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) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set (...) has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (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)

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 essay argues that current theories of action fail to explain agentive control because they have left out a psychological capacity central to control: attention. This makes it impossible to give a complete account of the mental antecedents that generate action. By investigating attention, and in particular the intention-attention nexus, we can characterize the functional role of intention in an illuminating way, explicate agentive control so that we have a uniform explanation of basic cases of causal deviance in action as (...) well as other defects of agency, explain cases of skilled agency and sharpen questions about the role of thought in agency. This provides for a different orientation in the theory of action. (shrink)

Milner and Goodale's influential account of the primate cortical visual streams involves a division of consciousness between them, for it is the ventral stream that has the responsibility for visual consciousness. Hence, the dorsal visual stream is a ‘zombie’ stream. In this article, I argue that certain information carried by the dorsal stream likely plays a central role in the egocentric spatial content of experience, especially the experience of visual spatial constancy. Thus, the dorsal stream contributes to a pervasive feature (...) of consciousness. (shrink)

In response to Mole 2009, I present an argument for zombie action. The crucial question is not whether but rather to what extent we are zombie agents. I argue that current evidence supports only minimal zombie agency.

Do self-monitoring accounts, a dominant account of the positive symptoms, explain auditory verbal hallucination (AVH)? In this essay, I argue that the account fails to answer many crucial questions any explanation of AVH must address. Where the account provides a plausible answer, I make a case for an alternative explanation: AVH is not the result of a failed control mechanism, namely failed self-monitoring, but the persistent automaticity of auditory experience of a voice. The argument emphasizes the importance of careful examination (...) of phenomenology as a constraint on causal models of the positive symptoms in schizophrenia. (shrink)

In this paper, I argue that visual attention is cognitively penetrated by intention. I present a detailed account of attention and its neural basis, drawing on a recent computational model of neural modulation during attention: divisive normalization. I argue that intention shifts computations during divisive normalization. The epistemic consequences of attentional bias are discussed.

This paper considers the connection between automaticity, control and agency. Indeed, recent philosophical and psychological works play up the incompatibility of automaticity and agency. Specifically, there is a threat of automaticity, for automaticity eliminates agency. Such conclusions stem from a tension between two thoughts: that automaticity pervades agency and yet automaticity rules out control. I provide an analysis of the notions of automaticity and control that maintains a simple connection: automaticity entails the absence of control. An appropriate analysis, however, shows (...) that actions are forms of control and pervasively automatic even if automaticity implies the absence of control. Consequences are drawn for the theory of mental agency and the psychological concepts of automaticity and control. (shrink)

In his rich and provocative paper, Peter Carruthers announces two related theses: (a) a positive thesis that “central cognition is sensory based, depending on the activation and deployment of sensory images of various sorts” (Carruthers 2013) and (b) a negative thesis that the “central mind does not contain any workspace within which goals, decisions, intentions, or non-sensory judgments can be active” (Carruthers 2013). These are striking claims suggesting that a natural view about cognition, namely that explicit theoretical reasoning involves direct (...) operations over beliefs, is wrong. Our beliefs, on this natural view, interact with each other to yield new beliefs. If Carruthers is right, beliefs have only an indirect or mediated influence in cognition with sensory states playing the direct role. I think it an important feature of Carruthers’ discussion that he draws support from work on the neural circuits and mechanisms that subserve these processes. In what follows, I want to regis. (shrink)

In this review of Eric Schwitzgebel's "Perplexities of Consciousness", we discuss the book's arguments in light of the role of attention in introspection.

We respond to Moseley and Wilkinson's defense of inner speech models of AVH.

This paper examines the relationship of ethical decision-making by individuals to corporate business ethics and organizational performance of three groups: SMEs, Outstanding SMEs and Large Enterprises, in order to provide a reference for Taiwanese entrepreneurs to practice better business ethics. The survey method involved random sampling of 132 enterprises within three groups. Some 524 out of 1320 questionnaires were valid. The survey results demonstrated that ethical decision-making by individuals, corporate business ethics and organizational performance are highly related. In summary, then, (...) high levels of organizational performance were directly attributable to high levels of applied corporate and individual ethics. Furthermore, there is a demonstrable tendency for Outstanding SMEs to reject ethically unsound practices such as padded expense accounts, tax evasion and misleading advertising. The measurement criteria used to assess organizational performance, however, did not include an objective evaluation of financial performance. (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)

Derrida’s thought on “trace,” “différance,” “writing,” and “supplement” is always thought the breaking of logocentrism, the essence, the positive meaning, and the closure of the metaphysics of presence; this thinking is accordingly regarded the thinking with the fundamental structure of difference and openness. By tracking back to Saussure, Husserl and Levinas, this fundamental difference breaks the myth of ideal meaning as well as the illusion of the absolute open; its lack of ideality and absoluteness contains the fundamental difference within itself (...) and thus has the structure of open. However, from a broader perspective, I will re-ask the question “Whether or not Derrida’s ‘trace,’ ‘différance,’ ‘writing,’ and ‘supplement’ have a structure of open.” When the web of differences encompasses everything even its own “exit,” this “open” thus conceals and denies other modes of thinking. With the impossibility of going out of this mode of thinking, the structure of différance is closed. (shrink)

The psychology of consciousness as explained by Vygotsky is the ability of one to focus on the inner state of being. Vygotsky’s proposition of external tools redistributing mental and external processes into internalized acts lacks the concept of embodied mediational tools existing in the current world as computational artifacts extending or augmenting human capabilities. This paper proposes sociocultural embodied augmentation theory (SEAT) as a means to explain the impact of augmenting technologies on Vygotsky’s original notion of “psychological tool,” therefore initiating (...) an inevitable transformation of the sociocultural mind. Hence, a new social mind is posited as an evolving symbiosis between human life and artificial life that extends consciousness: a symbiont consciousness. (shrink)

Virtues are acquirable, so if intellectual humility is a virtue, it’s acquirable. But there is something deeply problematic—perhaps even paradoxical—about aiming to be intellectually humble. Drawing on Edward Slingerland’s analysis of the paradoxical virtue of wu-wei in Trying Not To Try (New York: Crown, 2014), we argue for an anti-individualistic conception of the trait, concluding that one’s intellectual humility depends upon the intellectual humility of others. Slingerland defines wu-wei as the “dynamic, effortless, and unselfconscious state of mind of a person (...) who is optimally active and effective” (Trying Not to Try, 7). Someone who embodies wu-wei inspires implicit trust, so it is beneficial to appear wu-wei. This has led to an arms race between faking wu-wei on the one hand and detecting fakery on the other. Likewise, there are many benefits to being (or seeming to be) intellectually humble. But someone who makes conscious, strategic efforts to appear intellectually humble is ipso facto not intellectually humble. Following Slingerland’s lead, we argue that there are several strategies one might pursue to acquire genuine intellectual humility, and all of these involve commitment to shared social or epistemic values, combined with receptivity to feedback from others, who must in turn have and manifest relevant intellectual virtues. In other words, other people and shared values are partial bearers of a given individual’s intellectual humility. If this is on the right track, then acquiring intellectual humility demands epistemic anti-individualism. (shrink)

By rethinking the meaning of a central idiom in the Great Learning, this essay intends to open up a new horizon for the hermeneutics of early Confucian thinking, which has little to do with metaphysics. Through a careful etymological study of ge wu and a dialogue between the Great Learning and Heidegger's phenomenology of human affection, I demonstrate the critical position of the human heart in early Chinese thinking. This new interpretation of early Confucian moral teachings also recovers an invigorating (...) possibility for contemporary discourse on the question of ethics. (shrink)

This article presents a critical reevaluation of the thesis – closely associated with H.L.A. Hart, and central to the views of most recent legal philosophers – that the idea of state coercion is not logically essential to the definition of law. The author argues that even laws governing contracts must ultimately be understood as “commands of the sovereign, backed by force”. This follows in part from recognition that the “ sovereign ”, defined rigorously, at the highest level of abstraction, is (...) that person or entity identified by reference to game theory and the philosophical idea of “convention” as the source of signals to which the subject population has become effectively locked, as a group, into conformity. (shrink)

The National Library of Finland and the Von Wright and Wittgenstein Archives at the University of Helsinki keep the collected correspondence of Georg Henrik von Wright, Wittgenstein’s friend and successor at Cambridge and one of the three literary executors of Wittgenstein’s Nachlass. Among von Wright’s correspondence partners, Elizabeth Anscombe and Rush Rhees are of special interest to Wittgenstein scholars as the two other trustees of the Wittgenstein papers. Thus, von Wright’s collections held in Finland promise to shed light on the (...) context of decades of editorial work that made Wittgenstein’s later philosophy available to all interested readers. In this text, we present the letters which von Wright received from Anscombe and Rhees during the first nine months after Wittgenstein’s death. This correspondence provides a vivid picture of the literary executors as persons and of their developing relationships. The presented letters are beautiful examples of what the correspondence as a whole has to offer; it depicts – besides facts of editing – the story of three philosophers, whose conversing voices unfold the human aspects of inheriting Wittgenstein’s Nachlass. Their story does not only deal with editing the papers of an eminent philosopher, but with the attempt to do justice to the man they knew, to his philosophy and to his wishes for publication. (shrink)

Jest to wybór z pracy Gadamera "Idea dobra..." Zawiera Przedmowę, Zakres problemu, Rozdział I (Sokratejska wiedza i niewiedza) oraz Posłowie tłumacza. This is the opening part of the Polish translation of Gadamers' The idea of the good... with the Translator's afterword.

The law presents itself as a body of meaning, open to discovery, interpretation, application, criticism, development and change. But what sort of meaning does the law possess? Legal theory provides three sorts of answers. The first portrays the law as a mode of communication through which law-makers convey certain standards or norms to the larger community. The law's meaning is that imparted by its authors. On this view, law is a vehicle, conveying a message from a speaker to an intended (...) audience. The second theory portrays the law as a mode of interpretation, whereby judges, officials, and ordinary citizens make decisions about how the law applies in various practical contexts. The law's meaning is that furnished by its interpreters. According to this theory, law is a receptacle into which decision-makers pour meaning. The third viewpoint argues that these theories, while not altogether wrong, are incomplete because they downplay or ignore the autonomous meaning that the law itself possesses. This theory suggests that the law is basically a mode of participation, whereby legislators, judges, officials, and ordinary people attune themselves to an autonomous field of legal meaning. The law's meaning is grounded in a body of social practice which is independent of both the law's authors and its interpreters and which is infused with basic values and principles that transcend the practice. On this view, law is the emblem of meaning that lies beyond it. -/- Elements of all three theories are present in H.L.A. Hart's influential work, The Concept of Law, which attempts to fuse them into a single, all-encompassing theory. Nevertheless, as we will argue here, the attempt is not successful. Any true reconciliation of the communication and interpretation theories can only take place within the framework of a fully developed participation theory. In the early stages of his work, Hart lays the foundation for such a theory. However, his failure to elaborate it in a thoroughgoing way renders the work incomplete and ultimately unbalanced. As we will see, there is something to be learned from this failure. (shrink)

In this essay I argue that the central problem of Aristotle’s Metaphysics H (VIII) 6 is the unity of forms and that he solves this problem in just the way he solves the problem of the unity of composites – by hylomorphism. I also discuss the matter– form relationship in H 6, arguing that they have a correlative nature as the matter of the form and the form of the matter.

Although Wayne Wu correctly identifies a flaw in the way in which my 2009 article frames the debate about ‘zombie action’, he fails in his attempts to strengthen the case for thinking that our actions are under less conscious control than we usually imagine. His argument, like the arguments that my earlier paper addressed, can be blocked by allowing that an embodied demonstrative concept can contribute contents to a visual experience.

In response to Fred Adams and Charlotte Shreve’s (2016) paper entitled “What Can Synesthesia Teach Us about Higher Order Theories of Consciousness?”, previously published in Symposion, I argue that H.O.T. theory does have the resources to account for synesthesia and the specific worries that they advance in their paper, such as the relationship between concepts and experience and the ability to handle instances of ‘pop-out’ experiences.

In this retrospective for Ethics, I discuss H.M. Oliver’s “Established Expectations and American Economic Policies.” This article, by a then-modestly-famous economist, has been ignored (no citations) since its 1940 publication. Yet it bears directly on a normative problem at the intersection of ethics and economics that challenges today’s policymakers but has received comparatively little philosophical attention: how should we balance potentially desirable institutional change against the disruption of established expectations? -/- Oliver details how the principle of fulfilling established expectations cuts (...) across political lines. Conservatives, he observes, criticized inflation for disrupting expectations, and demanded the protection of established corporations. New Deal progressives achieved “the safeguarding of the economic positions of certain important sections of the American people” (104) via statutes designed to protect income and homeownership status. And labor leaders lobbied for the preservation of occupational status. Oliver criticizes these demands on two grounds. First, they are noncompossible: they can’t simultaneously be fulfilled. Second, they are economically inefficient. He concludes that “in a modern dynamic economy, the preservation of status is not and cannot be a feasible criterion of economic justice” (107). -/- I argue that Oliver accurately recognizes both the wide endorsement and the moral ill-foundedness of fulfilling expectations. However, I criticize Oliver’s belief in the noncompossibility of expectations. The established expectations of the wealthy, middle-class homeowners and retirees, and current workers can all be maintained, but at the price of constricting the opportunities of new graduates, immigrants, and the poor—all groups yet to develop settled expectations. This insight renders the protection of expectations not merely inefficient but also unjust. (shrink)

Why is humour so hard to understand? Rather like attempts to explain how music can move us, attempts to explain why things are funny seem doomed from the outset. Discussions of humour typically distinguish three kinds of theory: the incongruity theory (we are amused by the incongruous), the relief theory (humour is an expression of relief in difficult situations) and the superiority theory (we laugh to express our sense of superiority over others). In the face of genuine humour, theories like (...) these can seem pedestrian and unconvincing. F.H. Buckley’s book is, unfortunately, no exception to this rule. Coming from the superiority camp, the book defends two theses about humour. (Professor Buckley’s own word is ‘laughter’, but it is clear that he is really interested in why we laugh rather than laughter itself.) The first is what he calls the ‘Positive’ thesis: that all humour is the expression of a sense of superiority over someone else, whom he names ‘the butt’. The second he calls the ‘Normative’ thesis: that those who laugh really are superior to the butt. (shrink)

This book is a translation of W.V. Quine's Kant Lectures, given as a series at Stanford University in 1980. It provide a short and useful summary of Quine's philosophy. There are four lectures altogether: I. Prolegomena: Mind and its Place in Nature; II. Endolegomena: From Ostension to Quantification; III. Endolegomena loipa: The forked animal; and IV. Epilegomena: What's It all About? The Kant Lectures have been published to date only in Italian and German translation. The present book is filled out (...) with the translator's critical Introduction, "The esoteric Quine?" a bibliography based on Quine's sources, and an Index for the volume. (shrink)

This review shows how Auden was a philosopher of religion and therefore, this review calls for reassessing the poet Auden as a philosopher concerned with prayer and the necessity of the transcendent in life.

Jordan agreed to extensive liberalization undertakings under the General Agreement on Trade in Services (“GATS”) that would open some sectors that were previously closed or restricted to foreign suppliers and investors. It undertook horizontal commitments in cross-border movement of individuals and commercial presence covering all types of services.

"Capital is moved as much and as little by the degradation and final depopulation of the human race, as by the probable fall of the earth into the sun. Apres moi le deluge! is the watchword of every capitalist and of every capitalist nation" (Marx, CAPITAL Vol 1, 380-381).

A case to be taken up by the Criminal Appeals Commission because the decision of the appeal court was flawed- a miscarriage of justice against Dr Stephen Hamilton, formerly, a most respected senior family general practitioner.

Though almost forty years have elapsed since its first publication, it is a testament to the philosophical acumen of its author that 'The Matter of Chance' contains much that is of continued interest to the philosopher of science. Mellor advances a sophisticated propensity theory of chance, arguing that this theory makes better sense than its rivals (in particular subjectivist, frequentist, logical and classical theories) of ‘what professional usage shows to be thought true of chance’ (p. xi) – in particular ‘that (...) chance is objective, empirical and not relational, and that it applies to the single case’ (ibid.). The book is short and dense, with the serious philosophical content delivered thick and fast. There is little by way of road-mapping or summarising to assist the reader: the introduction is hardly expansive and the concluding paragraph positively perfunctory. The result is that the book is often difficult going, and the reader is made to work hard to ensure correct understanding of the views expressed. On the other hand, the author’s avoidance of unnecessary use of formalism and jargon ensures that the book is still reasonably accessible. In the following, I shall first summarise the key features of Mellor’s propensity theory, and then offer a few critical remarks. (shrink)

Short review of Helge Kragh's excellent book on the contest between big bang and steady state theories of the universe.

This is a case that should go to the European Court of Human Rights. A decent, senior qualified family doctor was accused by his mentally ill daughter of sex abuse. Without real evidence except for what the girl told another mentally ill patient at a psychiatric hospital she stayed at for several years, and wit just two witnesses, one a younger child wo saw none of the accused offences, and the other parent, struck off the General Medical Council Register for (...) drunk driving more than once, the case was fitted up by those who are rampantly seeking to raise statistical numbers for child sex abuse offences by high level persons- a bizarre situation and a travesty against tis family doctor's human rights, because a judge can use his 'discretion' to send a much needed family doctor to 18 years in jail. The International Community should scrutinize the United Kingdom's Criminal Justice System. (shrink)

Law is traditionally related to the practice of command and hierarchy. It seems that a legal rule should immediately establish a relation between a superior and an inferior. This hierarchical and authoritharian view might however be challenged once the phenomenology of the rule is considered from the internal point of view, that is, from the stance of those that can be said to “use” rather than to “suffer” the rules themselves. A practice oriented approach could in this way open up (...) a more liberal, and also somehow less parochial and ideological, road for legal theory. This is – it is argued in the paper – the programme, or better, the promise we can find in Herbert Hart’s main work, The Concept of Law. The article tries to render this promise more transparent while, nonetheless, not eschewing the blind sides of its narrative and argumentative strategy. (shrink)