Bunge (2000) distinguishes two main methodological approaches of holism and individualism, and associates with them policy prescriptions of centralism and laissez-faire. He identifies systemism as a superior approach to both the study and management of society. The present paper, seeking to correct and develop this line of thought, suggests a more complex relation between policy and methodology. There are two possible methodological underpinnings for laissez-faire: while writers such as Friedman and Lucas fit Bunge’s pattern, more sophisticated advocates of laissez-faire, such (...) as Smith and Hayek, base their policy prescription in a methodology quite divergent from the individualism Bunge describes. (shrink)

This thesis argues for the fundamental importance of the opposition between holistic and reductionistic world-views in economics. Both reductionism and holism may nevertheless underpin laissez-faire policy prescriptions. Scrutiny of the nature of the articulation between micro and macro levels in the writings of economists suggests that invisible hand theories play a key role in reconciling reductionist policy prescriptions with a holistic world. An examination of the prisoners' dilemma in game theory and Arrow's impossibility theorem in social choice theory sets the (...) scene. The prisoners' dilemma epitomises the collective irrationality coordination problems lead to. The source of the dilemma is identified as the combination of interdependence in content and independence in form of the decision making process. Arrovian impossibility has been perceived as challenging traditional views of the relationship between micro and macro levels in economics. Conservative arguments against the possibility in principle of a social welfare function are criticised here as depending on an illicit dualism. The thesis then reviews the standpoints of Smith, Hayek and Keynes. For Smith, the social desirability of individual self-seeking activity is ensured by the 'invisible hand' of a god who has moulded us so to behave, that the quantity of happiness in the world is always maximised. Hayek seeks to re-establish the invisible hand in a secular age, replacing the agency of a deity with an evolutionary mechanism. Hayek's evolutionary theory, criticised here as being based on the exploded notion of group selection, cannot underpin the desirability of spontaneous outcomes. I conclude by arguing that Keynes shares the holistic approach of Smith and Hayek, but without their reliance on invisible hand mechanisms. If spontaneous processes cannot be relied upon to generate desirable social outcomes then we have to take responsibility for achieving this ourselves by establishing the appropriate institutional framework to eliminate macroeconomic prisoners' dilemmas. (shrink)

In a world of partially overlapping and partially conflicting interests there is good reason to doubt that self-seeking behaviour at the micro-level will spontaneously lead to desirable social outcomes at the macro-level. Nevertheless, some sophisticated economic writers advocating a laissez-faire policy prescription have proposed various 'invisible hand' mechanisms which can supposedly be relied upon to 'educe good from ill'. Smith defended the 'simple system of natural liberty' as giving the greatest scope to the unfolding of God's will and the (...) working out of 'natural' providential processes free of interference by 'artificial' state intervention - the expression not of divine order but of fallible human reason. Hayek, adopting a similar policy stance, based it in an evolutionary process in which those institutional forms best adapted to reconciling individual interests would, he believed, spontaneously be selected for in the inter-group struggle for survival. Keynes shares the holistic approach of Smith and Hayek, but without their reliance on invisible hand mechanisms. If spontaneous processes cannot be relied upon to generate desirable social outcomes then we have to take responsibility for achieving this ourselves by establishing the appropriate institutional framework. Keynes takes a historical view of the role of capitalism and analyses its pathology as rooted in what we would now refer to as a multi-player prisoners' dilemma. The paper draws out the significance of his methodological standpoint here. Keynes's policy standpoint assigns a critical role to his own class, the 'educated bourgeoisie' in the reform process he maps out. A distinction, but also an intimate connection, is highlighted between, on the one hand, micro-level individualism (the 'Manchester System, and, on the other, the macro-level collective action ('planning') required to preserve it. Finally Keynes is considered in relation to the themes of laissez-faire, holism, reductionism, providentialism and the invisible hand. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

The moral status of animals is a subject of controversy both within and beyond academic philosophy, especially regarding the question of whether and when it is ethical to eat meat. A commitment to animal rights and related notions of animal protection is often thought to entail a plant-based diet, but recent philosophical work challenges this view by arguing that, even if animals warrant a high degree of moral standing, we are permitted - or even obliged - to eat meat. (...) class='Hi'>Andy Lamey provides critical analysis of past and present dialogues surrounding animal rights, discussing topics including plant agriculture, animal cognition, and in vitro meat. He documents the trend toward a new kind of omnivorism that justifies meat-eating within a framework of animal protection, and evaluates for the first time which forms of this new omnivorism can be ethically justified, providing crucial guidance for philosophers as well as researchers in culture and agriculture. (shrink)

A very simple contextualist treatment of a sentence containing an epistemic modal, e.g. a might be F, is that it is true iff for all the contextually salient community knows, a is F. It is widely agreed that the simple theory will not work in some cases, but the counterexamples produced so far seem amenable to a more complicated contextualist theory. We argue, however, that no contextualist theory can capture the evaluations speakers naturally make of sentences containing epistemic modals. If (...) we want to respect these evaluations, our best option is a relativist theory of epistemic modals. On a relativist theory, an utterance of a might be F can be true relative to one context of evaluation and false relative to another. We argue that such a theory does better than any rival approach at capturing all the behaviour of epistemic modals. (shrink)

Hohwy (Hohwy 2016, Hohwy 2017) argues there is a tension between the free energy principle and leading depictions of mind as embodied, enactive, and extended (so-called ‘EEE1 cognition’). The tension is traced to the importance, in free energy formulations, of a conception of mind and agency that depends upon the presence of a ‘Markov blanket’ demarcating the agent from the surrounding world. In what follows I show that the Markov blanket considerations do not, in fact, lead to the kinds of (...) tension that Hohwy depicts. On the contrary, they actively favour the EEE story. This is because the Markov property, as exemplified in biological agents, picks out neither a unique nor a stationary boundary. It is this multiplicity and mutability– rather than the absence of agent-environment boundaries as such - that EEE cognition celebrates. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

Philosophers have highlighted a dilemma for the criminal law. Unjust, racist policies in the United States have produced conditions in which the dispossessed are more likely to commit crime. This complicity undermines the standing of the state to blame their offenses. Nevertheless, the state has reason to punish those crimes in order to deter future offenses. Tommie Shelby proposes a way out of this dilemma. He separates the state’s right to condemn from its right to punish. I raise doubts about (...) Shelby’s proposed resolution. So long as punishment is widely and reasonably understood to condemn crime, Shelby’s proposal does not resolve the dilemma. Moreover, there is reason to think the blaming aspect of punishment plays a role in the justification of its hard treatment. I conclude by considering some other ways out of the dilemma, focusing especially on how the United States might take responsibility for its complicity. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (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)

This article brings animal protection theory to bear on Temple Grandin’s work, in her capacity both as a designer of slaughter facilities and as an advocate for omnivorism. Animal protection is a better term for what is often termed animal rights, given that many of the theories grouped under the animal rights label do not extend the concept of rights to animals. I outline the nature of Grandin’s system of humane slaughter as it pertains to cattle. I then outline four (...) arguments Grandin has made defending meat-eating. On a protection-based approach, I argue, Grandin’s system of slaughter is superior to its traditional counterpart. Grandin’s success as a designer of humane slaughterhouses however is not matched by any corresponding success in offering a moral defence of meat-eating. Despite, or perhaps because of, the popularity of her work, Grandin’s arguments for continuing to eat animals are noteworthy only in how disappointing and rudimentary they are. If we can thank Grandin for making a difference in the lives of millions of farm animals, her work can also be criticized for not engaging the moral status of animals with the depth and rigor that it deserves. (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)

The Handmaid’s Tale depicts a United States taken over by a fundamentalist dictatorship called Gilead that also resembles Plato’s ideal city. Attempts to explain Gilead’s debt to Plato face two challenges. First, aspects of Gilead that recall Plato also contain features that differ, at times dramatically, from the Platonic original. Second, Gilead invokes distorted versions of ideas from philosophies other than Plato’s. I explore two ways of making sense of Gilead’s distorted philosophical appropriations. The explanations differ over whether such distortions (...) are best explained by the nature of the philosophies they misrepresent, or by the nature of Gilead. The explanation that emphasizes Gilead’s own agency is ultimately best able to make sense of how illiberal regimes misappropriate philosophical concepts, both in the novel and in reality, in order to limit the political imagination of their subjects. (shrink)

During long-term refugee displacements, it is common for the refugees’ country of origin to be called on to recognize a right of return. A long-standing tradition of philosophical theorizing is sceptical of such a right. Howard Adelman and Elazar Barkan are contemporary proponents of this view. They argue that, in many cases, it is not feasible for entire refugee populations to return home, and so the notion of a right of return is no right at all. We can call Adelman (...) and Barkan’s view the feasibility objection. Many defenders of rights will deny that empirical facts such as the kind to which Adelman and Barkan appeal are relevant to determining whether a moral entitlement amounts to a right. In contrast, I offer a response to the feasibility objection that does admit the relevance of facts. In my view, considerations of feasibility do matter when determining what rights human beings possess. Nevertheless, the feasibility objection is undone by its failure to acknowledge a distinction between two different kinds of feasibility constraints. ‘Hard’ constraints include logical, nomological and biological considerations. ‘Soft’ constraints include political, cultural and institutional factors. A necessary condition of a moral entitlement achieving the status of a right, I argue, is that it be feasible in the hard sense. Crucially, however, a right need not always be feasible in the soft sense. Refugees can have rights that it is not currently possible to implement politically. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

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

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)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

Freeganism is the practice of eating food that is free. It is commonly associated with recovering food that grocery stores and restaurants have thrown away, but vegetables grown in one’s garden and other free foods, such as leftovers from a work event, would also qualify. It is worth asking whether there is a form of freeganism that can be justified in new omnivorist terms. Could it be consistent with animal protection to eat meat, just so long as we don’t pay (...) for it? -/- I argue that from an animal protection point of view, freegan meat consumption faces two difficulties. The first is that when it involves the consumption of animal flesh conventionally regarded as edible (chicken, pork, beef, etc.) but not other types of flesh commonly considered inedible (mice, dogs, etc.), the practice is likely to be rooted in speciesism. This runs contrary to new omnivorism’s own principles, which are anti-speciesist. In addition, when the meat in question is the product of animal agriculture, consuming it will amount to a form of complicity in the industry’s wrong-doing, as the rationale for the animal’s slaughter will be retroactively endorsed. Either of these two considerations taken by itself will suffice to generate a presumption against freegan meat consumption. -/- My analysis, however, does not address every conceivable defense of freegan meat consumption. In particular, neither consideration generates a reason to avoid all animal by-products, such as eggs from backyard chickens that are well cared for. But given that the by-products in question will not be industrially produced, such consumption is likely to be permissible only in exceptional instances, rather than a practice available to society at large. (shrink)

Hannah Arendt argued that refugees pose a major problem for liberalism. Most liberal theorists endorse the idea of human rights. At the same time, liberalism takes the existence of sovereign states for granted. When large numbers of people petition a liberal state for asylum, Arendt argued, these two commitments will come into conflict. An unwavering respect for human rights would mean that no refugee is ever turned away. Being sovereign, however, allows states to control their borders. States supposedly committed to (...) human rights will thus often violate the rights of refugees by denying them entry. I attempt to defend liberalism from Arendt’s criticism by outlining a rights-based model of asylum that is enforceable by sovereign states. This approach avoids the question of what border-enforcement measures, if any, are defensible at the level of ideal justice, and instead seeks to outline a framework of refugee rights that can be realized in a world in which migration controls are a fact of life. Central to my argument is a distinction between the place where a person is recognized as a rights-bearing agent and the potentially different place where he or she exercises those rights. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

One of the starting assumptions in the debate over the ethical status of animals is that someone who is committed to reducing animal suffering should not eat meat. Steven Davis has recently advanced a novel criticism of this view. He argues that individuals who are committed to reducing animal suffering should not adopt a vegetarian or vegan diet, as Tom Regan an other animal rights advocates claim, but one containing free-range beef. To make his case Davis highlights an overlooked form (...) of animal harm, that done to field animals in crop production. Yet while Davis's argument is ingenious and thought-provoking, it is not a successful challenge to vegetarianism and veganism's status as the diets that most advance animal rights. Scientific studies of crop production that Davis draws on document two different forms of harm done to field animals: those that are directly killed by harvesting equipment and those that are killed by other animals. Once this distinction is made explicit, the degree to which such studies pose a problem for animal protection theory considerably weakens. Davis also overlooks philosophically significant forms of harm to human beings that are present in beef production but not crop harvesting. Finally, he bases his argument on the controversial assumption that there is no difference between deliberate and accidental killing - either of animals or people. Although these problems defeat Davis's attempt to offer an immanent critique of Regan's animal rights position, his analysis does have important dietary ramifications that animal advocates should take into account. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Recent work in moral theory has seen the refinement of theories of moral standing, which increasingly recognize a position of intermediate standing between fully self-conscious entities and those which are merely conscious. Among the most sophisticated concepts now used to denote such intermediate standing is that of primitive self-consciousness, which has been used to more precisely elucidate the moral standing of human newborns. New research into the structure of the avian brain offers a revised view of the cognitive abilities of (...) birds. When this research is approached with a species-specific focus, it appears likely that one familiar species, the chicken (Gallus gallus domesticus), also exhibits primitive self-consciousness. Given the likelihood that they are primitively self-consciousness, chickens warrant a degree of moral standing that falls short of that enjoyed by persons, but which exceeds the minimal standing of merely conscious entities. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Jurisdictionism offers a new rationale for restricting immigration. Immigrants impose new obligations on the people whose territories they enter. Insofar as these obligations are unwanted, polities are justified in turning immigrants away, so long as the immigrants are from a country that respects their rights. The theory, however, employs a flawed account of obligation, which overlooks how we can be obliged to take on new duties to immigrants. Jurisdictionism also employs different standards when determining whether an obligation exists, only one (...) of which is sensitive to consequences. Finally, the theory falsely claims that obligations necessarily reduce the freedom of the obliged. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (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)

The notion of a spontaneous order has a long history in the philosophy of economics, where it has been used to advance a view of markets as complex networks of information that no single mind can apprehend. Traditionally, the impossibility of grasping all of the information present in the spontaneous order of the market has been invoked as grounds for not subjecting markets to central planning. A less noted feature of the spontaneous order concept is that when it is applied (...) to ecosystems it yields a reasonably strong environmental ethic. Thinking of ecosystems as spontaneous orders generates a presumption against interfering with their natural functioning in a manner that results in anthropogenic species loss. Such a presumption will permit some interventions in nature while precluding others. Environmental ethics could potentially make valuable use of the spontaneous order idea, without necessarily endorsing its traditional application to markets. (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)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, and we outline an associated knowledge modelling language called GOL – for: General Ontological Language. It turns out that the upper-level ontology underlying well-known standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. In a set theory which allows Urelements, however, there (...) will be ontological relations between these Urelements which the set-theoretic machinery cannot capture. In contrast to standard modelling and representation formalisms, GOL provides a machinery for representing and analysing such ontologically basic relations. GOL is thus a genuine extension of KIF and of similar languages. In GOL entities are divided into sets and Urelements, the latter being divided in their turn into individuals and universals. Foremost among the individuals are things or substances, tropes or moments, and situoids: entities containing facts as components. (shrink)

I argue against two of the most influential contemporary theories of moral responsibility: those of Harry Frankfurt and John Martin Fischer. Both propose conditions which are supposed to be sufficient for direct moral responsibility for actions. (By the term direct moral responsibility, I mean moral responsibility which is not traced from an earlier action.) Frankfurt proposes a condition of 'identification'; Fischer, writing with Mark Ravizza, proposes conditions for 'guidance control'. I argue, using counterexamples, that neither is sufficient for direct moral (...) responsibility. -/- My counterexample cases are based on recent research in psychology which reveals many surprising causes of our actions. Some of this research comes from the field of situationist social psychology; some from experiments which reveal the influence of automatic processes in our actions. Broadly, I call such causes 'subverting' when the agent would not identify with her action, if she knew all the causes of the action. When an action has subverting causes, the agent is not directly morally responsible for it, even though she may meet the conditions specified by Frankfurt and Fischer. -/- I also criticise the theories of Eddy Nahmias and John Doris, who have both engaged specifically with the threats posed to moral responsibility by situationist research. Against Doris and Nahmias, I argue that their conditions are neither necessary nor sufficient for direct moral responsibility. -/- My final objective is to argue that there are many everyday actions for which we mistakenly hold agents morally responsible. I review evidence that there are many everyday actions which have subverting causes. Many of those are actions for which we currently hold agents morally responsible. But I argue that, in many of those same actions, the agents are not in fact morally responsible – they bear neither direct nor traced moral responsibility. (shrink)

This study aims to evaluate whether the idea of ultimate reality in world religions contributes to the characteristics of the world religion paradigm, which is hierarchical cosmology or “subject-object cosmology.” Several research on this topic claims that one of the characteristics of the world religion paradigm is its hierarchical perspective. Discussing this issue is important to distinguish the world religions as the paradigm and the world religions as the most widely embraced religion. This study argues that the hierarchical perspective of (...) the world religion paradigm can be rooted in the idea of ultimate reality, that there is a supreme, foremost, and most principal reality in the continuity of this universe, namely the supernatural or God. The hierarchical cosmology consists of three main domains: supernatural/God, culture/human, and nature. This study uses a literature study methodology, relying on books, journals, and texts related to research questions. This study finds that the world religion paradigm or hierarchical cosmology or “subject-object cosmology” is prominent, especially in Abrahamic religions such as Islam, Christianity, and Judaism, even though the concept of ultimate reality in these three religions is different. (shrink)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

Calls to recognize a right of return are a recurring feature of refugee crises. Particularly when such crises become long-term, advocates of displaced people insist that they be allowed to return to their country of origin. I argue that this right is best understood as the right of refugees to return, not to a prior territory, but to a prior political status. This status is one that sees not just any state, but a refugee's state of origin, take responsibility for (...) safeguarding their welfare. This entitlement I characterize as an institutional right: a right that presupposes, and is a necessary feature of, a particular institution. The institution of which the right of return is an indispensable part is the international political system that sees authority exercised by sovereign states. The institutional argument for a right of refugee return presupposes two basic factual claims about states: they play a central role in safeguarding rights and they pursue exclusionary policies of border control. Importantly, the institutional view presupposes only that states do perform both functions, not that they are justified in doing so. On a purely normative level, the institutional account assumes little more than the moral equality of human beings. (shrink)