We analyse Hutto & Myin's three arguments against computationalism [Hutto, D., E. Myin, A. Peeters, and F. Zahnoun. Forthcoming. “The Cognitive Basis of Computation: Putting Computation In Its Place.” In The Routledge Handbook of the Computational Mind, edited by M. Sprevak, and M. Colombo. London: Routledge.; Hutto, D., and E. Myin. 2012. Radicalizing Enactivism: Basic Minds Without Content. Cambridge, MA: MIT Press; Hutto, D., and E. Myin. 2017. Evolving Enactivism: Basic Minds Meet Content. Cambridge, MA: MIT Press]. The Hard Problem (...) of Content targets computationalism that relies on semantic notion of computation, claiming that it cannot account for the natural origins of content. The Intentionality Problem is targeted against computationalism using non-semantic accounts of computation, arguing that it fails in explaining intentionality. Theion Problem claims that causal interaction between concrete physical processes and abstract computational properties is problematic. We argue that these a... (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

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

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

Theoretical arguments and empirical investigations indicate that a high proportion of published findings do not replicate and are likely false. The current position paper provides a broad perspective on scientific error, which may lead to replication failures. This broad perspective focuses on reform history and on opportunities for future reform. We organize our perspective along four main themes: institutional reform, methodological reform, statistical reform and publishing reform. For each theme, we illustrate potential errors by narrating the story of a fictional (...) researcher during the research cycle. We discuss future opportunities for reform. The resulting agenda provides a resource to usher in an era that is marked by a research culture that is less error-prone and a scientific publication landscape with fewer spurious findings. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

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

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (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)

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)

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

The precarious rights of senior citizens, especially those who are highly educated and who are expected to counsel and guide the younger generations, has stimulated the creation internationally of advocacy associations and opinion leader groups. The strength of these groups, however, varies from country to country. In some countries, they are supported and are the focus of intense interest; in others, they are practically ignored. For this is reason we believe that the creation of a network of all these associations (...) is essential. The proposed network would act as a support for the already-existing policies of the United Nations’ High Commission for Human Rights, of independent experts, and of the Global Alliance for the Rights of Older People. All three have long ago recommended the creation of a recognized instrument for uniting presently scattered efforts. The proposed network, therefore, will seek to promote the international exchange of relevant expertise, and it will reinforce the commitments and actions that single countries are currently taking to meet these objectives. For example, informative public events can be organised to promote particular support initiatives and to provide an opportunity for new members of the network to be presented. The network will promote health for senior citizens, disease prevention, senior mobility, safe free time for seniors, alimentary education, protection against new risks and dangers, as well as equity in the services necessary for seniors to adopt new information and communication technologies. In the case of retired academic members, the network will promote equality with respect to continuing use of digital technologies (particularly email), continuing access to research libraries, and the guaranteed ability for seniors to fund their own research programs and to deliver free seminars. (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)

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)

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...) of its anticipated uses. (shrink)

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

In their article ’Is Pregnancy a Disease? A Normative Approach’, Anna Smajdor and Joona Räsänen contend that, on several of the most prominent accounts of disease, pregnancy should be considered a disease. More specifically, of the five accounts they discuss, each renders pregnancy a disease or suffers serious conceptual problems otherwise. They take issue specifically with the dysfunction account of disease and argue that it suffers several theoretical difficulties. In this response, we focus on defending the dysfunction account against (...) their main objections and show why a version of the dysfunction account is viable on account of the indispensability of normativity in biology and medicine. After disarming their main objections to the dysfunction account, we briefly respond to their treatment of the normality of pregnancy and then draw a distinction between adverse symptoms and underlying causes to show why even though pregnancy may have ’disease-like’ features, it is not a disease. (shrink)

In the paper, I pose the question of how, on artistic, aesthetic, and philosophical levels, decoration and domestic handicrafts as subversive strategies enable the undermining and breakdown of class-based and patriarchal divisions into high and low, objective and subjective, public and private, masculine and feminine. I explore whether handicrafts, in accordance with feminist postulates, are transgressive, transformative, and inclusive. I link handicrafts with the feminist perspective, since, in the second half of the twentieth century, it was precisely the feminist movement (...) that initiated significant changes in the social and cultural perception of women, femininity, and gender relations. Thus I apply this perspective in the first place to the analysis of selected works of contemporary art in which handicrafts is used not only as a means of artistic expression but also as a subversive aesthetic strategy. I also demonstrate how the world of fashion transforms and aesthetizes handicrafts, whose presence in fashion makes it an area in which, in addition to imperatives and aesthetic values, social attitudes, ethical values, and world views are shaped. Finally, referring to the works of selected feminist authors (Mary Field Belenky, Mary Daly, Evelyn Fox-Keller, Donna Haraway), I show how these researchers have metaphorically interpreted handicrafts as specifically feminine ways of creating and developing knowledge. (shrink)

The central aim of this article is to specify the ontological nature of constitutive mechanistic phenomena. After identifying three criteria of adequacy that any plausible approach to constitutive mechanistic phenomena must satisfy, we present four different suggestions, found in the mechanistic literature, of what mechanistic phenomena might be. We argue that none of these suggestions meets the criteria of adequacy. According to our analysis, constitutive mechanistic phenomena are best understood as what we will call ‘object-involving occurrents’. Furthermore, on the basis (...) of this notion, we will clarify what distinguishes constitutive mechanistic explanations from etiological ones. 1 Introduction 2 Criteria of Adequacy 2.1 Descriptive adequacy 2.2 Constitutive–etiological distinction 2.3 Constitution 3 The Ontological Nature of Constitutive Mechanistic Phenomena 3.1 Phenomena as input–output relations 3.2 Phenomena as end states 3.3 Phenomena as dispositions 3.4 Phenomena as behaviours 4 Phenomena as Object-Involving Occurrents 4.1 What object-involving occurrents are and why we need them 4.2 The object in the phenomenon 4.3 The adequacy of option 5 Conclusion. (shrink)

Leuridan (2011) questions whether mechanisms can really replace laws at the heart of our thinking about science. In doing so, he enters a long-standing discussion about the relationship between the mech-anistic structures evident in the theories of contemporary biology and the laws of nature privileged especially in traditional empiricist traditions of the philosophy of science (see e.g. Wimsatt 1974; Bechtel and Abrahamsen 2005; Bogen 2005; Darden 2006; Glennan 1996; MDC 2000; Schaffner 1993; Tabery 2003; Weber 2005). In our view, Leuridan (...) misconstrues this discussion. His weak positive claim that mechanistic sciences appeal to generalizations is true but uninteresting. His stronger claim, that all causal claims require laws, is unsupported by his arguments. Though we proceed by criticizing Leuridan’s arguments, our greater purpose is to embellish his arguments in order to show how thinking about mechanisms enriches and transforms old philosophical debates about laws in biology and provides new insights into how generalizations afford prediction, explanation and control. (shrink)

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

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a biological process that must make a necessary contribution (...) to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism. (shrink)

A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar, we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the (...) account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. In contrast to this, we uphold the mutual independence of logical and ontological complexity, and the authors outline formal principles of truthmaking taking account of both kinds of complexity. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...) archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...) an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in Smith's "Acta cum fundamentis in re". The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception. (shrink)

Mimesis can refer to imitation, emulation, representation, or reenactment - and it is a concept that links together many aspects of ancient Greek Culture. The Western Greek bell-krater on the cover, for example, is painted with a scene from a phlyax play with performers imitating mythical characters drawn from poetry, which also represent collective cultural beliefs and practices. One figure is shown playing a flute, the music from which might imitate nature, or represent deeper truths of the cosmos based upon (...) Pythagorean views (which were widespread in Western Greece at the time). The idea that mimesis should be restricted to ideals was made famous by Plato (whose connections to Pythagoreanism and Siracusa are well-known), and famously challenged by his student Aristotle (not to mention by the mimetic character of Plato’s own poetry). This volume gathers essays not only on the philosophical debate about mimesis, but also on its use in architecture, drama, poetry, history, music, ritual, and visual art. The emphasis is on examples from Hellenic cities in Southern Italy and Sicily, but the insights apply far beyond – even to modern times. Contributors include: Thomas Noble Howe, Francisco J. Gonzalez, Gene Fendt, Guilherme Domingues da Motta, Jeremy DeLong, Carolina Araújo, Marie-Élise Zovko, Lidia Palumbo, Sean Driscoll, Konstantinos Gkaleas, Anna Motta, Jure Zovko, Alexander H. Zistakis, Christos C. Evangeliou, Dorota Tymura, Iris Sulimani, Elliott Domagola, Jonah Radding, Giulia Corrente, Laura Tisi, Ewa Osek, Argyri G. Karanasiou, Rocío Manuela Cuadra Rubio, Jorge Tomás García, Aura Piccioni, and José Miguel Puebla Morón. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Biological individuality is a notoriously thorny topic for biologists and philosophers of biology. In this paper we argue that biological individuality presents multiple, interconnected questions for biologists and philosophers that together form a problem agenda. Using a case study of an interdisciplinary research group in ecology, behavioral and evolutionary biology, we claim that a debate on biological individuality that seeks to account for diverse practices in the biological sciences should be broadened to include and give prominence to questions about uniqueness (...) and temporality. We show that broadening the problem agenda of biological individuality draws attention to underrecognized philosophical issues and discussions and thereby organizes and enriches the existing debate. (shrink)

Philosophy has long either dismissed or paid only minimal attention to creativity, and even with the rise of research on imagination, the creative imagination has largely been ignored as well. The aim of this volume is to correct this neglect. By bringing together existing research in various sub-disciplines, we also aim to open up new avenues of research. The chapters in Part I provide some framing and history on the philosophical study of imagination and creativity, along with an overview of (...) the empirical literature. Part II explores imagination and creativity as they manifest in, and in turn shape, the individual. Part III surveys the role of imagination and creativity across a wide variety of artistic domains, and the chapters of Part IV turn to societal domains. Part V focuses on the interplay of imagination and creativity with regard to particular features of creative subjects and different kinds of creative subjects. *** -/- Part I: Theories and Approaches 1. Theories of Imagination (Peter Kung) 2. Theories of Creativity (Julia Langkau) 3. Historical Treatments of Imagination in the Western Tradition (Lucia Oliveri) 4. Historical Treatments of Creativity in the Western Tradition (Elliot Paul) 5. Non-Western Treatments of Imagination (Reza Hadisi and Jing Iris Hu) 6. Non-Western Treatments of Creativity (Nicolas B. Verger and Vlad Glăveanu) 7. Empirical Treatments of Imagination and Creativity (Dustin Stokes) 8. Experimental Philosophy of Imagination and Creativity (Michael T. Stuart) 9. The Relationship between Imagination and Creativity (Margherita Arcangeli) -/- Part II: Imagination and Creativity in Mind and Action 10. Imagination, Creativity, and Skill (Amy Kind) 11. Imagination, Creativity, and Attention (Bence Nanay) 12. Imagination, Creativity, and Agency (Caterina Moruzzi) 13. Imagination, Creativity, and Emotion (Julien Deonna and Fabrice Teroni) 14. Imagination, Creativity, and Embodiment (Adriana Clavel-Vázquez and María Jimena Clavel Vázquez) 15. Imagination, Creativity, and Gender (Luke Roelofs) 16. Imagination, Creativity, and Race (Nicholas Whittaker) 17. Imagination, Creativity, and Child Development (Thalia Goldstein, Anna Sofia Caruso, Darian Stapleton, and Lamin Fatty) -/- Part III: Imagination and Creativity in the Arts 18. Imagination, Creativity, and the Visual Arts (Claire Anscomb) 19. Imagination, Creativity, and Music (Matteo Ravasio) 20. Imagination, Creativity, and Fiction (Hannah H. Kim) 21. Imagination, Creativity, and Dance (David Davies and Anna Pakes) 22. Imagination, Creativity, and the Culinary Arts (Patrik Engisch) 23. Imagination, Creativity, and Film (Murray Smith) 24. Imagination, Creativity, and Acting (Tzachi Zamir) 25. Imagination, creativity, and fashion (Laura T. Di Summa) -/- Part IV: Imagination and Creativity in Society 26. Imagination and Creativity in the Scientific Realm (Alice Murphy) 27. Imagination and Creativity in the Moral Realm (Tim Mulgan) 28. Imagination and Creativity in the Political Realm (Avshalom Schwartz) 29. Imagination and Creativity in the Law (Maksymilian Del Mar) 30. Imagination and Creativity in the Religious Realm (Neil Van Leeuwen) 31. Imagination and Creativity in Business (Eric Peterson) 32. Imagination and Creativity in Times of Crisis (Jennifer Fraser and Noah Stemeroff) Part V: Emerging Issues in Imagination and Creativity Research 33. Imagination, Creativity, and Aphantasia (Andrea Blomkvist) 34. Imagination, Creativity, and Neurodivergence (Sofia Ortiz-Hinojosa) 35. Imagination, Creativity, and Non-Human Animals (Henry Shevlin) 36. Imagination, Creativity, and Artificial Intelligence (Peter Langland-Hassan) 37. Collective Imagination and Collective Creativity (Nick Wiltsher) . (shrink)

This document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity—Guidance for research performing organisations. The aim of the statement is to complement existing instruments by focusing specifically on institutional responsibilities for strengthening integrity. It takes into account the daily challenges and organisational contexts of most researchers. The statement intends to make research integrity challenges recognisable from the work-floor perspective, providing concrete advice on organisational measures to strengthen integrity. The statement, which was concluded February 7th 2018, provides guidance on (...) the following key issues: § 1.Providing information about research integrity § 2.Providing education, training and mentoring § 3.Strengthening a research integrity culture § 4.Facilitating open dialogue § 5.Wise incentive management § 6.Implementing quality assurance procedures § 7.Improving the work environment and work satisfaction § 8.Increasing transparency of misconduct cases § 9.Opening up research § 10.Implementing safe and effective whistle-blowing channels § 11.Protecting the alleged perpetrators § 12.Establishing a research integrity committee and appointing an ombudsperson § 13.Making explicit the applicable standards for research integrity. (shrink)

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

The Austrian philosopher Christian von Ehrenfels published his essay "On 'Gestalt Qualities'" in 1890. The essay initiated a current of thought which enjoyed a powerful position in the philosophy and psychology of the first half of this century and has more recently enjoyed a minor resurgence of interest in the area of cognitive science, above all in criticisms of the so-called 'strong programme' in artificial intelligence. The theory of Gestalt is of course associated most specifically with psychologists of the Berlin (...) school such as Max Wertheimer, Wolfgang Kohler and Kurt Koffka. We shall see in what follows, however, that an adequate philosophical understanding of the Gestalt idea and of Ehrenfels' achievement will require a close examination not merely of the work of the Berlin school but also of a much wider tradition in Austrian and German philosophy in general. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Say that two goals are normatively coincident just in case one cannot aim for one goal without automatically aiming for the other. While knowledge and justification are distinct epistemic goals, with distinct achievement conditions, this paper begins from the suggestion that they are nevertheless normatively coincident—aiming for knowledge and aiming for justification are one and the same activity. A number of surprising consequences follow from this—both specific consequences about how we can ascribe knowledge and justification in lottery cases and more (...) general consequences about the nature of justification and the relationship between justification and evidential probability. Many of these consequences turn out to be at variance with conventional, prevailing views. (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)

An introduction to our edited volume, The Metaphysics of Relations, covering a range of issues including the problem of order, the ontological status of relations, reasons for ancient scepticism about relational properties, and two ways of drawing the distinction between internal and external relations.

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

Charles Darwin hat eindrucksvoll gezeigt, dass der Mensch ebenso wie alle anderen Lebewesen ein Produkt der biologischen Evolution ist. Die sich an Darwin anschließende Forschung hat außerdem plausibel gemacht, dass sich nicht nur viele der körperlichen Merkmale des Menschen, sondern auch (zumindest einige) seiner Verhaltensdispositionen in adaptiven Selektionsprozessen herausgebildet haben. Die Vorstellung, dass auch die menschliche Moralität evolutionär bedingt ist, scheint daher auf den ersten Blick ganz überzeugend. Schließlich hat die Evolutionstheorie in den vergangenen Jahrzehnten in vielen Bereichen (auch außerhalb (...) der Biologie) ihre weitreichende Bedeutung unter Beweis gestellt. Warum sollte, so könnte man beispielsweise fragen, gerade die Fähigkeit des Menschen, moralische Normen aufzustellen und gemäß ihnen zu handeln, nicht evolutionär erklärt werden können? Und warum sollte eine solche evolutionäre Erklärung der menschlichen Moralität irrelevant für die Rechtfertigung moralischer Normen sein? Warum sollte die Ethik eine Bastion der Philosophen bleiben, für die evolutionsbiologische Forschungsergebnisse über den Menschen und seine nächsten Verwandten keinerlei Relevanz besitzen? (shrink)

What should we do when we won't do as we ought? Suppose it ought to be that the procrastinating professor accept the task of reviewing a book, and actually review the book. It seems clear that given he won't review it, he ought not to accept the task. That is a genuine moral obligation in light of less than perfect circumstances. I want to entertain the possibility that a set of such obligations form something like a 'practical morality'; that which (...) we ought to do given that we're unlikely or unwilling to do much of what ideal morality demands. If it is possible to give a coherent account of these kinds of obligations, then it is possible to entertain the idea that these obligations are in fact what morality demands. The conceptual truths about justice (good, right, fairness) that come from ideals are one thing; the actions that morality demands of people given their actual circumstances are quite another. In this paper I will ask about the kinds of facts that can be used to establish a more circumscribed set of obligations than we get from the orthodox view about moral obligation. (shrink)

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate that the concept of (...) a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology. (shrink)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

A number of logicians and philosophers have turned their attention in recent years to the problem of developing a logic of interrogatives. Their work has thrown a great deal of light on the formal properties of questions and question-sentences and has led also to interesting innovations in our understanding of the structures of performatives in general and, for example, in the theory of presuppositions. When, however, we examine the attempts of logicians such as Belnap or Åqvist to specify what, precisely, (...) a question is, or what it is to ask or raise a question, then what we are offered is somewhat less illuminating. Two alternative reductionist accounts seem in particular to have gained most favor: questions are identified either as special sorts of statements, or as special sorts of requests. As we hope will become clear in what follows, neither of these accounts is even nearly adequate; and matters are not improved if questions are identified, by force majeure, as combinations of statements and requests. (shrink)

Both ‘Sachverhalt’ and ‘state of affairs’ seem to have been derived from the juridical ‘status’ in the sense of 'status rerum' meaning: state or constitution of things. ‘Status’ signifies also in an extended sense ‘the way things stand, the condition or peculiarity of a thing in regard to its circumstances, position, order’. We describe the history of usage of ‘Sachverhalt’ from these beginnings, addressing the role of Goclenius, Lotze, Stumpf, Husserl and Adolf Reinach, whose theory of the relations between judgment (...) and Sachverhalt served as one starting point for the development of Reinach’s theory of speech acts in 1913. (shrink)

This paper uses a partially ordered set of syntactic categories to accommodate optionality and licensing in natural language syntax. A complex but well-studied data set pertaining to the syntax of quantifier scope and negative polarity licensing in Hungarian is used to illustrate the proposal. The presentation is geared towards both linguists and logicians. The paper highlights that the main ideas can be implemented in different grammar formalisms, and discusses in detail an implementation where the partial ordering on categories is given (...) by the derivability relation of a calculus with residuated and Galois-connected unary operators. (shrink)

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