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)

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) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (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.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

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)

Hope as a virtue is an acquired disposition, shaped by reflection; as a civic virtue it must serve the good of the community. Ernst Bloch and Lord Buddha offer help in constructing such a virtue. Using a taxonomy developed by Darren Webb I distinguish open hope from goal-oriented hope, and use each thinker to develop the former. Bloch and Buddha are very different (and notoriously obscure; I do not attempt an exegesis). But they share a metaphysics of change, foundational (...) for making any sense of hope.Buddhism would seem to repudiate hope; it is a source of suffering (i.e., pain in living with reality). Seen more deeply, however, Buddhism offers material for a carefully limited virtue of hope: the habits of noticing good and acknowledging transience. This disposition, acquired through Buddhist practice among other ways, shields one against despair. The habit also frees up energy that would otherwise be wasted. Ernst Bloch gives us insight into how to use that energy, teaching us to value the yearning implicit throughout culture. Open hope becomes a civic virtue when it concerns civic matters; it can be threatened by hyperbolic discourse in political life. (shrink)

Hope as a virtue is an acquired disposition, shaped by reflection; as a civic virtue it must serve the good of the community. Ernst Bloch and Lord Buddha offer help in constructing such a virtue. Using a taxonomy developed by Darren Webb I distinguish open hope from goal-oriented hope, and use each thinker to develop the former. Bloch and Buddha are very different (and notoriously obscure; I do not attempt an exegesis). But they share a metaphysics of change, foundational (...) for making any sense of hope.Buddhism would seem to repudiate hope; it is a source of suffering (i.e., pain in living with reality). Seen more deeply, however, Buddhism offers material for a carefully limited virtue of hope: the habits of noticing good and acknowledging transience. This disposition, acquired through Buddhist practice among other ways, shields one against despair. The habit also frees up energy that would otherwise be wasted. Ernst Bloch gives us insight into how to use that energy, teaching us to value the yearning implicit throughout culture. Open hope becomes a civic virtue when it concerns civic matters; it can be threatened by hyperbolic discourse in political life. (shrink)

In this paper, we build on recent work on the role of the ‘utopian pedagogue’ to explore how utopian thinking can be developed within contemporary higher education institutions. In defending a utopian orientation on the part of HE lecturers, we develop the notion of ‘minimal utopianism’; a notion which, we suggest, expresses the difficult position of critical educators concerned to offer their students the tools with which to imagine and explore alternatives to current social and political reality, while acknowledging the (...) contingent ethical constraints of the system within which they and their students are working. While agreeing with utopian theorists such as Darren Webb who have defended the need for ‘blueprint utopias’ in education in the face of the reduction of the idea of utopia to a purely process-oriented pedagogy, our focus here is on the prior educational task of providing the conceptual and communicative tools for utopian thinking to emerge. The collaborative nature of this paper is ref... (shrink)

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)

Seth MacFarlane’s space adventure, The Orville, is not “Family Guy in Space.” It is a social commentary of the most direct and compelling sort. Through satire, humor, and symbolism, The Orville explores the potential dangers of religion. It does so in individual episodes, such as “If the Stars Should Appear” and “Mad Idolatry,” as well as through the series as a whole in its depiction of how the Union resolves its political differences with the Krill and the Moclans. In this (...) chapter, we will look at how The Orville criticizes religion, both generally and specifically. We will see that while it is not a condemnation of all religious believers, it is a critique of religion itself, suggesting that it can become dangerous when it merges religious dogma with political power. (shrink)

How do we access the authentic self in order to live fulfilling, meaningful lives? In straightforward terms, The Heart of the Matter: Gifts in Strange Wrapping Paper explains a simple but extraordinarily powerful technique called the See, Feel, Hear Challenge that enables people to easily gain entry into the storehouse of their subconscious core beliefs. In the process, it cracks the coded messages that those beliefs release in the form of disease, suffering, addictions, unhappy relationships, and victimized circumstances. Based in (...) the latest findings in neuroscience and neurocardiology, this book guides readers to an uncomplicated understanding of the astounding power of our emotions and how life automatically delivers experiences that trigger negative reactions that subconsciously impact us. These emotions form the foundation of core beliefs that create unhealthy attitudes and dis-ease patterns that keep us from experiencing the authentic, satisfying lives we desire. Using clear examples and true stories from clients, Dr. Weissman’s latest work demonstrates how we can release these stored emotions and their wisdom via the See, Feel, Hear Challenge. It then explains how to use this simple method to evoke feelings that positively impact the quantum field, remolding our bodies, minds, and everyday lives into purposeful expressions of inner joy and radiant well-being. Whether you’re dealing with addictions, dysfunctional relationships, or illness, or are focused on becoming an Olympic champion, The Heart of the Matter gives you a potent tool for positive change and transformation that you can use for the rest of your life. (shrink)

The book moves from descriptive through to more interpretative phenomenological methods to enable the reader to learn to use the main approaches to ...

In The Realm of Rights Judith Thomson provides a full-scale, systematic theory of human and social rights, bringing out what in general makes an attribution of ...

The “practice turn” in philosophy of science has strengthened the connections between philosophy and scientific practice. Apart from reinvigorating philosophy of science, this also increases the relevance of philosophical research for science, society, and science education. In this paper, we reflect on our extensive experience with teaching mandatory philosophy of science courses to science students from a range of programs at University of Copenhagen. We highlight some of the lessons we have learned in making philosophy of science “fit for teaching” (...) outside of philosophy circles by taking selected cases from the students’ own field as the starting point. We argue for adapting philosophy of science teaching to particular audiences of science students, and discuss the benefits of drawing on research within science education to inform curriculum and course design. This involves reconsidering teaching resources, assumptions about students, intended learning outcomes, and teaching formats. We also argue that to make philosophy of science relevant and engaging to science students, it is important to consider their potential career trajectories. By anticipating future contexts and situations in which methodological, conceptual, and ethical questions could be relevant, philosophy of science can demonstrate its value in the education of science students. (shrink)

Interpreting the world through a social lens is a central characteristic of human cognition. Humans ascribe intentions to the behaviors of other individuals and groups. Humans also make inferences about others’ emotional and mental states. This capacity for social attribution underlies many of the concepts at the core of legal and political systems. The developing scientific understanding of the neural mechanisms used in social attribution may alter many earlier suppositions. However, just as often, these new methods will lead back to (...) old conundrums. Cognitive neuroscience will not dispel the hard problems of social judgment. (shrink)

Incisively and stylishly written, this book constitutes an open challenge to reconsider the fundamental question of the relationship of law to society.

In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...) against the possibility of building a machine that passes the Turing test. Finally, I respond to objections against the proposed link between questions in the philosophy of mind and philosophy of computer science. (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.

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)

The essay reflects on how Hans-Georg Gadamer and Karl Barth view interpretation of the Christian Bible. It proceeds in three main sections. The first contends that Gadamer secularizes Christian theology, and that this has drawbacks for the sort of reading his hermeneutic can give to Christian Scripture. The second part turns to Barth, arguing that the whole structure of his approach to the Bible factors in theological commitment, with benefits for the readings he can deliver. The final part makes a (...) case that contemporary reflection on interpretation can nonetheless glean important insights from Gadamer, especially regarding the readerly reception of texts, because his perspective has a certain sort of richness that Barth’s cannot match. The overall suggestion emerging from the interrogation of these two thinkers is that phenomenology and theology might learn from one another, that they each contribute something valuable to discussions of biblical interpretation. (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 which is rooted in a philosophical world view called functional contextualism. 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)

A political philosophy classic from one of the foremost political thinkers of the twentieth century After Utopia was Judith Shklar’s first book, a harbinger of her renowned career in political philosophy. Throughout the many changes in political thought during the last half century, this important work has withstood the test of time. In After Utopia, Shklar explores the decline of political philosophy, from Enlightenment optimism to modern cultural despair, and she offers a critical, creative analysis of this downward trend. (...) She looks at Romantic and Christian social thought, and she shows that while the present political fatalism may be unavoidable, the prophets of despair have failed to explain the world they so dislike, leaving the possibility of a new and vigorous political philosophy. With a foreword by Samuel Moyn, examining After Utopia’s continued relevance, this current edition introduces a remarkable synthesis of ideas to a new generation of readers. (shrink)

I argue that Diogenes and early Cynicism can be understood in an explicitly social and political context, where Cynic praxis, performative public action, can be seen to make visible oppositions inherent to the polity. In doing so, Diogenes’ praxis should be understood as a form of immanent critique, one that demonstrates, for example, that nature and custom are interrelated oppositions in the polis. Cynicism here is understood as a form of immanent critique because Diogenes challenges the social norms of the (...) polis without endorsing external universal standards or predetermined models, but from illuminating dynamics from within the polis and polity. (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)

In this paper I argue that Turing’s responses to the mathematical objection are straightforward, despite recent claims to the contrary. I then go on to show that by understanding the importance of learning machines for Turing as related not to the mathematical objection, but to Lady Lovelace’s objection, we can better understand Turing’s response to Lady Lovelace’s objection. Finally, I argue that by understanding Turing’s responses to these objections more clearly, we discover a hitherto unrecognized, substantive thesis in his philosophical (...) thinking about the nature of mind. (shrink)

Large prospective biobanks are being established containing DNA, lifestyle and health information in order to study the relationship between diseases, genes and environment. Informed consent is a central component of research ethics protection. Disclosure of information about the research is an essential element of seeking informed consent. Within biobanks, it is not possible at recruitment to describe in detail the information that will subsequently be collected because people will not know which disease they will develop. It will also be difficult (...) to describe the specific research that will be performed using the biobank, other than to stipulate categories of research or diseases that are not included. Potential subjects can only be given information about the sorts of research that will be performed and by whom. Organisations responsible for biobanks usually argue that this disclosure of information is adequate when seeking informed consent, especially if coupled with a right to withdraw, as it would not be feasible or it would be too expensive to seek consent renewal on a regular basis. However, there are concerns about this ‘blanket consent’ approach’. Consent waivers have also been proposed in which research subjects entrust their consent with an independent third party to decide whether subsequent research using the biobank is consistent with the original consent provided by the subject. (shrink)