Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

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

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

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

Sometimes someone does something morally wrong in clear-eyed awareness that what she is doing is wrong. More commonly, a wrongdoer fails to see that her conduct is wrong. Call the latter behavior unwitting wrongful conduct. It is generally agreed that an agent can be blameworthy for such conduct, but there is considerable disagreement about how one’s blameworthiness in such cases is to be explained, or what conditions must be satisfied for the agent to be blameworthy for her conduct. Many theorists (...) hold that an agent’s blameworthiness for unwitting wrongful conduct must stem from—or trace back to—her blameworthiness for something else. And appeals to tracing in these cases lead some writers to a highly revisionist view, on which people are blameworthy for wrongdoing much less often than we ordinarily think (and our mistake, unfortunately, isn’t about how much wrongdoing there is). In this chapter, I set out the main claims of an argument for such a view and respond to it. I offer grounds for retaining a good many of the judgments that the revisionist would have us reject. The defense rests to a significant extent on commonsense views about the psychological capacities and abilities to act that people ordinarily possess, views that, as far as I can tell, revisionists have not shown to be mistaken. (shrink)

As genealogy has gained greater disciplinary recognition over the last two decades, it has become increasingly common to call any historically oriented philosophy, such as Theodor W. Adorno’s, “genealogy.” In this article, I show that Adorno’s philosophy indeed performs genealogy’s defining functions of “problematization” and “possibilization.” Moreover, it does so in unique ways that constitute a significant contribution to genealogical practice. Adorno’s method, here called “tragic genealogy,” is particularly well-suited to the genealogical analysis of traditional philosophical problems and to the (...) critical reanimation of declining, but ethically significant, values. Nevertheless, I also argue that Adorno’s philosophy cannot be assimilated into genealogical practice without rejecting or revising some of its Hegelian influences, particularly its philosophy of history and its modal metaphysics. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

Many philosophical theories of causation are egalitarian, rejecting a distinction between causes and mere causal conditions. We sought to determine the extent to which people's causal judgments discriminate, selecting as causes counternormal events—those that violate norms of some kind—while rejecting non-violators. We found significant selectivity of this sort. Moreover, priming that encouraged more egalitarian judgments had little effect on subjects. We also found that omissions are as likely as actions to be judged as causes, and that counternormative selectivity appears to (...) apply equally to actions and omissions. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

A growing number of philosophers now hold that agent causation is required for agency, or free will, or moral responsibility. To clarify what is at issue, this paper begins with a distinction between agent causation that is ontologically fundamental and agent causation that is reducible to or realized in causation by events or states. It is widely accepted that agency presents us with the latter; the view in question claims a need for the former. The paper then examines a “disappearing (...) agent” argument from Derk Pereboom that is aimed at showing that free will requires agent causation that is ontologically fundamental. It is argued that the argument fails. Further, it is argued that, contrary to Pereboom’s claim, the issue raised by his disappearing agent argument is distinct from the problem of present luck that libertarian theories of free will face. The paper concludes with an assessment of the prospects for success of a disappearing agent argument showing that agent causation that is ontologically fundamental is required for agency tout court. (shrink)

Waiting for Godot’s many commentators have emphasized the absurdity of hope in the play, but there has not been an account of how the play reprises hope’s historical transformation and weakening in modernity. This essay provides that account, arguing that Beckett’s Waiting for Godot sponsors a form of hope appropriate to the predicaments of modern societies. Godot stages the blockage of hope by reflecting the obsolescence and fragmentation of the religious and progressive legitimations for the concept that used to be (...) broadly convincing. Despite this blockage, however, Godot does not give in to nihilism. It, rather, models a form of responsible, self-aware hope appropriate to an historical situation where hope does not admit of rational justification. To develop this interpretation of the play and to defend its minimalist conception of hope, the essay draws on Theodor W. Adorno’s Negative Dialectics and aesthetics. (shrink)

Several philosophers claim that the phenomenology of one’s own agency conflicts with standard causal theories of action, couched in terms of causation by mental events or states. Others say that the phenomenology is prima facie incompatible with such a theory, even if in the end a reconciliation can be worked out. Here it is argued that the type of action theory in question is consistent with what can plausibly be said to be presented to us in our experience of our (...) agency. Several routes to a claim that there is nevertheless a prima facie incompatibility are examined, and all are found wanting. The phenomenology of agency, it is argued, is no threat to a standard causal theory of action. (shrink)

Certain states in the Global North have responded to refugees seeking safety on their territories through harmful practices of border violence, detention, encampment and containment that serve to prevent and deter refugee arrivals. These practices are ostensibly justified through an appeal to a right to control borders. This paper therefore assesses whether these harmful practices can indeed be morally justified by a state’s right to control borders. It analyses whether Christopher Heath Wellman’s account of a state’s right to freedom of (...) association, which represents the most restrictive account of a state’s right to control borders available in the literature, can extend to justify current harmful practices against refugees. If not, then no available justification will be able to do so, and thus contemporary harmful practices used against refugees cannot be justified by a state’s right to control borders. (shrink)

In this paper I defend an eudaimonistic reading of Spinoza’s ethical philosophy. Eudaimonism refers to the mainstream ethical tradition of the ancient Greeks, which considers happiness a naturalistic, stable, and exclusively intrinsic good. Within this tradition, we can also draw a distinction between weak eudaimonists and strong eudaimonists. Weak eudaimonists do not ground their ethical conceptions of happiness in complete theories of metaphysics, epistemology, or psychology. Strong eudaimonists, conversely, build their conceptions of happiness around an overall philosophical system that extends (...) far beyond ethics, while nevertheless being directed at the promotion of a happy life. I will show that Spinozistic happiness is not only naturalistic, stable, and exclusively intrinsically good, but that Spinoza is also a strong eudaimonist because his ethical account of happiness is incomprehensible without appeal to metaphysical, epistemological, and psychological doctrines. As well, I will explain how the apparent subjective and relativistic features of Spinoza’s ethics do not undermine the eudaimonistic reading, because both Spinoza and the ancient eudaimonists grant that the beliefs/feelings of the subject play a necessary (but insufficient) role in happiness as the highest good. (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)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

Let F be a fact in virtue of which an agent, S, is blameworthy for performing an act of A-ing. We advance a slightly qualified version of the following thesis: -/- (Reason) F is (at some time) a reason for S to feel guilty (to some extent) for A-ing. -/- Leaving implicit the qualification concerning extent, we claim as well: -/- (Desert) S's having this reason suffices for S’s deserving to feel guilty for A-ing. -/- We also advance a third (...) thesis connecting desert of feeling guilty with the fittingness of this response. -/- In light of our three theses, we address several claims that have been made regarding responsibility and desert. We take issue with the divorce of desert from responsibility. We find acceptable a claim regarding blameworthiness and reason to induce guilt, and we defend the idea that it is noninstrumentally good that one who is blameworthy be subject to a fitting feeling of guilt. We argue against a view on which desert of blame has a teleological dimension. (shrink)

This interview, conducted over the span of several months, tracks the respective journeys of Constantin V. Boundas and Daniel W. Smith with the philosophy of Gilles Deleuze. Rather than “becoming Deleuzian,” which is neither desirable nor possible, these exchanges reflect an array of encounters with Deleuze. These include the initial discoveries of Deleuze’s writings by Boundas and Smith, in-person meetings between Boundas and Deleuze, and the wide-ranging and influential philosophical work on Deleuze’s concepts produced by both Boundas and (...) Smith. At stake in this discussion are key contributions by Deleuze to continental philosophy, including the distinction between the virtual and the actual and the very nature of a “concept.” Also at stake is the formative or pedagogical impact of a philosopher, like Deleuze, on those who find and fully engage with his texts, concepts, and project. Cette interview, menée sur plusieurs mois, suit les parcours respectifs de Constantin V. Boundas et Daniel W. Smith avec la philosophie de Gilles Deleuze. Au lieu de « devenir Deleuzien, » ce qui n’est ni souhaitable ni possible, ces échanges reflètent un éventail de rencontres avec Deleuze. Il s’agit notamment des premières découvertes des écrits de Deleuze par Boundas et Smith, des rencontres en personne entre Boundas et Deleuze, et du travail philosophique vaste et in????luent sur les concepts de Deleuze produit par Boundas et Smith. L’enjeu ici étant les contributions clés de Deleuze à la philosophie continentale, y compris la distinction entre le virtuel et l’actuel, et la nature même d’un « concept. » Mais il y a aussi l’impact formateur ou pédagogique d’un philosophe, comme Deleuze, sur ceux qui trouvent et s’engagent pleinement dans ses textes, ses concepts et ses projets. (shrink)

Often when one omits to do a certain thing, there's no action that is one's omission; one's omission, it seems, is an absence of any action of some type. This paper advances the view that an absence of an action--and, in general, any absence--is nothing at all: there is nothing that is an absence. Nevertheless, it can result from prior events that one omits to do a certain thing, and there can be results of the fact that one omits to (...) do something. This is so even if absences cannot be causes or causal effects. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

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

One of the most intriguing claims in Sven Rosenkranz’s Justification as Ignorance is that Timothy Williamson’s celebrated anti-luminosity argument can be resisted when it comes to the condition ~K~KP—the condition that one is in no position to know that one is in no position to know P. In this paper, I critically assess this claim.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The problem I want to discuss has to do with believing as distinct from perceiving, imagining, positing, resolving, and hoping, as well as from knowing. Since these distinctions are not always observed, we must remind ourselves what ‘belief’ means when it is deliberately preferred to other intentional descriptions, and we ought to characterize it in such a way that we can see why it matters immediately , not just consequentially, whether one believes in something or not. I propose putting it (...) this way: Believing in X means taking X to be real, which in turn means accepting X as something to be dealt with. Unlike knowledge, which is originally conceived, so to speak, from the object to the subject – given that X is there, if I come along and see it there, then I am among those who know it is there – belief is conceived from the subject to the object: given that I am looking about me, if I see X there, then X is among the things I believe in, unless I mistrust it for some reason. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

Deleuze argued that a fundamental mutation in the concept of time occurred in Kant. In antiquity, the concept of time was subordinated to the concept of movement: time was a ‘measure’ of movement. In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an autonomy of its own: time becomes "the pure and empty form" of everything that moves and changes. What is essential in the theory of time is not the distinction between objective ‘clock (...) time’ (or physical time) and the subjective experience of ‘time consciousness,’ since both of them measure movements, whether the movement of extensive objects or intensive states. What is fundamental is rather the relation between time and movement, since time can only assume its own concept when it ceases to be subordinate to movement, whether that movement is objective or subjective. This article examines how Kant inverted the relation between time and movement, and how Deleuze’s own theory of time builds on Kant’s revolution and extends it further. (shrink)

We take it for granted that commonly we act freely and we are generally morally responsible for what we do when we so act. Can there be such a thing as freely omitting to act, or freely refraining or forbearing, and can we be similarly responsible for omitting, refraining, and forbearing? This paper advances a view of freely omitting to act. In many cases, freedom in omitting cannot come to the same thing as freedom in acting, since in many cases (...) omitting to do a certain thing is not a matter of performing an action of any sort. There are nevertheless important similarities. It is argued, further, that we should view responsibility for omitting to act as capable of being basic or underived, not needing to derive from one’s responsibility for prior actions. Finally, brief consideration is given to a proposal concerning what is required for responsibility for omitting to do a certain thing. (shrink)

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

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

The “Treatise on Nomadology: The War Machine" is one of the most important and innovative chapters in Gilles Deleuze and Felix Guattari's book, A Thousand Plateaus. It is a highly original text in political philosophy whose implications have yet to be fully mined—or even partially mined, for that matter. This short text analyzes the "noumenal" status that Deleuze assigns to the nomadic war machine, and analyzes the fundamental role that the nomadology plays in Deleuze and Guattari's political philosophy.

For centuries it has been a mainstay of European and American moral thought that keeping promises—and the allied activity of upholding contracts—is one of the most important requirements of morality. On some historically powerful views the obligation to uphold promises or contracts not only regulates private relationships, but also provides the moral foundation for our duty to support and obey legitimate governments. Some theorists believe that the concept of keeping promises has gradually moved to center stage in European moral thought. (...) They see this movement as part of an historical shift from a moral conception in which an individual’s duties are mainly externally imposed and unalterable, to a conception in which duties are largely chosen by the individual. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in his "Understanding models understanding language" (2022) for a thesis of this sort. His idea is that (1) where there is semantics there is also understanding and (2) machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics. We show that he goes wrong because he pays insufficient (...) attention to the difference between language as used by humans and the sequences of inert symbols which arise when language is stored on hard drives or in books in libraries. (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...) from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

A belief one has is safe if either (i) it could not easily be false or (ii) in any nearby world in which it is false, it is not formed using the method one uses to form one’s actual belief. It seems our mathematical beliefs are safe if mathematical pluralism is true: if, loosely put, almost any consistent mathematical theory is true. It seems, after all, that in any nearby world where one’s mathematical beliefs differ from one’s actual beliefs, one (...) would believe some other true, consistent theory. Focusing on Justin Clarke-Doane’s recent discussion, I argue the thesis that mathematical beliefs are safe given pluralism faces some obstacles. I argue (i) is true of mathematical belief given pluralism only if we deny plausible claims about the interpretation of non-pluralists who many of us could easily be. Unless strong metasemantic theses are true, it is plausible many of us could easily deny or refuse to believe a consistent and true mathematical theory we actually believe. Since philosophical arguments and controversies permeate the methodology of foundational mathematics, I argue we cannot confidently distinguish the methods we use in mathematics between worlds, thus raising doubts about (ii). (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

From a radical feminist perspective, gender is a cage. Or to be more precise, it’s two cages. If genders are cages, then surely we want to let people out. Being less constrained in our choices is something we all have reason to want: theorists in recent years have emphasized the importance of the capability to do and be many different things. At the very least, we should want an end to sex-based oppression. But what does this entail, when it comes (...) to gender? In this paper, I’ll compare four ‘transitional pathways’, with a view to considering how each relates to the ultimate end of ending sex-based oppression. Should we open the doors to the cages, so that people can move freely between them, but leave the cages themselves in place?. Should we add more cages?. Should we make the cages bigger, so that people have a lot more room to move around inside them? Or should we dismantle the cages, so there are no more genders at all?. Some of these options are ‘gender revisionist’, others are gender abolitionist. I’ll argue in favour of a gender abolitionist pathway. (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)

Richard Rorty's rejection of prevailing interior-mirror understandings of the presumed relationship between “minds” and “nature,” along with his promotion of nonrepresentational accounts of knowledge, truth, and science, participates in a rich tradition of jointly pragmatist and constructivist views that spans the twentieth century. This contribution to the symposium “Whatever Happened to Richard Rorty?” considers Rorty's complex and ambivalent relation to that tradition, particularly to the work of his American pragmatist predecessors, William James and John Dewey, and to subsequent pragmatist-constructivist antirepresentationalism (...) in contemporary science and technology studies (STS) and “4E” (embodied, embedded, extended, enactive) cognitive theory. A final section on Nicholas Gaskill's contribution to the symposium questions his sense of Rorty's rhetorical recklessness and suggests that his worries over relativism, in Rorty's texts and more generally, are misplaced. (shrink)

The standard of proof applied in civil trials is the preponderance of evidence, often said to be met when a proposition is shown to be more than 50% likely to be true. A number of theorists have argued that this 50%+ standard is too weak – there are circumstances in which a court should find that the defendant is not liable, even though the evidence presented makes it more than 50% likely that the plaintiff’s claim is true. In this paper, (...) I will recapitulate the familiar arguments for this thesis, before defending a more radical one: The 50%+ standard is also too strong – there are circumstances in which a court should find that a defendant is liable, even though the evidence presented makes it less than 50% likely that the plaintiff’s claim is true. I will argue that the latter thesis follows naturally from the former once we accept that the parties in a civil trial are to be treated equally. I will conclude by sketching an alternative interpretation of the civil standard of proof. (shrink)

In the literature on philosophical progress it is often assumed that agreement is a necessary condition for progress. This assumption is sensible only if agreement is a reliable sign of the truth, since agreement on false answers to philosophical questions would not constitute progress. This paper asks whether agreement among philosophers is (or would be) likely to be a reliable sign of truth. Insights from social choice theory are used to identify the conditions under which agreement among philosophers would be (...) a reliable indicator of the truth, and it is argued that we lack good reason to think that philosophical inquiry meets these conditions. The upshot is that philosophical agreement is epistemically uninformative: agreement on the answer to a philosophical question does not supply even a prima facie reason to think that the agreed-upon view is true. However, the epistemic uninformativeness of philosophical agreement is not an indictment of philosophy's progress, because philosophy is valuable independent of its ability to generate agreement on the correct answers to philosophical questions. (shrink)