction with our background evidence) and propositions about God. Our model offers (...) advantages such as eliminating the need for a sui generis religious faculty, harmonizing the sensus divinitatis with prominent theories in the cognitive science of religion, and providing a superior account of natural revelation. (shrink)

Early moderns such as Locke and Descartes thought we could guarantee the justification of our beliefs, even in worlds most hostile to their truth, if only we form those beliefs with sufficient care. That is, they thought it possible for us to be impeccable with respect to justification. This principle has traditionally been used to argue for internalism. By placing all of the normatively relevant conditions in our minds, we ensure reflective access to what those norms require of us and (...) so sustain the possibility of impeccability (unlike externalism). However, recent challenges to transparency leave this reasoning vulnerable. In response, I show how impeccability can be sustained without requiring transparency. The account only works if we define internal states as those directly accessible to our rational belief forming systems. I argue that this sort of causal internalism, while somewhat revisionary, preserves traditional motivations for internalism while avoiding problems faced by other varieties. The result is a renewed argument for internalism that simultaneously moves us away from access internalism and towards a species of mentalism. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

According to the Standard View, a doctor who withdraws life-sustaining treatment does not kill the patient but rather allows the patient to die—an important distinction, according to some. I argue that killing can be understood in either of two ways, and given the relevant understanding, the Standard View is insulated from typical criticisms. I conclude by noting several problems for the Standard View that remain to be fully addressed.

I offer a novel two-stage reconstruction of Hume’s general-point-of-view account, modeled in part on his qualified-judges account in ‘Of the Standard of Taste.’ In particular, I argue that the general point of view needs to be jointly constructed by spectators who have sympathized with (at least some of) the agents in (at least some of) the actor’s circles of influence. The upshot of the account is two-fold. First, Hume’s later thought developed in such a way that it can rectify the (...) problems inherent in his Treatise account of the general point of view. Second, the proposed account provides the grounds for an adequate and well-motivated modest ideal observer theory of the standard of virtue. (shrink)

Arguably, the original conception of epistemic justification comes from Descartes and Locke, who thought of justification deontologically. Moreover, their deontological conception was especially strict: there are no excuses for unjustified beliefs. Call this the “classical deontologist” conception of justification. As the original conception, we ought to accept it unless proven untenable. Nowadays, however, most have abandoned classical deontologism as precisely that—untenable. It stands accused of requiring doxastic voluntarism and normative transparency. My goal is to rescue classical deontologism from these accusations. (...) I show how, given a specific form of internalism coupled with a plausible theory of epistemic blame, we can be blameworthy for all of our (non-exempt) unjustified beliefs without transparency or voluntarism. The result is that the classical deontological conception of justification should regain its privileged status. (shrink)

Logical pluralism is the view that there is more than one correct logic. A key objection to logical pluralism is that it collapses into monism. The core of the Collapse Objection is that only the pluralist’s strongest logic does any genuine normative work; since a logic must do genuine normative work, this means that the pluralist is really a monist, who is committed to her strongest logic being the one true logic. This paper considers a neglected question in the collapse (...) debate: what is it for a logic to do genuine normative work? As well as having wider upshot for the connection between logic and normativity, grappling with this question provides a new response to the Collapse Objection on behalf of the pluralist. I suggest that we should allow logics to generate pro tanto reasons in a way that bears not just on combinations of attitudes but on how an agent’s attitudes are based on one another. This motivates adopting normative principles that allow the pluralist’s weaker logics to earn their normative keep. Rather than being ad hoc, these principles capture a sense in which good reasoning goes beyond the consistency of an agent’s attitudes. Good reasoning is also concerned with how an agent’s attitudes are based on one another. (shrink)

I defend the feasibility of a medical conscience in the following sense: a medical professional can object to the prevailing medical norms because they are incorrect as medical norms. In other words, I provide an account of conscientious objection that makes use of the idea that the conscience can issue true normative claims, but the claims in question are claims about medical norms rather than about general moral norms. I further argue that in order for this line of reasoning to (...) succeed, there needs to be an internal morality of medicine that determines what medical professionals ought to do qua medical professionals. I utilize a constructivist approach to the internal morality of medicine and argue that medical professionals can conscientiously object to providing treatment X, if providing treatment X is not in accordance with norms that would have been constructed, in light of the end of medicine, by the appropriate agents under the appropriate conditions. (shrink)

Subjectivists think that our well-being is grounded in our subjective attitudes. Many such views are vulnerable to variations on the ‘paradox of desire’, where theories cannot make determinate judgements about the well-being of agents who take a positive valuing attitude towards their life going badly. However, this paradox does not affect all subjectivist theories; theories grounded on agents’ prudential values can avoid it.This paper suggests a new paradox for subjectivist theories which has a wider scope, and includes such prudential judgement (...) theories. I outline the new paradox and show how two plausible idealisztions (coherence and consideration) will not help. Subjectivists about well-being must either add an additional idealization that can solve the paradox of judgement or explain why such paradoxes do not constitute serious objections to a theory of well-being. (shrink)

According to hedonism about well-being, lives can go well or poorly for us just in virtue of our ability to feel pleasure and pain. Hedonism has had many advocates historically, but has relatively few nowadays. This is mainly due to three highly influential objections to it: The Philosophy of Swine, The Experience Machine, and The Resonance Constraint. In this paper, I attempt to revive hedonism. I begin by giving a precise new definition of it. I then argue that the right (...) motivation for it is the ‘experience requirement’ (i.e., that something can benefit or harm a being only if it affects the phenomenology of her experiences in some way). Next, I argue that hedonists should accept a felt-quality theory of pleasure, rather than an attitude-based theory. Finally, I offer new responses to the three objections. Central to my responses are (i) a distinction between experiencing a pleasure (i.e., having some pleasurable phenomenology) and being aware of that pleasure, and (ii) an emphasis on diversity in one’s pleasures. (shrink)

Doxastic involuntarists have paid insufficient attention to two debates in contemporary epistemology: the permissivism debate and the debate over norms of assertion and belief. In combination, these debates highlight a conception of belief on which, if you find yourself in what I will call an ‘equipollent case’ with respect to some proposition p, there will be no reason why you can’t believe p at will. While doxastic involuntarism is virtually epistemological orthodoxy, nothing in the entire stock of objections to belief (...) at will blocks this route to doxastic voluntarism. Against the backdrop of the permissivism debate and the literature on norms of belief and assertion, doxastic involuntarism emerges as an article of faith, not the obvious truth it’s usually purported to be. (shrink)

A book chapter (about 8,000 words, plus references) summarizing Part One of Reasons and Persons, with particular attention to the Self-interest Theory, Consequentialism, Common-Sense Morality, and how critical scrutiny of Consequentialism and Common-Sense Morality points the way toward a unified theory of morality.

We criticize the classical evidentialist approach to religious epistemology as articulated by John DePoe from the perspective of phenomenal conservatism.

Logical pluralism is the view that there is more than one logic. Logical normativism is the view that logic is normative. These positions have often been assumed to go hand-in-hand, but we show that one can be a logical pluralist without being a logical normativist. We begin by arguing directly against logical normativism. Then we reformulate one popular version of pluralism—due to Beall and Restall—to avoid a normativist commitment. We give three non-normativist pluralist views, the most promising of which depends (...) not on logic’s normativity but on epistemic goals. (shrink)

ABSTRACT Katherine Dormandy argues that there is no partiality in virtuous faith. Partiality biases and leads to noetic entrenchment. In response, I contend there is an important sense in which virtuous faith is partial towards its object. Namely, it disposes one to perceive the object as more trustworthy and to rely on this partialist evidence in forming beliefs, even when the impartialist evidence points in the other direction. There are, after all, situations in which impartialist evidence is apt to mislead (...) or to fail to bring one to the truth. In such cases, faith attunes one to the subject’s true motivations and intentions. Here the partiality of faith constitutes a kind of social acuity or expertise, not a bias. Indeed, to lack faith in such situations—and to give impartialist evidence equal weight with the partial—might constitute a kind of bias against the subject, casting his or her actions in an overly negative light. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

I defend two collapsing or reductionist arguments against Weak Pro-Natalism (WPN), the view that procreation is generally merely permissible. In particular, I argue that WPN collapses into Strong Pro-Natalism (SPN), the view that procreation is generally obligatory. Because SPN conflicts with the dominant view that procreation is never obligatory, demonstrating that WPN collapses into or entails SPN establishes epistemic parity (at least as concerns reproductive liberty) between WPN and Anti-Natalism (AN), the view that procreation is always impermissible. First, I distinguish (...) between two moral goods: the good of procreation itself and the good of procreative potential. Second, I contend that the average moral agent is obligated to assist needy children via adoption, fostering, or other financial or interpersonal support. Third, I present the first collapsing argument: If an agent’s justification for not assisting needy children is preservation of their resources (financial or interpersonal) for their actual future offspring, that justification is preserved only if they eventually and actually procreate. Thus, their eventual procreation is morally obligatory, and SPN follows. Fourth, I present the second collapsing argument, which assumes procreative potential as the relevant good: If an agent’s justification for not assisting needy children is preservation of their resources for their potential future offspring, that justification holds only if (a) the objective or subjective valuation of the opportunity is of the relevant type and valence to justify not assisting needy children and (b) the agent sincerely values the opportunity. Fifth, I argue that (a) is unsatisfied and that while (b) is satisfied in most cases, it entails that most agents are obligated to desire or be behaviorally disposed to pursue procreation for themselves (i.e., SPN). Thus, I conclude that both actual procreation and procreative potential are either insufficient justifications for not assisting needy children or that they entail obligatory pro-reproductive attitudes or behaviors. (shrink)

Physicalism is incompatible with what is known as the possibility of zombies, that is, the possibility of a world physically like ours, but in which there are no conscious experiences. But it is compatible with what is known as the possibility of ghosts, that is, the possibility of a world which is physically like ours, but in which there are additional nonphysical entities. In this paper we argue that a revision to the traditional definition of physicalism designed to accommodate the (...) possibility of ghosts inadvertently accommodates what is known as the possibility of inverted spectra, that is, the possibility of a world which is physically like ours, but in which colour experience is inverted. This consequence is unwelcome, because it is widely agreed that the possibility of inverted spectra is incompatible with physicalism. We argue for a revised definition of physicalism which resolves this problem. We then use our definition to argue that physicalism is not compatible with what is known as the possibility of blockers, that is, the possibility of a world which is physically like ours, but in which additional nonphysical entities have prevented the existence of conscious experience. This undermines Stephan Leuenberger's attempt to defend physicalism from arguments which purport to establish the possibility of zombies. (shrink)

We suggest that the emerging field of the conservation humanities can play a valuable role in biodiversity protection in Papua New Guinea (PNG), where most land remains under collective customary clan ownership. As a first step to mobilising this scholarly field in PNG and to support capacity development for PNG humanities academics, we conducted a landscape review of PNG humanities teaching and research relating to biodiversity conservation and customary land rights. We conducted a systematic literature review, a PNG teaching programme (...) review, and a series of online workshops between the authors (10 PNG-based, 7 UK-based). We found a small but notable amount of PNG research and teaching focused on biodiversity conservation or customary land rights. This included explicit discussion of these topics in 8 of 156 PNG-authored humanities texts published 2010-2020 and related teaching content in the curricula of several different humanities-based programmes. We discuss current barriers to PNG academic development. The growth of fully fledged in-country conservation humanities will require a joint collaborative effort by PNG researchers, who are best placed to carry out such work, and researchers from abroad who can access resources to support the process. (shrink)

The recent explosion of philosophical papers on Confederate and Colonialist statues centers on a central question: When, if ever, is it permissible to admire a person? This paper contends it’s not just Confederates and slavers whose reputations are on the line, but also pacifists like Martin Luther King, Jr., and Daisy Bates whose commitments to pacifism meant they were unwilling to save others using defensive violence, including others they talked into endangering themselves for the sake of racial equality. Other things (...) being equal, that’s gravely immoral if pacifism is false, and we shouldn’t admire people guilty of grave immorality. So, it appears that we shouldn’t admire Bates or King, which is counterintuitive. To solve this problem, I explore several possibilities: that only selective traits of Bates and King are admirable, that Bates and King are admirable despite their grave immorality, and that Bates and King are admirable by virtue of their integrity. However, each of these proposals fails: the first because it inadequately captures our moral phenomenology (we admire people, not just their traits), the second because it ignores the extent to which gravely immoral commitments are constitutive of a person’s moral character, and the third because we ought not to admire people for acting on their immoral beliefs. The paper concludes, first, that either pacifists like Bates and King aren’t admirable or they are, and the latter presupposes the truth of pacifism. Second, I borrow from Vanessa Carbonell’s ratcheting-up argument from moral sainthood to argue that pacifists like Bates and King provide epistemic defeaters to the objection that pacifism is unreasonably costly. Thus, not only are pacifists admirable only if they’re right—they are right. (shrink)

Virtue epistemology is among the dominant influences in mainstream epistemology today. An important commitment of one strand of virtue epistemology – responsibilist virtue epistemology (e.g., Montmarquet 1993; Zagzebski 1996; Battaly 2006; Baehr 2011) – is that it must provide regulative normative guidance for good thinking. Recently, a number of virtue epistemologists (most notably Baehr, 2013) have held that virtue epistemology not only can provide regulative normative guidance, but moreover that we should reconceive the primary epistemic aim of all education as (...) the inculcation of the intellectual virtues. Baehr’s picture contrasts with another well-known position – that the primary aim of education is the promotion of critical thinking (Scheffler 1989; Siegel 1988; 1997; 2017). In this paper – that we hold makes a contribution to both philosophy of education and epistemology and, a fortiori, epistemology of education – we challenge this picture. We outline three criteria that any putative aim of education must meet and hold that it is the aim of critical thinking, rather than the aim of instilling intellectual virtue, that best meets these criteria. On this basis, we propose a new challenge for intellectual virtue epistemology, next to the well-known empirically-driven ‘situationist challenge’. What we call the ‘pedagogical challenge’ maintains that the intellectual virtues approach does not have available a suitably effective pedagogy to qualify the acquisition of intellectual virtue as the primary aim of education. This is because the pedagogic model of the intellectual virtues approach (borrowed largely from exemplarist thinking) is not properly action-guiding. Instead, we hold that, without much further development in virtue-based theory, logic and critical thinking must still play the primary role in the epistemology of education. (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)

A number of philosophers, going back at least to Kierkegaard, argue that to have faith in something is, in part, to have a passion for that thing—to possess a lasting, formative disposition to feel certain positive patterns of emotion towards the object of faith. I propose that (at least some of) the intellectual dimensions of faith can be modeled in much the same way. Having faith in a person involves taking a certain perspective towards the object of faith—in possessing a (...) lasting, formative disposition for things to seem as though the object of faith is worthy of one’s trust. After developing the view, I briefly discuss its epistemic implications. I suggest that, by systematically reorienting how one experiences the world, faith can actually change one’s total body of evidence (or perhaps even how one weighs that evidence), thereby altering what one is justified in believing about the object of faith. (shrink)

According to attitudinal theories of pleasure and pain, what makes a given sensation count as a pleasure or a pain is just the attitudes of the experiencing agent toward it. In a previous article, I objected to such theories on the grounds that they cannot account for pleasures and pains whose subjects are entirely unaware of them at the time of experience. Recently, Chris Heathwood and Fred Feldman, the two leading contemporary defenders of attitudinal theories, have responded to this objection, (...) in very different ways. In this paper, I reconstruct and evaluate these responses. My conclusion is that neither response succeeds. (shrink)

Two problems seem to plague Adam Smith’s account of sympathy and approbation in The Theory of Moral Sentiments (TMS). First, Smith’s account of sympathy at the beginning of TMS appears to be inconsistent with the account of sympathy at the end of TMS. In particular, it seems that Smith did not appreciate the distinction between ‘self-oriented sympathy’ and ‘other-oriented sympathy’, that is, between imagining being oneself in the actor’s situation and imagining being the actor in the actor’s situation. Second, Smith’s (...) account of approbation, according to which a sentiment of approval arises when there is recognition of concordance between the spectator’s sympathetic passion and the actor’s original passion, seems to face the following problem: since the spectator attains both his own sympathetic passion and the actor’s original passion by sympathizing with the actor, the sympathetic passion of the spectator and the original passion of the actor will necessarily be identical. Therefore, Smith’s account of approbation requires that the spectator utilize both self-oriented and other-oriented sympathy (‘the double-sympathy model of approbation’). I offer a novel developmental account of sympathy in TMS that renders Smith’s account of sympathy consistent and allows for the utilization of the double-sympathy model of approbation. (shrink)

A clear and provocative introduction to the ethics of COVID-19, suitable for university-level students, academics, and policymakers, as well as the general reader. It is also an original contribution to the emerging literature on this important topic. The author has made it available Open Access, so that it can be downloaded and read for free by all those who are interested in these issues. Key features include: -/- A neat organisation of the ethical issues raised by the pandemic. An exploration (...) of the many complex interconnections between these issues. A succinct case for a continued lockdown until we develop a vaccine. An original account of the Deep Moral Problem of the Pandemic, and a Revolutionary Argument for how we should change society post-pandemic. References to, and engagement with, many of the best writings on the pandemic so far (both in popular media and academic journals). -/- ISBN: 978-0-6489016-0-0. (shrink)

Physicians frequently ask whether they should give patients what they want, usually when there are considerations pointing against doing so, such as medicine’s values and physicians’ obligations. It has been argued that the source of medicine’s values and physicians’ obligations lies in what has been dubbed “the internal morality of medicine”: medicine is a practice with an end and norms that are definitive of this practice and that determine what physicians ought to do qua physicians. In this paper, I defend (...) the claim that medicine requires a morality that is internal to its practice, while rejecting the prevalent characterization of this morality and offering an alternative one. My approach to the internal morality of medicine is constructivist in nature: the norms of medicine are constructed by medical professionals, other professionals, and patients, given medicine’s end of “benefitting patients in need of prima facie medical treatment and care.” I make the case that patients should be involved in the construction of medicine’s morality not only because they have knowledge that is relevant to the internal morality of medicine—namely, their own values and preferences—but also because medicine is an inherently relational enterprise: in medicine the relationship between physician and patient is a constitutive component of the craft itself. The framework I propose provides an authoritative morality for medicine, while allowing for the incorporation, into that very morality, of qualified deference to patient values. (shrink)

An influential way of distinguishing inferential from non-inferential processes appeals to representational states: an agent infers a conclusion from some premises only if she represents those premises as supporting that conclusion. By contrast, when some premises merely cause an agent to believe the conclusion, there is no relevant representational state. While promising, the appeal to representational states invites a regress problem, first famously articulated by Lewis Carroll. This paper develops a novel account of inference that invokes representational states without succumbing (...) to regress. The key move is to reject the tempting idea that the relevant representational states are causally prior to inferences. I argue, instead, that an inference constitutes the relevant representational state. To infer is thus—in the very drawing of the conclusion—to represent the premises as supporting the conclusion, and thereby to commit to that support relation. (shrink)

I explain why model theory is unsatisfactory as a semantic theory and has drawbacks as a tool for proofs on logic systems. I then motivate and develop an alternative, the truth-valuational substitutional approach (TVS), and prove with it the soundness and completeness of the first order Predicate Calculus with identity and of Modal Propositional Calculus. Modal logic is developed without recourse to possible worlds. Along the way I answer a variety of difficulties that have been raised against TVS and show (...) that, as applied to several central questions, model-theoretic semantics can be considered TVS in disguise. The conclusion is that the truth-valuational substitutional approach is an adequate tool for many of our logic inquiries, conceptually preferable over model-theoretic semantics. Another conclusion is that formal logic is independent of semantics, apart from its use of the notion of truth, but that even with respect to it its assumptions are minimal. (shrink)

It is natural to think that there is a tight connection between whether someone is responsible for some outcome and whether it is appropriate to hold her accountable for that outcome. And this natural thought naturally extends to health: if someone is responsible for her health, then, all else being equal, she is accountable for it. Given this, some have thought that responsibility for health has an important role to play in distributing the benefits and burdens of healthcare. But there (...) is a reason for caution. That health is influenced by social, economic, and environmental factors is a matter of consensus. And some have argued that in light of these social determinants of health, individuals are not typically responsible for their health, rendering inappropriate policies that employ a responsibility‐for‐health criterion. This debate implicates a number of overlapping concepts and questions that are often difficult to pull apart. And I worry that those who maintain that social determinants undermine responsibility for health have latched on to the wrong target. The social determinants of health are relevant to such policies, but, I argue, not by globally undermining responsibility. Rather, social determinants are sometimes responsibility‐undermining, sometimes responsibility‐preserving, and often relevant to whether we should hold individuals accountable for their health regardless of their responsibility. This calls for a more nuanced appraisal of the ways in which the social determinants of health are relevant to such policies. And here I attempt to provide one. (shrink)

I demonstrate that analogies, both explicit and implicit, between Wittgenstein’s discussion of rituals, aesthetics, and psychoanalysis (and, indeed, his own philosophical methodology) suggest that he entertained the idea that Freud’s psychoanalytic project, when understood correctly—that is, as a descriptive project rather than an explanatory-hypothetical one—provides a “surveyable representation” (übersichtliche Darstellung) of certain psychological facts (as opposed to psychological concepts). The consequences of this account are that it offers an explanation of Wittgenstein’s admiration for and self-perceived affinity to Freud, as well (...) as of his apparent “know-nothing approach” to empirical psychology. (shrink)

This paper attempts to evaluate the AIME project immanently, from the perspective of a participant, in terms of five criteria: digitality, diplomacy, religiosity, testability, and democracy. A sixth criterion runs through the other five: pluralism. I distinguish between AIME as project, as process, and as party line.

I build on Adam Smith’s account of the impartial spectator in The Theory of Moral Sentiments in order to offer a modest ideal observer theory of moral judgment that is adequate in the following sense: the account specifies the hypothetical conditions that guarantee the authoritativeness of an agent’s (or agents’) responses in constituting the standard in question, and, if an actual agent or an actual community of agents are not under those conditions, their responses are not authoritative in setting this (...) standard. However, in the account that I provide, the hypothetical conditions can themselves be constructed from the psychology and interactions of actual human beings. In other words, facts about the morally appropriate and inappropriate are determined from hypothetical conditions that––while agents in a given society might have yet to attain them––can be constructed from those agents’ shared experiences. Thus, the account offers both an attainable standard of moral judgment and a standard that can transcend the biases of the society which gave rise to it. I also defend the account against three challenges: (a) ideal observer theories do not offer the right kind of motivation to act on the verdicts of the ideal observer; (b) ideal observer theories cannot explain why the idealization in question is well-motivated and not objectionably ad hoc; (c) the standard used in ideal observer theories cannot be defended upon further reflection, because we would need a non-arbitrary, second-order standard to govern our reflection on the first-order standard of moral judgment. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Epistemic conservatism maintains that some beliefs are immediately justified simply because they are believed. The intuitive implausibility of this claim sets the burden of proof against it. Some epistemic conservatives have sought to lessen this burden by limiting its scope, but I show that they cannot remove it entirely. The only hope for epistemic conservativism is to appeal to its theoretical fruit. However, such a defense is undercut by the introduction of phenomenal conservatism, which accomplishes the same work from a (...) more intuitive starting point. Thus, if one opts for conservatism, better to choose the phenomenal kind. (shrink)

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

This paper defends the view, put roughly, that to think that p is to guess that p is the answer to the question at hand, and that to think that p rationally is for one’s guess to that question to be in a certain sense non-arbitrary. Some theses that will be argued for along the way include: that thinking is question-sensitive and, correspondingly, that ‘thinks’ is context-sensitive; that it can be rational to think that p while having arbitrarily low credence (...) that p; that, nonetheless, rational thinking is closed under entailment; that thinking does not supervene on credence; and that in many cases what one thinks on certain matters is, in a very literal sense, a choice. Finally, since there are strong reasons to believe that thinking just is believing, there are strong reasons to think that all this goes for belief as well. (shrink)

I argue that in addressing worries about the validity and reliability of implicit measures of social cognition, theorists should draw on research concerning “entitativity perception.” In brief, an aggregate of people is perceived as highly “entitative” when its members exhibit a certain sort of unity. For example, think of the difference between the aggregate of people waiting in line at a bank versus a tight-knit group of friends: The latter seems more “groupy” than the former. I start by arguing that (...) entitativity perception modulates the activation of implicit biases and stereotypes. I then argue that recognizing this modulatory role will help researchers to address concerns surrounding the validity and reliability of implicit measures. (shrink)

This paper provides an opinionated guide to discussions of acting and believing on the basis of reasons. I aim to bring closer together largely separate literatures in practical rea- son and in epistemology. I focus on three questions. First, is basing causing? Causal theories of basing remain popular despite the notorious Problem of Deviant Causal Chains. Causal theorists in both the epistemic and practical domains have begun to appeal to dispositions to try and solve the problem. Second, how unified are (...) acting and believing on the basis of reasons? I consider an important challenge to their unity due to Setiya. I sketch a response, which posits unity of causal structure across acting and believing on the basis of reasons. Third, how does acting or believing on the basis of a good reason relate to acting or believing on the basis of a reason simpliciter? I generalize a recent argument of Lord and Sylvan's to include acting as well as believing. The conclusion is that, for both believing and acting, ϕing on the basis of a good reason does not amount to ϕing on the basis of a reason that just so happens to be good. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Intellectualists disagree with anti-intellectualists about the relationship between knowledge and truth. According to intellectualists, this relationship is intimate. Knowledge entails true belief, and in fact everything required for knowledge is somehow relevant to the probability that the belief in question is true. According to anti-intellectualists, this relationship isn’t intimate. Or, at least, it’s not as intimate as intellectualists think. Factors that aren’t in any way relevant to the probability that a belief is true can make a difference to whether it (...) counts as knowledge. In this paper, I give a new argument for anti-intellectualism and draw out consequences of this argument for the pragmatic encroachment debate. The standard purist objection to pragmatism is that pragmatism entails anti-intellectualism. As I show, anti-intellectualism follows from premises that are plausible even if purism is true, so the standard purist objection to pragmatism fails. (shrink)