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)

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)

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)

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)

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)

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)

I focus on the No-Paradise Dilemma, which results from some initially plausible epistemic ideals, coupled with an assumption concerning our evidence. Our evidence indicates that we are not in an epistemic paradise, in which we do not experience cognitive failures. I opt for a resolution of the dilemma that is based on an evidentialist position that can be motivated independently of the dilemma. According to this position, it is rational for an agent to believe a proposition on the agent’s total (...) evidence just in case the (total) evidence stably supports the proposition. Based on this evidentialist position, I argue that it is not an epistemic ideal in the actual world that we hold rational beliefs that are logically equivalent to our rational beliefs. The dilemma is resolved by giving up this ideal for the actual world and adopting the evidentialist position in terms of stable evidential support. (shrink)

Enjoying great popularity in decision theory, epistemology, and philosophy of science, Bayesianism as understood here is fundamentally concerned with epistemically ideal rationality. It assumes a tight connection between evidential probability and ideally rational credence, and usually interprets evidential probability in terms of such credence. Timothy Williamson challenges Bayesianism by arguing that evidential probabilities cannot be adequately interpreted as the credences of an ideal agent. From this and his assumption that evidential probabilities cannot be interpreted as the actual credences of human (...) agents either, he concludes that no interpretation of evidential probabilities in terms of credence is adequate. I argue to the contrary. My overarching aim is to show on behalf of Bayesians how one can still interpret evidential probabilities in terms of ideally rational credence and how one can maintain a tight connection between evidential probabilities and ideally rational credence even if the former cannot be interpreted in terms of the latter. By achieving this aim I illuminate the limits and prospects of Bayesianism. (shrink)

This book explores the question of whether the ideal right to science and culture exists. It proposes that the human right to science and culture is of a utopian character and argues for the necessity of the existence of such a right by developing a philosophical project situated in postmodernity, based on the assumption of ‘thinking in terms of excendence’. The book offers a new way of thinking about access to knowledge in the postanalogue, postmodern society, and is inspired by (...) twentieth-century critical theorists such as Levinas, Gadamer, Bauman and Habermas. (shrink)

In everyday life and in science we acquire evidence of evidence and based on this new evidence we often change our epistemic states. An assumption underlying such practice is that the following EEE Slogan is correct: 'evidence of evidence is evidence' (Feldman 2007, p. 208). We suggest that evidence of evidence is best understood as higher-order evidence about the epistemic state of agents. In order to model evidence of evidence we introduce a new powerful framework for modelling epistemic states, Dyadic (...) Bayesianism. Based on this framework, we then discuss characterizations of evidence of evidence and argue for one of them. Finally, we show that whether the EEE Slogan holds, depends on the specific kind of evidence of evidence. (shrink)

On an evidentialist position, it is epistemically rational for us to believe propositions that are (stably) supported by our total evidence. We are epistemically permitted to believe such propositions, and perhaps even ought to do so. Epistemic rationality is normative. One popular way to explain the normativity appeals to epistemic teleology. The primary aim of this paper is to argue that appeals to epistemic teleology do not support that we ought to believe what is rational to believe, only that we (...) are permitted to do so. In arguing for that, I defend an epistemic teleological position that is radical in nature. It involves no commitment to aiming at the truth. I conclude by dispelling some worries that have been raised about my position. (shrink)

The Stoic theory of knowledge was founded by Zeno on a perceptual and crudely materialistic base, but subsequently developed into an elaborate theory involving λεκτ which has proved difficult to reconstruct. The evolution of the school, influenced not only by internal differences but also by interaction with the Platonic Academy, certainly contributed to this development. Hence any adequate reconstruction of the Stoic theory of knowledge must take account of the differences among the positions of the different representatives of the school (...) with respect to the criticism put foward by the Academics. I propose here to clarify Zeno's position, showing how Arcesilaus' criticism helped to expose certain lacunae and thus to bring about changes in doctrine on the part both of Zeno himself and of his immediate successors. (shrink)

In the literature, one finds two accounts of the normative status of rational belief: the ought account and the permissibility account. Both accounts have their advantages and shortcomings, making it difficult to favour one over the other. Imagine that there were two principles of rational belief or rational degrees of belief commonly considered plausible, but which, however, yielded a paradox together with one account, but not with the other. One of the accounts therefore requires us to give up one of (...) the plausible principles; whereas the other allows us to save them both. The fact that it allows us to save both of the plausible principles might well be considered a strong reason in favour of the relevant account. The permissibility-account-based resolution of the lottery paradox suggests that the permissibility account is a candidate for being supported in this way, since the account seems to save two plausible principles of rational belief and rational degrees of belief. I argue that even if the permissibility account were supported in this way the support would be defeated, since one cannot provide an analogous resolution of the preface paradox. The principles remain unsaved by the permissibility account. (shrink)

In March 1986, a public symposium took place in Heidelberg about the “unresolved potential dangers of genetic engineering”. The event was organized by institutions affiliated with the environmental movement. Choosing this symposium as an example, the article shows how the public appearance of scientists can be understood as a form of political activism. The article shows how specialists from fields as diverse as biology, chemistry, physics, law and political sciences tried to place political messages by putting themselves in the limelight (...) as independent scientists. I argue that the symposium was both: a place of science communication intertwined with political agitation that, as should be noted, happened in a time when the West German government was working on the legislation of genetic engineering, legitimated by relying on independent expertise. It can be concluded that the discourse of scientific independence became a strategic tool in the controversial debate about the uses and dangers of genetic engineering. Thus, it draws attention to a dimension of political-scientific activity which cannot be fully grasped by the concept of ‘the expert’ that is established in the history of science. (shrink)

This paper is the introduction to the Special Issue “Philosophical Methods”. The Special Issue will be published by Synthese.

Semantyka teoriomonogościowa dla wielowartościowych rachunków pozycyjnych Celem artykułu jest zdefiniowanie adekwatnych semantyk teoriomonogościowych dla rachunków pozycyjnych.

Material artefacts consist of many smaller – and ultimately natural – objects such as molecules and atoms that have been intentionally rearranged in such a way as to take the shape of a particular artefact and fulfil its functions. Whenever the arrangement of several parts results in properties that go beyond the properties of the individual parts or their sum, it can be said that this arrangement has resulted in a new object. Once created, material artefacts may take part in (...) natural processes such as reproduction and evolution and cannot be fundamentally distinguished from fully natural objects. This article provides a number of – mainly biological – examples that show the traditional Aristotelian dichotomy between nature and artefacts to be highly problematic and suggest a continuum instead. Most importantly, it is argued that living beings and artefacts are equally capable – or sometimes incapable – of self-reproduction and that there are numerous objects which are both living beings and artefacts. (shrink)

The aim of the study was to examine the role of self-esteem in resisting the influence of materialistic goals of four social role models in adolescents. Previous studies showed a negative correlation between the psychological health of teens and striving for materialistic goals, one of the main sources is the social modeling of materialism. Two studies were carried out. The first, correlational study, was conducted on target teens and their mothers, fathers, and peers of their choice. It examined if self-esteem (...) is a moderator of the relationship between the materialism of social role models and the materialism of teens. The second, experimental study, was conducted on target teens only. It examined how boosting the self-esteem of teens and activating materialism of social role models may affect the materialism of teens. Study 1 showed a significant interaction effect of self-esteem and the materialism of peers on the materialism of teens. The interaction effects of self-esteem and other role models were not significant. Study 2 showed that elevated self-esteem lowered the influence of the materialism of peers on the materialism of teens. The results were not significant when other role models were analyzed. The results obtained in the presented studies indicate that the self-esteem of teens may have an important role in resisting the influence of materialism role models of peers. Practical implications of the studies for the psychological health of teens are also discussed. (shrink)

Nostalgia is a fond longing for the past that has been shown to increase feelings of meaning, social connectedness, and self-continuity. Although nostalgia for personal memories provides intra- and interpersonal benefits, there may be negative consequences of group-based nostalgia on the perception and acceptance of others. The presented research examined national nostalgia, and its effects on group identification and political attitudes in the United States. In a sample of US voters, tendencies to feel personal and national nostalgia are associated with (...) markedly different emotional and attitudinal profiles. Higher levels of national nostalgia predicted both positive attitudes toward President Trump and racial prejudice, though there was no evidence of such relationships with personal nostalgia. National nostalgia most strongly predicted positive attitudes toward president Trump among those high in racial prejudice. Furthermore, nostalgia's positive relationship with racial prejudice was partially mediated by perceived outgroup threat. Results from this study will help us better understand how the experience of national nostalgia can influence attitudes and motivate political behavior. (shrink)

When members of a group doxastically disagree with each other, decisions in the group are often hard to make. The members are supposed to find an epistemic compromise. How do members of a group reach a rational epistemic compromise on a proposition when they have different (rational) credences in the proposition? I answer the question by suggesting the Fine-Grained Method of Aggregation, which is introduced in Brössel and Eder 2014 and is further developed here. I show how this method faces (...) challenges of the standard method of aggregation, Weighted Straight Averaging, in a successful way. One of the challenges concerns the fact that Weighted Straight Averaging does not respect the evidential states of agents. Another challenge arises because Weighted Straight Averaging does not account for synergetic effects. (shrink)

In his treatise "Elementa harmonica," Aristoxenus of Tarentum formulated a distinctive philosophical framework within the realm of sound exploration, deviating from the harmonics theory advanced by the Pythagoreans. A pivotal disparity lies in the methodological approach to research. Aristoxenus posited meticulous observation of acoustic phenomena as the foundational step in all inquiries, constituting a fundamental criterion for truth. He asserted that perception alone could authenticate the fidelity of the observed state of affairs. Aristoxenus vehemently opposed the Pythagorean disregard for auditory (...) testimony, deeming it a notable methodological lapse. According to him, the harmonikos must serve as a vigilant observer of acoustic phenomena, equipped with a discerning and cultivated musical ear. (shrink)

Bien qu’il tende à interpréter l’ἐποχή comme une position personnelle d’Arcésilas, Thomas Bénatouïl admet cependant que cette interprétation n’est pas pleinement justifiée par nos sources, lesquelles, loin d’être unanimes, font également état d’une interprétation exclusivement dialectique de l’ἐποχή περὶ πάντων. Mais s’il en est ainsi, il est également difficile de soutenir qu’Arcésilas utilise un vocabulaire qui lui est propre pour exposer son point de vue ; en conséquence de quoi le mot ἄδη...