In the Nintendo game Animal Crossing: New Horizons, players move to an uninhabited island and quickly become instrumental to the naming, aesthetic development, and biodiversity of the island. In some ways, the game can foster a love for and curiosity about nature. In other ways, the game reinforces harmful colonialist values and attitudes that are ultimately an obstacle to conservation in the real world. Here I critique the game values relevant to conservation, both the values that benefit and the values (...) that hinder conservation. I discuss possibilities for a future version of the game that reinforces values better aligned with conservation. (shrink)

To Aaron Pacitti and Michael Cauvel–whose journal article, “Rent-Seeking Behavior and Economic Justice: A Classroom Exercise” broadly argues that “understanding the [complexities] of rent-seeking behavior helps fill the gap between economics and politics”–the varieties of rent are wide and, therefore, can only be described in their category-specific positions. I will discuss three of these categories in more detail below, but for now, I propose that a useful working grasp of economic rent involves “the amount paid to the owner of a (...) factor of production over the cost that is to be necessarily incurred on utilizing such elements in the production process.” In math terms, ‘economic rent’ equals the agreed-upon-amount paid by the consumer (when that amount far exceeds the market value of the product) minus the cost spent by the producer to make the product (when that cost is far below the typical amount to produce the product). Originally, the concept of economic rent concerned land ownership and the production of natural goods. Two major economists, Adam Smith and David Ricardo, offered insights into the general makeup and logic of what they called, the rent of land and simply rent, respectively. (shrink)

Simon Blackburn has not shied away from the use of vivid imagery in developing, over a long and prolific career, a large-scale philosophical vision. Here one might think, for instance, of ‘Practical Tortoise Raising’ or ‘Ramsey's Ladder’ or ‘Frege's Abyss’. Blackburn develops a ‘quasi-realist’ account of many of our philosophical and everyday commitments, both theoretical (e.g., modality and causation) and practical (e.g., moral judgement and normative reasons). Quasi-realism aims to provide a naturalistic treatment of its targeted phenomena while earning the (...) right to deploy all of the ‘trappings’ of realism—i.e., while eschewing any idea that our normal thought and talk about such phenomena are pervasively in error. The quasi-realist project is that of explaining how (as Huw Price puts it here) ‘the folk come to “talk the realist talk” without committing ourselves—us theorists, as it were—to “walking the metaphysical walk”’ (p. 136). Quasi-realism, too, can speak of truth, facts, properties, belief, knowledge, and so on. The imagery in this collection also abounds, though, in capturing a different view of quasi-realism: No fewer than three of the contributors picture Blackburn as wanting to have his cake and eat it too (Louise Antony asking, in addition, ‘Who doesn't? It's cake’ [p. 19]). (shrink)

This essay is my brief review of Nicholas Phillipson’s biography of Adam Smith. I discuss the highlights of his treatment of Smith’s fascinating life. Phillipson does a beautiful job of surveying Smith’s academic career. Especially useful is Phillipson’s discussion of the influence David Hume had on Smith’s thought, as well as the influences of Montesquieu, Samuel Johnson, Voltaire, Rousseau, and others.

Reasons internalism holds that reasons for action contain an essential connection with motivation. I defend an account of reasons internalism based on the advisor model. The advisor model provides an account of reasons for action in terms of the advice of a more rational version of the agent. Contrary to Pettit and Smith's proposal and responding to Sobel's and Johnson's objections, I argue that the advisor model can provide an account of internal reasons and that it is too (...) caught up in the psychology of the actual agent to be able to account for anything other than internal reasons. (shrink)

How can a business institution function as an ethical institution within a wider system if the context of the wider system is inherently unethical? If the primary goal of an institution, no matter how ethical it sets out to be, is to function successfully within a market system, how can it reconcile making a profit and keeping its ethical goals intact? While it has been argued that some ethical businesses do exist, e.g., Johnson and Johnson, the argument I (...) would like to put forth is that no matter how ethical a business institution is, or how ethical its goals are, its capacity to act in an ethical manner is restricted by the wider system in which it must operate, the market system. Unless there is a fundamental change in the notion of the market system itself, the capacity for individual businesses to act in an ethical manner will always be restricted. My argument is divided into two parts. The first part is to show the inherent bias towards unethical outcomes that is inherent in the market system. The second part is to suggest how to reorient the general economic framework in order to make ethical institutions more possible. The question then becomes, how to define economic behavior in terms other than competition for profit. (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)

Albert Camus’ views contributed to the rise of the philosophy known as Absurdism, he defines the Absurd “as the conflict between the human tendency to seek inherent value and meaning in life, and the human inability to find any meaning in a purposeless, meaningless, and irrational universe, with the ‘unreasonable silence’ of the universe in response.” However, this world in itself is not absurd, what is absurd is our relationship with the universe, which is irrational. Camus is considered to be (...) an existentialist, even though he firmly rejected the term throughout his lifetime. He is properly categorised as an atheist existentialist. However, he would also disagree with this label. In his notebooks, he presents the following contradictory statement: -/- “I do not believe in God and I am not an atheist.” -/- This reflects the notion of the Absurd. The search of the possibility of the existence of God is humanly impossible, but this also entails that the proof that God does not exist is impossible too. He writes in The Myth of Sisyphus: “In a universe suddenly divested of illusions and lights, man feels an alien, a stranger. His exile is without remedy since he is deprived of the memory of a lost home or the hope of a promised land. This divorce between man and his life, the actor and his setting, is properly the feeling of absurdity.” The Myth of Sisyphus is a fierce expression of the Absurd. It starts off with a powerful and thought-provoking statement: “There is but one truly serious philosophical problem and that is suicide. Judging whether life is or is not worth living amounts to answering the fundamental question of philosophy.” . (shrink)

An interview by Alex Thomson of UKColumn on Landgrebe and Smith's book: Why Machines Will Never Rule the World. The subtitle of the book is Artificial Intelligence Without Fear, and the interview begins with the question of the supposedly imminent takeover of one profession or the other by artificial intelligence. Is there truly reason to be afraid that you will lose your job? The interview itself is titled 'Where this is no will there is no way', drawing on one (...) thesis of the book to the effect that there will never be anything like the human will on the part of a machine. This is for mathematical reasons. AI is always and in every case a matter of algorithms; thus of applied mathematics. And algorithms are not the sorts of things that can want or desire or intend to do something. It is the human will of those who work at OpenAI or google or microsoft which have given rise to the new shiny objects of AI (ChatGPT and other Large Language Models). And it is the human will of the users of these shiny objects which gives them the resources and power to work their apparent miracles. (shrink)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (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)

Individuals have various kinds of obligations: keep promises, don’t cause harm, return benefits received from injustices, be partial to loved ones, help the needy and so on. How does this work for group agents? There are two questions here. The first is whether groups can bear the same kinds of obligations as individuals. The second is whether groups’ pro tanto obligations plug into what they all-things-considered ought to do to the same degree that individuals’ pro tanto obligations plug into what (...) they all-things-considered ought to do. We argue for parity on both counts. (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.

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)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (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)

As with so many mystics, Alexis karpouzos intuitively know the oneness of cosmic creation and historic humanity as part of all that is and all there isn't. So, the originality of Alexis Karpouzos thought is that it crosses the most diverse fields, the most opposing philosophies, to unite them into an often contradictory and broken whole. Marx and Heidegger, Nietzsche, Freud and Heraclitus, poets and political theorists all come together in the same distance and the same unusual proximity. (...) Alexis karpouzos use Pre-Socratics philosophy and generally the ancient Greek philosophy, as well as the pre-philosophical thinking of The Upanishads, the Vedas and Buddhism in India, of Lao Tzu, of Zen Buddhism and the Taoist tradition in China, of the Arab mystics and poets, with their metaphysical religiosity as the metaphysical basis for the interpretation and understanding of the world and existence. At the same time the ancient metaphysics is connect with Hegel’s dialectical ontology and with the modern thinking of Marx, Nietzsche, Freud, Heidegger, and others as the interpretive context for understanding the central problems of the technical and scientific world during his time. Novalis, Hölderlin, Rimbaud, Whitman, Eliot and others show the dreamy nature of existence, the transcendence of the Cosmos, welcome the infinity. For Alexis karpouzos the combination of ancient and modern thought creates the holistic experience of universal space-time and the consciousness of the unity. The poetic thought of Alexis karpouzos is a expressions of soul's inner experiences, expression of universality. The inspiring visual images and the symbolic use of language offer a description of elevating experiences of consciousness, a glimpse of higher worlds. The philosophy of Alexis karpouzos speak to the human experience from a universal perspective, transcending all religions, cultural and national boundaries. Using vivid images and a direct language that speaks to the heart, his philosophy evokes a sense of deep communication with the collective unconscious, a sense of connection to all the creatures of the world, compassion for others, admiration for the beauty of nature, reverence for all life, and an abiding faith in the invisible touch of world. Alexis karpouzos thoughts are often terse and paradoxical, challenging us to to break out of the box of limiting beliefs and see things from a new perspective. Above all, Alexis karpouzos continually calls to us to wake up and explore the mysteries within our own selves, i.e the mysteries of universe. (shrink)

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or (...) subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

Gödel's Philosophical Legacy Kurt Gödel's contributions to philosophy extend beyond his incompleteness theorems. He engaged deeply with the work of other philosophers, including Immanuel Kant and Edmund Husserl, and explored topics such as the nature of time, the structure of the universe, and the relationship between mathematics and reality. Gödel's philosophical writings, though less well-known than his mathematical work, offer rich insights into his views on the nature of existence, the limits of human knowledge, and the interplay between the finite (...) and the infinite. His work continues to inspire and challenge philosophers, mathematicians, and scientists, inviting them to explore the profound and often enigmatic questions at the heart of human understanding. -/- Kurt Gödel's Broader Contributions to Philosophy Kurt Gödel, while primarily known for his monumental incompleteness theorems, made significant contributions that extended beyond the realm of mathematical logic. His philosophical pursuits deeply engaged with the works of eminent philosophers like Immanuel Kant and Edmund Husserl. Gödel's explorations into the nature of time, the structure of the universe, and the relationship between mathematics and reality reveal a profound and multifaceted intellectual legacy. -/- Engagement with Immanuel Kant Gödel held a deep interest in the philosophy of Immanuel Kant. He admired Kant's critical philosophy, particularly the distinction between the noumenal and phenomenal worlds. Kant posited that human experience is shaped by the mind’s inherent structures, leading to the conclusion that certain aspects of reality (the noumenal world) are fundamentally unknowable. Gödel’s incompleteness theorems echoed this Kantian theme, illustrating the limits of formal systems in capturing the totality of mathematical truth. Gödel believed that mathematical truths exis t independently of human thought, akin to Kant's noumenal realm. This philosophical alignment provided a robust foundation for Gödel's Platonism, which asserted the existence of mathematical objects as real, albeit abstract, entities. -/- Influence of Edmund Husserl Gödel was also profoundly influenced by Edmund Husserl, the founder of phenomenology. Husserl's phenomenology emphasizes the direct investigation and description of phenomena as consciously experienced, without preconceived theories about their causal explanation. Gödel saw Husserl's work as a pathway to bridge the gap between the abstract world of mathematics and concrete human experience. Husserl's ideas about the structures of consciousness and the intentionality of thought resonated with Gödel's views on mathematical intuition. Gödel believed that human minds could access mathematical truths through intuition, a concept that draws on Husserlian phenomenological methods. -/- The Nature of Time and the Universe Gödel's philosophical inquiries extended to the nature of time and the structure of the universe. His collaboration with Albert Einstein at the Institute for Advanced Study led to the development of the "Gödel metric" in 1949. This solution to Einstein's field equations of general relativity described a rotating universe where time travel to the past was theoretically possible. Gödel's model challenged conventional notions of time and causality, suggesting that the universe might have a more intricate structure than previously thought. Gödel's exploration of time was not just a mathematical curiosity but a profound philosophical statement about the nature of reality. He questioned whether time was an objective feature of the universe or a construct of human consciousness. His work hinted at a timeless realm of mathematical truths, aligning with his Platonist view. -/- Mathematics and Reality Gödel's philosophical outlook extended to the broader relationship between mathematics and reality. He believed that mathematics provided a more profound insight into the nature of reality than empirical science. For Gödel, mathematical truths were timeless and unchangeable, existing independently of human cognition. This perspective led Gödel to critique the materialist and mechanistic views that dominated 20th-century science and philosophy. He argued that a purely physicalist interpretation of the universe failed to account for the existence of abstract mathematical objects and the human capacity to understand them. Gödel's philosophy suggested a more integrated view of reality, where both physical and abstract realms coexist and inform each other. -/- Gödel's Exploration of Time Kurt Gödel, one of the most profound logicians of the 20th century, ventured beyond the confines of mathematical logic to explore the nature of time. His inquiries into the concept of time were not merely theoretical musings but were grounded in rigorous mathematical formulations. Gödel's exploration of time challenged conventional views and opened new avenues of thought in both physics and philosophy. -/- Gödel and Einstein Gödel’s interest in the nature of time was significantly influenced by his friendship with Albert Einstein. Both were faculty members at the Institute for Advanced Study in Princeton, where they engaged in deep discussions about the nature of reality, time, and space. Gödel's exploration of time culminated in his solution to Einstein's field equations of general relativity, known as the Gödel metric. -/- The Gödel Metric In 1949, Gödel presented a model of a rotating universe, which became known as the Gödel metric. This solution to the equations of general relativity depicted a universe where time travel to the past was theoretically possible. Gödel’s rotating universe contained closed timelike curves (CTCs), paths in spacetime that loop back on themselves, allowing for the possibility of traveling back in time. The Gödel metric posed a significant philosophical challenge to the conventional understanding of time. If time travel were possible, it would imply that time is not linear and absolute, as commonly perceived, but rather malleable and subject to the geometry of spacetime. This raised profound questions about causality, the nature of temporal succession, and the very structure of reality. -/- Philosophical Implications Gödel’s exploration of time extended beyond the mathematical implications to broader philosophical inquiries: Nature of Time: Gödel questioned whether time was an objective feature of the universe or a construct of human consciousness. His work suggested that our understanding of time as a linear progression from past to present to future might be an illusion, shaped by the limitations of human perception. -/- Causality and Free Will: The existence of closed timelike curves in Gödel’s model raised questions about causality and free will. If one could travel back in time, it would imply that future events could influence the past, potentially leading to paradoxes and challenging the notion of a deterministic universe. -/- Temporal Ontology: Gödel's work contributed to debates in temporal ontology, particularly the debate between presentism (the view that only the present exists) and eternalism (the view that past, present, and future all equally exist). Gödel’s rotating universe model seemed to support eternalism, suggesting a block universe where all points in time are equally real. Philosophy of Science: Gödel’s exploration of time had implications for the philosophy of science, particularly in the context of understanding the limits of scientific theories. His work underscored the importance of considering philosophical questions when developing scientific theories, as they shape our fundamental understanding of concepts like time and space. -/- Legacy Gödel’s exploration of time remains a significant and controversial contribution to both physics and philosophy. His work challenged established notions and encouraged deeper inquiries into the nature of reality. Gödel’s rotating universe model continues to be a topic of interest in theoretical physics and cosmology, inspiring new research into the nature of time and the possibility of time travel. In philosophy, Gödel’s inquiries into time have prompted ongoing debates about the nature of temporal reality, the relationship between mathematics and physical phenomena, and the limits of human understanding. His work exemplifies the intersection of mathematical rigor and philosophical inquiry, demonstrating the profound insights that can emerge from such an interdisciplinary approach. The Temporal Ontology of Kurt Gödel Kurt Gödel's profound contributions to mathematics and logic extend into the realm of temporal ontology—the philosophical study of the nature of time and its properties. Gödel's insights challenge conventional perceptions of time and suggest a more intricate, layered understanding of temporal reality. This essay explores Gödel's contributions to temporal ontology, particularly through his engagement with relativity and his philosophical reflections. -/- Gödel's Rotating Universe One of Gödel’s most notable contributions to temporal ontology comes from his work in cosmology, specifically his solution to Einstein’s field equations of general relativity, known as the Gödel metric. Introduced in 1949, the Gödel metric describes a rotating universe with closed timelike curves (CTCs). These curves imply that, in such a universe, time travel to the past is theoretically possible, presenting a significant challenge to conventional views of linear, unidirectional time. -/- Implica tions for Temporal Ontology Gödel's rotating universe model has profound implications for our understanding of time: Eternalism vs. Presentism: Gödel’s model supports the philosophical stance known as eternalism, which posits that past, present, and future events are equally real. In contrast to presentism, which holds that only the present moment exists, eternalism suggests a "block universe" where time is another dimension like space. Gödel’s rotating universe, with its CTCs, reinforces this view by demonstrating that all points in time could, in principle, be interconnected in a consistent manner. Non-linearity of Time: The possibility of closed timelike curves challenges the idea of time as a linear sequence of events. In Gödel’s universe, time is not merely a straight path from past to future but can loop back on itself, allowing for complex interactions between different temporal moments. This non-linearity has implications for our understanding of causality and the nature of temporal succession. Objective vs. Subjective Time: Gödel’s work invites reflection on the distinction between objective time (the time that exists independently of human perception) and subjective time (the time as experienced by individuals). His model suggests that our subjective experience of a linear flow of time may not correspond to the objective structure of the universe. This raises questions about the relationship between human consciousness and the underlying temporal reality. -/- Gödel and Philosophical Reflections on Time Gödel’s engagement with temporal ontology was not limited to his cosmological work. He also reflected deeply on philosophical questions about the nature of time and reality, drawing on the ideas of other philosophers and integrating them into his own thinking. Kantian Influences: Gödel was influenced by Immanuel Kant’s distinction between the noumenal world (things as they are in themselves) and the phenomenal world (things as they appear to human observers). Gödel’s views on time echoed this distinction, suggesting that our perception of time might be a phenomenon shaped by the limitations of human cognition, while the true nature of time (the noumenal aspect) might be far more complex and non-linear. Husserlian Phenomenology: Gödel’s interest in Edmund Husserl’s phenomenology also informed his views on time. Husserl’s emphasis on the structures of consciousness and the intentionality of thought resonated with Gödel’s belief in the importance of intuition in accessing mathematical truths. Gödel’s reflections on time incorporated a phenomenological perspective, considering how temporal experience is structured by human consciousness. Mathematical Platonism: Gödel’s Platonist views extended to his understanding of time. Just as he believed in the independent existence of mathematical objects, Gödel saw time as an objective entity with a structure that transcends human perception. His work on the Gödel metric can be seen as an attempt to uncover this objective structure, revealing the deeper realities that underlie our experience of time. (shrink)

Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...) the classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with multiple inheritance. (shrink)

The relationship between the One and the Multiple in mystic philosophy is a profound and central theme that explores the nature of existence, the cosmos, and the divine. This theme is present in various mystical traditions, including those of the East and West, and it addresses the paradoxical coexistence of the unity and multiplicity of all things. -/- In mystic philosophy, the **One** often represents the ultimate reality, the source from which all things emanate and to which all things return. (...) It is the absolute, the infinite, and the unchanging. The One is beyond all attributes and is often associated with the divine or the absolute truth. -/- The **Multiple**, on the other hand, represents the manifest world, the diversity of forms, and the realm of change and plurality. It is the world we experience through our senses, the domain of time and space, where differentiation and individuality are apparent. -/- The relationship between the One and the Multiple is not one of opposition but of emanation and unity. The Multiple is seen as a reflection, expression, or manifestation of the One. In this sense, the diversity of the world doesn’t contradict the unity of the One but rather demonstrates it in a myriad of forms. -/- Mystics seek to understand and experience this relationship through various practices and insights. They aim to transcend the illusion of separation and duality to experience the non-dual reality where the One and the Multiple are recognized as inseparable. -/- This concept can be illustrated by the metaphor of the ocean and its waves. The ocean represents the One—vast, deep, and all-encompassing—while the waves represent the Multiple—distinct, diverse, and ever-changing. Each wave is unique, yet it is not separate from the ocean. The wave’s existence is dependent on and made of the same substance as the ocean. In the same way, each individual entity in the Multiple is an expression of the One. -/- In summary, the relationship between the One and the Multiple in mystic philosophy is a dynamic interplay that challenges the conventional understanding of separation. It invites a deeper exploration of reality, where the apparent multiplicity of the world is a direct expression of the singular, underlying essence of all that is. -/- The relationship between the One and the Multiple in the context of mathematical philosophy is a profound topic that touches upon the very foundations of existence and knowledge. It’s a theme that has been explored by philosophers and mathematicians alike, often leading to the contemplation of unity and diversity within the structures of reality. -/- In mathematics, the concept of the One can be seen as the basis of unity from which all numbers derive. It’s the identity element in multiplication, the starting point in counting, and the foundation of dimension in geometry. The One is often associated with the concept of monism in philosophy, which posits that there is a single, underlying substance or principle that constitutes reality. -/- On the other hand, the Multiple represents the infinite variety and diversity of forms and numbers that arise from the One. It’s the embodiment of plurality and the complex interplay of different entities that mathematics seeks to understand and describe. This reflects the philosophical stance of pluralism, which acknowledges the existence of multiple realities or truths. -/- The interplay between the One and the Multiple can be seen in the mathematical concept of sets. A set can be thought of as a unity, a whole composed of distinct elements. Yet, each element within the set also retains its individuality, contributing to the diversity of the set’s composition. This duality is mirrored in the philosophical exploration of the universal and the particular, where the universal represents the One, and the particulars represent the Multiple. -/- In the realm of mathematical philosophy, this relationship often leads to questions about the nature of mathematical objects: Are they discovered as part of an objective reality (the One), or are they constructed by the human mind from a multitude of experiences (the Multiple)? This debate resonates with the philosophical inquiry into the nature of truth and reality. -/- Reflecting on the One and the Multiple can also lead to a deeper understanding of the self and the cosmos. Just as the number one is integral to the existence of all other numbers, the individual self can be seen as a unique expression of the universal whole. Similarly, the cosmos can be viewed as a grand unity composed of a multiplicity of forms and phenomena. -/- Gödel’s incompleteness theorems have a fascinating connection to the philosophical concepts of the One and the Multiple. These theorems, which are pivotal in mathematical logic and philosophy of mathematics, articulate the inherent limitations of formal axiomatic systems, particularly those sufficient to express the arithmetic of natural numbers. -/- Gödel’s incompleteness theorems have a fascinating connection to the philosophical concepts of the One and the Multiple. These theorems, which are pivotal in mathematical logic and philosophy of mathematics, articulate the inherent limitations of formal axiomatic systems, particularly those sufficient to express the arithmetic of natural numbers⁴. -/- The **first incompleteness theorem** reveals that within any such consistent system, there are propositions that are true but cannot be proven within the system itself. This reflects the idea of the Multiple in that there is an abundance of mathematical truths, a multiplicity that exceeds the unifying framework of any one system. It suggests that the realm of mathematical truth is more extensive than any single formal system can fully capture. -/- The **second incompleteness theorem** extends this by showing that a system cannot prove its own consistency. This relates to the concept of the One, as it implies that a system’s complete self-understanding, its unity and coherence, is unattainable from within. It must look beyond itself, to an external vantage point, to ascertain its consistency. -/- In the context of the One and the Multiple, Gödel’s theorems imply that the One (a consistent formal system) is inherently incomplete and cannot encompass the Multiple (the totality of mathematical truths). This resonates with philosophical discussions about the relationship between unity and plurality. Just as a single philosophical system cannot capture the entirety of truth, a single formal mathematical system cannot encapsulate all mathematical truths. -/- Moreover, Gödel’s work suggests that the pursuit of a single, unified theory of everything in mathematics—a One that encompasses all Multiples—is an inherently Sisyphean task. There will always be more truths (Multiples) than can be derived from any given set of axioms (the One). -/- In essence, Gödel’s incompleteness theorems provide a formal underpinning to the philosophical notion that the One cannot exist without the Multiple, and vice versa. They are interdependent, with the One giving rise to the Multiple, and the Multiple necessitating the One for its expression and comprehension. This interplay is a dance of limitations and possibilities, where the boundaries of logic, mathematics, and philosophy blur into one another. -/- The relationship between the One and the Multiple in the context of the mathematics of zero is a deeply philosophical inquiry that bridges the abstract world of numbers with the existential questions of being and non-being. -/- Zero, in mathematics, is a symbol of absence, a representation of nothingness, yet it holds a pivotal position as a number. It is the void from which all things emerge and to which they return. In the philosophy of mathematics, zero is the paradoxical junction where the One and the Multiple converge and diverge. -/- From the perspective of the One, zero can be seen as the origin—the singular point that precedes the existence of numbers. It is the empty set, the foundation upon which the edifice of mathematics is constructed. As the identity element in addition, zero maintains the integrity of numbers, for adding zero to any number leaves it unchanged, reflecting the immutable nature of the One. -/- Conversely, when we consider the Multiple, zero represents the infinite potentiality of creation. It is the canvas upon which the integers, both positive and negative, express their multitude. Zero is the balance point, the fulcrum around which the symphony of numbers dances. It embodies the plurality of possibilities, the beginning of the number line that stretches infinitely in both directions. -/- Philosophically, zero challenges our understanding of existence. It is both something and nothing—a number that quantifies the absence of quantity. This duality echoes the philosophical struggle to comprehend how the One gives rise to the Multiple. How does the unity of being manifest the diversity of the cosmos? Zero offers a mathematical metaphor for this mystery, as it encapsulates the transition from non-existence to existence, from the undifferentiated One to the differentiated Multiple. -/- In the realm of set theory, zero corresponds to the empty set—a set with no elements. This set is unique in that it is the only set that contains nothing, yet it is the foundation upon which all other sets are built. The empty set is the mathematical embodiment of the One, and all other sets, containing multiple elements, arise from it. -/- Reflecting on zero in the context of Gödel’s incompleteness theorems, we find a resonance with the idea that the One (a consistent formal system) cannot capture the entirety of the Multiple (the totality of mathematical truths). Zero, as the foundation of numbers, similarly suggests that from the nothingness of the One, the infinite complexity of the Multiple emerges—yet it can never be fully encompassed or expressed by any single system. -/- In conclusion, the mathematics of zero offers a profound reflection on the relationship between the One and the Multiple. It serves as a bridge between the abstract and the concrete, the known and the unknowable, challenging us to ponder the origins of existence and the nature of reality itself. -/- . (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

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.

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)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (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)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...) this paper, we describe the theoretical foundations of this paradigm and show how it is being applied to the solution of analogous problems of ambiguous identification in the fields of digital rights management, corporate memories and decision algorithms. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (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)

Difference and Repetition: Deleuze’s magnum opus, “Difference and Repetition” (1968), explores the interplay between difference and repetition. He argues that difference is fundamental to reality, and repetition is not mere duplication but a creative force. Deleuze challenges conventional notions of identity and sameness, emphasizing the productive potential of difference. Gilles Deleuze’s “Difference and Repetition” is a seminal work that challenges traditional Western metaphysics and offers a fresh perspective on concepts like identity, repetition, and creativity. Let’s explore some key ideas from (...) this remarkable book: Pure Difference: Deleuze argues that difference is fundamental to reality. Unlike classical philosophy that seeks universal truths, he emphasizes divergence and decentering. Each moment contains unique differences, and these differences shape our understanding of the world. Complex Repetition: Repetition, for Deleuze, isn’t mere duplication. Instead, it involves displacement and disguising. While repetition contributes to generality and thought, it’s the differences within each repetition that account for change and novelty. Concepts and things derive meaning from these differences. Shift Away from Hegel and Marx: “Difference and Repetition” played a crucial role in shifting French thought away from Hegel and Marx toward Nietzsche and Freud. Deleuze’s exploration of difference challenged established philosophical norms and paved the way for new perspectives. The Image of Thought: Deleuze critiques the traditional “image of thought,” which often relies on fixed identities and binary oppositions. Instead, he encourages us to embrace multiplicities, complexities, and the perpetual process of becoming. Asymmetrical Synthesis of the Sensible: Deleuze introduces the concept of asymmetrical synthesis, emphasizing the interplay between perception and affect. Reality is a dynamic, ever-changing process, not a static being. Copies are never identical; they’re something new. “Difference and Repetition” invites us to rethink how we perceive reality, emphasizing creativity, multiplicity, and the constant flux of existence. Deleuze’s work continues to inspire thinkers across disciplines, bridging philosophy with art, literature, and mysticism. (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)

Abstract: We propose a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this semantic view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this (...) theory provides a general framework within which we can understand the relation between vague terms and concepts and the corresponding crisp portions of reality. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches. Central to our approach is the idea that judgments about reality involve in every case (1) a separation of reality into foreground and background of attention and (2) the feature of granularity. On this basis we attempt to show that even vague judgments made in naturally occurring contexts are not marked by truth-value indeterminacy. We distinguish, in addition to crisp granular partitions, also vague partitions, and reference partitions, and we explain the role of the latter in the context of judgments that involve vagueness. We conclude by showing how reference partitions provide an effective means by which judging subjects are able to temper the vagueness of their judgments by means of approximations. (shrink)

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)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (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 introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it has not been able to keep pace (...) with recent developments either in semantics and ontology or in computer science and engineering. HL7’s response has been to develop its “Services-Aware Interoperability Framework” (SAIF), which is intended to provide a foundation for work on all aspects of standardization in HL7 henceforth. We here summarise the major design principles that must be satisfied by a semantic interoperability framework – principles relating both to static semantics and to computational behaviour. We then assess the SAIF in light of these principles. We conclude that the SAIF is not in a position to support the needed reform of the HL7 v3 family of standards. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

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)

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