Radical democratic thinking is becoming intrigued by the material situatedness of its political agents and by the role of nonhuman participants in political interaction. At stake here is the displacement of narrow anthropocentrism that currently guides democratic theory and practice, and its repositioning into what we call ‘the nonhuman condition’. This Critical Exchange explores the nonhuman condition. It asks: What are the implications of decentering the human subject via a new materialist reading of radical democracy? Does this reading dilute political (...) agency? Or should this be seen, on the contrary, as an invitation for new voices and demands to enter into democratic assemblages? How might engagement with the more-than-human disrupt or extend theories of radical democracy? Hans Asenbaum and Amanda Machin discuss the human democratic subject both through radical democratic and new materialist lenses. They suggest that a new materialist decentred subject does not lose agency but further gains political responsibility in radical democracy. Jean-Paul Gagnon highlights the possibility of becoming through loss. In losing our anthropocentric arrogance—our understanding of being other and better than animal—we become more connected and discover our place in human-nonhuman assemblages. Melissa Orlie agrees that something can be gained through renouncing dominant human fantasies and presents a ‘radical democratic naturalism’. By renouncing land violence and acknowledging nature’s subjectivity, we can further nonexploitative radical democratic politics. This is where the notion of ‘tidalectic’ processes introduced by James L. Smith is helpful. Focusing on water and the Indigenous knowledges around rivers, he considers how democracy and community can be reimagined as plural, cyclical and attentive to the nonhuman with which the human is inevitably entangled. Diana Leong offers a different approach. Considering the nonhuman from the perspective of Black Studies demands an awareness to how blackness has long been constituted as non- or partially human. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

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

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

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

Many extant theories of placebo focus on their causal structure wherein placebo effects are those that originate from select features of the therapy (e.g., client expectations or “incidental” features like size and shape). Although such accounts can distinguish placebos from standard medical treatments, they cannot distinguish placebos from everyday occurrences, for example, when positive feedback improves our performance on a task. Providing a social-epistemological account of a treatment context can rule out such occurrences, and furthermore reveal a new way to (...) distinguish clinical placebos from standard medical treatments. (shrink)

There can be no doubt that Kant thought we should be reflective: we ought to care to make up our own minds about how things are and what is worth doing. Philosophical objections to the Kantian reflective ideal have centred on concerns about the excessive control that the reflective person is supposed to exert over her own mental life, and Kantians who feel the force of these objections have recently drawn attention to Kant’s conception of moral virtue as it is (...) developed in his later work, chiefly the Metaphysics of Morals. Melissa Merritt’s book is a distinctive contribution to this recent turn to virtue in Kant scholarship. Merritt argues that we need a clearer, and textually more comprehensive, account of what reflection is, in order not only to understand Kant’s account of virtue, but also to appreciate how it effectively rebuts long-standing objections to the Kantian reflective ideal. (shrink)

Noah Rosenberg et al.'s 2002 article “Genetic Structure of Human Populations” reported that multivariate genomic analysis of a large cell line panel yielded reproducible groupings (clusters) suggestive of individuals' geographical origins. The paper has been repeatedly cited as evidence that traditional notions of race have a biological basis, a claim its authors do not make. Critics of this misinterpretation have often suggested that it follows from interpreters' personal biases skewing the reception of an objective piece of scientific writing. I contend, (...) however, that the article itself to some degree facilitates this misrepresentation. I analyze in detail several verbal and visual features of the original article that may predispose aspects of its racial interpretation; and, tracing the arguments of one philosopher and one popular science writer, I show how these features are absorbed, transformed into arguments for a biological basis of race, and re-attributed to the original. The essay demonstrates how even slight ambiguities can enable the misappropriation of scientific writing, unintentionally undermining the authors' stated circumspection on the relationship between cluster and race. (shrink)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

The chapter replies to Paul Guyer’s (2020) account of the debate between Mendelssohn and Kant about whether humankind makes continual moral progress. Mendelssohn maintained that progress can only be the remit of individuals, and that humankind only “continually fluctuates within fixed limits”. Kant dubs Mendelssohn’s position “abderitism” and explicitly rejects it. But Guyer contends that Kant’s own theory of freedom commits him, malgré lui, to abderitism. Guyer’s risky interpretive position is not supported by examination of the relevant texts in their (...) intellectual context. I first identify the historical origins of the term abderitism, which here signifies the independence of individual progress from social conditions. By contrast, Kant argues that individual progress cannot be independent of the progress of the species, acting as a corporate agent. This arresting position, I argue, must be understood in light of the Stoic ethical-teleological presuppositions generally accepted in eighteenth-century German discussion of human progress. (shrink)

I respond to a dilemma for Causal Decision Theory (CDT) under determinism, posed in Adam Elga's paper “Confessions of a Causal Decision Theorist”. The treatment I present highlights (i) the status of laws as predictors, and (ii) the consequences of decision dependence, which arises natively out of Jeffrey Conditioning and CDT's characteristic equation. My argument leverages decision dependence to work around a key assumption of Elga's proof: to wit, that in the two problems he presents, the CDTer must employ subjunctive‐suppositional (...) (rather than evidential) transformations of a shared prior. (shrink)

I propose a unified solution to two puzzles: Ross's puzzle and free choice permission. I begin with a pair of cases from the decision theory literature illustrating the phenomenon of act dependence, where what an agent ought to do depends on what she does. The notion of permissibility distilled from these cases forms the basis for my analysis of 'may' and 'ought'. This framework is then combined with a generalization of the classical semantics for disjunction — equivalent to Boolean disjunction (...) on the diagonal, but with a different two-dimensional character — that explains the puzzling facts in terms of semantic consequence. (shrink)

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

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

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

In the Doctrine of Virtue Kant divides duties of love into three categories: beneficent activity , gratitude and Teilnehmung – commonly referred to as the duty of sympathy . In this paper I will argue that the content and scope of the third duty of love has been underestimated by both critics and defenders of Kant's ethical theory. The account which pervades the secondary literature maintains that the third duty of love includes only two components: an obligation to make use (...) of our natural receptivity to sympathetic feelings as a means to fulfilling other duties of love, and an indirect duty to cultivate these feelings. As a result, Kant's duty of sympathy has been widely regarded as a duty whose value is derived from the way in which it serves other duties, in particular, the duty of beneficent activity, which obliges agents ‘to promote according to one's means the happiness of others in need’ . Teilnehmung has thus assumed something of a second-class status among the duties to others. My aim in this paper is to demonstrate that the prevailing account of Kant's third duty of love is incomplete. (shrink)

The Free Choice effect—whereby \\) seems to entail both \ and \—has traditionally been characterized as a phenomenon affecting the deontic modal ‘may’. This paper presents an extension of the semantic account of free choice defended by Fusco to the agentive modal ‘can’, the ‘can’ which, intuitively, describes an agent’s powers. On this account, free choice is a nonspecific de re phenomenon that—unlike typical cases—affects disjunction. I begin by sketching a model of inexact ability, which grounds a modal approach to (...) agency in a Williamson -style margin of error. A classical propositional semantics combined with this framework can reflect the intuitions highlighted by Kenny ’s dartboard cases, as well as the counterexamples to simple conditional views recently discussed by Mandelkern et al.. In Section 3, I turn to an independently motivated actual-world-sensitive account of disjunction, and show how it extends free choice inferences into an object language for propositional modal logic. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

“Everyone has a price at which he sells himself”: Immanuel Kant quotes this remark in the 1793 _Religion within the Bounds of Reason Alone_, attributing it to “a member of English Parliament”. I argue, however, that the context of the quotation in the _Religion_ alludes to the arresting pedagogical practices of the Stoic philosopher Epictetus, who famously said that “different people sell themselves at different prices” (Discourses 1.2). I argue that there are two sides of Epictetus’s pedagogical strategies: a jolting (...) side meant to expose self-deception and practical inconsistency; and an uplifting side meant to arouse the resources by which it is possible to progress towards virtue — specifically, our sense of kinship with the divine insofar as we are rational. I argue that Kant develops a conception of self-respect in later practical works that plausibly draws on Epictetus, and his distinctive version of the traditional Stoic account of rational agency. (shrink)

I reconsider the relation between love and respect in Kantian ethics, taking as my guide Iris Murdoch's view of love as the fundamental moral attitude and a kind of attention to individuals. It is widely supposed that Kantian ethics disregards individuals, since we don't respect individuals but the universal quality of personhood they instantiate. We need not draw this conclusion if we recognise that Kant and Murdoch share a view about the centrality of love to virtue. We can then see (...) that respect in the virtuous person cannot be blind to the individual, as critics of Kantian ethics contend. My approach contrasts recent efforts to assimilate Kantian respect to Murdochian love, which overlook Murdoch's distinctive claims about the singularity of moral activity. This idea is not as un-Kantian as it seems, and it should inform any Kantian ethics that aims to address the charge about individuals. (shrink)

The chapter examines Kant’s thesis about the ‘radical evil in human nature’ developed in his Religion within the Boundaries of Mere Reason. According to this thesis, the human moral condition is corrupt by default and yet by own deed; and this corruption is the origin (root, radix) of human badness in all its variety, banality, and ubiquity. While Kant clearly takes radical evil to be endemic in human nature, controversy reigns about how to understand this. Some assume this can only (...) be a synthetic a priori claim about the necessity of radical evil (and thus one requiring a transcendental deduction). However, Kant indicates that while radical evil is inevitable it is not, for that, strictly necessary. The best way to understand this is through a teleological approach that explains how we inevitably bring this corruption upon ourselves in the course of our development. The chapter thereby joins other teleological accounts, but distinctively argues that Kant draws on Stoic natural teleology (specifically the doctrine of oikeiōsis), which he knows through Seneca and Cicero. This background allows us to make sense of the structure of Kant’s argument in ways that shed fresh light on the philosophical content of the thesis about radical evil. It also allows us to see that another hotly debated issue — namely, whether radical evil should be understood in ‘psychological’ or ‘social’ terms — is spurious: we see that these are flip sides of one coin, and are better placed to register the broader ethical significance of this result. (shrink)

This paper addresses a little puzzle with a surprisingly long pedigree and a surprisingly large wake: the puzzle of Free Choice Permission. I begin by presenting a popular sketch of a pragmatic solution to the puzzle, due to Kratzer and Shimoyama, which has received a good deal of discussion, endorsement and elaboration in recent work :535–590, 2006; Fox, in: Sauerland and Stateva Presupposition and implicature in compositional semantics, 2007; Geurts, Mind Lang 24:51–79, 2009; von Fintel, Central APA session on Deontic (...) Modals, 2012). I then explain why the general form of the Kratzer and Shimoyama explanation is not extensionally adequate. This leaves us with two possibilities with regard to the original solution-sketch; either the suggested pragmatic route fails, or it succeeds in a particularly strange way: Free Choice permission is rendered a kind pragmatic illusion on the part of both speakers and hearers. Finally, I discuss some ramifications. (shrink)

This chapter argues that Kant’s aesthetic theory of the sublime has particular relevance for his ethics of virtue. Kant contends that our readiness to revel in natural sublimity depends upon a background commitment to moral ends. Further lessons about the emotional register of the sublime allow us to understand how Kant can plausibly contend that the temperament of virtue is both sublime and joyous at the same time.

For Kant, ‘reflection’ is a technical term with a range of senses. I focus here on the senses of reflection that come to light in Kant's account of logic, and then bring the results to bear on the distinction between ‘logical’ and ‘transcendental’ reflection that surfaces in the Amphiboly chapter of the Critique of Pure Reason. Although recent commentary has followed similar cues, I suggest that it labours under a blind spot, as it neglects Kant's distinction between ‘pure’ and ‘applied’ (...) general logic. The foundational text of existing interpretations is a passage in Logik Jäsche that appears to attribute to Kant the view that reflection is a mental operation involved in the generation of concepts from non-conceptual materials. I argue against the received view by attending to Kant's division between ‘pure’ and ‘applied’ general logic, identifying senses of reflection proper to each, and showing that none accords well with the received view. Finally, to take account of Kant's notio.. (shrink)

Disclosure in clinical practice is aimed at promoting patient autonomy, usually culminating in patient choice (e.g., to consent to an operation or not, or between different medications). In medical ethics, there is an implicit background assumption that knowing more about (X) automatically translates to greater, or more genuine, autonomy with respect to one's choices involving (X). I challenge this assumption by arguing that in rare cases, withholding information can promote a patient's autonomy (understood as the capacity for rational choice in (...) alignment with one's values and goals). (shrink)

Two-dimensional semantics, which can represent the distinction between a priority and necessity, has wielded considerable influence in the philosophy of language. In this paper, I axiomatize the dagger operator of Stalnaker’s “Assertion” in the formal context of two-dimensional modal logic. The language contains modalities of actuality, necessity, and a priority, but is also able to represent diagonalization, a conceptually important operation in a variety of contexts, including models of the relative a priori and a posteriori often appealed to Bayesian and (...) Gricean contexts. Finally, I sketch the prospects for extending this two-dimensional upgrade to other kinds of modal logics for natural language. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

The debate between ΛCDM and MOND is often cast in terms of competing gravitational theories. However, recent philosophical discussion suggests that the ΛCDM–MOND debate demonstrates the challenges of multiscale modeling in the context of cosmological scales. I extend this discussion and explore what happens when the debate is thought to be about modeling rather than about theory, offering a model-focused interpretation of the ΛCDM–MOND debate. This analysis shows how a model-focused interpretation of the debate provides a better understanding of challenges (...) asso- ciated with extension to a different scale or domain, which are tied to commitments about explanatory fit. (shrink)

A crucial feature of Kant's critical-period writing on the sublime is its grounding in moral psychology. Whereas in the pre-critical writings, the sublime is viewed as an inherently exhausting state of mind, in the critical-period writings it is presented as one that gains strength the more it is sustained. I account for this in terms of Kantian moral psychology, and explain that, for Kant, sound moral disposition is conceived as a sublime state of mind.

My project is to reconsider the Kantian conception of practical reason. Some Kantians think that practical reasoning must be more active than theoretical reasoning, on the putative grounds that such reasoning need not contend with what is there anyway, independently of its exercise. Behind that claim stands the thesis that practical reason is essentially efficacious. I accept the efficacy principle, but deny that it underwrites this inference about practical reason. My inquiry takes place against the background of recent Kantian metaethical (...) debate — each side of which, I argue, correctly points to issues that need to be jointly accommodated in the Kantian account of practical reason. The constructivist points to the essential efficacy of practical reason, while the realist claims that any genuinely cognitive exercise of practical reason owes allegiance to what is there anyway, independently of its exercise. I argue that a Kantian account of respect for persons (“recognition respect”) suggests how the two claims might be jointly accommodated. The result is an empirical moral realism that is itself neutral on the received Kantian metaethical debate. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...) performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

This forthcoming edited volume is written by expert women in philosophy for younger women and girls ages 16-20. It features a range of ethical, metaphysical, social and political, and other philosophical chapters divided into four main sections. Each chapter features an opening anecdote involving women and/or girls from historical, literary, artistic, scientific, mythic, and other sources to lead into the main topic of the chapter.

Scholars have widely assumed that the aspects of Kant’s virtue theory that nod to ancient ethics must be cashed out with reference to Aristotle. Interpreters then worry that Kant's conception of virtue as a “moral strength of will” (Doctrine of Virtue, 6:405) must be tantamount to Aristotle’s notion of “continence” (enkrateia) — the state of a person who knows the good, and acts accordingly, but must overcome strong countervailing impulses in order to do so. The result plays into caricatures of (...) Kantian ethics as valorising a joyless standard of duty, which these Aristotelian-oriented commentators (rightly) wish to resist. However, the worry is misplaced. I show that Kant is not thinking about Aristotle here, but is instead engaged with a specifically Stoic approach to ethics as a dimension of natural teleology. I draw on this context to show that Kant’s virtue-as-strength idea is not marred in the ways it appears to be when read through an Aristotelian lens. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

Kant’s account of “the radical evil in human nature” in the 1793 Religion within the Bounds of Reason Alone is typically interpreted as a reworking of the Augustinian doctrine of original sin. But Kant doesn’t talk about Augustine explicitly there, and if he is rehabilitating the doctrine of original sin, the result is not obviously Augustinian. Instead Kant talks about Stoic ethics in a pair of passages on either end of his account of radical evil, and leaves other clues that (...) his argument is a reworking of an old Stoic problem. “Radical evil” refers to the idea that our moral condition is — by default and yet by our own deed — bad or corrupt; and that this corruption is the root (radix) of human badness in all its variety, ubiquity, and sheer ordinariness. Kant takes as his premise a version of the Stoic idea that nature gives us “uncorrupted starting points” (Diogenes Laertius 7.89). What sense can be made of the origin of human badness, given such a premise? Kant’s account of radical evil is an answer to this old Stoic problem, which requires a conception of freedom that is not available in his Stoic sources. (shrink)

For Kant, the ideal of enlightenment is most fundamentally expressed as a self-developed soundness of judgment. But what does this mean when the judgment at issue is practical, i.e., concerns the good to be brought about through action? I argue that the moral context places special demands on the ideal of enlightenment. This is revealed through an interpretation of Kant’s prescription for moral pedagogy in the Critique of Practical Reason. The goal of the pedagogy is to cultivate the moral disposition, (...) and the method consists of training in judgment. Unfortunately, Kant seems to wind up somewhere short of this goal, leaving the young person with only an idle wish for a properly cultivated moral disposition. In this paper, I argue that when we address the special issues that arise when the enlightenment ideal is brought to bear on practical judgment — issues that stem from the intrinsic connection between practical judgment and agency — we will see that there is no lacuna in Kant’s account. (shrink)

Why did Kant write the Critique of Judgment, and why did he say that his analysis of the judgment of taste — his technical term for our enjoyment of beauty — is the most important part of it? Kant claims that his analysis of taste “reveals a property of our faculty of cognition that without this analysis would have remained unknown” (KU §8, 5:213). The clue lies in Kant’s view that while taste is an aesthetic, and non-cognitive, mode of judgment, (...) it nevertheless involves the “free play” of cognitive capacities that is pleasurable in some way that ordinary cognitive business is not. My thesis is that the judgment of taste reveals a pleasure that is not usually apparent when we understand something in particular, but which is nevertheless proper to the activity of understanding as such. This matters, I argue, because in this way the judgment of taste points to a standard of cognitive virtue. (shrink)

In an intriguing but neglected passage in the Transcendental Deduction, Kant appears to link the synthetic activity of the understanding in experience with the phenomenon of attention (B156-7n). In this paper, we take up this hint, and draw upon Kant's remarks about attention in the Anthropology to shed light on the vexed question of what, exactly, the understanding's role in experience is for Kant. We argue that reading Kant's claims about synthesis in this light allows us to combine two aspects (...) of Kant's views that many commentators have thought are in tension with one another: on the one hand, Kant's apparent commitment to naïve realism about perception and, on the other, his apparent commitment to the necessity of synthetic activity by the understanding for any kind of cognitive contact with external objects. (shrink)

It is widely assumed that Kant’s moral psychology draws from the dualist tradition of Plato and Aristotle, which takes there to be distinct rational and non-rational parts of the soul. My aim is to challenge the air of obviousness that psychological dualism enjoys in neo-Kantian moral psychology, specifically in regard to Tamar Schapiro’s account of the nature of inclination. I argue that Kant’s own account of inclination instead provides evidence of his commitment to psychological monism, the idea that the mentality (...) of an adult human being is rational through and through. I first consider Schapiro’s “intuitions” in favour of dualism: inclination must have a non-rational source, she contends, because they assail us unbidden and are not immediately responsive to volition, and because we are not responsible simply for having inclinations (only for acting on them). I explain how a monistic account of the nature of inclination can accommodate the first two points, and explain why the third neither is a point a Kantian can accept, nor is its denial the affront to common sense that Schapiro supposes. Then I turn to Schapiro’s aim to conceive of reflection as non-rational and thus independent of justificatory thought, and yet such as to induce rational reflection. I argue that it remains mysterious how inclination, on her account, could be resourced to play this role; and with that criticism in mind, I conclude by making a positive case for Kant’s conceiving of inclination in monistic terms, as an expression of rational mindedness. (shrink)

Alix Cohen argues that the function of feeling in Kantian psychology is to appraise and orient activity. Thus she sees feeling and agency as importantly connected by Kant’s lights. I endorse this broader claim, but argue that feeling, on her account, cannot do the work of orientation that she assigns to it.

It has been insufficiently remarked that Murdoch deems “Kant’s ethical theory” to be “one of the most beautiful and exciting things in the whole of philosophy” in her 1959 essay “The Sublime and the Good”. Murdoch specifically has in mind the connection between Kant’s ethics and his theory of the sublime, which runs via the moral feeling of respect (Achtung). The chapter examines Murdoch’s interest in Kant on this point as a way to tease out the range of issues that (...) complicate Kant’s significance for the development of Murdoch’s distinctive conception of ethics as it is articulated in _The Sovereignty of Good_ and earlier essays. It focuses on her particular concerns about the moral dangers of consolation, and why this led her to propose reworking the Kantian theory of the sublime as a theory of art, and specifically of tragedy. (shrink)

Existing interpretations of Kant’s appeal to the spontaneity of the mind focus almost exclusively on the discussion of pure apperception in the Transcendental Deduction. The risk of such a strategy lies in the considerable degree of abstraction at which the argument of the Deduction is carried out: existing interpretations fail to reconnect adequately with any ground-level perspective on our cognitive lives. This paper works in the opposite direction. Drawing on Kant’s suggestion that the most basic picture we can have of (...) our cognitive capacity already makes reference to its state of excellence, or health (“sound understanding”), I set out by assembling Kant’s normative ground-level view of our cognitive lives, and then search for the fundamental condition of its possibility. This leads me to Kant’s conception of reflection as a normative requirement of judgment. Through examination of Kant’s remarks on reflection, I connect Kant’s preoccupation with the enlightenment ideal of originality (thinking for oneself) with his central appeal to the spontaneity of the mind. (shrink)

This Element considers Kant's account of the sublime in the context of his predecessors both in the Anglophone and German rationalist traditions. Since Kant says with evident endorsement that 'we call sublime that which is absolutely great' and nothing in nature can in fact be absolutely great, Kant concludes that strictly speaking what is sublime can only be the human calling to perfect our rational capacity according to the standard of virtue that is thought through the moral law. The Element (...) takes account of the difference between respect and admiration as the two main varieties of sublime feeling, and concludes by considering the role of Stoicism in Kant's account of the sublime, particularly through the channel of Seneca. (shrink)

I examine the significance of the Stoic theory of pathē for Kant’s moral psychology, arguing against the received view that systematic differences block the possibility of Kant’s drawing anything more than rhetoric from his Stoic sources. More particularly, I take on the chronically underexamined assumption that Kant is committed to a psychological dualism in the tradition of Plato and Aristotle, positing distinct rational and nonrational elements of human mentality. By contrast, Stoics take the mentality of an adult human being to (...) be rational through and through, while recognising that this rationality is not normally in a state of health or excellence. I show how Kant’s account of affections—chiefly the “affects” and “passions” that he identifies as targets of a duty of apathy—draws substantive lessons from his Stoic sources, and how he accepts on his own terms the monistic principles of Stoic moral psychology. (shrink)

Kant’s Prolegomena is a piece of philosophical advertising: it exists to convince the open-minded “future teacher” of metaphysics that the true critical philosophy — i.e., the Critique — provides the only viable solution to the problem of metaphysics (i.e. its failure to make any genuine progress). To be effective, a piece of advertising needs to know its audience. This chapter argues that Kant takes his reader to have some default sympathies for the common-sense challenge to metaphysics originating from Thomas Reid (...) and his followers; this fact in turn explains his rhetorical strategies in the Prolegomena, particularly regarding the presentation of the problem of metaphysics. The chapter draws attention to the importance of Shaftesbury, who, with a nod to Horace, had argued for the deployment of humour to disarm fraudulent claims to epistemic and moral authority. Kant looks to Horace himself to poke fun at the common-sense challenge to metaphysics, and from there to indicate the general shape of the particular argumentative strategies of the Critique — that project that alone, in his view, can promise some kind of future for metaphysics. (shrink)

The idea that virtue can be profitably conceived as a certain sort of skill has a long history. My aim is to examine a neglected episode in this history — one that focuses on the pivotal role that Moses Mendelssohn played in rehabilitating the skill model of virtue for the German rationalist tradition, and Immanuel Kant’s subsequent, yet significantly qualified, endorsement of the idea. Mendelssohn celebrates a certain automatism in the execution of skill, and takes this feature to be instrumental (...) in meeting an objection against perfectionist, agent-based ethics: namely, that a virtuous person would seem to act for the sake of realising his own perfection in everything that he does, thereby taking a morally inappropriate interest in his own character. Kant rejects the automatism featured in Mendelssohn’s account, on grounds that it would make virtue mindless and unreflective. But he does not reject the skill model of virtue wholesale. Rather, he calls for considering how reflection can be embedded in the expression of certain kinds of skill, enabling him to endorse, and arguably adopt, the model on his own terms. (shrink)

How, as Caldwell puts it, does one choose between rival systems all of which claim to rest on a priori foundations? On the nonfallibilistic conception it is difficult to make sense even of the possibility of rival systems of this sort. On the conception here defended, in contrast, the existence of such rival systems can be seen to be a perfectly natural and acceptable consequence of the just-mentioned difficulties we will often fact in coming to know even the intelligible traits (...) of reality: one adjudicates between such systems in the same way in which one adjudicates between all rival scientific hypotheses, namely via a complex mixture of empirical and a priori considerations. (shrink)