Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

According to essentialism, metaphysical modality is founded in the essences of things, where the essence of a thing is roughly akin to its real definition. According to potentialism (also known as dispositionalism), metaphysical modality is founded in the potentialities of things, where a potentiality is roughly the generalized notion of a disposition. Essentialism and potentialism have much in common, but little has been written about their relation to each other. The aim of this paper is to understand better the relations (...) between essence and potentiality, on the one hand, and between essentialism and potentialism, on the other. It is argued, first, that essence and potentiality are not duals but interestingly linked by a weaker relation dubbed ‘semi-duality’; second, that given this weaker relation, essentialism and potentialism are not natural allies but rather natural competitors; and third, that the semi-duality of essence and potentiality allows the potentialist to respond to an important explanatory challenge by using essentialist resources without thereby committing to essentialism. (shrink)

My aim in this paper is to sketch, with a broad brush and in bare outlines, an approach to modal epistemology that is characterized by three distinctive features. First, the approach is agency-based: it locates the roots of our modal thought and knowledge in our experience of our own agency. Second, the approach is ambitious in that it takes the experience of certain modal properties in agency to be the sole distinctive feature of specifically modal thought and knowledge; everything that (...) we know about modality beyond the experience of agency is a matter of applying standard methods of inquiry such as deduction, induction and abductive methods for choosing between theories. Third, the account holds that modal thought and knowledge is, first and foremost, about modal properties that are sufficiently like those encountered in agency. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

According to ecological psychology, animals perceive not just the qualities of things in their environment, but their affordances: in James Gibson’s words, ’what things furnish, for good or ill’. I propose a metaphysics for affordances that fits into a contemporary anti-Humean metaphysics of powers or potentialities. The goal is to connect two debates, one in the philosophy of perception and one in metaphysics, that stand to gain much from each other.

Abilities are in many ways central to what being an agent means, and they are appealed to in philosophical accounts of a great many different phenomena. It is often assumed that abilities are some kind of dispositional property, but it is rarely made explicit exactly which dispositional properties are our abilities. Two recent debates provide two different answers to that question: the new dispositionalism in the debate about free will, and virtue reliabilism in epistemology. This paper argues that both answers (...) fail as general accounts of abilities, and discusses the ramifications of this result. (shrink)

Dispositionalism about modality is the view that metaphysical modality is a matter of the dispositions possessed by actual objects. In a recent paper, David Yates has raised an important worry about the formal adequacy of dispositionalism. This paper responds to Yates’s worry by developing a reply that Yates discusses briefly but dismisses as ad hoc: an appeal to a ’plenitude of powers’ including such powers as the necessarily always manifested power for 2+2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} (...) \begin{document}$$2+2$$\end{document} to be 4. I argue that the reply is not ad hoc at all, by defending the metaphysics of dispositions that should underly it. I then argue, first, that a proper understanding of dispositions’ degrees provides us with an argument for such necessarily always manifested dispositions; second, that all the natural attempts to block that argument can be resisted without being ad hoc; and third, that pragmatic considerations explain our intuitive resistance to the ascription of necessarily always manifested dispositions. Dispositionalism can be formally adequate after all. (shrink)

Williamsonian modal epistemology is characterized by two commitments: realism about modality, and anti-exceptionalism about our modal knowledge. Williamson’s own counterfactual-based modal epistemology is the best known implementation of WME, but not the only option that is available. I sketch and defend an alternative implementation which takes our knowledge of metaphysical modality to arise, not from knowledge of counterfactuals, but from our knowledge of ordinary possibility statements of the form ‘x can F’. I defend this view against a criticism indicated in (...) Williamson’s own work, and argue that it is better connected to the semantics of modal language. (shrink)

Modal dispositionalism is the view that possibilities are a matter of the dispositions of individual objects: it is possible that p if and only if something has a disposition for p to be the case. We raise a problem for modal dispositionalism: nothing within the theory rules out that there could be necessary, perfect masks, which make the manifestation of a disposition impossible. Unless such necessary perfect masks are ruled out, modal dispositionalism runs the risk of failing to provide a (...) sufficient condition for possibility, and indeed of engendering contradictions. But to rule them out, modal dispositionalism would have to revise a crucial tenet of the view, its localism. (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)

Dispositionalists try to provide an account of modality—possibility, necessity, and the counterfactual conditional—in terms of dispositions. But there may be a tension between dispositionalist accounts of possibility on the one hand, and of counterfactuals on the other. Dispositionalists about possibility must hold that there are no impossible dispositions, i.e., dispositions with metaphysically impossible stimulus and/or manifestation conditions; dispositionalist accounts of counterfactuals, if they allow for non-vacuous counterpossibles, require that there are such impossible dispositions. I argue, first, that there are in (...) fact no impossible dispositions; and second, that the dispositionalist can nevertheless acknowledge the non-vacuity of some counterpossibles. The strategy in the second part is one of ‘divide and conquer’ that is not confined to the dispositionalist: it consists in arguing that counterpossibles, when non-vacuous, are read epistemically and are therefore outside the purview of a dispositional account. (shrink)

Alexander Bird puts forward a modest version of anti-Humeanism about the non-fundamental, by providing an argument for the existence of a certain select class of non-fundamental but sparse dispositions: those that have an evolutionary function. I argue that his argument over-generates, so much so that the sparse–abundant distinction, and with it the tenet of his anti-Humean view, becomes obsolete. I suggest an alternative way of understanding anti-Humeanism in the non-fundamental realm, one which is not concerned with the existence of sparse (...) properties but with explanatory relations. (shrink)

This paper explores the prospects for dispositional accounts of abilities. According to so-called new dispositionalists, an agent has the ability to Φ iff they have a disposition to Φ when trying to Φ. We show that the new dispositionalism is beset by some problems that also beset its predecessor, the conditional analysis of abilities, and bring up some further problems. We then turn to a different approach, which links abilities not to motivational states but to the notion of success, and (...) consider ways of implementing that approach. Our results suggest that there are principled disanalogies between abilities and disposition which prevent any dispositional account of abilities from succeeding. (shrink)

In this paper I investigate central temporal and spatial notions in the second part of Plato’s Parmenides and argue that also these notions, and not only the metaphysical ones usually discussed in the literature, can be understood as a response to positions and problems put on the table by Parmenides and Zeno. Of the spatial notions examined in the dialogue, I look at the problems raised for possessing location and shape, while with respect to temporal notions, I focus on the (...) discussion of ‘being in time’ and exaiphnês (the latter notion will be shown to be also an important influence for Aristotle’s Physics). In displaying a paradoxical character and taking up crucial notions from Parmenides, the second part of the Parmenides seems to display some resemblance to Zeno’s paradoxes. I will show, however, that in contrast to Zeno, the second part of Plato’s Parmenides also demonstrates Parmenides’ One to be problematic on its own terms. Furthermore, the dialogue presents not only important problems that these spatial and temporal notions seem to lead us into, but also establishes some positive features necessary to think of time and space. In this way, Plato’s Parmenides can be seen as contributing to the development of temporal and spatial conceptualisations in ancient Greek thought. (shrink)

It is a familiar point that many ordinary dispositions are multi-track, that is, not fully and adequately characterisable by a single conditional. In this paper, I argue that both the extent and the implications of this point have been severely underestimated. First, I provide new arguments to show that every disposition whose stimulus condition is a determinable quantity must be infinitely multi-track. Secondly, I argue that this result should incline us to move away from the standard assumption that dispositions are (...) in some way importantly linked to conditionals, as presupposed by the debate about various versions of the ‘conditional analysis’ of dispositions. I introduce an alternative conception of dispositionality, which is motivated by linguistic observations about dispositional adjectives and links dispositions to possibility instead of conditionals. I argue that, because of the multi-track nature of dispositions, the possibility-based conception of dispositions is to be preferred. (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)

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

This paper responds to the contributions by Alexander Bird, Nathan Wildman, David Yates, Jennifer McKitrick, Giacomo Giannini & Matthew Tugby, and Jennifer Wang. I react to their comments on my 2015 book Potentiality: From Dispositions to Modality, and in doing so expands on some of the arguments and ideas of the book.

Dispositions are modal properties. The standard conception of dispositions holds that each disposition is individuated by its stimulus condition(s) and its manifestation(s), and that their modality is best captured by some conditional construction that relates stimulus to manifestation as antecedent to consequent. I propose an alternative conception of dispositions: each disposition is individuated by its manifestation alone, and its modality is closest to that of possibility — a fragile vase, for instance, is one that can break easily. The view is (...) expounded in some detail and defended against the major objections. (shrink)

This paper surveys recent "new actualist" approaches to modality that do without possible worlds and locate modality squarely in the actual world. New actualist theories include essentialism and dispositionalism about modality, each of which can come in different varieties. The commonalities and differences between these views, as well as their shared motivations, are layed out.

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

Contemporary issues involving knowledge and science examined from a constructivist-pragmatist perspective often labeled "relativism." Individual chapters include a review of the difference between constructivist-pragmatist epistemology and "social constructivism;" an examination of recent writings by Bruno Latour; a critique of computational methods in literary studies; a skeptical look at current efforts to "integrate" the humanities and the natural sciences; and reflections on the social dynamics of belief in relation to denials of climate change and to hopes expressed by environmentalists.

In this review of Ann Whittle's book, I take a closer look at, and raise some concerns about, two crucial steps in the argument of the book. First, I consider the ‘all-in can’, the sense of ‘can’ that is relevant for freedom, and argue that it sits uneasily with Whittle’s foundation in the semantics of agentive modals. Second, I take a closer look at the notion of ‘robust control’ and its role in Whittle's argument for contextualism about moral responsibility, and (...) argue that Whittle’s own conception of control is in tension with her argument for contextualism about moral responsibility. (shrink)

This chapter explores the different dimensions of domination, including whether it has a structural approach, its relation to race and imperialism, and how non-domination can be institutionalized and achieved at a global level.

Manley and Wasserman (2008) have provided a convincing case against analyses of dispositions in terms of one conditional, and a very interesting positive proposal that links any disposition to a ‘suitable proportion’ of a particular set of precise conditionals. I focus on their positive proposal and ask just how precise those conditionals are to be. I argue that, contrary to what Manley and Wasserman imply in their paper, they must be maximally specific, describing in their antecedents complete centred worlds. This (...) suggests a natural semantics for dispositional expressions, which I briefly explore to argue that it lacks uniformity. I end by suggesting a variation on Manley and Wasserman's view which would preserve uniformity, though at the cost of some new puzzling questions. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

This paper provides a philosophical analysis and a new edition of an anonymous Epitome of John Dumbleton’s solution to the semantic paradoxes. The first part of this paper briefly presents Dumbleton’s cassationist solution to the semantic paradoxes, which the English philosopher proposes in his Summa Logicae, written in the 1330s–40s. The second part investigates the solution to various types of insolubles proposed by the anonymous author of the Epitome. The third part provides a new critical edition of the Latin text (...) – a first edition was edited by Bottin in 1978 – and an English translation. (shrink)

In this paper I show that one of the most fruitful ways of employing paradoxes has been as a philosophical method that forces us to reconsider basic assumptions. After a brief discussion of recent understandings of the notion of paradoxes, I show that Zeno of Elea was the inventor of paradoxes in this sense, against the background of Heraclitus’ and Parmenides’ way of argumentation: in contrast to Heraclitus, Zeno’s paradoxes do not ask us to embrace a paradoxical reality; and in (...) contrast to Parmenides, Zeno shows common assumptions to be internally problematic, not just in light of Eleatic positions. (shrink)

In May 2021, Royal Dutch Shell was ordered by the Hague District Court to significantly reduce its CO2 emissions. This ruling is unprecedented in that it attributes the responsibility for mitigating climate change directly to a specific corporate emitter. Shell neither directly causes climate change alone nor can alleviate it by itself; therefore, what grounds this responsibility attribution? I maintain that this question can be answered via Young’s social connection model of responsibility for justice. I defend two claims: First, I (...) argue that the model explains Shell’s connection to climate change and that this relationship grounds Shell’s responsibility. Second, by identifying a way in which the social connection model could be applied to corporations in legal practice, I further develop Young’s model. I question Young’s distinction between political and legal responsibility for justice and propose that courts could mediate citizens’ actions regarding political responsibilities. (shrink)

Advocates of literary Darwinism, cognitive cultural studies, neuroaesthetics, digital humanities, and other such hybrid fields now seek explicitly to make the aims and methods of one or another humanities discipline approximate more closely the aims and methods of science, and at their most visionary, they urge as well the overall integration of the humanities and natural sciences. This essay indicates some major considerations—historical, conceptual, and pragmatic—that may be useful for assessing these efforts and predicting their future. Arguments promoting integration often (...) involve dubious teleological models of intellectual history and betray limited understandings of the distinctive epistemic orientations and cultural functions of the humanities vis-à-vis the sciences. Recurrent institutional difficulties encountered by scholars and/or scientists in hybrid fields reflect steep prestige differentials between the humanities and sciences, along with significant differences of training, experience, style, and temperament. Meanwhile, both the sciences and humanities are being shaken up by technological and related intellectual developments. Though worrisome, the new disciplinary configurations are thus likely to play out in surprising and, not inconceivably, positive ways. (shrink)

In this thesis, I develop a nonreductive and general conception of potentiality, and explore the prospects of a realist account of possibility based on this account of potentiality. Potentialities are properties of individual objects; they include dispositions such as fragility and abilities such as the ability to play the piano. Potentialities are individuated by their manifestation alone. In order to provide a unified account of potentialities, I argue in chapter 2 that dispositions, contrary to philosophical orthodoxy, are best understood in (...) terms only of their manifestations (as disposi- tions to ...), rather than in terms of a stimulus and a manifestation condition (as dispositions to ... if ...). Chapter 3 provides some preliminary motivation for a nonreductive and gen- eral account of potentiality, and chapter 4 develops such an account. The guiding question is how far the notion of potentiality can be extended from the initial ex- amples of familiar dispositions and abilities, and it is argued that it can be extended very far. Various features of potentialities are explored, among them extrinsicality, iterations of potentiality, and the behaviour of potentiality with regard to logical equivalence. In chapter 5, the account is set to work in providing the outlines and a defense of a potentiality-based account of possibility. The basic idea of such an account is that it is possible that p just in case some thing has a potentiality for p. The account is defended against the objection that there may not be enough potential- ities to ground all the possibilities that there are. Finally, in chapter 6, a logic of potentiality is formulated and the logic of possibility derived from it, showing that the potentiality-based account of possibility is formally adequate: it provides pos- sibility with the formal features that modal logicians have studied. I conclude that the proposed account of possibility is a promising research programme. (shrink)

An analysis of Cardinal Joseph Ratzinger's statements regarding relativism in his 2005 homily to the conclave meeting to elect the new pope in the context of the charge of "relativism" in 20th-century philosophy. Parts of this essay are adapted from Barbara Herrnstein Smith,"Pre-Post-Modern Relativism," in *Scandalous Knowledge: Science, Truth and the Human* (Edinburgh: Edinburgh University Press, 2005; Durham, NC: Duke University Press, 2006), 18 – 45.

A critical examination of the charge of self-refutation, particularly as leveled by orthodoxy-defending philosophers against those maintaining epistemologically unorthodox, especially relativistic or skeptical, views. Beginning with an analysis of its classic illustration in Plato’s *Theaetetus* as leveled against Protagoras’s “Man is the measure ...,” I consider various aspects of the charge, including logical, rhetorical, pedagogic, affective, and cognitive.

This paper aims to show that—and how—Plato’s notion of the receptacle in the Timaeus provides the conditions for developing a mathematical as well as a physical space without itself being space. In response to the debate whether Plato’s receptacle is a conception of space or of matter, I suggest employing criteria from topology and the theory of metric spaces as the most basic ones available. I show that the receptacle fulfils its main task–allowing the elements qua images of the Forms (...) to exist as sensible things by being that in which the elements appear, change and move–in virtue of being pure continuity. All further qualifications required for a full notion of space are derived solely from the content of the receptacle. (shrink)

This paper argues that the problem of how to act in the face of radical contingency is of central importance in Musil’s novel and intimately connected to what Musil calls the sense of possibility. There is a variety of different strategies by which individuals, and the state of Kakania as a whole, deal with contingency, and they all involve a claim to a kind of grounding or necessity; for example, the Parallel Campaign is one big attempt to ground Kakania in (...) what can be perceived as a form of metaphysical necessity. With the figure of Ulrich, Musil radicalizes the problem by showing the consequences of viewing even the relationship one has to one’s own self as contingent – the ultimate outcome of which is self-alienation. (shrink)

The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...) formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Who and how revised Marxism in Poland? The simple answer is that it was done by young intellectuals seeing themselves as obligated to social and political activity, eager to participate in the process of the constitution of a new postwar Communist society. Marxism was for them a philosophical world-view and a political program rising hopes for a better socio-economic reality. Revisionists were committed Communists and their attitude toward Marxism was almost religious. Marxism, Promethean and scientific at the same time, was (...) supposed to replace religion, for which the radically secular revisionists saw no place in the new society. (See: Mikołajczyk 2013, p. 44-48) After the shock of 1956 they stuck by the slogan: ’socialism–yes, distortions–no,’ they thought that “Marxist socialism was possible without Leninist political forms, that Communism might be attacked within «the framework of Marxism»,” and they “believed for some time ... that Stalinism was curable in the sense that Communism could be restored or «democratized» without questioning its foundations” (Kolakowski 1978, p. 461). They saw themselves in an elitist way, i.e., as true and devoted Marxists fighting with dogmas, orthodoxy, myths, and unfounded faith both within Marxism-Leninism and outside it. They were willing to accept the position of sectarians, heretics, or apostates. Their political and ideological involvement forced them to attack pre-war but still active Polish philosophers of the Lvov-Warsaw School and other nonMarxist thinkers (Roman Ingarden, Władysław Tatarkiewicz, Stanisław Ossowski), who were classified as “bourgeois thinkers” unable to understand and assimilate Marxism. (shrink)

While Aristotle provides the crucial testimonies for the paradoxes of motion, topos, and the falling millet seed, surprisingly he shows almost no interest in the paradoxes of plurality. For Plato, by contrast, the plurality paradoxes seem to be the central paradoxes of Zeno and Simplicius is our primary source for those. This paper investigates why the plurality paradoxes are not examined by Aristotle and argues that a close look at the context in which Aristotle discusses Zeno holds the answer to (...) this question. (shrink)

This paper argues that processes in the sensible realm can be in accord with reason in the Timaeus, since rationality is understood here as being based on regularity, which is conferred onto processes by time. Plato uses two different temporal structures in the Timaeus, associated with the contrast there drawn between Greek and Egyptian approaches to history. The linear order of before and after marks natural processes as rational and underlies the Greek treatment of history. By contrast, a bidirectional temporal (...) structure is the basis for the Egyptian approach to historical processes: present actions are not only determined by preceding ones in the past, but can also be influenced by the future (plans, aims). This latter temporal structure is shown to be necessary for learning from history, which makes human actions more regular. (shrink)

Risk communication has been generally categorized as a warning act, which is performed in order to prevent or minimize risk. On the other side, risk analysis has also underscored the role played by information in reducing uncertainty about risk. In both approaches the safety aspects related to the protection of the right to health are on focus. However, it seems that there are cases where a risk cannot possibly be avoided or uncertainty reduced, this is for instance valid for the (...) declaration of side effects associated with pharmaceutical products or when a decision about drug approval or retirement must be delivered on the available evidence. In these cases, risk communication seems to accomplish other tasks than preventing risk or reducing uncertainty. The present paper analyzes the legal instruments which have been developed in order to control and manage the risks related to drugs – such as the notion of “development risk” or “residual risk” – and relates them to different kinds of uncertainty. These are conceptualized as epistemic, ecological, metric, ethical, and stochastic, depending on their nature. By referring to this taxonomy, different functions of pharmaceutical risk communication are identified and connected with the legal tools of uncertainty management. The purpose is to distinguish the different functions of risk communication and make explicit their different legal nature and implications. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)