Ioannis G. Ntagkas

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.

Contemporary epistemologists typically define a priori justification as justification that is independent of sense experience. However, sense experience plays at least some role in the production of many paradigm cases of a priori justified belief. This raises the question of when experience is epistemically relevant to the justificatory status of the belief that is based on it. In this paper, I will outline the answers that can be given by the two currently dominant accounts of justification, i.e. evidentialism and reliabilism. While for the evidentialist, experience is epistemically relevant only if it is used as evidence, the reliabilist requires that the reliability of the relevant process depends on the reliability of experiential processes. I will argue that the reliabilist account accommodates our pre-theoretic classifications much better. In the final part of my paper I will use the reliabilist criterion to defend the a priori—a posteriori distinction against recent challenges by Hawthorne and Williamson

The distinction between a priori knowledge and a posteriori knowledge has come under attack in the recent literature by Philip Kitcher, John Hawthorne, C. S. Jenkins, and Timothy Williamson. Evaluating the attacks requires answering two questions. First, have they hit their target? Second, are they compelling? My goal is to argue that the attacks fail because they miss their target. Since the attacks are directed at a particular concept or distinction, they must accurately locate the target concept or distinction. Accurately locating the target concept or distinction requires correctly articulating that concept or distinction. The attacks miss their target because they fail to correctly articulate the target concept or distinction. I go on to present a different challenge to the a priori-a posteriori distinction. This challenge is not directed at the coherence or significance of the distinction. Its target is the traditional view that all knowledge (or justified belief) is either a priori or a posteriori.

Kant contends that necessity is a criterion of the a priori—that is, that all knowledge of necessary propositions is a priori. This contention, together with two others that Kant took to be evident—we know some mathematical propositions and such propositions are necessary—leads directly to the conclusion that some knowledge is a priori. Although many contemporary philosophers endorse Kant’s criterion, supporting arguments are hard to come by. Gordon Barnes provides one of the few examples. My purpose in this chapter is to articulate and examine his argument. I have two goals in doing so. The first is to uncover several significant gaps in the argument. The second is to show that it suffers from a common defect in rationalist arguments. If the argument were successful against empiricist accounts of modal knowledge, it would apply with equal force to extant rationalist accounts of such knowledge. Hence, the cost of refuting modal empiricism is modal scepticism.

In Necessary Beings, Bob Hale addresses two questions: What is the source of necessity? What is the source of our knowledge of it? He offers novel responses to them in terms of the metaphysical notion of nature or, more familiarly, essence. In this paper, I address Hale’s response to the first question. My assessment is negative. I argue that his essentialist explanation of the source of necessity suffers from three significant shortcomings. First, Hale’s leading example of an essentialist explanation merely asserts that the nature of an entity explains some necessity, but leaves unexplained how it does so. Second, his essentialist explanation of particular necessities introduces new necessities that remain unexplained. Third, Hale’s version of essentialism presupposes a controversial metaphysical theory of properties, for which he offers no defense.

For much of the past two millennia philosophers have embraced a priori knowledge and have thought that the a priori plays an important role in philosophy itself. Philosophers from Plato to Descartes, Kant to Kripke, all endorse the a priori and engage in a priori reasoning in their philosophical discussions. Recent work in epistemology and experimental philosophy, however, has raised questions about both the existence of a priori knowledge and the centrality of the a priori for philosophy. This collection of essays aims to advance the discussion of the a priori and its role in philosophy. The contributors include a mix of young and established philosophers, including some of the most prominent voices in philosophy today.

The paper proposes a synthesis between human scientists and artificial representation learning models as a way of augmenting epistemic warrants of realist theories against various anti-realist attempts. Towards this end, the paper fleshes out unconceived alternatives not as a critique of scientific realism but rather a reinforcement, as it rejects the retrospective interpretations of scientific progress, which brought about the problem of alternatives in the first place. By utilising adversarial machine learning, the synthesis explores possibility spaces of available evidence for unconceived alternatives providing modal knowledge of what is possible therein. As a result, the epistemic warrant of synthesised realist theories should emerge bolstered as the underdetermination by available evidence gets reduced. While shifting the realist commitment away from theoretical artefacts towards modalities of the possibility spaces, the synthesis comes out as a kind of perspectival modelling.

Pierre Duhem and Jacques Maritain, influenced by positivist philosophies of science that prevailed in the late nineteenth and early twentieth centuries, adopted markedly non-realist views about the mathematical theories of the modern physical sciences. The philosophies of science they developed were a hybrid of Thomism and positivism. This paper argues that the ideas of Duhem and Maritain about the relation of the mathematical theories of modern physics to physical reality are inadequate in light of the insights modern physics has yielded about the physical world.

Perspectival realism combines two apparently contradictory aspects: the epistemic relativity of perspectives and the mind-independence of realism. This paper examines the prospects for a coherent perspectival realism, taking the literature on scientific representation as a starting point. It is argued that representation involves two types of norms, referred to as norms of relevance and norms of accuracy. Norms of relevance fix the domain of application of a theory and the way it categorises the world, and norms of accuracy give the conditions for the theory to be true. Perspectival realism could be made coherent by taking a realist stance towards one type of norm, and a perspectival stance towards the other, by assuming they are relative to a community. This provides two versions of perspectival realism, called relevance perspectivism and accuracy perspectivism. How each option fares with respect to the challenge of incompatible models is examined. Finally, the prospects of full perspectivism are evaluated.

What are the philosophical views of contemporary professional philosophers? We surveyed many professional philosophers in order to help determine their views on 30 central philosophical issues. This article documents the results. It also reveals correlations among philosophical views and between these views and factors such as age, gender, and nationality. A factor analysis suggests that an individual's views on these issues factor into a few underlying components that predict much of the variation in those views. The results of a metasurvey also suggest that many of the results of the survey are surprising: philosophers as a whole have quite inaccurate beliefs about the distribution of philosophical views in the profession.

This paper replies to objections from perceptual distortion against the representationalist thesis that the phenomenal characters of experiences supervene on their intentional contents. It has been argued that some pairs of distorted and undistorted experiences share contents without sharing phenomenal characters, which is incompatible with the supervenience thesis. In reply, I suggest that such cases are not counterexamples to the representationalist thesis because the contents of distorted experiences are always impoverished in some way compared to those of normal experiences. This can be shown by considering limit cases of perceptual distortion, for example, maximally blurry experiences, which manifestly lack details present in clear experiences. I argue that since there is no reasonable way to draw the line between distorted experiences that have degraded content and distorted experiences that do not, we should allow that an increase in distortion is always accompanied by a change in content. This applies to perceptual distortions due to blur, double vision, perspective, and illumination conditions.

Intermodal representationalists hold that the phenomenal characters of experiences are fully determined by their contents. In contrast, intramodal representationalists hold that the phenomenal characters of experiences are determined by their contents together with their intentional modes or manners of representation, which are nonrepresentational features corresponding roughly to the sensory modalities. This paper discusses a kind of experience that provides evidence for an intermodal representationalist view: intermodal experiences, experiences that unify experiences in different modalities. I argue that such experiences are much easier to explain on the intermodal view.

We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology. We show how a combination of classification systems and mixed-membership models trained over large digital libraries can inform resource discovery in this domain. Through a novel approach of “drill-down” topic modeling—simultaneously reducing both the size of the corpus and the unit of analysis—we are able to reduce a large collection of fulltext volumes to a much smaller set of pages within six focal volumes containing arguments of interest to historians and philosophers of comparative psychology. The volumes identified in this way did not appear among the first ten results of the keyword search in the HathiTrust digital library and the pages bear the kind of “close reading” needed to generate original interpretations that is the heart of scholarly work in the humanities. Zooming back out, we provide a way to place the books onto a map of science originally constructed from very different data and for different purposes. The multilevel approach advances understanding of the intellectual and societal contexts in which writings are interpreted.

One central brand of representationalism claims that the specific phenomenal character of an experience is fully determined by its content. A challenge for this view is that cognitive and perceptual experiences sometimes seem to have the same representational content while differing in phenomenal character. In particular, it might seem that one can have faint imagery experiences or conscious thoughts with the same contents as vivid perceptual experiences. This paper argues that such cases never arise, and that they are probably metaphysically impossible. I also suggest a fully representational account of differences in vividness between phenomenal experiences.

If there is content that we reason on, cognitive content, it is in the head and accessible to reasoning mechanisms. This paper discusses the phenomenal theory of cognitive content, according to which cognitive contents are the contents of phenomenal consciousness. I begin by distinguishing cognitive content from the closely associated notion of narrow content. I then argue, drawing on prior work, that the phenomenal theory can plausibly account for the cognitive contents of many relatively simple mental states. My main focus in this paper is the question whether the phenomenal theory can account for the apparently abstract and complex cognitive contents of "high-level" thoughts. It might seem dubious that the theory can account for such cognitive contents, because cognitive phenomenology is too scarce and too thin. However, I argue there are in fact few abstract or complex cognitive contents, so the phenomenal theory's predictions are correct. This position explains some apparently irrational behavior that is otherwise hard to explain, and it makes sense of the central role of inner speech and other forms of consciousness in reasoning.

Philosophers traditionally recognize two main features of mental states: intentionality and phenomenal consciousness. To a first approximation, intentionality is the aboutness of mental states, and phenomenal consciousness is the felt, experiential, qualitative, or "what it's like" aspect of mental states. In the past few decades, these features have been widely assumed to be distinct and independent. But several philosophers have recently challenged this assumption, arguing that intentionality and consciousness are importantly related. This article overviews the key views on the relationship between consciousness and intentionality and describes our favored view, which is a version of the phenomenal intentionality theory, roughly the view that the most fundamental kind of intentionality arises from phenomenal consciousness.

One sometimes believes a proposition without grasping it. For example, a complete achromat might believe that ripe tomatoes are red without grasping this proposition. My aim in this paper is to shed light on the difference between merely believing a proposition and grasping it. I focus on two possible theories of grasping: the inferential theory, which explains grasping in terms of inferential role, and the phenomenal theory, which explains grasping in terms of phenomenal consciousness. I argue that the phenomenal theory is more plausible than the inferential theory.

This paper aims to shed new light on certain philosophical theories of perceptual experience by examining the semantics of perceptual ascriptions such as “Jones sees an apple.” I start with the assumption, recently defended elsewhere, that perceptual ascriptions lend themselves to intensional readings. In the first part of the paper, I defend three theses regarding such readings: I) intensional readings of perceptual ascriptions ascribe phenomenal properties, II) perceptual verbs are not ambiguous between intensional and extensional readings, and III) intensional perceptual ascriptions have a relational form. The second part of the paper describes the implications of I-III for theories of perceptual experience. I argue that I-III support and reconcile the three main views of perceptual experience, relationalism, disjunctivism, and representationalism. However, I-III leave open at least one important point of contention: particularism, the view that we experience external objects. I conclude by exploring the implications of accepting or denying particularism given I-III.

When we philosophers think about causation we are primarily interested in what causation is—what exactly is the relation between cause and effect? Or, more or less equivalently, how and in virtue of what is the cause connected to the effect? But we are also interested in an epistemic issue, viz., the possibility of causal knowledge: how, if at all, can causal knowledge be obtained? The two issues are, of course, conceptually distinct—but to many thinkers, there is a connection between them. A metaphysical account of causation would be useless if it did not make, at least in principle, causal knowledge possible. Conversely, many philosophers, mostly of an empiricist persuasion, have taken the possibility of causal knowledge to act as a constraint on the metaphysics of causation: no feature that cannot in principle become the object of knowledge can be attributed to causation

Sellars was one of the few systematic philosophers in the analytic tradition but he never published a magnum opus. Though his profound and complex philosophical endeavours were all tied together into a many-dimensional worldview, the dimensions of this worldview were built bit-bybit throughout his philosophical career. His papers, collections of essays, public lectures and lecture notes deal with almost every philosophical issue. One can easily see in them a megaintellect—a genius—thinking deeply and carefully about hard philosophical problems, taking the reader by the hand, as it were, and unveiling to her not only the complexity of the problems under discussion but also the hard-won truth that in philosophy there is no black and white: new insights can be gained and fresh light can be cast on old problems only by utilising the best thoughts of, and striking a balance between, competing philosophical traditions and thinkers

Philosophy of science emerged as a distinctive part of philosophy in the twentieth century. Its defining moment was the meeting (and the clash) of two courses of events: the breakdown of the Kantian philosophical tradition and the crisis in the sciences and mathematics in the beginning of the century. But what we now call philosophy of science has a rich intellectual history that goes back to the ancient Greeks. It is intimately connected with the efforts made by many thinkers to come to terms with the distinctive kind of knowledge (episteme; scientia) that science offers. Though science proper was distinguished from natural philosophy only in the nineteenth century, the philosophy of natural philosophy has had almost the very same agenda that current philosophy of science has

This paper formulates what I think is the basic problem of any attempt to characterise the abstract structure of scientific method, viz., that it has to satisfy two conflicting desiderata: it should be ampliative (contentincreasing) and it should confer epistemic warrant on its outcomes. Then, after two extreme solutions to the problem of the method, viz., Enumerative Induction and the Method of Hypothesis, are examined, the paper argues that abduction, suitably understood as Inference to the Best Explanation, offers the best description of scientific method and solves the foregoing problem in the best way: it strikes the best balance between ampliation and epistemic warrant.

Traditionally, philosophers have focused mostly on the logical template of inference. The paradigm-case has been deductive inference, which is topic-neutral and context-insensitive. The study of deductive rules has engendered the search for the Holy Grail: syntactic and topic-neutral accounts of all prima facie reasonable inferential rules. The search has hoped to find rules that are transparent and algorithmic, and whose following will just be a matter of grasping their logical form. Part of the search for the Holy Grail has been to show that the so-called scientific method can be formalised in a topic-neutral way. We are all familiar with Carnap’s inductive logic, or Popper’s deductivism or the Bayesian account of scientific method.

A natural way to think of models is as abstract entities. If theories employ models to represent the world, theories traffic in abstract entities much more widely than is often assumed. This kind of thought seems to create a problem for a scientific realist approach to theories. Scientific realists claim theories should be understood literally. Do they then imply the reality of abstract entities? Or are theories simply—and incurably—false? Or has the very idea of literal understanding to be abandoned? Is then fictionalism towards scientific theories inevitable? This paper argues that scientific realism can happily co-exist with models qua abstracta

Alan Musgrave has been one of the most important philosophers of science in the last quarter of the 20th century. He has exemplified an exceptional combination of clearheaded and profound philosophical thinking. Two seem to be the pillars of his thought: an uncompromising commitment to scientific realism and an equally uncompromising commitment to deductivism. The essays reprinted in this volume (which span a period of 25 years, from 1974 to 1999) testify to these two commitments. (There are two omissions from this collection: “Realism, Truth and Objectivity” in Realism and Anti-realism in the PhilosophyofScience(1996,Kluwer)and“HowtoDowithoutInductiveLogic” (Science&Educationvol.8,1999.Iwillmakesomereferencestothesepapersin what follows.) In the present review, instead of giving an orderly summary of the 16 papers of Essays, I discuss Musgrave’s two major commitments and raise some worries about their combination.

Mumford presents the friends of laws with a Central Dilemma, either horn of which is supposed to be utterly unpalatable. The thrust of the dilemma is this: laws are either external or internal to their instances. If they are external, they cannot govern (or determine) their instances. If they are internal, they cannot govern (or determine) their instances. Ergo, laws cannot govern (or determine) their instances. The role of this dilemma is central to Mumford’s argument against laws: they are supposed to have no credible role to play. The dilemma rests on the premise that laws, if they exist, must do something: they must play a governing role. Of course, it is one thing to say that laws play a governing role and it is quite another to say that laws must play some role. Mumford (§9.4) agonises a lot about this, but his considered view is that laws must play an x- role in virtue of which they make a difference in the determination of the world’s history. As Mumford is fully aware, the supposed ‘governing role’ of laws might be just a metaphor. Still, he thinks his Central Dilemma is powerful against any x-role that laws are supposed to play. We shall see later that this is not so. For the time being, let us play along. The central dilemma is faulty, anyway.