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)

This chapter explores the place of remorse in Sophie de Grouchy’s moral theory, as presented in her 1798 work, Letters on Sympathy, which was originally published with her translation of Adam Smith’s Theory of Moral Sentiments. I argue that, for Grouchy, a cultivated sense of remorse weakens our self-conceit by drawing our attention to the ways in which we harm others, even for seemingly justifiable reasons. In so doing, we are led to recognize the equal standing of others, (...) which gives rise to the “sentiment of natural equality.” This “sentiment of natural equality” places a check on our norms and institutions and allows for the potential of moral progress. While Grouchy frames the Letters as a commentary on Smith’s writings, her discussion of remorse, equality, and moral progress shows her to be a bold and original thinker, and one worth taking seriously. (shrink)

William James famously tells us that there are two main goals for rational believers: believing truth and avoiding error. I argues that epistemic consequentialism—in particular its embodiment in epistemic utility theory—seems to be well positioned to explain how epistemic agents might permissibly weight these goals differently and adopt different credences as a result. After all, practical versions of consequentialism render it permissible for agents with different goals to act differently in the same situation. -/- Nevertheless, I argue that epistemic consequentialism (...) doesn’t allow for this kind of permissivism and goes on to argue that this reveals a deep disanalogy between decision theory and the formally similar epistemic utility theory. This raises the question whether epistemic utility theory is a genuinely consequentialist theory at all. (shrink)

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study to (...) highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

This paper introduces and motivates the claim that we possess doxastic agent’s awareness. I argue that this is a form of agentive awareness concerning our belief states that we enjoy in virtue of deliberating and judging. Namely, we experience these activities as those of making up our mind and keeping it made up regarding our beliefs. Following related work in the philosophy of action, I understand this awareness as a form of conscious experience which can then ground our self-ascriptions. As (...) such, this enables me to also propose a new account of self-knowledge of belief and the way in which deliberating and concluding that p can warrant us in self-ascribing the belief that p (i.e., employing the so-called ‘transparency method’). Philosophers often appeal to our arguably agentive relation to our beliefs in explaining this. I, though, I extend work in the philosophy of action in a way that is surprisingly flatfooted way given that belief is a state and not an action. (shrink)

This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...) evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

Do conceivability arguments work against physicalism if properties are causal powers? By considering three different ways of understanding causal powers and the modality associated with them, I will argue that most, if not all, physicalist powers theorists should not be concerned about the conceivability argument because its conclusion that physicalism is false does not hold in their favoured ontology. I also defend specific powers theories against some recent objections to this strategy, arguing that the conception of properties as powerful blocks (...) conceivability arguments unless a rather implausible form of emergence is true. (shrink)

Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, based (...) on the Analytic Hierarchy Process (AHP) method, that aims to avoid overcrowding and outpacing the capacity of a hospital to effectively provide the best care to victims by finding out the most appropriate hospital that meets the victims’ needs. The proposed approach searches for the most appropriate healthcare institution that can effectively deal with the victims’ needs by considering the availability of the needed resources in the hospital, the victim’s wait time to receive the healthcare, and the transfer time that represents the hospital proximity to the disaster site. The evaluation and validation results showed that the assignment of hospitals was done successfully considering the needs of each victim and without overwhelming any single hospital. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (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)

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.

Short piece for The Philosophers' Magazine on why philosophers should pay attention to olfaction.

Philosophical discussion on control has largely centred around control over our actions and beliefs. Yet this overlooks the question of whether we also have control over the reasons for which we act and believe. To date, the overriding assumption appears to be that we do not, and with seemingly good reason. We cannot choose to act for a reason and acting-for-a-reason is not itself something we do. While some have challenged this in the case of reasons for action, these claims (...) seem especially untenable regarding believing for a reason. And extending the scope of control in this way also faces the threat of regress. In the face of this orthodoxy, the present paper argues that we do in fact have control over both believing and acting for a particular reason. It also starts to develop an account of the way in which this would be possible. Given the broad importance of understanding control and agency, this paper bears on a number of topics in epistemology, the philosophy of mind, and ethics. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

White, Christensen, and Feldman have recently endorsed uniqueness, the thesis that given the same total evidence, two rational subjects cannot hold different views. Kelly, Schoenfield, and Meacham argue that White and others have at best only supported the weaker, merely intrapersonal view that, given the total evidence, there are no two views which a single rational agent could take. Here, we give a new argument for uniqueness, an argument with deliberate focus on the interpersonal element of the thesis. Our argument (...) is that the best explanation of the value of promoting rationality is an explanation that entails uniqueness. (shrink)

I talk about the relation between the direct encounters with values that I take to be a key part of ordinary moral phenomenology, and the well-worn topic of demandingness. I suggest that an ethical philosophy based on (inter alia) such encounters sheds interesting light on some familiar problems.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (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 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)

Recent years have seen increased interest among 4E cognition scholars in physical disability, leading to the development of the EE-model of disability. This paper contributes to the literature on disability and 4E cognition in three key ways. First, it examines the relationship between the EE-model and social constructivist views that address the bodily reality of disablement, highlighting commonalities and distinctions. Second, it critiques the EE-model’s focus on individual strategies for expanding disabled persons’ affordance landscapes, arguing that disability policy should integrate (...) insights from both the EE-model and social constructivist approaches. Finally, it assesses the EE-model against the 'dogma of harmony'. We argue that while the EE-model’s focus on active human-environment collaboration is valuable, it can inadvertently perpetuate this dogma. We contend that integrating certain social constructivist insights can help the EE-model avoid the dogma of harmony. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

In this article we explore an argumentative pattern that provides a normative justification for expected utility functions grounded on empirical evidence, showing how it worked in three different episodes of their development. The argument claims that we should prudentially maximize our expected utility since this is the criterion effectively applied by those who are considered wisest in making risky choices (be it gamblers or businessmen). Yet, to justify the adoption of this rule, it should be proven that this is empirically (...) true: i.e. that a given function allows us to predict the choices of that particular class of agents. We show how expected utility functions were introduced and contested in accordance with this pattern in the 18th century and how it recurred in the 1950s when Allais made his case against the neo-Bernoullians. (shrink)

Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...) resolves inconsistent terminologies and promotes semantic interoperability among ERs. In this work, we discuss developing POLARISCO as an extension of Basic Formal Ontology and the Common Core Ontologies. We conclude by presenting a real use-case to check the efficiency and applicability of the proposed ontology. (shrink)

This paper concerns a specific epistemic feature of believing for a reason (e.g., believing that it will rain on the basis of the grey clouds outside). It has commonly been assumed that our access to such facts about ourselves is akin in all relevant respects to our access to why other people hold their beliefs. Further, discussion of self-intimation - that we are necessarily in a position to know when we are in certain conditions - has centred largely around mental (...) states. In contrast to both assumptions, this paper argues that believing for a reason is (at least) very nearly self-intimating: necessarily, if a subject believes that q for the reason that p, then, provided relevant conceptual and rational capacities, she is in a position to form a justified true belief that she believes that q for the reason that p. We should think this on the basis of the role that believing for a reason plays from the subjects’ perspective, and in particular, the way in which it intellegises one’s belief. (shrink)

Metaethics tends to take for granted a bare Democritean world of atoms and the void, and then worry about how the human world that we all know can possibly be related to it or justified in its terms. I draw on Wittgenstein to show how completely upside-down this picture is, and make some moves towards turning it the right way up again. There may be a use for something like the bare-Democritean model in some of the sciences, but the picture (...) has no standing as the basic objective truth about the world; if anything has that standing, it is ordinary life. I conclude with some thoughts about how the notion of bare, “thin” perception of non-evaluative reality feeds a number of philosophical pathologies, such as behaviourism, and show how a “thicker”, more value-laden, understanding of our perceptions of the world can be therapeutic against them. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient (...) exchange of data and information among those involved, which can impede the response process and slow decision making. We, therefore, hypothesize that promoting semantic interoperability across ERO information systems might improve information exchange among stakeholders and thereby allow a more coherent response to the disaster. We propose an ontology‐based messaging service on the basis of the Emergency Data Exchange Language (EDXL) standards. The parties involved will continue to use the terminologies to which they are accustomed, but the system will resolve inconsistencies and thereby enhance mutual understanding among EROs by ensuring semantic translation of the exchanged information. The evaluation of the semantic translation demonstrated the effectiveness and accuracy of the proposed service. (shrink)

On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing a joint (...) intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

Sophie Roux confronte la critique du « sokalisme » qu’on trouve dans La Querelle des imposteurs d’Yves Jeanneret et la manière dont Impostures intellectuelles dessine le partage entre « littéraires » et « scientifiques ».

On sait peu de choses d’Edme Mariotte, membre de l’Académie royale des sciences de 1668 à 1684. Une analyse de son Essai de logique montre cependant que, pour défendre ses pratiques expérimentales, il s’appropria des bribes venues de différentes traditions intellectuelles. Ainsi, ce livre examine ce qu’on entendait par « méthode » à la fin du XVIIe siècle, les épistémologies de la physique qui s’affrontaient alors, quelques débats ouverts par la gestion de l’héritage cartésien. Mais l’essentiel sera peut-être la question (...) suivante : comment reconstituer les idées d’un savant ordinaire, qui n’a ni bouleversé l’ordre des sciences, ni montré une perspicacité épistémologique exceptionnelle ? (shrink)

The History of scepticism from Erasmus to Spinoza is often called upon to support three theses: first, that Descartes had a dogmatic notion of systematic knowledge, and therefore of physics; second, that the hypothetical epistemology of physics which spread during the xviith century was the result of a general sceptical crisis; third, that this epistemology was more successful in England than in France. I reject these three theses: I point first to the tension in Descartes’ works between the ideal of (...) a completely certain science and a physics replete with hypotheses; further, I argue that the use of hypotheses by mechanical philosophers cannot be separated from their conception of physics; finally I show that, at the end of the xviith century, physicists in France as well as in England spoke through hypotheses and I examine different ways of explaining this shared practice. Richard H. Popkin’s book serves therefore as a starting point for insights into the general problem: to what extent and for what reasons some propositions in physics have been presented as hypotheses in the xviith century? (shrink)

Should citizens have equal say regarding the running of society? Following the principles of democracy, and most of political philosophy: yes (at least at a fundamental level, thus allowing for representatives and the like). Indeed, comparing the main alternative seemingly supports this intuition. Epistocracy would instead give power just to the most epistemically competent. Yet testing citizens’ political and economic knowledge looks apt to disproportionately disempower marginalised groups, making the position seem like a nonstarter and democracy the clear winner. Nevertheless, (...) this paper argues against giving citizens equal say, or at least, it offers the strongest possible motivation for this position. In particular, I introduce the progressive case for epistocracy, and what I term standpoint epistocracy. This account refigures the relevant notion of political competence such that it is not the most privileged classes who would most likely constitute our epistocracy, but rather, the least. The resulting picture considerably improves on traditional versions of epistocracy and also democracy. (shrink)

Dans un texte court, dense, poétique et technique à la fois, Martin Buber nous invite à considérer autrement nos compagnes végétales. Cette forme de considération nouvelle peut s’étendre aux autres humains, aux autres vivants. Les êtres humains constituent une espèce vivante qui entretient des relations, de toutes natures, avec quantité d’espèces vivantes, très diverses, plus ou moins visibles ou perceptibles, selon des modalités conscientes ou pas. Les humains se sont entourés d’espèces domestiquées, végétales et animales, avec lesquelles les relations sont (...) anciennes, conscientes et proches. Partis d’un arbre et de sa contemplation, nous sommes invités à une prise de conscience de son existence d’être vivant face à la nôtre, de notre puissance, éventuellement destructive, jusqu’à notre capacité à lui reconnaître sa dignité et à la possibilité d’entrer en relation réciproque avec lui. Dans la continuité de cette démarche, nous nous tournons vers les autres vivants, jusqu’à atteindre une forme d’invisibilité qui n’est ni la réciprocité de la relation ni la conscience de l’arbre mais l’existence des micro-organismes, qui ne nous sont pas accessibles directement, mais qui se révèlent être, également, dans des relations fortes avec les autres vivants. (shrink)

We give an overview of Lakatos’ life, his philosophy of mathematics and science, as well as of this issue. Firstly, we briefly delineate Lakatos’ key contributions to philosophy: his anti-formalist philosophy of mathematics, and his methodology of scientific research programmes in the philosophy of science. Secondly, we outline the themes and structure of the masterclass Lakatos’ Undone Work – The Practical Turn and the Division of Philosophy of Mathematics and Philosophy of Science, which gave rise to this special issue. Lastly, (...) we provide a summary of the contributions to this issue. (shrink)

We debate whether permissivism is true. We start off by assuming an accuracy-oriented framework, and then discuss metaepistemological questions about how our epistemic evaluations promote accuracy.

This collection of papers builds on the idea that the bioeconomy provides a framework for potentially effective solutions addressing the grand global challenges by a turn towards an increased use of biological resources, towards renewability and circularity. Consequently, it cannot be perceived as an end in itself. Thus, innovative endeavors within this bioeconomy framework require a serious examination of their normative premises and implications. From different perspectives, the five contributions to the collection demonstrate that for a bioeconomy that is to (...) contribute to the transformation towards sustainability, inquiries into norms, values, and paradigms of innovators and other stakeholders are indispensable. Originating in the spirit of an interdisciplinary workshop on the "The Normative Dimension of Transformations towards a Sustainable Bioeconomy", the collection at hand provides an attempt to facilitate an increased commitment of social sciences into bioeconomy discourses. We learn: the bioeconomy is on the rise as it is, but whether it will guide us the way towards an equitable, environmentally sound, and future-proof economy, heavily depends on the normative guardrails imposed by science, society, and business. Recent discussions have shown that the pressing problems and complex challenges humanity is currently facing cannot be adequately tackled by approaches that. (shrink)

Four propositions relative to the laws of nature in the classical period must be noted. 1. Certain regularities in phenomena had been discovered. 2. A concept of law had emerged. 3. Classical science is characterized by the introduction of the notion of the legality of nature. 4. New uses of the word «law» had appeared in scientific texts. This article is devoted to the analysis of only this last proposition, that is to say to a terminological problem. First we will (...) describe the semantic uses of the word «law» that may have contributed to the constitution of its classical meaning: its specific usage, disciplinary usage, usage in physics, in mathematics, in metaphysics. Second we will analyze the various moments of the diffusion of the word in the sciences in the xviith century. The general thesis defended in the end is that if the term «law» had indeed been used in science with no reference to a law-giving God prior to the xviith century, only this reference, that is, the coming together of its physical and its metaphysical usage, allowed its generalization in the period between the xviith and xviiith centuries. (shrink)

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

In an influential paper, L. A. Paul argues that one cannot rationally decide whether to have children. In particular, she argues that such a decision is intractable for standard decision theory. Paul's central argument in this paper rests on the claim that becoming a parent is ``epistemically transformative''---prior to becoming a parent, it is impossible to know what being a parent is like. Paul argues that because parenting is epistemically transformative, one cannot estimate the values of the various outcomes of (...) a decision whether to become a parent. In response, we argue that it is possible to estimate the value of epistemically transformative experiences. Therefore, there is no special difficulty involved in deciding whether to undergo epistemically transformative experiences. Insofar as major life decisions do pose a challenge to decision theory, we suggest that this is because they often involve separate, familiar problems. (shrink)

Essay review of Roger Ariew, Descartes and the first Cartesians. Oxford: Oxford University Press 2014. xix + 236 S.

As its Latin title says, this article inquires whether there is a single correct list of the moral virtues. Virtue ethics tells us to “act in accordance with the virtues” but can often be accused, for example in Aristotle's Ethics, of helping itself without argument to an account of what the virtues are. This paper is, stylistically, an affectionate tribute to the Angelic Doctor, and it works with a correspondingly Thomistic background and approach. It argues for the view that there (...) is at least one correct list of the virtues, and that we can itemise at least seven items in the list, namely, the four cardinal and the three theological virtues. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)