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.

​I use network models to simulate social learning situations in which the dominant group ignores or devalues testimony from the marginalized group. I find that the marginalized group ends up with several epistemic advantages due to testimonial ignoration and devaluation. The results provide one possible explanation for a key claim of standpoint epistemology, the inversion thesis, by casting it as a consequence of another key claim of the theory, the unidirectional failure of testimonial reciprocity. Moreover, the results complicate the understanding (...) and application of previously discovered network epistemology effects, notably the Zollman effect (Zollman 2007, 2010). (shrink)

I analyze the role of infinite idealizations used in the renormalization group (RG hereafter) method in explaining universality across microscopically different physical systems in critical phenomena. I argue that despite the reference to infinite limit systems such as systems with infinite correlation lengths during the RG process, the key to explaining universality in critical phenomena need not involve infinite limit systems. I develop my argument by introducing what I regard as the explanatorily relevant property in RG explanations: linearization* property; I (...) then motivate and prove a proposition about the linearization* property in support of my view. As a result, infinite limit systems in RG explanations are dispensable. (shrink)

关于人类意识起源和本质问题的探讨由来已久，各领域如哲学、社会学、生物学和心理学等都有不同定义和解释，但是至今为止都没有得到广泛的认同，主要原因是由意识的复杂性导致了各领域都不能全面、合理和充分地认识其 起源和本质，成为千古奇案，所以有必要对其进行深入探讨。 本文根据各学科的知识分析、汇总和归纳，得出如下结论：意识的起源来自自然物质；意识的本质为物质信息；意识的能力是物质信息的复杂度和有序度的利用程度；意识具有先天性、物质性、系统性、复杂性、动态性、差异性 和自我性属性 .

Diversity of practice is widely recognized as crucial to scientific progress. If all scientists perform the same tests in their research, they might miss important insights that other tests would yield. If all scientists adhere to the same theories, they might fail to explore other options which, in turn, might be superior. But the mechanisms that lead to this sort of diversity can also generate epistemic harms when scientific communities fail to reach swift consensus on successful theories. In this paper, (...) we draw on extant literature using network models to investigate diversity in science. We evaluate different mechanisms from the modeling literature that can promote transient diversity of practice, keeping in mind ethical and practical constraints posed by real epistemic communities. We ask: what are the best ways to promote an appropriate amount of diversity of practice in scientific communities? (shrink)

Joe Horton argues that partial aggregation yields unacceptable verdicts in cases with risk and multiple decisions. I begin by showing that Horton’s challenge does not depend on risk, since exactly similar arguments apply to riskless cases. The underlying conflict Horton exposes is between partial aggregation and certain principles of diachronic choice. I then provide two arguments against these diachronic principles: they conflict with intuitions about parity, prerogatives, and cyclical preferences, and they rely on an odd assumption about diachronic choice. Finally, (...) I offer an explanation, on behalf of partial aggregation, for why these diachronic principles fail. (shrink)

古代中国明朝哲学家王阳明创立的心学已有七百多年，它继承了中国古代的哲学，比如孔孟之道和宋明理学等的内容，创立了心学。其理念在社会哲学领域深深地影响了中国、日本和朝鲜等东亚国家，甚至于间接地推动了日本的 明治维新运动，成为千年一圣。同时世界各地的学者对心学的研究和探讨也是层出不穷，但是总体而言，缺乏对心学理论体系性的探讨和研究。 本文从体系概念着手，结合心学的内容，经过梳理后整合成一个完整的、逻辑的和全面的心学体系。.

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)

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)

Attention has become an important focal point of recent work in ethics and epistemology, yet philosophers continue to be noncommittal about what attention is. In this paper, I defend attention as selection for action in a weak form, namely that selection for action is sufficient for attention. I show that selection for action in this form is part of how we, the folk, experience it and how the cognitive scientist studies it. That is, selection for action pulls empirical and folk-psychology (...) together. Accordingly, philosophers who take seriously either source have reason to work with selection for action as their starting conception of attention. This conception provides a way to bridge empirical and philosophical concerns where attention is central. The theoretical advantages of selection for action have been obscured by the common opinion that it is easily refuted. I defend the position against many of the published objections and then deploy it to provide a foundation for the intuitive, but inchoate idea of attention being more or less, focusing on recent work in the ethics of attention. (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)

目前，世界上的哲学简单地可分两类，一是：唯物主义，二是：唯心主义，它们统治了哲学史几千年，相互争斗了几千年，但是都存在着，不分胜负，至少说明都有合理之处，当然也包括不合理之处。 如果把两者进行了升华，就是集合唯心主义和唯物主义各自的合理部分，摈弃了不合理部分，把它们合二为一，统一成一个系统的、合理的和广泛的哲学体系，那就是唯能主义。 .

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.

In Movements of the Mind (MoM; Wu, 2023a), I give a theory of agency that uncovers its internal psychological structure, revealing how creatures with minds do things. While my focus is on things we do 'in our heads', mental actions, the theory concerns all forms of agency. The book also provides a theory of attention and its essential connection to action. It characterizes intention in action as a type of memory for work, drawing on empirical theories of working memory. Further, (...) it reveals the essential role of bias in action, providing an account of various psychological biases. The theory is then applied to three phenomena prominent in philosophical practice: implicit (better, automatic) bias, reasoning deductively, and introspection of conscious perceptual experience. (shrink)

In the domain of cognitive science, understanding consciousness through the investigation of neural correlates has been the primary research approach. The exploration of neural correlates of consciousness is focused on identifying these correlates and reducing consciousness to a physical phenomenon, embodying a form of reductionist physicalism. This inevitably leads to challenges in explaining consciousness itself. The computational interpretation of consciousness takes a functionalist view, grounded in physicalism, and models conscious experience as a cognitive function, elucidated through computational means. This paper (...) posits that predictive processing offers a fresh paradigm for comprehending human cognition and serves as a neural foundation for the computational elucidation of consciousness. Additionally, free energy theory, as a mathematical construct explaining the predictive processing model, furnishes a theoretical scaffold for understanding consciousness computationally. (shrink)

A longstanding orthodoxy holds that the Mohists regard the promotion of li (benefit, 利) as their ultimate normative criterion, meaning that they measure what is yi (just, 義) or buyi (unjust, 不義) depending on whether it maximizes li or not. This orthodoxy dates back at least to Joseph Edkins (1859), who saw Mozi as a utilitarian and an ally of Bentham. In this paper, we will argue that this orthodoxy should be reconsidered because it does not square with several passages (...) from the Mozi. That the Mohists place a strong weight on the promotion of ‘li for the whole world (tianxia zhi li, 天下之利)’ is uncontroversial. We argue, however, that in certain cases the Mohist moral calculus diverges in its rationale or outcome from li-promotionalism. This position rejects the orthodoxy by showing that Mohism and li-promotionalism are not entirely coterminous. (shrink)

It has a long history for the exploration of the origin and essence of human consciousness with different definitions and explanations in various fields such as philosophy, medicine, sociology, biology, and psychology. However, all of them had not been recognized so far. The main reason is that the complexity of consciousness leads to the inability of various fields to understand its essence fully, reasonably, and comprehensively, and there are still significant differences for it, and which have become an eternal mystery. (...) So, it is necessary to delve deeper into it. Here we show that this article concludes that the origin of consciousness comes from natural matter, the essence of consciousness is material information, the ability of consciousness is the degree to which the complexity and orderliness of material information are utilized, and consciousness has the attributes of congenital, materiality, systematicness, complexity, dynamics, difference, and selfness according to the analysis, summary and induction of knowledge from various disciplines. (shrink)

Xinxue （The philosophy of mind） founded by ancient Chinese philosopher Wang Yangming of the Ming Dynasty for over 700 years. Its ideas have deeply influenced East Asian countries such as China, Japan, and Korea in the field of social philosophy, and even indirectly promoted Japan's Meiji Restoration movement. At the same time, scholars from all over the world have conducted numerous studies and explorations on it, but overall, there is a lack of systematic exploration and research on it. This article (...) starts with the concept of a system, combines the content of Xinxue and integrates it into a complete, logical, and comprehensive system of Xinxue. (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)

The literature on algorithmic fairness has examined exogenous sources of biases such as shortcomings in the data and structural injustices in society. It has also examined internal sources of bias as evidenced by a number of impossibility theorems showing that no algorithm can concurrently satisfy multiple criteria of fairness. This paper contributes to the literature stemming from the impossibility theorems by examining how informational richness affects the accuracy and fairness of predictive algorithms. With the aid of a computer simulation, we (...) show that informational richness is the engine that drives improvements in the performance of a predictive algorithm, in terms of both accuracy and fairness. The centrality of informational richness suggests that classification parity, a popular criterion of algorithmic fairness, should be given relatively little weight. But we caution that the centrality of informational richness should be taken with a grain of salt in light of practical limitations, in particular, the so-called bias-variance trade off. (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)

The question of Who am I?” is the end of philosophy. The famous ancient Greek philosopher Socrates raised three ultimate questions in philosophy when he looked up at the starry sky: “Who am I?” “Where do I come from?” “Where am I going？”. For thousands of years, humans have explored and answered questions about them, including various disciplines such as philosophy, psychology, biology, and neurology etc., but none of them have been recognized. This article starts with the cosmology and worldview (...) of “Who am I?” and elaborates on the origin of “Who am I?” and the concept of “center”. (shrink)

Aiming at the allocation of scarce medical resources, Immanuel and other scholars have put forward a set of influential ethical values and guiding principles. It assigns the priority of resource allocation to those whose lives can be saved and maximized, those who can bring the greatest instrumental value, and those who are the worse off. For other members of society, random selection under the same conditions is adopted. Following the Rawlsian "lexical order, lexicographical" rule, this priority arrangement requires that the (...) "utilitarian principle" should be placed before the "equality principle", and the "instrumental difference principle", the "integrity difference principle" and the "fair opportunity principle" in turn acts on specific distribution agents. Although the framework and its priority rules have obvious drawbacks when faced with Medical Resources Squeeze and other dilemmas, with the help of an understanding of its internal structure, it can effectively respond to the four core issues in the allocation of scarce medical resources. (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 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)

In the evolution of Chinese and Western literatures, the emphasis on the "strength" of "courage" is gradually given to the "mind" of "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)

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 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 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)

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)

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 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)

In defense of anti-essentialism, pragmatist Richard Rorty holds that we may think of all objects as if they were numbers. I find that Rorty’s metaphysics hinges on two rather weak arguments against the essences of numbers. In contrast, Plato’s metaphysics offers a plausible definition of essentiality by which numbers do have essential properties. Further, I argue that Rorty’s argumentative mistake is mischaracterizing Plato’s definition. I conclude that Plato’s definition of “essential” is a robust one which implies that many properties, beyond (...) those we might intuitively think of, can count as essential properties of objects. (shrink)

Recently, there is a renewed debate concerning the role of perspective in vision. Morales et al. (2020) present evidence that, in the case of viewing a rotated coin, the visual system is sensitive to what has often been called “perspectival shapes.” It has generated vigorous discussions, including an online symposium by Morales and Cohen, an exchange between Linton (2021) and Morales et al. (2021), and most recently, a fierce critique by Burge and Burge (2022), in which they launch various conceptual (...) and empirical objections. Although Morales and Firestone (2022) have responded to them recently, and we are in agreement with Morales and Firestone in general, there are further problems in Burge and Burge (2022) that are worth highlighting. The main point of this comment is that what the Burge–Burge team call “viewpoint-dependent relational properties” are simply instances of what the Morales–Firestone team call “perspectival shapes”; the confusion arises from Burge and Burge’s misconstrual of Morales et al.’s claims. This shows that conceptually, the two teams are in large agreement, as Morales and Firestone (2022) also point out, and the focus should be put on the empirical disagreements, which has been covered by Morales and Firestone (2022). Relatedly, we argue that Burge and Burge (2022) misinterpret Morales et al. (2020) as supporting a new entity in perception science, and that this misinterpretation is a primary source of their apparent disagreement. This is worth pointing out because such misunderstanding generates many unnecessary quarrels that hinder progress. (shrink)

This essay explores the meaning of Kant's transcendental definition of pleasure and displeasure. I will explain the meaning of "definition" and "transcendental" respectively in relation to the feeling of pleasure and displeasure, contrasting with the interpretations of Guyer (2018) and Deimling (2018). Not only will I show how they are wrong, but I will also offer reasons for their misinterpretations. This essay proposes that the transcendental definition of pleasure and displeasure bears more systematic significance in Kant's philosophy than previous researchers (...) might have thought. My analysis also leads back to Kant's conception of the anthropological relation between life, desire, and pleasure. (shrink)

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

De-anthropocentrism is the leitmotif of philosophy in the twenty-first century, encouraging diverse and competing thoughts as to how this goal may be achieved. This article argues that the method by which we may achieve de-anthropocentrism is ethical rather than metaphysical – it must involve a creation of the self, rather than an interpretation of the given human conditions. Through engagements with the thought of Nietzsche, Levinas, and Foucault, and a close reading of Baudelaire’s poem “La Beauté,” I will illustrate three (...) ethical commitments essential to de-anthropocentrism: to abandon the claim to knowledge associated with human reason, to remain in perpetual quest of an object, and to transgress the given perceptual structure through aesthetic experience. In contrast to Kantian philosophy built upon universal human reason, art is the ethical arena where each artist creates their own way to relate to the object, while de-anthropocentrism occurs – this article argues – when the artist includes the self as the field of creation. Object-Oriented Ontology in my assessment is the only branch of philosophy that truly achieves de-anthropocentrism. (shrink)

One famous debate in contemporary epistemology considers whether there is always one unique, epistemically rational way to respond to a given body of evidence. Generally speaking, answering “yes” to this question makes one a proponent of the Uniqueness thesis, while those who answer “no” are called “permissivists”. Another influential recent debate concerns whether non-truth-related factors can be the basis of epistemic justification, knowledge, or rational belief. Traditional theories answer “no”, and are therefore considered “purists”. However, more recently many theorists have (...) argued to the contrary, claiming that impurist factors, such as practical stakes, can sometimes encroach or even override truth-related considerations. This paper bridges the two debates by presenting and defending what I call “Impurist Permissivism”. I support Impurist Permissivism by showing how it can resist Roger White’s famous Argument from Arbitrariness (2005). (shrink)

This article compares the use of Romantic metaphor with the Chinese literary device xiang 象 (which I translate as “thing-metaphor”) in regard to how they embody different metaphysical relations between humans and things. Whereas Romantic metaphor transports a physical thing to the immaterial realm of imagination, xiang is a literary device in which the material qualities of the thing, while creatively interpreted to generate human meaning, retain ontologically a strong physical presence. Xiang therefore epitomizes a theory of creation that challenges (...) the Western dualistic paradigm: that the poet creates not virtual copies of the thing, but meanings of the thing, and therefore our relationships with things. The article concludes with Heidegger’s discourses on metaphor to suggest that my discussion of thing-metaphor has universal applicability. (shrink)

IPCC SPECIAL REPORT ON CLIMATE CHANGE AND LAND (SRCCL) -/- Chapter 3: Climate Change and Land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.

When solving a complex problem in a group, should group members always choose the best available solution that they are aware of? In this paper, I build simulation models to show that, perhaps surprisingly, a group of agents who individually randomly follow a better available solution than their own can end up outperforming a group of agents who individually always follow the best available solution. This result has implications for the feminist philosophy of science and social epistemology.

The Protein Ontology 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 present study aimed to explore the effect of subliminal priming on team trust and the mechanism through the mediating role of perceived trustworthiness. A total of 144 participants were asked to complete a lexical decision task that was embedded with the “trust” or “suspicion” Chinese words as the subliminal stimuli. Then, they played a public good game and evaluated the perceived trustworthiness of the team. The results of the study showed that subliminal stimuli had a significant effect on team (...) trust [β = –0.99, 95% CI = (−1.64, −0.33)]. Perceived trustworthiness was found to have a significant mediating effect between the priming condition and team trust [β = −0.35, 95% CI = (−0.72, −0.02)]. The current study revealed the underlying mechanism through which subliminal priming techniques influence team trust and informed efforts by altering perceived trustworthiness. (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)

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)

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)

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.

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)

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)