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)

Engineering ethics calls the attention of engineers to professional codes of ethical responsibility and personal values, but the practice of ethics in corporate settings can be more complex than either of these. Corporations too have cultures that often include corporate social responsibility (CSR) practices and policies, but few discussions of engineering ethics make any explicit reference to CSR. This article proposes critical attention to CSR and role ethics as an opportunity to help prepare engineers to think through the ethics of (...) their professional practice. After a brief overview of the evolution of social responsibility within engineering ethics in the United States, this article shares empirical research with practicing engineers in the mining and energy industries to explore how their formal ethics training did and did not prepare them to grapple with the ethical dimensions of their professional practice. It then illustrates the ways in which these dilemmas and the strategies employed for navigating them are framed within CSR policies and practices and resonate more strongly with role ethics rather than ethical theory as currently taught in most US engineering programs. The article concludes that engineering ethics teaching and learning would benefit from explicitly incorporating critical discussions of role ethics and CSR. (shrink)

The mining and energy industries present unique challenges to engineers, who must navigate sometimes competing responsibilities and codes of conduct, such as personal senses of right and wrong, professional ethics codes, and their employers’ corporate social responsibility policies. Corporate social responsibility is the current dominant framework used by industry to conceptualize firms’ responsibilities to their stakeholders, yet has it plays a relatively minor role in engineering ethics education. In this article, we report on an interdisciplinary pedagogical intervention in a petroleum (...) engineering seminar that sought to better prepare engineering undergraduate students to critically appraise the strengths and limitations of CSR as an approach to reconciling the interests of industry and communities. We find that as a result of the curricular interventions, engineering students were able to expand their knowledge of the social, rather than simply environmental and economic dimensions of CSR. They remained hesitant, however, in identifying the links between those social aspects of CSR and their actual engineering work. The study suggests that CSR may be a fruitful arena from which to illustrate the profoundly sociotechnical dimensions of the engineering challenges relevant to students’ future careers. (shrink)

Sterols and the reductant nicotinamide adenine dinucleotide phosphate (NADPH), essential for eukaryotic life, arose because of, and as an adaptation to, rising levels of molecular oxygen (O2). Hence, the NADPH and O2‐intensive process of sterol biosynthesis is inextricably linked to redox status. In mammals, cholesterol biosynthesis is exquisitely regulated post‐translationally by multiple E3 ubiquitin ligases, with membrane associated Really Interesting New Gene (RING) C3HC4 finger 6 (MARCHF6) degrading at least six enzymes in the pathway. Intriguingly, all these MARCHF6‐dependent enzymes require (...) NADPH. Moreover, MARCHF6 is activated by NADPH, although what this means for control of cholesterol synthesis is unclear. Indeed, this presents a paradox for how NADPH regulates this vital pathway, since NADPH is a cofactor in cholesterol biosynthesis and yet, low levels of NADPH should spare cholesterol biosynthesis enzymes targeted by MARCHF6 by reducing its activity. We speculate MARCHF6 helps mammalian cells adapt to oxidative stress (signified by low NADPH levels) by reducing degradation of cholesterogenic enzymes, thereby maintaining synthesis of protective cholesterol. (shrink)

This paper argues that “backstage” gallows humor among clinical mentors not only affects medical students’ perceptions of what it means to be a doctor but is also symptomatic and indicative of a much larger problem in medicine—namely, the failure to attend fully to the complexity and profundity of the lived experiences of illness, suffering, and death. Reorienting the discourse surrounding gallows humor away from whether or in what context it is acceptable and toward the reasons why doctors feel the need (...) to use such humor in the first place addresses this issue in a more illuminating way. (shrink)

Hastings Center Report, Volume 52, Issue S1, Page S57-S59, March‐April 2022.

This study investigated the roles of problem structure and strategy use in problem encoding. Fourth‐grade students solved and explained a set of typical addition problems (e.g., 5 + 4 + 9 + 5 = _) and mathematical equivalence problems (e.g., 4 + 3 + 6 = 4 + _ or 6 + 4 + 5 = _ + 5). Next, they completed an encoding task in which they reconstructed addition and equivalence problems after viewing each for 5 s. Equivalence problems (...) of the form 4 + 3 + 6 = 4 + _ overlap with a perceptual pattern found in traditional arithmetic problems (i.e., answer blank in final position), and students' encoding was poorest on problems of this type. Individual differences in encoding the equivalence problems were related to variations in strategy use. Some students solved blank‐final equivalence problems using the standard arithmetic strategy of performing all given operations on all given numbers. These students made more errors in encoding problem structure, but fewer errors in encoding the numbers, than did students who solved the problems using correct or other incorrect strategies. Moreover, students who expressed many strategies for solving the blank‐final equivalence problems made fewer errors in encoding problem structure, but more errors in encoding the numbers, than did students who expressed only a single strategy. Results highlight that encoding is intended to guide action and that prior experience can simultaneously facilitate and interfere with accurate encoding. (shrink)

In the current U.S. context, we are facing a Constitutional crisis with frequent government shutdowns and new policy debates surrounding immigration, climate change, budgeting practices, and the balance of power. With competing interests, unclear policy, and inconsistent leadership directives, the question becomes: How do contemporary bureaucrats make sense of this ethically turbulent environment? This collection provides a lens for viewing administrative decision-making and behavior from a Constitutional basis, as contemporary bureaucrats attempt to navigate uncharted territory. Ethics for Contemporary Bureaucrats is (...) organized around three constitutional values: freedom, property, and social equity. These themes are based on emerging trends in public administration and balanced with traditional ethical models. Each chapter provides an overview of a contemporary ethical issue, identifies key actors, institutions, legal and legislative policy, and offers normative and practical recommendations to address the challenges the issue poses. Rooted in a respected and time-tested intellectual history, this volume speaks to bureaucrats in a modern era of governance. It is ideally suited to educate students, scholars, and public servants on Constitutional values and legal precedent as a basis for ethics in the public sector. (shrink)

We examined the management of completed advance directives including why participants completed a document, what procedures and values they chose, with whom they held end-of-life conversations, and where they stored their document. Participants elected to complete a SurveyMonkey survey that was made available to individuals who wrote an advance directive through Texas-LivingWill.org; 491 individuals elected to fill out the survey, aged 19 to 94 years. The survey asked multiple questions about why participants completed an advance directive, where they would store (...) it, and with whom they had conversations about their end-oflife wishes. A list of procedures and values allowed participants to indicate what they refused or requested in their advance directive. Advance directives are most often completed to allow patients to prepare and control the healthcare they wish to receive when dying. One-half to two-thirds of individuals refuse common end-of-life medical procedures, and the rest request the procedures. We found a correlation between the choice to refuse or request a procedure and the age of the participant. Participants reported that their end-of-life conversations most often occurred with their spouse. Respondents often reported that their advance directive was stored with their physician and power of attorney for healthcare, conversations with those individuals rarely happened. Advance directives document patients’ requests for and refusals of end-of-life care. Physicians and surrogates need to be better educated so that the documents are part of a meaningful conversation with the patient. Because patients’ choices change over their lifespan, these documents need to be revisited regularly and not completed as a onetime event. (shrink)

In describing the foundations of our pedagogical approaches to service-learning, we seek to go beyond the navel-gazing—at times, paralyzing—paradoxes of neoliberal forces, which can do “good” for students and their communities, yet which also call students into further calculative frameworks for understanding the “value” of pre-health humanities education and social engagement. We discuss methods to create quiet forms of subversion that call for a moral imagination in extending an ethics of care to students as well as to the communities with (...) which they engage. While we recognize the partiality and limitations of our attempts, framing mentored service-learning in unexpected ways can help students and practitioners to understand their role within broader social, historical, cultural, and emotional contexts and encourage them to act intentionally toward the communities they seek to serve in response to this new self-knowledge. To that end, we outline an academically rigorous service-learning intervention at one of our universities. (shrink)

Recent efforts by legislative officials and public health advocates to reform the US food stamp program, or Supplemental Nutrition Assistance Program, have focused on restricting the types of foods eligible for purchase with SNAP benefits, specifically sugar-sweetened beverages. We argue that it is, in principle, permissible for the US government to enact a SNAP-specific SSB ban prohibiting the purchase of SSBs with SNAP benefits. While the government has a duty to ensure that citizens meet their nutritional needs, since SSBs provide (...) negligible nutrition, it has no obligation to subsidize them. Additionally, there is good reason to think that a SNAP-specific SSB ban would enable the government to better fulfill two other duties—improving citizens’ health and providing public services like Medicaid and Medicare in a more cost-effective manner. Still, because the costs and benefits of such a ban remain uncertain, we argue that the government should conduct well-designed pilot projects to help determine the effects of an SSB ban. (shrink)

Samuel H. LiPuma and Joseph P. DeMarco argue for a positive right to continuous sedation until death (CSD) for any patient with a life expectancy less than six months. They reject any requirement of proportionality. Their proposed guideline makes CSD an option for a decisional adult patient with an appropriate terminal diagnosis regardless of whether suffering (physical or existential) is present. This guideline purports to “empower” the patient with the ability to control the timing and manner of her death. This (...) extends even to the option to “opt out” of the awareness and experience of dying and to avoid suffering altogether, even if one’s symptoms and suffering could be effectively treated.We respond first with a critique of their terminology. We then turn to some purely practical considerations of how this guideline might be enacted in the current atmosphere of American hospice and palliative care medicine. We close with a consideration of one philosophical concern that might ground the discussion of risks, benefits, and alternatives necessary for informed consent. (shrink)

If engaging in end of life conversations and advance care planning not only is desired by many Americans but also might significantly improve patient care at the end of life, then why was a provision that provided reimbursement for physicians to engage in end of life planning through Medicare removed from legislation? If, as some researchers have suggested, reimbursements under Medicare “would have been a start” for encouraging these conversations, then why was the Advance Care Planning Consultation provision in the (...) 2008 health reform effort so vehemently opposed by politicians and citizens alike? The heated and misleading rhetoric employed against the ACPC undoubtedly contributed to intractable polarization surrounding this portion of the health reform bill and assured its failure. But the ACPC's emphasis on “checklists” and regulation may also have served as fodder for these fiery critiques. If that's right, legislation that focuses squarely on the broader and more fundamental goals of end of life consultations and deemphasizes administrative and documentary concerns may have a greater chance for success in years to come, as health reform is implemented and the battle over the ACPC fades from memory. (shrink)

How medical education and practice can move beyond a narrow focus on biological intervention to recognize the lived experiences of illness, suffering, and death. In Afflicted, Nicole Piemonte examines the preoccupation in medicine with cure over care, arguing that the traditional focus on biological intervention keeps medicine from addressing the complex realities of patient suffering. Although many have pointed to the lack of compassion and empathy in medical practice, few have considered the deeper philosophical, psychological, and ontological reasons for (...) it. Piemonte fills that gap, examining why it is that clinicians and medical trainees largely evade issues of vulnerability and mortality and, doing so, offer patients compromised care. She argues that contemporary medical pedagogy and epistemology are not only shaped by the human tendency to flee from the reality of death and suffering but also perpetuate it. The root of the problem, she writes, is the educational and institutional culture that promotes reductionist understandings of care, illness, and suffering but avoids any authentic confrontation with human suffering and the fear and self-doubt that can come with that confrontation. Through a philosophical analysis of the patient-practitioner encounter, Piemonte argues that the doctor, in escaping from authentic engagement with a patient who is suffering, in fact “escapes from herself.” Piemonte explores the epistemology and pedagogy of medicine, examines its focus on calculative or technical thinking, and considers how “clinical detachment” diminishes physicians. She suggests ways that educators might cultivate the capacity for authentic patient care and proposes specific curricular changes to help students expand their moral imaginations. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

Topics in Cognitive Science, Volume 14, Issue 1, Page 163-188, January 2022.

The fact that many modal operators are part of an adjunction is probably folklore since the discovery of adjunctions. On the other hand, the natural idea of a minimal propositional calculus extended with a pair of adjoint operators seems to have been formulated only very recently. This recent research, mainly motivated by applications in computer science, concentrates on technical issues related to the calculi and not on the significance of adjunctions in modal logic. It then seems a worthy enterprise (both (...) for these contemporary topical pursuits and also for historical interest) to trace the concept of adjunction back to the origins of the algebraic semantics of modal logic and to make explicit its ubiquity in this branch of mathematics. (shrink)

This paper makes a conceptual inquiry into the notion of ‘publics’, and forwards an understanding of this notion that allows more responsible forms of decision-making with regards to technologies that have localized impacts, such as wind parks, hydrogen stations or flood barriers. The outcome of this inquiry is that the acceptability of a decision is to be assessed by a plurality of ‘publics’, including that of a local community. Even though a plurality of ‘publics’ might create competing normative demands, its (...) acknowledgment is necessary to withstand the monopolization of the process of technology appraisal. The paper presents four ways in which such an appropriation of publicness takes place. The creation of dedicated ‘local publics’, in contrast, helps to overcome these problems and allows for more responsible forms of decision-making. We describe ‘local publics’ as those in which stakeholders from the different publics that are related to the process of technology implementation are brought together, and in which concerns and issues from these publics are deliberated upon. The paper will present eight conditions for increasing the effectiveness of such ‘local publics’. (shrink)

The feuding factions of the memory wars, that is, those concerned with the validity of recovered memories versus those concerned with false memories, are unified by Erdelyi's theory of repression. Evidence shows suppression, inhibition, and retrieval blocking can have profound yet reversible effects on a memory's accessibility, and deserve as prominent a role in the recovered memory debate as evidence of false memories. Erdelyi's theory shows that both inhibitory and elaborative processes cooperate to keep unwanted memories out of consciousness.

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

To assess whether and how environmental values and sense of place relate to sustainable farming practices, we conducted a study in South Kona, Hawaii, addressing environmental values, sense of place, and farm sustainability in five categories: environmental health, community engagement and food security, culture and history, education and research, and economics. We found that the sense of place and environmental values indexes showed significant correlation to each category of sustainability in both independent linear regressions and multivariate regression. In total, sense (...) of place explained a larger share of the overall farm performance. However, each indicator showed relative strengths; environmental values showed significantly higher correlation to environmental and educational practices. Furthermore the scales were complimentary, and the use of both scales greatly improved prediction of good farming practices from a multiple-impact perspective. With implications for community and environmental impacts, results suggest that a more comprehensive view of farmers’ environmental values and place connections may help illuminate individual farmers’ decisions and sustainability-related practices. (shrink)

This article aims to contribute to the literature on conceptual change by engaging in direct theoretical and empirical comparison of contrasting views. We take up the question of whether naïve physical ideas are coherent or fragmented, building specifically on recent work supporting claims of coherence with respect to the concept of force by Ioannides and Vosniadou [Ioannides, C., & Vosniadou, C. (2002). The changing meanings of force. Cognitive Science Quarterly 2, 5–61]. We first engage in a theoretical inquiry on the (...) nature of coherence and fragmentation, concluding that these terms are not well‐defined, and proposing a set of issues that may be better specified. The issues have to do with contextuality, which concerns the range of contexts in which a concept (meaning, model, theory) applies, and relational structure, which is how elements of a concept (meaning, model, or theory) relate to one another. We further propose an enhanced theoretical and empirical accountability for what and how much one needs to say in order to have specified a concept. Vague specification of the meaning of a concept can lead to many kinds of difficulties.Empirically, we conducted two studies. A study patterned closely on Ioannides and Vosniadou's work (which we call a quasi‐replication) failed to confirm their operationalizations of “coherent.” An extension study, based on a more encompassing specification of the concept of force, showed three kinds of results: (1) Subjects attend to more features than mentioned by Ioannides and Vosniadou, and they changed answers systematically based on these features; (2)We found substantial differences in the way subjects thought about the new contexts we asked about, which undermined claims for homogeneity within even the category of subjects (having one particular meaning associated with “force”) that best survived our quasi‐replication; (3) We found much reasoning of subjects about forces that cannot be accounted for by the meanings specified by Ioannides and Vosniadou. All in all, we argue that, with a greater attention to contextuality and with an appropriately broad specification of the meaning of a concept like force, Ioannides and Vosniadou's claims to have demonstrated coherence seem strongly undermined. Students' ideas are not random and chaotic; but neither are they simply described and strongly systematic. (shrink)

The effects of parent rewards on youth outcomes have been studied extensively; however, research has not systematically categorized parent rewards. Centralizing the analysis of rewards within a given study would help compare the prevalence of reward types at superordinate and subordinate levels. Moreover, it could reveal which level is the most effective for assessing cultural group similarities and differences in a globalizing world. Mother-child conversations between European-American (n = 51) and Hispanic-American (n = 44) dyads were transcribed. A content analysis (...) assessed material and social reward talk themes and created new subthemes. A series of 2 (culture) × 2 (gender) ANCOVAs assessed cultural differences in reward talk themes and subthemes. Results revealed the prevalence of certain reward subthemes, like praise, significantly differed by cultural group. In conclusion, investigations with different cultural groups should consider reward talk on a subordinate level rather than superordinate. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

BackgroundPublic Safety Personnel are routinely exposed to human suffering and need to make quick, morally challenging decisions. Such decisions can affect their psychological wellbeing. Participating in or observing an event or situation that conflicts with personal values can potentially lead to the development of moral injury. Common stressors associated with moral injury include betrayal, inability to prevent death or harm, and ethical dilemmas. Potentially psychologically traumatic event exposures and post-traumatic stress disorder can be comorbid with moral injury; however, moral injury (...) extends beyond fear to include spiritual, cognitive, emotional or existential struggles, which can produce feelings of severe shame, guilt, and anger.ObjectiveThis scoping review was designed to identify the extant empirical research regarding the construct of moral injury, its associated constructs, and how it relates to moral distress in firefighters, paramedics, and police officers.MethodsA systematic literature search of peer-reviewed research was conducted using databases MEDLINE, EMBASE, APA PsychInfo, CINHAL PLUS, Web of Science, SCOPUS, and Google Scholar. Included studies were selected based on the inclusion criteria before being manually extracted and independently screened by two reviewers.ResultsThe initial database search returned 777 articles, 506 of which remained after removal of duplicates. Following review of titles, abstracts, and full texts, 32 studies were included in the current review. Participants in the articles were primarily police officers, with fewer articles focusing on paramedics and firefighters. There were two studies that included mixed populations. Most studies were qualitative and focused on four topics: values, ethical decision-making, organizational betrayal, and spirituality.ConclusionPublic safety organizations appear to recognize the experience of moral distress or moral injury among public safety personnel that results from disconnects between personal core values, formal and informal organizational values, vocational duties, and expectations. Further research is needed to better understand moral distress or moral injury specific to public safety personnel and inform training and treatment in support of public safety personnel mental health. (shrink)

This paper examines the effects of a decrease in auditor litigation risk in a setting that isolates a change in auditor litigation risk from changes in auditor reputation. _StoneRidge Investment Partners v. Scientific Atlanta_ is a 2008 U.S. Supreme Court ruling that restricted secondary actor liability in class action suits, resulting in a decrease in class actions that listed auditors as defendants. We document that the _StoneRidge_ decision is associated with a negative CAR for clients of Big 4 auditors and (...) industry specialist auditors, in particular those associated with high-litigation risk, low cash, and past incidences of modified going concern opinions. These findings are consistent with investor perception of lower potential payoffs from secondary defendants in class action suits, in particular auditors, following the _StoneRidge_ decision. We also document that auditors are more (less) likely to accept (reject) risky clients and charge lower audit fees to risky clients after _StoneRidge_, consistent with a decrease in auditor litigation risk that increases auditor risk tolerance. Finally, we provide evidence that audit firms issue fewer going concern opinions following _StoneRidge_, consistent with a decrease in litigation risk leading to lower audit quality_._ Our results are relevant to policy makers as they consider the disciplinary role of litigation on audit markets. (shrink)