Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices address the (...) challenges and constraints of interdisciplinary research in different contexts. In this paper we draw from our 5-year empirical ethnographic study of two systems biology labs and their collaborations with experimental biologists to analyze a significant problem-solving approach in ISB, which we call adaptive problem solving. ISB lacks much of the methodological and theoretical resources usually found in disciplines in the natural sciences, such as methodological frameworks that prescribe reliable model-building processes. Researchers in our labs compensate for the lack of these and for the complexity of their problems by using a range of heuristics and experimenting with multiple methods and concepts from the background fields available to them. Using these resources researchers search out good techniques and practices for transforming intractable problems into potentially solvable ones. The relative freedom lab directors grant their researchers to explore methodological options and find good practices that suit their problems is not only a response to the complex interdisciplinary nature of the specific problem, but also provides the field itself with an opportunity to discover more general methodological approaches and develop theories of biological systems. Such developments in turn can help to establish the field as an identifiably distinct and successful approach to understanding biological systems. (shrink)

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the (...) role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration. (shrink)

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory (...) will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. (shrink)

Ludwik Fleck, Edmund Husserl : on the historicity of scientific knowledge -- Gaston Bachelard : the concept of "phenomenotechnique" -- Georges Canguilhem : epistemological history -- Pisum : Carl Correns's experiments on Xenia, 1896-99 -- Eudorina : Max Hartmann's experiments on biological regulation in protozoa, 1914-21 -- Ephestia : Alfred Kähn's experimental design for a developmental physiological -- Genetics, 1924-45 -- Tobacco mosaic virus : virus research at the Kaiser Wilhelm Institutes for Biochemistry and Biology, 1937-45 -- The concept of (...) the gene : molecular biological perspectives -- The liquid scintillation counter : traces of radioactivity -- The concept of information : the writings of François Jacob -- Intersections -- Preparations -- The economy of the scribble. (shrink)

This paper analyzes the generation and function of hitherto ignored or misrepresented interfield theories , theories which bridge two fields of science. Interfield theories are likely to be generated when two fields share an interest in explaining different aspects of the same phenomenon and when background knowledge already exists relating the two fields. The interfield theory functions to provide a solution to a characteristic type of theoretical problem: how are the relations between fields to be explained? In solving this problem (...) the interfield theory may provide answers to questions which arise in one field but cannot be answered within it alone, may focus attention on domain items not previously considered important, and may predict new domain items for one or both fields. Implications of this analysis for the problems of reduction and the unity and progress of science are mentioned. (shrink)

This article examines to what extent a particular case of cross-disciplinary research in the 1930s was structured by mechanistic reasoning. For this purpose, it identifies the interfield theories that allowed biologists and chemists to use each other’s techniques and findings, and that provided the basis for the experiments performed to identify plant growth hormones and to learn more about their role in the mechanism of plant growth. In 1930, chemists and biologists in Utrecht and Pasadena began to cooperatively study plant (...) growth. I will argue that these researchers decided to join forces because they believed to rely on each other’s findings and methods to solve their research problems adequately. In the course of the cooperation, organic chemists arrived at isolating plant growth hormones by using a test method developed in plant physiology. This achievement, in turn, facilitated biologists’ investigation of the mechanism of plant growth. Researchers eventually believed to have the means to study the relation between a substance’s molecular structure and its physiological activity. The way they conceptualized the problem of identifying hormones and unraveling the mechanism of plant growth, as well as their actual research actions are compatible with the new mechanists’ account of mechanism research. The study illustrates that focusing on researchers’ mechanistic reasoning can contribute considerably to explaining the structure of cross-disciplinary research projects. (shrink)

The question whether research techniques are producing artifacts or data is often a crucial one for scientists. The potential for artifacts results from the fact that generating data often requires numerous procedures that are often brutal, poorly understood, and very sensitive to details of the procedure. Through a case-study of the introduction of electron microscopy as a tool for studying cells, I examine how scientists judge whether new techniques are introducing artifacts. Three factors seem to be most salient in their (...) judgments: determinateness of the results, consilience of different procedures, and ability of the results to fit into emerging theories. (shrink)

We examine the emergence of the field of life-history strategies during the 1950s. (We consider a 'field' an area of scientific activity consisting of a theoretical core, a subject of research, a vocabulary and research tools). During the late 1940s and early 1950s, population ecology faced many problems, concerning its conceptual framework, its mathematical models, experimental deficiencies, etc. Research on life-history characteristics remained descriptive, lacking explanations about the causes and significance of phenomena. This was due to the deficiencies of the (...) theoretical framework of population ecology up to the 1950s. The catalyzing factor for the emergence of the new field was the interdisciplinary impacts, and especially the impact of neodarwinism. The elaboration of a new theoretical core, invoking also methodological shifts, was the triggering factor, conditioning the emergence of the new field. (shrink)

This article is about the beginnings of tissue culture-the culture of living, reproducing cells of complex organisms outside the body. It argues that Ross Harrison's experiments in nerve culture between 1907 and 1910 should be viewed as part of a larger shift in early twentieth-century laboratory practice from in vivo to in vitro experimentation. Via a focus on the temporality of experiment-contrasting the live object of Harrison's investigation with the static object of histological representations-this article details the production of a (...) new and surprising form of life, cellular life in vitro. Tissue culture, developed from Harrison's experiments, was greeted with great surprise and disbelief, despite Harrison's protestations that he had merely juxtaposed extant techniques. An analysis of these initial reactions to tissue culture illuminates the extent to which cells living visibly outside of the body in glass broke with in vivo practices and assumptions of the hiddenness and interiority of certain processes of growth and change. (shrink)