Ioannis G. Ntagkas

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

This paper examines whether biblical descriptions of the intermediate state imply dualism of the sort that rules out physicalism. Certain passages in the Bible seem to describe persons or souls existing without their bodies in an intermediate state between death and resurrection. For this reason, these passages appear to imply a form of dualism. Some Christian physicalists have countered that the passages in question are in fact compatible with physicalism. For it is compatible with physicalism that, although we are necessarily constituted by physical bodies, we can continue to exist without our current bodies in the intermediate state by being constituted by replacement bodies. I argue that broadly Gricean considerations significantly weaken this response. In its place, I propose a new, linguistic objection to the biblical argument for dualism. The linguistic objection says that biblical descriptions of an intermediate state cannot imply dualism in the sense that contradicts physicalism because physicalism is defined by a concept of the physical derived from modern physics, and no term in the biblical languages expresses that concept. I argue that the linguistic objection is less vulnerable to Gricean considerations than the constitution objection. On the other hand the linguistic objection also makes concessions to dualism that some Christian physicalists will find unacceptable. And it may be possible to reinforce the biblical argument for dualism by appeal to recent research on ‘common-sense dualism’. The upshot for Christian physicalists who wish to remain open to the biblical case for an intermediate state is therefore partly good, partly bad. The prospects for a Biblical argument for dualism in the sense that contradicts physicalism are limited but remain open.

This book evaluates the widespread preference in philosophy of mind for varieties of property dualism over other alternatives to physicalism. It takes the standard motivations for property dualism as a starting point and argues that these lead directly to nonphysical substances resembling the soul of traditional metaphysics. In the first half of the book, the author clarifies what is at issue in the choice between theories that posit nonphysical properties only and those that posit nonphysical substances. The crucial question, he argues, is whether one posits nonphysical things that satisfy an Aristotelian-Cartesian independence definition of substance: nonphysical things that could exist in the absence of anything else. In the second half, the author argues that standard and Russellian monist forms of property dualism are far less plausible than we usually suppose. Most significantly, the presuppositions of one of the leading arguments for property dualism, the conceivability argument, lead by parity of reasoning to the view that conscious subjects are nonphysical substances. He concludes that if you posit nonphysical properties in response to the mind-body problem then you should be prepared to posit nonphysical substances as well. Mainstream philosophy of mind must take nonphysical substances far more seriously than it has done for the best part of a century. The Mind-Body Problem and Metaphysics will be of interest to scholars and advanced students working in philosophy of mind, metaphysics, and the history of philosophy.

In Galileo's Error, Philip Goff sets out a manifesto for a post-Galilean science of consciousness. Article four of the manifesto reads: 'Anti-Dualism: Consciousness is not separate from the physical world; rather consciousness is located in the intrinsic nature of the physical world.' I argue that there is an important sense of ‘dualism’ in which Goff’s arguments are not only compatible with but entail dualism, and not only dualism but substance dualism. Substance dualism, in the sense I have in mind, is the view that (i) there are two sides to reality, a fundamentally mental side and a fundamentally nonmental side; and (ii) the fundamentally mental side consists of mental substances resembling Cartesian souls. I do not suggest that this is bad news for post-Galilean science of consciousness. My aim is rather to push for a certain view about what a theory of consciousness motivated by Goff’s arguments must look like.

This groundbreaking, open access volume analyses and compares data practices across several fields through the analysis of specific cases of data journeys. It brings together leading scholars in the philosophy, history and social studies of science to achieve two goals: tracking the travel of data across different spaces, times and domains of research practice; and documenting how such journeys affect the use of data as evidence and the knowledge being produced. The volume captures the opportunities, challenges and concerns involved in making data move from the sites in which they are originally produced to sites where they can be integrated with other data, analysed and re-used for a variety of purposes. The in-depth study of data journeys provides the necessary ground to examine disciplinary, geographical and historical differences and similarities in data management, processing and interpretation, thus identifying the key conditions of possibility for the widespread data sharing associated with Big and Open Data. The chapters are ordered in sections that broadly correspond to different stages of the journeys of data, from their generation to the legitimisation of their use for specific purposes. Additionally, the preface to the volume provides a variety of alternative “roadmaps” aimed to serve the different interests and entry points of readers; and the introduction provides a substantive overview of what data journeys can teach about the methods and epistemology of research.

I present two relatively independent sets of remarks on common causes and the violation of Bell inequalities in algebraic quantum field theory. The first set of remarks concerns the possibility of reconciling Reichenbachian ideas on common causes with quantum field theory in the face of an already known difficulty: the event shown to satisfy statistical relations for being the common cause of two correlated events has been associated with the union, rather than the intersection, of the backward light cones of the correlated events. I explore a way of overcoming this difficulty by considering the common cause to be a conjunction of suitably located events. But I show that this line of thought too is beset with interpretational problems. My second set of remarks concerns the type of inequality one may derive from the common-common cause hypothesis: I argue, on grounds of interpretation, that the Clauser-Horne type, and not the Bell type, of inequalities emerge more naturally in this context

In this paper, we attempt to explicate Salmon’s idea of a causal process, as defined in terms of the mark method, in the context of C*-dynamical systems. We prove two propositions, one establishing mark manifestation infinitely many times along a given interval of the process, and, a second one, which establishes continuous manifestation of mark with the exception of a countable number of isolated points. Furthermore, we discuss how these results can be implemented in the context of the Haag–Araki theories of relativistic quantum fields on Minkowski spacetime.

In 2013, we welcomed the paperback edition of this voluminous work, authored by Bernard d’Espagnat—a theoretical physicist having a special interest in philosophy and, particularly, in the investigation of the conceptual foundations of physics, dated from the mid 60s. The book tries to articulate a view on realism, open realism, abiding it by the developments in the twentieth-century physics.The work consists of two parts. In the first one, the author undertakes a negative task: to question what he calls objectivist realism in the light of quantum theory. Firstly, the author rejects the view, inherited by Descartes, that there is an ultimate reality which can be described using familiar concepts such as figures, sizes, shapes and motions of bodies. Secondly, he rejects what he calls multitudinist view of the world—i.e., the view on which the ultimate reality consists of separate things and that the wholes are just the sum of their constituent parts—in favor of a holistic view which sug ..

Anything other than paraphrasing the well-known Heraclitean aphorism would not be more appropriate to portray the crux of the contribution of the three philosophers of the Budapest School, Gábor Hofer-Szabó, Miklós Rédei and Lázló E. Szabó, in the ongoing discussion of the principle of the common cause . Indeed, ‘common causes love to hide’ and for that reason critics and aspirant falsifiers of PCC find correlations which, at a first level of analysis, might lack a common cause explanation. But as the authors argue such correlations do not amount to disconfirming evidence for the principle, since PCC does not specify where to search for a common cause of a correlation; it just states that there is one. PCC is neither falsifiable, nor verifiable; it is a metaphysical doctrine that can only be assessed for its plausibility in the light of theories of empirical science. This idea fosters the investigation of the existence of common causes of correlations in two fundamental physical t ..

To consider metaphysical claims a priori and devoid of empirical content, is a rather commonplace received opinion. This paper attempts an exploration of a contemporary philosophical heresy: it is possible to test metaphysical claims if they play an indispensable role in producing empirical success, i.e. novel predictions. To do so one, firstly, needs to express the metaphysical claims employed in the logico-mathematical language of a scientific theory, i.e. to explicate them. Secondly, one should have an understanding of what it is to test and to verify or to falsify a metaphysical claim. Finally, one also need to consider the philosophical practice of testing a metaphysical claim. These three aspects are introduced in this paper and they are illustrated by means of the metaphysical concept of common cause and the principle of the common cause.

What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends the LRQ to characterize approaches with sequences of questions and factors. I highlight the importance that ordering one’s investigation plays in approaches at the level of adaptationism by analyzing two research programs in community ecology: competitionists and neutralists. Competitionists and neutralists take opposed starting points and use explanatory and developmental heuristics to consider more factors in due time. On the Ordered Factors Proposal, these approaches are not only the ecological factors they are open to considering but also the order in which they will consider them. My disagreement with Lloyd’s over how to characterize methodological approaches reflects different views about methodological monism and pluralism.

The Quine-Putnam Indispensability argument is the argument for treating mathematical entities on a par with other theoretical entities of our best scientific theories. This argument is usually taken to be an argument for mathematical realism. In this chapter I will argue that the proper way to understand this argument is as putting pressure on the viability of the marriage of scientific realism and mathematical nominalism. Although such a marriage is a popular option amongst philosophers of science and mathematics, in light of the indispensability argument, the marriage is seen to be very unstable. Unless one is careful about how the Quine-Putnam argument is disarmed, one can be forced to either mathematical realism or, alternatively, scientific instrumentalism. I will explore the various options: (i) finding a way to reconcile the two partners in the marriage by disarming the indispensability argument (Jody Azzouni [2], Hartry Field [13, 14], Alan Musgrave [18, 19], David Papineau [21]); (ii) embracing mathematical realism (W.V.O. Quine [23], Michael Resnik [25], J.J.C. Smart [27]); and (iii) embracing some form of scientific instrumentalism (Ot´ avio Bueno [7, 8], Bas van Fraassen [30]). Elsewhere [11], I have argued for option (ii) and I won’t repeat those arguments here. Instead, I will consider the difficulties for each of the three options just mentioned, with special attention to option (i). In relation to the latter, I will discuss an argument due to Alan Musgrave [19] for why option (i) is a plausible and promising approach. From the discussion of Musgrave’s argument, it will emerge that the issue of holist versus separatist theories of confirmation plays a curious role in the realism–antirealism debate in the philosophy of mathematics. I will argue that if you take confirmation to be an holistic matter—it’s whole theories (or significant parts thereof) that are confirmed in any experiment—then there’s an inclination to opt for (ii) in order to resolve the marital tension outlined above..

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

It is my aim in this paper to show that the contemporary assimilation of essence to modality is fundamentally misguided and that, as a consequence, the corresponding conception of metaphysics should be given up. It is not my view that the modal account fails to capture anything which might reasonably be called a concept of essence. My point, rather, is that the notion of essence which is of central importance to the metaphysics of identity is not to be understood in modal terms or even to be regarded as extensionally equivalent to a modal notion. The one notion is, if I am right, a highly refined version of the other; it is like a sieve which performs a similar function but with a much finer mesh.

Contemporary process metaphysics has achieved a number of important results, most significantly in accounting for emergence, a problem on which substance metaphysics has foundered since Plato. It also faces trenchant problems of its own, among them the related problems of boundaries and individuation. Historically, the quest for ontology may thus have been largely responsible for the persistence of substance metaphysics. But as Plato was well aware, an ontology of substantial things raises serious, perhaps insurmountable problems for any account of our epistemic access to such things. Physical things are subject to change, and as such, they are poor objects of knowledge—if knowledge is to be more reliable than mere opinion. There is a reading of Plato’s Theaetetus on which knowledge may be understood as a relation between an epistemic subject and a logos, where logoi are intrinsically dialectical, and where dialectic is a kind of intersubjective activity. Insofar as this epistemology may be attributed to Plato, the project of this paper is Platonic in spirit. It is also, in a sense, Kantian, in that it divorces ontology from the search for things-in-themselves, redirecting our attention from things to objects: epistemic objects. Such objects can be understood, as Maurice Merleau-Ponty proposed, as shared by multiple subjects by virtue of their participation in an intersubjective world, constituted by what Shaun Gallagher calls participatory sense-making. On an epistemology constructed in this way, the fact that both epistemic objects and their subject are mutable is no obstacle to knowledge. Far-from-equilibrium systems are forever mutable; at thermodynamic equilibrium, there would be neither subject, nor object. Epistemic objects, on this picture, are metastable loci of interactive potential

This chapter provides an overview of the basic research strategies and analytic techniques deployed in computational cognitive neuroscience. On the one hand, “top-down” strategies are used to infer, from formal characterizations of behavior and cognition, the computational properties of underlying neural mechanisms. On the other hand, “bottom-up” research strategies are used to identify neural mechanisms and to reconstruct their computational capacities. Both of these strategies rely on experimental techniques familiar from other branches of neuroscience, including functional magnetic resonance imaging, single-cell recording, and electroencephalography. What sets computational cognitive neuroscience apart, however, is the explanatory role of analytic techniques from disciplines as varied as computer science, statistics, machine learning, and mathematical physics. These techniques serve to describe neural mechanisms computationally, but also to drive the process of scientific discovery by influencing which kinds of mechanisms are most likely to be identified. For this reason, understanding the nature and unique appeal of computational cognitive neuroscience requires not just an understanding of the basic research strategies that are involved, but also of the formal methods and tools that are being deployed, including those of probability theory, dynamical systems theory, and graph theory.

Scientific realism is a thesis about the success of science. Most traditionally: science has been so successful at prediction and guiding action because its best theories are true (or approximately true or increasing in their degree of truth). If science is in the business of doing its best to generate true theories, then we should turn to those theories for explanatory knowledge, predictions, and guidance of our actions and decisions. Views that are popular in contemporary philosophy of science about scientific modeling and the centrality of idealization create several challenges for this traditional form of scientific realism. Yet the basic idea behind scientific realism that science has been and will continue to be epistemically successful is deeply appealing. This chapter explores the challenges posed by idealization and scientific modeling to motivate a scientific realism fully divorced from the idea that science is in the business of generating true theories. On the resulting view, the objects of scientific knowledge are causal patterns, so this knowledge only ever provides partial, simplified accounts of a complex reality. This variety of selective realism better accommodates the nature of our present-day scientific successes and offers an interpretation of scientific progress that resists the antirealist’s pessimism.

In his chapter in this volume, Christopher Pincock develops an argument for scientific realism based on scientific understanding, and he argues that Giere’s (2006) and my (2017, 2020) commitment to the context-dependence of scientific understanding or knowledge renders our views unable to account for an essential step in how scientists come to know. Meanwhile, in my chapter in this volume, I motivate a view that I call "causal pattern realism." In this response to Pincock's chapter, I will sketch a revised version of Pincock’s argument for realism that is consistent with causal pattern realism. Then I will respond to Pincock’s concern that the context-dependence of understanding on my view would interfere with the scientific community’s ability to extrapolate from specific experimental and observational contexts as needed to develop knowledge. My goal is not to convince anyone to be a causal pattern realist but rather to create the space for such a view, taking into account the concerns motivating Pincock.

There is widespread recognition at universities that a proper understanding of science is needed for all undergraduates. Good jobs are increasingly found in fields related to Science, Technology, Engineering, and Medicine (STEM), and science now enters almost all aspects of our daily lives. For these reasons, scientific literacy and an understanding of scientific methodology are a foundational part of any undergraduate education. Recipes for Science provides an accessible introduction to the main concepts and methods of scientific reasoning. With the help of an array of contemporary and historical examples, definitions, visual aids, and exercises for active learning, the textbook helps to increase students’ scientific literacy. The first part of the book covers the definitive features of science: naturalism, experimentation, modeling, and the merits and shortcomings of both activities. The second part covers the main forms of inference in science: deductive, inductive, abductive, probabilistic, statistical, and causal. The book concludes with a discussion of explanation, theorizing and theory-change, and the relationship between science and society. The textbook is designed to be adaptable to a wide variety of different kinds of courses. In any of these different uses, the book helps students better navigate our scientific, 21st-century world, and it lays the foundation for more advanced undergraduate coursework in a wide variety of liberal arts and science courses. Selling Points Helps students develop scientific literacy—an essential aspect of _any_ undergraduate education in the 21 st century, including a broad understanding of scientific reasoning, methods, and concepts Written for all beginning college students: preparing science majors for more focused work in particular science; introducing the humanities’ investigations of science; and helping non-science majors become more sophisticated consumers of scientific information Provides an abundance of both contemporary and historical examples Covers reasoning strategies and norms applicable in all fields of physical, life, and social sciences, _as well as_ strategies and norms distinctive of specific sciences Includes visual aids to clarify and illustrate ideas Provides text boxes with related topics and helpful definitions of key terms, and includes a final Glossary with all key terms Includes Exercises for Active Learning at the end of each chapter, which will ensure full student engagement and mastery of the information include earlier in the chapter Provides annotated ‘For Further Reading’ sections at the end of each chapter, guiding students to the best primary and secondary sources available Offers a Companion Website, with: For Students: direct links to many of the primary sources discussed in the text, student self-check assessments, a bank of exam questions, and ideas for extended out-of-class projects For Instructors: a password-protected Teacher’s Manual, which provides student exam questions with answers, extensive lecture notes, classroom-ready Power Point presentations, and sample syllabi Extensive Curricular Development materials, helping any instructor who needs to create a Scientific Reasoning Course, ex nihilo.

Biology seems to present local and transitory regularities rather than immutable laws. To account for these historically constituted regularities and to distinguish them from mathematical invariants, Montévil and Mossio (Journal of Theoretical Biology 372:179–191, 2015) have proposed to speak of constraints. In this article we analyse the causal power of these constraints in the evolution of biodiversity, i.e., their positivity, but also the modality of their action on the directions taken by evolution. We argue that to fully account for the causal power of these constraints on evolution, they must be thought of in terms of normativity. In this way, we want to highlight two characteristics of the evolutionary constraints. The first, already emphasised as reported by Gould (The structure of evolutionary theory, Harvard University Press, 2002), is that these constraints are both produced by and producing biological evolution and that this circular causation creates true novelties. The second is that this specific causality, which generates unpredictability in evolution, stems not only from the historicity of biological constraints, but also from their internalisation through the practices of living beings.