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)

For nearly two decades, the process of reviewing the ethical merit of research involving human subjects has been based on the application of principles initially described in the U.S. National Commission's Belmont Report, and later articulated more fully by Beauchamp and Childress in their Principles of Biomedical Ethics. Recently, the use of ethical principles for deliberating about moral problems in medicine and research, referred to in the pejorative sense as “principlism”, has come under scrutiny. In this paper we argue that (...) these principles can provide a foundation for the source of ethical appraisal of human research, but are not themselves wholly adequate for this purpose. Therefore, we further propose that (1) principles should be understood as heuristics that can be “specified” as described by DeGrazia (1992), and (2) that the principle‐based approach should be supplemented by formally incorporating “sensitivity to context” into the evaluation of clinical trials. (shrink)

This case study details how and why integrating storytelling, empathy, and inclusive practice shifted QSuper, a large Australian finance organisation, from minimal awareness to moral awareness then moral capability in the delivery of services to Indigenous customers. During the Royal Commission into Misconduct in the Banking, Superannuation, and Financial Services Industry, QSuper were recognised for their exemplary service with Indigenous customers (Hayne, Interim report: Royal commission into misconduct in the banking, superannuation and financial services industry, Volume 1. Commonwealth of Australia, (...) 2018; _Transcript of Proceedings, 13 August_, Commonwealth of Australia, 2018). This position was in stark contrast to the inaccessible service offerings of other financial organisations where some used predatory practices to sell unethical financial products to Indigenous Australians (Hayne, Interim report: Royal commission into misconduct in the banking, superannuation and financial services industry, Volume 1. Commonwealth of Australia, 2018; Hayne, Final report: Royal commission into misconduct in the banking, superannuation and financial services industry, Volume 1. Commonwealth of Australia, 2019a). Storytelling garned from visiting customers in remote communities and other meaningful activities involving inclusive practice to facilitate ethical decision-making in finance is different to standard functionalist finance approaches (Schinckus, Int Rev Financ Anal 40:103–106, 2015). Two empathetic questions asked within QSuper complementing the storytelling, were: “What is the right thing to do by the customer?” and “How would I feel if this were my mother?” Exploration into the lived reality of moral capacity is important based on the Commission finding many of the 490,000 finance staff do not know how to provide ethical services to vulnerable customers, in particular remote Indigenous customers (Australian Bureau of Statistics. Labour force, Australia, detailed. ABS. Retrieved from https://www.abs.gov.au/statistics/labour/employment-and-unemployment/labour-force-australia-detailed /latest-release, 2021; Hayne, Final report: Royal commission into misconduct in the banking, superannuation and financial services industry, Volume 1. Commonwealth of Australia, 2019a). Furthermore, there is minimal literature on the role of Indigenous storytelling to heighten moral awareness in the finance industry which was found to lead to better ethical outcomes. (shrink)

Interest in and initiation of farm-to-school (FTS) programs have increased in recent years, spurred on by converging public concerns about child obesity trends and risks associated with industrialization and distancing in the modern food system. A civic agriculture framework that more specifically considers civic engagement and problem solving offers insights about variations in the development and prospects for FTS programs. Drawing on comparative case studies of two emerging FTS initiatives in Pennsylvania—one in a rural setting and one in an urban (...) setting—this article examines the role of internal and external “champions” in launching FTS programs and fostering civic engagement. Farm-to-school community stakeholders across the two cases framed FTS in broadly similar terms of (1) redressing poor food environments; (2) improving student nutrition, health and well-being; and (3) revitalizing rural community through support of local agriculture. However, specific concerns and emphases differed across the rural and urban cases, illustrating the significance of local context for such programs. The article concludes by discussing the importance of frame bridging and frame extension as strategies for expanding the FTS movement, and also ensuring programs that correspond to the specific circumstances and possibilities of their social and geographic settings. (shrink)

In a recent unit of study in an undergraduate Health Sciences pathway course, we identified a set of essays which exhibited similarity of content but demonstrated the use of bizarre and unidiomatic language. One of the distinct features of the essays was the inclusion of unusual synonyms in place of expected standard medical terminology.We suspected the use of online paraphrasing tools, but were also interested in investigating the possibility of the use of online language translation tools. In order to test (...) the outputs of these tools, we used as a seed document a corpus of text which had been provided to the students as prompt for the essay. This document was put through six free online paraphrasing tools and six separate iterative language translations through the online Google Translate™ tool.The results demonstrated that free online paraphrasing tools did not identify medical terminology as standardised or accepted nomenclature and substituted synonyms, whereas Google Translate™ largely preserved medical terminology.We believe that textual indicators such as the absence of standard discipline-based terminology may be of assistance in the identification of machine paraphrased text. (shrink)

When people think about how a situation might have turned out differently, they tend to imagine counterfactual alternatives to their actions. We report the results of three experiments which show that people imagine alternatives to actions differently when they know about a reason for the action. The first experiment ( n = 36) compared reason - action sequences to cause - effect sequences. It showed that people do not imagine alternatives to reasons in the way they imagine alternatives to causes: (...) they imagine an alternative to an action more than an effect, and to a cause more than a reason. The second experiment ( n = 214) and the third experiment ( n = 190) both show that different sorts of reasons have different sorts of effects on how people imagine alternatives to actions. People imagine an alternative to an action (the protagonist went to a ball) less often when they know the reason for the action was an obligation (he had to participate in fundraising) compared to when they know about a weaker reason (he wanted to meet a famous violinist) or no reason. The second experiment shows the effect for a social obligation and the third experiment replicates and extends it to a health obligation. We interpret the results in terms of the possibilities that people keep in mind about actions and their reasons. (shrink)

The relationship between tenure and principled reasoning is of vital importance to the fields of management and business ethics, as more tenured managers often hold influential posts and have the ability to affect the overall ethical tones of their organizations. Few researchers have studied this relationship, however, and those studies that have been conducted have produced mixed results. While some researchers have found that greater tenure is associated with higher levels of ethical reasoning, others have found the reverse to be (...) true. The findings of this particular study of 270 current U.S. corporate managers, who responded to a nationwide survey, indicated that there is indeed a link between tenure and principled reasoning. More tenured managers demonstrated lower principled reasoning than their less tenured counterparts. As the number of years of tenure increased, principled reasoning scores declined. The results of this study, as well as a comparison to the results of previous studies that have been conducted, are discussed within this paper. (shrink)

For nearly two decades, the process of reviewing the ethical merit of research involving human subjects has been based on the application of principles initially described in the U.S. National Commission's Belmont Report, and later articulated more fully by Beauchamp and Childress in their Principles of Biomedical Ethics. Recently, the use of ethical principles for deliberating about moral problems in medicine and research, referred to in the pejorative sense as “principlism”, has come under scrutiny. In this paper we argue that (...) these principles can provide a foundation for the source of ethical appraisal of human research, but are not themselves wholly adequate for this purpose. Therefore, we further propose that principles should be understood as heuristics that can be “specified” as described by DeGrazia , and that the principle‐based approach should be supplemented by formally incorporating “sensitivity to context” into the evaluation of clinical trials. (shrink)

ABSTRACTGrounded in Emotional Cascade Theory, we explored whether rumination and multisensory imagery-based cognitions moderated the relationships between affect and both odds of non-suicidal self-injury, and frequency of the behaviour. A sample of 393 university students completed self-report questionnaires assessing the constructs of interest. Contrary to expectations, rumination did not emerge as a significant moderator of the affect-NSSI relationship. However, the relationship between affect and frequency of NSSI was moderated by the use of imagery. Further, the relationship between negative affect and (...) NSSI was moderated by positive affect, underscoring the need to consider both negative and positive affect in models of NSSI. Most youth who self-injured reported thinking in images while the urge to self-injure was strong, with 53% thinking in images at least half the time. Future work is needed to explore how positive and negative affect work in concert to govern NSSI, and how imagery might eit... (shrink)

Some species face extinction if they are unable to keep pace with climate change. Yet proposals to assist threatened species’ poleward or uphill migration (‘assisted migration’) have caused significant controversy among conservationists, not least because assisted migration seems to threaten some values, even as it protects others. To date, however, analysis of ethical and value questions about assisted migration has largely remained abstract, removed from the ultimately pragmatic decision about whether or not to move a particular species. This paper uses (...) the case study of the whitebark pine, a keystone species of sub-alpine habitats in western North America, to consider how particular cases of assisted migration may be ethically approached. After taking into account the value of species, wildness, place, ecosystems, culture and sentient animals, we conclude that, on balance, there appear to be good reasons to move the whitebark pine. (shrink)

Responsible research and innovation has come to represent a change in the relationship between science, technology and society. With origins in the democratisation of science, and the inclusion of ethical and societal aspects in research and development activities, RRI offers a means of integrating society and the research and innovation communities. In this article, we frame RRI activities through the lens of layers of science and technology governance as a means of characterising the context in which the RRI activity is (...) positioned and the goal of those actors promoting the RRI activities in shaping overall governance patterns. RRI began to emerge during a time of considerable deliberation about the societal and governance challenges around nanotechnology, in which stakeholders were looking for new ways of integrating notions of responsibility in nanotechnology research and development. For this reason, this article focuses on nanotechnology as the site for exploring the evolution and growth of RRI. (shrink)

The purpose of the work was to produce a framework to guide the development of meritorious clinical trial proposals. The framework consists of essential features of rigourous methodology, ethical acceptability, and a component referred to as "community context". These three domains were woven together in a checklist format under the headings of general, scientific and ethical considerations. Since texts concerning clinical trial methodology do not integrate ethics criteria and ethics guidelines do not provide detailed scientific criteria in obvious and practical (...) ways, we outline a more contemporary and comprehensive set of guidelines. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

BackgroundRandomized controlled trials (RCTs) are often complex and expensive to perform. Less than one third achieve planned recruitment targets, follow-up can be labor-intensive, and many have limited real-world generalizability. Designs for RCTs conducted using cohorts and routinely collected health data, including registries, electronic health records, and administrative databases, have been proposed to address these challenges and are being rapidly adopted. These designs, however, are relatively recent innovations, and published RCT reports often do not describe important aspects of their methodology in (...) a standardized way. Our objective is to extend the Consolidated Standards of Reporting Trials (CONSORT) statement with a consensus-driven reporting guideline for RCTs using cohorts and routinely collected health data.MethodsThe development of this CONSORT extension will consist of five phases. Phase 1 (completed) consisted of the project launch, including fundraising, the establishment of a research team, and development of a conceptual framework. In phase 2, a systematic review will be performed to identify publications (1) that describe methods or reporting considerations for RCTs conducted using cohorts and routinely collected health data or (2) that are protocols or report results from such RCTs. An initial “long list” of possible modifications to CONSORT checklist items and possible new items for the reporting guideline will be generated based on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) and The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statements. Additional possible modifications and new items will be identified based on the results of the systematic review. Phase 3 will consist of a three-round Delphi exercise with methods and content experts to evaluate the “long list” and generate a “short list” of key items. In phase 4, these items will serve as the basis for an in-person consensus meeting to finalize a core set of items to be included in the reporting guideline and checklist. Phase 5 will involve drafting the checklist and elaboration-explanation documents, and dissemination and implementation of the guideline.DiscussionDevelopment of this CONSORT extension will contribute to more transparent reporting of RCTs conducted using cohorts and routinely collected health data. (shrink)

Population-based research is enhanced by biological measures, but biological sampling raises complex ethical issues. The third British National Survey of Sexual Attitudes and Lifestyles (Natsal-3) will estimate the population prevalence of five sexually transmitted infections (STIs) (Chlamydia trachomatis, Neisseria gonorrhoeae, human papillomavirus (HPV), HIV and Mycoplasma genitalium) in a probability sample aged 16–44 years. The present work describes the development of an ethical approach to urine testing for STIs, including the process of reaching consensus on whether to return results. The (...) following issues were considered: (1) testing for some STIs that are treatable and for which appropriate settings to obtain free testing and advice are widely available (Natsal-3 provides all respondents with STI and healthcare access information), (2) limits on test accuracy and timeliness imposed by survey conditions and sample type, (3) testing for some STIs with unknown clinical and public health implications, (4) how a uniform approach is easier to explain and understand, (5) practical difficulties in returning results and cost efficiency, such as enabling wider STI testing by not returning results. The agreed approach, to perform voluntary anonymous testing with specific consent for five STIs without returning results, was approved by stakeholders and a research ethics committee. Overall, this was acceptable to respondents in developmental piloting; 61% (68 of 111) of respondents agreed to provide a sample. The experiences reported here may inform the ethical decision making of researchers, research ethics committees and funders considering population-based biological sampling. (shrink)

Ronald Sandler's ‘Climate change and ecosystem management’ provides a fine summary of reasons to modify our approach to ecosystem management given ‘rapid and uncertain ecological change’. We...

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 41.3 (2003) 426-427 [Access article in PDF] Timothy Smiley, editor. Mathematics and Necessity: Essays in the History of Philosophy. New York: Oxford University Press, 2000. Pp. ix + 166. Cloth, $35.00.Mathematics and Necessity contains essays by M. F. Burnyeat, Ian Hacking, and Jonathan Bennett based on lectures given to the British Academy in 1998. All concern the history of the philosophical treatment of (...) mathematics, necessity, or both, although there is no single thread running through all three essays.Burnyeat focuses on Plato's understanding of mathematics in the Republic, making use of the Timeaus in particular to defend his interpretation. Plato claimed that in the ideal society mathematics should be studied for a full ten years, which many have thought excessive. To explain it, Burnyeat argues that the role of mathematics is pervasive: ethics and politics are mathematical, because in Plato's view mathematics is a constitutive part of ethical understanding. On Burnyeat's interpretation, goodness is part of the objective world, and mathematics is a science of values. The link between mathematics and goodness in the objective world is forged by the concord, harmony, and unity of proportions, which express the goodness of the Divine Craftsman's beneficent design. Proportions are both intrinsically good and the proper study of mathematics.Burnyeat explains why Plato thinks abstract kinematics (the pure non-sensible counterpart to astronomy) and abstract harmonics lead to knowledge of the good. Abstract kinematics concerns the "harmony of the spheres" described in the Republic. Drawing heavily on the Timeaus, Burnyeat argues that the circular motions of the spheres are motions in the intelligence of the world soul and that there are similar motions in human souls. The world soul and human souls are spatial and have circular motions (invisibility and intangibility make them incorporeal). Souls are the most important subject matter of abstract harmonics—the study of good proportions. A soul that understands the various mathematical disciplines and their relations takes on the harmony and hence goodness of the world soul. Such a soul serves as a model for organizing the social world, a model which properly trained rulers can use to shape a community. Burnyeat's well-argued essay is compelling and exciting. [End Page 427]Ian Hacking's views provide a great contrast to Burnyeat's Plato. Hacking conducts a phenomenological inquiry into why some philosophers have become obsessed by mathematics as a source of philosophical inspiration. He holds that mathematics concerns a relatively minor part of human culture and that the influence of mathematics on philosophy is pernicious; he even describes it as an infection.Hacking examines the views of six philosophers: Plato, Leibniz, Mill, Descartes, Lakatos, and Wittgenstein. Hacking's assessment of the six philosophers is at times disputable, but it is also interesting and stimulating, and serves his phenomenological inquiry.Hacking traces philosophy's infection by mathematics to two factors. A mathematical proof can be perspicuous; that is, a proof can be "grasped," which requires seeing directly why something must be true and being able to recapitulate it. A mathematical proof can also anticipate facts about the world. He thinks that these two factors affect us in two ways: they give us the idea of a priori knowledge, and they dazzle us into unreasoned conviction in proofs. One might respond that, setting aside the feeling proofs give us, we are still justified in being impressed by them. Hacking argues that much of what impresses is based on a misunderstanding of their nature, which he attempts to correct.According to Hacking, a mathematical demonstration involves shifts of meaning that analytically bind the proof and the theorem it establishes. They thereby mutually support each other and provide what he calls self-authentication. The correctness of the proof is supported by the "analytified" truth of the theorem and the theorem is considered true because proven.This bootstrapping feature of mathematical proofs supports Hacking's deflationary account of necessity. Hacking suggests that the "must" of logical necessity rests upon our unwillingness to accept empirical counter-examples to the... (shrink)

I introduce a perceptual phenomenon so far overlooked in the philosophical literature: ‘visual evanescence’. ‘Evanescent’ objects are those that due to their structured visible appearances have a tendency to vanish or evanesce from sight at certain places and for certain ‘biologically apt’ perceivers. Paradigmatically evanescent objects are those associated with certain forms of animal camouflage. I show that reflection on visual evanescence helps create conceptual room for a treatment of looks statements not explicit in the contemporary literature, one which takes (...) its cue from the relatively neglected philosophy of perception of G.E.M. Anscombe. In sensory contexts in which evanescence is known to have occurred, the use of ‘looks invisible’ seems to be intelligible, a fact that sensationalist and objectivist treatments of the nature of looks, as I call them, cannot obviously accommodate - at least, as I explain, when coupled with what Cora Diamond (1981) describes as a ‘natural’ understanding of nonsense. Focusing on a number of imaginative scenarios in which the statement ‘looks invisible’ is permissible, I oppose these ontological treatments with the grammatical approach I draw from Anscombe and in doing so I uncover a degree of unity across the cases I consider: something can intelligibly be said to ‘look invisible’ if one can see or appears to see the entirety of the region that the ‘invisible’ thing occupies. The region ‘looks empty’ but is full. (shrink)

Animal ethicists have recently debated the ethical questions raised by disenhancing animals to improve their welfare. Here, we focus on the particular case of breeding hens for commercial egg-laying systems to become blind, in order to benefit their welfare. Many people find breeding blind hens intuitively repellent, yet ‘welfare-only’ positions appear to be committed to endorsing this possibility if it produces welfare gains. We call this the ‘Blind Hens’ Challenge’. In this paper, we argue that there are both empirical and (...) theoretical reasons why even those adopting ‘welfare-only’ views should be concerned about breeding blind hens. But we also argue that alternative views, which (for example) claim that it is important to respect the telos or rights of an animal, do not offer a more convincing solution to questions raised by the possibility of disenhancing animals for their own benefit. (shrink)

In his reference letter for Murdoch’s 1947 fellowship application at Newnham College, Cambridge, her erstwhile Oxford undergraduate tutor, Donald MacKinnon, remarks that Murdoch is ‘on the threshold of creative work of a high order’. This chapter outlines the nature of that ‘creative work’ and its early development. We show how Murdoch’s close study of the Christian existentialist philosopher and playwright Gabriel Marcel (1883–1973) came to inflect both her early critique of Jean Paul Sartre’s existentialism and her first attempts to show (...) the limits of logical positivism. We explain how once at Cambridge, Murdoch’s exposure to Wittgenstein’s method, through her philosophical friendship with Elizabeth Anscombe, gave her the conceptual means to recast those aspects of Marcel’s thought (as well as those of Martin Buber) that she believed were important but, as she wrote in her application, ‘vague’. We show, finally, how both strands of Murdoch’s thinking are later brought into synchrony in the much-discussed example of M&D. This, in turn, allows us to isolate Murdoch’s understanding of the individual’s relation to their own ‘ghostly past’ and to reveal the importance of Murdoch’s early encounters with Anscombe and Marcel. (shrink)

I consider the first part of Marty’s Raum und Zeit, which treats of both the nature of space and spatial perception. I begin by sketching two charges that Marty raises against Kantian and Brentanian conceptions of space (and spatial perception) respectively, before detailing what I take to be a characteristically Martyan picture of space perception, though set against the backdrop of contemporary philosophy of perception. Marty has it that spatial relations are non-real but existent, causally inert relations that are grounded (...) in space, which is itself non-real but existent. Objects do not inhere in space in the way properties inhere in substances. Rather, there is a ‘non-real’ relation of ‘fulfillment’ (Erfüllung) that holds between objects and places in space, which itself subsists. I consider whether any contemporary philosophy of perception is equipped to make sense of Martyan space perception and I suggest that the most promising conception is Naïve Realism. I then outline a difficulty for this theoretical translation. Naïve Realism is a direct theory of perception whereby S is said to perceive O just in case S stands in a psychological relation of acquaintance with O, where this relation is both non-representational and explanatorily primitive. For Marty however, all relations are non-real and, insofar as they are grounded, are neither fundamental, nor brute or primitive in an explanatory sense. I close by detailing what I thereby take a distinctively Martyan form of Naïve Realism to involve. The central theoretical tenet that phenomenal character is fundamentally constituted by worldly objects is preserved; but the manifestly relational structure of the acquaintance relation, construed in particular as a relation of awareness, is treated as derivative. I make headway in spelling out the latter claim by bringing Marty into fleeting conversation with another Thomist - G.E.M. Anscombe. (shrink)

I ask whether figure-ground structure can be realized in touch, and, if so, how. Drawing on the taxonomy of touch sketched in Katz's 1925 The World of Touch, I argue that the form of touch that is relevant to such consideration is a species of immersed touch. I consider whether we can feel the space we are immersed in and, more specifically, the empty space against which the surfaces of objects, as I shall urge, “stand out.” Harnessing M. G. F. (...) Martin's account of bodily awareness and touch, I defend a positive thesis, pace Graham Nerlich on whose The Shape of Space I otherwise rely, both to defend the supposition that empty space can in principle be felt and to argue that touching empty space is not a mere species of absence perception. Along the way, I defuse a causal worry that might be thought to arise in the case of touching empty space. (shrink)

I present a novel anti-sceptical BIV argument by focusing on conditions on the production and use of the locative preposition ‘in’. I distinguish two uses of ‘in’—material and descriptive phenomenological—and I explain in what respect movement is central to the concept that our use of ‘in’ expresses. I go on to argue that a functionalist semantics of the intelligible use of ‘in’ demands a materialist philosophy of action in the spirit of G.E.M. Anscombe, but also why the structure of space (...) is not irrelevant either; appeal to the structure of space unsettles the causal-empirical assumptions that ground the picture of subjectivity and agency that the biv narrative assumes. Finally, I explain why a functionalist semantics demands a Naïve Realist metaphysics of perception, consistent with some of Putnam’s last writings on philosophy of perception. (shrink)