The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution (...) class='Hi'>; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Is de herhaling mogelijk? Deze ogenschijnlijk simpele vraag vormt het uitgangspunt van De herhaling. Een proeve van experimenterende psychologie door Constantin Constantius (1843), een van de meest (...) curieuze geschriften uit het oeuvre van Søren Kierkegaard. In dit artikel worden twee aspecten aan de orde gesteld die De herhaling tot een nog altijd belangrijk boek maken: 1) De ongewone filosofische stijl die in dit boek ontwikkeld wordt en 2) De eigenzinnige opvatting over vrijheid en subjectiviteit die er onder de noemer 'de herhaling' in naar voren wordt gebracht. Zoals de ondertitel 'een proeve van experimenterende psychologie' al aangeeft, is De herhaling geen klassieke filosofische verhandeling waarin op systematische wijze wordt uitgelegd wat er onder de herhaling - als filosofische begrip - verstaan moet worden. Integendeel, het is een uiterst experimenteel boek waarin een nieuwe filosofische stijl wordt geïntroduceerd. Er wordt zodoende nergens een eenduidige definitie gegeven van de herhaling in filosofische zin die ik in het vervolg zal aanduiden als de 'existentiële herhaling'. Sterker nog, de twee verschijningsvormen van de herhaling - de alledaagse en de existentiële herhaling - worden telkens welbewust met elkaar verward. Pas in de afsluitende brief aan de echte lezer van dit boek wordt duidelijk in welke richting we het verschil tussen deze twee vormen van herhaling moeten zoeken. (shrink)

This article tries to make sense of the concept of repetition in Søren Kierkegaard’s works. According to Kierkegaard repetition is a temporal movement of existence. What (...) class='Hi'>is repetition and what is its meaning for human existence? In answering this question the Danish philosopher depicts repetition by comparing three different approaches to life. Throughout the article I try to develop a coherent argument on ‘the new philosophical category’by analysing the three types of repetition and their corresponding human prototypes. I consider repetition a key concept in summarizing Kierkegaard’s theory of existence, where existence pictures the becoming of the human-self that follows several stages. Constantin Constantius’s repetition is an unsuccessful attempt, an aesthetic expression of human-life. The young lover’s repetition is spiritual, albeit not yet authentic, religious, but more poetic, even if he regains his self. Only Job’s repetition is an authentic movement of existence, an expression of a spiritual trial and of genuine faith. (shrink)

This essay calls attention to an aspect of Confucius's notion of ren that has often been overlooked or even denied in much recent discussion of the (...) class='Hi'>topic. While the egalitarian aspect of ren, i.e., the idea that every human being has the potential to become a ren person, is frequently asserted, the leadership dimension of ren has for the most part been given short shrift. I argue that for Confucius, ren is the leadership virtue. This conclusion is mainly based on a careful and systematic analysis of what may be called ?the definitional ren passages? and some ?elucidative ren passages? in the Analects. (shrink)

In this essay, I argue that Søren Kierkegaard’s oeuvre can be seen as a theater of ideas. This argument is developed in three steps. First, I (...) class='Hi'>will briefly introduce a theoretical framework for addressing the theatrical dimension of Kierkegaard’s works. This framework is based on a distinction between“performative writing strategies” and “categories of performativity.” As a second step, I will focus on Repetition: A Venture in Experimenting Psychology, by Constantin Constantius, one of the best examples of Kierkegaard’s innovative way of doing philosophy. This strange and elusive book introduces the difficult and counter-intuitive notion of repetition. Repetition is a category of performativity that aims to activate the subjectivity of the reader. This performative effect is achieved by confronting the reader with an “unresolved”existential problem that is not yet drawn into clarity but is staged in all its confusions and contradictions. Kierkegaard’s pseudonym Constantius relies here on a performative writing strategy that is animated by a dialectic of advance and withdrawal. In the last and third step, I will analyze Constantius’s own reflection on the performative dimension of his text. Constantius has left several clues behind, each of which suggests that he deliberately developed a performative writing strategy. (shrink)

Søren Kierkegaard’s influence on the thought of Mikhail Bakhtin has received relatively little attention from Bakhtin scholars (and hardly any attention from Bakhtin scholars in the (...) class='Hi'>English-speaking world). Yet, as I argue in this paper, Kierkegaard was among the most important formative influences on Bakhtin's work. This influence is most evident in Bakhtin's early ethical philosophy, but remains highly relevant in later periods. Reading Bakhtin as a follower and developer of Kierkegaard's fundamental philosophical insights provides us with a key to the unity of Bakhtin's thought. (shrink)

‘Transcendence’ has been a key subject of Western philosophy of religion and history of ideas. The meaning of transcendence, however, has changed over time. The article looks (...) at some perspectives o ered by the nineteenth and the twentieth century Anglo‐American and con‐ tinental European philosophers of religion and presents their views in relation to the concept of transcendence formulated by the Bengali Hindu traditionalist Bhaktisiddhanta Sarasvati (1874–1937). The questions raised are what transcendence in the philosophy of religion is, how one can speak of it, and what its goal is. The paper points to parallels and di erences in epistemology, ontology and practice. One di erence is that the nineteenth and the twentieth century Western philosophy of religion tended to assume an ontological di erence between self and transcendence inherited om personalities such as Søren Kierkegaard, but also to explore the concept of transcendence beyond the idea of a metaphysical God. Bhaktisiddhanta, whose foundational thought mirrors medieval Hindu philosophy of religion and the theistic schools of Vedānta, suggests that transcendence has a metaphysical and personal dimension that is to some degree ontologically similar to and directly knowable by the self. Bhaktisid‐ dhanta’s approach to transcendence di ers om Kierkegaard’s and other Western philosophers’ and revolves around the idea of God as a transcendent person that can be directly known mor‐ phologically and ontologically through devotion. The article is a contribution to the history of ideas and the philosophy of religion in Eurasia and beyond. (shrink)

It was the emphasis of Søren Kierkegaard's railing against 19th-century Danish Christianity in all its ruthlessness that eventually led him to utterly reject and actively fight (...) class='Hi'> the majority of the contemporary as well as important aspects of the historical discourse on Christianity. One of the aspects that Kierkegaard distanced himself from sharply consists in the long tradition of Christian mysticism. Nevertheless his concept of the “knight of faith” reveals several deliberations that appear to be close to mystical Christian conceptions (e.g. the meaning of suffering or despair for the leap of faith, an increasing awareness of sin and guilt as well as the conditions for the knight of faith's secular ministry). Thus, Kierkegaard's critique of mysticism suggests his misunderstanding of the mystical perspective's implications. This essay tries to solve said misunderstanding between Kierkegaard and christian tradition by interrelating the process of becoming a knight of faith with the mystical responsibility before the divine and the ethical responsibility before all of humanity. (shrink)

Abstract: This essay examines the thoughts and actions of the eponymous hero Hamlet of Shakespeare's tragedy from the perspective of existential philosophy. The death of his (...) class='Hi'>father, the prompt remarriage of his mother and Ophelia's rejection of his love are interpreted as Jaspersian boundary situations. Burdened with the responsibility to avenge his father's murder, Hamlet faces an existential dilemma of either being a dutiful son or being true to himself. As he loses faith in the goodness of the world and confronts death, Hamlet enters a protracted phase of foundering, suffused with despair and self-loathing. The customary rational way of thinking fails him and his soul becomes shipwrecked. But this is also the beginning of Hamlet's journey toward authentic selfhood and becoming the Existenz that he potentially is. Affirming life with all of its absurdity in a moment of transcendence, he attains a kind of happiness that Camus addresses in The Myth of Sisyphus. Keywords: Hamlet; Jaspers, Karl; Kierkegaard, Søren; Nietzsche, Friedr. (shrink)

The project described here is carried out within the framework of the publication of Søren Kierkegaard's (1813 –55) collected writings, Søren Kierkegaards Skrifter (SKS). The edition (...) class='Hi'>consists of Kierkegaard's works, posthumous writings, journals, and papers, and appears in a printed version as well as a digital one. The printed version will eventually consist of 28 volumes with accompanying volumes of explanatory notes. The digital version (SKS-E) will consist of additional texts, including the author's manuscripts and preparatory studies for the published works; it will also include various computer tools such as a search engine, concordances, indices of names, illustrations, maps, and other useful tools that we shall collectively call resource files. SKS-E was presented on the internet in its initial version March 30, 2007, at http://sks.dk. (shrink)

This essay examines the analysis of language in The Concept of Anxiety and argues that language ultimately reveals itself as both dangerous and salvific. The pseudonymous author, (...) Vigilius Haufniensis, is suspicious of language, for it divides the individual from herself and thereby makes possible the self-forgetfulness of objective chatter. Indeed, this warning (which commenters have tended to follow uncritically) is a legitimate one – yet it fails to grasp that by rendering the self other than itself, language constitutes the self. In other words, the individual’s very existence depends on language. Moreover, the attempt to establish oneself as absolutely self-identical is precisely sin. Language opens us to alterity, and for this reason the demonic cannot endure it and seeks to control it. Language is uncontrollable, however, to the point that no sign permits us to be certain that we have rightly distinguished good from evil, the salvific from the demonic – and salvation can come only if we renounce the attempt to establish distinctions that are beyond our power. By employing a pseudonymous figure who views language with suspicion, Kierkegaard shows that language is dangerous, even deadly, but also allows us to realize that language is the condition of possibility for salvation. (shrink)

In this review, I will focus on how William Irwin’s The Free Market Existentialist manages to take a broad definition of existentialism and narrow it into (...) class='Hi'>dogma. Such narrowing limits the appeal of this book and causes an interesting discussion to fall short of its promised goal: a demonstration that libertarianism is compatible, and perhaps a natural fit, with existentialism. (shrink)

A mysterious remark to Friedrich Waismann on 30 December 1929 marks the only occasion where Wittgenstein refers to both Heidegger and Kierkegaard. Yet although this has generated (...) much controversy, little attention has been paid to the charge of nonsense that Wittgenstein here appears to bring against Heidegger; thus, the supporting argument that may be latent has not been unearthed. Through analysis of this remark, Wittgenstein's arguments in the Tractatus and 'A Lecture on Ethics', and Heidegger's account of anxiety (Angst) in Being and Time, I argue that we can extract an argument against the central question of Heidegger's philosophy: the question of being. To understand this, I examine the Kierkegaardian ideas employed by Wittgenstein and Heidegger and attempt to show that this argument can be partly understood in Kierkegaardian terms. I further argue that examining what Heidegger means by 'being' (Sein) shows that Wittgenstein's argument does not meet its target. (shrink)

Alison Assiter has put together a work that has the potential to create an exciting and stimulating debate in Kierkegaard circles. Mostly because she portrays Kierkegaard as (...) an idealist ontologist, that is, a philosopher of not just human nature (i.e. subjectivity), but also nature in its cosmic totality. Thus, what I find most admirable is that with Assiter we have a thinker who has the philosophical courage to suggest that the purported relationship between Schelling and Kierkegaard leads necessarily to bold philosophical consequences. Since Günther Figal’s 1980 article, Schelling und Kierkegaards Freiheitsbegriff, which gave us the first clue of the Kierkegaardian connection to Schelling’s Freiheitsschrift, scholars have primarily focused on reemphasizing the actual possibility of (the early) Schellingean heritage in Kierkegaard, meanwhile forgetting to ask themselves what consequences this connection might have on our interpretation of Kierkegaard’s corpus. Assiter’s book is an attempt to draw such a long needed consequence. (shrink)

The problem of other minds has a distinguished philosophical history stretching back more than two hundred years. Taken at face value, it is an epistemological question: it (...) concerns how we can have knowledge of, or at least justified belief in, the existence of minds other than our own. In recent decades, philosophers, psychologists, neuroscientists, anthropologists and primatologists have debated a related question: how we actually go about attributing mental states to others (regardless of whether we ever achieve knowledge or rational justification in this domain). Until the mid-nineties, the latter debate – which sometimes goes under the name of the “mindreading” debate – was characterized by a fairly clear-cut opposition between two theoretical outlooks: “theory-theory” (TT) and “simulation theory” (ST). Theory-theorists typically argued that we attribute mental states to others on the basis of a “theory of mind” that is either constructed in early infancy and subsequently revised and modified (Gopnik 1996), or else is the result of maturation of innate mindreading “modules” (Baron-Cohen 1995). (shrink)

This essay narrates what I have learned from Søren Kierkegaard & John Dewey about teaching philosophy. It consists of three sections: 1) a Deweyan pragmatist’s translation of (...) Kierkegaard’s religious insights on Christianity, as a way of life, into ethical insights on philosophy, as a way of life; 2) a brief description of the introductory course that I teach most frequently: Ethics, Happiness, & The Good Life; and 3) an exploration of three spiritual exercises from the course: a) self-cultivation by means of writing in an Ethics Notebook, b) an “existential experiment” in which we practice one of Aristotle’s virtues for a week, and c) a 15-hour service-learning component. (shrink)

At the turn of the nineteenth century, Friedrich Schlegel developed an influential theory of irony that anticipated some of the central concerns of postmodernity. His most vocal (...) contemporary critic, the philosopher Hegel, sought to demonstrate that Schlegel’s theory of irony tacitly relied on certain problematic aspects of Fichte’s philosophy. While Schlegel’s theory of irony has generated seemingly endless commentary in recent critical discourse, Hegel’s critique of Schlegelian irony has gone neglected. This essay’s primary aim is to defend Hegel’s critique of Schlegel by isolating irony’s underlying Fichtean epistemology. Drawing on Søren Kierkegaard’s The Concept of Irony in the final section of this essay, I argue that Hegel’s critique of irony can motivate a dialectical hermeneutics that offers a powerful alternative both to Paul de Man’s poststructuralist hermeneutics and to recent cultural-studies-oriented criticism that tends to reduce literary texts to sociohistorical epiphenomena. (shrink)

This essay critically examines a suggestion proposed by some Confucianists that Confucianism and Care Ethics share striking similarities and that feminism in Confucian societies might take “a (...) new form of Confucianism.” Aspects of Confucianism and Care Ethics that allegedly converge are examined, including the emphasis on human relationships, and it is argued that while these two perspectives share certain surface similarities, moral injunctions entailed by their respective ideals of ren and caring are not merely distinctive but in fact incompatible. (shrink)

Classically, gratitude is a tri-polar construal, logically ordering a benefactor, a benefice, and a beneficiary in a favour-giving-receiving situation. Grammatically, the poles are distinguished and (...) bound together by the prepositions ”to’ and ”for’; so I call this classic concept ”to-for’ gratitude. Classic religious gratitude follows this schema, with God as the benefactor. Such gratitude, when felt, is a religious experience, and a reliable readiness or ”habit’ of such construal is a religious virtue. However, atheists have sometimes felt an urge or need for an analogous experience and virtue of gratitude, and theists sometimes feel intellectual discomfort with classical theistic gratitude on consideration of the misfortunes that characterize our life along with its blessings. In response, another conception of religious gratitude has been attempted, a construal that lacks the to-for structure. This paper probes the significance of the benefactor for gratitude, both secular and religious, and, with Søren Kierkegaard’s help, some features of the theology of classical religious gratitude that dissolve the problem of misfortunes. (shrink)

Nineteenth century Christian thought about self and relationality was stamped by the reception of Kant’s groundbreaking revision to the Cartesian cogito. For René Descartes (1596-1650), the (...) class='Hi'> self is a thinking thing (res cogitans), a simple substance retaining its unity and identity over time. For Immanuel Kant (1724-1804), on the other hand, consciousness is not a substance but an ongoing activity having a double constitution, or two moments: first, the original activity of consciousness, what Kant would call original apperception, and second, the reflected self, the “I think” as object of reflection. Both are essential to the possibility of an awareness of a unified experience. Such an awareness is achieved only insofar as the self is capable of reflecting on its activity of thinking. As such, the possibility of self-consciousness, or the capacity to reflect on one’s own acts of thought is essential to the constitution of the self. This new model of the mind became the starting point to the thought of central 19th century figures such as Friedrich Schleiermacher (1768-1834), J. G. Fichte (1762-1814), Friedrich Hegel (1770-1831) and Søren Kierkegaard (1813-1855). This chapter will explore their reception of Kant’s model of self-consciousness, the controversies surrounding its development and exposition, and the advantages of this model for theological reflection. The idea of mind as essentially capable of reflection provided an account of how the self can stand in an ontologically immediate relation to God constitutive of the self, while at the same time allowing that the self’s consciousness of itself is distinct from this original moment, so that a limited or false consciousness of self is possible. As such the task of the self is to recognize (that is, to realize in and through self-consciousness) who it most truly is, both in relation to God, and in relation to self and other. (shrink)