Waiting is a mundane yet inevitable customer experience. Surprisingly, little research has analyzed the effects of waiting on subsequent customer behavior. The current research explores a counterintuitive effect of waiting times on behavior during a shopping trip: Longer waits, compared with shorter waits, can lead to a larger number of purchases despite generating more negative emotional reactions. Results of a field study and three lab experiments demonstrate this effect in the context of waiting for hedonic products. Consistent with a social-inference (...) account, the experiments further show that the effect of waiting duration occurs when wait times are thought to depend on others’ preferences. This article explores the multifaceted effects of waiting duration on purchase behavior of hedonic products and sheds light on the social cognitions that underlie these effects. (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)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

I argue that there is a flaw in the way that response-dependence has been formulated in the literature, and this flawed formulation has been correctly attacked by Mark Johnston’s Missing Explanation Argument (1993, 1998). Moving to a better formulation, which is analogous to the move from behaviourism to functionalism, avoids the Missing Explanation Argument.

Supporters of neutrality as benign neglect argue that a neutral state should not grant any type of recognition to cultural or religious groups. Liberal multiculturalists argue instead that due to the non-neutral nature of public institutions, democratic states must adopt policies that recognize and accommodate the distinctive needs of ethnocultural groups. This article examines a different way of conceiving the principle of neutrality. In this conception, developed by Alan Patten in the framework of liberal multiculturalism, a state can only (...) be neutral when it extends equivalent levels of assistance/hindrance to rival conceptions of the good. Neutrality is thus reinterpreted to become a principle justifying the religious exemptions. The article highlights some aspects of this theory that should be reconsidered.// -/- Les défenseurs de la neutralité bienveillante soutiennent qu’un État neutre ne doit accorder aucun type de reconnaissance aux groupes culturels ou religieux. Les multiculturalistes libéraux avancent pour leur part que, en raison de la nature non neutre des institutions publiques, les États démocratiques doivent adopter des politiques vi-sant la reconnaissance et l’accommodement des besoins distinctifs des groupes ethnoculturels. Cet article examine une manière diffé-rente de concevoir le principe de neutralité. Dans cette conception, développée par Alan Patten dans le cadre du multiculturalisme libé-ral, un État ne peut être neutre que s’il assiste ou entrave de manière équivalente les différentes conceptions du bien. La neutralité est ainsi réinterprétée pour devenir un principe permettant de justifier les exemptions religieuses. L’article souligne certains aspects de cette théorie qui méritent d’être repensés. (shrink)

Humans think and communicate in very flexible and schematic ways, and a Spatial Data Infrastructure (SDI) for the Amazon and associated information system ontologies should reflect this flexibility and the adaptive nature of human cognition in order to achieve semantic interoperability. In this paper I offer a conceptual investigation of SDI and explore the nature of cultural schemas as expressions of indigenous ontologies and the challenges of semantic interoperability across cultures. Cultural schemas are, in essence, our ontologies, but they are (...) markedly different than classical formal ontologies. They shape our ontological commitments to what exists in the world as well as the ways in which we approach and engage the world. And while they help structure our understanding of the world in which we are embedded, they are associative and flexible. They help to focus our attention to particular details of our experiences and give them salience, yet they cannot be simply reduced to a series of extracted features. They allow us to make meaning of the contextualized, cultural experience in which we are always immersed. An SDI is a shared social-technological-informational structure that, if it is to be useful and successful for sustainability in the Amazon, must incorporate and use indigenous cultural schemas. Indigenous communities must have the ability to contribute to the collection of geospatial data and their contributions recognized as legitimate forms of knowledge. In order for the SDI to work, it must recognize the larger cultural landscape to which cultural schemas can connect to the ready-to-hand elements of salient cultural experiences. (shrink)

Ontologies are being used by information scientists in order to facilitate the sharing of meaningful information. However, computational ontologies are problematic in that they often decontextualize information. The semantic content of information is dependent upon the context in which it exists and the experience through which it emerges. For true semantic interoperability to occur among diverse information systems, within or across domains, information must remain contextualized. In order to bring more context to computational ontologies, we introduce culture as an essential (...) concept for information science. Culture helps to focus our attention on and make meaning of relevant extrapersonal structures and their qualities and dimensions that comprise the context and background of the world. In our approach, culture is integral to the study of semantics and, consequently, the study of ontologies and information technologies. The meaning we make of entities and phenomena in the world is always shaped by our cultural experience. If we understand culture as the emergent interplay of intrapersonal cognitive structures and extrapersonal structures of the world, then the notion of cognitive and cultural schemas becomes essential to understanding ontology and the ways in which we might achieve authentic semantic interoperability among diverse information systems. We explore the nature of ontologies and reconceptualize them as cultural schemas. Our proposal is an alternative to the historical path from philosophical ontology to computational ontologies as one that adheres primarily to the notion of ontology as a categorization and classification system. The obvious implication for ontology as categorization is that there is a single objective world that exists and that it can be described as entirely separate from the person observing it. We draw upon Heidegger’s examination of ontology to ground ontology in a phenomenological perspective, enabling it to remain flexible and adaptable and to accommodate context. (shrink)

Upon what philosophical foundation are semantic network graphs based? Does this foundation allow for the legitimization of other semantic networks and ontological diversity? How can we design our computational and informational systems to accommodate this ontological diversity and the variety of semantic networks? Are semantic networks segmentations of larger semantic landscapes? This paper explores semantic networks from a Heideggerian existentialist and phenomenological perspective. The analysis presented uses cultural schema theory to bridge the syntactic and lexical elements to the semantic and (...) conceptual dimensions of semantic network graphs and offers reasons why the viability of such graphs as they are currently constructed are insufficient for creating semantic interoperability for our informationtechnologies. Reconceptualizing semantic networks as cultural landscapes offers us. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

While the image of the slave as the antithesis of the freeman is central to republican freedom, it is striking to note that slaves themselves have not contributed to how this condition is understood. The result is a one-sided conception of both freedom and slavery, which leaves republicanism unable to provide an equal and robust protection for historically outcast people. I draw on the work of Frederick Douglass – long overlooked as a significant contributor to republican theory – to show (...) one way why this is so. Focusing the American Revolution, the subsequent republican government established new political institutions to maintain the collective interests of the whole population. The political revolution was held in place by processes of public reason that reflected the values and ideas of the people that had rebelled. The black population, however, had not been part of this revolution. After emancipation, black Americans were required to accept terms of citizenship that had already been defined, leaving them socially dominated, subject to the prejudices and biases within the prevailing ideas of public discourse. Douglass argued that republican freedom under law is always dependent on a more fundamental revolution, that he calls a ‘radical revolution in thought’, in which the entire system of social norms and practices are reworked together by members of all constituent social groups – women and men, black and white, rich and poor – so that it reflects a genuinely collaborative achievement. Only then can we begin the republican project of contestatory freedom as independence or non-domination that today’s republicans take for granted. (shrink)

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: (...) this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper. (shrink)

Although they were never to meet and corresponded only briefly, Catharine Macaulay and Mary Wollstonecraft shared a mutual admiration and a strong intellectual bond. Macaulay’s work had a profound and lasting effect on Wollstonecraft, and she developed and expanded on many of Macaulay’s ideas. While she often took these in a different direction, there remains a great synergy between their ideas to the extent that we can understand Wollstonecraft’s own feminist arguments by approaching them through the frameworks and ideas that (...) Macaulay provided. These included the principles of classical republicanism, particularly in its understanding of the values of freedom, equality and virtue, and an understanding of reason as grounded in immutable principles that apply equally to both sexes. On the question of women’s freedom and social equality with men, I argue that though Macaulay sets up the problem in far richer and more detailed philosophical terms, in the end it is Wollstonecraft that has the more compelling account of its far-reaching social implications and of how this might be addressed. (shrink)

There is a standard story told about the rise and fall of ordinary language philosophy: it was a widespread, if not dominant, approach to philosophy in Great Britain in the aftermath of World War II up until the early 1960s, but with the development of systematic approaches to the study of language—formal semantic theories on one hand and Gricean pragmatics on the other—ordinary language philosophy more or less disappeared. In this paper we present quantitative evidence to evaluate the standard story (...) of the rise and fall of ordinary language philosophy, building on the topic model of over 30,000 philosophy articles in Weatherson (2022). Using a combination of qualitative judgment and a topic-model-based measurement of similarity between individual articles, we find evidence that supports the first part of the standard story, according to which ordinary language philosophy arises in the 1940s, peaks between the early 1950s and the late 1960s, and then rapidly declines. But we argue that there is also evidence of a "new wave" of ordinary language philosophy in the early 21st century that defies the second part of the standard story. (shrink)

In spite of its everyday connotations, the term independence as republicans understand it is not a celebration of individualism or self-reliance but embodies an acknowledgement of the importance of personal and social relationships in people’s lives. It reflects our connectedness rather than separateness and is in this regard a relational ideal. Properly understood, independence is a useful concept in addressing a fundamental problem in social philosophy that has preoccupied theorists of relational autonomy, namely how to reconcile the idea of individual (...) human agency with the inevitable and necessary influence of other people, both directly and indirectly. I derive my account from the work of Mary Wollstonecraft and Catharine Macaulay, whose contributions have remained largely overlooked by current republican theorists. I have three purposes in this chapter. First, I set out the relational character of independence. Secondly, I outline a republican approach to the problem of structural social threats to agency. Finally, I hope to establish the basis for a fruitful dialogue between republicans and relational autonomy theorists on the requirements and dynamics of individual agency and freedom in oppressive social situations. I identify three distinctive features of the internal logic of freedom as independence that give it a relational character: it always locates the person within a community; there is a mediating role played by the notion of arbitrariness in connecting individual and collective perspectives; a causal relationship exists linking each person’s freedom as independence such that that the dependence of one class of persons jeopardizes the independence of the whole community. (shrink)

Catharine Macaulay was one of the most significant republican writers of her generation. Although there has been a revival of interest in Macaulay amongst feminists and intellectual historians, neo-republican writers have yet to examine the theoretical content of her work in any depth. Since she anticipates and addresses a number of themes that still preoccupy republicans, this neglect represents a serious loss to the discipline. I examine Macaulay’s conception of freedom, showing how she uses the often misunderstood notion of virtue (...) to reconcile the individual and collective elements inherent in the republican model. In her own analysis of the deep-rooted social obstacles that stand in the way of women becoming free, Macaulay identifies a serious problem that confronts all republicans, namely how to secure freedom in the face of entrenched structural imbalances that systematically disadvantage certain classes of person. In the end, I conclude that Macaulay herself cannot overcome the issues she raises. This in no way diminishes the importance of her work since her diagnosis is as relevant today as in her own time. (shrink)

Williams, Elster and Pears hold that an effort to induce in oneself a belief in the truth of some proposition that one believes to be false can succeed only if one manages, somewhere along the way, to forget that one is engaged in such an effort. Although this view has strong intuitive appeal, it is false, and in this paper it is shown to be false by example.

In recent years, bioethical discourse around the topic of ‘genetic enhancement’ has become increasingly politicized. We fear there is too much focus on the semantic question of whether we should call particular practices and emerging bio-technologies such as CRISPR ‘eugenics’, rather than the more important question of how we should view them from the perspective of ethics and policy. Here, we address the question of whether ‘eugenics’ can be defended and how proponents and critics of enhancement should engage with each (...) other. (shrink)

The papers in the following volume are the outcome of a three-year long interdisciplinary research project. The project began with an in-person meeting hosted and funded by the Daimler und Benz Stiftung in Germany in March 2020 (the world was shutting down one nation at a time as we met). During the pandemic we continued to meet monthly online with support from Memorial University of Newfoundland. From the beginning it was the goal of the Working Group on Intelligence (WGI), as (...) we called ourselves, to broaden and deepen the AI debate with a more nuanced understanding of intelligence than is common in cognitive and computer science discussions of AI. We wished to draw on the history of philosophy, ecology, and the philosophy of mind to establish that intelligence is meant in many senses, to use an Aristotelian expression. The clarification of these various meanings is essential to the discussion around the ethics of AI, especially the question concerning the possibility of strong AI or Artificial General Intelligence. (shrink)

Allocation of very scarce medical interventions such as organs and vaccines is a persistent ethical challenge. We evaluate eight simple allocation principles that can be classified into four categories: treating people equally, favouring the worst-off, maximising total benefits, and promoting and rewarding social usefulness. No single principle is sufficient to incorporate all morally relevant considerations and therefore individual principles must be combined into multiprinciple allocation systems. We evaluate three systems: the United Network for Organ Sharing points systems, quality-adjusted life-years, and (...) disability-adjusted life-years. We recommend an alternative system—the complete lives system—which prioritises younger people who have not yet lived a complete life, and also incorporates prognosis, save the most lives, lottery, and instrumental value principles. (shrink)

According to Colerus, Spinoza replied affirmatively when his landlady asked if she "...could be saved in her faith." This paper asks what Spinoza could have meant -- and what his landlady would have thought he meant. She was asking about salvation of a certain kind -- a kind that Spinoza did not in fact believe to be possible. When he talks about salvation in his writings, he has in mind a different kind of salvation -- one that his landlady will (...) certainly not achieve "in her faith." So, when he assured her that she could be saved in her faith was he simply lying to her? This question is explored against the background of the controversies regarding Spinoza's sincerity in the Tractatus Theologico-politicus. (shrink)

In this paper we compare the propositional logic of Frege’s Grundgesetze der Arithmetik to modern propositional systems, and show that Frege does not have a separable propositional logic, definable in terms of primitives of Grundgesetze, that corresponds to modern formulations of the logic of “not”, “and”, “or”, and “if…then…”. Along the way we prove a number of novel results about the system of propositional logic found in Grundgesetze, and the broader system obtained by including identity. In particular, we show that (...) the propositional connectives that are definable in terms of Frege’s horizontal, negation, and conditional are exactly the connectives that fuse with the horizontal, and we show that the logical operators that are definable in terms of the horizontal, negation, the conditional, and identity are exactly the operators that are invariant with respect to permutations on the domain that leave the truth-values fixed. We conclude with some general observations regarding how Frege understood his logic, and how this understanding differs from modern views. (shrink)

"No, your honor. I didn't know who or what he was when I first came across the book -- they don't exactly love him in the synagogue, if you've read the story of his life. I found it in a junkyard in a nearby town, paid a kopek, and left cursing myself for wasting money hard to come by. Later I read through a few pages and kept on going as though there were a whirlwind at my back. As I (...) say, I didn't understand every word but when you're dealing with such ideas you feel as though you were taking a witch's ride. After that I wasn't the same man. That's in a manner of speaking, of course, because I've changed little since my youth.". The speaker is Yakov Bok, the unlikely hero of Bernard Malamud's The Fixer. At this point, early in the novel, Yakov speaks truthfully when he says that he has changed little since his youth. But over the next two and a half years (the time-period covered in the novel), he will undergo profound change and impressive moral growth. He suffers; he learns; he grows. Spinoza's name and ideas appear again and again at crucial moments in the course of the hero's moral development. Yakov Bok's verbal account of Spinoza's ideas is often comically primitive, but his understanding far outstrips his ability to articulate. By the end of the novel, his sufferings have led him to a deep grasp of certain of Spinoza's ethical and political doctrines. (shrink)

This paper examines narrativism’s claim that the historical past cannot be known once and for all because it must be continuously re-described from the standpoint of the present. We argue that this claim is based on a non sequitur. We take narrativism’s claim that the past must be re-described continuously from the perspective of the present to be the result of the following train of thought: 1) “all knowledge is conceptually mediated”; 2) “the conceptual framework through which knowledge of reality (...) is mediated changes with every new generation of historians”; therefore (narrativism’s claim) “the historical past changes with every new generation of historians”. The idea of an unchanging past, for the narrativist, requires denying premise 1 (all knowledge is conceptually mediated”) and therefore rests on a problematic commitment to the chimerical notion of the past as it is in-itself, wie es eigentlich gewesen. We argue that the narrativist’s conclusion does not follow unless one adds a further premise, namely 3) “it is not possible to view reality through the categorial framework of historical agents”. If one asserts the possibility of grasping reality through the categorial framework of others, be they contemporary or past agents (as much philosophy of history written in an idealist key does), then one no longer has to accept the narrativist’s inference that since the past cannot be known in-itself or independently of conceptual mediation, then it cannot be known as it always was for the historical agents. Narrativism’s inference that the past cannot be known as it always was does not follow from premises 1 and 2 unless one smuggles in another problematic premise, premise 3. In this paper we defend the claim that the past can be known as it always was (not as it is in-itself) by invoking a different conception of the role of conceptual mediation in historical knowledge, one which assumes the possibility of viewing reality through the categorial framework of others. This notion of the role of conceptual mediation in historical knowledge is prevalent in the idealist tradition but, in the interest of brevity, we will defend this notion of mediacy by specific reference to the idealist philosophy of R.G. Collingwood. (shrink)

Review of Daniel Cook, Hartmut Rudolph, and Christoph Schulte, editors. _Leibniz und das Judentum_. Studia Leibnitiana Sonderhefte, 34. Stuttgart: Steiner, 2008. Pp. 283.

A vexing problem in contemporary epistemology—one with origins in Plato’s Meno—concerns the value of knowledge, and in particular, whether and how the value of knowledge exceeds the value of mere true opinion. The recent literature is deeply divided on the matter of how best to address the problem. One point, however, remains unquestioned: that if a solution is to be found, it will be at the personal level, the level at which states of subjects or agents, as such, appear. We (...) take exception to this orthodoxy, or at least to its unquestioned status. We argue that subpersonal states play a significant—arguably, primary—role in much epistemically relevant cognition and thus constitute a domain in which we might reasonably expect to locate the “missing source” of epistemic value, beyond the value attached to mere true belief. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Purpose – To review and discuss Luciano Floridi’s 2019 book The Logic of Information: A Theory of Philosophy as Conceptual Design, the latest instalment in his philosophy of information (PI) tetralogy, particularly with respect to its implications for library and information studies (LIS). Design/methodology/approach – Nine scholars with research interests in philosophy and LIS read and responded to the book, raising critical and heuristic questions in the spirit of scholarly dialogue. Floridi responded to these questions. Findings – Floridi’s PI, including (...) this latest publication, is of interest to LIS scholars, and much insight can be gained by exploring this connection. It seems also that LIS has the potential to contribute to PI’s further development in some respects. Research implications – Floridi’s PI work is technical philosophy for which many LIS scholars do not have the training or patience to engage with, yet doing so is rewarding. This suggests a role for translational work between philosophy and LIS. Originality/value – The book symposium format, not yet seen in LIS, provides forum for sustained, multifaceted and generative dialogue around ideas. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This essay series explores the human costs and policy challenges associated with the displacement crises in the Mediterranean and Andaman Seas. The essays explore the myths or misconceptions that have pervaded discussions about these two crises, as well as the constraints or capacity deficiencies have hampered the responses to them.

Clark and Chalmers (1998) defend the hypothesis of an ‘Extended Mind’, maintaining that beliefs and other paradigmatic mental states can be implemented outside the central nervous system or body. Aspects of the problem of ‘language acquisition’ are considered in the light of the extended mind hypothesis. Rather than ‘language’ as typically understood, the object of study is something called ‘utterance-activity’, a term of art intended to refer to the full range of kinetic and prosodic features of the on-line behaviour of (...) interacting humans. It is argued that utterance activity is plausibly regarded as jointly controlled by the embodied activity of interacting people, and that it contributes to the control of their behaviour. By means of specific examples it is suggested that this complex joint control facilitates easier learning of at least some features of language. This in turn suggests a striking form of the extended mind, in which infants’ cognitive powers are augmented by those of the people with whom they interact. (shrink)

This study focused on determining the attitudes and academic performance of engineering students in Technological University of the Philippines-Manila. A total of 139 male engineering and 47 female engineering students were the respondents of the study. This only dwell on the attitude in learning English Language Vocabulary in terms of their behavioral aspects, cognitive aspects, and emotional aspects. This is a quantitative study utilized by descriptive and inferential method as the research design. Based on the findings, academic grades strongly correlate (...) with their attitude in learning English vocabulary which is a negative correlation coefficient in all its components with r value of -0.3695 in behavioral, -0.5261 in Cognitive, and -0.4332 in emotional aspect. Their P values is less than .00001 which is significant at p<0.05. Thus, the null hypothesis where there is no significant relationship between their ALEV and academic performance is rejected. The researcher recommends that teachers should enhance creativity in teaching vocabulary which inculcate the positive attitudes and motivation towards learning process. Teachers and parents should encourage the learners to read and watch educational related materials. (shrink)

Debate on free will with Christian List, Gregg Caruso, and Cory Clark. The exchange is focused on Christian List's book Why Free Will Is Real.

In this short response to Kerstein and Bognar, we clarify three aspects of the complete lives system, which we propose as a system of allocating scarce medical interventions. We argue that the complete lives system provides meaningful guidance even though it does not provide an algorithm. We also defend the investment modification to the complete lives system, which prioritizes adolescents and older children over younger children; argue that sickest-first allocation remains flawed when scarcity is absolute and ongoing; and argue that (...) Kerstein and Bognar are mistaken to base their allocation principles on differences in personhood. (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)

In this article, we aim to map out the complexities which characterise debates about the ethics of vaccine distribution, particularly those surrounding the distribution of the COVID-19 vaccine. In doing so, we distinguish three general principles which might be used to distribute goods and two ambiguities in how one might wish to spell them out. We then argue that we can understand actual debates around the COVID-19 vaccine – including those over prioritising vaccinating the most vulnerable – as reflecting disagreements (...) over these principles. Finally, we shift our attention away from traditional discussions of distributive justice, highlighting the importance of concerns about risk imposition, special duties, and social roles in explaining debates over the COVID-19 vaccine. We conclude that the normative complexity this article highlights deepens the need for decision-making bodies to be sensitive to public input. (shrink)

In Big Gods, Norenzayan (2013) presents the most comprehensive treatment yet of the Big Gods question. The book is a commendable attempt to synthesize the rapidly growing body of survey and experimental research on prosocial effects of religious primes together with cross-cultural data on the distribution of Big Gods. There are, however, a number of problems with the current cross-cultural evidence that weaken support for a causal link between big societies and certain types of Big Gods. Here we attempt to (...) clarify these problems and, in so doing, correct any potential misinterpretation of the cross-cultural findings, provide new insight into the processes generating the patterns observed, and flag directions for future research. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of (...) which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

Shortages of new therapeutics to treat coronavirus disease (COVID-19) have forced clinicians, public health officials, and health systems to grapple with difficult questions about how to fairly allocate potentially life-saving treatments when there are not enough for all patients in need (1). Shortages have occurred with remdesivir, tocilizumab, monoclonal antibodies, and the oral antiviral Paxlovid (2) -/- Ensuring equitable allocation is especially important in light of the disproportionate burden experienced during the COVID-19 pandemic by disadvantaged groups, including Black, Hispanic/Latino and (...) Indigenous communities, individuals with certain disabilities, and low-income persons. However, many health systems have resorted to first-come, first-served approaches to allocation, which tend to disadvantage individuals with barriers in access to care (3). There is mounting evidence of racial, ethnic, and socioeconomic disparities in access to medications for COVID-19 (4, 5). -/- One potential method to promote equitable allocation is to use a weighted lottery, which is an allocation strategy that gives all eligible patients a chance to receive the scarce treatment while also allowing the assignment of higher or lower chances according to other ethical considerations (6). We sought to assess the feasibility of implementing a weighted lottery to allocate scarce COVID-19 medications in a large U.S. health system and to determine whether the weighted lottery promotes equitable allocation. (shrink)

Standard Analytic Epistemology (SAE) names a contingently clustered class of methods and theses that have dominated English-speaking epistemology for about the past half-century. The major contemporary theories of SAE include versions of foundationalism, coherentism, reliabilism, and contextualism. While proponents of SAE don’t agree about how to define naturalized epistemology, most agree that a thoroughgoing naturalism in epistemology can’t work. For the purposes of this paper, we will suppose that a naturalistic theory of epistemology takes as its core, as its starting-point, (...) an empirical theory. The standard argument against naturalistic approaches to epistemology is that empirical theories are essentially descriptive, while epistemology is essentially prescriptive, and a descriptive theory cannot yield normative, evaluative prescriptions. In short, naturalistic theories cannot overcome the is-ought divide. Our main goal in this paper is to show that the standard argument against naturalized epistemology has it almost exactly backwards. (shrink)

Our aim in this paper is to bring the woefully neglected literature on predictive modeling to bear on some central questions in the philosophy of science. The lesson of this literature is straightforward: For a very wide range of prediction problems, statistical prediction rules (SPRs), often rules that are very easy to implement, make predictions than are as reliable as, and typically more reliable than, human experts. We will argue that the success of SPRs forces us to reconsider our views (...) about what is involved in understanding, explanation, good reasoning, and about how we ought to do philosophy of science. (shrink)

We investigate claims about the frequency of "know" made by philosophers. Our investigation has several overlapping aims. First, we aim to show what is required to confirm or disconfirm philosophers’ claims about the comparative frequency of different uses of philosophically interesting expressions. Second, we aim to show how using linguistic corpora as tools for investigating meaning is a productive methodology, in the sense that it yields discoveries about the use of language that philosophers would have overlooked if they remained in (...) their "armchairs of an afternoon", to use J.L. Austin’s phrase. Third, we discuss facts about the meaning of "know" that so far have been ignored in philosophy, with the aim of reorienting discussions of the relevance of ordinary language for philosophical theorizing. (shrink)