In this article, I examine the historiographical ideas of the historian of chemistry Hélène Metzger against the background of the ideas of the members of the groups and institutions in which she worked, including Alexandre Koyré, Gaston Bachelard, Abel Rey, Henri Berr and Lucien Febrve. This article is on two interdependent levels: that of particular institutions and groups in which she worked and the École Pratique des Hautes Études) and that of historiographical ideas. I individuate two particular theoretical aspirations pursued (...) by the historians in Metzger's milieu: the ideal of total history and the study of the human mind. These two objectives were seen by Metzger and many others as implicating each other. Moreover, Metzger and other historians wanted to integrate the practice of commentary of texts in the realisations of those ideals. I argue, however, that these objectives proved very difficult to realise at the same time. One tradition which stemmed out of these discussions, exemplified by Bachelard, Canguilhem and Foucault, focused on the mind and knowledge, and renounced commentary of texts and total history as it was understood by the historians of the Centre de Synthèse. The latter, however, did not really pursue the study of the mind. Moreover, historians like Metzger and Koyré who practised an attentive analysis of texts could not realise total history. (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)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed (...) and applied styles, paradigms, and models simultaneously? I address these questions in general and for a specific case study: a brief history of systematics. (shrink)

In “The Toolbox of Science” (1995) together with Towfic Shomar we advocated a form of instrumentalism about scientific theories. We separately developed this view further in a number of subsequent works. Steven French, James Ladyman, Otavio Bueno and Newton Da Costa (FLBD) have since written at least eight papers and a book criticising our work. Here we defend ourselves. First we explain what we mean in denying that models derive from theory – and why their failure to do so should (...) be lamented. Second we defend our use of the London model of superconductivity as an example. Third we point out both advantages and weaknesses of FLBD’s techniques in comparison to traditional Anglophone versions of the semantic conception. Fourth we show that FLBD’s version of the semantic conception has not been applied to our case study. We conclude by raising doubts about FLBD’s overall project. (shrink)

Historians and philosophers of science have interpreted the taxonomic theory of Carl Linnaeus as an ‘essentialist’, ‘Aristotelian’, or even ‘scholastic’ one. This interpretation is flatly contradicted by what Linnaeus himself had to say about taxonomy in Systema naturae , Fundamenta botanica and Genera plantarum . This paper straightens out some of the more basic misinterpretations by showing that: Linnaeus’s species concept took account of reproductive relations among organisms and was therefore not metaphysical, but biological; Linnaeus did not favour classification by (...) logical division, but criticized it for necessarily failing to represent what he called ‘natural’ genera; Linnaeus’s definitions of ‘natural’ genera and species were not essentialist, but descriptive and polytypic; Linnaeus’s method in establishing ‘natural’ definitions was not deductive, but consisted in an inductive, bottom-up procedure of comparing concrete specimens. The conclusion will discuss the fragmentary and provisional nature of Linnaeus’s ‘natural method’. I will argue in particular that Linnaeus opted for inductive strategies not on abstract epistemological grounds, but in order to confer stability and continuity to the explorative practices of contemporary natural history. (shrink)

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)

A number of recent discussions comparing computer simulation and traditional experimentation have focused on the significance of “materiality.” I challenge several claims emerging from this work and suggest that computer simulation studies are material experiments in a straightforward sense. After discussing some of the implications of this material status for the epistemology of computer simulation, I consider the extent to which materiality (in a particular sense) is important when it comes to making justified inferences about target systems on the basis (...) of experimental results. (shrink)

Bogen and Woodward claim that the function of scientific theories is to account for 'phenomena', which they describe both as investigator-independent constituents of the world and as corresponding to patterns in data sets. I argue that, if phenomena are considered to correspond to patterns in data, it is inadmissible to regard them as investigator-independent entities. Bogen and Woodward's account of phenomena is thus incoherent. I offer an alternative account, according to which phenomena are investigator-relative entities. All the infinitely many patterns (...) that data sets exhibit have equal intrinsic claim to the status of phenomenon: each investigator may stipulate which patterns correspond to phenomena for him or her. My notion of phenomena accords better both with experimental practice and with the historical development 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)

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)

Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that (...) they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online. (shrink)

The focus of this volume, which collects both recent and now-classic essays, is the historical emergence of concepts and objects, through new uses of words and ...

Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state of (...) a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege’s idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction. (shrink)

Developmental systems theory (DST) expands the unit of replication from genes to whole systems of developmental resources, which DST interprets in terms of cycling developmental processes. Expansion seems required by DST's argument against privileging genes in evolutionary and developmental explanations of organic traits. DST and the expanded replicator brook no distinction between biological and cultural evolution. However, by endorsing a single expanded unit of inheritance and leaving the classical molecular notion of gene intact, DST achieves only a nominal reunification of (...) heredity and development. I argue that an alternative conceptualization of inheritance denies the classical opposition of genetics and development while avoiding the singularity inherent in the replicator concept. It also yields a new unit--the reproducer--which genuinely integrates genetic and developmental perspectives. The reproducer concept articulates the non-separability of "genetic" and "developmental" roles in units of heredity, development, and evolution. DST reformulated in terms of reproducers rather than replicators preserves an empirically interesting distinction between cultural and biological evolution. (shrink)

Debate over the nature of science has recently moved from the halls of academia into the public sphere, where it has taken shape as the "science wars." At issue is the question of whether scientific knowledge is objective and universal or socially mediated, whether scientific truths are independent of human values and beliefs. Ronald Giere is a philosopher of science who has been at the forefront of this debate from its inception, and Science without Laws offers a much-needed mediating perspective (...) on an increasingly volatile line of inquiry. Giere does not question the major findings of modern science: for example, that the universe is expanding or that inheritance is carried by DNA molecules with a double helical structure. But like many critics of modern science, he rejects the widespread notion of science--deriving ultimately from the Enlightenment--as a uniquely rational activity leading to the discovery of universal truths underlying all natural phenomena. In these highly readable essays, Giere argues that it is better to understand scientists as merely constructing more or less abstract models of limited aspects of the world. Such an understanding makes possible a resolution of the issues at stake in the science wars. The critics of science are seen to be correct in rejecting the Enlightenment idea of science, and its defenders are seen to be correct in insisting that science does produce genuine knowledge of the natural world. Giere is utterly persuasive in arguing that to criticize the Enlightenment ideal is not to criticize science itself, and that to defend science one need not defend the Enlightenment ideal. Science without Laws thus stakes out a middle ground in these debates by showing us how science can be better conceived in other ways. (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.

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

It has increasingly been recognised that units of biological classification cannot be identified with the units of evolution. After briefly defending the necessity of this distinction I argue, contrary to the prevailing orthodoxy, that species should be treated as the fundamental units of classification and not, therefore, as units of evolution. This perspective fits well with the increasing tendency to reject the search for a monistic basis of classification and embrace a pluralistic and pragmatic account of the species category. It (...) also provides a diagnosis of the paradoxical but popular idea that species are individuals: Species are not individuals, but the units of evolution are. (shrink)

This book is Dewey's most fully developed treatment of logic as the theory of Inquiry. It is a later work which reflects, in part, Dewey's readings of C.S. Peirce during the 1930's. -/- Reprinted in Series: The collected works of John Dewey / ed. by Jo Ann Boydston, 3,12.; The later works, 1925 - 1953, Vol. 12.

This book is about the methods used for unifying different scientific theories under one all-embracing theory. The process has characterized much of the history of science and is prominent in contemporary physics; the search for a 'theory of everything' involves the same attempt at unification. Margaret Morrison argues that, contrary to popular philosophical views, unification and explanation often have little to do with each other. The mechanisms that facilitate unification are not those that enable us to explain how or why (...) phenomena behave as they do. A feature of this book is an account of many case studies of theory unification in nineteenth- and twentieth-century physics and of how evolution by natural selection and Mendelian genetics were unified into what we now term evolutionary genetics. (shrink)

Models as Mediators discusses the ways in which models function in modern science, particularly in the fields of physics and economics. Models play a variety of roles in the sciences: they are used in the development, exploration and application of theories and in measurement methods. They also provide instruments for using scientific concepts and principles to intervene in the world. The editors provide a framework which covers the construction and function of scientific models, and explore the ways in which they (...) enable us to learn about both theories and the world. The contributors to the volume offer their own individual theoretical perspectives to cover a wide range of examples of modelling, from physics, economics and chemistry. These papers provide ideal case-study material for understanding both the concepts and typical elements of modelling, using analytical approaches from the philosophy and history of science. (shrink)

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