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)

This paper argues that satire constitutes a particularly effective strategy for feminist philosophy through an analysis of Simone de Beauvoir’s account of motherhood. Feminists have grappled at length with how to interpret Beauvoir’s focus on the unpleasantness of pregnancy and challenges of motherhood. In this paper, I suggest a new interpretive strategy. My view is that Beauvoir’s disparaging depiction of motherhood cannot be read by the letter; rather, it is an exercise in satire. By overemphasizing its strangeness and difficulty, Beauvoir (...) dethrones motherhood as the pinnacle of feminine existence, transforming it from women’s only possible destiny into a contingent feature of existence. My underlying contention here is that such feminist satirizing speaks to the aims of feminist philosophy more generally: the satirical subversion of our buried assumptions opens the possibility of imagining the world anew. (shrink)

Voor het eerst hebben jongeren onder de achttien in Duitsland en België deze maand gestemd, bij de Europese verkiezingen. Nederlandse leeftijdsgenoten hebben dit recht (nog) niet. Te beïnvloedbaar, ze kunnen nog niet verantwoord stemmen, klinkt het. Deze tegenwerpingen zijn oneerlijk. Ze gelden ook voor miljoenen anderen die al wel stemrecht hebben.

Communication and cultivation accounts of responsibility argue that blaming has an important communicative and agency-cultivating function when addressed at someone we consider to be deserving of blame. On these accounts, responsible agents are agents who can understand negative reactive attitudes and are sensitive to their moral-agency cultivating function. In this paper I examine our reproachful engagements with agents whose moral agency is underdeveloped or compromised. I discuss how these engagements compare to blaming on CC accounts and argue reproachful engagements can (...) have an important communicative and agency-cultivating pointe. I then go on to propose an addition to CC-accounts that explains how underdeveloped and compromised agents can be held responsible. I will show how this addition resolves ambiguities in accounts from McKenna, Vargas and McGeer. I conclude the paper by anticipating an objection CC accounts could raise: that reproach and blame are co-extensive. (shrink)

Abstract: In this article, we explore what are ethical forms of holding service users responsible in mental health care contexts. Hanna Pickard has provided an account of how service users should be held responsible for morally wrong or seriously harmful conduct within contexts of mental health care, called the clinical stance. From a clinical stance one holds a person responsible for harm, but refrains from emotionally blaming the person and only considers the person responsible for this conduct in a detached (...) sense. Her account is based on what are considered best practices in the treatment of people with borderline personality disorder and addiction. We ask if this account generalizes across different diagnostic criteria and different clinical contexts. To begin to answer this question, we compare the clinical stance to an account of what are considered best practices in the treatment of service users at a specialized clinic for people with autism spectrum disorder in the Netherlands. We refer to this alternative account as the nurturing stance and highlight relevant similarities and differences between the clinical stance and the nurturing stance. We conclude with suggestions for further research and theorizing. (shrink)

In this paper I provide a forward-looking account of the difference between the responsibility of children and the responsibility of adults. I do so by means of criticizing agency-cultivation accounts of responsibility. According to these accounts, the justification for holding a person to a norm is the cultivation of their moral agency, and children are, just like adults, considered responsible to the extent that they can have their moral agency cultivated in this manner. Like many forward-looking accounts, these accounts claim (...) that the purpose of holding adults to norms is similar to the purpose of holding children to norms. I argue that the justifications for holding adults to norms are different because of the particular ways in which adults can be in moral disagreement with one another, and the consequences that this has. Moral disagreement is relevant to consequentialist accounts because it impacts on whether and how we can secure beneficial outcomes via holding someone to a norm. One of the upshots of this analysis is that the forward-looking justification for holding adults to norms is qualitatively different from how and why we should hold children to norms. (shrink)

Whataboutism is een strategie waarbij op een beschuldiging wordt gereageerd met een wedervraag die eveneens een beschuldiging impliceert, waardoor de oorspronkelijke vraag eerder wordt ontweken dan beantwoord. Het is een effectieve methode om de aandacht te verplaatsen naar een andere situatie door een vergelijkbaar, dan wel onvergelijkbaar, contrast te bieden, waardoor de beschuldigde het eigen gedrag probeert te rechtvaardigen en verantwoordelijkheid probeert te ontlopen. Maar niet alle vormen van whataboutism impliceren echter een drogredenering, noch worden ze altijd verkeerd toegepast. Het (...) contrast dat voortkomt uit de vraag ‘what about’ kan dan een cruciale bijdrage leveren aan een situatie die een verdere kritische analyse vereist, en daarmee de geloofwaardigheid van de argumentatie versterken. (shrink)

Synthetic biology is often seen as the engineering turn in biology. Philosophically speaking, entities created by synthetic biology, from synthetic cells to xenobots, challenge the ontological divide between the organic and inorganic, as well as between the natural and the artificial. Entities such as synthetic cells can be seen as hybrid or transitory objects, or neo–things. However, what has remained philosophically underexplored so far is the impact these hybrid neo–things will have on (our phenomenological experience of) the living world. By (...) extrapolating from Walter Benjamin’s account of how technological reproducibility affects the aura of art, we embark upon an exploratory inquiry that seeks to fathom how the technological reproducibility of life itself may influence our experience and understanding of the living. We conclude that, much as technologies that enabled reproduction corroded the aura of original artworks (as Benjamin argued), so too will the aura of life be under siege in the era of synthetic lifeforms. This article zooms in on a specific case study, namely the research project Building a Synthetic Cell (BaSyC) and its mission to create a synthetic cell–like entity, as autonomous as possible, focusing on the properties that differentiate organic from synthetic cells. (shrink)

Throughout his work, Deleuze not only draws on literature in order to address philosophical problems but he seeks to map out the ‘mobile relations’ between philosophy and literature. After an initial overview, I will focus on A Thousand Plateaus (1980), a book co-authored with Guattari, and in particular, on plateaus “1874: Three Novellas or ‘What happened?’” and “1730: Becoming-intense, becoming-animal, becoming-imperceptible…” In doing so, I aim to explore: (a) how the relation between literature and philosophy is refracted in Novellas Plateau (...) and (b) the way in which Deleuze and Guattari articulate their key philosophical notion of becoming-imperceptible via Kierkegaard’s knight of faith. The novella as a literary genre by essentially relating to secrecy also advances a distinctive way of relation between the three dimensions of time (the past, present and future). I argue that novella-time could be extended beyond the limits of the literary genre ‘novella.’ To this end, I propose a reading of Kierkegaard’s Repetition (1843) and selected entries from his Journals in order to identify his contribution as a religious writer to the discussion of philosophy as literature. I conclude that time, change and faith stand out as a common problematic of philosophy, literature, and life. (shrink)

A quotation from the early Platonic dialogue Hippias Major is used as an epigraph to Concluding Unscientific Postscript. Apart from this paratextual (and liminal) presence of the Platonic text, “the Hippias as an introduction to the beautiful” could serve, according to Climacus’ words, “as a kind of analogy to an introduction such as that” his own book aims to be; that is, an introduction which will throw light “on what Christianity is” but make “it difficult to become a Christian”. The (...) aim of the present paper is to investigate whether the above claim of Climacus could be attested in the Postscript and how the Platonic dialogue helps him reiterate a “new approach” to the problem of the Crumbs and orient his reader to the particularity of the Crumbs’ crumb philosophy. (shrink)

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)

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.

A dominant view of guilt and shame is that they have opposing action tendencies: guilt- prone people are more likely to avoid or overcome dysfunctional patterns of behaviour, making amends for past misdoings, whereas shame-prone people are more likely to persist in dysfunctional patterns of behaviour, avoiding responsibility for past misdoings and/or lashing out in defensive aggression. Some have suggested that addiction treatment should make use of these insights, tailoring therapy according to people’s degree of guilt-proneness versus shame-proneness. In this (...) paper, we challenge this dominant view, reviewing empirical findings from others as well as our own to question (1) whether shame and guilt can be so easily disentangled in the experience of people with addiction, and (2) whether shame and guilt have the opposing action tendencies standardly attributed to them. We recommend a shift in theoretical perspective that explains our main finding that both emotions can be either destructive or constructive for recovery, depending on how these emotions are managed. We argue such management depends in turn on a person’s quality of self-blame (retributive or ‘scaffolding’), impacting upon their attitude towards their own agency as someone with fixed and unchanging dispositions (shame and guilt destructive for recovery) or as someone capable of changing themselves (shame and guilt productive for recovery). With an eye to therapeutic intervention, we then explore how this shift in attitude towards the self can be accomplished. Specifically, we discuss empathy-driven affective and narratively-driven cognitive components of a process that allow individuals to move away from the register of retributive self-blame into a register of scaffolding ‘reproach’, thereby enabling them to manage their experiences of both shame and guilt in a more generative way. (shrink)

Three recent research reports by Topping and Trickey, by Fair and colleagues, and by Gorard, Siddiqui and Huat See have produced data that support the conclusion that a Philosophy for Children program of one-hour-per-week structured discussions has a marked positive impact on students. This article presents data from a follow up study done three years after the completion of the study reported in Fair et al.. The data show that the positive gains in scores on the Cognitive Abilities Test were (...) still present and had not faded after three years. Given the strength of these confirmations of the positive durable impact of the P4C program of structured discussions and given the relatively low cost of implementing the P4C program, it is recommended that it become a standard part of the school curriculum. (shrink)

The study area was a small lowland river valley within a range of 4750 m length and approx. 150 m width (about 62 ha), situated in the south-east of Poland, in the middle of Sandomierz Basin (Fig. 1). Flora and the chosen most valuable plant communities of the river bed with adjacent ecotone zone were investigated in 2007. During the study 291 species of vascular plants were found. Among them 10 are protected: Batrachium peltatum, Convallaria majalis, Dactylorhiza majalis, Daphne (...) mezereum, Frangula alnus, Hedera helix, Lycopodium annotium, Nuphar lutea, Utricularia vulgaris, and Viburnum opulus. Other species were considered to be value-raising, e.g. Achillea ptarmica, Batrachium circinatum, Calla palustris, Crepis paludosa, Hottonia palustris, Hypochoeris glabra, Senecio ovatus or Valeriana dioica. The number of antropophytes with the amount of 10% is relatively low. Most valuable plant communities represent 3 types of Nature 2000 habitats: natural eutrophic lakes with Magnopotamion or Hydrocharition – code 3150, transition and quaking bogs – code 7140-1, and alluvial forests with Alnus glutinosa and Fraxinus excelsior – code 91E0-3. Human activities brought about the emergence of 3 different areas within the valley: channeled river site (K), natural river bed site (N) and agricultural field site (P). Those areas differ significantly in terms of the composition of flora, vegetation and biological diversity. Most valuable is (P) and the least is (K). The greatest potential source of danger for biodiversity is the wrong forester’s management, especially interference in the natural processes (the planned building of the extra pond) and preventing wooden biomass accumulation. (shrink)