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)

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)

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)

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.

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://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)

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)

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)

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)

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)

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)

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)

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)

Logical consequence is typically construed as a metalinguistic relation between sentences. Deflationism is an account of logic that challenges this orthodoxy. In Williamson’s recent presentation of deflationism, logic’s primary concern is with universal generalizations over absolutely everything. As well as an interesting account of logic in its own right, deflationism has also been recruited to decide between competing logics in resolving semantic paradoxes. This paper defends deflationism from its most important challenge to date, due to Ole Hjortland. It then presents (...) two new problems for the view. Hjortland’s objection is that deflationism cannot discriminate between distinct logics. I show that his example of classical logic and supervaluationism depends on equivocating about whether the language includes a “definitely” operator. Moreover, I prove a result that blocks this line of objection no matter the choice of logics. I end by criticizing deflationism on two fronts. First, it cannot do the work it has been recruited to perform. That is, it cannot help adjudicate between competing logics. This is because a theory of logic cannot be as easily separated from a theory of truth as its proponents claim. Second, deflationism currently has no adequate answer to the following challenge: what does a sentence’s universal generalization have to do with its logical truth? I argue that the most promising, stipulative response on behalf of the deflationist amounts to an unwarranted change of subject. (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)

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)

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)

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)

Many think that the perceptual theory known as “conceptualism” cannot honor a common and intuitive constraint on concept acquisition—that we gain the initial power to deploy primitive concepts through experience. Their argument is: if experience involves the deployment of concepts, then one must possess the power to deploy those concepts prior to experience. I argue that the plausibility of this argument rests on a subtle equivocation. It’s true that conceptualism requires a particular kind of power to deploy concepts prior to (...) experience, but not the sort referenced in the intuitive constraint mentioned above. I end by proposing how the conceptualist might satisfy this constraint. I conclude that conceptualism is better situated to account for primitive concept acquisition than typically thought. (shrink)

Many theists believe both (1) that Heaven will be infinitely or maximally good for its residents and (2) that most humans will, eventually, reside in Heaven. Further, most theists believe (3) that human procreation is often all-things-considered morally permissible. I defend three novel arguments for the impermissibility of procreation predicated on the possibility of heavenly overpopulation. First, we shouldn’t be rude to hosts by bringing more people to a party than were invited, which we do if we continue to procreate. (...) Second, justice requires that the goods of Heaven be supremely good for those for whom heavenly existence is (even partially) compensatory, but if Heaven has a fixed and finite number of goods, each successful act (or enough acts) of procreation lowers the expected goodness for those persons and threatens to undermine justice. Third, we should choose the course of action with the least-worst outcome, and it would be worse to overpopulate Heaven than underpopulate it. (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)

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)

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)

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)

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)

According to attributor virtue epistemology (the view defended by Ernest Sosa, John Greco, and others), S knows that p only if her true belief that p is attributable to some intellectual virtue, competence, or ability that she possesses. Attributor virtue epistemology captures a wide range of our intuitions about the nature and value of knowledge, and it has many able defenders. Unfortunately, it has an unrecognized consequence that many epistemologists will think is sufficient for rejecting it: namely, it makes knowledge (...) depend on factors that aren't truth-relevant, even in the broadest sense of this term, and it also makes knowledge depend in counterintuitive ways on factors that are truth-relevant in the more common narrow sense of this term. As I show in this paper, the primary objection to interest-relative views in the pragmatic encroachment debate can be raised even more effectively against attributor virtue epistemology. (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)

The problem of evil is broadly considered to be one of the greatest intellectual threats to traditional brands of theism. And William Rowe’s 1979 formulation of the problem in “The Problem of Evil and Some Varieties of Atheism” is the most cited formulation in the contemporary philosophical literature. In this paper, we explore how the tools and resources of experimental philosophy might be brought to bear on Rowe’s seminal formulation, arguing that our empirical findings raise significant questions regarding the ultimate (...) success of Rowe’s argument. Such a result would be quite notable within philosophy of religion, since this is considered one of the most formidable arguments against theism. However, further testing is needed before any firm conclusions can be drawn. -/- In section 1, we elucidate Rowe’s formulation of the problem of evil and the intuitions that seem to underwrite it. In section 2, we explore how the tools and resources of experimental philosophy might be brought to bear on Rowe’s formulation, outlining our hypotheses and our methods for testing them before showcasing our results. In section 3, we discuss the philosophical import of our results–arguing that our results, when taken together, pose an initial challenge to Rowe’s seminal argument. (shrink)

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

In 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)

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)

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)

Kenneth Einar Himma (2009, 2016) argues that the existence of Hell renders procreation impermissible. Jason Marsh (2015) contends that problems of evil motivate anti-natalism. Anti-natalism is principally rejected for its perceived conflict with reproductive rights. I propose a theistic solution to the latter problem. Universalism says that all persons will, postmortem, eventually be eternally housed in Heaven, a superbly good place wherein harm is fully absent. The acceptance of universalism is now widespread, but I offer further reason to embrace one (...) variant of it. If universalism is true and there are opportunities to procreate in Heaven, then reproductive autonomy is largely preserved for everyone. Assuming Heaven is a harm-free place, there are no risks to children born in Heaven, unlike Earth or Hell. While this requires human persons to accept temporary restrictions on procreation during our premortem lives, the bulk of reproductive autonomy is preserved since one will have infinite opportunities to reproduce in Heaven. (shrink)

Adequate and inadequate ideas play a central role in Spinoza’s system. A number of recent commentators have suggested that the internality or externality of an idea’s immediate cause is a necessary and sufficient condition of the idea’s adequacy or inadequacy, respectively. I show that this thesis is subject to counterexample and briefly explore the significance of this critique for recent interpretations. I offer an alternative interpretation on which adequate and inadequate ideas are characterized by the manner in which they grasp (...) their objects. Adequate ideas conceive of their objects as following from God. Inadequate ideas conceive of their objects as affecting the body at a time and place. (shrink)

Alexander Campbell once declared “a solemn league and covenant” between philosophy and common sense. Campbell’s pronouncement is representative of a broader trend in the Restorationist movement to look favorably on the common sense response to skepticism—a response originating in the work of Scottish philosopher and former minister Thomas Reid. I recount the tumultuous history between philosophy and common sense followed by the efforts of Campbell and Reid to reunite them. Turning to the present, I argue that an epistemic principle known (...) as phenomenal conservatism best embodies the core insights contained within Reid and Campbell's common sense response to skepticism. I finish by arguing for phenomenal conservatism. (shrink)

Philosophy of religion is dominated by Christianity and by Christians. This, in conjunction with the historically anti-LGBTQIA bent of Christian thinking, has resulted in the exclusion of less dominant and often marginalized perspectives, including queer ones. This essay charts a normative direction for Christian philosophers and for philosophy of religion, a subfield they dominate. First, given some of the unique ways Christian philosophy and philosophers have unjustly harmed queers, Christian philosophers as a group have a responsibility to communities their group (...) has oppressed to prioritize the interests of the oppressed. Second, Christian philosophers must prioritize queer voices by creating or furthering academic space for those who publicly and professionally identify as queer. Third, Christian philosophers must mitigate their criticisms of queers and queerness where such criticisms would undermine their efforts toward compensatory/reparative justice. (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)

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)

Most epistemologists hold that knowledge entails belief. However, proponents of this claim rarely offer a positive argument in support of it. Rather, they tend to treat the view as obvious and assert that there are no convincing counterexamples. We find this strategy to be problematic. We do not find the standard view obvious, and moreover, we think there are cases in which it is intuitively plausible that a subject knows some proposition P without—or at least without determinately—believing that P. Accordingly, (...) we present five plausible examples of knowledge without (determinate) belief, and we present empirical evidence suggesting that our intuitions about these scenarios are not atypical. (shrink)

We criticize the approach of covenantal epistemology to religious epistemology as articulated by Scott Oliphint from the perspective of phenomenal conservatism.

Mark Murphy argues that the property identity version of divine command theory, coupled with the doctrine that God has freedom in commanding, violates the supervenience of the moral on the nonmoral. In other words, they permit two situations exactly alike in nonmoral facts to differ in moral facts. I give three arguments to show that a divine command theorist of this sort can consistently affirm moral supervenience. Each argument contends that there are always nonmoral differences between worlds with different divine (...) commands. If there are such nonmoral differences, then there’s no conflict between divine command theory and moral supervenience. (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)

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.

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)

Many people who have achieved a certain age, live in a certain sense of bewilderment. How can people, companies, and countries do the things they do? How can our neighbors, our co-workers, our bosses, our employees, and our family members do the things that they do? How can the opposing political party do the things they do? Why are things so unfair? It just doesn’t make sense! -/- Many people think that if we just got together and talked it through, (...) we can resolve our differences. But man has been talking for thousands of years. That isn’t working. This paper is not about resolving those differences. It is about understanding why those differences exist. (shrink)

We criticize the proper functionalist approach to religious epistemology as articulated by Tyler McNabb from the perspective of phenomenal conservatism.

Graham Harman judges science and common sense in terms of the crude philosophical criteria of another age and finds them lacking in knowledge of reality. He posits a shadowy "withdrawn" realm of real objects in order to explain the discrepancies between his naive abstract model of knowledge as access and the concrete reality of the sciences. Works such as THE QUADRUPLE OBJECT, THE THIRD TABLE and BELLS AND WHISTLES, like the whole of his philosophy, are the record of Harman noticing (...) the discrepancies, but refusing to revise the model. His solution is a dead-end, the timid, nostalgic, and fundamentally misleading propounding of an antiquated epistemology under the cover of a "new" ontology. (shrink)

We critique MacIntyre's traditions-based perspectivalist approach to religious epistemology as articulated by Erik Baldwin from the perspective of phenomenal conservatism.

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