Philosophers of science traditionally have ignored the details of scientific research, and the result has often been theories that lack relevance either to science or to philosophy in general. In this volume, leading philosophers of biology discuss the limitations of this tradition and the advantages of the "naturalistic turn"—the idea that the study of science is itself a scientific enterprise and should be conducted accordingly. This innovative book presents candid, informal debates among scholars who examine the benefits and problems of (...) studying science in the same way that scientists study the natural world. Callebaut achieves the effect of face-to-face engagement through separate interviews with participants. Contributors include William Bechtel, Robert Brandon, Richard M. Burian, Donald T. Campbell, Patricia Churchland, Jon Elster, Ronald N. Giere, David L. Hull, Philip Kitcher, Karin Knorr Cetina, Bruno Latour, Richard Levins, Richard C. Lewontin, Elisabeth Lloyd, Helen Longino, Thomas Nickles, Henry C. Plotkin, Robert J. Richards, Alexander Rosenberg, Michael Ruse, Dudley Shapere, Elliott Sober, Ryan Tweney, and William Wimsatt. "Why can't we have both theoretical ecology and natural histories, lovingly done?"—Philip Kitcher "Don't underestimate the arrogance of philosophers!"—Elisabeth Lloyd. (shrink)

This collection broadens the scientific discussion of modularity by bringing together experts from a variety of disciplines, including artificial life, ...

This volume has its already distant or1g1n in an inter national conference on Evolutionary Epistemology the editors organized at the University of Ghent in November 1984. This conference aimed to follow up the endeavor started at the ERISS (Epistemologically Relevant Internalist Sociology of Science) conference organized by Don Campbell and Alex Rosen berg at Cazenovia Lake, New York, in June 1981, whilst in jecting the gist of certain current continental intellectual developments into a debate whose focus, we thought, was in (...) danger of being narrowed too much, considering the still underdeveloped state of affairs in the field. Broadly speaking, evolutionary epistemology today con sists of two interrelated, yet qualitatively distinct inves tigative efforts. Both are drawing on Darwinian concepts, which may explain why many people have failed to discriminate them. One is the study of the evolution of the cognitive apparatus of living organisms, which is first and foremost the province of biologists and psychologists (H. C. Plotkin, Ed. , Learning, Development, and Culture: Essays in Evolu tionary Epistemology, New York, Wiley, 1984), although quite a few philosophers - professional or vocational - have also felt the need to express themselves on this vast subject (F. M. Wuketits, Ed. , Conce ts and Approaches in Evolutionary Epistemology, Dordrecht Boston, Reidel, 1984). The other approach deals with the evolution of science, and has been dominated hitherto by (allegedly) 'naturalized' philosophers; no book-length survey of this literature is available at present. (shrink)

Moral perceptualism is the theory that perception and perceptual experience is attuned to moral features in our environment. This idea has received renewed attention in the last 15–20 years, for its potential to do theoretical work in moral epistemology and moral psychology. In this paper, I review the main motivations and arguments for moral perceptualism, the variety of theories that go under the heading of “moral perception,” and the three biggest challenges to moral perception. https://youtu.be/9cc_1zykq80.

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science to slip into (...) the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena. (shrink)

Proponents of impure moral perception claim that, while there are perceptual moral experiences, these experiences epistemically depend on a priori moral knowledge. Proponents of pure moral perception claim that moral experiences can justify independently of substantive a priori moral knowledge. Some philosophers, most notably David Faraci, have argued that the pure view is mistaken, since moral perception requires previous moral background knowledge, and such knowledge could not itself be perceptual. I defend pure moral perception against this objection. I consider two (...) ways to understand the notion of “background knowledge” that is crucial to the objection. On a reading, the claim that background knowledge is necessary for moral perception is likely false. On a second and weaker reading, the claim is true, but the background knowledge in question could be perceptual, and thus compatible with pure moral perception. Thus, the objection fails. (shrink)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

Against the background of the contemporary debate about financialisation, the paper conceptualises the capitalist labour economy as fundamentally a monetary system. It argues that money is not a capitalist means of organising its labour economy but that it is rather a capitalist end. The argument examines and finds wanting conceptions of money in political economy, including Keynesianism and neoliberalism, and argues that the debate about financialisation is fundamentally based on the propositions of political economy. It holds that Marx’s critique of (...) political economy conceives of money as the form of value and expounds money-making as the purpose of the capital labour economy. Thus, the labour theory of value is fundamentally a monetary theory of value, labour is the means of valorisation, and that is, of money in process, and as such capital. Making money out of money is capital as its most rational. In the form of credit, money posits wealth as a claim on future surplus value. (shrink)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or (...) subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

Two major philosophical movements have sought to fundamentally rethink the relationship between humans and their environment(s): environmental ethics and enactivism. Surprisingly, they virtually never refer to or seek inspiration from each other. The goal of this analysis is to bridge the gap. Our main purpose, then, is to address, from the enactivist angle, the conceptual backbone of environmental ethics, namely the concept of intrinsic value. We argue that intrinsic value does indeed exist, yet its "intrinsicality" does not boil down to (...) being independent of the interests and needs of humans. Rather, it is brought forth by what we callshared enactionof an axiological domain. The latter is built upon such core posits of enactivism as autonomy, enaction, participatory sense-making as well as the most recent concept of loving as knowing proposed by Hanne De Jaegher. (shrink)

Plato's dialogues frequently criticize traditional Greek myth, yet Plato also integrates myth with his writing. Daniel S. Werner confronts this paradox through an in-depth analysis of the Phaedrus, Plato's most mythical dialogue. Werner argues that the myths of the Phaedrus serve several complex functions: they bring nonphilosophers into the philosophical life; they offer a starting point for philosophical inquiry; they unify the dialogue as a literary and dramatic whole; they draw attention to the limits of language and the (...) limits of knowledge; and they allow Plato to co-opt cultural authority as a way of defining and legitimating the practice of philosophy. Platonic myth, as a species of traditional tale, is thus both distinct from philosophical dialectic and similar to it. Ultimately, the most powerful effect of Platonic myth is the way in which it leads readers to participate in Plato's dialogues and to engage in a process of self-examination. (shrink)

Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European (...) philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.”. (shrink)

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...) which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems. (shrink)

This paper aims to elucidate a kind of ignorance that is more fundamental than a momentary lack of information, but also not a kind of ignorance that is built into the subject’s cognitive apparatus such that the subject can’t do anything about it. The paper sets forth the notion of cognitive confinement, which is a contingent, yet relatively stable state of being structurally or systematically unable to gain information from an environment, determined by patterns of interaction between the subject and (...) the world. In order to unpack the idea of cognitive confinement the paper discusses niche construction theory, and then, in greater detail, the notion of cognitive niche once proposed by John Tooby and Irven DeVore. Cognitive confinement is here imagined as a pathologized form of cognitive niche. This posit is substantiated by referring to a case that has come to the fore in recent years and raised debate around the world: the rise of so-called filter bubbles. They turn out to be instantiations of a more general phenomenon of cognitive confinement. (shrink)

We explore the different meanings of “quantum uncertainty” contained in Heisenberg’s seminal paper from 1927, and also some of the precise definitions that were developed later. We recount the controversy about “Anschaulichkeit”, visualizability of the theory, which Heisenberg claims to resolve. Moreover, we consider Heisenberg’s programme of operational analysis of concepts, in which he sees himself as following Einstein. Heisenberg’s work is marked by the tensions between semiclassical arguments and the emerging modern quantum theory, between intuition and rigour, and between (...) shaky arguments and overarching claims. Nevertheless, the main message can be taken into the new quantum theory, and can be brought into the form of general theorems. They come in two kinds, not distinguished by Heisenberg. These are, on one hand, constraints on preparations, like the usual textbook uncertainty relation, and, on the other, constraints on joint measurability, including trade-offs between accuracy and disturbance. (shrink)

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

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...) this paper, we describe the theoretical foundations of this paradigm and show how it is being applied to the solution of analogous problems of ambiguous identification in the fields of digital rights management, corporate memories and decision algorithms. (shrink)

Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...) clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We here address a challenge to this realist approach relating to the diagnosis of malaria, and show how this challenge can be resolved by appeal to Basic Formal Ontology (BFO) and to the Ontology for General Medical Science (OGMS) constructed in its terms. (shrink)

This is the second of two articles in which I reflect on “generalized Darwinism” as currently discussed in evolutionary economics. In the companion article (Callebaut, Biol Theory 6. doi: 10.1007/s13752-013-0086-2, 2011, this issue) I approached evolutionary economics from the naturalistic perspectives of evolutionary epistemology and the philosophy of biology, contrasted evolutionary economists’ cautious generalizations of Darwinism with “imperialistic” proposals to unify the behavioral sciences, and discussed the continued resistance to biological ideas in the social sciences. Here I assess Generalized Darwinism (...) as propounded by Geoffrey Hodgson, Thorbjørn Knudsen, and others, concentrating on the roles of theory and model building in science (and the roles of analogy and metaphor therein), generative replication, and the relation between selection and self-organization. I then point to advances in current biology that promise to be more fruitful as sources of inspiration for evolutionary economics than the project to generalize Darwinism in its current, “hardened Modern Synthesis” form; and I draw some conclusions. (shrink)

Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus on business (...) aspects and not enough on involvement of the right sorts of researchers, in particular those that are able to see how the data and information relate to the entities of concern on the side of the patient. The lack of a central focus on the patient, and the associated focus on ‘concepts’, have spawned a variety of mutually incompatible terminologies exhibiting non-resolvable overlap. The predominance of the healthcare IT industry in the writing and selection of semantic interoperability standards mitigates against the benefits that standards, when well designed, can bring about. (shrink)

In experimental economics one can confront a “don’t!”, as in “do not deceive your participants!”, as well as a “do!”, as in “incentivize choice making!”. Neither exists in experimental psychology. Further controversies exist in data collection methods, e.g., play strategy (vector) method in game experiments, and how to guarantee external and internal validity by describing experimental scenarios by field-related vignettes or by abstract, often formal, rules as it is used in decision and game theory. We emphasize that differences between the (...) experimental methodology of the two disciplines are minor rather than substantial and suggest that such differences should be resolved, as much as possible, through empirical research. Rather than focusing on familiar debates, we suggest to substitute the revealed-motive approach in experimental economics by designs whose data not only inform about choice, but also about the reasoning dynamics. (shrink)

Repetitive thinking predicts and maintains depression and anxiety, yet the role of RT in the perinatal context has been under-researched. Further, the content and themes that emerge during RT in the perinatal period have been minimally investigated. We recruited an online community sample of women who had their first baby within the past 12 months. Participants completed a battery of self-report questionnaires which included four open-ended questions about the content of their RT. Responses to the latter were analyzed using an (...) inductive thematic analysis approach. Participants reported RT about a range of unexpected emotional responses to becoming a new mother, impact on their sleep and cognitive functioning, as well as the impact on their identity, sense of self, lifestyle, achievements, and ability to function. RT was commonly experienced in first-time mothers, and the themes that emerged conveyed an overall sense of discrepancy between expectations and reality, as well as adjustment to profound change. By providing insight into the content of RT in new mothers, the findings of our study have scope to inform the content of interventions that seek to prevent and treat postnatal mental health problems, particularly those which target key psychological processes such as RT. (shrink)

For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...) realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future. (shrink)

According to an epistemically optimistic view of empathy – understood as the simulation of another person’s state – agents learn (1) in which state the target is and (2) what it is like for her to be in this state. Assuming the necessity of justification for knowledge, this view faces the challenge of how imagination can justify beliefs. Constraining simulation to match the target’s state seems to be a solution. Because of the abundance of plausible psychological reactions towards a specific (...) situation, however, we need to know how the target reacts in order to simulate the correct mental state. According to narrativists, we gain this knowledge by means of testimony, which makes simulation superfluous. For those who accept that (2) has epistemic value, the paper presents a solution to the problem of justification that assigns a central role to both testimony and imagination. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...) comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...) such real things in information artifacts? We here outline the problems faced by HL7 in providing answers to such questions, problems which arise because of the lack of anything like a coherent ontology in the HL7 standard, and we make some recommendations for future improvements. (shrink)