The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The surface grammar of reports such as ‘I have a pain in my leg’ suggests that pains are objects which are spatially located in parts of the body. We show that the parallel construction is not available in Mandarin. Further, four philosophically important grammatical features of such reports cannot be reproduced. This suggests that arguments and puzzles surrounding such reports may be tracking artefacts of English, rather than philosophically significant features of the world.

On the question of whether the universe should be infinite or finite, there has been throughout the history of physics a struggle between materialism and idealism, between dialectics and metaphysics. Materialism asserts that the universe is infinite, while idealism advocates finitude. At every stage in the history of physics, these two philosophical lines have engaged in fierce struggle. Although developments in physics always demonstrate the failure of the finite universe doctrine, with every new advance in science the idealists distort and (...) take advantage of the latest results of physics to "prove" with varying sleights of hand that the universe is finite, serving the reactionary rule of the moribund exploiting classes. In the early part of this century after the rise of quantum theory and relativity theory, physics arrived at a new stage of development. After General Relativity was announced in 1916, a lot of people used it and similar theories of gravity to produce all sorts of models of the universe. The "finite universe" point of view became even more fashionable. Lenin pointed out that "That certain schools of the new physics have various dealings with Machism and other variants of modern idealism, is a fact not to be doubted for a moment." It is clear from reading all sorts of foreign literature that the schools of physics promoting a finite universe are linked up with all sorts of idealist philosophy, including theology. (shrink)

Philosophers disagree about what the folk concept of pain is. This paper criticises existing theories of the folk concept of pain, i.e. the mental view, the bodily view, and the recently proposed polyeidic view. It puts forward an alternative proposal – the polysemy view – according to which pain terms like “sore,” “ache” and “hurt” are polysemous, where one sense refers to a mental state and another a bodily state, and the type of polysemy at issue reflects two distinct but (...) related concepts of pain. Implications with respect to issues in philosophy of pain are also drawn. (shrink)

In The Specter of Materialism Petrus Liu examines what "materialism" means for progressive queer theory and Marxist approaches to China's postsocialist economy. Liu recasts the history of queer theory in light of the Beijing Consensus, arguing that North American queer theory's inability to sustain a materialist analysis is the result of its positioning of the United States, rather than China, as the focal point of contemporary global capitalism. Analyzing relations of gender and sexuality that have been reconfigured by China's global (...) capitalist accumulation-such as dagongmei (female migrant laborers in China's export-oriented sunbelt) and money boys (rural-to-urban sex workers)-Liu argues for a materialist queer theory that positions China at the center. (shrink)

Against a backcloth of philosophical debates on science and technology, and in particular the viewpoints of Karl Marx, this three-volume set proposes to reconsider science and technology and explores how the philosophy of science and technology responds to scientific and technological evolutions and an ever-changing world. The first volume analyses Marx's reconsideration of science and technology in five parts: its positioning, its historical practice, alienation of science and technology, and its relationship with productivity and human liberty. In the second volume, (...) viewpoints and problems of scientism and anti-scientism are discussed, covering topics such as instrumental reason, scientific optimism and pessimism, irrationalism and the deconstruction of scientism. The final volume discusses complementary value choices, the loss and awakening of scientific culture and reveals a vison for a liberal and open world of science and technology. The volumes will appeal to scholars and students interested in Marxist philosophy, the philosophy of science and technology and topics related to scientific culture. (shrink)

The problem of consciousness has been an issue in philosophy of mind for decades, and in recent years panpsychism and panprotopsychism have gained attention among philosophers who are still dedicated to finding a complete explanation of consciousness. In this dissertation, I criticize panpsychism and panprotopsychism by examining their metaphysical plausibility and their epistemic prospects. Concerning the metaphysical plausibility of panpsychism and panprotopsychism, I explain the “combination problem” of panpsychism and criticize several major accounts of panpsychism and panprotopsychism that aim at (...) solving this problem, including Seager’s panpsychist infusionism, Goff’s phenomenal bonding proposal, and Coleman’s panqualityism. I also examine the proposal of motivating panpsychism and panprotopsychism by drawing support from the integrated information theory (IIT) of consciousness. I argue that this proposal to merge panpsychism or panprotopsychism with IIT does not work. Concerning the epistemic prospect of panpsychism and panprotopsychism, I raise concerns about whether panpsychism and panprotopsychism can guide a fruitful research program about the nature of consciousness. First, I argue that a theory based on Russellian Monism would not have a promising epistemic prospect. I compare Russellian Monism to Thomistic Hylomorphism and argue that Russellian Monism faces similar epistemic challenges that plagued Thomistic Hylomorphism. Since most theories of contemporary panpsychism and panprotopsychism rely on the metaphysical framework of Russellian Monism, the challenges to Russellian Monism also undermine the epistemic prospects of panpsychism and panprotopsychism. Second, I challenge the epistemic prospects of panpsychism and panprotopsychism by examining if there can be a viable method to study the consciousness of micro-level entities. After revisiting the reasoning process that guided the study of atoms, I argue that studying micro-level facts requires “analogies” that compare micro-level facts with macro-level models. Then I argue that an analogy that fits the need of panpsychism or panprotopsychism is hard to achieve, because we have no macro-level models to be compared to the hypothesized systems of micro-level consciousness. (shrink)

本书收录了刘文英先生1978年到2004年发表的论文及未刊稿53篇,文章主题分为"天论新诠""时空纵横谈""科学史话""意识观与认识论""梦的解析""原始思维探秘"等专题.

Representationalism is a philosophical position which reduces all phenomenal conscious states to intentional states. However, starting from the phenomenal consciousness, the phenomenal intentionality theory provides an explanation of all sorts of intentionality. Against Michael Shim's interpretation, I argue that, although Hussserl's phenomenology is certainly considered as an antipode of strong representationalism, Husserl does not stand in opposition the weak representationalists, because Husserl maintains an essential connection between the senses of noemata and the hyletic data. In addition, Husserl's phenomenology is also (...) consistent with the phenomenal theory of intentionality. According to him, statically and genetically, all non-phenomenal intentional states take a recourse to phenomenal intentional states and eventually to sensual perceptions. (shrink)

本书选辑了作者自1982年以来公开发表的学术论文和学术评论50余篇。学术论文部分主要是围绕重大现实课题,探讨了马克思主义哲学历史观、真理观、价值观和文化研究的方法论等问题;学术评论部分主要针对社会上和 学术理论界存在的思想路线、思维方式、思想作风、学风、文风等方面的问题及其实质和根源,作了分析和评论。.

本书内容包括:物质第一性精神第二性关于哲学基本问题的对话、批判林彪“四人帮”的“精神万能论”、论矛盾诸方面同一性在事物发展中的作用、关于实践标准的几个问题等。.