(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

This article seeks to describe in general terms what has become the standard way of conceptualizing moral injury in the clinical psychological and psychiatric literature, which is the key source for applications of the concept in other domains. What we call “the standard model” draws on certain assumptions about beliefs, mental states, and emotions as well as an implicit theory of causation about how various forms of harm arise from certain experiences or “events” that violate persons’ moral beliefs and systems. (...) Our analysis makes these assumptions more explicit and subjects them to critical scrutiny. In so doing, we survey the current literature and identify basic features of how moral injuries are defined, how they are thought to occur, and the forms of treatment or repair that appear to be indicated. We caution that it matters how moral experience is characterized and argue that an alternative understanding of what is the moral in moral injury is important for overcoming critical challenges to the standard model. Moreover, recently evolving approaches to moral repair could be more consistent with an alternative model. Our concluding suggestion is that a more robust account of the nature of moral experience and its relations to self-identity and social experience more generally could advance understanding of the etiology of moral injury and promote rehabilitation. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

In this paper, I investigate under-explored moments in Rousseau’s and Adam Smith’s writings in which each presents speech, and particularly testimony, as a manifestation of the desire for others’ recognition. I begin by considering some features of Rousseau’s understanding of amour-propre (or the desire for recognition from others) as well as that desire’s relevance for the conception of vocal speech (as in its nature passional) at the center of Rousseau’s Essay on the Origin of Languages. Since a feeling of (...) insult is the characteristic response to the thwarting of amour-propre, this connection between amour-propre and vocal speech might help to illuminate the distinctive insult (remarked upon by several philosophers) in having one’s speech act rejected. But there is also something incomplete in this thought insofar as it cannot yet distinguish the rejection involved in, say, not being believed from just any thwarting of amour-propre (or any instance of taking oneself to be demoted in another’s opinion). I then consider the possibility that this latter sort of observation might lie behind not only Adam Smith’s interest in what he calls our “mortification” in not being believed, but also his interest in a distinctive kind of response that we typically think of ourselves as owed, especially in the context of our addressing another person, but whose satisfactoriness consists in its being unforced. I end the paper by considering how Rousseau’s egalitarian political prescriptions (which contrast with the individual psychological maneuvers that Smith offers to those who go unbelieved) can be understood, in part, as aiming to limit the social significance of our dependence on another’s capricious judgment about our trustworthiness. (shrink)

In this paper we explore the idea that Pentecostalism is best supported by conjoining it to a postmodern, narrative epistemology in which everything is a text requiring interpretation. On this view, truth doesn’t consist in a set of uninterpreted facts that make the claims of Christianity true; rather, as James K. A. Smith says, truth emerges when there is a “fit” or proportionality between the Christian story and one’s affective and emotional life. We argue that Pentecostals should reject this (...) account of truth, since it leads to either a self-refuting story-relativism or the equally problematic fallacy of story-ism: favoring one’s own story over others without legitimate reason. In either case, we contend, the gospel itself is placed at risk. (shrink)

Can new technology enhance purpose-driven, democratic dialogue in groups, governments, and societies? Online Deliberation: Design, Research, and Practice is the first book that attempts to sample the full range of work on online deliberation, forging new connections between academic research, technology designers, and practitioners. Since some of the most exciting innovations have occurred outside of traditional institutions, and those involved have often worked in relative isolation from each other, work in this growing field has often failed to reflect the full (...) set of perspectives on online deliberation. This volume is aimed at those working at the crossroads of information/communication technology and social science, and documents early findings in, and perspectives on, this new field by many of its pioneers. -/- CONTENTS: -/- Introduction: The Blossoming Field of Online Deliberation (Todd Davies, pp. 1-19) -/- Part I - Prospects for Online Civic Engagement -/- Chapter 1: Virtual Public Consultation: Prospects for Internet Deliberative Democracy (James S. Fishkin, pp. 23-35) -/- Chapter 2: Citizens Deliberating Online: Theory and Some Evidence (Vincent Price, pp. 37-58) -/- Chapter 3: Can Online Deliberation Improve Politics? Scientific Foundations for Success (Arthur Lupia, pp. 59-69) -/- Chapter 4: Deliberative Democracy, Online Discussion, and Project PICOLA (Public Informed Citizen Online Assembly) (Robert Cavalier with Miso Kim and Zachary Sam Zaiss, pp. 71-79) -/- Part II - Online Dialogue in the Wild -/- Chapter 5: Friends, Foes, and Fringe: Norms and Structure in Political Discussion Networks (John Kelly, Danyel Fisher, and Marc Smith, pp. 83-93) -/- Chapter 6: Searching the Net for Differences of Opinion (Warren Sack, John Kelly, and Michael Dale, pp. 95-104) -/- Chapter 7: Happy Accidents: Deliberation and Online Exposure to Opposing Views (Azi Lev-On and Bernard Manin, pp. 105-122) -/- Chapter 8: Rethinking Local Conversations on the Web (Sameer Ahuja, Manuel Pérez-Quiñones, and Andrea Kavanaugh, pp. 123-129) -/- Part III - Online Public Consultation -/- Chapter 9: Deliberation in E-Rulemaking? The Problem of Mass Participation (David Schlosberg, Steve Zavestoski, and Stuart Shulman, pp. 133-148) -/- Chapter 10: Turning GOLD into EPG: Lessons from Low-Tech Democratic Experimentalism for Electronic Rulemaking and Other Ventures in Cyberdemocracy (Peter M. Shane, pp. 149-162) -/- Chapter 11: Baudrillard and the Virtual Cow: Simulation Games and Citizen Participation (Hélène Michel and Dominique Kreziak, pp. 163-166) -/- Chapter 12: Using Web-Based Group Support Systems to Enhance Procedural Fairness in Administrative Decision Making in South Africa (Hossana Twinomurinzi and Jackie Phahlamohlaka, pp. 167-169) -/- Chapter 13: Citizen Participation Is Critical: An Example from Sweden (Tomas Ohlin, pp. 171-173) -/- Part IV - Online Deliberation in Organizations -/- Chapter 14: Online Deliberation in the Government of Canada: Organizing the Back Office (Elisabeth Richard, pp. 177-191) -/- Chapter 15: Political Action and Organization Building: An Internet-Based Engagement Model (Mark Cooper, pp. 193-202) -/- Chapter 16: Wiki Collaboration Within Political Parties: Benefits and Challenges (Kate Raynes-Goldie and David Fono, pp. 203-205) -/- Chapter 17: Debian’s Democracy (Gunnar Ristroph, pp. 207-211) -/- Chapter 18: Software Support for Face-to-Face Parliamentary Procedure (Dana Dahlstrom and Bayle Shanks, pp. 213-220) -/- Part V - Online Facilitation -/- Chapter 19: Deliberation on the Net: Lessons from a Field Experiment (June Woong Rhee and Eun-mee Kim, pp. 223-232) -/- Chapter 20: The Role of the Moderator: Problems and Possibilities for Government-Run Online Discussion Forums (Scott Wright, pp. 233-242) -/- Chapter 21: Silencing the Clatter: Removing Anonymity from a Corporate Online Community (Gilly Leshed, pp. 243-251) -/- Chapter 22: Facilitation and Inclusive Deliberation (Matthias Trénel, pp. 253-257) -/- Chapter 23: Rethinking the ‘Informed’ Participant: Precautions and Recommendations for the Design of Online Deliberation (Kevin S. Ramsey and Matthew W. Wilson, pp. 259-267) -/- Chapter 24: PerlNomic: Rule Making and Enforcement in Digital Shared Spaces (Mark E. Phair and Adam Bliss, pp. 269-271) -/- Part VI - Design of Deliberation Tools -/- Chapter 25: An Online Environment for Democratic Deliberation: Motivations, Principles, and Design (Todd Davies, Brendan O’Connor, Alex Cochran, Jonathan J. Effrat, Andrew Parker, Benjamin Newman, and Aaron Tam, pp. 275-292) -/- Chapter 26: Online Civic Deliberation with E-Liberate (Douglas Schuler, pp. 293-302) -/- Chapter 27: Parliament: A Module for Parliamentary Procedure Software (Bayle Shanks and Dana Dahlstrom, pp. 303-307) -/- Chapter 28: Decision Structure: A New Approach to Three Problems in Deliberation (Raymond J. Pingree, pp. 309-316) -/- Chapter 29: Design Requirements of Argument Mapping Software for Teaching Deliberation (Matthew W. Easterday, Jordan S. Kanarek, and Maralee Harrell, pp. 317-323) -/- Chapter 30: Email-Embedded Voting with eVote/Clerk (Marilyn Davis, pp. 325-327) -/- Epilogue: Understanding Diversity in the Field of Online Deliberation (Seeta Peña Gangadharan, pp. 329-358). -/- For individual chapter downloads, go to odbook.stanford.edu. (shrink)

In this paper I draw attention to a peculiar epistemic feature exhibited by certain deductively valid inferences. Certain deductively valid inferences are unable to enhance the reliability of one's belief that the conclusion is true—in a sense that will be fully explained. As I shall show, this feature is demonstrably present in certain philosophically significant inferences—such as GE Moore's notorious 'proof' of the existence of the external world. I suggest that this peculiar epistemic feature might be correlated with the much (...) discussed phenomenon that Crispin Wright and Martin Davies have called 'transmission failure'—the apparent failure, on the part of some deductively valid inferences to transmit one's justification for believing the premises. (shrink)

In this paper we respond to three objections raised by Joshua Harris to our article, “Against a Postmodern Pentecostal Epistemology,” in which we express misgivings about the conjunction of Pentecostalism with James K. A. Smith’s postmodern, story-based epistemolo- gy. According to Harris, our critique: 1) problematically assumes a correspondence theory of truth, 2) invalidly concludes that “Derrida’s Axiom” conflicts with “Peter’s Axiom,” and 3) fails to consider an alternative account of the universality of Christian truth claims. We argue that (...) Harris’s objections either demonstrate a deficient interpretation of the relevant biblical pas- sages or are not directed at us at all. (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)

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

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)

I argue that Adam Smith does more than providing an account of competitive behavior loosely linked to an underlying psychology since the joint between the complex psychology of The Theory of Moral Sentiments and the invisible hand pages in The Wealth of Nations explains why some of the basest affections, greed and ambition, prevail over other tendencies in certain social groups, namely merchants and manufacturers, in a commercial and urban society.

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)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

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)

Most philosophers writing on the ethics of war endorse “reductivist individualism,” a view that holds both that killing in war is subject to the very same principles of ordinary morality ; and that morality concerns individuals and their rights, and does not treat collectives as having any special status. I argue that this commitment to individualism poses problems for this view in the case of national defense. More specifically, I argue that the main strategies for defending individualist approaches to national (...) defense either fail by their own lights or yield deeply counterintuitive implications. I then offer the foundations for a collectivist approach. I argue that such an approach must do justice to the collective goods that properly constituted states make possible and protect through certain acts of defensive war; and that any such picture of national defense must make room for some form of national partiality. (shrink)

Epistemologists typically assume that the acquisition of knowledge from testimony is not threatened at the stage at which audiences interpret what proposition a speaker has asserted. Attention is instead typically paid to the epistemic status of a belief formed on the basis of testimony that it is assumed has the same content as the speaker’s assertion. Andrew Peet has pioneered an account of how linguistic context sensitivity can threaten the assumption. His account locates the threat in contexts in which an (...) audience’s evidence under-determines which proposition a speaker is asserting. I argue that Peet’s epistemic uncertainty account of the threat is mistaken and I propose an alternative. The alternative locates the threat in contexts that provide factors that give audiences a mistaken psychological certainty or confidence that a speaker has asserted a proposition she has not. (shrink)

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (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)

In the 1980s and 1990s, a series of attempts were made to put into U.S. law a civil rights ordinance that would make it possible to sue the makers and distributors of pornography for doing so (under certain conditions). One defence of such legislation has come to be called "the free speech argument against pornography." Philosophers Rae Langton, Jennifer Hornsby and Caroline West have supposed that this defence of the legislation can function as a liberal defence of the legislation: in (...) particular, a defence of the legislation based on the value of women's liberty. This would be somewhat unexpected given MacKinnon's own antipathy toward liberalism. In this paper, I argue that the free speech argument against pornography cannot be used as a liberal defence of the ordinances. The legislation is, to some extent, self-defeating insofar as it understood in terms acceptable to a fairly standard kind of liberal. This becomes apparent when we consider the value pornography can have for women, which we can see if we consider what female makers, distributors and consumers of pornography have to say about why they make, distribute and consume it. (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)

Computer-Assisted Argument Mapping (CAAM) is a new way of understanding arguments. While still embryonic in its development and application, CAAM is being used increasingly as a training and development tool in the professions and government. Inroads are also being made in its application within education. CAAM claims to be helpful in an educational context, as a tool for students in responding to assessment tasks. However, to date there is little evidence from students that this is the case. This paper outlines (...) the use of CAAM as an educational tool within an Economics and Commerce Faculty in a major Australian research university. Evaluation results are provided from students from a CAAM pilot within an upper-level Economics subject. Results indicate promising support for the use of CAAM and its potential for transferability within the disciplines. If shown to be valuable with further studies, CAAM could be included in capstone subjects, allowing computer technology to be utilised in the service of generic skill development. (shrink)

We analyze the logical form of the domain knowledge that grounds analogical inferences and generalizations from a single instance. The form of the assumptions which justify analogies is given schematically as the "determination rule", so called because it expresses the relation of one set of variables determining the values of another set. The determination relation is a logical generalization of the different types of dependency relations defined in database theory. Specifically, we define determination as a relation between schemata of first (...) order logic that have two kinds of free variables: (1) object variables and (2) what we call "polar" variables, which hold the place of truth values. Determination rules facilitate sound rule inference and valid conclusions projected by analogy from single instances, without implying what the conclusion should be prior to an inspection of the instance. They also provide a way to specify what information is sufficiently relevant to decide a question, prior to knowledge of the answer to the question. (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)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

According to telling based views of testimony (TBVs), B has reason to believe that p when A tells B that p because A thereby takes public responsibility for B's subsequent belief that p. Andrew Peet presents a new argument against TBVs. He argues that insofar as A uses context-sensitive expressions to express p, A doesn't take public responsibility for B's belief that p. Since context-sensitivity is widespread, the kind of reason TBVs say we have to believe what we're told, is (...) not widespread. Peet doesn't identify any problem with his own argument though he does attempt to limit its sceptical potential by identifying special contexts in which TBVs stand a chance of success. A more general defence of TBVs can be provided by showing Peet's argument to be unsound. I argue that Peet's argument is unsound because it requires us to wrongly suppose that speakers do far less labour than their audiences in context-sensitive linguistic communication. I aim to show why—in the context of the epistemology of testimony and the philosophy of language—it's important to recognize the labour that speakers can do, and so can can be held responsible for not doing, in episodes of context-sensitive linguistic communication. (shrink)

_ Source: _Page Count 25 This is a pre-print. Please cite only the revised published version. This paper presents an original, ambitious, truth-directed transcendental argument for the existence of an ‘external world’. It begins with a double-headed starting-point: Stroud’s own remarks on the necessary conditions of language in general, and Hegel’s critique of the “fear of error.” The paper argues that the sceptical challenge requires a particular critical concept of thought as that which may diverge from reality, and that this (...) concept is possible only through reflection on situations of error, in which how things are thought to be diverges from how things really are with independent items in an objective world. The existence of such a world is therefore a necessary condition of the possibility of scepticism: such scepticism is therefore false. I defend the argument against objections from Stroud’s sceptic and others. Drawing on Heidegger, the paper concludes by indicating that the chain of necessary conditions includes practical engagement with the world. (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)

Georgalis claimed that when Frege wrote ‘Über Sinn und Bedeutung’ Frege thought that the indirect [ungerade] sense of an expression was identical to its normal [gewöhnlich] sense (Georgalis 2022: e.g. 4, 5, 13). In this paper, I present five arguments for the falsity of Georgalis’ claim which are based on three pieces of apparent counterevidence: a passage from Frege’s letter to Russell dated 28.12.1902; a passage from Frege’s letter to Russell dated 20.10.1902; and a passage from ‘Über Sinn und Bedeutung’. (...) I outline possible counter-arguments and responses. (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)

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.

This paper resolves a paradox concerning colour constancy. On the one hand, our intuitive, pre-theoretical concept holds that colour constancy involves invariance in the perceived colours of surfaces under changes in illumination. On the other, there is a robust scientific consensus that colour constancy can persist in cerebral achromatopsia, a profound impairment in the ability to perceive colours. The first stage of the solution advocates pluralism about our colour constancy capacities. The second details the close relationship between colour constancy and (...) contrast. The third argues that achromatopsics retain a basic type of colour constancy associated with invariants in contrast processing. The fourth suggests that one person-level, conscious upshot of such processing is the visual awareness of chromatic contrasts ‘at’ the edges of surfaces, implicating the ‘colour for form’ perceptual function. This primitive type of constancy sheds new light on our most basic perceptual capacities, which mark the lower borders of representational mind. (shrink)

Stephen Davies taught philosophy at the University of Auckland, Auckland, New Zealand. His research specialty is the philosophy of art. He is a former President of the American Society for Aesthetics. His books include Definitions of Art (Cornell UP, 1991), Musical Meaning and Expression (Cornell UP, 1994), Musical Works and Performances (Clarendon, 2001), Themes in the Philosophy of Music (OUP, 2003), Philosophical Perspectives on Art (OUP, 2007), Musical Understandings and Other Essays on the Philosophy of Music (OUP, 2011), The Artful (...) Species: Aesthetics, Art, and Evolution (OUP, 2012), The Philosophy of Art (Wiley-Blackwell, 2016 second ed.), and Adornment: What Self-decorations Tells Us about Who We Are, (Bloomsbury Academic, 2020). (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

A considerable literature has emerged around the idea of using ‘personal responsibility’ as an allocation criterion in healthcare distribution, where a person's being suitably responsible for their health needs may justify additional conditions on receiving healthcare, and perhaps even limiting access entirely, sometimes known as ‘responsibilisation’. This discussion focuses most prominently, but not exclusively, on ‘luck egalitarianism’, the view that deviations from equality are justified only by suitably free choices. A superficially separate issue in distributive justice concerns the two–way relationship (...) between health and other social goods: deficits in health typically undermine one's abilities to secure advantage in other areas, which in turn often have further negative effects on health. This paper outlines the degree to which this latter relationship between health and other social goods exacerbates an existing problem for proponents of responsibilisation (the ‘harshness objection’) in ways that standard responses to this objection cannot address. Placing significant conditions on healthcare access because of a person's prior responsibility risks trapping them in, or worsening, negative cycles where poor health and associated lack of opportunity reinforce one another, making further poor yet ultimately responsible choices more likely. It ends by considering three possible solutions to this problem. (shrink)

Buddhism originated and developed in an Indian cultural context that featured many first-person practices for producing and exploring states of consciousness through the systematic training of attention. In contrast, the dominant methods of investigating the mind in Western cognitive science have emphasized third-person observation of the brain and behavior. In this chapter, we explore how these two different projects might prove mutually beneficial. We lay the groundwork for a cross-cultural cognitive science by using one traditional Buddhist model of the mind (...) – that of the five aggregates – as a lens for examining contemporary cognitive science conceptions of consciousness. (shrink)

The Food and Drug Administration (FDA) recently issued its first approval of an oral contraceptive medication for access without a clinician’s prescription. One might expect this will lead to fewer people seeking to terminate unplanned pregnancies, including in states that imposed severe restrictions on abortion care following the Supreme Court’s reversal on abortion rights in Dobbs v. Jackson Women’s Health Organization. Despite the clear potential health benefits, increased accessibility of oral contraceptives offers no real solution to ongoing threats to patients’ (...) reproductive health and moral rights created by post-Dobbs abortion restrictions. To secure their patients’ reproductive health and well-being, clinicians must work to maximize the benefits of OTC oral contraceptives without relenting in their advocacy for safe and accessible abortion care. (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.

At some point in the future – perhaps within the next few decades – it will be possible for foetuses to develop completely outside the womb. Ectogenesis, as this technology is called, raises substantial issues for the abortion debate. One such issue is that it will become possible for a woman to have an abortion, in the sense of having the foetus removed from her body, but for the foetus to be kept alive. We argue that while there is a (...) right to an abortion, there are reasons to doubt that there is a right to the death of the foetus. Our strategy in this essay is to consider and reject three arguments in favour of this latter right. The first claims that women have a right not to be biological mothers, the second that women have a right to genetic privacy, and the third that a foetus is one's property. Furthermore, we argue that it follows from rejecting the third claim that genetic parents also lack a right to the destruction of cryopreserved embryos used for in vitro fertilization. The conclusion that a woman possesses no right to the death of the foetus builds upon the claims that other pro-choice advocates, such as Judith Jarvis Thomson, have made. (shrink)

In anticipation of the journal’s centenary in 2027 this paper provides a citation network analysis of all available citation and publication data of the Australasian Journal of Philosophy (1923–2017). A total of 2,353 academic articles containing 21,772 references were collated and analyzed. This includes 175 articles that contained author-submitted keywords, 415 publisher-tagged keywords and 519 articles that had abstracts. Results initially focused on finding the most published authors, most cited articles and most cited authors within the journal, followed by most (...) discussed topics and emerging patterns using keywords and abstracts. The analysis then proceeded to apply social network analysis using Kumu© – a visualization platform for mapping systems and relationships using large datasets. Analysis reveals topic clusters both unique to the journal, and inclusive of the journal’s history. Results from this analysis reaffirm the journal’s continuing focus on topics in traditional analytic philosophy such as morality, epistemology and knowledge, whilst also featuring topics associated with logic and paradox. This paper presents a new approach to analysing and understanding the historic and emerging topics of interest to the journal, and its readership. This has never previously been done for single philosophy journal. This is historically important given the journal’s forthcoming centenary. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

This paper argues that private property and rights assignment, especially as applied to communication infrastructure and information, should be informed by advances in both technology and our understanding of psychology. Current law in this area in the United States and many other jurisdictions is founded on assumptions about human behavior that have been shown not to hold empirically. A joint recognition of this fact, together with an understanding of what new technologies make possible, leads one to question basic assumptions about (...) how law is made and what laws we should have in a given area, if any. I begin by analyzing different aspects of U.S. law, from a high-level critique of law making to a critique of rights assignment for what I call 'simple nonrival goods.' I describe my understanding, as a non-lawyer with a background in psychology and computing, of the current conventions in U.S. law, consider the foundational assumptions that justify current conventions, describe advances in psychology and technology that call these conventions into question, and briefly note how the law might normatively change in this light. I then apply this general analysis to the question of domain name assignment by the Internet Corporation for Assigned Names and Numbers (ICANN). (shrink)

This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information scientists.

Throughout the COVID-19 pandemic, shortages of scarce healthcare resources consistently presented significant moral and practical challenges. While the importance of vaccines as a key pharmaceutical intervention to stem pandemic scarcity was widely publicized, a sizable proportion of the population chose not to vaccinate. In response, some have defended the use of vaccination status as a criterion for the allocation of scarce medical resources. In this paper, we critically interpret this burgeoning literature, and describe a framework for thinking about vaccine-sensitive resource (...) allocation using the values of responsibility, reciprocity, and justice. Although our aim here is not to defend a single view of vaccine-sensitive resource allocation, we believe that attending critically with the diversity of arguments in favor (and against) vaccine-sensitivity reveals a number of questions that a vaccine-sensitive approach to allocation should answer in future pandemics. (shrink)