In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (shrink)

This article seeks to describe in general terms what has become the standard way of conceptualizing moral injury in the clinical psychological and psychiatric literature, which is the key source for applications of the concept in other domains. What we call “the standard model” draws on certain assumptions about beliefs, mental states, and emotions as well as an implicit theory of causation about how various forms of harm arise from certain experiences or “events” that violate persons’ moral beliefs and systems. (...) Our analysis makes these assumptions more explicit and subjects them to critical scrutiny. In so doing, we survey the current literature and identify basic features of how moral injuries are defined, how they are thought to occur, and the forms of treatment or repair that appear to be indicated. We caution that it matters how moral experience is characterized and argue that an alternative understanding of what is the moral in moral injury is important for overcoming critical challenges to the standard model. Moreover, recently evolving approaches to moral repair could be more consistent with an alternative model. Our concluding suggestion is that a more robust account of the nature of moral experience and its relations to self-identity and social experience more generally could advance understanding of the etiology of moral injury and promote rehabilitation. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

The verb ‘to know’ can be used both in ascriptions of propositional knowledge and ascriptions of knowledge of acquaintance. In the formal epistemology literature, the former use of ‘know’ has attracted considerable attention, while the latter is typically regarded as derivative. This attitude may be unsatisfactory for those philosophers who, like Russell, are not willing to think of knowledge of acquaintance as a subsidiary or dependent kind of knowledge. In this paper we outline a logic of knowledge of acquaintance in (...) which ascriptions like ‘Mary knows Smith’ are regarded as formally interesting in their own right, remaining neutral on their relation to ascriptions of propositional knowledge. The resulting logical framework, which is based on Hintikka’s modal approach to epistemic logic, provides a fresh perspective on various issues and notions at play in the philosophical debate on acquaintance. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

PREMISSA No século XIX, ocorreram transformações impulsionadas pela emergência de novas fontes energéticas (água e petróleo), por novos ramos industriais e pela alteração profunda nos processos produtivos, com a introdução de novas máquinas e equipamentos. Depois de 300 anos de exploração por parte das nações europeias, iniciou -se, principalmente nas colônias latino-americanas, um processo intenso de lutas pela independência. É no século XIX, já com a consolidação do sistema capitalista na Europa, que se encontra a herança intelectual mais próxima da (...) qual surgirá a Sociologia como ciência particular. No início desse século, as ideias do Conde de Saint-Simon (1760-1825), de Georg Wilhelm Friedrich Hegel (1770-1831), de David Ricardo (1772-1823) e de Charles Darwin (1809-1882), entre outros, foram o elo para que Alexis de Tocqueville (1805-1859), Auguste Comte (1798-1857), Karl Marx (1818 -1883) e Herbert Spencer (1820-1903), entre outros, desenvolvessem reflexões sobre a sociedade de seu tempo. Auguste Comte e Karl Marx foram os pensadores que lançaram as bases do pensamento sociológico e de duas grandes tradições – a positivista e a socialista – que muito influenciaram o desenvolvimento da Sociologia no Brasil. 1 AUGUSTE COMTE E A TRADIÇÃO POSITIVISTA Isidore Auguste Marie François Xavier Comte nasceu em Montpellier, na França, em 19 de janeiro de 1798. Com 16 anos de idade, ingressou na Escola Politécnica de Paris, fato que teria significativa influência na orientação posterior de seu pensamento. De 1817 a 1824, foi secretário do Conde de Saint-Simon. Comte declarou que, com Saint -Simon, aprendeu muitas coisas que jamais encontraria nos livros e que, no pouco tempo em que conviveu com o conde, fez mais progressos do que faria em muitos anos, se estivesse sozinho. Toda a obra de Comte está permeada pelos acontecimentos que ocorreram após a Revolução Francesa de 1789. Ele defendeu parte dos princípios revolucionários e criticou a restauração da monarquia, preocupando-se fundamentalmente em reorganizar a sociedade, que, no seu entender, estava em ebulição e mergulhada no caos. Para Comte, a desordem e a anarquia imperavam em virtude da confusão de princípios (metafísicos e teológicos), que não se adequavam à sociedade industrial em expansão. Era, portanto, necessário superar esse estado de coisas, usando a razão como fundamento da nova sociedade. Propôs, então, a mudança da sociedade por meio da reforma intelectual plena das pessoas. De acordo com o pensador, com a modificação do pensamento humano, por meio do método científico, que ele chamava de “filosofia positiva”, haveria uma reforma das instituições. Com a proposta do estudo da sociedade por meio da análise de seus processos e estruturas, e da reforma prática das instituições, Comte criou uma nova ciência, à qual deu o nome de “física social”, passando a chamá-la posteriormente de Sociologia. A Sociologia representava, para Comte, o coroamento da evolução do conhecimento, mediante o emprego de métodos utilizados por outras ciências, que buscavam conhecer os fenômenos constantes e repetitivos da natureza: a observação, a experimentação, a comparação e a classificação. De acordo com esse pensador, a Sociologia, como as ciências naturais, deve sempre procurar a reconciliação entre os aspectos estáticos e os dinâmicos do mundo natural ou, no caso da sociedade humana, entre a ordem e o progresso. O lema da “filosofia positiva” proposta por Comte era “conhecer para prever, prever para prover”, ou seja, o conhecimento é necessário para fazer previsões e também para solucionar possíveis problemas. A influência de Comte no desenvolvimento da Sociologia foi marcante, sobretudo, na escola francesa, evidenciando-se em Émile Durkheim e seus contemporâneos e seguidores. Seu pensamento esteve presente em muitas das tentativas de criar tipologias para explicar a sociedade. Suas principais obras são: Curso de filosofia positiva (1830-1842), Discurso sobre o espírito positivo (1848), Catecismo positivista (1852) e Sistema de política positiva (1854). Para concluirmos, Comte explanava que para a superação da anarquia reinante na nova sociedade industrial, a filosofia positivista defendia a subordinação do progresso à ordem. O mesmo era contra o retorno de Luís XVIII ao trono: em sua concepção, a sociedade industrial que emergia requeria um governo fundado na razão. 2 A TRADIÇÃO SOCIALISTA: KARL MARX E FRIEDRICH ENGELS Karl Heinrich Marx nasceu em Tréveris, na antiga Prússia, hoje Alemanha, em 1818 e, em 1830, ingressou no Liceu Friedrich Wilhelm, nessa mesma cidade. Anos depois, foi cursar Direito na Universidade de Bonn, transferindo-se para Berlim em seguida. Pouco a pouco, entretanto, seus interesses migraram para a Filosofia, área na qual defendeu, em 1841, a tese de doutorado A diferença da filosofia da natureza em Demócrito e Epicuro. Sua vida universitária foi marcada pelo debate político e intelectual influenciado pelo pensamento de Ludwig Feuerbach (1804-1872) e, principalmente, pelo de Georg Wilhelm Friedrich Hegel (1770- 1831). Friedrich Engels (1820-1895) nasceu em Barmen (Renânia), na antiga Prússia, hoje Alemanha, filho mais velho de um rico industrial do ramo têxtil. Terminou sua formação secundária em 1837 e a partir de então sua formação intelectual foi por conta própria (autodidata), com alguns cursos universitários esparsos e de curta duração. Desde cedo começou a trabalhar nas empresas de seu pai e foi nessa condição que se deslocou para Bremen por três anos e depois foi enviado pelos pais a Manchester, na Inglaterra, onde trabalhou nas fábricas da família. Engels ficou impressionado com a miséria na qual viviam os trabalhadores das fábricas inglesas. Os dois, Marx e Engels, se encontraram em 1842, quando Marx passou a escrever para A Gazeta Renana, jornal da província de Colônia, do qual Engels era colaborador e mais tarde editor-chefe. O jornal, que criticava o poder prussiano, foi fechado em 1843, e Marx se viu desempregado. Ao perder o emprego, mudou-se para Paris, na França. Ali escreveu, em 1844, os Manuscritos econômico-filosóficos (só publicados em 1932) e, junto com F. Engels, o livro A sagrada família. Por sua vez, F. Engels, em 1844, decidiu voltar para a Alemanha, onde publicou, em 1845, A situação da classe trabalhadora na Inglaterra. Entre 1845 e 1847, Marx exilou-se em Bruxelas, na Bélgica, onde escreveu A ideologia alemã (em parceria com Friedrich Engels) e Miséria da filosofia (1847), obra na qual criticou o filósofo Pierre-Joseph Proudhon (1809-1865). Em 1848, ainda na Bélgica, a parceria com Engels se solidificou ao escreverem juntos o livreto O Manifesto Comunista. Em 1848, Marx foi expulso da Bélgica e retornou a Colônia, na Alemanha (Prússia), sempre pensando na possibilidade de uma mudança estrutural em sua terra natal. Isso, entretanto, não aconteceu e Marx foi expulso da Alemanha em 1849, ano em que migrou para Londres, na Inglaterra, onde permaneceu até o fim da vida. Lá escreveu O 18 Brumário de Luís Bonaparte (1852), sua mais importante obra de reflexão sobre a vida política europeia do século XIX, desenvolveu pesquisas e concluiu seu maior trabalho: O capital: crítica da economia política. O primeiro volume dessa obra foi publicado em 1867; os outros três, em 1885, 1894 e 1905, após a morte de Marx, revisados por F. Engels. 2.1 O contexto histórico e a obra de Marx e Engels Para situar a obra de Marx e Engels, é necessário conhecer um pouco do que acontecia em meados do século XIX. Com as transformações que ocorriam no mundo ocidental, principalmente na esfera da produção industrial, houve um crescimento expressivo no número de trabalhadores industriais urbanos, com uma consequência evidente: precariedade da vida dos operários nas cidades. As condições de trabalho no interior das fábricas eram péssimas. Os empregados eram superexplorados, alimentavam-se mal e trabalhavam em ambientes insalubres. Para enfrentar essa situação e tentar modificá-la, os trabalhadores passaram a se organizar em associações e sindicatos e a promover movimentos de reivindicação. Desenvolveu-se, então, uma discussão das condições sociais, políticas e econômicas para se definirem as possibilidades de intervenção nessa realidade. Desde o início do século XIX, muitos pensadores discutiram essas questões, nas perspectivas socialista e anarquista. Na Inglaterra podem ser citados, entre outros: William Godwin (1756-1836), Thomas Spence (1750-1814), Thomas Paine (1737-1809), Robert Owen (1771-1858) e Thomas Hodgkin (1787-1866). Na França, destacaram-se Étienne Cabet (1788- 1856), Flora Tristan (1803-1844), Charles Fourier (1772-1837) e Pierre-Joseph Proudhon (1809-1865). Marx e Engels levaram em conta esses pensadores, debatendo com alguns contemporâneos e criticando-os. Além disso, incorporaram a tradição da economia clássica inglesa, presente principalmente nas obras de Adam Smith e de David Ricardo. Pode-se dizer, portanto, que Marx e Engels desenvolveram seu trabalho com base na análise crítica da economia política inglesa, do socialismo utópico francês e da filosofia alemã. Esses dois autores não buscavam definir uma ciência específica para estudar a sociedade (como a Sociologia, para Auguste Comte) ou situar seu trabalho em um campo científico particular. Em alguns escritos, Marx afirmou que a História seria a ciência que mais se aproximava de suas preocupações, por abarcar as múltiplas dimensões da sociedade, a qual deveria ser analisada na totalidade, não havendo uma separação rígida entre os aspectos sociais, econômicos, políticos, ideológicos, religiosos, culturais etc. O objetivo de Marx e Engels era estudar criticamente a sociedade capitalista com base em seus princípios constitutivos e em seu desenvolvimento, visando dotar a classe trabalhadora de uma análise política da sociedade de seu tempo. Assim, a tradição socialista nascida da luta dos trabalhadores, muitos anos antes e em situações diferentes, tem como expressão intelectual o pensamento de Karl Marx e Friedrich Engels. Para entender as concepções fundamentais de Marx e Engels é necessário fazer a conexão entre as lutas da classe trabalhadora, suas aspirações e as ideias revolucionárias que estavam presentes no século XIX na Europa. Para eles, o conhecimento científico da realidade só tem sentido quando visa à transformação dessa mesma realidade. A separação entre teoria e prática não é discutida, pois a “verdade histórica” não é algo abstrato e que se define teoricamente; sua verificação está na prática. Apesar de haver algumas diferenças em seus escritos, os elementos essenciais do pensamento de Marx e Engels podem ser assim sintetizados: • historicidade das ações humanas – crítica ao idealismo alemão; • divisão social do trabalho e o surgimento das classes sociais – a luta de classes; • o fetichismo da mercadoria e o processo de alienação; • crítica à economia política e ao capitalismo; • transformação social e revolução; • utopia – sociedade comunista. A obra desses dois autores é muito vasta e não ficou vinculada estritamente aos movimentos sociais dos trabalhadores. Pouco a pouco foi introduzida nas universidades como parte do estudo em diferentes áreas do conhecimento. Estudiosos de Filosofia, Sociologia, Ciência Política, Economia, História e Geografia, entre outras áreas, foram influenciados por ela. Na Sociologia, como afirma Irving M. Zeitlin, no livro Ideología y teoría sociológica, tanto Max Weber quanto Émile Durkheim fizeram, em suas obras, um debate com as ideias de Karl Marx. Pelas análises da sociedade capitalista de seu tempo e a repercussão que tiveram em todo o mundo, principalmente no século XX, nos movimentos sociais e nas universidades, Marx e Engels são considerados autores clássicos da Sociologia. No campo dessa disciplina, porém, o pensamento deles ficou um pouco restrito, pois perdeu aquela relação entre teoria e prática (práxis), ou seja, entre a análise crítica e a prática revolucionária. Essa relação esteve presente, por exemplo, na vida e na obra dos russos Vladimir Ilitch Ulianov, conhecido como Lênin (1870-1924), e Leon D. Bronstein, conhecido como Trotsky (1879-1940), da alemã Rosa Luxemburgo (1871-1919) e do italiano Antonio Gramsci (1891- 1937), que tiveram significativa influência no movimento operário do século XX. Com base no trabalho de Marx e Engels, muitos autores desenvolveram estudos acadêmicos em vários campos do conhecimento. Podemos citar, por exemplo, Georg Lukács (1885-1971), Theodor Adorno (1903-1969), Walter Benjamin (1892-1940), Henri Lefebvre (1901-1991), Lucien Goldmanm (1913 -1970), Louis Althusser (1918 -1990), Nikos Poulantzas (1936-1979), Edward P. Thompson (1924-1993) e Eric Hobsbawm (1917 -2012). O pensamento de Marx e Engels continua, assim, presente em todo o mundo, com múltiplas tendências e variações, sempre gerando controvérsias. REFERENCIAL TEÓRICO GEMKOW, H.; PSUA, I. M. L. Marx e Engels: Vida e Obra. São Paulo: Alfa e Ômega, 1984. 232 pp. GIANOTTI, J. A. Comte. São Paulo: Abril Cultural, 1978. 318 pp. (Col. Os Pensadores) KONDER, L. Marx: vida e obra. 7ª ed. São Paulo: Paz e Terra, 2007. 154 pp. (Col. Vida e Obra). (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

The last decade has witnessed the beginnings of a remarkable convergence of Husserlian phenonenology and analytic philosophy of language, and the present volumes provide original and important texts of the phenomenological philosophy of language. Powerfully influenced by the writings of the early Husserl, Reinach fashioned Husserl’s ideas into a rigorous analytical methodology of his own, which he applied in particular to problems in logic and the theory of knowledge, and to the philosophies of law and psychology. The central role of (...) the concept of state of affairs in Reinach’s philosophy will bring to mind immediately the formal ontology of Wittgenstein’s Tractatus. Reinach’s most significant contribution, however, is contained in his The a priori foundations of civil law (1913), above all in the detailed analysis of the a priori structure of the act of promising. This amounts to an elaborate phenomenological theory of speech acts which anticipates, and in some respects goes beyond, the later theories of Austin and Searle. The present edition is in two volumes. Volume 1, which includes a biographical and thematic introduction by the editors, contains critical editions of those pieces published by Reinach himself. Volume II is a collection of all those items in Reinach’s surviving Nachlass which are in publishable form, including a number of important pieces not hitherto obtainable on such themes as ethical predicates, speech acts (“soziale Akte”), perception and the theory of number, together with a comprehensive sketch of the problems in the theory of knowledge, logic and ethics. Appended to this is a text-critical apparatus which also contains extensive discussions of the origins and sources of the materials in question. (shrink)

A collaborative article by the Editorial Collective of Social Imaginaries. Investigations into social imaginaries have burgeoned in recent years. From ‘the capitalist imaginary’ to the ‘democratic imaginary’, from the ‘ecological imaginary’ to ‘the global imaginary’ – and beyond – the social imaginaries field has expanded across disciplines and beyond the academy. The recent debates on social imaginaries and potential new imaginaries reveal a recognisable field and paradigm-in-the-making. We argue that Castoriadis, Ricoeur, and Taylor have articulated the most important theoretical frameworks (...) for understanding social imaginaries, although the field as a whole remains heterogeneous. We further argue that the notion of social imaginaries draws on the modern understanding of the imagination as authentically creative. We contend that an elaboration of social imaginaries involves a significant, qualitative shift in the understanding of societies as collectively and politically-instituted formations that are irreducible to inter-subjectivity or systemic logics. After marking out the contours of the field and recounting a philosophical history of the imagination, the essay turns to debates on social imaginaries in more concrete contexts, specifically political-economic imaginaries, the ecological imaginary, multiple modernities and their inter-civilisational encounters. The social imaginaries field imparts powerful messages for the human sciences and wider publics. In particular, social imaginaries hold significant implications for ontological, phenomenological and philosophical anthropological questions; for the cultural, social, and political horizons of contemporary worlds; and for ecological and economic phenomena. The essay concludes with the argument that social imaginaries as a paradigm-in-the-making offers valuable means by which movements towards social change can be elucidated as well providing an open horizon for the critiques of existing social practices. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)

The paper challenges the assumption, common amongst philosophers, that the reality described in the fundamental theories of microphysics is all the reality we have. It will be argued that this assumption is in fact incompatible with the nature of such theories. It will be shown further that the macro-world of three-dimensional bodies and of such qualitative structures as colour and sound can be treated scientifically on its own terms, which is to say not only from the perspective of psychology but (...) also ontologically. A new sort of emergentist position will be defended, one which yields the basis of a method for describing the perceptually salient macroscopic world in mathematical terms. Broadly, it will be argued that the macroscopic world exists in virtue of certain specific sorts of boundary-patterns in the field of what is captured by the theories of microphysics. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed analyses of (...) pertinent examples. But his writings leave no doubt that he is acutely aware of the very problems concerning language structure and use out of which contemporary speech act theory has evolved and that he goes a good way towards solving these problems in the spirit of the modern theory. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Physical reality is all the reality we have, and so physical theory in the standard sense is all the ontology we need. This, at least, was an assumption taken almost universally for granted by the advocates of exact philosophy for much of the present century. Every event, it was held, is a physical event, and all structure in reality is physical structure. The grip of this assumption has perhaps been gradually weakened in recent years as far as the sciences of (...) mind are concerned. When it comes to the sciences of external reality, however, it continues to hold sway, so that contemporary philosophers B even while devoting vast amounts of attention to the language we use in describing the world of everyday experience B still refuse to see this world as being itself a proper object of theoretical concern. Here, however, we shall argue that the usual conception of physical reality as constituting a unique bedrock of objectivity reflects a rather archaic view as to the nature of physics itself and is in fact incompatible with the development of the discipline since Newton. More specifically, we shall seek to show that the world of qualitative structures, for example of colour and sound, or the commonsense world of coloured and sounding things, can be treated scientifically (ontologically) on its own terms, and that such a treatment can help us better to understand the structures both of physical reality and of cognition. (shrink)

Individuals sometimes pass their duties on to collectives, which is one way in which collectives can come to have duties. The collective discharges its duties by acting through its members, which involves distributing duties back out to individuals. Individuals put duties in and get (transformed) duties out. In this paper we consider whether (and if so, to what extent) this general account can make sense of states' duties. Do some of the duties we typically take states to have come from (...) individuals having passed on certain individual duties? There are complications: states can discharge their duties by contracting fulfilment out to non-members; states seem able to dissolve the duties of non-members; and some of states' duties are not derived in this way. We demonstrate that these complicate, but do not undermine, the general account and its application to states. And the application has an interesting upshot: by asking which individuals robustly participate in this process of duty transfer-and-transformation with a given state, we can begin to get a grip on who counts as a member of that state. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

In 1929 when Aurel Kolnai published his essay “On Disgust” in Husserl's ]ahrbuch he could truly assert that disgust was a "sorely neglected" topic. Now, however, this situation is changing as philosophers, psychologists, and historians of culture are turning their attention not only to emotions in general but more specifically to the large and disturbing set of aversive emotions, including disgust. We here provide an account of Kolnai’s contribution to the study of the phenomenon of disgust, of his general theory (...) of emotions and of the phenomenological methodology he employed in his work. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics (...) domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

Artificial intelligence is man's attempt to use software to emulate the intelligence of human beings. But the complexity of the human neurological system formed in the course of evolution is impossible to replicate: "Human languages and societies are complex systems, indeed complex systems of many complex systems," so much so that their mathematical modeling is impossible. Barry Smith, philosopher and professor at the University at Buffalo. shows no uncertainty about this. His latest book written with Jobst Landgrebe, a mathematician (...) and entrepreneur in the AI field, leaves no doubt – starting with the title: Why machines will never rule the world (Routledge 2023). The book was presented in Turin during an evening organized by the Fondazione CRT and the Bruno Leoni Institute, in which Smith was interviewed based on questions developed by generative Ai. We have accepted the challenge to conduct an interview parallel to the one done with GPT4. (shrink)

We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) is about. (shrink)

Learner’s attitude towards modular distance learning catches uncertainties as a world crisis occurs up to this point. As self-learning modules (SLMs) become a supplemental means of learning in new normal education, this study investigated efficiency towards the learners’ attitude and performance. Specifically, the study described the learners’ profile and their attitude and performance towards SLMs. It also ascertained the relationship between the learner’s profile with their attitude and performance, as well as the relationship between attitude and performance relevant to SLMs. (...) A descriptive-correlational research design was employed in the study with 88 non-randomly chosen participants from secondary schools in West Philippines. The learners’ GWA (general weighted average) was used to determine their performance and a survey questionnaire for their profile and attitude. Frequency counts, percentage, and Spearman’s rank correlation coefficient were used to analyze the data gathered with the aid of Jamovi software. Results revealed a strong correlation between attitude and performance, but there was no link between learner’s attitude and performance as to the learner’s profile. It was affirmed that attitude is a compelling factor that is related with performance. Hence, this research has broader ramifications that can direct the Bureau of Learning Delivery to orient the module writers to further contextualize the learning materials that can compound learner’s disposition and academic performance. (shrink)

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. (...) Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

Disputes over territory are a major contributing factor to the disruption of international relations. We believe that a cumulative, integrated, and continuously updated resource providing information about such disputes in an easily accessible form would be of benefit to intelligence analysts, military strategists, political scientists, and also to historians and others concerned with international disputes. We propose an ontology-based strategy for creating such a resource. The resource will contain information about territorial disputes, arguments for and against claims pertaining to sovereignty, (...) proffered evidence for such claims, political and military motives (overt or hidden), and associated conflicts. Our approach is designed to address several issues surrounding the representation of geopolitical conflict, including the tracking and individuation of disputes and the validation of disseminated information. (shrink)

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.

For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...) realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future. (shrink)

Part One of Montesquieu's Idea of Justice comprises a survey of the currency in philosophical, ethical and aesthetic debate during the second half of the 17th century of the terms rapport and convenance, which are central to the enigmatic definition given to justice by Mon tesquieu in Lettres Persanes LXXXllI. In this survey, attention is concen trated on the way in which the connotations of these terms fluctuate with the divergent development of the methodological and speculative outgrowths of Cartesian ism (...) into two schools of thought, materialist and idealist, often widely at variance in their views of the nature and orga nization of the universe. In Part Two, Montesquieu's definition of justice is set against this background, whose doctrinal conflicts, because of the characteristic as sociations of its key terms, it may be taken to reflect, just as it may be held to epitomize, by virtue of its elaboration in the opening chapter of De l' Esprit des Lois and its close terminological affinities with the defini tion of law there given, an undoubtedly related conflict between the implications of causal determinism and the aspirations of idealist meta physics surviving at the heart of Montesquieu's outlook, and, remaining unresolved, often said to impair the coherence if not the validity of his theory of society. (shrink)

The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...) the theory to the IPAP schizophrenia algorithm results in a representation that can be used by software agents to perform monitoring and control in a referent tracking environment. (shrink)

Radical democratic thinking is becoming intrigued by the material situatedness of its political agents and by the role of nonhuman participants in political interaction. At stake here is the displacement of narrow anthropocentrism that currently guides democratic theory and practice, and its repositioning into what we call ‘the nonhuman condition’. This Critical Exchange explores the nonhuman condition. It asks: What are the implications of decentering the human subject via a new materialist reading of radical democracy? Does this reading dilute political (...) agency? Or should this be seen, on the contrary, as an invitation for new voices and demands to enter into democratic assemblages? How might engagement with the more-than-human disrupt or extend theories of radical democracy? Hans Asenbaum and Amanda Machin discuss the human democratic subject both through radical democratic and new materialist lenses. They suggest that a new materialist decentred subject does not lose agency but further gains political responsibility in radical democracy. Jean-Paul Gagnon highlights the possibility of becoming through loss. In losing our anthropocentric arrogance—our understanding of being other and better than animal—we become more connected and discover our place in human-nonhuman assemblages. Melissa Orlie agrees that something can be gained through renouncing dominant human fantasies and presents a ‘radical democratic naturalism’. By renouncing land violence and acknowledging nature’s subjectivity, we can further nonexploitative radical democratic politics. This is where the notion of ‘tidalectic’ processes introduced by James L. Smith is helpful. Focusing on water and the Indigenous knowledges around rivers, he considers how democracy and community can be reimagined as plural, cyclical and attentive to the nonhuman with which the human is inevitably entangled. Diana Leong offers a different approach. Considering the nonhuman from the perspective of Black Studies demands an awareness to how blackness has long been constituted as non- or partially human. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...) diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

Academic institutions migrated to modular teaching-learning amid the COVID-19 pandemic. To ensure the quality of the pedagogical innovations employed, the study determined the students’ evaluation of the faculty prepared instructional modules for the courses they enrolled in during the first and second semesters of Academic Year 2020-2021. Employing a descriptive-correlational research design, the study was participated by 644 students from three colleges who were then available during the data gathering. Data gathered through online surveys were then analyzed using descriptive statistics (...) and Spearman's rank correlation coefficient utilizing jamovi software. Results revealed that the faculty-prepared instructional modules were acceptable and satisfactory to the students. Besides, the students' evaluation of the instructional modules was positively related to their level of satisfaction. Still, the students recommended that a review of the modules be done before sending the modules; a more extended time allotment is considered, and sufficient concrete examples are given in the modules. With this, the faculty concerned are encouraged to review the phases involved in the design, development, and distribution of the instructional modules to make them highly acceptable and very satisfactory to the students while maintaining the quality of both the content and aesthetics of the learning materials. Considering the study’s limitations, further endeavors may be carried out to validate this pedagogical innovation. (shrink)

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)