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)

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)

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.

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

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

As a non-cognitivist analysis of moral language, Charles Stevenson's sophisticated emotivism is widely regarded by moral philosophers as a substantial improvement over its historical antecedent, radical emotivism. None the less, it has come in for its share of criticism. In this essay, Leslie Allan responds to the key philosophical objections to Stevenson's thesis, arguing that the criticisms levelled against his meta-ethical theory rest largely on a too hasty reading of his works.

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)

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)

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)

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)

The lunar Three-Body problem is a famously intractable problem of Newtonian mechanics. The demand for accurate predictions of lunar motion led to practical approximate solutions of great complexity, constituted by trigonometric series with hundreds of terms. Such considerations meant there was demand for high speed machine computation from astronomers during the earliest stages of computer development. One early innovator in this regard was Wallace J. Eckert, a Columbia University professor of astronomer and IBM researcher. His work illustrates some interesting features (...) of the interaction between computers and astronomy. (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)

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 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)

This paper concerns would-be necessary connections between doxastic attitudes about the epistemic statuses of your doxastic attitudes, or ‘higher-order epistemic attitudes’, and the epistemic statuses of those doxastic attitudes. I will argue that, in some situations, it can be reasonable for a person to believe p and to suspend judgment about whether believing p is reasonable for her. This will set the stage for an account of the virtue of intellectual humility, on which humility is a matter of your higher-order (...) epistemic attitudes. Recent discussions in the epistemology of disagreement have assumed that the question of the proper response to disagreement about p concerns whether you ought to change your doxastic attitude towards p. My conclusion here suggests an alternative approach, on which the question of the proper response to disagreement about p concerns the proper doxastic attitude to adopt concerning the epistemic status of your doxastic attitude towards p.Send article to KindleTo send this article to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle. Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply. Find out more about the Kindle Personal Document Service.HIGHER-ORDER EPISTEMIC ATTITUDES AND INTELLECTUAL HUMILITYVolume 9, Issue 3Allan HazlettDOI: https://doi.org/10.1017/epi.2012.11Your Kindle email address Please provide your Kindle [email protected]@kindle.com Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Dropbox To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Dropbox. HIGHER-ORDER EPISTEMIC ATTITUDES AND INTELLECTUAL HUMILITYVolume 9, Issue 3Allan HazlettDOI: https://doi.org/10.1017/epi.2012.11Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Google Drive To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Google Drive. HIGHER-ORDER EPISTEMIC ATTITUDES AND INTELLECTUAL HUMILITYVolume 9, Issue 3Allan HazlettDOI: https://doi.org/10.1017/epi.2012.11Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Export citation Request permission. (shrink)

David Lewis maintained that epistemological contextualism (on which the truth-conditions for utterances of “S knows p” change in different contexts depending on the salient “alternative possibilities”) could solve the problem of skepticism as well as the Gettier problem. Contextualist approaches to skepticism have become commonplace, if not orthodox, in epistemology. But not so for contextualist approaches to the Gettier problem: the standard approach to this has been to add an “anti-luck” condition to the analysis of knowledge.

The soul-making theodicy seeks to explain how belief in the existence of God is compatible with the evil, pain and suffering we experience in our world. It purports to meet the problem of evil posed by non-theists by articulating a divine plan in which the occurrence of evil is necessary for enabling the greater good of character building of free moral agents. Many philosophers of religion have levelled strong objections against this theodicy. In this essay, Leslie Allan considers the (...) effectiveness of the counterarguments advanced by theist philosopher, Clement Dore, to two key objections to the soul-making theodicy. (shrink)

Leslie Allan defends his thesis that ethics is objective in the sense of requiring moral agents to offer impartial reasons for acting. Radical subjectivists have attacked this requirement for impartiality on a number of grounds. Some critics make the charge that Allan's thesis is simply a version of subjectivism in disguise. He responds by showing how a broadly naturalist view of ethics accommodates objective moral constraints. Allan also counters cases in which impartiality is purportedly not morally required (...) and considers the subjectivists' response to the problem of demarcating moral from non-moral judgements. (shrink)

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

The 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)

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)

Leslie Allan reviews Professor Losee's tracing of the history of the philosophy of science from its beginning with Aristotle in Ancient Greece, through the Middle Ages and the Enlightenment to the work of contemporary philosophers. In this review, Allan also provides a summary of each chapter and commentary on Losee's analysis.

Imre Lakatos holds a well-deserved primary place in current philosophy of science. In this essay, Leslie Allan critically examines Lakatos' theory of knowledge in two key areas. The first area of consideration is Lakatos' notion that knowledge is gained through a process of competition between rival scientific research programmes. Allan identifies and discusses four problems with Lakatos' characterization of a research programme. Next, Allan considers Lakatos' proposed test of adequacy for theories of rationality using his methodology of (...) historiographical research programmes. Allan discovers tensions within Lakatos' criteria and suggests ways of strengthening his test. (shrink)

In “The Myth of Factive Verbs” (Hazlett 2010), I had four closely related goals. The first (pp. 497-99, p. 522) was to criticize appeals to ordinary language in epistemology. The second (p. 499) was to criticize the argument that truth is a necessary condition on knowledge because “knows” is factive. The third (pp. 507-19) – which was the intended means of achieving the first two – was to defend a semantics for “knows” on which <S knows p> can be true (...) even if p isn’t true. The fourth (Ibid.) – which seemed necessary for the success of the third – was to defend a pragmatic account of the fact that utterances of <S knows p> typically imply p, on which the implication in those cases is down to conversational implicature. In this paper I’ll go after these goals again, with an emphasis on the second. Our topic will be whether the factivity of “knows” (whatever this amounts to) supports the truth condition on knowledge. A new goal will be to defend my argument against some criticisms from John Turri (2011) and Savas Tsohatzidis (forthcoming). We’ll first look at the truth condition (§1) and factive presupposition (§§2 – 3), before turning to replies to Turri and Tsohatzidis (§§4 – 7). (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)

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)

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)

This participatory study, conducted in an introductory psychology class, recounts self-reflections of 22 undergraduate students and their instructor engaging in an GenAI-mediated storyboard generation process. It relies on Gordon Pask’s conversation theory, structuring out the nature of interactions between students, instructor, and GenAI, and then uses a qualitative narrative to describe these conversational feedback loops constituting the creation of draft and final storyboards. Results suggest students engaged in cyclical feedback driven processes to master their creations, used elements of photography related (...) to the relationships between objects in frame, image processing, and cultural objects/themes to generate narratives. Issues were faced with generating text on images, and the consistency and style of generated frames as they interacted with GenAI tools. This study provides guidelines to university teaching professionals to design effective activities mediated by text-to-image GenAI. (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)

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)

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)

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)

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)

Conservative and liberal approaches to the problem of abortion are oversimplified and deeply flawed. Accepting that the moral status of the conceptus changes during gestation, the author advances a more nuanced perspective. Through applying a form of rules in practice utilitarianism within the context of overall population policy, he provides a compelling ethical and legal framework for regulating contraception and abortion practices.

In this paper, we develop an analysis of unrealistic fiction that captures the everyday sense of ‘unrealistic’. On our view, unrealistic fictions are a species of inconsistent fictions, but fictions for which such inconsistency, given the supporting role we claim played by genre, needn’t be a critical defect. We first consider and reject an analysis of unrealistic fiction as fiction that depicts or describes unlikely events; we then develop our own account and make an initial statement of it: unrealistic fictions (...) are those that invite us to believe something false. We further develop this account and restate it in terms of the notion of “import-export inconsistency.” That is, unrealistic fictions invite us to import certain propositions true in the actual world then invite us to export propositions entailing the negation of those imported. Finally, we consider whether for fiction being unrealistic is always an aesthetic flaw. (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)

The precarious rights of senior citizens, especially those who are highly educated and who are expected to counsel and guide the younger generations, has stimulated the creation internationally of advocacy associations and opinion leader groups. The strength of these groups, however, varies from country to country. In some countries, they are supported and are the focus of intense interest; in others, they are practically ignored. For this is reason we believe that the creation of a network of all these associations (...) is essential. The proposed network would act as a support for the already-existing policies of the United Nations’ High Commission for Human Rights, of independent experts, and of the Global Alliance for the Rights of Older People. All three have long ago recommended the creation of a recognized instrument for uniting presently scattered efforts. The proposed network, therefore, will seek to promote the international exchange of relevant expertise, and it will reinforce the commitments and actions that single countries are currently taking to meet these objectives. For example, informative public events can be organised to promote particular support initiatives and to provide an opportunity for new members of the network to be presented. The network will promote health for senior citizens, disease prevention, senior mobility, safe free time for seniors, alimentary education, protection against new risks and dangers, as well as equity in the services necessary for seniors to adopt new information and communication technologies. In the case of retired academic members, the network will promote equality with respect to continuing use of digital technologies (particularly email), continuing access to research libraries, and the guaranteed ability for seniors to fund their own research programs and to deliver free seminars. (shrink)

In the Phaedrus, Socreates sympathetically describes the ability “to cut up each kind according to its species along its natural joints, and to try not to splinter any part, as a bad butcher might do.” (265e) In contemporary philosophy, Ted Sider (2009, 2011) defends the same idea. As I shall put it, Plato and Sider’s idea is that limning structure is an epistemic goal. My aim in this paper is to articulate and defend this idea. First, I’ll articulate the notion (...) of a structural proposition (§1), and the notion of an epistemic goal (§2), where I’ll assume that epistemic goals are species of accuracy. Then (§3), I’ll argue against some proposals for understanding the idea that limning structure is an epistemic goal: limning structure is neither an aim of belief (§3.1), nor of inquiry (§3.2), nor of concept possession (§3.3). Importantly, non-structural belief is not thereby inaccurate; belief does not “aim” at being structural. Next (§4), I’ll propose a framework for understanding the idea that limning structure is an epistemic goal, and defend that idea. What is required, to defend the view that limning structure is an epistemic goal, is the notion of (what I call) theorizing – a propositional attitude that, unlike belief, does “aim” at being structural (§4.1). I’ll argue that structural truths constitute a species of “important” truths (§4.2), and that apt theorizing is a species of understanding (§4.3). Finally (§5), I’ll discuss the possibility that there is no structure. (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)

Most people not only think that it is possible for reasonable people to disagree, but that it is possible for people to recognize that they are parties to a reasonable disagreement. The aim of this paper is to explain how such mutually recognized reasonable disagreements are possible. I appeal to an which implies a form of relativism about reasonable belief, based on the idea that whether a belief is reasonable for a person can depend on the fact that she has (...) inherited a particular worldview from her community. (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)

In a recent article, Jack Mulder, Jr., gives a Plantinga-style defense of the Virgin Mary’s free consent to bear Jesus at the Annunciation. Against Mulder, I argue that a theodicy (rather than a defense) is necessary to undermine my arguments, that Mulder’s Catholic appeal to Mary’s Immaculate Conception amounts to a kind of freedom-undermining metaphysical grooming, and therefore Marian consent remains invalid.

there seems to be some kind of asymmetry, at least in some cases, between moral testimony and non-moral testimony, between aesthetic testimony and non-aesthetic testimony, and between religious testimony and non-religious testimony. In these domains, at least in some cases, we object to deference, and for this reason expect people to form their beliefs on non-testimonial grounds, in a way that we do not object to deference in paradigm cases of testimonial knowledge. Our philosophical puzzle is therefore: what explains these (...) (apparent) asymmetries (or are they merely apparent)? My aim here is to criticize three accounts of these testimonial asymmetries and to suggest an alternative strategy for solving our puzzle. I’ll consider the idea that testimony cannot be a source of understanding (§2), the idea that testimony cannot be a source of acquaintance (§3), and the idea that testimonial belief is not conducive to moral virtue (§4). These accounts all explain the badness of testimonial belief, in the relevant cases, by appeal to its consequences for the believer—respectively, a lack of understanding, acquaintance, or moral virtue. I’ll conclude by suggesting a way forward (§5): we should try to understand the badness of testimonial belief, in the relevant cases, as deriving from its consequences for the believer’s society. (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)

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)

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)

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)

There is, I shall assume, such a thing as moral evil (more on which below). My question is whether is also such a thing as non-moral evil, and in particular whether there are such things as aesthetic evil and epistemic evil. More exactly, my question is whether there is such a thing as moral evil but not such a thing as non-moral evil, in some sense that reveals something special about the moral, as opposed to such would-be non-moral domains as (...) the aesthetic and the epistemic. The philosophical issue at stake here is that of the nature of these different normative domains, and the nature and extent of their difference. (shrink)