This paper defends “Animal Universalism,” the thesis that all sentient non-human animals will be brought into Heaven and remain there for eternity. It assumes that God exists and is all-powerful, perfectly loving, and perfectly just. From these background theses, the authors argue that Animal Universalism follows. If God is perfectly loving, then God is concerned about the well-being of non-human animals, and God chooses to maximize the well-being of each individual animal when doing so does not harm other individual creatures (...) or violate creaturely freedom. If God is perfectly just, then God does not arbitrarily discriminate against non-human animals by offering humans an opportunity to enter Heaven but not offering the same to each animal. Each of these conclusions implies Animal Universalism. (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)

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)

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)

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)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (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.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Cross cultural studies have played a pivotal role in elucidating the extent to which behavioral and mental characteristics depend on specific environmental influences. Surprisingly, little field research has been carried out on a fundamentally important perceptual ability, namely the perception of biological motion. In this report, we present details of studies carried out with the help of volunteers from the Mundurucu indigene, a group of people native to Amazonian territories in Brazil. We employed standard biological motion perception tasks inspired by (...) over 30 years of laboratory research, in which observers attempt to decipher the walking direction of point-light (PL) humans and animals. Do our effortless skills at perceiving biological activity from PL animations, as revealed in laboratory settings, generalize to people who have never before seen representational depictions of human and animal activity? The results of our studies provide a clear answer to this important, previously unanswered question. Mundurucu observers readily perceived the coherent, global shape depicted in PL walkers, and experienced the classic inversion effects that are typically found when such stimuli are turned upside down. In addition, their performance was in accord with important recent findings in the literature, in the abundant ease with which they extracted direction information from local motion invariants alone. We conclude that the effortless, veridical perception of PL biological motion is a spontaneous and universal perceptual ability, occurring both inside and outside traditional laboratory environments. (shrink)

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.

In this article I take a critical look at the origins and sources of Bruno Latour's pluralism as it is expressed in his book AN INQUIRY INTO MODES OF EXISTENCE, and compare it to other similar projects (Wittgenstein, Feyerabend, Badiou). I consider the accusations of reductionism and of relativism, and demonstrate that Latour's «empirical metaphysics» is not an ontological reductionism but a pluralist ontology recognising the existence of a plurality of entities and of types of entities. Nor is it an (...) epistemological relativism but an ontological pluralism affirming the existence of a plurality of types of existence. These two strands, pluralist ontology and ontological pluralism, mutually reinforce each other to produce at least the outlines of a robust pluralist realism. (shrink)

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)

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)

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

I begin by “deconstructing” the title and explaining that Feyerabend does not really use the word “ontology”, though he does call his position sometimes (and the “sometimes” is important) ontological realism. I explain that he talks about his position as indifferently a “general methodology” or a “general cosmology”, and that he seems to be be hostile to the very enterprise of ontology, conceived of as “school philosophy”. I then go on to say that there is perhaps a concept of a (...) different type of ontology, that I call a “diachronic ontology” that perhaps he would have accepted,and that is very different from ontology as ordinarily thought, which I claim to be synchronic ontology (having no room for the dialogue with Being, but just supposing that Being is already and always there without our contribution). I discuss Althusser and Graham Harman as exemplifying synchronic ontology, giving a reading of Harman’s recent book THE THIRD TABLE. I then discuss Feyerabend’s ideas as showing a different way, that of a diachronic ontology, in which there is no stable framework or fixed path. I end with Andrew Pickering whose essay NEW ONTOLOGIES makes a similar distinction to mine, expressing it in the imagistic terms of a De Kooningian (diachronic) versus a Mondrianesque (synchronic) approach. (shrink)

This discussion interprets William Blake's poetry and painting across the hermeneutic philosophy of Martin Heidegger and his analysis of Dasein. It shows Blake's eighteenth-century discourse to be, like Heidegger's philosophy of Dasein, a radical critique of philosophical, scientific, and artistic thinking. To better understand the connections between Blake and Heidegger, the development of aesthetic philosophy from classical aesthetics through Nietzsche is charted. The parameters of eighteenth-century aesthetics, and the rise of hermeneutics in the nineteenth and early twentieth (...) century, are discussed as a response to the limitations of the neoclassical. On this basis, ideas and practices central to Blake's poetry such as "eternity" and "Albion" are compared to Heidegger's concepts of Dasein in order to shed additional light on the pioneering nature of Blake's work, and to see that he may be understood in terms of later aesthetic philosophies. (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)

In this chapter, we argue for a phenomenal conservative perspective on religious epistemology and attempt to answer some common criticisms of this perspective.

This study aims to identify the different managerial styles employed by owners of legitimate micro, small and medium enterprises (MSME) in different localities within the city of Manila in the day-to-day management and supervision of their enterprises. According to the Department of Trade and Industry of the Philippines (2003), micro, small and medium enterprises (MSMEs) are defined as any business activity/enterprise engaged in industry, agribusiness/services, whether single proprietorship, cooperative, partnership, or corporation whose number of employees are categorized as follows: for (...) micro-enterprises, 1 – 9 employees; for small enterprise, 10 – 99 employees; and for medium enterprises, 100 – 199 employees. Out of the 99.6% MSMEs, the average micro-enterprises share 91.5 and the remainder is the share of SMEs. Unlike large firms, a micro, small, or medium enterprise is managed by an individual who is usually the owner-manager. Management style in large firms is mostly systematic and procedural while MSMEs management and operation are flexible, personal, and direct. This research used a self-assessment questionnaire formulated by two American psychologists Robert Blake and Jane Mouton. Face-to-face interviews were also administered to several MSME owner-managers. The interviews revealed that owner-managers are inclined to being task-oriented and people-oriented. However, women are more task-oriented than men. Based on the result of the self-assessment test the dominant management style among owner-managers is Team management. (shrink)

The main objection to pragmatism about knowledge is that it entails that truth-irrelevant factors can make a difference to knowledge. Blake Roeber (2018) has recently argued that this objection fails. I agree with Roeber. But in this paper, I present another way of thinking about the dispute between purists and pragmatists about knowledge. I do so by formulating a new objection to pragmatism about knowledge. This is that pragmatism about knowledge entails that factors irrelevant to both truth and “cognitive (...) agency” can make a difference to knowledge. An interesting additional upshot of my argument is the connection revealed between the debate between pragmatists and purists about knowledge, and the debate between “alethists” and pragmatists about reasons for belief. (shrink)

Does knowledge depend in any interesting way on our practical interests? This is the central question in the pragmatic encroachment debate. Pragmatists defend the affirmative answer to this question while purists defend the negative answer. The literature contains two kinds of arguments for pragmatism: principle-based arguments and case-based arguments. Principle-based arguments derive pragmatism from principles that connect knowledge to practical interests. Case-based arguments rely on intuitions about cases that differ with respect to practical interests. I argue that there are insurmountable (...) problems for both kinds of arguments, and that it is therefore unclear what motivates pragmatism. (shrink)

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

For the theorists of crisis, the revolutionary state comes into existence through violence, and due to its inability to provide an authoritative katechon (restrainer) against internal and external violence, it perpetuates violence until it self-destructs. Writing during extreme economic depression and growing social and political violence, the crisis theorists––Joseph de Maistre, Juan Donoso Cortés, and Carl Schmitt––each sought to blame the chaos of their time upon the Janus-faced postrevolutionary ideals of liberalism and socialism by urging a return to pre-revolutionary moral (...) and religious values. They are united by three counterrevolutionary principles, all of which are purported to remedy revolutionary violence: traditional constitutional fidelity, the philosophy of the decision, and opposition to bourgeois liberalism. This essay is followed by the first complete English translation and publication of Donoso’s letter of October 24, 1851, which contains Donoso’s only reference to the “discussing class,” a political entity later popularized by Schmitt in his 1922 work Political Theology. (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)

Purists think that changes in our practical interests can’t affect what we know unless those changes are truth-relevant with respect to the propositions in question. Impurists disagree. They think changes in our practical interests can affect what we know even if those changes aren’t truth-relevant with respect to the propositions in question. I argue that impurists are right, but for the wrong reasons, since they haven’t appreciated the best argument for their own view. Together with “Minimalism and the Limits of (...) Warranted Assertability Maneuvers,” “The Pragmatic Encroachment Debate,” and “Anti-Intellectualism” (below), this paper constitutes my attempt to refute the entire pragmatic encroachment debate. As I show in this paper, there is an argument for impurism sitting in plain sight that is considerably more plausible than any extant argument for pragmatism. (shrink)

For Hegel, personhood is developed primarily through the possession, ownership, and exchange of property. Property is crucial for individuals to experience freedom as persons and for the existence of Sittlichkeit, or ethical life within a community. The free exchange of property serves to develop individual personalities by mediating our intersubjectivity between one another, whereby we share another’s subjective experience of the object by recognizing their will in it and respecting their ownership of it. This free exchange is grounded the abstract (...) right to property which is defined by the liberal institution of private property. Like all legal/juridical rights, the abstract property right and its related institution are productions of the state, which can also claim priority over them. This prioritization reveals the dialectic inherent in the both the conception and exercise of the right, in which the private right to property at the level of civil society confronts the public right of the state, resulting in both the preservation and uplifting of the right, and, at the same time, its cancellation or annihilation. (shrink)

In “Reasons to Believe and Reasons to Act,” Stewart Cohen argues that balance of reasons accounts of rational action get the wrong results when applied to doxastic attitudes, and that there are therefore important differences between reasons to believe and reasons to act. In this paper, I argue that balance of reasons accounts of rational action get the right results when applied to the cases that Cohen considers, and that these results highlight interesting similarities between reasons to believe and reasons (...) to act. I also consider an argument for Cohen's conclusion based on the principle that Adler, Moran, Shah, Velleman and others call “transparency.” I resist this argument by explaining why transparency is itself doubtful. (shrink)

This work explores the increasing militarization of borders throughout the world, particularly the United States border with Mexico. Rather than further rhetoric of "border security," this work views increases in guards, technology and the building of walls as militarized action. The goal of this essay is to place the onus upon states to justify their actions at borders in ways that do not appeal to tropes of terrorism. This work then explores how a logic of security infiltrates philosophical discussions of (...) "the right to exclude," thereby curtailing the ability to see borders in any other way than as a locale that must be militarized. Specifically, I analyze the work of Michael Blake and his juridical theory of immigration restrictions. I argue that his work necessitates the walling of borders and removal of those who create new obligations for current members of existing political institutions. (shrink)

This is the first complete English translation and publication of Donoso’s carta de 24 de octubre, 1851, a letter encapsulating many of his views on revolution and decision. This remarkable letter, sent as a diplomatic missive while he was serving the Spanish crown in Paris, describes how Napoleon III––stuck between the 1848 constitution’s prohibition against his election and his impending coup that will crown him emperor––must gain the support of the liberal bourgeoise middle class if he is to maintain his (...) rule over France. The letter is also of great importance to Donoso and Schmitt scholars because it contains the first and only time Donoso uses the complete term “las clases discutidoras,” which, through Schmitt’s injudicious and repeated misspellings as “una clasa discutidora” has become famous for its characterization of the liberal bourgeoisie as the “discussing” or “disputing” class that is incapable of action at the precise historical moment when a decision is most direly needed to save the constitution from inner or outer existential threats. (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)

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)

The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” or (...) “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. -/- In the following, we first offer a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance. We do not take these to be an exhaustive taxonomy of all possible ways in which chance meaningfully figures in explanations in evolutionary biology. These are simply five common uses of the term by biologists at this period. They will serve to organize our summary of the collected references to chance and the analysis and discussion of the following questions: • What did synthesis authors understand by chance? • How did these authors see chance operating in evolution? • Did their appeals to chance increase or decrease over time during the synthesis? That is, was there a “hardening” of the synthesis, as Gould claimed (1983)? (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 Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (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)

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)

Michael Blake’s excellent book 'Justice and Foreign Policy' makes an important contribution to the ongoing debates about the kinds of values that should inform the foreign policy of liberal states. In this paper I evaluate his defence of the view that egalitarianism applies within the state but not globally. I discuss two arguments he gives for this claim - one appealing to the material preconditions of democracy and the other grounded in a duty to justify coercive power. I argue (...) that neither argument succeeds. I then identify a general problem with his approach. If states adopted Blake’s principles for their foreign policy we would have a much better world than currently exists. But it would not – I submit - be a fair world. (shrink)

During much of the past century, it was widely believed that phonemes--the human speech sounds that constitute words--have no inherent semantic meaning, and that the relationship between a combination of phonemes (a word) and its referent is simply arbitrary. Although recent work has challenged this picture by revealing psychological associations between certain phonemes and particular semantic contents, the precise mechanisms underlying these associations have not been fully elucidated. Here we provide novel evidence that certain phonemes have an inherent, non-arbitrary emotional (...) quality. Moreover, we show that the perceived emotional valence of certain phoneme combinations depends on a specific acoustic feature--namely, the dynamic shift within the phonemes' first two frequency components. These data suggest a phoneme-relevant acoustic property influencing the communication of emotion in humans, and provide further evidence against previously held assumptions regarding the structure of human language. This finding has potential applications for a variety of social, educational, clinical, and marketing contexts. (shrink)

Humphry Osmond wrote to Aldous Huxley in 1956 proposing the term “psychedelic,” coined from two Greek words to mean “mind manifesting.” The scholars, one a psychiatrist and the other a celebrated novelist and philosopher, were exuberant about the potential of drugs for accessing the mind. Huxley favored a phrase from William Blake: -/- If the doors of perception were cleansed everything would appear to man as it is, infinite. -/- He postulated that psychedelics disturbed the “cerebral reducing valve” (1954), (...) and that this was in fact the shared mechanism for regular drug trips, as well as schizophrenic and mystical experiences. If it were the case, the drugs could offer a chemical shortcut to the divine, and a reasonable way to scientifically study mental illness. -/- With such ideas in vogue, the 1950s were heady years, at least for research on psychedelic drugs. More than 750 articles were published on LSD alone. Some studies made use of the drug experience to model schizophrenia, others to develop treatments for alcoholism. And as Nicolas Langlitz explains in Neuropsychedelia: The Revival of Hallucinogen Research Since the Decade of the Brain, the brain as filter – the idea of gates or doors (which, yes, also gave name to the band) – would go on to serve as a significant shared conceptual matrix for psychopharmacologic research, from experimental psychosis to experimental mysticism (10). (shrink)

Science has been under attack ever since William Blake and Romantic movement. In our time, criticisms of modern science have led to Alan Sokal's spoof, and the so-called science wars. Both sides missed the point. Science deserves to be criticized for seriously misrepresenting its highly problematic aims, which have metaphysical, value and political assumptions associated with them. Instead of repressing these problematic aims, science ought rather to make them explicit, so that they can be critically assessed and, we may (...) hope, improved. (shrink)

Recent iterations of Alvin Plantinga’s “evolutionary argument against naturalism” bear a surprising resemblance to a famous argument in Descartes’s Third Meditation. Both arguments conclude that theists have an epistemic advantage over atheists/naturalists vis-à-vis the question whether or not our cognitive faculties are reliable. In this paper, I show how these arguments bear an even deeper resemblance to each other. After bringing the problem of evil to bear negatively on Descartes’s argument, I argue that, given these similarities, atheists can wield a (...) recent solution to the problem of evil against theism in much the way Plantinga wields the detailsof evolutionary theory against naturalism. I conclude that Plantinga and Descartes give us insufficient reason for thinking theists are in a better epistemic position than atheists and naturalists vis-à-vis the question whether or not our cognitive faculties are reliable. (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)

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)

Bashabi Fraser is known the world over as a Scottish-Bengali aka diasporic writer. Further she has also been slotted as a feminist scholar with a huge corpus on Tagore. This essay proves the fallacy of such pigeon-holeing of Fraser and shows that she is as mainstream as Yeats and even before that, like unto Blake. The essay also makes a point for rejecting every other mode of poetry except the Romantic mode. It established the Vedantic nature of the poetic (...) genius. The endnotes are copious and comment on how/why/(what of) Fraser should compulsory reading at which age. The essay speaks at length on the nature of poetry. It stresses the value of Vedanta in assessing true poetry written even in English. This essay is also valuable since it has within it acute observations on Fraser as a Tagore scholar. (shrink)