This book argues that the only kind of metaphysics that can contribute to objective knowledge is one based specifically on contemporary science as it really is, and not on philosophers' a priori intuitions, common sense, or simplifications of science. In addition to showing how recent metaphysics has drifted away from connection with all other serious scholarly inquiry as a result of not heeding this restriction, this book demonstrates how to build a metaphysics compatible with current fundamental physics, which, when combined (...) with metaphysics of the special sciences, can be used to unify physics with the other sciences without reducing these sciences to physics itself. Taking science metaphysically seriously, this book argues, means that metaphysicians must abandon the picture of the world as composed of self-subsistent individual objects, and the paradigm of causation as the collision of such objects. The text assesses the role of information theory and complex systems theory in attempts to explain the relationship between the special sciences and physics, treading a middle road between the grand synthesis of thermodynamics and information, and eliminativism about information. The consequences of the books' metaphysical theory for central issues in the philosophy of science are explored, including the implications for the realism versus empiricism debate, the role of causation in scientific explanations, the nature of causation and laws, the status of abstract and virtual objects, and the objective reality of natural kinds. (shrink)

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French (...) & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...) term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed into their (...) parts and their activities can be decomposed into component operations. A potent bridge between flat networks and hierarchical mechanisms is provided by biological ontologies, both those curated by hand such as Gene Ontology and those extracted directly from databases such as Network Extracted Ontology. I examine several examples in which by applying ontologies to networks, systems biologists generate new hypotheses about mechanisms and characterize these novel strategies for developing mechanistic explanations. (shrink)

Bas C. van Fraassen presents an original exploration of how we represent the world.

This paper proposes an account of scientific data that makes sense of recent debates on data-driven and ‘big data’ research, while also building on the history of data production and use particularly within biology. In this view, ‘data’ is a relational category applied to research outputs that are taken, at specific moments of inquiry, to provide evidence for knowledge claims of interest to the researchers involved. They do not have truth-value in and of themselves, nor can they be seen as (...) straightforward representations of given phenomena. Rather, they are fungible objects defined by their portability and prospective usefulness as evidence. (shrink)

I argue for the claim in the title. Along the way, I also address an independently interesting question: what is metaphysics, anyway? I think that the typical characterizations of metaphysics are inadequate, that a better one is available, and that the better one helps explain why metaphysics is no more problematic than the rest of philosophy.

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

The Health Level 7 Reference Information Model (HL7 RIM) is lauded by its authors as ‘the foundation of healthcare interoperability’. Yet even after some 10 years of development work, the RIM is still subject to a variety of logical and ontological flaws which have placed severe obstacles in the way of those who are called upon to develop implementations. We offer evidence that these obstacles are insurmountable and that the time has come to abandon an unworkable paradigm.

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Critics of contemporary metaphysics argue that it attempts to do the hard work of science from the ease of the armchair. Physics, not metaphysics, tells us about the fundamental facts of the world, and empirical psychology is best placed to reveal the content of our concepts about the world. Exploring and understanding the world through metaphysical reflection is obsolete. In this paper, I will show why this critique of metaphysics fails, arguing that metaphysical methods used to make claims about the (...) world are similar to scientific methods used to make claims about the world, but that the subjects of metaphysics are not the subjects of science. Those who argue that metaphysics uses a problematic methodology to make claims about subjects better covered by natural science get the situation exactly the wrong way around: metaphysics has a distinctive subject matter, not a distinctive methodology. The questions metaphysicians address are different from those of scientists, but the methods employed to develop and select theories are similar. In the first section of the paper, I will describe the sort of subject matter that metaphysics tends to engage with. In the second section of the paper, I will show how metaphysical theories are classes of models and discuss the roles of experience, common sense and thought experiments in the construction and evaluation of such models. Finally, in the last section I will discuss the way these methodological points help us to understand the metaphysical project. Getting the right account of the metaphysical method allows us to better understand the relationship between science and metaphysics, to explain why doing metaphysics successfully involves having a range of different theories, to understand the role of thought experiments involving fictional worlds, and to situate metaphysical realism in a scientifically realist context. (shrink)

This essay introduces the volume Scientific Pluralism (Volume 19 of Minnesota Studies in Philosophy of Science). Varieties of recent pluralisms are surveyed, the difference between monism and pluralism vis a vis the sciences is clarified, and the authors’ notion of scientific pluralism is advanced.

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)

In “Ontological realism: Methodology or misdirection?” I offered a detailed critique of the position referred to as “realism” taken by Barry Smith and Werner Ceusters. This position is claimed to serve as the basis for a “realist methodology” that they seek to impose on the development of scientific ontologies, particularly within the biomedical sciences. Here, in part responding to a reply to those criticisms by Smith and Ceusters, I return the focus to an examination of fundamental incoherencies in this realist (...) approach and propose an alternative that is amenable to much of what Smith and Ceusters hope to accomplish. And I sketch what I believe is needed to advance ontology theory and practice in the sciences. (shrink)

In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...) fact necessary for understanding and using terminologies and ontologies in science. -/- This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose. (shrink)

With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

Every Thing Must Go aruges that the only kind of metaphysics that can contribute to objective knowledge is one based specifically on contemporary science as it ...

A systematic overview of modern metaphysics, A Survey of Metaphysics covers all of the most important topics in the field. It adopts the fairly traditional conception of metaphysics as a subject that deals with the deepest questions that can be raised concerning the fundamental structure of reality as a whole. The book is divided into six main sections that address the following themes: identity and change, necessity and essence, causation, agency and events, space and time, and universals and particulars. It (...) focuses on contemporary views and issues throughout, rather than on the history of metaphysics. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential (...) ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (shrink)

The paper indicates how social kinds may be internally and objectively unified in a way continuous with physical kinds. It argues that the practice of theorizing is continuous with other practices to the extent that theorists, like anyone engaged in a practice, needs to make choices that are responsive to purposes (and corresponding values) guiding the practice. The paper discusses Epstein's theory of anchoring, and argues for a theory of scaffolding social kinds.

This paper aims to better motivate the naturalization of metaphysics by identifying and criticizing a class of theories I call ’free range metaphysics’. I argue that free range metaphysics is epistemically inadequate because the constraints on its content—consistency, simplicity, intuitive plausibility, and explanatory power—are insufficiently robust and justificatory. However, since free range metaphysics yields clarity-conducive techniques, incubates science, and produces conceptual and formal tools useful for scientifically engaged philosophy, I do not recommend its discontinuation. I do recommend, however, ending the (...) discipline’s bad faith. That is, I urge that free range metaphysics not be taken to have fully satisfactory epistemic credentials over and above its pragmatic ones. (shrink)

This book introduces a new approach to the issue of radical scientific revolutions, or "paradigm-shifts," given prominence in the work of Thomas Kuhn. The book articulates a dynamical and historicized version of the conception of scientific a priori principles first developed by the philosopher Immanuel Kant. This approach defends the Enlightenment ideal of scientific objectivity and universality while simultaneously doing justice to the revolutionary changes within the sciences that have since undermined Kant's original defense of this ideal. Through a modified (...) Kantian approach to epistemology and philosophy of science, this book opposes both Quinean naturalistic holism and the post-Kuhnian conceptual relativism that has dominated recent literature in science studies. Focussing on the development of "scientific philosophy" from Kant to Rudolf Carnap, along with the parallel developments taking place in the sciences during the same period, the author articulates a new dynamical conception of relativized a priori principles. This idea applied within the physical sciences aims to show that rational intersubjective consensus is intricately preserved across radical scientific revolutions or "paradigm-shifts and how this is achieved. (shrink)

This fine collection of essays by a leading philosopher of science presents a defence of integrative pluralism as the best description for the complexity of scientific inquiry today. The tendency of some scientists to unify science by reducing all theories to a few fundamental laws of the most basic particles that populate our universe is ill-suited to the biological sciences, which study multi-component, multi-level, evolved complex systems. This integrative pluralism is the most efficient way to understand the different and complex (...) processes - historical and interactive - that generate biological phenomena. This book will be of interest to students and professionals in the philosophy of science. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

Recent philosophy of science has been seized by what may appear a schizophrenic attitude towards analytic metaphysics. Some philosophers of science have embraced metaphysical theorizing as an important tool for interpreting and extending scientific theories, while others reject analytic metaphysics as misguided, futile, or epistemically impotent. The idea of naturalized metaphysics—metaphysics appropriately ‘grounded’ in the details of empirical science—offers one possibility of a rapprochement between these seemingly conflicting attitudes. In this chapter, however, it is argued that the crucial notion of (...) ‘grounding’, and hence the idea of naturalized metaphysics itself, have not yet been articulated in a compelling manner. The beginnings of an articulation are sketched. (shrink)

This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of integration, so that rather than attempting to offer (...) a universal construal of what integrations is, philosophers have to analyze in concrete cases in what respects particular aspects of scientific theorizing and/or practice are ‘integrative’ and how this instance of integration works and was achieved. (shrink)

This chapter introduces a distinctive approach for scientific metaphysics. Instead of drawing metaphysical conclusions by interpreting the most basic theories of science, this approach draws metaphysical conclusions by analyzing how multifaceted practices of science work. Broadening attention opens the door to drawing metaphysical conclusions from a wide range of sciences. This chapter analyzes conceptual practice in genetics to argue that the reality investigated by biologists lacks an overall structure. It expands this conclusion to motivate the no general structure thesis, which (...) states that the world lacks a general, overall structure that spans scales. It concludes that the no general structure thesis counts as metaphysics because it says something very important and general about the world. This thesis informs science as well as philosophy of science, and it provides a useful perspective for societies that look upon science to help solve complex problems in our changing world. (shrink)

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...) settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)