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.

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)

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)

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)

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 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)

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)

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)

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)

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.

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)

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)

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)

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)

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)

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)

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)

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)

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)

This article questions the commonly held view that professional ethics is grounded in general ethical principles, in particular, respect for client (or patient) autonomy and beneficence in the treatment of clients (or patients). Although these are admirable as general ethical principles, we argue that there is considerable logical difficulty in applying them to the professional-client relationship. The transition from general principles to professional ethics cannot be made because the intended conclusion applies differently to each of the parties involved, whereas the (...) premise is a general principle that applies equally to both parties. It is widely accepted that professionals are required to recognize that clients or patients possess rights to autonomy that are more than the general rights to personal autonomy accepted in ordinary social life, and that professionals are expected to display beneficence toward their clients that is more than the beneficence expected of anyone in ordinary social life. The comparative component of professional ethics is an intrinsic feature of the professional situation, and thus it cannot be bypassed in working out a proper professional ethics. Thus, we contend, the proper professional treatment of clients or patients has not been explained by appeal to general ethical principles. (shrink)

Pascal’s Wager involves expected utilities. In this chapter, we examine the Wager in light of two main features of expected utility theory: utilities and probabilities. We discuss infinite and finite utilities, and zero, infinitesimal, extremely low, imprecise, and undefined probabilities. These have all come up in recent literature regarding Pascal’s Wager. We consider the problems each creates and suggest prospects for the Wager in light of these problems.

The topic ‘ethics in politics’ might cover a multitude of sins. Here it will be restricted to the ethics of politicians in representative liberal democracies. The ethics of public servants will be left aside, as will be the ethics of politicians in other political systems. Plain criminal wrongdoing by politicians will also be outside our scope. The subject is still very large. It includes all those matters that reflect on a politician’s ethical reputation. Political wrongdoing can range in magnitude from (...) taking a country to war on inadequate grounds to fiddling with one’s parliamentary expenses. (shrink)

There is increasing concern about “surveillance capitalism,” whereby for-profit companies generate value from data, while individuals are unable to resist (Zuboff 2019). Non-profits using data-enabled surveillance receive less attention. Higher education institutions (HEIs) have embraced data analytics, but the wide latitude that private, profit-oriented enterprises have to collect data is inappropriate. HEIs have a fiduciary relationship to students, not a narrowly transactional one (see Jones et al, forthcoming). They are responsible for facets of student life beyond education. In addition to (...) classrooms, learning management systems, and libraries, HEIs manage dormitories, gyms, dining halls, health facilities, career advising, police departments, and student employment. HEIs collect and use student data in all of these domains, ostensibly to understand learner behaviors and contexts, improve learning outcomes, and increase institutional efficiency through “learning analytics” (LA). ID card swipes and Wi-Fi log-ins can track student location, class attendance, use of campus facilities, eating habits, and friend groups. Course management systems capture how students interact with readings, video lectures, and discussion boards. Application materials provide demographic information. These data are used to identify students needing support, predict enrollment demands, and target recruiting efforts. These are laudable aims. However, current LA practices may be inconsistent with HEIs’ fiduciary responsibilities. HEIs often justify LA as advancing student interests, but some projects advance primarily organizational welfare and institutional interests. Moreover, LA advances a narrow conception of student interests while discounting privacy and autonomy. Students are generally unaware of the information collected, do not provide meaningful consent, and express discomfort and resigned acceptance about HEI data practices, especially for non-academic data (see Jones et al. forthcoming). The breadth and depth of student information available, combined with their fiduciary responsibility, create a duty that HEIs exercise substantial restraint and rigorous evaluation in data collection and use. (shrink)

ABSTRACT: One important criticism of algorithmic systems is that they lack transparency. Such systems can be opaque because they are complex, protected by patent or trade secret, or deliberately obscure. In the EU, there is a debate about whether the General Data Protection Regulation (GDPR) contains a “right to explanation,” and if so what such a right entails. Our task in this chapter is to address this informational component of algorithmic systems. We argue that information access is integral for respecting (...) autonomy, and transparency policies should be tailored to advance autonomy. -/- To make this argument we distinguish two facets of agency (i.e., capacity to act). The first is practical agency, or the ability to act effectively according to one’s values. The second is what we call cognitive agency, which is the ability to exercise what Pamela Hieronymi calls “evaluative control” (i.e., the ability to control our affective states, such as beliefs, desires, and attitudes). We argue that respecting autonomy requires providing persons sufficient information to exercise evaluative control and properly interpret the world and one’s place in it. We draw this distinction out by considering algorithmic systems used in background checks, and we apply the view to key cases involving risk assessment in criminal justice decisions and K-12 teacher evaluation. -/- The link below is to an open access version of the chapter. (shrink)

Despite widespread agreement that privacy in the context of education is important, it can be difficult to pin down precisely why and to what extent it is important, and it is challenging to determine how privacy is related to other important values. But that task is crucial. Absent a clear sense of what privacy is, it will be difficult to understand the scope of privacy protections in codes of ethics. Moreover, privacy will inevitably conflict with other values, and understanding the (...) values that underwrite privacy protections is crucial for addressing conflicts between privacy and institutional efficiency, advising efficacy, vendor benefits, and student autonomy. -/- My task in this paper is to seek a better understanding of the concept of privacy in institutional research, canvas a number of important moral values underlying privacy generally (including several that are explicit in the AIR Statement), and examine how those moral values should bear upon institutional research by considering several recent cases. (shrink)

Julius Kovesi was a moral philosopher whose work rested on a theory of concepts and concept-formation, which he outlined in his 1967 book Moral Notions. But his contribution goes further than this. In sketching a theory of concepts and concept-formation, he was entering the philosophy of language. To make his account of moral concepts credible, he needs a broader story about how moral concepts compare with other sorts of concepts. Yet philosophy of language, once dominated by Wittgenstein and Austin, came (...) rather suddenly in the 1960s to be dominated by metaphysicians and philosophers of science trying to give an account of natural science concepts. How then does Kovesi’s theory of concepts fare when viewed in the light of this shift of interests? Does he have a theory of natural world concepts that can stand scrutiny? I will try to show that he does. To show this, I will focus on the concept of water. However, before doing this we need an outline of Kovesi’s account of what he called ‘notions formed about the inanimate world’. (shrink)

In this state-of-the-field article, I examine some of the problems plaguing present-day analytic Hegel studies and try to find out what can be done to remedy the situation as scholars collectively (and finally) begin grappling with the metaphysico-logical core of Hegel’s thought. In so doing, I go over the various currents of Hegelian interpretation and describe some of the limitations behind the usual analytic approaches which have often tended to downplay key aspects of Hegel’s thought, like his dialectical logic, and (...) which have also partly helped create enthusiasm for metaphysically deflationary approaches to Hegel’s thought. I then propose three practical directives for the betterment of the field in terms of future research, ones which essentially advocate for the generalized adoption of a more historicist approach to certain matters, one that is not mutually exclusive with the overarching scholarly desire to extract something that is philosophically relevant or contemporarily useful from Hegel’s thought, which is what seems to drive analytic Hegel studies in general. (shrink)

Humans were once purely animal, the same as all the other animal species, implying that the practice of ethics must have been nonexistent until quite recently in human history. It has been during the species’ turn towards behavioral modernity that ethical precepts and systems have been formed, eventually becoming an integral part of modern human existence. This essay will explore the cause for this transition, emphasizing the idea that there are now two different sources of modern human behavior. On the (...) one hand, modern humans are still animal, and they must still engage in biologically driven behaviors. At the same time, modern humans have become increasingly influenced and guided by the many artificial constructions that have been accruing over time and are now saturating the human landscape, with the response to these artificial constructions producing a wide range of behaviors heretofore unwitnessed on the planet Earth. These two aspects of modern humanity—the animal aspect and the constructed aspect—they find themselves often in conflict, each striving to gain ascendency over each individual and over the species as a whole. It is to negotiate this inherent conflict that ethics and morality are formed. (shrink)

This article reexamines Vico’s early critique of Cartesian reasoning and of how the Cartesian method, which comes from epistemology, creates problems for the sciences once embedded into their methodologies and given a foundational role. The focus will be on De nostri temporis studiorum ratione (1709), where Vico argues against generalizing the Cartesian method and overemphasizing clarity and distinctness in the search for truth. To this end, Vico’s relation to Cartesianism is first carefully contextualized. Then, Vico is presented as a hylomorphist (...) when it comes to how scientific disciplines and their instruments interrelate, something key for understanding why he questions the “instrumentalization” of the Cartesian method in the first place. Afterwards, Vico’s account of the impossibility of maximal scientific progress when the Cartesian method is prioritized across the sciences is presented, as probabilistic reasoning and the importance of the imagination and memory take centerstage. Lastly, the article looks at Vico’s opposition to the geometrical method’s role in physics and his defense of visual thinking in mathematics. The hope throughout is to advance a picture of the early Vico as being not only a neo- Baconian pragmatist, but a hypermodern ”meta-Cartesian” thinker concerned with humanity’s optimizing its creative potential in order to achieve scientific advances. (shrink)

Joseph Priestley was a man of many and varied intellectual interests. This thesis surveys his philosophical thought, with a central focus on his philosophical theology. The subject can be divided into two parts, natural theology and moral theology. Priestley's natural theology is a perhaps unique attempt to combine and harmonize materialism, determinism and theism, under the auspices of Newtonian methodology. His materialism is based on three arguments: that interaction between matter and spirit is impossible; that a dynamic theory of matter (...) breaks down the active/passive dichotomy assumed by many dualists; and that Newton's "Rules of Reasoning in Philosophy" require the rejection of the "hypothesis" of the soul. His determinism arises from his theory of causation. He attempts to show that the only acceptable account of causation is one in which every cause is invariably followed by the same effect, and that libertarianism violates this central assumption of scientific thought. His theism rests on the Argument from Design. He defends the Argument by trying to show that none of the alternatives to Design advanced in Hume's Dialogues concerning Natural Religion constitute a plausible scientific hypothesis. His critics accused his synthesis of materialism, determinism and theism of leading to atheism or pantheism. His defence against these charges is that his system is essentially theistic, and that its ontology is determined by the Argument from Design. Priestley's moral theology is also in part a response to Hume's Dialogues. He offers a number of replies to the "problem of evil". Evil and adversity heighten our appreciation of good; they are a consequence of the finitude of the creation; they follow from the desirability of having a world governed by general laws; and they make possible the achievement of moral character. Character-formation is his main defence, and his methodology requires him to show that adversity leads more often than not to positive results. This requirement is embodied in his progressivist philosophy of history. History, he holds, exhibits temporal purpose and Design, just as nature exhibits atemporal purpose and Design. Priestley's political thought can be seen as arising from his moral theology, mediated by the notions of "luxury", which he regards as morally harmless, and "idleness", which is the main source of moral evil. His combination of liberalism and radicalism is examined both for internal consistency and as a response to the events of his day, ending with the French Revolution. Priestley is interesting partly for his unorthodoxy, partly for the inter-connectedness of his diverse concerns, and partly because he debated with distinguished contemporaries. Throughout the thesis his views are juxtaposed with those of Hume, Reid, Price, Boscovich, Burke and a number of other thinkers. (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.

In this article, I re-examine Kant’s many senses of cognition, thought, and object in order to better understand his account of logic, and, in particular, transcendental logic. In laying out the multiple and conflicting ways Kant defines each of those terms, the relation between transcendental logic and pure general logic can be revealed as analogous to, and, indeed, linked to, the isomorphism that exists between the categories of the understanding and the logical forms of judgment, which are equivalent if one (...) ignores the manifold of intuition. This means transcendental logic is a general logic, even as a logic of (some) cognizing. (shrink)

In this paper, we consider the role of conversations in contributing to healthcare quality improvement. More specifically, we suggest that conversations can be important in responding to what we call ’normative complexity’. As well as reflecting on the value of conversations, the aim is to introduce the dimension of normative complexity as something that requires theoretical and practical attention alongside the more recognised challenges of complex systems, which we label, for short, as ’explanatory complexity’. In brief, normative complexity relates to (...) the inherent difficulty of deciding what kinds of changes are ’improvements’ or, more broadly, what is valuable in healthcare. We suggest that explanatory and normative complexity intersect and that anyone interested in healthcare improvement needs to be sensitive to both. After briefly introducing the idea of normative complexity, we consider some contrasting examples of conversations, reflecting on how they do and might contribute to healthcare quality. We discuss both conversations that are deliberately organised and facilitated (’orchestrated conversations’) and more informally occurring and routine conversations. In the first half of the paper, we draw on some examples of orchestrated and routine conversations to open up these issues. In the second half of the paper, we bring some more theoretical lenses to bear on both conversations and normative complexity, summarise what we take to be the value of conversations and draw together some of the implications of our discussion. In summary, we argue that conversations can play a crucial role in negotiating the normative complexity of healthcare quality improvement because of their capacity to hold together a plurality of perspectives, to contribute and respond to emergence and to help underpin institutional conditions for empathy and imagination. (shrink)

The purpose of this article is to discuss the concept and the content of courses on “social ethics”. I will present a dilemma that arises in the design of such courses. On the one hand, they may present versions of “applied ethics”; that is, courses in which moral theories are applied to moral and social problems. On the other hand, they may present generalised forms of “occupational ethics”, usually professional ethics, with some business ethics added to expand the range of (...) the course. Is there, then, not some middle ground that is distinctively designated by the term “social ethics”? I will argue that there is such a ground. I will describe that ground as the ethics of “social practices”. I will then illustrate how this approach to the teaching of ethics may be carried out in five domains of social practice: professional ethics, commercial ethics, corporate ethics, governmental ethics, and ethics in the voluntary sector. My aim is to show that “social ethics” courses can have a clear rationale and systematic content. (shrink)

In his day, Joseph Priestley (1733-1804) was a philosopher of some importance. He argued the case for materialism perhaps more cogently than did any British thinker before recent times. He presented determinism vigorously, with a focus on the central issue of the nature of causation. He defended scientific realism against Reid’s Common Sense realism and against Hume’s phenomenonalism. He articulated a working scientist’s account of causation, induction and scientific progress. He defended the Argument from Design against Hume’s criticisms. His attempt (...) to combine theism, materialism and determinism is audacious and original. As a political thinker, he argued the case for extensive civil liberties. He was perhaps the most thorough British exponent of a Providentialist account of progress. His ultimate aim was to combine Enlightenment principles with a modernized Christian theism. (shrink)

How should historians treat one another? More generally, what are the ethical obligations that go with belonging to the profession of history? And more generally still, in what ways and in what sense is history a profession and how are professional ethics manifested in the profession? These are the questions I will canvass in this essay. In his introduction to The Historian’s Conscience, Stuart Macintyre observes that in the recent ‘public dispute over Australian history … there is surprisingly little attention (...) to the ethical dimensions of historical scholarship’. I will suggest that this lack of attention is a problem, and I will try to clarify the nature of the problem. (shrink)

I argue that most counterfactuals are false.

I begin by describing the hideous nature of sexuality, that which makes sexual desire and activity morally suspicious, or at least what we have been told about the moral foulness of sex by, in particular, Immanuel Kant, but also by some of his predecessors and by some contemporary philosophers.2 A problem arises because acting on sexual desire, given this Kantian account of sex, apparently conflicts with the Categorical Imperative. I then propose a typology of possible solutions to this sex problem (...) and critically discuss recent philosophical ethics of sex that fall into the typology's various categories. (shrink)

Discussion of Darwinian evolutionary theory by philosophers has gone through a number of historical phases, from indifference (in the first hundred years), to criticism (in the 1960s and 70s), to enthusiasm and expansionism (since about 1980). This paper documents these phases and speculates about what, philosophically speaking, underlies them. It concludes with some comments on the present state of the evolutionary debate, where rapid and important changes within evolutionary theory may be passing by unnoticed by philosophers.

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?

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)

In this article, I reconstruct and interpret the early Vico’s oft-neglected theory of scientific cognition, as found in his 1710 metaphysical treatise On the Most Ancient Wisdom of the Italians, a work whose aim was to be the handmaid to experimental physics. In particular, I offer a new reading of his verum-factum principle, which holds that the true and the made are interchangeable, by examining this doctrine in light of its unexpected connections to much later trends in philosophy. I also (...) present his criticism of Descartes’ cogito and, finally, Vico’s own solution to the problem of skepticism, which is meant to provide a new foundation for the sciences. (shrink)

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)

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)