Ioannidis [Why most published research findings are false. PLoS Med 2: e124 ] identifies six factors that contribute to explaining why most of the current published research findings are more likely to be false than true, and argues that for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this article, we argue that three “hot” areas in current biological research, viz., agent-based modeling, evolutionary developmental biology, and systems biology, are especially (...) prone to the flaws. (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)

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

Complexity and integration are longstanding widely debated issues in philosophy of science and recent contributions have largely focused on biology and biomedicine. This paper specifically considers some methodological novelties in cancer research, motivated by various features of tumours as complex diseases, and shows how they encourage some rethinking of philosophical discourses on those topics. In particular, we discuss the integrative-cluster approach, and analyse its potential in the epistemology of cancer. We suggest that, far from being the solution to tame cancer (...) complexity, this approach offers a philosophically interesting new manner of considering integration, and show how it can help addressing the apparent contrast between a pluralistic and a unitary account. (shrink)

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

Ioannidis [Why most published research findings are false. PLoS Med 2: e124 ] identifies six factors that contribute to explaining why most of the current published research findings are more likely to be false than true, and argues that for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this article, we argue that three “hot” areas in current biological research, viz., agent-based modeling, evolutionary developmental biology , and systems biology, are (...) especially prone to the flaws. (shrink)

ZusammenfassungDer Beitrag nimmt den heute allgegenwärtigen Begriff „Daten“ als historische Kategorie in den Blick. Er geht der langsamen Verbreitung des Wortes unter Statistikern im 19. Jahrhundert nach und untersucht die materielle Kultur derjenigen Konzepte und Praktiken, die mit seiner Verwendung einhergingen. Am Beispiel der preußischen Volkszählung legt der Beitrag mit diesem Vorgehen bislang unbeachtete Genealogien datengetriebener Forschung frei: Nicht erst Computerspezialisten des 20. und 21. Jahrhunderts, sondern Wissenschaftler des 19. Jahrhunderts machten sich den Begriff für die Produktion streng abstrahierter, numerischer (...) Information zunutze. Sie entwickelten hochflexible Aufbereitungsverfahren von Massenerhebungen, lange bevor Maschinen wie das Hollerith-System oder der Computer die Kompilierung per Hand ersetzten. Bei der preußischen Volkszählung war das Werkzeug dieser „Verdatung“ die sogenannte Zählkarte, ein beweglicher Papierträger, der ein komplexes System der Auswertung erzwang. Der Beitrag rekonstruiert die Logistik dieses Verfahrens und verfolgt die durch ganz Berlin zirkulierenden Papiermassen. Er analysiert die Organisation der meist weiblichen, in Heimarbeit beschäftigten Auszähler und ermisst die sozialen und intellektuellen Anforderungen, die erforderlich wurden, um die auf den beweglichen Zählkarten eingeschriebenen Informationen möglichst schnell und fehlerlos in numerische Aggregate umzuwandeln. Der Beitrag argumentiert, dass die Verdatung nicht nur in der Bevölkerungsstatistik zu neuen Darstellungsformen und Erkenntnissen führte, sondern auch die Forschungspraktiken etlicher anderer „baconischer“ Wissenschaften prägte. Von der Nationalökonomie über die Taxonomie bis zur Paläontologie stärkte das Sehen und Verarbeiten von „Daten“ historische Sensibilitäten und führte zu überraschenden, epochalen Einsichten. (shrink)

ABSTRACT This essay explores ways to “write together” the awkwardly jointed histories of “science” and “medicine”—but it also includes other “arts” (in the old sense) and technologies. It draws especially on the historiography of medicine, but I try to use terms that are applicable across all of science, technology, and medicine (STM). I stress the variety of knowledges and practices in play at any time and the ways in which the ensembles change. I focus on the various relations of “science” (...) and “medicine,” as they were understood for a succession of periods—from mainly agricultural societies, through industrial societies, to our biomedical present—trying to sketch a history that encompasses daily practices and understandings as well as major conceptual and technical innovations. The model is meant to facilitate inquiry across topics and across times, including those to come. (shrink)

Meeting grand challenges requires responses that constructively combine multiple forms of expertise, both academic and non-academic; that is, it requires cross-disciplinary integration. But just what is cross-disciplinary integration? In this paper, we supply a preliminary answer by reviewing prominent accounts of cross-disciplinary integration from two literatures that are rarely brought together: cross-disciplinarity and philosophy of biology. Reflecting on similarities and differences in these accounts, we develop a framework that integrates their insights—integration as a generic combination process the details of which (...) are determined by the specific contexts in which particular integrations occur. One such context is cross-disciplinary research, which yields cross-disciplinary integration. We close by reflecting on the potential applicability of this framework to research efforts aimed at meeting grand challenges. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include (...) the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data. (shrink)

Bogen and Woodward characterized data as embedded in the context in which they are produced (‘local’) and claims about phenomena as retaining their significance beyond that context (‘nonlocal’). This view does not fit sciences such as biology, which successfully disseminate data via packaging processes that include appropriate labels, vehicles, and human interventions. These processes enhance the evidential scope of data and ensure that claims about phenomena are understood in the same way across research communities. I conclude that the degree of (...) locality of both data and claims about phenomena varies depending on the packaging used to make them travel and on the research setting in which they are used. †To contact the author, please write to: ESRC Centre for Genomics in Society, University of Exeter, Byrne House, St. Germans Road, EX4 4PJ Exeter, United Kingdom; e‐mail: [email protected]. (shrink)

We demonstrate a heterogeneity of representation types for breast cancer phenotypes and stress that the characterisation of a tumour phenotype often includes parameters that go beyond the representation of a corresponding empirically observed tumour, thus reflecting significant functional features of the phenotypes as well as epistemic interests that drive the modes of representation. Accordingly, the represented features of cancer phenotypes function as epistemic vehicles aiding various classifications, explanations, and predictions. In order to clarify how the plurality of epistemic motivations can (...) be integrated on a formal level, we give a distinction between six categories of human agents as individuals and groups focused around particular epistemic interests. We analyse the corresponding impact of these groups and individuals on representation types, mapping and reasoning scenarios. Respecting the plurality of representations, related formalisms, expressivities and aims, as they are found across diverse scientific communities, we argue for a pluralistic ontology integration. Moreover, we discuss and illustrate to what extent such a pluralistic integration is supported by the distributed ontology language DOL, a meta-language for heterogeneous ontology representation that is currently under standardisation as ISO WD 17347 within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. We particularly illustrate how DOL supports representations of parthood on various levels of logical expressivity, mapping of terms, merging of ontologies, as well as non-monotonic extensions based on circumscription allowing a transparent formal modelling of the normal/abnormal distinction in phenotypes. (shrink)

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...) the cultures is necessary for understanding how they collaborate or compete, and how they are fragmented or integrated, in the rich interdisciplinary /trading zone/ (Galison 1997) of Evo-Devo. Evo-Devo is an important example of how science can progress through a radical plurality of perspectives and cultures. (shrink)