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)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

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)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...) approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including boththe Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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

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

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

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

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

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the (...) body fluids ontology initiative may provide support to basic and translational science. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

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

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

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

This paper lays out the basic structure of any view involving coincident entities, in the light of the grounding problem. While the account is not novel, I highlight fundamental features, to which attention is not usually properly drawn. With this in place, I argue for a number of further claims: The basic differences between coincident objects are modal differences, and any other differences between them need to be explained in terms of these differences. More specifically, the basic difference is not (...) a difference in sort. A number of recent defenses of coincidence, which share the basic structure I outline, misidentify what, in their accounts, plays the basic role of addressing the grounding problem. More tentatively, I argue Coincident entities differ only in these modal properties, and properties they entail. In particular, they do not differ in properties like ‘being a tree,’ ‘being a statue,’ or aesthetic properties, and finally in light of how the account of coincidence offered addresses the grounding problem, the grounding problem provides no reason to prefer monism to pluralism. (shrink)

Quine's views on semantic holism and observation statements appear to be incompatible. My paper is an attempt to alleviate this tension.

If the begriffsschrift from Frege does represent the logical form of natural language it either lacks a logical form itself, or its logical form is different to that of natural language. But Frege insists that his notation has a logical form. So the second disjunct holds. This suggests that Frege's notation will generate consequences different to those that can be derived with natural language, with its different logical form. For anyone looking for "a means of avoiding misunderstandings", as Frege does, (...) this would be unpalatable, to say the least. (shrink)

I argue that most counterfactuals are false.

Bayesianism is our leading theory of uncertainty. Epistemology is defined as the theory of knowledge. So “Bayesian Epistemology” may sound like an oxymoron. Bayesianism, after all, studies the properties and dynamics of degrees of belief, understood to be probabilities. Traditional epistemology, on the other hand, places the singularly non-probabilistic notion of knowledge at centre stage, and to the extent that it traffics in belief, that notion does not come in degrees. So how can there be a Bayesian epistemology?

Human social intelligence comprises a wide range of complex cognitive and affective processes that appear to be selectively impaired in autistic spectrum disorders. The study of these neuro- developmental disorders and the study of canonical social intelligence have advanced rapidly over the last twenty years by investigating the two together. Specifically, studies of autism have provided important insights into the nature of ‘theory of mind’ abilities, their normal development and underlying neural systems. At the same time, the idea of impaired (...) development of the neurocognitive mechanisms underlying ‘theory of mind’ has shed new light on the nature of autistic disorders. This general approach is not restricted to the study of impairments but extends to mapping areas of social intelligence that are spared in autism. Here we investigate basic moral judgment and find that it appears to be substantially intact in children with autism who are severely impaired in ‘theory of mind’. At the same time, we extend studies of moral reasoning in normal development by way of a new control task, the ‘cry baby’ task. Cry baby scenarios, in which the distress of the victim is ‘unreasonable’ or ‘unjustified,’ do not elicit moral condemnation from normally developing preschoolers or from children with autism. Judgments of moral transgressions in which the victim displays distress are therefore not likely the result of a simple automatic reaction to the distress and more likely involve moral reasoning. Mapping the cognitive co-morbidity patterns of disordered development should encompass both impairments and sparings because both will be needed to make sense of the neural and genetic levels. (shrink)

So-called “traditional epistemology” and “Bayesian epistemology” share a word, but it may often seem that the enterprises hardly share a subject matter. They differ in their central concepts. They differ in their main concerns. They differ in their main theoretical moves. And they often differ in their methodology. However, in the last decade or so, there have been a number of attempts to build bridges between the two epistemologies. Indeed, many would say that there is just one branch of philosophy (...) here—epistemology. There is a common subject matter after all. In this paper, we begin by playing the role of a “bad cop,” emphasizing many apparent points of disconnection, and even conflict, between the approaches to epistemology. We then switch role, playing a “good cop” who insists that the approaches are engaged in common projects after all. We look at various ways in which the gaps between them have been bridged, and we consider the prospects for bridging them further. We conclude that this is an exciting time for epistemology, as the two traditions can learn, and have started learning, from each other. (shrink)

In this chapter, Ricardo Silvestre and Alan Herbert offer a reconstruction of the Gītā’s concept of God with a focus on the relationship between God and the world. They try to explain the claim that the Gītā is panentheistic. This is done with the help of some key notions of contemporary metaphysics (such as ontological dependence and fundamentality) along with the Indic notion of prakṛti, considered as a metaphysical primitive denoting the intimate relationship that exists between matter and conscious (...) living beings on the one hand, and God on the other. (shrink)

A comprehensive introduction to the ways in which meaning is conveyed in language. Alan Cruse covers semantic matters, but also deals with topics that are usually considered to fall under pragmatics. A major aim is to highlight the richness and subtlety of meaning phenomena, rather than to expound any particular theory.

There have long been calls from industry for guidance in implementing strategies for sustainable development. The Circular Economy represents the most recent attempt to conceptualize the integration of economic activity and environmental wellbeing in a sustainable way. This set of ideas has been adopted by China as the basis of their economic development, escalating the concept in minds of western policymakers and NGOs. This paper traces the conceptualisations and origins of the Circular Economy, tracing its meanings, and exploring its antecedents (...) in economics and ecology, and discusses how the Circular Economy has been operationalized in business and policy. The paper finds that while the Circular Economy places emphasis on the redesign of processes and cycling of materials, which may contribute to more sustainable business models, it also encapsulates tensions and limitations. These include an absence of the social dimension inherent in sustainable development that limits its ethical dimensions, and some unintended consequences. This leads us to propose a revised definition of the Circular Economy as “an economic model wherein planning, resourcing, procurement, production and reprocessing are designed and managed, as both process and output, to maximize ecosystem functioning and human well-being”. (shrink)

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct (...) facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

When agents insert technological systems into their decision-making processes, they can obscure moral responsibility for the results. This can give rise to a distinct moral wrong, which we call “agency laundering.” At root, agency laundering involves obfuscating one’s moral responsibility by enlisting a technology or process to take some action and letting it forestall others from demanding an account for bad outcomes that result. We argue that the concept of agency laundering helps in understanding important moral problems in a number (...) of recent cases involving automated, or algorithmic, decision-systems. We apply our conception of agency laundering to a series of examples, including Facebook’s automated advertising suggestions, Uber’s driver interfaces, algorithmic evaluation of K-12 teachers, and risk assessment in criminal sentencing. We distinguish agency laundering from several other critiques of information technology, including the so-called “responsibility gap,” “bias laundering,” and masking. (shrink)

A central task of schooling is to cultivate reasonableness in students. In this chapter we show how the teaching of reasonableness can be practiced successfully in secondary schools, using materials from the Western Australian curriculum. The discussion proceeds in four stages. We first defend the claim that the teaching of reasonable is a key aim of schooling. Here we offer an account of reasonableness, which we take to be both a skill and a disposition. Students learn reasonableness through the practice (...) of specific skills such as open and curious questioning, clarifying, and categorizing, and evaluating the merits of each contribution toward the problem or question under consideration. Reasonableness comes about as a joint commitment between the individual and the group to be honest in their views, to take care of those views, and for everyone to recognize that each member is a partial bearer of truth. Secondly, we discuss the pedagogies that cultivate reasonableness. The Philosophical Community of Inquiry is a natural pedagogy for this purpose. This can be supplemented with the thinking tools approach of Cam’s Twenty Thinking Tools or Harvard Project Zero’s Thinking Routines. In addition, we introduce our own two skill-building exercises, the Reasoning Game and the Argument Game. Thirdly, we show how this approach can be applied not just in Philosophy classes, but in the Humanities and Social Sciences. We argue that our approach brings these subjects to life, it develops understanding and reasonableness, and it bumps up student engagement. Fourthly, we discuss the assessment of reasonableness. In this type of learning environment, the way students perform in the philosophical community of inquiry is the focus of assessment. The desirable qualities of being reasonable become the assessment criteria for an on-balanced judgment about the student. (shrink)

Algorithmic systems and predictive analytics play an increasingly important role in various aspects of modern life. Scholarship on the moral ramifications of such systems is in its early stages, and much of it focuses on bias and harm. This paper argues that in understanding the moral salience of algorithmic systems it is essential to understand the relation between algorithms, autonomy, and agency. We draw on several recent cases in criminal sentencing and K–12 teacher evaluation to outline four key ways in (...) which issues of agency, autonomy, and respect for persons can conflict with algorithmic decision-making. Three of these involve failures to treat individual agents with the respect they deserve. The fourth involves distancing oneself from a morally suspect action by attributing one’s decision to take that action to an algorithm, thereby laundering one’s agency. (shrink)

ABSTRACT: So far in this book, we have examined algorithmic decision systems from three autonomy-based perspectives: in terms of what we owe autonomous agents (chapters 3 and 4), in terms of the conditions required for people to act autonomously (chapters 5 and 6), and in terms of the responsibilities of agents (chapter 7). -/- In this chapter we turn to the ways in which autonomy underwrites democratic governance. Political authority, which is to say the ability of a government to exercise (...) power, may be justifiable or not. Whether it is justified and how it can come to be justified is a question of political legitimacy. Political legitimacy is another way in which autonomy and responsibility are linked. This relationship is the basis of the current chapter, and it is important in understanding the moral salience of algorithmic systems. We will draw the connection as follows. We begin, in section 8.1, by describing two uses of technology: crime predicting technology used to drive policing practices and social media technology used to influence elections (including by Cambridge Analytica and by the Internet Research Agency). In section 8.2 we consider several views of legitimacy and argue for a hybrid version of normative legitimacy based on one recently offered by Fabienne Peter. In section 8.3 we will explain that the connection between political legitimacy and autonomy is that legitimacy is grounded in legitimating processes, which are in turn based on autonomy. Algorithmic systems—among them PredPol and the Cambridge Analytica-Facebook-Internet Research Agency amalgam—can hinder that legitimation process and conflict with democratic legitimacy, as we argue in section 8.4. We will conclude by returning to several cases that serve as through-lines to the book: Loomis, Wagner, and Houston Schools. -/- The link below is to an open-access copy of the chapter. (shrink)

Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...) outstanding moral obligations. It is engaged scholarship because it required building relationships with affected persons and taking responsibility for his institution’s legacy, as well as transforming Wilson’s own outlook along the way. It is socially relevant philosophy and history of science because it brings to light issues that remain salient today, especially how eugenic themes are ubiquitous in societal discourse and evinced in everyday decisions. It is interdisciplinary because to accomplish this type of analysis requires intellectual gymnastics that range over diverse domains of research: from standpoint theory and disability studies to oral history and governmental policy; from the evolutionary biology of prosociality and variation to conceptual questions about the categorization of human traits and types. (shrink)

I argue that metaphysical views of material objects should be understood as 'packages', rather than individual claims, where the other parts of the package include how the theory addresses 'recalcitant data', and that when the packages meet certain general desiderata - which all of the currently competing views *can* meet - there is nothing in the world that could make one of the theories true as opposed to any of the others.

In this article we revisit the concept of a profession. Definitions of the concept are readily encountered in the literature on professions and we have collected a sample of such definitions. From this sample we distil frequently occurring elements and ask whether a synthesis of these elements adequately explains the concept. We find that bringing the most frequently occurring elements together does not adequately address the reason that society differentiates professions from other occupations or activities -- why there is a (...) concept of ‘profession’ at all. We suggest an alternative approach that attempts to make sense of the concept at a more general level. This more philosophical approach employs analytical tools from Julius Kovesi, Patricia Hanna and Bernard Harrison to address the question of what is the point of the concept. (shrink)

Responds to two other chapters that describe what they identify as the "Socratic Method." Our claim is that the elenchos is not sufficiently methodical as to qualify as a "method.".

In recent years, educational institutions have started using the tools of commercial data analytics in higher education. By gathering information about students as they navigate campus information systems, learning analytics “uses analytic techniques to help target instructional, curricular, and support resources” to examine student learning behaviors and change students’ learning environments. As a result, the information educators and educational institutions have at their disposal is no longer demarcated by course content and assessments, and old boundaries between information used for assessment (...) and information about how students live and work are blurring. Our goal in this paper is to provide a systematic discussion of the ways in which privacy and learning analytics conflict and to provide a framework for understanding those conflicts. -/- We argue that there are five crucial issues about student privacy that we must address in order to ensure that whatever the laudable goals and gains of learning analytics, they are commensurate with respecting students’ privacy and associated rights, including (but not limited to) autonomy interests. First, we argue that we must distinguish among different entities with respect to whom students have, or lack, privacy. Second, we argue that we need clear criteria for what information may justifiably be collected in the name of learning analytics. Third, we need to address whether purported consequences of learning analytics (e.g., better learning outcomes) are justified and what the distributions of those consequences are. Fourth, we argue that regardless of how robust the benefits of learning analytics turn out to be, students have important autonomy interests in how information about them is collected. Finally, we argue that it is an open question whether the goods that justify higher education are advanced by learning analytics, or whether collection of information actually runs counter to those goods. (shrink)

The paper is an introduction to geometric algebra and geometric calculus for those with a knowledge of undergraduate mathematics. No knowledge of physics is required. The section Further Study lists many papers available on the web.

Questions of privacy have become particularly salient in recent years due, in part, to information-gathering initiatives precipitated by the 2001 World Trade Center attacks, increasing power of surveillance and computing technologies, and massive data collection about individuals for commercial purposes. While privacy is not new to the philosophical and legal literature, there is much to say about the nature and value of privacy. My focus here is on the nature of informational privacy. I argue that the predominant accounts of privacy (...) are unsatisfactory and offer an alternative: for a person to have informational privacy is for there to be limits on the particularized judgments that others are able to reasonably make about that person. (shrink)

While the image of the slave as the antithesis of the freeman is central to republican freedom, it is striking to note that slaves themselves have not contributed to how this condition is understood. The result is a one-sided conception of both freedom and slavery, which leaves republicanism unable to provide an equal and robust protection for historically outcast people. I draw on the work of Frederick Douglass – long overlooked as a significant contributor to republican theory – to show (...) one way why this is so. Focusing the American Revolution, the subsequent republican government established new political institutions to maintain the collective interests of the whole population. The political revolution was held in place by processes of public reason that reflected the values and ideas of the people that had rebelled. The black population, however, had not been part of this revolution. After emancipation, black Americans were required to accept terms of citizenship that had already been defined, leaving them socially dominated, subject to the prejudices and biases within the prevailing ideas of public discourse. Douglass argued that republican freedom under law is always dependent on a more fundamental revolution, that he calls a ‘radical revolution in thought’, in which the entire system of social norms and practices are reworked together by members of all constituent social groups – women and men, black and white, rich and poor – so that it reflects a genuinely collaborative achievement. Only then can we begin the republican project of contestatory freedom as independence or non-domination that today’s republicans take for granted. (shrink)

Allocation of very scarce medical interventions such as organs and vaccines is a persistent ethical challenge. We evaluate eight simple allocation principles that can be classified into four categories: treating people equally, favouring the worst-off, maximising total benefits, and promoting and rewarding social usefulness. No single principle is sufficient to incorporate all morally relevant considerations and therefore individual principles must be combined into multiprinciple allocation systems. We evaluate three systems: the United Network for Organ Sharing points systems, quality-adjusted life-years, and (...) disability-adjusted life-years. We recommend an alternative system—the complete lives system—which prioritises younger people who have not yet lived a complete life, and also incorporates prognosis, save the most lives, lottery, and instrumental value principles. (shrink)

Although they were never to meet and corresponded only briefly, Catharine Macaulay and Mary Wollstonecraft shared a mutual admiration and a strong intellectual bond. Macaulay’s work had a profound and lasting effect on Wollstonecraft, and she developed and expanded on many of Macaulay’s ideas. While she often took these in a different direction, there remains a great synergy between their ideas to the extent that we can understand Wollstonecraft’s own feminist arguments by approaching them through the frameworks and ideas that (...) Macaulay provided. These included the principles of classical republicanism, particularly in its understanding of the values of freedom, equality and virtue, and an understanding of reason as grounded in immutable principles that apply equally to both sexes. On the question of women’s freedom and social equality with men, I argue that though Macaulay sets up the problem in far richer and more detailed philosophical terms, in the end it is Wollstonecraft that has the more compelling account of its far-reaching social implications and of how this might be addressed. (shrink)

Taurek cases focus a choice between two views of permissible action, Can Save One and Must Save Many . It is argued that Taurek cases do illustrate the rationale for Can Save One , but existing views do not highlight the fact that this is because they are examples of claims grounded on non-comparative justice. To act to save the many solely because they form a group is to discriminate against the one for an irrelevant reason. That is a canonical (...) form of non-comparative injustice. The error lies in taking a contingency of some presentations of some Taurek cases, namely, that they involve distribution, to introduce the claims of comparative as opposed to non-comparative justice. But cases of non-comparative justice can, contingently, also involve distribution. In order to settle which form of justice applies it is necessary to examine the nature of the distribution involved and the nature of “classes” to which individuals can be assigned. (shrink)