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 (...) class='Hi'>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)

Scholars working in philosophy of action still struggle with the freedom/determinism dichotomy that stretches back to Hellenist philosophy and the metaphysics that gave rise to it. (...) class='Hi'>Although that metaphysics has been repudiated in current philosophy of mind and cognitive science, the dichotomy still haunts these fields. As such, action is understood as distinct from movement, or motion. In early China, under a very different metaphysical paradigm, no such distinction is made. Instead, a notion of self-caused movement, or spontaneity, is elaborated. In this article a general conception of spontaneity from early Daoism is explained, detailing its constituent aspects. Similar notions appeared from time to time in Western philosophy, and these instances are pursued, exploring how their instantiations differed from Daoist spontaneity and why. Based on these approximate examples of spontaneity and on early Daoist spontaneity, new criteria are postulated for a plausible theory of action that dispenses with presuppositions that eventuate in a freedom/determinism dichotomy, and instead the possibility is offered of a general model of action that can be applied smoothly across current philosophical and cognitive scientific subdisciplines. (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. (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 (...) class='Hi'>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)

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

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 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. (shrink)

This paper is mainly about Brentano’s commentaries on Ernst Mach in his lectures “Contemporary philosophical questions” which he held one year before he left Austria. I (...) class='Hi'>will first identify the main sources of Brentano’s interests in Comte’s and J. S. Mill’s positivism during his Würzburg period. The second section provides a short overview of Brentano’s 1893-1894 lectures and his criticism of Comte, Kirchhoff, and Mill. The next sections bear on Brentano’s criticism of Mach’s monism and Brentano’s argument against the reduction of the mental based on his theory of intentionality. The last section is about Brentano’s proposal to replace the identity relation in Mach’s theory of elements by that of intentional correlation. I conclude with a remark on the history of philosophy in Austria. (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)

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, (...) class='Hi'>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)

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

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)

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.

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)

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. (shrink)

Different understanding on Aristotelian distributive justice results in two main factions: holism and egalitarianism. Dennis McKerlie, one of the representatives of holism, criticized Martha Nussbaum's interpretation (...) class='Hi'>as an egalitarian. McKerlie argued that Nussbaum did not attach enough importance to the Proportional equality and Aristotelian Common good, as well as a deviation in the understanding of the concept of distribution. The defense of egalitarianism is that Aristotle's emphasis on the rational equality of citizens and the ontological presupposition of primal equality show Aristotelian egalitarian tendencies. (shrink)

Hans Jonas 's responsibility ethics is an important achievement of modern technology criticism and ethical theory innovation. The maturity of Jonas's ethical thought has gone through (...) class='Hi'>three main stages, namely, the critique of modern technology, the reflection of traditional ethics and the construction of the " Future-oriented " Responsibility Ethics. Jonas's criticism of modern technology not only has a strong epochal character but also carries on the spirit of social criticism since Marx. His insight into the traditional ethics theory and the ethical characteristics of the technical age constituted the background of the Responsibility ethics. Jonas's responsibility ethics is not only the return of "responsibility" spirit in ethics but also the dimension of "Future", which is the characteristic of his theory. Through criticism, reflection and construction, Jonas formed this kind of asymmetrical ethics thought of "Future-oriented" Responsibility and faced the challenge of modern technology. (shrink)

With the development of sharing economy, a consensus to study this area from the perspective of morality and ethics has been recently reached. The key point of (...) this study is the ethical basis of sharing economy. It should be noticed that the conceptual framework of sharing economy must be grounded within the market economy, technological innovation, and the spirit of "rational cooperation". It is, therefore, necessary to realize that the sharing economy is based on the Contractual Ethics internally rooted in the market economy, the Technical Ethics which is coordinated with technological innovation, and the Universal Ethics produced by the cooperative reason. The three concept of ethics lay the ethical foundation of sharing economy together. (shrink)

In the evolution of Chinese and Western literatures, the emphasis on the "strength" of "courage" is gradually given to the "mind" of " (...) class='Hi'>courage", that is the intention of the Agent. The connotation of Chinese and Western traditional thoughts of "courage" reflected in the distinction between the "physical courage" and "moral courage". Philosophers distinguish moral courage from physical courage, which does not seem to be clear and complete. Moral courage however as moral elements have been distinguished from "courage as a virtue". The behavior of "moral courage" must be "supernormal behavior", which is the embodiment of moral choice and moral practice in a specific situation. The Agent of "moral courage" has particularity, the behavior itself is in a certain situation, and the behavioral consequences show severe. (shrink)

The Concept of Life and Death of Chuang-tzu have inherited and developed Confucianism and Taoism thoughts, establishing Ontological foundation of "Life - Body", distinguishing the transcendental (...) class='Hi'> concept of "Dead Heart" and the empirical concept of "Death Body", as well as proposing the thought of "Equivalence of Life and Death" finally. The logic Reasoning of Chuang-tzu "Equivalence of Life and Death", start from constructing the equal status of "Life" and “Death" from ontological argument. Life and Death then are reduced to be a natural phenomenon to dispel its mystery. With emphasizing the social connotation of life and death, the difference between them has been removed, and finally the Thought experiment of "Chuang-tzu dreaming butterfly" has deepened the idea of "Equivalence of Life and Death". The Ideological Characteristic of the Concept of Life and Death of Chuang-tzu mainly reflects in the aspects of Ontology, Epistemology and Ethical practice. (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 (...) class='Hi'>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)

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 (...) class='Hi'>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)

Empirical work and philosophical analysis have led to widespread acceptance that vision for action, served by the cortical dorsal stream, is unconscious. I argue that the empirical (...) argument for this claim is unsound. That argument relies on subjects’ introspective reports. Yet on biological grounds, in light of the theory of primate cortical vision, introspection has no access to dorsal stream mediated visual states. It is thus wrongly assumed that introspective reports speak to absent phenomenology in the dorsal stream. In light of this, I consider a different conception of consciousness’s relation to agency in terms of access. While theoretical reasons suggest that the inaccessibility of the dorsal stream to conceptual report is evidence that it is unconscious, this position begs important questions. I propose a broader notion of access in respect of the guidance of intentional agency and not, narrowly, conceptual report (Note: this paper contradicts my earlier paper, "The Case for Zombie Agency"). (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist (...) that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

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)