Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

We revisit an important exchange on the problem of radical skepticism between Richard Rorty and Michael Williams. In his contribution to this exchange, Rorty defended the kind of transcendental approach to radical skepticism that is offered by Donald Davidson, in contrast to Williams’s Wittgenstein-inspired view. It is argued that the key to evaluating this debate is to understand the particular conception of the radical skeptical problem that is offered in influential work by Barry Stroud, a conception of the skeptical problem (...) which generates metaepistemological ramifications for anti-skeptical theories. In particular, we argue that, contra Williams, Rorty’s view that Davidson was offering a theoretical diagnosis of radical skepticism can be consistently maintained with his transcendental approach. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (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 chapter looks at the discussion of materialism in John Locke’s Essay concerning Human Understanding, and then at parts of the Anglophone reaction to those discussions. It considers the early criticisms of Locke by Edward Stillingfleet and the anonymous author of three sets of Remarks on Locke’s Essay. It then looks at some other ways in which readers reacted to Locke’s discussions: the views of Anthony Collins and John Toland, which one might be tempted to think of as Lockean materialism; (...) William Carroll’s reading of Locke as a Spinozistic materialist; and the dualistic Lockeanism of William Duncan’s Lockean logic textbook. (shrink)

Quentin Smith argues that if God exists, He had a duty to ensure life's existence; and He couldn't rationally have done so and made a big bang unless a counter-factual like "If God had made a big bang, there would have been life," was true pre-creation. But such counter-factuals are not true pre-creation. I argue that God could have made a big bang without irrationality; and that He could have ensured life without making big bangs non-random. Further, a proper understanding (...) of the truth-conditions of counter-factuals like the one above lets them have determinate truth-values pre-creation. But the explanation of how the above counter-factual can be true pre-creation is more complicated than that offered by William Lane Craig. (shrink)

Experiential acquaintance is an alleged relation between ourselves and our experiences that has sometimes been hypothesised as necessary for knowledge of our experiences. This paper begins with a clarification of ‘acquaintance’ and an explanation of ‘experience’ that focuses attention on a famous, but flawed, argument by G. E. Moore. It goes on to critically examine several recent arguments concerning experiential acquaintance and to show how internalist foundationalism can respond to a famous Sellarsian dilemma without appeal to a relation of acquaintance (...) with our experiences. It concludes that we can dispense with experiential acquaintance. (shrink)

We present Backward Clock, an original counterexample to Robert Nozick’s truth-tracking analysis of propositional knowledge, which works differently from other putative counterexamples and avoids objections to which they are vulnerable. We then argue that four ways of analysing knowledge in terms of safety, including Duncan Pritchard’s, cannot withstand Backward Clock either.

According to Duncan Pritchard, there are two kinds of radical sceptical problem; the closure-based problem, and the underdetermination-based problem. He argues that distinguishing these two problems leads to a set of desiderata for an anti-sceptical response, and that the way to meet all of these desiderata is by supplementing a form of Wittgensteinian contextualism with disjunctivist views about factivity. I agree that an adequate response should meet most of the initial desiderata Pritchard puts forward, and that some version of (...) Wittgensteinian contextualism shows the most promise as a starting point for this, but I argue, contra Pritchard, that the addition of disjunctivism is unnecessary and potentially counter-productive. If we draw on lessons from Michael Williams's inferential contextualism then it is both possible, and preferable, to meet the most important of Pritchard's desiderata, undercutting both closure-based and underdetermination-based sceptical problems in a unified way, without the need to resort to disjunctivism. (shrink)

The ways in which Wittgenstein was directly influenced by William James (by his early psychological work as well his later philosophy) have been thoroughly explored and charted by Russell B. Goodman. In particular, Goodman has drawn attention to the pragmatist resonances of the Wittgensteinian notion of hinge propositions as developedand articulated in the posthumously edited and published work, On Certainty. This paper attempts to extend Goodman’s observation, moving beyond his focus on James (specifically, James’s Pragmatism) as his pragmatist reference (...) point. It aims to articulate the affinity between Wittgenstein’s thought on the topic of certainty and that of the neglected pragmatist thinker, George Santayana. -/- The paper draws on Duncan Pritchard’s recent reading of Wittgenstein’s On Certainty in order to articulate the concept of certainty involved in the notion of hinge propositions. It identifies two important and related points of affinity between this Wittgensteinian line of thought on certainty and the line of thought on the same topic articulated in Santayana’s Scepticism and Animal Faith. The paper argues, firstly, that, both lines of thought reflect a pragmatist concept of certainty, according to which our most fundamental certainties are not conceived as purely theoretical objects of belief or knowledge but rather as thearational presuppositions of beliefs and practical action. Secondly, it examines the way inwhich the pragmatist concept of certainty functions, for the two thinkers as a response to scepticism. It argues that although the two thinkers’ responses are very different, they are mutually compatible and, together, point towards the possibility of a distinctively pragmatist response to scepticism, which involves an anti-epistemological model of the intimate relation of the human self to the world. (shrink)

This article seeks the origin, in the theories of Ibn al-Haytham (Alhazen), Descartes, and Berkeley, of two-stage theories of spatial perception, which hold that visual perception involves both an immediate representation of the proximal stimulus in a two-dimensional ‘‘sensory core’’ and also a subsequent perception of the three dimensional world. The works of Ibn al-Haytham, Descartes, and Berkeley already frame the major theoretical options that guided visual theory into the twentieth century. The field of visual perception was the first area (...) of what we now call psychology to apply mathematics, through geometrical models as used by Euclid, Ptolemy, Ibn al-Haytham, and Descartes (among others). The article shows that Kepler’s discovery of the retinal image, which revolutionized visual anatomy and entailed fundamental changes in visual physiology, did not alter the basic structure of theories of spatial vision. These changes in visual physiology are advanced especially in Descartes' Dioptrics and his L'Homme. Berkeley develops a radically empirist theory vision, according to which visual perception of depth is learned through associative processes that rely on the sense of touch. But Descartes and Berkeley share the assertion that there is a two-dimensional sensory core that is in principle available to consciousness. They also share the observation that we don't usually perceived this core, but find depth and distance to be phenomenally immediate, a point they struggle to accommodate theoretically. If our interpretation is correct, it was not a change in the theory of the psychology of vision that engendered the idea of a sensory core, but rather the introduction of the theory into a new metaphysical context. (shrink)

How does empire become transposed onto justice? There are two kinds of question here, one historical the other conceptual, though they are often entwined. First, we may ask whether there are particular arguments about justice that were subsequently used in the justification of empire or colonialism. Or, we may seek to trace the conceptual structure of argu- ments justifying imperialism to their roots in particular philosophical views, debunking their supposed universalism.3 Second, we may ask about the very nature of the (...) concept of global justice and the values it expresses in relation to other important values. Is the very notion of global justice imperialistic, just because it claims there are universal values applicable to everyone everywhere, whatever their particular ways of life or worldviews? (shrink)

First published in the International Encyclopaedia of Social and Behavioural Sciences (Pergamon Press, 2001); reprinted in the 2nd edition (2015). An overview of different justifications of multiculturalism in contemporary political theory, as well as various challenges to and critiques of those arguments.

Suppose that disgust can provide evidence of moral wrongdoing. What account of disgust might make sense of this? A recent and promising theory is the social contagion view, proposed by Alexandra Plakias. After criticizing both its descriptive and normative claims, I draw two conclusions. First, we should question the wisdom of drawing so straight a line from biological poisons and pathogens to social counterparts. Second, we don’t need to explain the evidential value of disgust by appealing to what the response (...) tracks. These lessons point toward an alternative: namely, that disgust is a moral heuristic. On the heuristic view, disgust is a trigger for the subconscious use of a particular rule: I show how this view fits with a plausible hypothesis about the social function of disgust, and then apply it to Leon Kass’s famous use of repugnance to criticize cloning. (shrink)

When we experience the world – see, hear, feel, taste, or smell things – we gain all sorts of knowledge about the things around us. And this knowledge figures heavily in our reasoning about the world – about what to think and do in response to it. But what is the nature of this knowledge? On one commonly held view, all knowledge is constituted by beliefs in propositions. But in this paper I argue against this view. I argue that some (...) knowledge is constituted, not by beliefs in propositions, but by awareness of properties and objects. To make my case, I focus on the role of visual perception in reasoning. I start by introducing a principle about the relationship between knowledge and reasoning, which says that to learn something new by reasoning, one must know the bases of one’s reasoning. Then I argue that in some cases of genuine, knowledge-conferring reasoning, the bases of our reasoning are not propositions that we believe; rather, they’re properties or objects that we see. Thus, I conclude that some such knowledge is non-propositional and is rather what some call “knowledge of things”. (shrink)

In his Enquiry concerning the Principles of Morals David Hume said that a group of earlier modern philosophers, beginning with Malebranche, held that morality was founded on relations. In this paper I follow up on that suggestion by investigating pre-Humean views in moral philosophy according to which morality is founded on relations. I do that by looking at the work of Nicolas Malebranche, John Locke, and Samuel Clarke. Each of them talked prominently about relations in their accounts of basic aspects (...) of morality. Beyond that, each of them turns out to have held both metaphysical and epistemological views that might be described as founding morality on relations. Despite the definite differences between the three philosophers’ approaches, Hume does seem to have noticed a genuine connection here—even though he himself tended to ignore significant versions of this approach when criticizing it. (shrink)

In a recent paper Shieva Kleinschmidt has argued that if certain scenarios involving extended simple regions are possible (so-called ‘Place Cases’), then no logic of location with only one primitive locative notion (i.e., no ‘parsimonious logic of location’) will suffice to describe all of the locative possibilities. Since almost all existing logics of location are parsimonious (and apparently for good reason) the argument is a considerable obstacle to the development of a satisfactory logic of location. Kleinschmidt suggests that the best (...) way out of the difficulty is to deny the possibility of Place Cases by denying that extended simple regions are possible. I argue that much the same problem arises even in cases not involving extended simple regions or indeed exotic regions of any kind. Thus, simply denying the possibility of extended simple regions will not save parsimonious logics of location. (shrink)

Chapin reviewed this 1972 ZEITSCHRIFT paper that proves the completeness theorem for the logic of variable-binding-term operators created by Corcoran and his student John Herring in the 1971 LOGIQUE ET ANALYSE paper in which the theorem was conjectured. This leveraging proof extends completeness of ordinary first-order logic to the extension with vbtos. Newton da Costa independently proved the same theorem about the same time using a Henkin-type proof. This 1972 paper builds on the 1971 “Notes on a Semantic Analysis of (...) Variable Binding Term Operators” (Co-author John Herring), Logique et Analyse 55, 646–57. MR0307874 (46 #6989). A variable binding term operator (vbto) is a non-logical constant, say v, which combines with a variable y and a formula F containing y free to form a term (vy:F) whose free variables are exact ly those of F, excluding y. Kalish-Montague 1964 proposed using vbtos to formalize definite descriptions “the x: x+x=2”, set abstracts {x: F}, minimization in recursive function theory “the least x: x+x>2”, etc. However, they gave no semantics for vbtos. Hatcher 1968 gave a semantics but one that has flaws described in the 1971 paper and admitted by Hatcher. In 1971 we give a correct semantic analysis of vbtos. We also give axioms for using them in deductions. And we conjecture strong completeness for the deductions with respect to the semantics. The conjecture, proved in this paper with Hatcher’s help, was proved independently about the same time by Newton da Costa. (shrink)

The classical theory of probability has long been abandoned and is seen by most philosophers as a non-contender—a mere precursor to newer and better theories. In this paper I argue that this is a mistake. The main reasons for its rejection—all related to the notorious principle of indifference—are that it is circular, of limited applicability, inconsistent, and dependent upon unjustified empirical assumptions. I argue that none of these claims is true and that the classical theory remains to be refuted.

This is an earlier version of the argument presented as the appendix to the author's final book, Peri Physeos.

Psychological construction represents an important new approach to psychological phenomena, one that has the promise to help us reconceptualize the mind both as a behavioral and as a biological system. It has so far been developed in the greatest detail for emotion, but it has important implications for how researchers approach other mental phenomena such as reasoning, memory, and language use. Its key contention is that phenomena that are characterized in (folk) psychological vocabulary are not themselves basic features of the (...) mind, but are constructed from more basic psychological operations. The framework of mechanistic explanation, currently under development in philosophy of science, can provide a useful perspective on the psychological construction approach. A central insight of the mechanistic account of explanation is that biological and psychological phenomena result from mechanisms in which component parts and operations do not individually exhibit the phenomena of interest but function together in an orchestrated and sometimes in a complex dynamical manner to generate it. While at times acknowledging the compatibility of the mechanist approach with constructionist approach (Lindquist, Wager, Kober, Bliss-Moreau, & Barrett, 2012), proponents of the constructionist approach have at other times pitched their approach as anti-mechanist. For example, Barrett (2009) claims that the psychological constructionist approach rejects machines as the primary metaphor for understanding the mind, instead favoring a recipe metaphor; constructionism also purportedly rejects the “mechanistic” picture of causation, which it portrays as linear or sequential in nature (see also Barrett, Wilson-Mendenhall, & Barsalou, in press). While some mechanistic accounts do fit this description, we will see that the mechanisms generating phenomena can be complex and dynamic, producing phenomena far less stereotypic and more adaptive than people often associate with machines. Our goal, however, is not just to render constructionism and mechanism compatible. Philosophers of science have been examining the nature of mechanistic explanation in biology with the goal of gaining new insights into the operation of science. We will identify some of the places where the mechanistic account can shed new light on the constructionist project. (shrink)

Public discussions of political and social issues are often characterized by deep and persistent polarization. In social psychology, it’s standard to treat belief polarization as the product of epistemic irrationality. In contrast, we argue that the persistent disagreement that grounds political and social polarization can be produced by epistemically rational agents, when those agents have limited cognitive resources. Using an agent-based model of group deliberation, we show that groups of deliberating agents using coherence-based strategies for managing their limited resources tend (...) to polarize into different subgroups. We argue that using that strategy is epistemically rational for limited agents. So even though group polarization looks like it must be the product of human irrationality, polarization can be the result of fully rational deliberation with natural human limitations. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

To be acquainted with something (in the philosophical sense of “acquainted” discussed here) is to be directly aware of it. The idea that we are acquainted with certain things we experience has been discussed throughout the history of Western Philosophy, but in the early 20th century it gained especially focused attention among analytic philosophers who drew their inspiration from Bertrand Russell's work on acquaintance. Since then, many philosophers—particularly those working on self‐knowledge or perception—have used the notion of acquaintance to explain (...) various facts about human experience and knowledge. In this paper, I offer an overview of this work, with particular focus on the resurgent literature on acquaintance in contemporary analytic philosophy. After more fully explaining what acquaintance is (or is supposed to be), I describe some reasons for thinking that we are indeed acquainted with certain things we experience, and then I survey some of the facts about experience and knowledge that acquaintance may help explain. (shrink)

The Repugnant Conclusion served an important purpose in catalyzing and inspiring the pioneering stage of population ethics research. We believe, however, that the Repugnant Conclusion now receives too much focus. Avoiding the Repugnant Conclusion should no longer be the central goal driving population ethics research, despite its importance to the fundamental accomplishments of the existing literature.

Proponents of the extended mind have suggested that phenomenal transparency may be important to the way we evaluate putative cases of cognitive extension. In particular, it has been suggested that in order for a bio-external resource to count as part of the machinery of the mind, it must qualify as a form of transparent equipment or transparent technology. The present paper challenges this claim. It also challenges the idea that phenomenological properties can be used to settle disputes regarding the constitutional (...) status of bio-external resources in episodes of extended cognizing. Rather than regard phenomenal transparency as a criterion for cognitive extension, we suggest that transparency is a feature of situations that support the ascription of certain cognitive/mental dispositional properties to both ourselves and others. By directing attention to the forces and factors that motivate disposition ascriptions, we arrive at a clearer picture of the role of transparency in arguments for extended cognition and the extended mind. As it turns out, transparency is neither necessary nor sufficient for cognitive extension, but this does not mean that it is entirely irrelevant to our understanding of the circumstances in which episodes of extended cognizing are apt to arise. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Contemporary debates about scientific institutions and practice feature many proposed reforms. Most of these require increased efforts from scientists. But how do scientists’ incentives for effort interact? How can scientific institutions encourage scientists to invest effort in research? We explore these questions using a game-theoretic model of publication markets. We employ a base game between authors and reviewers, before assessing some of its tendencies by means of analysis and simulations. We compare how the effort expenditures of these groups interact in (...) our model under a variety of settings, such as double-blind and open review systems. We make a number of findings, including that open review can increase the effort of authors in a range of circumstances and that these effects can manifest in a policy-relevant period of time. However, we find that open review’s impact on authors’ efforts is sensitive to the strength of several other influences. (shrink)

This paper motivates the idea that social robots should be credited as moral patients, building on an argumentative approach that combines virtue ethics and social recognition theory. Our proposal answers the call for a nuanced ethical evaluation of human-robot interaction that does justice to both the robustness of the social responses solicited in humans by robots and the fact that robots are designed to be used as instruments. On the one hand, we acknowledge that the instrumental nature of robots and (...) their unsophisticated social capabilities prevent any attribution of rights to robots, which are devoid of intrinsic moral dignity and personal status. On the other hand, we argue that another form of moral consideration—not based on rights attribution—can and must be granted to robots. The reason is that relationships with robots offer to the human agents important opportunities to cultivate both vices and virtues, like social interaction with other human beings. Our argument appeals to social recognition to explain why social robots, unlike other technological artifacts, are capable of establishing with their human users quasi-social relationships as pseudo-persons. This recognition dynamic justifies seeing robots as worthy of moral consideration from a virtue ethical standpoint as it predicts the pre-reflective formation of persistent affective dispositions and behavioral habits that are capable of corrupting the human user’s character. We conclude by drawing attention to a potential paradox drawn forth by our analysis and by examining the main conceptual conundrums that our approach has to face. (shrink)

“We are animals.” That’s what animalists say—that’s their slogan. But what animalists mean by their slogan varies. Many animalists are adamant that what they mean—and, indeed, what the true animalist thesis is—is that we are identical to animals (human animals, to be precise). But others say that’s not enough. They say that the animalist thesis has to be something more—perhaps that we are essentially or most fundamentally human animals. This paper argues that, depending on how we understand it, animalism is (...) either false or uninteresting. If animalism is just the claim that we are identical to animals, then it is uninteresting. For it doesn’t provide an answer to the question it’s meant to address. On the other hand, if animalism entails a stronger claim, such as that we are essentially animals, then animalism is false. Either way, we should set animalism aside. (shrink)

The author presents reasons for thinking that the evil we observe in the world is not even prima facie evidence against the existence of God.

Child soldiers, who often appear to be both victims and perpetrators, present a vexing moral and legal challenge: how can we protect the rights of children while seeking justice for the victims of war crimes? There has been little stomach, either in domestic or international courts, for prosecuting child soldiers—but neither has this challenge been systematically addressed in international law. Establishing a uniform minimum age of criminal responsibility would be a major step in the right direction; we argue that such (...) a standard ought to be guided by the best evidence from neuropsychology about the development, during childhood and adolescence, of the executive functions that give rise to morally and legally responsible agents. In light of that evidence, which suggests that the brain’s executive functions are still maturing into early adulthood, we recommend a graded structure of culpability for child soldiers. (shrink)

It seems like experience plays a positive—even essential—role in generating some knowledge. The problem is, it’s not clear what that role is. To see this, suppose that when your visual system takes in information about the world around you it skips the experience step and just automatically and immediately generates beliefs in you about your surroundings. A lot of philosophers think that, in such a case, you would (or at least could) still know, via perception, about the world around you. (...) But then that raises the question: What epistemic role was the experience playing? How did it contribute to your knowledge of your surroundings? Philosophers have given many different answers to these questions. But, for various reasons, none of them has really stuck. In this paper I offer and defend a different answer to these questions—a solution to the problem—which avoids the pitfalls of other answers. I argue that experience is, all by itself, a kind of knowledge—it’s what Bertrand Russell (1912) calls “knowledge of things”. So I argue that experience helps generate knowledge simply by being knowledge. (shrink)

The Hong and Page ‘diversity trumps ability’ result has been used to argue for the more general claim that a diverse set of agents is epistemically superior to a comparable group of experts. Here we extend Hong and Page’s model to landscapes of different degrees of randomness and demonstrate the sensitivity of the ‘diversity trumps ability’ result. This analysis offers a more nuanced picture of how diversity, ability, and expertise may relate. Although models of this sort can indeed be suggestive (...) for diversity policies, we advise against interpreting such results overly broadly. (shrink)

This Article argues that a particular political theory underlies the judicial interpretation of ‘equality before the law’. The Canadian Courts at the date of writing have elaborated two tests for the signification of ‘equality before the law’. The Article traces the two tests to the utilitarian political theory outlined by John Stuart Mill. The one test sets out the ‘greatest happiness of the greatest number’ or ‘social interests’ as the criterion for adjudicating equality. The second test identifies the reasonable relationship (...) of an alleged statutory classification vis-à-vis the statutory purpose. The Article offers an alternative approach based upon democratic theory. Examples of the two tests and the alternative approach are drawn from judicial constitutional interpretations in the USA and Canada. (shrink)

My interest is the kind of philosophical vertigo that is a theme of Cavell’s work on scepticism. This describes the anxiety that is elicited via philosophical engagement with certain kinds of sceptical questions. There is a standing puzzle about this notion of vertigo, however, forcefully pressed, for example, by McDowell. Why should a resolution of the sceptical problem, one that putatively completely undercuts the motivation for scepticism in that domain, nonetheless generate vertigo in this sense? I aim to resolve the (...) puzzle, in a way that I believe underwrites this Cavellian notion, via consideration of Wittgenstein’s remarks on the structure of rational evaluation in his final notebooks, published as On Certainty. (shrink)

As I walk into a restaurant to meet up with a friend, I look around and see all sorts of things in my immediate environment—tables, chairs, people, colors, shapes, etc. As a result, I know of these things. But what is the nature of this knowledge? Nowadays, the standard practice among philosophers is to treat all knowledge, aside maybe from “know-how”, as propositional. But in this paper I will argue that this is a mistake. I’ll argue that some knowledge is (...) constituted, not by beliefs toward propositions, but by awareness of properties and objects. Seeing isn’t believing, but it is knowing. After further characterizing this type of knowledge, I will make the case for it. Then I will consider a variety of objections. Finally, I will indicate how our recognition of this knowledge may answer other questions, and solve other problems, in philosophy. (shrink)

This paper explores the implications of Zeynep Tufekci’s capacities approach to social movements, which explains the strength of social movements in terms of their capacities. Tufekci emphasises that the capacities of contemporary social movements largely depend upon their uses of new digital technologies, and of social media in particular. We show that Tufekci’s approach has important implications for the structure of social movements, whether and what obligations they can have, and for how these obligations distribute to their members. In exploring (...) these implications, we develop a tripartite taxonomy of social movements. Each type of social movement in the taxonomy corresponds to a different type of group: social campaigns, social struggles, and social agitations. We show that all three types of social movement can bear obligations in virtue of their capacities. Finally, we argue that a surprising upshot of the obligations of social movements is that members of oppressed groups can have obligations to resist their own oppression in virtue of being members of social movements. (shrink)

This article addresses two issues. First, it critiques a prominent position regarding how affluent states should balance their national interest on the one hand and their duty to aid developing states on the other. Second, it suggests that absent a principled way to balance national interest with international aid, a state’s more immediate concern is to comply with its negative duty to not harm other states. To support this position, the article constructs a conception of harm that may be applied (...) to questions regarding a state’s negative duties, focusing upon the example of the Trade-Related Aspects of Intellectual Property Rights Agreement (TRIPS). (shrink)

A powerful argument against the counterfactual comparative account of harm is that it cannot distinguish harming from failing to benefit. In reply to this problem, I suggest a new account of harm. The account is a counterfactual comparative one, but it counts as harms only those events that make a person occupy his level of well-being at the world at which the event occurs. This account distinguishes harming from failing to benefit in a way that accommodates our intuitions about the (...) standard problem cases. In laying the groundwork for this account, I also demonstrate that rival accounts of harm are able to distinguish harming from failing to benefit only if, and because, they also appeal to the distinction between making upshots happen and allowing upshots to happen. One important implication of my discussion is that preserving the moral asymmetry between harming and failing to benefit requires a commitment to the existence of a metaphysical and moral distinction between making and allowing. (shrink)

This paper analyzes ethical issues relating to lawyer mobility.

I can be aware of myself, and thereby come to know things about myself, in a variety of different ways. But is there some special way in which I—and only I—can learn about myself? Can I become aware of myself by introspecting? Do I somehow show up in my own conscious experiences? David Hume and most contemporary philosophers say no. They deny that the self shows up in experience. However, in this paper I appeal to research on schizophrenia—on thought insertion, (...) in particular—to argue that Hume and his follows are wrong: The self does, in fact, show up in experience. (shrink)