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.

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)

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)

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)

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)

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)

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.

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

This is a (likely incomplete) transcendental phenomenology of professional failure. You can read it, if you like. Or don't.

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)

Is knowledge consistent with literally any credence in the relevant proposition, including credence 0? Of course not. But is credence 0 the only credence in p that entails that you don’t know that p? Knowledge entails belief (most epistemologists think), and it’s impossible to believe that p while having credence 0 in p. Is it true that, for every value of ‘x,’ if it’s impossible to know that p while having credence x in p, this is simply because it’s impossible (...) to believe that p while having credence x in p? If so, is it possible to believe that p while having (say) credence 0.4 in p? These questions aren’t standard epistemological fare, at least in part because many epistemologists think their answers are obvious, but they have unanticipated consequences for epistemology. Let ‘improbabilism’ name the thesis that it’s possible to know that p while having a credence in p below 0.5. Improbabilism will strike many epistemologists as absurd, but careful reflection on these questions reveals that, if improbabilism is false, then all of the most plausible theories of knowledge are also false. Or so I argue in this paper. Since improbabilism is widely rejected by epistemologists (at least implicitly), this paper reveals a tension between all of the most plausible theories of knowledge and a widespread assumption in epistemology. (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 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)

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)

Pacifism is the view that necessarily, the nonconsensual harming of pro tanto rights-bearers is all-things-considered morally impermissible. Critics of pacifism frequently point to common moral intuitions about self-defenders and other-defenders as evidence that pacifism is false and that self- and other-defense are often morally justified. I call this the Justification View and defend its rival, the Excuse View. According to the latter, a robust view of moral excuse adequately explains the common moral intuitions invoked against pacifism and is compatible with (...) pacifism. The paper proceeds in five steps. First, I identify ten intuitive data points that require explanation. Second, I introduce the justification/excuse distinction. Third, I demonstrate the Excuse View’s equal explanatory power with respect to the intuitive data. Fourth, I defend the Fair Use Principle: When evaluating the plausibility of rival theories J and E, the use of datum d’s full intuitive force against E and for J is epistemically permissible only if (i) d is better explained by J than E and (ii) no intuitive components of d are equally well-explained by E. Finally, I conclude that the conjunction of pacifism and the Excuse View renders the intuitive defense of the Justification View largely moot, and that this is a substantial victory for pacifism. (shrink)

Contextualists and pragmatists agree that knowledge-denying sentences are contextually variable, in the sense that a knowledge-denying sentence might semantically express a false proposition in one context and a true proposition in another context, without any change in the properties traditionally viewed as necessary for knowledge. Minimalists deny both pragmatism and contextualism, and maintain that knowledge-denying sentences are not contextually variable. To defend their view from cases like DeRose and Stanley's high stakes bank case, minimalists like Patrick Rysiew, Jessica Brown, and (...) Wayne Davis forward ‘warranted assertability maneuvers.’ The basic idea is that some knowledge-denying sentence seems contextually variable because we mistake what a speaker pragmatically conveys by uttering that sentence for what she literally says by uttering that sentence. In this paper, I raise problems for the warranted assertability maneuvers of Rysiew, Brown, and Davis, and then present a warranted assertability maneuver that should succeed if any warranted assertability maneuver will succeed. I then show how my warranted assertability maneuver fails, and how the problem with my warranted assertability maneuver generalizes to pragmatic responses in general. The upshot of my argument is that, in order to defend their view from cases like DeRose and Stanley's high stakes bank case, minimalists must prioritize the epistemological question whether the subjects in those cases know over linguistic questions about the pragmatics of various knowledge-denying sentences. (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)

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)

Brian Leftow has argued in significant detail for a timeless conception of God. However, his work has been interacted with less than one might expect, especially given that some have contended that divine timelessness should be put to death and buried. Further, the work that has critically interacted with Leftow does a very poor job at discrediting it, or so I will contend. As we shall see, the main reason for this is either because what is central to Leftow’s view (...) is not affected by the objection, or because Leftow provides another way of getting his theory off the ground. Why, then, do so many objections miss the mark? I suspect it’s because many struggle to understand Leftow’s view and what is central to it. As such, one of the main goals of this paper will be to make Leftow’s account more accessible and to elucidate the main elements of the theory, whilst also providing responses to the main objections raised against his view. The overall result of this, I hope, will be a more fruitful examination of Leftow’s view in the future. (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)

A prominent argument for internalism appeals to the requirement that justified beliefs not be accidentally true from the subject’s perspective. Bergmann’s dilemma remains the most troublesome obstacle to those who defend internalism in this way. In a word, what is required for a belief to be non-accidental? If we require the subject to justifiably believe that one is aware of something counting in its favor, then a vicious regress results and one is never justified in believing anything. But we cannot (...) require less since beliefs can satisfy any lesser requirements and still be accidental. I argue here that phenomenal conservatism, which appeals to “seemings,” shows a way out of this dilemma. The key is that seemings, via their unique phenomenal character, make their content non-accidental for us simply by our being conscious of them and without our having to reflect on their significance. This is an important step in the larger project of re-envisioning traditional arguments for access internalism as supporting mentalism instead. (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)

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)

I argue that some of the most prominent interpretations of Reid's response to skepticism marginalize a crucial aspect of his thought: namely, that our common sense beliefs meet whatever normative standards of rationality the skeptic might fairly demand of them. This should be seen as supplementary to reliabilist or proper functionalist interpretations of Reid, which often ignore this half of the story. I also show how Reid defends the rationality of believing first principles by appealing to their naturalness and irresistibility. (...) The resulting interpretation supplies Reid with a more satisfying and formidable response to the skeptic than interpretations currently offer. (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)

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)

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. The NCRO ontology is free and open to all users. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Suppose that we think it important that people have the chance to enjoy autonomous lives. An obvious corollary of this thought is that people should, if they want it, have control over the time and manner of their deaths, either ending their own lives, or by securing the help of others in doing so. So, generally, and even if we overall think that the practice should not be legalized on other grounds, it looks like common sense to think that considerations (...) of autonomy tell at least somewhat in favour of legalizing at least some acts of suicide and voluntary euthanasia. In this paper, I argue that, in fact, when we scrutinize the reasons for most end of life decisions, it turns out that they are seriously problematic from the point of view of autonomy. Full autonomy requires that we are responsible for the consequences of our decisions, and responsibility is precluded by non-voluntariness, which is to say decisions made because there are no acceptable alternatives. Since most end of life decisions are made for precisely this reason, it looks as though most such decisions are non-voluntary, and therefore undermine our autonomy: a discomforting and paradoxical claim. I argue that we should respond by taking the paradox to illuminate the context required by an autonomy-respecting framework for legalizing assisted suicide and euthanasia. People should have a legal right to a reasonable choice about when and how to die. However, this must go hand in hand with institutions that ensure, as far as possible, that such choices are made against a background which ensures, as far as possible, that people choose death clear-sightedly and not because nothing else is acceptable. (shrink)

A plausible principle about the felicitous use of indicative conditionals says that there is something strange about asserting an indicative conditional when you know whether its antecedent is true. But in most contexts there is nothing strange at all about asserting indicative conditionals like ‘If Oswald didn’t shoot Kennedy, then someone else did’. This paper argues that the only compelling explanation of these facts requires the resources of contextualism about knowledge.

Take a strip of paper with 'once upon a time there'‚ written on one side and 'was a story that began'‚ on the other. Twisting the paper and joining the ends produces John Barth’s story Frame-Tale, which prefixes 'once upon a time there was a story that began'‚ to itself. I argue that the ability to understand this sentence cannot be explained by tacit knowledge of a recursive theory of truth in English.

One prominent argument in international law and religious thought for abolishing capital punishment is that it violates individuals’ right to life. Notably, this _right-to-life argument_ emerged from normative and legal frameworks that recognize deadly force against aggressors as justified when necessary to stop their unjust threat of grave harm. Can capital punishment be necessary in this sense—and thus justified defensive killing? If so, the right-to-life argument would have to admit certain exceptions where executions are justified. Drawing on work by Hugo (...) Bedau, I identify a thought experiment where executions are justified defensive killing but explain why they cannot be in our world. A state’s obligations to its prisoners include the _obligation to use nonlethal incapacitation_ (ONI), which applies as long as prisoners pose no imminent threat. ONI precludes executions for reasons of future dangerousness. By subjecting the right-to-life argument to closer scrutiny, this article ultimately places it on firmer ground. (shrink)

This article explains and defends a novel idea about how people can be misled by a discussion topic, even if the discussion itself does not explicitly involve the making of false claims. The crucial aspect of this idea is that people are liable to infer, from the fact that a particular topic is being discussed, that this topic is important. As a result, they may then be led to accept certain beliefs about the state of the world they consider necessary (...) for the topic’s importance. What the article calls “importance misrepresentation” occurs when these beliefs about the state of the world are false or otherwise mistaken. The article explores different ways in which importance misrepresentation can occur, and it uses this idea to help clarify and strengthen some well‐known criticisms of the topic choices of academic philosophers. (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.

Recently, I presented evidence that there are two broad kinds of dehumanization: descriptive dehumanization and normative dehumanization. An individual is descriptively dehumanized when they are perceived as less than fully human in the biological-species sense; whereas an individual is normatively dehumanized when they are perceived as lacking a deep-seated commitment to good moral values. Here, I develop the concept of normative dehumanization by addressing skepticism about two hypotheses that are widely held by dehumanization researchers. The first hypothesis is that dehumanization (...) is distinct from mere dislike and other non-dehumanizing attitudes. The second hypothesis is that dehumanization is an important predictor of intergroup hostility. Across four studies, I found evidence that normative dehumanization is distinct from mere dislike, and denials of ideal humanness. I also found that it is a unique predictor of intergroup hostility. These findings suggest that research into dehumanization and intergroup hostility will benefit from recognizing the distinction between descriptive and normative dehumanization. (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)

A puzzling feature of paradigmatic cases of dehumanization is that the perpetrators often attribute uniquely human traits to their victims. This has become known as the “paradox of dehumanization.” We address the paradox by arguing that the perpetrators think of their victims as human in one sense, while denying that they are human in another sense. We do so by providing evidence that people harbor a dual character concept of humanity. Research has found that dual character concepts have two independent (...) sets of criteria for their application, one of which is descriptive and one of which is normative. Across four experiments, we found evidence that people deploy a descriptive criterion according to which being human is a matter of being a Homo sapiens; as well as a normative criterion according to which being human is a matter of possessing a deep-seated commitment to do the morally right thing. Importantly, we found that people are willing to affirm that someone is human in the descriptive sense, while denying that they are human in the normative sense, and vice versa. In addition to providing a solution to the paradox of dehumanization, these findings suggest that perceptions of moral character have a central role to play in driving dehumanization. (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)