This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (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)

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

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

In this paper we respond to three objections raised by Joshua Harris to our article, “Against a Postmodern Pentecostal Epistemology,” in which we express misgivings about the conjunction of Pentecostalism with James K. A. Smith’s postmodern, story-based epistemolo- gy. According to Harris, our critique: 1) problematically assumes a correspondence theory of truth, 2) invalidly concludes that “Derrida’s Axiom” conflicts with “Peter’s Axiom,” and 3) fails to consider an alternative account of the universality of Christian truth claims. We argue that (...) Harris’s objections either demonstrate a deficient interpretation of the relevant biblical pas- sages or are not directed at us at all. (shrink)

A review of Gary Smith and Jay Cordes: The Phantom Pattern Problem: The Mirage of Big Data. New York: Oxford University Press, 2020.

In this paper we explore the idea that Pentecostalism is best supported by conjoining it to a postmodern, narrative epistemology in which everything is a text requiring interpretation. On this view, truth doesn’t consist in a set of uninterpreted facts that make the claims of Christianity true; rather, as James K. A. Smith says, truth emerges when there is a “fit” or proportionality between the Christian story and one’s affective and emotional life. We argue that Pentecostals should reject this (...) account of truth, since it leads to either a self-refuting story-relativism or the equally problematic fallacy of story-ism: favoring one’s own story over others without legitimate reason. In either case, we contend, the gospel itself is placed at risk. (shrink)

Metaethical expressivists claim that we can explain what moral words like ‘wrong’ mean without having to know what they are about – but rather by saying what it is to think that something is wrong – namely, to disapprove of it. Given the close connection between expressivists’ theory of the meaning of moral words and our attitudes of approval and disapproval, expressivists have had a hard time shaking the intuitive charge that theirs is an objectionably subjectivist or mind-dependent view of (...) morality. Expressivism, critics have charged over and again, is committed to the view that what is wrong somehow depends on or at least correlates with the attitudes that we have toward it. Arguments to this effect are sometimes subtle, and sometimes rely on fancy machinery, but they all share a common flaw. They all fail to respect the fundamental idea of expressivism: that ‘stealing is wrong’ bears exactly the same relationship to disapproval of stealing as ‘grass is green’ bears to the belief that grass is green. In this paper I rehearse the motivations for the fundamental idea of expressivism and show how the arguments of Frank Jackson and Philip Pettit [1998], Russ Shafer-Landau [2003], Jussi Suikkanen [2009], and Christopher Peacocke [2004] all fail on this same rock. In part 1 I’ll rehearse the motivation for expressivism – a motivation which directly explains why it does not have subjectivist consequences. Then in each of parts 2-5 I’ll illustrate how each of Jackson and Pettit’s, Peacocke’s, Shafer-Landau’s, and Suikkanen’s arguments work, respectively, and why each of them fails to respect the fundamental parity at the heart of expressivism. Though others have tried before me to explain why expressivism is not committed to any kind of subjectivism or mind-dependence – prominently including Blackburn [1973], [1998], Horgan and Timmons [2006], and, in response to Pettit and Jackson, Dreier [2004] and Smith and Stoljar [2003], the explanation offered in this article is distinguished by its scope and generality.. (shrink)

This book is an anthology with the following themes. Non-European Tradition: Bussanich interprets main themes of Hindu ethics, including its roots in ritual sacrifice, its relationship to religious duty, society, individual human well-being, and psychic liberation. To best assess the truth of Hindu ethics, he argues for dialogue with premodern Western thought. Pfister takes up the question of human nature as a case study in Chinese ethics. Is our nature inherently good (as Mengzi argued) or bad (Xunzi’s view)? Pfister ob- (...) serves their underlying agreement, that human beings are capable of becoming good, and makes precise the disagreement: whether we achieve goodness by cultivating autonomous feelings or by accepting external precepts. There are political consequences: whether government should aim to respect and em- power individual choices or to be a controlling authority. Early Greek Thinking: Collobert examines the bases of Homeric ethics in fame, prudence, and shame, and how these guide the deliberations of heroes. She observes how, by depending upon the poet’s words, the hero gains a quasi- immortality, although in truth there is no consolation for each person’s inevi- table death. Plato: Santas examines Socratic Method and ethics in Republic 1. There Socrates examines definitions of justice and tests them by comparison to the arts and sciences. Santas shows the similarities of Socrates’ method to John Rawls’ method of considered judgments in reflective equilibrium. McPherran interprets Plato’s religious dimension as like that of his teacher Socrates. McPherran shows how Plato appropriates, reshapes, and extends the religious conventions of his own time in the service of establishing the new enterprise of philosophy. Ac- cording to Taylor, Socrates believes that humans in general have the task of helping the gods by making their own souls as good as possible, and Socrates’ unique ability to cross-examine imposes on him the special task of helping others to become as good as possible. This conception of Socrates’ mission is Plato’s own, consisting in an extension of the traditional conception of piety as helping the gods. Brickhouse and Smith propose a new understanding of Socratic moral psychology—one that retains the standard view of Socrates as an intellectualist, but also recognizes roles in human agency for appetites and passions. They compare and contrast the Socratic view to the picture of moral psychology we get in other dialogues of Plato. Hardy also proposes a new, non-reductive understanding of Socratic eudaimonism—he argues that Socrates invokes a very rich and complex notion of the “Knowledge of the Good and Bad”, which is associated with the motivating forces of the virtues. Rudebusch defends Socrates’ argument that knowledge can never be impotent in the face of psychic passions. He considers the standard objections: that knowledge cannot weigh incom- mensurable human values, and that brute desire, all by itself, is capable of moving the soul to action. Aristotle: Anagnostopoulos interprets Aristotle on the nature and acquisition of virtue. Though virtue of character, aiming at human happiness, requires a complex awareness of multiple dimensions of one’s experience, it is not properly a cognitive capacity. Thus it requires habituation, not education, according to Aristotle, in order to align the unruly elements of the soul with reason’s knowledge of what promotes happiness. Shields explains Aristotle’s doctrine that goodness is meant in many ways as the doctrine that there are different analyses of goodness for different types of circumstance, just as for being. He finds Aristotle to argue for this conclusion, against Plato’s doctrine of the unity of the Good, by applying the tests for homonymy and as an immediate cons- equence of the doctrine of categories. Shields evaluates the issue as unresolved at present. Russell discusses Aristotle’s account of practical deliberation and its virtue, intelligence (phronesis). He relates the account to contemporary philo- sophical controversies surrounding Aristotle’s view that intelligence is neces- sary for moral virtue, including the objections that in some cases it is unnecessary or even impedes human goodness. Frede examines the advantages and disadvantages of Aristotle’s virtue ethics. She explains the general Greek con- ceptions of happiness and virtue, Aristotle’s conception of phronesis and compares the Aristotle’s ethics with modern accounts. Liske discusses the question of whether the Aristotelian account of virtue entails an ethical-psy- chological determinism. He argues that Aristotle’s understanding of hexis allows for free action and ethical responsibility : By making decisions for good actions we are able to stabilize our character (hexis). Hellenistic and Roman: Annas defends an account of stoic ethics, according to which the three parts of Stoicism—logic, physics, and ethics—are integrated as the parts of an egg, not as the parts of a building. Since by this analogy no one part is a foundation for the rest, pedagogical decisions may govern the choice of numerous, equally valid, presentations of Stoic ethics. Piering interprets the Cynic way of life as a distinctive philosophy. In their ethics, Cynics value neither pleasure nor tradition but personal liberty, which they achieve by self-suffi- ciency and display in speech that is frank to the point of insult. Plotinus and Neoplatonism: Gerson outlines the place of ordinary civic virtue as well as philosophically contemplative excellence in Neoplatonism. In doing so he attempts to show how one and the same good can be both action-guiding in human life and be the absolute simple One that grounds the explanation of everything in the universe. Delcomminette follows Plotinus’s path to the Good as the foundation of free will, first in the freedom of Intellect and then in the “more than freedom” of the One. Plotinus postulates these divinities as not outside but within each self, saving him from the contradiction of an external foundation for a truly free will. General Topics: Halbig discusses the thesis on the unity of virtues. He dis- tinguishes the thesis of the identity of virtues and the thesis of a reciprocity of virtues and argues that the various virtues form a unity (in terms of reciprocity) since virtues cannot bring about any bad action. Detel examines Plato’s and Aristotle’s conceptions of normativity : Plato and Aristotle (i) entertained hybrid theories of normativity by distinguishing functional, semantic and ethical normativity, (ii) located the ultimate source of normativity in standards of a good life, and thus (iii) took semantic normativity to be a derived form of normativity. Detel argues that hybrid theories of normativity are—from a mo- dern point of view—still promising. Ho ̈ffe defends the Ancient conception of an art of living against Modern objections. Whereas many Modern philosophers think that we have to replace Ancient eudaimonism by the idea of moral obligation (Pflicht), Ho ̈ffe argues that Eudaimonism and autonomy-based ethics can be reconciled and integrated into a comprehensive and promising theory of a good life, if we enrich the idea of autonomy by the central elements of Ancient eudaimonism. Some common themes: The topics in Chinese and Hindu ethics are perhaps more familiar to modern western sensibilities than Homeric and even Socratic. Anagnostopoulos, Brickhouse and Smith, Frede, Liske, Rudebusch, and Russell all consider in contrasting ways the role of moral character, apart from intellect, in ethics. Brickhouse / Smith, Hardy, and Rudebusch discuss the Socratic con- ception of moral knowledge. Brickhouse / Smith and Hardy retain the standard view of the so called Socratic Intellectualism. Shields and Gerson both consider the question whether there is a single genus of goodness, or if the term is a homonym. Bussanich, McPherran, Taylor, and Delcomminette all consider the relation between religion and ethics. Pfister, Piering, Delcomminette, and Liske all consider what sort of freedom is appropriate to human well-being. Halbig, Detel, and Ho ̈ffe propose interpretations of main themes of Ancient ethics. (shrink)

În această lucrare analizez posibilitatea călătoriei în timp pe baza mai multor lucrări de specialitate, printre care cele ale lui Nicholas J.J. Smith ("Time Travel", The Stanford Encyclopedia of Philosophy”), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller și Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius și Tim Maudlin ("Time Travel and Modern Physics") și David Lewis (“The Paradoxes of Time Travel”). Lucrarea începe cu o Introducere în care fac o scurtă (...) prezentare a călătoriei în timp, și continuă cu o Istoria conceptului de călătorie în timp, prezentarea principalelor Aspecte fizice ale călătoriei în timp, inclusiv călătoria în timp în trecut în relativitatea generală și în fizica cuantică și călătoria în timp în viitor, apoi o prezentare a Paradoxul bunicului care este abordat în aproape toate lucrările de specialitate, urmat de o secțiune dedicată Filosofiei călătoriei în timp, și o secțiune în care analizez Buclele cauzale pentru călătoria în timp. Finalizez lucrarea cu Concluzii, în care expun opiniile personale privind călătoria în timp, și Bibliografia pe care se bazează lucrarea. (shrink)

About the possibility of time traveling based on several specialized works, including those of Nicholas J. J. Smith ("Time Travel"), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller and Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius and Tim Maudlin ("Time Travel and Modern Physics"), and David Lewis (“The Paradoxes of Time Travel”). The article begins with an Introduction in which I make a short presentation of the time travel, and continues with (...) a History of the concept of time travel, main physical aspects of time travel, including backward time travel in the past in general relativity and quantum physics, and time travel in the future, then a presentation of the Grandfather paradox that is approached in almost all specialized works, followed by a section dedicated to the Philosophy of time travel, and a section in which I analyze Causal loops for time travel. I finish my work with Conclusions, in which I sustain my personal opinions on the time travel, and the Bibliography on which the work is based. -/- ISSN 978-606-033-195-7, DOI: 10.58679/TW82554. (shrink)

In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.

Moral particularism, on some interpretations, is committed to a shapeless thesis: the moral is shapeless with respect to the natural. (Call this version of moral particularism ‘shapeless moral particularism’). In more detail, the shapeless thesis is that the actions a moral concept or predicate can be correctly applied to have no natural commonality (or shape) amongst them. Jackson et al. (Ethical particularism and patterns, Oxford University Press, Oxford, 2000) argue, however, that the shapeless thesis violates the platitude ‘predication supervenes on (...) nature’—predicates or concepts apply because of how things are, and therefore ought to be rejected. I defend shapeless moral particularism by arguing that Jackson et al’s contention is less compelling than it firstly appears. My defense is limited in the sense that it does not prove shapeless moral particularism to be right and it leaves open the possibility that shapeless moral particularism might attract criticisms different from the ones advanced by Jackson et al. But at the very least, I hope to say enough to undermine Jackson et al’s powerful attack against it. The plan of this paper is as follows. Section 1 glosses the view of moral particularism and why it is taken to be essentially committed to the shapeless thesis. Section 2 examines a Wittgensteinian argument for the shapeless thesis. I shall argue that the Canberrans’ counter-arguments against it on grounds of disjunctive commonality and conceptual competence do not succeed. Section 3 explicates Canberrans’ predication supervenience argument against the shapeless thesis. Section 4 offers my criticisms of the Canberrans’ predication supervenience argument. In view of the above discussions, in Sect. 5, I conclude that there is no compelling argument (from the Canberrans) to believe that the shapeless thesis fails (as I have argued in Sect. 4). In fact, there is some good reason for us to believe it (as I have argued in Sect. 2). If so, I contend that moral particularism, when construed as essentially committed to the shapeless thesis, still remains as a live option. (shrink)

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...) approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy. (shrink)

À propos de la possibilité de voyager dans le temps sur la base de plusieurs ouvrages spécialisés, notamment ceux de Nicholas J. J. Smith (« Time Travel »), William Grey (« Troubles with Time Travel »), Ulrich Meyer (« Explaining causal loops »), Simon Keller and Michael Nelson (« Presentists should believe in time-travel »), Frank Arntzenius and Tim Maudlin (« Time Travel and Modern Physics »), et David Lewis (« The Paradoxes of Time Travel »). L'article commence (...) par une Introduction dans laquelle je fais une brève présentation du voyage dans le temps et poursuit par une Histoire du concept de voyage dans le temps, les principaux aspects physiques du voyage dans le temps, y compris les voyages dans le temps dans le passé dans la relativité générale et la physique quantique , et les voyages dans le temps dans le futur, puis une présentation du Paradoxe du grand-père abordé dans presque toutes les œuvres spécialisées, suivie d’une section consacrée à la Philosophie du voyage dans le temps et d’une section dans laquelle j’analyse les Boucles causales pour le voyage dans le temps. Je termine mon travail avec Conclusions, dans laquelle je maintiens mes opinions personnelles sur le voyage dans le temps et la Bibliographie sur laquelle repose le travail. -/- TABLE: -/- Abstract Introducere Istoria conceptului de călătorie în timp Paradoxul bunicului Filosofía călătoriei în timp Buclele cauzale Concluzii Note Bibliografie -/- DOI: 10.13140/RG.2.2.27116.51841. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

This chapter proposed a novel design methodology called Value-Sensitive Design and its potential application to the field of artificial intelligence research and design. It discusses the imperatives in adopting a design philosophy that embeds values into the design of artificial agents at the early stages of AI development. Because of the high risk stakes in the unmitigated design of artificial agents, this chapter proposes that even though VSD may turn out to be a less-than-optimal design methodology, it currently provides a (...) framework that has the potential to embed stakeholder values and incorporate current design methods. The reader should begin to take away the importance of a proactive design approach to intelligent agents. (shrink)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – and (...) this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Encouraging people to consider multiple alternatives appears to be a useful debiasing technique for reducing many biases (explanation, hindsight, and overconfidence), if the generation of alternatives is experienced as easy. The present research tests whether these alternative generation procedures induce a mental simulation mind-set (cf. Galinsky & Moskowitz, 2000), such that debiasing in one domain transfers to debias judgments in unrelated domains. The results indeed demonstrated that easy alternative generation tasks not only debiased judgments in the same domain but also (...) generalized to debias judgments in unrelated domains, provided that participants were low in the need for structure. The alternative generation tasks (even when they were easy to perform) showed no evidence of activating a mental simulation mind-set in individuals high in need for structure, as these individuals displayed no transfer effects. Implications of the results for understanding the role of the need for structure, ease of generation, and mental simulation mind-set activation for debiasing are discussed. (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)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

O livro reúne textos apresentados no II Workshop de Filosofia e Ensino, realizado na UFRGS em 2015, com a temática "Epistemologia e Currículo" -/- .

Durch genomweite Analysen werden vielfältige gesundheitsrelevante Informationen über eine Person gewonnen. Solche Informationen können die Behandlung von Krankheiten verbessern. Sie ermöglichen aber auch Vorhersagen, ob eine Person und deren Verwandte in Zukunft möglicherweise erkranken werden. Der neuartige Charakter des Informationseingriffs und sein prädiktive Potential bedürfen der ethischen, juristischen und ökonomischen Reflexion, damit diese Technologie zum Wohl der Patienten, der Familienangehörigen und der Solidargemeinschaft eingesetzt werden kann. Die vorliegende Schrift leistet mit ihren interdisziplinären, vom BMBF finanzierten Analysen dazu einen Beitrag. Grundlagen (...) für einen ethisch und juristisch verantwortbaren Einsatz der Genomsequenzierung zu medizinischen Zwecken werden erörtert und Eckpunkte für Kostenanalysen sowie Elemente einer “Guten klinischen Praxis” präsentiert. (shrink)

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)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much (...) to demonstrate the continued fertility of the ideas and methods of the Austrian philosophers in our own day. For some time now, historians of philosophy have been gradually coming to terms with the idea that post-Kantian philosophy in the German-speaking world ought properly to be divided into two distinct traditions which we might refer to as the German and Austrian traditions, respectively. The main line of the first consists in a list of personages beginning with Kant, Fichte, Hegel and Schelling and ending with Heidegger, Adorno and Bloch. The main line of the second may be picked out similarly by means of a list beginning with Bolzano, Mach and Meinong, and ending with Wittgenstein, Neurath and Popper. As should be clear, it is the Austrian tradition that has contributed most to the contemporary mainstream of philosophical thinking in the Anglo-Saxon world. For while there are of course German thinkers who have made crucial contributions to the development of exact or analytic philosophy, such thinkers were outsiders when seen from the perspective of native German philosophical culture, and in fact a number of them found their philosophical home precisely in Vienna. When, in contrast, we examine the influence of the Austrian line, we encounter a whole series of familiar and unfamiliar links to the characteristic concerns of more recent philosophy of the analytic sort. As Michael Dummett points out in his Origins of Analytic Philosophy, the newly fashionable habit of referring to analytic philosophy as "Anglo-American" is in this light a "grave historical distortion". If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy "could at least as well be called "Anglo-Austrian" (1988, p. 7). Much valuable scholarly work has been done on the thinking of Husserl and Wittgenstein, Mach and the Vienna Circle. The central axis of Austrian philosophy, however, which as I hope to show in what follows is constituted by the work of Brentano and his school, is still rather poorly understood. Work on Meinong or Twardowski by contemporary philosophers still standardly rests upon simplified and often confused renderings of a few favoured theses taken out of context. Little attention is paid to original sources, and little effort is devoted to establishing what the problems were by which the Austrian philosophers in general were exercised -- in spite of the fact that many of these same problems have once more become important as a result of the contemporary burgeoning of interest on the part of philosophers in problems in the field of cognitive science. (shrink)

This paper discusses the finite version of the two envelope paradox. (That is, we treat the paradox against the background assumption that there is only a finite amount of money in the world.).

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

Some properties are causally relevant for a certain effect, others are not. In this paper we describe a problem for our understanding of this notion and then offer a solution in terms of the notion of a program explanation.

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Definition of the problem The umbrella term “explicability” refers to the reduction of opacity of artificial intelligence (AI) systems. These efforts are challenging for medical AI applications because higher accuracy often comes at the cost of increased opacity. This entails ethical tensions because physicians and patients desire to trace how results are produced without compromising the performance of AI systems. The centrality of explicability within the informed consent process for medical AI systems compels an ethical reflection on the trade-offs. Which (...) levels of explicability are needed to obtain informed consent when utilizing medical AI? Arguments We proceed in five steps: First, we map the terms commonly associated with explicability as described in the ethics and computer science literature, i.e., disclosure, intelligibility, interpretability, and explainability. Second, we conduct a conceptual analysis of the ethical requirements for explicability when it comes to informed consent. Third, we distinguish hurdles for explicability in terms of epistemic and explanatory opacity. Fourth, this then allows to conclude the level of explicability physicians must reach and what patients can expect. In a final step, we show how the identified levels of explicability can technically be met from the perspective of computer science. Throughout our work, we take diagnostic AI systems in radiology as an example. Conclusion We determined four levels of explicability that need to be distinguished for ethically defensible informed consent processes and showed how developers of medical AI can technically meet these requirements. (shrink)

In this paper, I offer an analysis of the radical disagreement over the adequacy of string theory. The prominence of string theory despite its notorious lack of empirical support is sometimes explained as a troubling case of science gone awry, driven largely by sociological mechanisms such as groupthink (e.g. Smolin 2006). Others, such as Dawid (2013), explain the controversy by positing a methodological revolution of sorts, according to which string theorists have quietly turned to nonempirical methods of theory assessment given (...) the technological inability to directly test the theory. The appropriate response, according to Dawid, is to acknowledge this development and widen the canons of acceptable scientific methods. As I’ll argue, however, the current situation in fundamental physics does not require either of these responses. Rather, as I’ll suggest, much of the controversy stems from a failure to properly distinguish the “context of justification” from the “context of pursuit”. Both those who accuse string theorists of betraying the scientific method and those who advocate an enlarged conception of scientific methodology objectionably conflate epistemic justification with judgements of pursuit-worthiness. Once we get clear about this distinction and about the different norms governing the two contexts, the current situation in fundamental physics becomes much less puzzling. After defending this diagnosis of the controversy, I’ll show how the argument patterns that have been posited by Dawid as constituting an emergent methodological revolution in science are better off if reworked as arguments belonging to the context of pursuit. (shrink)

Recent years have witnessed intensive efforts to specify which requirements ethical artificial intelligence (AI) must meet. General guidelines for ethical AI consider a varying number of principles important. A frequent novel element in these guidelines, that we have bundled together under the term explicability, aims to reduce the black-box character of machine learning algorithms. The centrality of this element invites reflection on the conceptual relation between explicability and the four bioethical principles. This is important because the application of general ethical (...) frameworks to clinical decision-making entails conceptual questions: Is explicability a free-standing principle? Is it already covered by the well-established four bioethical principles? Or is it an independent value that needs to be recognized as such in medical practice? We discuss these questions in a conceptual-ethical analysis, which builds upon the findings of an empirical document analysis. On the example of the medical specialty of radiology, we analyze the position of radiological associations on the ethical use of medical AI. We address three questions: Are there references to explicability or a similar concept? What are the reasons for such inclusion? Which ethical concepts are referred to? (shrink)

In this paper, I consider the relationship between Inference to the Best Explanation and Bayesianism, both of which are well-known accounts of the nature of scientific inference. In Sect. 2, I give a brief overview of Bayesianism and IBE. In Sect. 3, I argue that IBE in its most prominently defended forms is difficult to reconcile with Bayesianism because not all of the items that feature on popular lists of “explanatory virtues”—by means of which IBE ranks competing explanations—have confirmational import. (...) Rather, some of the items that feature on these lists are “informational virtues”—properties that do not make a hypothesis \ more probable than some competitor \ given evidence E, but that, roughly-speaking, give that hypothesis greater informative content. In Sect. 4, I consider as a response to my argument a recent version of compatibilism which argues that IBE can provide further normative constraints on the objectively correct probability function. I argue that this response does not succeed, owing to the difficulty of defending with any generality such further normative constraints. Lastly, in Sect. 5, I propose that IBE should be regarded, not as a theory of scientific inference, but rather as a theory of when we ought to “accept” H, where the acceptability of H is fixed by the goals of science and concerns whether H is worthy of commitment as research program. In this way, IBE and Bayesianism, as I will show, can be made compatible, and thus the Bayesian and the proponent of IBE can be friends. (shrink)

The study focused on the persistent poverty status in Nigeria in spite of all the actions and activities directly and indirectly put in place to reduce it. Nigerian poverty statistics and government actions in tackling poverty were examined. Few countries that have succeeded in reducing poverty position were briefly examined. Specifically, we highlighted how Malaysia, China and South Korea aspired and attained high level poverty alleviation. The lessons of their success stories were the basis for recommendations for Nigeria as a (...) panacea for poverty reduction which has persevere in spite of every efforts over the years. Among the recommendations made include designing of poverty line for the entire geopolitical zone, stating target of poverty reduction within a time frame, and sincerely implementing and monitoring of strategies, programmes and policies. Kalu E. Uma | Paul C.Obidike | Frank O. Ozoh "Poverty and it's Alleviation: Lessons for Nigeria" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-4 , June 2017. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)

It is argued, on the basis of ideas derived from Wittgenstein's Tractatus and Husserl's Logical Investigations, that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The (...) paper concludes with a discussion of the relationship between formal logic, formal ontology, and mathematics. (shrink)

In this article, I will provide a critical overview of the form of non-deductive reasoning commonly known as “Inference to the Best Explanation” (IBE). Roughly speaking, according to IBE, we ought to infer the hypothesis that provides the best explanation of our evidence. In section 2, I survey some contemporary formulations of IBE and highlight some of its putative applications. In section 3, I distinguish IBE from C.S. Peirce’s notion of abduction. After underlining some of the essential elements of IBE, (...) the rest of the entry is organized around an examination of various problems that IBE confronts, along with some extant attempts to address these problems. In section 4, I consider the question of when a fact requires an explanation, since presumably IBE applies only in cases where some explanation is called for. In section 5, I consider the difficult question of how we ought to understand IBE in light of the fact that among philosophers, there is significant disagreement about what constitutes an explanation. In section 6, I consider different strategies for justifying the truth-conduciveness of the explanatory virtues, e.g., simplicity, unification, scope, etc., criteria which play an indispensable role in any given application of IBE. In section 7, I survey some of the most recent literature on IBE, much of which consists of investigations of the status of IBE from the standpoint of the Bayesian philosophy of science. (shrink)