As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

People have an “anomalous-is-bad” stereotype whereby they make negative inferences about the moral character of people with craniofacial anomalies like scars. This stereotype is hypothesized to be a byproduct of adaptations for avoiding pathogens. However, evidence for the anomalous-is-bad stereotype comes from studies of European and North American populations; the byproduct hypothesis would predict universality of the stereotype. We presented 123 Hadza across ten camps pairs of morphed Hadza faces—each with one face altered to include a scar—and asked who they (...) expected to be more moral and a better forager. Hadza with minimal exposure to other cultures chose at chance for both questions. Hadza with greater exposure to other cultures, however, expected the scarred face to be less moral and a better forager. These results suggest the anomalous-is-bad stereotype may be culturally shared or learned erroneously through associations with population-level differences, providing evidence against a universal pathogen avoidance byproduct hypothesis. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Current approaches used in educational research and practice to evaluate the quality of written arguments often rely on structural analysis. In such assessments, credit is awarded for the presence of structural elements of an argument, such as claims, evidence, and rebuttals. In this article, we discuss limitations of such approaches, including the absence of criteria for evaluating the quality of the argument elements. We then present an alternative framework, based on the Rational Force Model (RFM), which originated from the work (...) of a Nordic philosopher Næss. Using an example of an argumentative essay, we demonstrate the potential of the RFM to improve argument analysis by focusing on the acceptability and relevance of argument elements, two criteria widely considered to be fundamental markers of argument strength. We outline possibilities and challenges with using the RFM in educational contexts and conclude by proposing directions for future research. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

In this chapter, we will summarize recent empirical results highlighting how different groups of people solve pure coordination games. Such games are traditionally studied in behavioural economics, where two people need to coordinate without communicating with each other. Our results suggest that coordination choices vary across groups of people, and that people can adapt flexibly to these differences in order to coordinate between groups. We propose that pure coordination games are a useful empirical platform for studying aspects of mindshaping. Drawing (...) on existing psychological literature on alignment during interactions, we suggest that experience of successful interaction leads people to develop aligned intuitions about what is relevant and appropriate that support coordination when interaction and communication is not possible. Consistent with arguments made in the literature on mindshaping we believe that such alignment is more important for coordination than mindreading inferences about mental states, and indeed that mindreading is instead a form of coordination behaviour that is dependent upon intuitive alignment. (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)

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)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

Health services internationally struggle to ensure health care is “person-centered” (or similar). In part, this is because there are many interpretations of “person-centered care” (and near synonyms), some of which seem unrealistic for some patients or situations and obscure the intrinsic value of patients’ experiences of health care delivery. The general concern behind calls for person-centered care is an ethical one: Patients should be “treated as persons.” We made novel use of insights from the capabilities approach to characterize person-centered care (...) as care that recognizes and cultivates the capabilities associated with the concept of persons. This characterization unifies key features from previous characterisations and can render person-centered care applicable to diverse patients and situations. By tying person-centered care to intrinsically valuable capability outcomes, it incorporates a requirement for responsiveness to individuals and explains why person-centered care is required independently of any contribution it may make to health gain. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

The rejection of behaviorism in the 1950s and 1960s led to the view, due mainly to Noam Chomsky, that language must be studied by looking at the mind and not just at behavior. It is an understatement to say that Chomskyan linguistics dominates the field. Despite being the overwhelming majority view, it has not gone unchallenged, and the challenges have focused on different aspects of the theory. What is almost universally accepted, however, is Chomsky’s view that understanding language demands a (...) theory that posits mental states that represent rules of language. Call this claim, following Cowie (1999), Representationalism or (R). According to (R), ‘‘[e]xplaining language mastery and acquisition requires the postulation of contentful mental states and processes involving their manipulation’’ (Cowie, 1999, p. 154). Although (R) is nothing more than the general assumption on which cognitive psychology is founded applied to the case of language, even it has had its detractors. Critics have argued that linguistic competence should not in fact be thought of as based on the possession of a body of linguistic knowledge but should be thought of, rather, as a kind of skill. This is an important challenge because one might be inclined to think that no recognizable form of Chomskyan linguistics could withstand the falsification of (R). In this paper we attempt to show that in fact (R) could be false without doing much damage to Chomskyan linguistics at all. Indeed, it is possible that the Chomskyan position could be made more coherent by adopting the view we will sketch. Our claim, therefore, is that critics of (R) might be right, but that this does not obviously make them serious critics of the Chomskyan program. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

I build on Adam Smith’s account of the impartial spectator in The Theory of Moral Sentiments in order to offer a modest ideal observer theory of moral judgment that is adequate in the following sense: the account specifies the hypothetical conditions that guarantee the authoritativeness of an agent’s (or agents’) responses in constituting the standard in question, and, if an actual agent or an actual community of agents are not under those conditions, their responses are not authoritative in setting (...) this standard. However, in the account that I provide, the hypothetical conditions can themselves be constructed from the psychology and interactions of actual human beings. In other words, facts about the morally appropriate and inappropriate are determined from hypothetical conditions that––while agents in a given society might have yet to attain them––can be constructed from those agents’ shared experiences. Thus, the account offers both an attainable standard of moral judgment and a standard that can transcend the biases of the society which gave rise to it. I also defend the account against three challenges: (a) ideal observer theories do not offer the right kind of motivation to act on the verdicts of the ideal observer; (b) ideal observer theories cannot explain why the idealization in question is well-motivated and not objectionably ad hoc; (c) the standard used in ideal observer theories cannot be defended upon further reflection, because we would need a non-arbitrary, second-order standard to govern our reflection on the first-order standard of moral judgment. (shrink)

This paper describes a neglected aspect of the critique of academic ‘cultures of speed’ offered by Maggie Berg and Barbara Seeber in The Slow Professor. I argue internalisation of the values and imperatives of cultures of speed can encourage the erosion of a range of academic virtues while also facilitating the development of a range of academic vices. I focus on the ways that an internalised ‘psychology of speed’ erodes our capacity to exercise the virtues of intellectual beneficence – excellences (...) of character which advance the intellectual needs of others – by radically distorting our experience of time. (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)

Charitable interpreters of David Hume set aside his sprinkles of piety. Better to read him as lying than as clumsily inconsistent. We argue that the attribution of lies can pay dividends in historical scholarship no matter how strongly the theorist condemns lying. Accordingly, we show that our approach works even with one of the strongest condemners of lying: Immanuel Kant. We argue that Kant lied in his scholarly work and even in the first Critique. And we defend the claim that (...) this lie attribution, strange as it may sound, amounts to a kind of scholarly charity. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

A dealbreaker, in the sense developed in this essay, is a relationship between a person's psychology and an aspect of an artwork to which they are exposed. When a person has a dealbreaking aversion to an aspect of a work, they are blocked from embracing the work's aesthetically positive features. I characterize dealbreakers, distinguish this response from other negative responses to an artwork, and argue that the presence or absence of a dealbreaker is in some cases an appropriate target of (...) moral evaluation. I then use the concept of dealbreakers to develop a new approach to the question of our moral obligations with respect to the work of immoral artists, arguing that there is no general obligation binding us to cultivate or eliminate a dealbreaking aversion to their work. I conclude by suggesting several other philosophical debates that could benefit from a focus on dealbreakers. (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)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

A critique of Cora Diamond's influential approach to reading Wittgenstein's Tractatus. According to Diamond, the Tractatus contains no substantive philosophical theses, but is rather merely an especially subtle and sophisticated exercise in the unmasking of nonsense. I argue that no remotely convincing case for this interpretive thesis has yet been made--either by Diamond herself, or by the numerous defenders of this so-called "resolute" reading (so-called by those who wish to style themselves as resolute; their opponents tend to reject this characterization (...) as tendentious and rhetorically self-serving). Having critically scrutinized the arguments that have been offered in favor of the resolute reading, I proceed to amass evidence suggesting that, on the contrary, Wittgenstein advanced, and indeed took himself to have advanced, a host of substantive philosophical theses even in the (so-called) "body" of the Tractatus. I argue that resolute readers of the Tractatus have not begun to offer a plausible explanation of these problematic texts, and that the "frame/body" distinction alleged by resolute readers does not stand up to critical scrutiny. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

According to a venerable ideal, the core aim of philosophical practice is wisdom. The guiding concern of the ancient Greek, Indian, and Chinese traditions was the nature of the good life for human beings and the nature of reality. Central to these traditions is profound recognition of the subjection to adversities intrinsic to human life. I consider paradigmatic exemplars of wisdom, from ancient Western and Asian traditions, and the ways that experiences of adversity shaped their life. The suggestion is that (...) these exemplars, if any, will show how to live wisely in adversity. (shrink)

I offer a new interpretation of Feyerabend’s ‘conquest of abundance’ narrative. I consider and reject both the ontological reading as implausible and the ‘historical’ reading as uncompelling My own proposal is that the ‘conquest of abundance’ be understood in terms of an impoverishment of the richness of human experience. For Feyerabend, such abundance is ‘conquered’ when individuals internalize distorting epistemic prejudices including those integral to the theoretical conceptions associated with the sciences. I describe several ways, identified by Feyerabend, in which (...) individuals can be led to occlude the richness of their experience in ways that are existentially impoverishing. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The problem of evil is an ideal topic for experimental philosophy. Suffering--which is at the heart of most prominent formulations of the problem of evil--is a universal human experience and has been the topic of careful reflection for millennia. However, interpretations of suffering and how it bears on the existence of God are tremendously diverse and nuanced. We might immediately find ourselves wondering why (and how!) something so universal might be understood in so many different ways. Why does suffering push (...) some people toward atheism while pushing others toward deeper faith? What cultural, psychological, or sociological differences account for this diversity of responses? And, importantly, what light might this diversity of responses shed on the problem of evil and how it has been formulated by philosophers in recent years? The primary aim of this paper is to highlight how the tools and resources of experimental philosophy might be fruitfully applied to the problem of evil. In the first section, we review some recent work in this area and describe the current state of this emergent body of literature. In the second section, we review the broader and more recent theoretical developments on the problem of evil. Finally, in the final section, we outline some potential areas of future empirical research that we see as especially promising given those developments. (shrink)

In this paper, I will look at what role being able to provide justification plays in several prominent conceptions of epistemology, and argue that taking the ability to provide reasons as necessary for knowledge leads to a biasing toward false negatives. However, I will also argue that asking for reasons is a common practice among the general public, and one that is endorsed by “folk epistemology.” I will then discuss the fact that this asking for reasons is done neither constantly (...) nor arbitrarily, but rather in a systematic way that produces ignorance by oppressing some knowledge and some knowers, in particular those from already marginalized groups. After looking at the implications of all this, I will ultimately argue that we must be very careful when we ask for reasons, and acknowledge it as the powerful weapon it is. (shrink)

The 'Why ain'cha rich?' argument for one-boxing in Newcomb's problem allegedly vindicates evidential decision theory and undermines causal decision theory. But there is a good response to the argument on behalf of causal decision theory. I develop this response. Then I pose a new problem and use it to give a new 'Why ain'cha rich?' argument. Unlike the old argument, the new argument targets evidential decision theory. And unlike the old argument, the new argument is sound.

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 Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

For centuries it has been a mainstay of European and American moral thought that keeping promises—and the allied activity of upholding contracts—is one of the most important requirements of morality. On some historically powerful views the obligation to uphold promises or contracts not only regulates private relationships, but also provides the moral foundation for our duty to support and obey legitimate governments. Some theorists believe that the concept of keeping promises has gradually moved to center stage in European moral thought. (...) They see this movement as part of an historical shift from a moral conception in which an individual’s duties are mainly externally imposed and unalterable, to a conception in which duties are largely chosen by the individual. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

The introduction to a special issue of Religious Studies on the theme of experimental philosophy of religion.

It is widely held that episodic memory is constitutively connected with space and time. In particular, many contend that episodic memory constitutively has spatial and/or temporal content: for instance, necessarily representing a spatial scene, or when a given event occurred, or at the very minimum that it occurred in the past. Here, I critically assess such claims. I begin with some preparatory remarks on the nature of episodic memory. I then ask: How, if at all, is episodic memory constitutively spatial? (...) And, how, if at all, is episodic memory constitutively temporal? In answer, I argue that episodic memory need not have any spatial content, nor (in any substantial sense) need it represent when its events occur, nor even that they occur in the past. Instead, only a relatively modest connection holds between episodic memory and time in virtue of the temporal structure of its objects. Finally, I critically assess whether considerations concerning the organization and encoding of episodic memory in creatures like us provide stronger reason to posit a constitutive link between our episodic memories and space or time. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

Sustainability is commonly recognized as an important goal, but there is little agreement on what sustainability is, or what it requires. This paper looks at some common approaches to sustainability, and while acknowledging the ways in which they are useful, points out an important lacuna: that for something to be sustainable, people must be willing to work to sustain it. The paper presents a framework for thinking about and assessing sustainability which highlights people working to sustain. It also briefly discusses (...) Integrated Water Resource Management and the example of the California Water Plan to explore what such a perspective brings that is overlooked in other approaches, and how this approach might be pursued. Ultimately, this framework argues that a system can only be described as sustainable if people’s work to sustain the system is biophysically possible, socially possible, and if people would freely choose to do the sustaining work. -/- Read More: http://ascelibrary.org.proxy1.cl.msu.edu/doi/abs/10.1061/%28ASCE%29WR.1943-5452.0000526. (shrink)

This essay partly builds on and partly criticizes a striking idea of Dieter Henrich. Henrich argues that Kant's distinction in the first Critique between the question of fact (quid facti) and the question of law (quid juris) provides clues to the argumentative structure of a philosophical "Deduction". Henrich suggests that the unity of apperception plays a role analogous to a legal factum. By contrast, I argue, first, that the question of fact in the first Critique is settled by the Metaphysical (...) Deduction, which establishes the purity of origin of the Categories, and, second, that in the second Critique, the relevant factum is the Fact of Reason, which amounts to the fact that the Moral Law is pure in origin. (shrink)

Many people suspect it is morally wrong to watch the graphically violent horror films colloquially known as gorefests. A prominent argument vindicating this suspicion is the Argument from Reactive Attitudes (ARA). The ARA holds that we have a duty to maintain a well-functioning moral psychology, and watching gorefests violates that duty by threatening damage to our appropriate reactive attitudes. But I argue that the ARA is probably unsound. Depictions of suffering and death in other genres typically do no damage to (...) our appropriate reactive attitudes, and until we locate a relevant difference between these depictions in gorefests and in other genres, we should assume that the depictions in gorefests do no damage. I consider and reject three candidate differences: in artistic merit, meaningfulness, and audience orientation. Until genre skeptics identify a relevant difference, we should accept the taste for gory fictions as we would any other morally innocuous variation in taste. (shrink)

Many epistemologists have responded to the lottery paradox by proposing formal rules according to which high probability defeasibly warrants acceptance. Douven and Williamson present an ingenious argument purporting to show that such rules invariably trivialise, in that they reduce to the claim that a probability of 1 warrants acceptance. Douven and Williamson’s argument does, however, rest upon significant assumptions – amongst them a relatively strong structural assumption to the effect that the underlying probability space is both finite and uniform. In (...) this paper, I will show that something very like Douven and Williamson’s argument can in fact survive with much weaker structural assumptions – and, in particular, can apply to infinite probability spaces. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

This paper offers an overview of the philosophical work on epistemic injustices as it relates to psychiatry. After describing the development of epistemic injustice studies, we survey the existing literature on its application to psychiatry. We describe how the concept of epistemic injustice has been taken up into a range of debates in philosophy of psychiatry, including the nature of psychiatric conditions, psychiatric practices and research, and ameliorative projects. The final section of the paper indicates future directions for philosophical research (...) of epistemic injustices and psychiatry, concerning neurocognitive disorders, identity prejudices in psychiatric illness, concepts of epistemic privilege in psychiatry, and the prospects for combining phenomenological psychopathology and epistemic justice. We argue that much remains to be done in the conceptualization of these epistemic injustices and suggest that this future work should be multidisciplinary in character and sensitive to the phenomenology of psychiatric conditions. (shrink)