The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

This study aims to highlight how an existential-humanistic perspective can inform athlete support and in doing so, emphasize the importance of explicating the philosophical underpinnings of athlete lifestyle support. Drawing on applied experience with elite youth cricketers over a 12-month period, ethnographic data were collected through the observation, maintenance of case notes, and a practitioner reflective diary. Based on thematic analysis, we created three nonfictional vignettes that we use to illustrate how existential-humanistic theorizing can inform lifestyle support. We discuss the (...) implications of this professional philosophy in terms of considerations for performance and talent development programs, and how holistic support for athletes is positioned. We also discuss implications for athlete lifestyle and performance psychology practitioners, with regard to training, underpinning theoretical grounding of support and the strategic positioning of their practitioner roles. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

pt. 1. lecture 1. Issues and problems ; lecture 2. Mircea Eliade's Cosmos and history and cyclical time ; lecture 3. The early enlightenment and the search for the laws of history, Vico's New science of history ; lecture 4. The high enlightenment's cult of progress, Kant's idea for a universal history from a cosmopolitan point of view ; lecture 5. Hegel's philosophy of history ; lecture 6. Marx's historical materialism ; lecture 7. Nietzche's critique of historical consciousness, On the (...) advantages and disadvantages of history for life ; lecture 8. Weber's historical sociology -- pt. 2. lecture 9. Taking the long view, Arnold Toynbee and world historical speculation ; lecture 10. Twentieth-century neo-idealism, R.G. Collingwood's The idea of history ; lecture 11. The positivist conception of historical knowledge, Carl Hempel's The function of general laws in history ; lecture 12. Analytic musings, Arthur Danto's Narration and knowledge ; lecture 13. Social history, structuralism, and the long duree, Fernand Brandel's On history ; lecture 14. Post-structuralism and the linguistic turn, Hayden White's Introduction to metahistory ; lecture 15. Naturalism revisited, William McNeill's Plagues and peoples ; lecture 16. The heterogeneity of historical understanding. (shrink)

Contemporary emphasis on creating culturally relevant and context specific knowledge increasingly drives researchers to conduct their work in settings outside their home country. This often requires researchers to build relationships with various stakeholders who may have a vested interest in the research. This case study examines the tension between relationship development with stakeholders and maintaining study integrity, in the context of potential harms, data credibility and cultural sensitivity. We describe an ethical breach in the conduct of global health research by (...) a arising from the ad-hoc participation of a community stakeholder external to the visiting research group. A framework for reflection is developed from a careful examination of underlying factors and presented with a discussion of consequences and mitigation measures. This framework aims to present lessons learned for researchers working abroad who might face similar situations in their work. (shrink)

Sometimes we learn what the world is like, and sometimes we learn where in the world we are. Are there any interesting differences between the two kinds of cases? The main aim of this article is to argue that learning where we are in the world brings into view the same kind of observation selection effects that operate when sampling from a population. I will first explain what observation selection effects are ( Section 1 ) and how they are relevant (...) to learning where we are in the world ( Section 2 ). I will show how measurements in the Many Worlds Interpretation of quantum mechanics can be understood as learning where you are in the world via some observation selection effect ( Section 3 ). I will apply a similar argument to the Sleeping Beauty Problem ( Section 4 ) and explain what I take the significance of the analogy to be ( Section 5 ). Finally, I will defend the Restricted Principle of Indifference on which some of my arguments depend ( Section 6 ). (shrink)

In this paper, I argue that the notion of ‘reasonableness’ that is, for many, at the heart of the Philosophy for Children approach particularly and education for democratic citizenship more broadly, is constituted within the epistemology of ‘white ignorance’ and operates in such a way that it is unlikely to transgress the boundaries of white ignorance so as to view it from without. Drawing on scholarship in critical legal studies and social epistemology, I highlight how notions of reasonableness often include (...) consensus, ‘racialised common sense’ and the ‘typical’ view. In addition the promotion of particular dispositions on the grounds of ‘reasonableness’ both promotes stability and limits how one may think otherwise. Thus, P4C practices that fail to historicise, examine and challenge prevailing notions of reasonableness establish an epistemically ‘gated’ community of inquiry. (shrink)

Background: Alexithymia is a personality trait which is characterized by an inability to identify and describe conscious emotions of oneself and others.Aim: The present study aimed to determine whether various measures of mental health, interoception, psychological flexibility, and self-as-context, predicted through linear associations alexithymia as an outcome. This also included relevant mediators and non-linear predictors identified for particular sub-groups of participants through cluster analyses of an Artificial Neural Network output.Methodology: Two hundred and thirty participants completed an online survey which included (...) the following questionnaires: Toronto alexithymia scale; Acceptance and Action Questionnaire 2 ; Positive and Negative Affect Scale, Depression, Anxiety, and Stress Scale 21 ; Multidimensional Assessment of Interoceptive Awareness ; and the Self-as-Context scale. A stepwise backwards linear regression and mediation analysis were performed, as well as a cluster analysis of the non-linear ANN upper hidden layer output.Results: Higher levels of alexithymia were associated with increased psychological inflexibility, lower positive affect scores, and lower interoception for the subscales of “not distracting” and “attention regulation.” SAC mediated the relation between emotional regulation and total alexithymia. The ANNs accounted for more of the variance than the linear regressions, and were able to identify complex and varied patterns within the participant subgroupings.Conclusion: The findings were discussed within the context of developing a SAC processed-based therapeutic model for alexithymia, where it is suggested that alexithymia is a complex and multi-faceted condition, which requires a similarly complex, and process-based approach to accurately diagnose and treat this condition. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

Robert Elliot claims that the metaethical distinction between subjectivism and objectivism is unimportant in environmental ethics. He argues that because a sufficiently sophisticated subjectivist can accommodate all the intrinsic value an objectivist can, even in apparently problematic situations where humans either do not exist or do not have the relevant values, and because metaethical commitments fail to have any normative or motivational impact on rational debate, it makes no difference whether an environmental ethicist is a subjectivist or an objectivist. Elliot's (...) dismissal, however, is unjustified. As it turns out, objectivists argue differently from the way subjectivists do, are motivated differently from the way subjectivists are, and are able to make a greater range of intrinsic value claims than subjectivists are. If Elliot's arguments have any appeal at all, it is only because he blurs the fundamental metaethical distinction in the first place and defends a subjectivism so objectivist that it is almost unrecognizable as subjectivism. (shrink)

Daniel Bensaïd’s theoretical and political framework deserves to be habitually known in the English-speaking world. His philosophical work has a universal dimension, but because it was also the product of particular political upsurges and downturns, it is necessary to understand these particular political moments to thoroughly understand the universal scope and significance of his work. This paper will look at these political developments and pay particular attention to the crisis of the workers’ movement, strategy and Marxism.

The best way to divide control over children’s education between private and state authorities is unclear. This task has ethical implications that this thesis explores—in the context of a pluralist liberal democracy. In cases where authority over children’s education is granted to private groups, like ethnic or religious minorities, rights are often part of the default vocabulary adopted by politically liberal commentaries. These rights are often viewed as a shield that offers the group immunity from state interference. Some illiberal minority (...) groups argue that they need to be shielded from state interference because the persistence of their cultural or religious identity depends on it. For example, the Amish community in Wisconsin argued in Wisconsin v. Yoder that the future of their community would be jeopardized if they were forced to send their children to school beyond the age of fourteen. While a rights-based approach does explain many of the variables connected with cases like these, the explanation is incomplete. I will offer two clarifications to the rights-based view. First, in the event that a minority group is shielded from state interference, it is not clear that it would be morally legitimate for the group to take over the authority of the state. I will, then, offer a plausible theory that could justify the self-governing authority of minority groups in these situations. My second clarification is that the concept of individual autonomy, often the central liberal value protected by rights, is too broad to support a zero-tolerance approach toward illiberal groups. This indicates that illiberal minority groups might still have a claim to self-governing authority even though they arguably interfere with the autonomy of their children. Some interference with minor elements of individual autonomy should arguably be tolerated in cases where the ruination or assimilation of the group’s unique culture or religion is at stake. (shrink)

There are three main categories of rationale for withholding information or telling lies: if overwhelming harm can only be averted through deceit; complete triviality such that it is irrelevant whether the truth is told; a duty to protect the interests of others. Public health authorities are frequently having to form judgements about the public interest, whether to release information or issue warnings. In June 1992, routine surveillance detected patulin levels (a known carcinogen) in samples of apple juice exceeding safety threshold. (...) Remedial actions were promptly taken and it was planned to subsequently publish the information in the routine way. However, the media portrayed the handling of the problem as a conspiracy and there was a short term reduction in juice sales. In October 1995, the UK Committee on Safety of Medicines issued a warning about certain brands of the contraceptive pill, based on the interim results of three unpublished studies. The increased risk of thromboembolism was small, but the resulting scare led to an increase in unwanted pregnancies. The handling of the B.S.E. crisis in the U.K. also led to accusations of incompetence or conspiracy. Public health authorities have to handle uncertainty and frequently have to form judgements for public safety on the basis of evidence of poor quantity and quality. Their task is not helped by the sometimes conflicting agenda of scientists and media. The public also have differing perceptions and interpretations of risk. The series of scares and crises are having a detrimental effect on public confidence in public health authorities. (shrink)

We used social network analysis to examine a theoretical model exploring why, and under what circumstances, the perpetrators’ ostracizing behaviors are accurately perceived by the target employees. In turn, these perceptions of ostracism lead to the target employees’ counterproductive work behaviors. Adopting perspectives from both perpetrators and targets, we directly measured the ostracizing behaviors by all potential perpetrators and perceived workplace ostracism by target employees. We integrate Social information processing theory and conservation of resource theory to propose a moderated mediation (...) model, and found that employees who have a high level of need to belong are more likely to capture coworkers’ ostracizing behaviors, and those with low political skill are more likely to engage in counterproductive work behavior as their reaction to perceived workplace ostracism. Theoretical and practical implications are discussed. (shrink)

This article makes the political dimension of Gadamer's thought more explicit by examining the interplay of three concepts in his work: solidarity, friendship, and the other. Focusing primarily on certain post--"Truth and Method" writings, I argue that Gadamer's conception of solidarity has to do with historically contingent manifestations of bonds that reflect a civic life together of reciprocal co-perception. These bonds go beyond conscious recognition of observable similarities and differences and emerge from encounters among those who are, and remain, in (...) important ways other to each other. I make this case through an analysis of Gadamer's phenomenology of friendship and the crucial role of otherness in his accounts of both understanding and friendship. I suggest that Gadamer's political thought gives us a way of conceptualizing solidarity and otherness without making the other same or leaving the other completely other. (shrink)

Carrie Jenkins (2005, 2008) has developed a theory of the a priori that she claims solves the problem of how justification regarding our concepts can give us justification regarding the world. She claims that concepts themselves can be justified, and that beliefs formed by examining such concepts can be justified a priori. I object that we can have a priori justified beliefs with unjustified concepts if those beliefs have no existential import. I then argue that only beliefs without existential import (...) can be justified a priori on the widely held conceptual approach. This limits the scope of the a priori and undermines arguments for essentialism. (shrink)

ABSTRACT This article investigates the moral wrongness of joke theft. Working through a trove of real-world cases, and using the sitcom The Marvelous Mrs. Maisel as a touchstone, I argue, ultimately, for a pluralist approach, contending that there are several wrongs that may be present in any case of joke theft, but which cannot be reduced to each other and which are collectively irreducible to any sort of “superwrong.”.

Hoping is an integral part of what it is to be human, and its significance for education has been widely noted. Hope is, however, a contested category of human experience and getting to grips with its characteristics and dynamics is a difficult task. The paper argues that hope is not a singular undifferentiated experience and is best understood as a socially mediated human capacity with varying affective, cognitive and behavioural dimensions. Drawing on the philosophy, theology and psychology of hope, five (...) modes of hoping are outlined: patient, critical, sound, resolute and transformative. The key aim of the paper is to illustrate how different modes of hoping are associated with different pedagogical strategies. Phrased differently, the paper seeks to delineate a range of pedagogies of hope. The phrase ‘pedagogy of hope’ is very much associated with critical theory—one thinks instantly of, for example, Paulo Freire, Henry Giroux or bell hooks. There are many pedagogies of hope, however, and an explicitly conservative text such as William Bennett’s Book of Virtues has as strong a claim to the title as Freire’s radical and utopian ideas. A broader argument, therefore, is that there is nothing inherently radical or subversive about a pedagogy of hope. Pedagogies of hope can serve to reproduce social relations as well as to transform them. (shrink)

Formal methods are changing how epistemology is being studied and understood. A Critical Introduction to Formal Epistemology introduces the types of formal theories being used and explains how they are shaping the subject. Beginning with the basics of probability and Bayesianism, it shows how representing degrees of belief using probabilities informs central debates in epistemology. As well as discussing induction, the paradox of confirmation and the main challenges to Bayesianism, this comprehensive overview covers objective chance, peer disagreement, the concept of (...) full belief, and the traditional problems of justification and knowledge. Subjecting each position to a critical analysis, it explains the main issues in formal epistemology, and the motivations and drawbacks of each position. Written in an accessible language and supported study questions, guides to further reading and a glossary, positions are placed in an historic context to give a sense of the development of the field. As the first introductory textbook on formal epistemology, A Critical Introduction to Formal Epistemology is an invaluable resource for students and scholars of contemporary epistemology. (shrink)

Solving the problem of moral luck—the problem of dealing with conflicting intuitions about whether moral blameworthiness varies with luck in cases of negligence—is like repairing a dented fender in front of two kinds of critic. The one keeps telling you that there is no dent, and the other sees the dent but keeps warning you that repairing it will do more harm than good. It is time to straighten things out. As I argue elsewhere, the solution to the problem of (...) moral luck is finally revealed. Our task now is twofold: to hold a magnifying glass up to the initial problem, so that all might finally see it; and to dismiss unfounded fears about solving that problem, so that all might finally stop grinning and bearing it. (shrink)

Background: Humor, both producing and appreciating, underpins positive social interactions acting as a facilitator of communication. There are clear links to wellbeing that go along with this form of social engagement. However, humor appears to be a seldom studied, cross-disciplinary area of investigation when applied to people with an intellectual disability, this review collates the current state of knowledge regarding the role of humor behavior in the social interactions of people with intellectual disabilities and their carers. Method: A systematic review (...) utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was completed which aimed to explore the current state of knowledge and quality of empirical evidence relating to humor in people with intellectual disabilities. Following this, articles were grouped thematically and summarized. A comprehensive search of four electronic databases (1954–2017) and additional search strategies yielded 32 articles which met the final inclusion criteria. Results: Humor played a significant positive and negative role in the social interactions of people with intellectual disabilities. Research had investigated humor in the classroom and humor expression in different groups including those with autism, Down syndrome, Angelman syndrome, Williams syndrome and Rett syndrome. Few investigations directly studied humor appreciation and comprehension hence themes did not focus solely on humor production/appreciation. Humor comprehension was reportedly supported by gestures. Some groups with intellectual disabilities found non-literal humor (e.g. sarcasm, irony) more difficult to understand which may affect social relationships. Various types of humor were found to be appreciated. The role of humor in relationship development, social facilitation, creativity and stigma had all received some limited attention. Humor also played a role for carer groups in coping with and enjoying the caring role. Research varied in quality with few experimental studies and mainly quasi-experimental and well-conducted qualitative studies. Conclusions: This review revealed the importance of humor behavior in many aspects of the social lives of people with intellectual disabilities. Limited disparate research exists pertaining to humor in this group, suggesting the need for further robust research in this area, including more high quality primary research in the areas of humor production, appreciation, comprehension and stigma. (shrink)

The Government in the UK is encouraging consumerism within health care and is requiring Health Authorities to consult with the public on prioritisation of resources. Public consultation within the National Health Service (NHS) has had limited success in the past. Many of the techniques used are flawed. Despite the limited scope of the public surveys conducted so far, a number of themes have emerged: — a willingness to pay for experimental, ‘high‐tech’ life‐saving treatments rather than more cost‐effective treatments which will (...) improve quality of life, which are more likely to maximise utility from the scarce resources available; — preference for treating the young rather than the old; — preference for treating patients with dependants (e.g. spouse, children) rather than those who have none; — a willingness to discriminate against those patients who were partially responsible for their illness due to choice of `unhealthy' lifestyle (e.g. smoking cigarettes, drinking excess alcohol). These public preferences raise ethical problems. For example, is it just to spend more on heroic treatments which are likely to fail? Is there a right to health care irrespective of whether you have had ‘a fair innings’ or whether a patient is in part responsible for their illness due to an unhealthy lifestyle? If there are ethical concerns about these preferences, should health authorities consult with the public at all? Is human life and suffering incommensurable, and hence is it impossible to prioritise anyway? Some of the ethical consequences of using empirical data on public preferences are discussed. (shrink)

J. Baird Callicott defends a communitarian environmental ethic that grounds moral standing in shared kinship and community. This normative theory is unacceptable because it is out of synch with our considered moral judgments as environmental philosophers. Ecological communitarianism excludes in advance entities that would obviously qualify for moral standing, and scuttles itself in the process.

Many epistemological problems can be solved by the objective Bayesian view that there are rationality constraints on priors, that is, inductive probabilities. But attempts to work out these constraints have run into such serious problems that many have rejected objective Bayesianism altogether. I argue that the epistemologist should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.

Criticism of orthodox models of prejudice reduction is particularly relevant for lesbians, gay men, and bisexuals, particularly when considering stage models of coming-out. If social change is to be effected regarding endemic homonegativity and heterosexism, then it is argued that a radical rethink is needed to the understandable but misinformed desire to get us to like each other more.

This paper examines John Scottus Eriugena's account of material bodies. Some scholars have argued that Eriugena's account prefigures Berkeleyan idealism. The interpretation offered in the paper rejects the Berkeleyan interpretation on the grounds that Eriugena, unlike Berkeley, did not propose a thoroughly immaterialist view of reality.

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. (shrink)

This paper offers a theory of how epistemic and practical reasons for belief can be combined into all‐things‐considered reason. Unlike alternative theories, it does not involve any sharp cut‐offs or lexical priorities among types of reason. The theory allows that the relative strengths of the practical and epistemic reasons matter, as does the distance between the epistemically rational credence and the practically rational credence. Although there are important differences between the structure of epistemic and practical reason, they can still be (...) combined in a satisfactory way. The central idea is that epistemic reason determines an epistemically rational doxastic state, and practical reason can push it around. (shrink)

Psychology has benefited from an enormous wealth of knowledge about processes of cognition in relation to how the brain organizes information. Within the categorization literature, this behavior is often explained through theories of memory construction called exemplar theory and prototype theory which are typically based on similarity or rule functions as explanations of how categories emerge. Although these theories work well at modeling highly controlled stimuli in laboratory settings, they often perform less well outside of these settings, such as explaining (...) the emergence of background knowledge processes. In order to explain background knowledge, we present a non-similarity-based post-Skinnerian theory of human language called Relational Frame Theory (RFT) which is rooted in a philosophical world view called functional contextualism (FC). This theory offers a very different interpretation of how categories emerge through the functions of behavior and through contextual cues, which may be of some benefit to existing categorization theories. Specifically, RFT may be able to offer a novel explanation of how background knowledge arises, and we provide some mathematical considerations in order to identify a formal model. Finally, we discuss much of this work within the broader context of general semantic knowledge and artificial intelligence research. (shrink)