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)

Macphail’s ‘null hypothesis’, that there are no differences in intelligence, qualitative or quantitative, between non-human vertebrates has been controversial. This controversy can be useful if it encourages interest in acquiring a detailed understanding of how non-human animals express flexible problem-solving capacity (‘intelligence’), but limiting the discussion to vertebrates is too arbitrary. As an example, we focus here on Portia, a spider with an especially intricate predatory strategy and a preference for other spiders as prey. We review research on pre-planned detours, (...) expectancy violation and a capacity to solve confinement problems where, in each of these three contexts, there is experimental evidence of innate cognitive capacities and reliance on internal representation. These cognitive capacities are related to, but not identical to, intelligence. When discussing intelligence, as when discussing cognition, it is more useful to envisage a continuum instead of something that is simply present or not; in other words, a continuum pertaining to flexible problem-solving capacity for ‘intelligence’ and a continuum pertaining to reliance on internal representation for ‘cognition’. When envisaging a continuum pertaining to intelligence, Daniel Dennett’s notion of four Creatures (Darwinian, Skinnerian, Popperian, Gregorian) is of interest, with the distinction between Skinnerian and Popperian Creatures being especially relevant when considering Portia. When we consider these distinctions, a case can be made for Portia being a Popperian Creature. Like Skinnerian Creatures, Popperian Creatures express flexible problem solving capacity, but the manner in which this capacity is expressed by Popperian Creatures is more distinctively cognitive. (shrink)

This essay describes the value and validity of public dialogue on science?related issues. We define what is meant by ?dialogue?, the context within which dialogue takes place in relation to science, and the purposes of dialogue. We introduce a model to describe and analyse the practice of dialogue, at different stages in the development of science, its applications and their consequences. Finally, we place the practice of dialogue on science?related issues in relation to the wider political process and draw out (...) implications for scientists in particular. (shrink)

Human suffering is a complex phenomenon that can manifest physically or psychologically. As the negative valence of affective phenomena, with the positive being pleasure or happiness, human suffering could easily be interpreted as something to avoid. Sartre explored existential aspects of human suffering in Being and Nothingness. Examining each occurrence of the word suffering in that work provides a basis for understanding the roles Sartre assigned to it within the human experience and consequently provides a more nuanced appreciation of this (...) complex phenomenon. An electronic copy of Being and Nothingness was searched for all occurrences of the word suffering (N = 50), tabularized using the Key Word In Context (KWIC) approach at the sentence level, resulting in 40 sentences for thematic analysis. That analysis resulted in 5 themes, showing the complexity of suffering in Sartre’s major philosophical work and suggesting that suffering is quintessentially human, unavoidable, and potentially liberating. (shrink)

This paper advances a new paradigm in clinical ethics education that not only emphasizes development of individual cli but also focuses on the institutional context within which health care professionals work. This approach has been applied to the goal of improving the care provided to critically and terminally ill adults. The model has been adopted by about thirty hospitals and nursing homes; additional institutions will soon join the program, entitled Decisions Near the End of Life. Here, we describe the history (...) and rationale for this approach, its goals, pedagogical assumptions, and design. (shrink)

. This paper follows the journey of two small fluid units throughout the nineteenth century in Anglo-American medicine and pharmacy, explaining how the non-uniform “drop” survived while the standardized minim became obsolete. I emphasize two roles these units needed to fulfill: that of a physical measuring device, and that of a rhetorical communication device. First, I discuss the challenges unique to measuring small amounts of fluid, outlining how the modern medicine dropper developed out of an effort to resolve problems with (...) the “minimometer,” which measured minims. Second, I explain how drops, utilized in “the open drop method” of administering general anesthesia, effectively communicated a gradual process and epistemically valuable heuristic to the audience of practitioners, whose attention to individual medical outcomes was important for verifying the proper dosage. The standardized minim was never able to achieve success as the drop’s intended replacement; the non-uniform drop better served the relevant epistemic goals within the practical contexts for which these units were designed. The surprising historical trajectory of drops should cause us to question the common equivocation of “standardization” with “progress” in the history and philosophy of measurement. This study also exemplifies how examining non-standard measurement practices can be instructive for better understanding the role and function of standardization within epistemology of measurement. (shrink)

In the light of current events, particularly the ‘post September 11th’ debates with much focus on aspects of the ‘clash of civilisation’ thesis, the issue of Islamic identity is a crucial one. Whilst Friedrich Nietzsche was addressing an audience of a different culture and age, his own originality, creativity, psychological, philological and historical insights allows for a fresh and enlightening understanding of Islam within the context of our modern era. In this book, Roy Jackson sets out to determine: Why did (...) Nietzsche feel inclined to be so generous towards the Islamic tradition yet so critical of Western Christianity? How important was religion for Nietzsche’s views on such matters as moral and political philosophy and how does this help us to understand the Islamic response to modernity? How does Nietzsche’s distinctive outlook and methodology help us to understand such key Islamic paradigms as the Qur’an, the Prophet, and the ‘Rightly-Guided’ Caliphs? Nietzsche and Islam provides an original and fresh insight into Nietzsche’s views on religion and shows that his philosophy can make an important contribution to what is considered to be Islam’s key paradigms. As such it will be of interest to a diverse readership and will provide useful material for researchers when thinking about religion, Islam and the future. (shrink)

To the question ‘Why do you try to realize this?’ your answer may be ‘Because I desire that and I think that the realization of this would involve the realization of that.’ Or your answer may be ‘Because I desire this.’ If ‘Why?’ is interpreted as ‘Desiring what?’ the question ‘Why do you desire this?’ is improper. The word ‘desire’ is, however, frequently used in such a way as to countenance the impropriety. It is so used not only when what (...) is pursued only as a means is said to be desired, but also when a desire for what possesses one character is said to be a desire for what possesses a a concomitant character. Strictly, perhaps, an object of desire is describable in terms only of the character immediately relevant to the desire. The expression ‘to desire what is X qua X’ is perhaps redundant; and the expression ‘to desire what is X qua Y’ is perhaps self-contradictory. But those who think, so must admit that such expressions are current among even careful speakers. (shrink)

Betrayal is both a “people” problem and a philosopher’s problem. Philosophers should be able to clarify the concept of betrayal, compare and contrast it with other moral concepts, and critically assess betrayal situations. At the practical level people should be able to make honest sense of betrayal and also to temper its consequences: to handle it, not be assaulted by it. What we need is a conceptually clear account of betrayal that differentiates between genuine and merely perceived betrayal, and which (...) also provides systematic guidance for the assessment of alleged betrayal in real life. In what follows I offer an account of betrayal that attempts to meet the two requirements of conceptual clarity and contextual adequacy. There is a great temptation to use the events in Washington of the past few years as the case study for such an analysis, but I believe that, for a variety of reasons, including the difficulty of viewing events from “within,” this would only complicate matters rather than clarify them. Rather, I believe that betrayal in literature is fruitful ground for analysis. I have chosen Jane Austen’s Sense and Sensibility for examples of trust and betrayal, because Austen displays the needed complexity and subtlety of human relationships and because she recognizes that violations of trust come in a variety of shades and colors. This particular novel, moreover, not only supplies multiple instances of trusting relationships gone awry, but also a common, detailed, and intelligible landscape within which these relationships exist. Again, however, in order to illuminate betrayal and appropriately assess a purported betrayal, rich examples are not enough. We need a clear concept of betrayal. I will develop this concept by beginning with the related concept of trust. By starting with an explicit definition of trust and using this definition to analyze the various examples Austen provides, betrayal will emerge as but one of two types of violation of trust. This in turn will allow us to distinguish actual from merely “felt” betrayals. I will finally argue that understanding and being sensitive to the other form of violation of trust, which I call abandonment, may be even more significant to our moral life. (shrink)

Juvenile offenders are sometimes transferred to a criminal court where they may stand trial as adults. The rationale for this current trend cannot be justified based on evidence from developmental psychology, the evidence of consistent positive effects for particular intervention strategies, and ethical arguments for justification of punishment. The rationale in actuality reflects the selective manipulation of the alternative conceptions of young people as dependent and vulnerable or as autonomous and responsible to continue to justify policies that entail cultural and (...) racial discrimination. Discretionary decisions at various stages of the justice process amplify racial disparities as minority youths proceed through the system and result in more severe dispositions that for comparable White youths. (shrink)

SummaryJohn Tyndall, Irish-born natural philosopher, completed his PhD at the University of Marburg in 1850 while starting his first substantial period of research into the phenomenon of diamagnetism. This paper provides a detailed analysis and evaluation of his contribution to the understanding of magnetism and of the impact of this work on establishing his own career and reputation; it was instrumental in his election as a Fellow of the Royal Society in 1852 and as Professor of Natural Philosophy at the (...) Royal Institution in 1853. Tyndall's interactions and relationships with Michael Faraday, William Thomson, Julius Plücker and others are explored, alongside his contributions to experimental practice and to emerging theory. Tyndall's approach, challenging Faraday's developing field theory with a model of diamagnetic polarity and the effect of magnetic forces acting in couples, was based on his belief in the importance of underlying molecular structure, an idea which suffused his later work, for example in relation to the study of glaciers and to the interaction of substances with radiant heat. (shrink)

Bentham was an influential thinker with an ‘essentially practical mind’. His influence on British social and political reform, however, was indirect, coming largely after his death and largely through the work of his disciples. Bentham's own attempts to put his ideas directly into practice generally had little effect. He came closest to success in the area of penal policy, winning a contract from Pitt's government in the early 1790s to build and manage a penitentiary that was to be organized on (...) the panopticon principle. Bentham saw the penitentiary as the spearhead of prison reform and as a means of effecting a change from transportation to imprisonment as a punishment for serious crime. While Bentham's use of the panopticon principle itself has attracted most attention in the literature, there was more to his scheme than this. The penitentiary proposals were worked out in great detail, they were a conscious application of his theory of punishment, and they were consistent with and an element of his all-embracing plan of social, political, and constitutional reform. (shrink)

This article seeks to clarify the relation between arguments for atheism and descriptions of the summum bonum in Indian Buddhism, through the analysis of one influential text. I begin by noting that a number of writers have detected a tension between, on the one hand, Buddhist refutations of the existence of “God” (īśvara, ātman, puruşa) and, on the other, Buddhist (especially Mahāyāna) claims about the nature of the ultimate (nirvāna, buddha, dharmakāya), which often appears to have God-like qualities. I then (...) turn to a locus classicus of Mahāyāna Buddhist philosophy of religion, the Pramānasiddhi (“Establishment of Authority”) chapter of the Pramānāvarttika (“Commentary on Authority”) of Dharmakīrti (7th century CE). After briefly introducing Dharmakīrti and the Pramānasiddhi chapter, I examine first the chapter’s atheological passages, which include a systematic attack on a Hindu (Nyāya) “argument from design” and a number of important claims about the implausibility of any permanent “spiritual” principle. The arguments are complex and varied, but most turn on the crucial Buddhist assumption that a permanent entity is by definition incapable of interaction with the impermanent, hence utterly unsuitable as a cause or effect. I then examine the chapter’s buddha logical passages, which tend to stress that a Buddha is defined above all by his knowledge of what is to be avoided and adopted by those intent on freedom, i.e., his knowledge of the four noble truths. The Buddha thus described is less notable for his transcendental nature than for his wise, compassionate, and skillful engagement with the world and its creatures---hence less obviously Mahāyānist than the Buddha described by those who articulate a “three-body” (trikāya) theory. I note by way of conclusion that, though Dharmakīrti’s buddhalogy did not prove as influential as his atheology, the juxtaposition of the two reveals an overall metaphysical consistency, in which axiomatic assumptions about permanence, impermanence, and deity are in harmony rather than tension. (shrink)

Physician strikes in the United States have been relatively rare, although this has not been the case in other countries nor with other members of the healthcare community, such as nurses. This situation, however, could change. More physicians are either joining unions or seriously discussing doing so. The National Guild for Medical Providers, for example, is actively trying to expand its membership of 11,000 doctors in Michigan, Pennsylvania, and New Hampshire into Illinois, California, New Jersey, Colorado, Texas, and South Carolina. (...) The Federation of Physicians and Dentists, with 2,500 members in Florida and Connecticut, is trying to establish itself in Seattle, Las Vegas, Tucson, and Philadelphia. Although unions are neither necessary nor sufficient conditions for strikes, if physician unions do become more prevalent, the potential for collective work actions, including strikes, increases. (shrink)

Friendship between professors and students have the potential for hurting those involved and can be hurtful to the larger society in which they occur. This paper examines what sort of boundary lines can be drawn for appropriate faculty-student relationships by considering three arguments against faculty-student friendships. After rejecting these arguments on the grounds that they rely upon a flawed conceptualization of friendship, the paper, drawing on William Rawlins’s theory of friendship, argues that faculty-student relationships are neither desirable nor undesirable per (...) se. However, if such relationships do arise, it is possible that they can be conducted in an ethically responsible and professionally appropriate way. (shrink)

This article examines the relationship between teaching and trust and argues that a good trust relationship is essential to effective teaching. Unfortunately, the increasingly commercial nature of the modern university undermines this and contributes to the mistaken idea that teaching is a contractual one, thereby undermining a core feature of good teaching.

Debating Terrorism is an innovative new textbook, addressing a number of key issues in contemporary terrorism studies from both 'traditional' and 'critical' perspectives. In recent years, the terrorism studies field has grown in quantity and quality, with a growing number of scholars rooted in various professional disciplines beginning to debate the complex dynamics underlying this category of violence. Within the broader field, there are a number of identifiable controversies and questions which divide scholarly opinion and generate opposing arguments. These relate (...) to theoretical issues, such as the definition of terrorism and state terrorism, substantive issues like the threat posed by al Qaeda and the utility of different responses to terrorism, different pathways leading people to engage in terrorist tactics, and ethical issues such as the torture of terrorist suspects and targeted assassination. This volume aims to bring together in one place many of the field's leading scholars to debate the key issues relating a set of 12 important controversies and questions. The format of the volume involves a leading scholar taking a particular position on the controversy, followed by an opposing or alternative viewpoint written by another scholar. In addition to the pedagogic value of allowing students to read opposing arguments in one place, the volume will also be important for providing an overview of the state of the field and its key lines of debate. This textbook will be essential reading for all students of terrorism and political violence, critical terrorism studies, critical security studies, security studies and IR in general. (shrink)

Business management within the United States of America contains unacknowledged, inherent contradictions that constrain individual and collective action, and form barriers against the development of authenticity and solidarity within organizations. The Emersonian themes of conformity, consistency, and knowledge, as developed in his 1841 essay Self-Reliance, were used as constructive points of philosophical inquiry around which to interrogate the theory and praxis of current American business management. The need for such an examination of management is observable in recent social phenomena. Specifically, (...) the great resignation was explored as a potential representative response to dealing with the contradictions between management as currently practiced within the United States and the existential needs of those subjugated by and to its praxis. Philosophy emerges as an effective way to assess the degree to which organizations can achieve their emancipatory potential using the current theory and praxis of business management. (shrink)

Buddhisms and Deconstructions considers the connection between Buddhism and Derridean deconstruction, focusing on the work of Robert Magliola. Fourteen distinguished contributors discuss deconstruction and various Buddhisms—Indian, Tibetan, and Chinese —followed by an afterword in which Magliola responds directly to his critics.

With this special volume of Speculations, the editors wanted to challenge the contested term "speculative realism," offering scholars who have some involvement with it a space to voice their opinions of the network of ideas commonly associated with the name.

In this third volume of Speculations, a serial imprint created to explore post-continental philosophy and speculative realism, a wide range of topics are covered, from the philosophy of religion to psychoanalysis to the philosophy of science to gender studies, and in a wide variety of formats (articles, interviews, position pieces, translations, and review essays).

In this sixth issue of Speculations, a serial imprint created to explore post-continental philosophy and speculative realism, a wide range of contemporary philosophical issues pertaining to the contemporary philosophical scene is touched upon, from the continental realism of Tristan Garcia, Graham Harman and Quentin Meillassoux to the 'new realism' of Maurizio Ferraris, from Lacanian and Laurellian speculations to the synthetic philosophy of Fernando Zalamea's mathematics.

Objective: To determine the views of people with multiple sclerosis (MS) and professionals in relation to confidentiality, consent and access to data within a proposed MS register in the UK. Design: Qualitative study using focus groups (10) and interviews (13). Setting: England and Northern Ireland. Participants: 68 people with MS, neurologists, MS nurses, health services management professionals, researchers, representatives from pharmaceutical companies and social care professionals. Results: People with MS expressed open and altruistic views towards the use of their personal (...) information to facilitate service provision and research, placing trust in responsible guardianship and legitimate use of their information. Participant’s proposed that people with MS should be able to select their individual level of involvement in a register using levels of consent. It was agreed that access to the register should be governed by a guardianship committee composed of a range of stakeholders. People with MS did not wish their details to be used by marketing agencies and did not consider this a legitimate use of their data. Whilst participants were positive of the role a register could play in promoting research, participants felt that access to data by pharmaceutical industries should be administered by the guardianship committee. People with MS are concerned should their employers be able to access their personal information. Professionals were more cautious than people with MS in their approach to the use of patient personal data within a register. Conclusions: Whilst all stakeholders were positive of the benefits of an MS register, development of such a resource must incorporate robust data security and guardianship measures in order to ensure that, whilst opportunities are maximised, risks to the privacy of individuals and legal challenges to professionals are avoided. (shrink)

Understanding terrestrial carbon metabolism is critical because terrestrial ecosystems play a major role in the global carbon cycle. Furthermore, humans have severely disrupted the carbon cycle in ways that will alter the climate system and directly affect terrestrial metabolism. Changes in terrestrial metabolism may well be as important an indicator of global change as the changing temperature signal. Improving our understanding of the carbon cycle at various spatial and temporal scales will require the integration of multiple, complementary and independent methods (...) that are used by different research communities. Tools such as air sampling networks, inverse numerical methods, and satellite data allow us to study the strength and location of the global- and continental-scale carbon sources and sinks. Bottom-up studies provide estimates of carbon fluxes at finer spatial scales and examine the mechanisms that control fluxes at the ecosystem, landscape, and regional scales. Bottom-up approaches include comparative and process studies that provide the necessary mechanistic information to develop and validate terrestrial biospheric models. An iteration and reiteration of top-down and bottom-up approaches will be necessary to help constrain measurements at various scales. We propose a major international effort to coordinate and lead research programs of global scope of the carbon cycle. (shrink)