The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well (...) as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development (...) stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, (...) the scope of the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to (...) plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

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)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? In (...) this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which (...) may however provide general lessons for the developers of ontologies in the future. (shrink)

Before he reached his mature metaphysical view of being as gradual in the Republic (Allen 1961), Plato claims that neither can negative facts explain positive facts, nor vice versa (Phaedo 103b) (this is very likely a corollary of his principle of opposites according to which if A and B are of opposite ontological categories, A cannot explain B (González-Varela and Barceló 2023). Yet, it seems obvious that we explain positive facts by appealing to negative facts and vice versa, all the (...) time. We say things like "Pat must be sick, because she would not have missed the party otherwise", "The Plant died because we forgot to water it", "The suitcase was so large, it did not fit in the trunk", etc. So this seems like a strange and obviously wrong take on the limits of metaphysical explanation. Yet here I will defend that this counter-intuitive metaphysical thesis has been unjustly dismissed and will argue that, instead, it is a plausible metaphysical principle. My defense of this metaphysical principle can also be seen as part of a larger defense of an under-explored metaphysical hypothesis, Ontological Manichesim, according to which positive and negative facts, if both belong in our ontology, are separate realms of being with no interaction whatsoever. (shrink)

Vere Chappell has pointed out that it is not clear whether Locke has a well-developed ontology or even whether he is entitled to have one.2 Nevertheless, it is clear that Locke believes that there are organisms, and it is clear that he thinks that there are substances. But does he believe that organisms are substances? There are certainly parts of the Essay in which Locke seems unequivocally to state that organisms are substances. For instance, in 2.23.3 Locke uses men (...) and horses as examples of substances. In Locke’s most explicit the account of abstraction, given in 3.3.7-9, organism [vivens] is treated as a sub-species of body and body as a sub-species of substance; so, by transitivity, organism is a kind of substance. Finally, in his discussion of essences in 3.6, Locke uses all of the following organisms as examples of substances: horses, mules, men, sheep, goats, plants, drills, changelings, asses, bulls, cats, and rats. This textual evidence would seem to settle the matter about the ontological status of organisms. However, there are other parts of the Essay in which the ontological status of organisms is less clear, to say the least. In fact, there are texts in which Locke seems to state (or at least to be committed to the.. (shrink)

There are long-standing doubts about whether data from subjective scales—for instance, self-reports of happiness—are cardinally comparable. It is unclear how to assess whether these doubts are justified without first addressing two unresolved theoretical questions: how do people interpret subjective scales? Which assumptions are required for cardinal comparability? This paper offers answers to both. It proposes an explanation for scale interpretation derived from philosophy of language and game theory. In short: conversation is a cooperative endeavour governed by various maxims (Grice 1989); (...) because subjective scales are vague and individuals want to make themselves understood, scale interpretation is a search for a focal point (Schelling 1960). A specific focal point it hypothesised; if this hypothesis is correct, subjective data will be cardinally comparable. Four individually necessary and jointly sufficient conditions for cardinal comparability are specified. The paper then argues this hypothesis can be empirically be tested, makes an initial attempt to do so using subjective well-being data, and concludes it is supported. Numerous areas for further research are identified including, at the end of the paper, how certain tests could be used to ‘correct’ subjective data if they are not cardinal. (shrink)

While life satisfaction theories (LSTs) of well-being are barely discussed in philosophy, they are popular among social scientists and wider society. When philosophers have discussed LSTs, they are taken to be a distinct alternative to the three canonical accounts of well-being—hedonism, desire theories, the objective list. This essay makes three main claims. First, on closer inspection, LSTs are indistinguishable from a type of desire theory—the global desire theory. Second, the life satisfaction/global desire theories are the only subjectivist accounts of well-being (...) in the sense that they maintain individuals decide what makes their lives go well for them; hedonism and other desire theories are subjectivist only in some alternative senses. Third, subjectivism is implausible, although for different reasons from those that are usually given. I examine what I take to be the two main current objections to LSTs and argue that they are unproblematic. I then raise two different, challenging objections. The first is novel. The second has been noted in passing, but its seriousness underestimated. I close by sketching some non-obvious difficulties that subjectivists will face if they attempt to show rival objectivist theories suffer even more counterintuitive implications. Although subjectivism has a strong intuitive pull, we should be ready to abandon it in favour of an objectivist theory—although it is not my purpose here to say which one. (shrink)

Suppose you want to do as much good as possible. What should you do? According to members of the effective altruism movement—which has produced much of the thinking on this issue and counts several moral philosophers as its key protagonists—we should prioritise among the world’s problems by assessing their scale, solvability, and neglectedness. Once we’ve done this, the three top priorities, not necessarily in this order, are (1) aiding the world’s poorest people by providing life-saving medical treatments or alleviating poverty (...) itself, (2) preventing global catastrophic risks, such as those posed by nuclear war or rogue artificial intelligence, and (3) ending factory farming. These claims are both plausible and striking. If correct, they should prompt a stark revision of how we approach our altruistic activities. However, the project of determining how to do the most good—as opposed to say, whether we should do the most good—has only recently, within the last ten years, become the subject of serious academic attention. Many key claims have not yet been carefully scrutinised. This is a cause for concern: are effective altruists doing good badly? In this thesis, I critique and develop some of the latest claims about how individuals can do the most good. I do this in three areas: the value of saving lives (preventing premature deaths), how best to improve lives (making people happier during their lives), and cause prioritisation methodology (frameworks for determining which problems are the highest priorities). In each case, I raise novel theoretical considerations that, when incorporated, change the analysis. Roughly speaking, my main conclusions are (1) saving lives is not as straightforwardly good we tend to suppose, may not be good at all, and is not clearly a priority; (2) happiness can be measured through self-reports and, based on the self-reported evidence, treating mental health stands out as an overlooked problem that may be an even more cost-effective way to improve lives than alleviating poverty; (3) the cause prioritisation methodology proposed by effective altruists needs to be moderately reconceptualised and, when it is, it turns out it is not as illuminating a tool as we might have thought and hoped. (shrink)

As well as disagreeing about how much one should donate to charity, moral theories also disagree about where one should donate. In light of this disagreement, how should the morally uncertain philanthropist allocate her donations? In many cases, one intuitively attractive option is for the philanthropist to split her donations across all of the charities that are recommended by moral views in which she has positive credence, with each charity’s share being proportional to her credence in the moral theories that (...) recommend that particular charity. Despite the fact that something like this approach is already being used by real-world philanthropists to distribute billions of dollars of donations, it is not supported by any of the approaches to moral uncertainty that have been proposed thus-far in the philosophical literature. In this paper, we will develop a bargaining-based approach to moral uncertainty that honors the proportionality intuition in favor of splitting one’s donations. We also show how this bargaining-based approach has several further advantages over the best alternative proposals. (shrink)

African ontological discourse revolves around a few principles, the interrelatedness of being, what is variously interpreted as communalism, ubuntu, Holism, communitarianism etc. This is the view that every being in the world, animate and inanimate are interconnected into a whole. This makes it possible for African environmental attitude to claim to be holistic. Since we are one, we care for each other, humans care for animals, plants, and mountains not because of what to gain from them but because we are (...) the same and harming the river is same as harming oneself. The weakness of seeing African environmental ethics as only holistic is that it is not African enough as the paper will argue. The second principle in African ontological discourse is the human being. This principle has made scholars like Callicott and even some African scholars to describe African environmental ethics as anthropocentric. The paper also argues that branding African environmental ethics anthropocentric is not African enough. This is because Africans live in an interconnected world, comprising both the living, the dead and nature. Humans are only one privileged part of the whole and this is because of her obligatory role to nature and the world as a result of her capabilities. Through the method of analysis, the paper argues that a plausible African environmental ethics will be one that will blend the holistic nature of the African ontology and its pride of place given to humans. It will be discovered that obligatory anthropoholism can comfortably blend these two principles without necessarily being anthropocentric. (shrink)

In this work Husserl makes the distinction between expressions and indications that Derrida will later plant the bomb of Husserl's own Phenomenology of Internal Time Consciousness underneath it in order to undermine the dream for presence and inaugurate Deconstruction. Logic, as Husserl sees it, is concerned in the first place with meanings (propositions, concepts) and with associated meaning-instantiating acts. Most importantly, it is concerned with that sort of deductively closed collection of meanings which constitutes a scientific theory. For Husserl, (...) as for Bolzano, logic is a theory of science. Only where we have an appropriate unity and organization also on the side of the objects (states of affairs, properties) to which the relevant acts refer, however, will we have a scientific theory, so that the unity which is characteristic of the latter must involve both (1) an interconnection of truths (or of propositional meanings in general), and (2) an interconnection of the things to which these truths (and the associated cognitive acts) are directed. Where formal logic relates in the first place to meaning categories such as proposition, concept, subject and predicate, its sister discipline of formal ontology relates to object categories such as object and property, relation and relatum, manifold, part, whole, state of affairs, existence and so on. Logic in a broader sense therefore seeks to delimit the concepts which belong to the idea of a unity of theory in relation to both meanings and objects, and the truths of logic are all the necessary truths relating to those categories of constituents, on the side of both meanings and objects, from out of which science as such is necessarily constituted (including what we might think of as bridge-categories such as identity and truth which span the division between meanings and objects). The best way to deal with Husserl's theory of formal ontology, therefore, is to explicate both the connections between the formal and material, and those between the ontological and the logical. In introducing his distinction between formal and material ontology, Husserl asserts that the former is descriptive and involves analytic a priori judgements, and that the latter involves synthetic a priori judgements. In its most general sense formal ontology concerns itself with characterizing the simple 'something'. The sphere of material ontology in this sense are the laws of non-independence (2) which delimit the ontological regions. For the genetic interpretation, material ontology precedes formal ontology; for the descriptive interpretation it is the other way round (1913, art. 10). Here emerges 'the fundamental distinction between formal and material ontology': namely, the distinction between analytic a priori and synthetic a priori (Introduction to Formale und transzendentale Logik, 1929). (shrink)

Metamorphosis seems problematic for our occidental point of view. Becoming in general is viewed as an error or exception by our classic standpoint. In fact, it is strongly against identity and law of non-contradiction: A is fundamentally something different from B and for A it is impossible to be at the same time B. We need to think A as what-becomes-B in order to make metamorphosis possible. Anyway, how can A become B? As a matter of fact, this very claim (...) has been historically the most common critic opposed to becoming. Deleuze and Guattari in their monumental work had tried to offer an enormous contribution to a few related problems. Redefining the subject as an event described by movement and affect can exceed the metamorphosis’ aporia. This new principle of individuation provides a new look upon arisen questions primarily because affects and movements are constant coordinates that define how metamorphosis is experienced. The paper tries to show how the betweenness in action in the encounter with people, human beings, things, animals, plants and minerals defines the logic field of metamorphosis. This is shown in dialogue with the ontological turn in anthropology that is particularly focused on this affective and lively dimension of encounter especially among Amazonian populations. Actually this is also what happens in our – occidental and classical but live – relation with things and objects, as long as we try to think a real conceptualisation of experience. (shrink)

This essay examines Wolff’s science of teleology, which has historically been dismissed as a crude physico-theology resting on a simple confusion between uses and purposes. Focusing especially on his two German volumes (German Teleology, 1723, and German Physiology, 1725), I argue that, first, Wolff never intended teleology to be a self-standing theology; and second, that teleology, as a part of physics, is primarily an applied or practical discipline. In its theological function, teleology presupposes the ontological and cosmological arguments for the (...) being and attributes of God rendered in rational theology. As a part of physics, meanwhile, teleology presupposes the inert-mechanical view of nature which had emerged in the seventeenth century, and builds upon mechanistic physics by providing a perspective on nature as consisting of relations of benefit and advantage. The physiological part of teleology, or the study of plant and animal bodies, occupies a special place, for which Wolff deploys notions of health and sickness consistent with the mechanistic physics he accepts. With this in view, I argue that Wolff’s teleology could not be the proper target of Kant’s critique of physico-theology. Yet, there remain deeper differences between Wolff and Kant on the topic, which have to do with the sources and limits of teleological reasoning in general. (shrink)

Marriages come in a very wide variety: if the reports of anthropologists and historians are to be believed, an extraordinarily wide variety. This includes some of the more unusual forms, including marriage to the dead; to the gods; and even to plants. This does suggest that few proposed marriage relationships would require 'redefining marriage': but on the other hand, it makes giving a general theory of marriage challenging. So one issue we should face is how accepting we should be of (...) the reports: to what extent reported 'marriages' really are marriages. This paper defends the view that almost all of these reported marriages are in fact marriages, and suggests some theoretical approaches that may be generous enough to account for this. (shrink)

1 Introduction1 In the 1980s, hermeneutics was often incorporated into deconstructionism and literary theory. Rather than focus on authorial intentions, the nature of writing itself including codes used to construct meaning, socio-economic contexts and inequalities of power,2 Gadamer introduced a different perspective; the interplay between effects of history on a reader’s understanding and the tradition(s) handed down in writing. This interplay in which a reader’s prejudices are called into question and modified by the text in a fusion of understanding and (...) topic revitalized the study of the printed word. Gadamer’s turn to language for understanding the meaning of Being also appealed to the post-modern antipathy toward modernity and metaphysics.3 If the truth and validity of interpretations are limited to communities of language, then our mode of being in history cannot but be historical. This point of view rendered Gadamer’s phenomenological hermeneutics vulnerable to the critique of moral and epistemological relativism. However, Gadamer’s theory of interpretation also stems from re-examination of the beginning of knowledge in the Pre-Socratics and Plato, and on this basis, is receptive to another dimension of inquiry than that which was trending in North America. -/- At the East-West Center, University of Hawai’i at Manoa in 1982, Chung-ying Cheng for the first time introduced onto-hermeneutics to an audience of esteemed philosophers including Li Zehou, Ren Jiyu, Feng Youlan, and Zhang Liwen.4 In contrast to schools of deconstruction and literary theory that had disengaged the interpreter from trans-historical sources of meaning and truth, Cheng explained that interpreters exist within a cosmological order inextricable from responsibility to harmonize Heaven and Earth in creative acts of interpretation. By integrating Chinese cosmology into hermeneutics through ontology, he tacitly challenged philosophers in the West to re-examine assumptions about humanity’s place in nature and by implication, Gadamer’s recovery of the beginnings of knowledge in Western philosophy. -/- Cheng’s Neo-Confucianism is inspired by the method and goals of Thomé H. Fang. The following words by Fang seem to prefigure, although in an indistinct and bundled way, aspects of Cheng’s philosophy including a Mencian theory of human nature, comprehensive observation, and creativity: “In the very process of living in concord with creative Nature, Man is charged with an ideal to be fully realized in the light of the principle of comprehensive harmony.”5 Like Fang, Cheng reinvigorates Chinese culture and language, but not solely in order to vindicate the insights of Neo-Confucianism. He has studied Western thought, from pragmatism and the analytic school to German idealism and phenomenology, to unlock and clarify philosophical concepts within the Yijing tradition and thereby render them intelligible to Anglophones. The result has been an awakening of Western scholars to the moral and cultural consequences of decoupling their thought from metaphysical foundations that are neither dogmatic nor doctrinal. -/- Not unlike the dialectic of Gadamer’s dialogue form, onto-generative hermeneutics integrates contrary positions on the same topic in order to blend both sides into a world philosophy, or as Cheng says, a “totalizing or integrative theory,”6 not to be confused with a theoretical rewording of a theory. On the contrary, the universal scope and relevance of hermeneutics stems from personal experience. Just as Gadamer, in response to faction and strife, immersed himself in Plato during the war years, and developed a method with which to harmonize opposites, so too, according to On-cho Ng, was Cheng moved by faction, strife and political persecution to develop a path toward unity.7 Gadamer taught at McMaster University in Hamilton, Ontario, and Cheng at the University of Hawai’i at Manoa among other institutions in North America. They facilitated trans-continental educational and cultural ties. Similar experiences yield similar insights irrespective of differences of time and place. Hence, authors in this issue who reside in Europe, China and North America, delineate the differences between Gadamer and Cheng, yet also, in light of Cheng’s onto-generative method and cosmology, develop integrative theories. Due to the page-budget restriction of the publisher, certain articles of this special theme will be subsequently published in the next issue. -/- 2 Integrative Theory This special issue of The Journal of Chinese Philosophy confirms a dimension of hermeneutics that Cheng has both motivated and inspired. The contributors do not abide by the conviction that since thought is mediated by language, interpretations cannot transcend culture. On the contrary, their research exemplifies the fruits of trans-historical onto-dialogical hermeneutics within limits defined by their field inquiry, organized into Parts I and II, around three themes: language, the philosophy of history and ethics. -/- Andrew Fuyarchuk introduces the theme of ontology in relation to Gadamer’s turn to language. Fuyarchuk argues that Chung-ying Cheng’s criticism of Gadamer’s hermeneutics is informed by Heidegger’s concept of Dasein and thereby overlooks how Gadamer’s Platonic-Pythagorean problem of the division between the One and Many is harmonized in the event of language, which in turn positions Gadamer in proximity to the presupposed grounds of receptivity in Cheng’s onto-generative hermeneutics. Lauren Pfister’s contributing article addresses the year 2000 meeting between Cheng and Gadamer in Heidelberg and expands the transhistorical grounds of meaning in Gadamer to matters of theology. Pfister’s summary of the written Chinese record of their conversation indicates that Cheng does not address the role of Christian philosophy and hence, the role of the inner word in Gadamer’s hermeneutics. This is important not only for detecting changes in Cheng’s philosophical development, but also for modifying his hermeneutics along the lines of a living conversation, possibilities explored by Pfister in a sequel to the article submitted to this issue. Nevertheless, by raising the issue of how Gadamer’s turn to language for understanding the meaning of Being extends possibilities in Cheng’s thought, Pfister anticipates the article by Katarina Gajdosova. She returns to the roots of Chinese thought during the Warring States period and broadens the meaning of names in recently excavated texts. Contrary to the conventions about how to understand terms, she appeals to both Heidegger’s ontology and Cheng’s notion of receptivity and creativity to reinterpret naming in relation to cosmology. Along the same lines, insofar as the event of Being is lingual, Jay Goulding captures its emergent structure in an evolving community of scholars and scholarship. He recalls his philosophical journey toward Cheng’s philosophy that begins in conversations with Gadamer at McMaster University in Hamilton, leads to Heidegger and Asian thought, expands into turning points with teachers and colleagues from various backgrounds that by increments contributed to Goulding’s formulation of “Daoist phenomenology.” -/- Although differing traditions guide their inquiries and research, Cheng and Gadamer recall the wisdom of the past to ameliorate the fragmentation in contemporary life. This leads them to re-examine the origins of philosophy; historical roots and thus sources of creative re-interpretations East and West whose affinities are developed in contributions by Hyun Höchsmann and Friederike Assandri. Höchsmann assesses convergences and divergences in the origins of Chinese and Western philosophy (Confucius and Socrates, the Yijing and Pre-Socratics) that culminates in pairing Gadamer’s understanding of paideia in the context of Plato’s political cosmology in the Timaeus with moral and social cultivation in The Western Inscription. She delineates the limits of this comparison which in turn justifies introducing Vattimo’s notion of locality. Assandri’s comparative analysis moves between India and China, Buddhism and Tang Daoism. Based on Gadamer’s argument that writing detaches concepts from their cultural moorings, she defines and applies three levels of understanding in onto-generative hermeneutics to Buddhist terms that were assimilated into the Benji Jing and in so doing clarifies essential dimensions of Daoism. -/- Contributions by Stephen Palmquist and Nicholas Brasovan position Cheng in relation to Kant and Gadamer by way of Aristotle’s ethics respectively. On the one hand, Palmquist plots Cheng’s evolving criticism of Kant’s moral philosophy and draws on crucial dimensions of Gadamer’s hermeneutics to reposition that criticism in a constructive relation to Kant’s emphasis on the philosophical conditions of morality while also indicating how religious dimensions of his thought answer Cheng’s concerns for lived moral action. For Palmquist, Gadamer enables a constructive criticism of Cheng. On the other hand, Brasovan compares Cheng’s Yijing-based account of moral deliberation with Gadamer’s Aristotelian-based ethics and reasons that in contrast to Cheng, Gadamer’s hermeneutical consciousness is disengaged from practical knowledge. For Brasovan, Cheng is a constructive critic of Gadamer. Palmquist and Brasovan’s divergent angles on Gadamer and Cheng map onto a dialectic of contrast and complementarity that constitutes the inner logic of Cheng’s philosophy. In other words, Gadamer and Cheng ought to be read alongside one another for the sake of removing discrepancies and contradictions, which constitutes the organic structure of their thinking. -/- 3 Our Mode of Being in History Is Not Historical The conversations between Cheng and Gadamer in this issue of The Journal of Chinese Philosophy pivot on language, philosophy of history and ethics within a comparative framework of analysis, but also explore the grounds that make the comparisons possible. Those grounds are informed by Chinese cosmology, and function to wrest Gadamer from the shadow of Heideggerian facticity and reposition him within the range of Cheng’s ideas about our place in nature that is embedded in his question about how mind emerges from inorganic matter.8 -/- For Gadamer scholars of Heidegger, human finitude, our ownmost individuating death ensures that hermeneutics is always open to the other as other, always on the way toward understanding the meaning of Being. To arrest the process in a concept of “the Absolute” cannot but represent someone’s point of view, and thereby render hermeneutics indistinguishable from ideology. However, insofar as finitude is defined by them in terms of an onto-theological concept of immorality, finitude is a metaphysical concept consistent with epistemologies and confuse beings with the meaning of Being. As a result, the celebrated political value of hermeneutics to always be on the way toward an understanding of the meaning of Being admits subtle variations on the same worldview that are insufficiently self-critical. -/- Gadamer scholars of Heidegger are right. A transformation in ethos and opening to the meaning of Being depends on awareness of finitude. Yet this awareness does not yield openness to more of the same, i.e., discourse structurally incapable of coming to unity but instead, for both Gadamer and Cheng, openness to a distinctly different ontological dimension of reality. As Sandra Wawrytko and So-Seong Park indicate,9 this ontological dimension is prefigured in the experience of being-as-a-whole or the totality of all possible relations in both Chinese totemic shamanistic rituals,10 and Greek Dionysian festivals.11 Through these religious experiences human ethos and therefore consciousness is expanded and elevated from being centered on one’s ownmost concerns toward an affinity with all sentient beings from insects and plants to animals. The channel for this affinity is an auditory disposition and hence, the emotions, compassion, and feeling response. -/- The capacity for an auditory disposition, or as Gadamer calls it, listening consciousness to respond to the inter-relationality and therefore inherent balance of nature is developed through music, song and dance of the religious rituals and festivals. They facilitate the unity of mind with nature. This use of music, that transforms ordinary consciousness, explains Cheng’s emphasis on the receptivity of feeling response in comprehensive observation, and Gadamer’s emphasis on openness to the other in attunement. However, an auditory disposition characteristic of pre-literate oral cultures that reveals the “All” need not rely on religion. As theorists about the evolution of language have explained,12 modern languages preserve their pre-historical past in music or prosody. That is to say, the song and dance that revealed the totality of inter-related beings to an ethos of comprehensive observation and attunement toward beings in classical civilizations is retained in the back-and-forth movement or rhythm of the dialogue form. Our mode of being in history is a mode of being in nature – through the music of language. -/- While alerting the reader to the limits of a nominalist interpretation, Gadamer expresses the inner law of the nature as follows: “in perishing there is always becoming, and in becoming there is always perishing.”13 Considered in process, opposites generate and blend into each other. This law of nature applies to everything.14 Hence, in a manner comparable to Pfister’s concluding insights, onto-dialogical hermeneutics is not only open to discrete events of otherness but moreover, to the moving structure of reality expressed, as Gajdosova suggests, in the existential moment of naming. Considered as interplay of tension and resolution with a life of its own, the dialectic of a dialogue is self-similar to the way in which an organism grows (by instinct). There is, therefore, a sense in which the art of interpretation extends the human mind into the eternal cycles of nature such that we participate in the articulation of the inner telos/homeostasis toward which all beings strive and importantly for Gadamer scholars of Heidegger, within the material limits of energy to which our embodied minds are self-evidently subject. In mortality there is always immortality. (shrink)

In a very general sense, hybrid can be understood to be any organism that is the product of two (or more) organisms where each parent belongs to a different kind. For example; the offspring from two or more parent organisms, each belonging to a separate species (or genera), is called a “hybrid”. “Hybridity” refers to the phenomenal character of being a hybrid. And “hybridization ” refers to both natural and artificial processes of generating hybrids. These processes include mechanisms of selective (...) cross-breeding and cross-fertilization of parents of different species for the purpose of producing hybrid offspring. In addition to these processes, “hybridization ” also refers to natural and artificial processes of whole genome duplication that result in the doubling or trebling of the sets of chromosomes of the organism. This entry provides an overview of the impact of hybridity on agriculture. It begins with an historical sketch that traces the early horticulturalists’ and naturalists’ investigations of hybrids. This starts with the observations of Thomas Fairchild and Georges-Louis Leclerc, Comte de Buffon; and leads to the explanation of its mechanism by Gregor Mendel, James Watson and Francis Crick, and Ernst Mayr; and the eventual manipulation of hybrids and hybridization by Barbara McClintock. Following this, the reader is introduced to a number of key terms and concepts in use within current research as well as highlighting diverse ethical concerns that center on hybridization. Recent research that attempts to ascertain the role of hybridization in adaptive change will be introduced. This will include research on the evolution of crop species, increased biodiversity, and the use of hybrids to manipulate phenotypically desirable traits in agricultural crops. The focus of the discussion is on a particularly significant type of naturally occurring hybridization, polyploidy hybridization. Polyploids are organisms which have more than two complete genomes in each cell. This kind of hybridization is ubiquitous among crop plants. The role of polyploidy in plant evolution and the affects of polyploidy on plants and animals will be reviewed. A critical discussion of its agricultural value in the production of fertile polyploid hybrids highlights key epistemological, ontological, and ethical issues. These are illuminated with reference to the distinct processes of artificial and natural hybridization. A survey of these different kinds of hybridization includes the ethical and economic impacts of hybridity on global nutrition, the environment, and considerations of some practical implications for the agricultural industry. Tracking the role of hybrids, the process of hybridization, and the current impacts of it for agriculture requires knowledge of the history of its early conceptualization, understanding, and use. This is the topic of the following section. (shrink)

Unlike mainstream Western ethics, African environmental ethics recognizes the interconnectedness and interdependence of all beings than individuality of being. This implies that Africans have often lived in peace and harmony with nature, realizing that the environment is key to life and that everything possesses intrinsic value. It is on the strength of the prevailing observations that this paper is geared toward unraveling African philosophy of environment and in the process argues that Africans indeed do have a philosophy of environment due (...) to their respect and oneness to both the living and nonliving components within the ecosystem. This paper employs the method of exposition, critical analysis as well as argumentation to prove that indeed, Africans have good intentions of taking care of the environment and not abuse it. This is evident in some of their cultural heritage where during some planting seasons, some lands are left fallow for some years to avoid excessive use that leads to erosion, also, many forests and groves are tagged ‘taboo’ to scare away people in order to preserve them as well as the other non-human beings found in the forest. (shrink)

According to F. Adams [this journal, vol. 68, 2018] cognition cannot be realized in plants or bacteria. In his view, plants and bacteria respond to the here-and-now in a hardwired, inflexible manner, and are therefore incapable of cognitive activity. This article takes issue with the pursuit of plant cognition from the perspective of an empirically informed philosophy of plant neurobiology. As we argue, empirical evidence shows, contra Adams, that plant behavior is in many ways analogous to animal (...) behavior. This renders plants suitable to be described as cognitive agents in a non-metaphorical way. Sections two to four review the arguments offered by Adams in light of scientific evidence on plant adaptive behavior, decision-making, anticipation, as well as learning and memory. Section five introduces the ‘phyto-nervous’ system of plants. To conclude, section six resituates the quest for plant cognition into a broader approach in cognitive science, as represented by enactive and ecological schools of thought. Overall, we aim to motivate the idea that plants may be considered genuine cognitive agents. Our hope is to help propel public awareness and discussion of plant intelligence once appropriately stripped of anthropocentric preconceptions of the sort that Adams' position appears to exemplify. (shrink)

All living things have sensory capacities. Plants, in particular, have sensory receptors, transduce the activations of these receptors, and process these outputs in order to manage actions that demand sensory integration. However, there is a kind of sensory function that plants cannot perform. They cannot sense something as other than themselves. Animals, by contrast, perceive. They experience two kinds of "othering impressions"—impressions of entities as located outside and available for interaction, and hence as distinct from the perceiving subject. First, they (...) represent external entities in a "body scheme" that enables sensorimotor interaction with these entities. Second, higher animals such as mammals and birds and possibly fish, represent these entities as located relative to a "cognitive map." These othering impressions are very important because they are the foundation for the human conceptions of the self and other. (shrink)

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the (...) issues are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

This is an article in Thomas J.J. McCloughlin (Ed.) The Nature of Science in Biology: A Resource for Educators. Graphikon Teo, Dublin. -/- Abstract: Philosophers usually tend to think of animals when they think about life, plants often only appear in their works as on the margins, in the background; they are rarely in the centre. However, plant life involves unique processes, including remarkable modes of interaction between plants and their environments. Needless to say, plants are vital parts of (...) ecosystems. Serious attention to plants provides novel and interesting perspectives on many topics in philosophy of biology, including individuality, organisation and disease. Plant biology should have a substantial part in philosophy education. To support this assertion, this paper briefly describes three topics related to plant-environment interaction and explains some of their philosophical implications. These topics are growth, plant hormones and plant-plant microbiota interactions, all of which present crucial aspects related to some prevalent topics in philosophy of biology such as individuality, systems thinking, and holobiont. (shrink)

This chapter develops the idea that the germ-soma split and the suppression of individual fitness differences within the corporate entity are not always essential steps in the evolution of corporate individuals. It illustrates some consequences for multilevel selection theory. It presents evidence that genetic heterogeneity may not always be a barrier to successful functioning as a higher-level individual. This chapter shows that levels-of-selection theorists are wrong to assume that the central problem in transitions is always that of minimizing within-group competition. (...) Evidence of intralevel conflict does not qualify as evidence against the existence of a higher level of selection. (shrink)

Le texte suivant s'appuie assez largement sur des informations scientifiques de la biologie végétale. Ce choix de philosopher à partir de la technicité et de l'historicité des objets botaniques correspond à un parti pris. La proximité de l’humain à ses objets d’étude, sa tendance à anthropomorphiser, voire anthropocentrer, les observations ou les problèmes qui se présentent à lui, a fait l’objet de multiples réflexions philosophiques et épistémologiques. Kant, pour qui « tout intérêt est finalement pratique [...] même celui de la (...) raison spéculative n’est que conditionné et n’est complet que dans l’usage pratique » 1 , Bachelard, qui appelle à « substituer à la notion anthropomorphe de cause la notion scientifique de fonction » 2 , ou Canguilhem pour qui « l’anthropocentrisme est plus aisé à rejeter que l’anthropomorphisme [...] Peut-on être biologistes sans se sentir du côté des vivants ? » 3 . Ces réflexions ne sont-elles pas toujours centrées sur les modes de connaissance ou de pensée de l’humain, alors que les « objets d’étude » en question demeurent souvent dans un certain flou, voire une large indétermination ? La démarche suivie ici tente d’aller dans une autre direction. Elle interroge les effets de l’anthropocentrisation d’objets spécifiques à la biologie végétale, envisagée aussi bien dans sa profondeur historique que dans ses développements techniques récents. Nous tentons ici un pari : une analyse précise de nos connaissances botaniques, actuelles et passées, peut nourrir la réflexion philosophique sur notre rapport aux plantes et, à travers elles, sur nous-mêmes. (shrink)

It has recently been asserted that legislative moves to consider plants as ethical subjects are philosophically foolish because plants lack autonomy. While by no means the sole basis or driving criterion for moral behavior, it is possible to directly challenge skeptical attitudes by constructing a human-plant ethics centered on fundamental notions of autonomy. Autonomous beings are agents who rule themselves, principally for their own purposes. A considerable body of evidence in the plant sciences is increasingly recognizing the capacity (...) of plants to assess, perceive, and act on their environment. The primary purpose of their doing so is to generate the conditions for their own flourishing. With these plant purposes in mind, it is evidentially inappropriate to treat plants purely as instruments. In this age of environmental crisis, knowledge of plant intelligence and autonomy opens up a new debate on respecting and promoting the well-being of the plants that make life on Earth possible. (shrink)

This book assembles recent research on memory and learning in plants. Organisms that share a capability to store information about experiences in the past have an actively generated background resource on which they can compare and evaluate coming experiences in order to react faster or even better. This is an essential tool for all adaptation purposes. Such memory/learning skills can be found from bacteria up to fungi, animals and plants, although until recently it had been mentioned only as capabilities of (...) higher animals. With the rise of epigenetics the context dependent marking of experiences on the genetic level is an essential perspective to understand memory and learning in organisms. -/- Plants are highly sensitive organisms that actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behavior accordingly. -/- The book will guide scientists in further investigations on these skills of plant behavior and on how plants mediate signaling processes between themselves and the environment in memory and learning processes. (shrink)

Do plants represent according to Kant? This is closely connected to the question of whether he held plants are alive, because he explains life in terms of the faculty to act on one’s own representations. He also explains life as having an immaterial principle of self-motion, and as a body’s interaction with a supersensible soul. I argue that because of the way plants move themselves, Kant is committed to their being alive, to their having a supersensible ground of their self-activity, (...) and to their having desires (although these are not conscious). This has important ramifications for Kant’s teleology and philosophy of mind. (shrink)

Electromagnetism is usually understood as a theory describing how charged particles and eletromagnetic fields interact. In this paper I argue that a double ontology comprising both particles and fields is problematic. Either we should think of electromagnetism as a theory about charged particles directly interacting with each other, or as theory of fields whose local interactions are manifested as field quanta, called "particles." From a purely theoretical point of view the choice between a particle and a field interpretation does (...) not matter much when it concerns classical electromagnetism; both interpretations are possible and, as shown by Quine, there is a general method for translating a theory about one kind of objects into a theory assuming another kind of objects, provided these theories are empirically equivalent. From an empiricist point of view, however, the particle interpretation is the choice, since some particles are directly observable. Testable predictions of electromagnetism are predictions of the motion of charged bodies, in theory represented as particles, so this must be the empiricists' choice of ontology. In quantum electrodynamics one is however forced to chose a field ontology, since a particle ontology for this theory is impossible. So called "quantum particles" are field quanta, which cannot be treated as individuals making up a domain of quantification. There is thus a tension regarding ontology between classical and quantum electrodynamics. But this tension is nothing else than the much debated measurement problem of quantum mechanics. (shrink)

A scientific theory is successful, according to Stanford (2000), because it is suficiently observationally similar to its corresponding true theory. The Ptolemaic theory, for example, is successful because it is sufficiently similar to the Copernican theory at the observational level. The suggestion meets the scientific realists' request to explain the success of science without committing to the (approximate) truth of successful scientific theories. I argue that Stanford's proposal has a conceptual flaw. A conceptually sound explanation, I claim, respects the ontological (...) order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate between scientific realists and antirealists. Any philosophers should keep the point in mind when they attempt to give an explanation of a property in their field whatever it may be. (shrink)

One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...) other hand, its unpredictability, non-physicality, and the fact that the stock market trend is largely determined by investors’ beliefs, do make its nature difficult to grasp. -/- This special issue of Rivista di Estetica aims to explore the financial sector from an ontological point of view. While the ontology of money has been extensively studied, few scholars have focused on the stock market and, more generally, on those entities belonging to the investment landscape. Matters are made more complicated by the fact that the financial sector is characterized by an ever-increasing use of digital technology, including software elements that trade in the market themselves. We believe that a careful study of this phenomenon may help us better to understand the role of artificial agents in the social world. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...) the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

The aim of this paper is to summarize a particular approach of doing metaphysics through physics - the primitive ontology approach. The idea is that any fundamental physical theory has a well-defined architecture, to the foundation of which there is the primitive ontology, which represents matter. According to the framework provided by this approach when applied to quantum mechanics, the wave function is not suitable to represent matter. Rather, the wave function has a nomological character, given that its (...) role in the theory is to implement the law of evolution for the primitive ontology. (shrink)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in (...) terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (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)

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)

Chapter 3 of an e-book 'Handbook for Logotherapists' 2024 (Niiles-Mäki Anne). Institute for Purpose-centered Philosophy Finland.

This article examines the ontology and politics of Peter Sloterdijk's Spheres trilogy, focusing in particular upon the notion of microspherical enclosure explicated in the first volume of this series. Noting Sloterdijk's unusual alignment of his philosophy with media theory, three main contentions are put forward. Firstly, that Sloterdijk's reconfiguration of Heidegger's fundamental ontology represents a largely unacknowledged renunciation of the primacy of Being-towards-death in the authentic existence of Dasein, foregrounding instead an originary co-belonging between mother and child. Secondly, (...) that Sloterdijk borrows from media theory a concern regarding the facticity of all communication, grounding philosophical discourse in the determinate locality of its origin, but does so while exalting a pre-natal communicative immediacy that would seem to disparage the everydayness of Dasein. Finally, that Sloterdijk's oft-justified scepticism regarding globalization often retreats into an anti-cosmopolitanism that, in its nostalgia for the comfort, security and immediacy of the matrixial co-belonging, evinces a covert but potentially noxious politics of exclusion. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

We know that animals are harmed in plant production. Unfortunately, though, we know very little about the scale of the problem. This matters for two reasons. First, we can’t decide how many resources to devote to the problem without a better sense of its scope. Second, this information shortage throws a wrench in arguments for veganism, since it’s always possible that a diet that contains animal products is complicit in fewer deaths than a diet that avoids them. In this (...) paper, then, we have two aims: first, we want to collect and analyze all the available information about animal death associated with plant agriculture; second, we try to show just how difficult it’s to come up with a plausible estimate of how many animals are killed by plant agriculture, and not just because of a lack of empirical information. Additionally, we show that there are significant philosophical questions associated with interpreting the available data—questions such that different answers generate dramatically different estimates of the scope of the problem. Finally, we document current trends in plant agriculture that cause little or no collateral harm to animals, trends which suggest that field animal deaths are a historically contingent problem that in future may be reduced or eliminated altogether. (shrink)

Ontological pluralism is the view that there are different fundamental ways of being. Trenton Merricks has recently raised three objections to combining pluralism with a generic way of being enjoyed by absolutely everything there is: first, that the resulting view contradicts the pluralist’s core intuition; second, that it is especially vulnerable to the charge—due to Peter van Inwagen—that it posits a difference in being where there is simply a difference in kind; and, third, that it is in tension with various (...) historically influential motivations for pluralism. I reply to each of these objections in turn. My replies will help to bring out the true nature of the pluralist’s basic commitments. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...) philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

It is argued that the many-worlds interpretation is by far the best interpretation of quantum mechanics. The key points of this view are viewing the wave functions of worlds in three dimensions and understanding probability through self-locating uncertainty.