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.

Contour adaptation is a recently described paradigm that renders otherwise salient visual stimuli temporarily perceptually invisible. Here we investigate whether this illusion can be exploited to study visual awareness. We found that CA can induce seconds of sustained invisibility following similarly long periods of uninterrupted adaptation. Furthermore, even fragmented adaptors are capable of producing CA, with the strength of CA increasing monotonically as the adaptors encompass a greater fraction of the stimulus outline. However, different types of adaptor patterns, such as (...) distinctive shapes or illusory contours, produce equivalent levels of CA suggesting that the main determinants of CA are low-level stimulus characteristics, with minimal modulation by higher-order visual processes. Taken together, our results indicate that CA has desirable properties for studying visual awareness, including the production of prolonged periods of perceptual dissociation from stimulation as well as parametric dependencies of that dissociation on a host of stimulus parameters. (shrink)

"The Blackwell Guide to Philosophy of Education" is state-of-the-art map to the field as well as a valuable reference book.

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)

Anticipating Mikhail Bakhtin’s appreciation for the unfinalizability of Fedor Dostoevskij’s universe, prominent Protestant theologian Karl Barth celebrates the Russian novelist’s presentation of “the impenetrable ambiguity of human life” characteristic of both the ending of Dostoevsky’s novels and Paul’s Epistle to the Romans. Barth’s unique reading of The Brothers Karamazov not only demonstrates the barrenness of the “theocratic dream” but also complements Bakhtin’s discussion of polyphony with an explicitly theological dimension by focusing on the dialogue between Creator and the created. Dostoevsky’s (...) prophetic voice provides Barth with a poetic expression of the divine command that highlights the ethical dimension inherent in every theological choice. (shrink)

Anticipating Mikhail Bakhtin’s appreciation for the unfinalizability of Fedor Dostoevskij’s universe, prominent Protestant theologian Karl Barth celebrates the Russian novelist’s presentation of “the impenetrable ambiguity of human life” characteristic of both the ending of Dostoevsky’s novels and Paul’s Epistle to the Romans. Barth’s unique reading of The Brothers Karamazov not only demonstrates the barrenness of the “theocratic dream” but also complements Bakhtin’s discussion of polyphony with an explicitly theological dimension by focusing on the dialogue between Creator and the created. Dostoevsky’s (...) prophetic voice provides Barth with a poetic expression of the divine command that highlights the ethical dimension inherent in every theological choice. (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)

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.

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)

Purpose This paper aims to focus on the role of information and communication technologies in preparation for and management of human and/or nature induced disasters. Design/methodology/approach Drawing from the phenomenal growth of ICTs, initiatives aimed at disaster management, stakeholder theory, prior research and the successful development and implementation of 9-1-1, this paper explores ICTs in the context of human and/or nature induced disasters. Findings This paper discusses a new ICT for mitigating disaster management, scans, using stakeholder theory, relevant initiatives and (...) prior research to identify the stakeholders relevant for successful preparation for and management of disasters, and draws from the 9-1-1 example to discuss how ICTs can be successfully developed and adopted. Research limitations/implications There are opportunities for researchers to develop ICTs that can make countries, developing and developed, more efficient and effective in their preparation for and management of nature and human induced disasters. In addition, researchers can investigate the role of stakeholders in facilitating the adoption of new ICTs developed for disaster management. Researchers could also help public policy in designing the most efficient and effective programs for the adoption of new ICTs. Practical/implications As an example of new ICTs that can potentially mitigate the effect of disasters, this paper discusses the E711 text-message mobile phone service and provides a description of how this protocol operates and can be implemented. There are tremendous opportunities to develop new ICTs in the context of disaster management. Social/implications This paper argues that ICTs such as E711 can have a major impact on all countries in general and poor and developing nations in particular. Specifically, in the bottom of the pyramid markets, developing ICTs for BOP market in the context of managing human and nature induced disasters and ensuring the diffusion of such ICT innovations is both critical and challenging. Originality/value This paper discusses the role and importance of ICTs in disaster management, identifies relevant stakeholders, discusses how ICTs can be diffused and implemented and calls on and hopes to provide an impetus to research on ICTs that can aid in the preparation for and the management of disasters. (shrink)

Doxastic involuntarists have paid insufficient attention to two debates in contemporary epistemology: the permissivism debate and the debate over norms of assertion and belief. In combination, these debates highlight a conception of belief on which, if you find yourself in what I will call an ‘equipollent case’ with respect to some proposition p, there will be no reason why you can’t believe p at will. While doxastic involuntarism is virtually epistemological orthodoxy, nothing in the entire stock of objections to belief (...) at will blocks this route to doxastic voluntarism. Against the backdrop of the permissivism debate and the literature on norms of belief and assertion, doxastic involuntarism emerges as an article of faith, not the obvious truth it’s usually purported to be. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

According to what I will call ‘the disanalogy thesis,’ beliefs differ from actions in at least the following important way: while cognitively healthy people often exhibit direct control over their actions, there is no possible scenario where a cognitively healthy person exhibits direct control over her beliefs. Recent arguments against the disanalogy thesis maintain that, if you find yourself in what I will call a ‘permissive situation’ with respect to p, then you can have direct control over whether you believe (...) p, and you can do so without manifesting any cognitive defect. These arguments focus primarily on the idea that we can have direct doxastic control in permissive situations, but they provide insufficient reason for thinking that permissive situations are actually possible, since they pay inadequate attention to the following worries: permissive situations seem inconsistent with the uniqueness thesis, permissive situations seem inconsistent with natural thoughts about epistemic akrasia, and vagueness threatens even if we push these worries aside. In this paper I argue that, on the understanding of permissive situations that is most useful for evaluating the disanalogy thesis, permissive situations clearly are possible. (shrink)

BackgroundAdvances in healthcare artificial intelligence (AI) are occurring rapidly and there is a growing discussion about managing its development. Many AI technologies end up owned and controlled by private entities. The nature of the implementation of AI could mean such corporations, clinics and public bodies will have a greater than typical role in obtaining, utilizing and protecting patient health information. This raises privacy issues relating to implementation and data security. Main bodyThe first set of concerns includes access, use and control (...) of patient data in private hands. Some recent public–private partnerships for implementing AI have resulted in poor protection of privacy. As such, there have been calls for greater systemic oversight of big data health research. Appropriate safeguards must be in place to maintain privacy and patient agency. Private custodians of data can be impacted by competing goals and should be structurally encouraged to ensure data protection and to deter alternative use thereof. Another set of concerns relates to the external risk of privacy breaches through AI-driven methods. The ability to deidentify or anonymize patient health data may be compromised or even nullified in light of new algorithms that have successfully reidentified such data. This could increase the risk to patient data under private custodianship.ConclusionsWe are currently in a familiar situation in which regulation and oversight risk falling behind the technologies they govern. Regulation should emphasize patient agency and consent, and should encourage increasingly sophisticated methods of data anonymization and protection. (shrink)

Alvin Plantinga theorizes the existence of a sensus divinitatis – a special cognitive faulty or mechanism dedicated to the production and non-inferential justification of theistic belief. Following Chris Tucker, we offer an evidentialist-friendly model of the sensus divinitatis whereon it produces theistic seemings that non-inferentially justify theistic belief. We suggest that the sensus divinitatis produces these seemings by tacitly grasping support relations between the content of ordinary experiences (in conjunction with our background evidence) and propositions about God. Our model offers (...) advantages such as eliminating the need for a sui generis religious faculty, harmonizing the sensus divinitatis with prominent theories in the cognitive science of religion, and providing a superior account of natural revelation. (shrink)

All justified beliefs ultimately rest on attitudes that are immediately justified. This book illuminates the nature of immediate justification and the states that provide it. Simply put, immediate justification arises from how things appear to us--from all and only our "seemings." The author defends each aspect of this "seemings foundationalism," including the assumption of foundationalism itself. Most notably, the author draws from common sense philosopher Thomas Reid to present new and improved arguments for phenomenal conservatism and gives the first systematic (...) argument that seemings alone are capable of immediately justifying. The discussion also delves deeply into the nature of seemings and how it is that their assertive phenomenal character makes them (and them alone) capable of immediately justifying. Along the way, the author makes novel contributions to perennial debates about justification such as: internalism versus externalism, deontologism and epistemic blame, epistemic circularity, and the common sense response to skepticism. Seemings and the Foundations of Justification will appeal to scholars and advanced students interested in epistemology, Thomas Reid, or the common sense tradition. (shrink)

Intellectualists disagree with anti-intellectualists about the relationship between knowledge and truth. According to intellectualists, this relationship is intimate. Knowledge entails true belief, and in fact everything required for knowledge is somehow relevant to the probability that the belief in question is true. According to anti-intellectualists, this relationship isn’t intimate. Or, at least, it’s not as intimate as intellectualists think. Factors that aren’t in any way relevant to the probability that a belief is true can make a difference to whether it (...) counts as knowledge. In this paper, I give a new argument for anti-intellectualism and draw out consequences of this argument for the pragmatic encroachment debate. The standard purist objection to pragmatism is that pragmatism entails anti-intellectualism. As I show, anti-intellectualism follows from premises that are plausible even if purism is true, so the standard purist objection to pragmatism fails. (shrink)

Early moderns such as Locke and Descartes thought we could guarantee the justification of our beliefs, even in worlds most hostile to their truth, if only we form those beliefs with sufficient care. That is, they thought it possible for us to be impeccable with respect to justification. This principle has traditionally been used to argue for internalism. By placing all of the normatively relevant conditions in our minds, we ensure reflective access to what those norms require of us and (...) so sustain the possibility of impeccability (unlike externalism). However, recent challenges to transparency leave this reasoning vulnerable. In response, I show how impeccability can be sustained without requiring transparency. The account only works if we define internal states as those directly accessible to our rational belief forming systems. I argue that this sort of causal internalism, while somewhat revisionary, preserves traditional motivations for internalism while avoiding problems faced by other varieties. The result is a renewed argument for internalism that simultaneously moves us away from access internalism and towards a species of mentalism. (shrink)

The cornerstone of contemporary nursing practice is the provision of individualised nursing care. Sustaining and nourishing the stream of research frameworks that inform individualised care are the findings from qualitative research. At the centre of much qualitative research practice, however, is an assumption that experiential understanding can be delivered through a thematisation of meaning which, it will be argued, can lead the researcher to make unsustainable assumptions about the relations of language and meaning‐making to experience. We will show that an (...) uncritical subscription to such assumptions can undermine the researcher's capacity to represent experience at the high level of abstraction consistent with experience itself and to thus inform genuinely individualised care. Instead, using qualia as a touchstone for the possibilities of understanding and representing experience, we trace the ‘designative’ and ‘expressive’ distinction to language in order to raise critical questions concerning both these assumptions and common practices within qualitative research. Following the ‘expressive’ account of language, we foreground in particular the hermeneutic work of Gadamer through which we explore the possibilities for a qualitative research approach that would better seek the mot juste of individual experience and illuminate qualia in order to better inform genuinely individualised care. (shrink)

In this paper I present two reasons why generalized skill-selection--a policy whereby skill, education, and economic independence are indefinitely prioritized in immigration decisions--is pro tanto unjust. First, such policies feed into existing biases, exacerbating status harms for low-SES citizens. The claim that we prefer the skilled to the unskilled, the educated to the uneducated, and the financially secure to the insecure is also heard by citizens. And there is considerable overlap between this message and the stereotypes and biases that set (...) their social status. Skill-selection can reinforce these biases, offering state support for the claim that they are less desirable as members of the society. -/- Second, the need for skilled immigrants ordinarily depends upon and reinforces failures of fair equality of opportunity (FEO). According to the dependency thesis, the need for skilled migrants stems from a failure to ensure domestic FEO. Many low-SES residents would desire to work, for example, as doctors or nurses. However, unequal education, as well as poverty and debt, have made such opportunities largely inaccessible. According to the reinforcement thesis, skill-selection disincentivizes the pursuit of FEO. A state that can meet domestic labor needs through less costly immigration policies will be disinclined to pursue programs designed to equalize opportunities for low-SES residents. -/- Generalized skill-selection in high-income countries like the US is, therefore, pro tanto unjust. However, this is not an argument for excluding the skilled. Skilled immigrants can be admitted through other policies—open borders, family-reunification, or a lottery—without the state signaling that the skilled are more desirable or perpetuating failures of FEO. And states can, responding to local emergencies, temporarily select for particular professions without contributing to these injustices. These concerns only arise when skill is generally and indefinitely prioritized. (shrink)

There is a growing movement advocating for using closed border policies as a tool for solving the climate crisis. On this view, which I call the green border argument, fighting climate change requires drastic reductions in the global population and/or per capita greenhouse gas (GHG) emissions. However, immigration into high-income countries—particularly from low-income countries—increases per capita emissions while leaving the population untouched. Therefore, the green border theorist argues, we should limit entry into high-income countries. I explain why this is a (...) mistake and why the political left should embrace a pro climate and pro migrant politic. -/- First, the argument significantly overstates the impact of immigration on global GHG emissions. Second, the progressive green border argument is normatively incoherent. It advocates for closing borders and eliminating poverty and other rights violations in sending countries. However, given the relationship between emissions and income, this argument would require rejecting all poverty reduction strategies—a conclusion the progressive theorist wants to avoid. Third, the argument is counterproductive. An open border politic better promotes climate justice. A key reason is that high-income countries perceive immigration to be one of the most serious short- and medium- term costs of climate change. Whereas closure allows them to avoid this “cost,” open borders would force them to eliminate push factors, incentivizing global adaptation and mitigation strategies. Moreover, a closed border politic creates divisions between those affected, undermining cross-border solidarity and contributing to the perception that environmentalism is a white, middle-class movement. (shrink)

The paper highlights the urgent and radical questions and problems which postmodernism poses for educational studies in general, and the philosophy of education in particular. First, it outlines and interrelates the legacies of modernism in social and cultural theory. Next, it describes the reactionary anti- modernism of the Right, and contrasts this with traditionalism. It is argued that the current political and economic context of education is largely anti-modernist, not traditionalist. The stirrings of radical doubts about modernism are described and (...) contrasted with the antimodernism of the Right. A salient theme to this point is the variety of conceptions of the relationship between knowledge and power. Mature postmodernism is characterised centrally in terms of a reconceptualisation of that relationship. The metamorphosis of the concept of the self in postmodernism is described and related to new problems about ethics and a newly emerging importance for the aesthetic. Finally, the paper argues that while the fundamental issues for philosophy of education are unchanged - problems about instrumentalism and various issues of autonomy - these are radically recast in postmodernism, and present new difficulties. (shrink)

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

Central to Perelman and Olbrechts-Tyteca’s philosophical revival of rhetoric and dialectic is the importance given to the temporal character of argumentation. Unlike demonstration, situated within the “empty time” of a single instant, the authors of The New Rhetoric understand argumentation as an action that unfolds within the “full time” of meaningful human life. By taking a broader view of his work beyond The New Rhetoric, I first outline Perelman’s understanding of time and temporality and the challenge that it poses for (...) the study of argumentation. Next, I emphasize the distinction between argumentation’s internal and external temporal structures, and then show how Perelman problematizes a static view of a number of basic argumentative concepts by bringing out their essentially temporal character. Finally, in clarifying what is at stake in Perelman’s account, I conclude by drawing attention to a number of issues in contemporary argumentation studies that may benefit from a reconsideration of Perelman’s analysis of time. (shrink)

Is knowledge consistent with literally any credence in the relevant proposition, including credence 0? Of course not. But is credence 0 the only credence in p that entails that you don’t know that p? Knowledge entails belief (most epistemologists think), and it’s impossible to believe that p while having credence 0 in p. Is it true that, for every value of ‘x,’ if it’s impossible to know that p while having credence x in p, this is simply because it’s impossible (...) to believe that p while having credence x in p? If so, is it possible to believe that p while having (say) credence 0.4 in p? These questions aren’t standard epistemological fare, at least in part because many epistemologists think their answers are obvious, but they have unanticipated consequences for epistemology. Let ‘improbabilism’ name the thesis that it’s possible to know that p while having a credence in p below 0.5. Improbabilism will strike many epistemologists as absurd, but careful reflection on these questions reveals that, if improbabilism is false, then all of the most plausible theories of knowledge are also false. Or so I argue in this paper. Since improbabilism is widely rejected by epistemologists (at least implicitly), this paper reveals a tension between all of the most plausible theories of knowledge and a widespread assumption in epistemology. (shrink)

Many supporters of open borders argue that restrictions on immigration are unjust in part because they undermine equal opportunity. Borders prevent the globally least-advantaged from pursuing desirable opportunities abroad, cementing arbitrary facts about birth and citizenship. In this paper I advance an argument from equal opportunity to global freedom of movement. In addition to preventing people from pursuing desirable opportunities, borders also create a prone, segregated population that can be dominated and exploited. Restrictions on mobility do not just trap people (...) in bad opportunity sets—they help create bad opportunities by isolating the negative externalities of production and foreign policy. Freedom of movement can play a vital role in spreading risks and burdens, incentivizing their mitigation. Using an analysis of feudalism, segregation, and the transnational economy, I illustrate the centrality of space and mobility, showing why freedom of movement is a necessary tool for preventing political and economic oppression. (shrink)

In a landmark text, ‘The Theological Turn of French Phenomenology’, Dominique Janicaud posits a boundary that sharply divides the legitimate phenomenological tradition from a problematic variant seen to be fundamentally compromised by theology. This article develops an immanent critique of Janicaud’s position. It demonstrates that his boundary relies on the mature work of Maurice Merleau-Ponty as a constitutive exemplar of the tradition, that this work is centrally concerned with beauty, and that its notion of beauty is irreducibly theological. Merleau-Ponty himself (...) will thus be shown to enact his own version of the theological turn. I shall consequently propose a reconstrual of the boundary of phenomenology. My argument relies fundamentally on Merleau-Ponty’s essay, ‘Eye and Mind’, and includes a critical restatement of Galen Johnson’s reading of this text. In addition to its direct relevance to phenomenology, this article bears upon broader concerns, including the relationships between theory, the body, aesthetics, and the post-secular. (shrink)