The paper presents an argument for treating certain types of computer simulation as having the same epistemic status as experimental measurement. While this may seem a rather counterintuitive view it becomes less so when one looks carefully at the role that models play in experimental activity, particularly measurement. I begin by discussing how models function as “measuring instruments” and go on to examine the ways in which simulation can be said to constitute an experimental activity. By focussing on the connections (...) between models and their various functions, simulation and experiment one can begin to see similarities in the practices associated with each type of activity. Establishing the connections between simulation and particular types of modelling strategies and highlighting the ways in which those strategies are essential features of experimentation allows us to clarify the contexts in which we can legitimately call computer simulation a form of experimental measurement. (shrink)

This paper examines the relationship between simulation and experiment. Many discussions of simulation, and indeed the term "numerical experiments," invoke a strong metaphor of experimentation. On the other hand, many simulations begin as attempts to apply scientific theories. This has lead many to characterize simulation as lying between theory and experiment. The aim of the paper is to try to reconcile these two points of viewto understand what methodological and epistemological features simulation has in common with experimentation, while at the (...) same time keeping a keen eye on simulation's ancestry as a form of scientific theorizing. In so doing, it seeks to apply some of the insights of recent work on the philosophy of experiment to an aspect of theorizing that is of growing philosophical interest: the construction of local models. (shrink)

The ArgumentIn its reconstruction of scientific practice, philosophy of science has traditionally placed scientific theories in a central role, and has reduced the problem of mediating between theories and the world to formal considerations. Many applications of scientific theories, however, involve complex mathematical models whose constitutive equations are analytically unsolvable. The study of these applications often consists in developing representations of the underlying physics on a computer, and using the techniques of computer simulation in order to learn about the behavior (...) of these systems. In many instances, these computer simulations are not simple number-crunching techniques. They involve a complex chain of inferences that serve to transform theoretical structures into specific concrete knowledge of physical systems. In this paper I argue that this process of transformation has its own epistemology. I also argue that this kind of epistemology is unfamiliar to most philosophy of science, which has traditionally concerned itself with the justification of theories, not with their application. Finally, I urge that the nature of this epistemology suggests that the end results of some simulations do not bear a simple, straightforward relation to the theories from which they stem. (shrink)

Integrative systems biology is among the most innovative fields of contemporary science, bringing together scientists from a range of diverse backgrounds and disciplines to tackle biological complexity through computational and mathematical modeling. The result is a plethora of problem-solving techniques, theoretical perspectives, lab-structures and organizations, and identity labels that have made it difficult for commentators to pin down precisely what systems biology is, philosophically or sociologically. In this paper, through the ethnographic investigation of two ISB laboratories, we explore the particular (...) structural features of ISB thinking and organization and its relations to other disciplines that necessitate cognitive innovation at all levels from lab PI’s to individual researchers. We find that systems biologists face numerous constraints that make the production of models far from straight-forward, while at the same time they inhabit largely unstructured task environments in comparison to other fields. We refer to these environments as adaptive problem spaces. These environments they handle by relying substantially on the flexibility and affordances of model-based reasoning to integrate these various constraints and find novel adaptive solutions. Ultimately what is driving this innovation is a determination to construct new cognitive niches in the form of functional model building frameworks that integrate systems biology within the biological sciences. The result is an industry of diverse and different innovative practices and solutions to the problem of modeling complex, large-scale biological systems. (shrink)

Designing, building, and experimenting with physical simulation models are central problem‐solving practices in the engineering sciences. Model‐based simulation is an epistemic activity that includes exploration, generation and testing of hypotheses, explanation, and inference. This paper argues that to interpret and understand how these simulation models function in creating knowledge and technologies requires construing problem solving as accomplished by a researcher–artifact system. It draws on and further develops the framework of “distributed cognition” to interpret data collected in ethnographic and cognitive‐historical studies (...) of two biomedical engineering research laboratories, and articulates the notion of distributed model‐based cognition to answer the question posed in the title. (shrink)

In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large‐scale molecular interactions; the other, which we shall refer to as ‘systems‐theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems (...) and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. BioEssays 27:1270–1276, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...) we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory. (shrink)

We are quickly passing through the historical moment when people work in front of a single computer, dominated by a small CRT and focused on tasks involving only local information. Networked computers are becoming ubiquitous and are playing increasingly significant roles in our lives and in the basic infrastructure of science, business, and social interaction. For human-computer interaction o advance in the new millennium we need to better understand the emerging dynamic of interaction in which the focus task is no (...) longer confined to the desktop but reaches into a complex networked world of information and computer-mediated interactions. We think the theory of distributed cognition has a special role to play in understanding interactions between people and technologies, for its focus has always been on whole environments: what we really do in them and how we coordinate our activity in them. Distributed cognition provides a radical reorientation of how to think about designing and supporting human-computer interaction. As a theory it is specifically tailored to understanding interactions among people and technologies. In this article we propose distributed cognition as a new foundation for human-computer interaction, sketch an integrated research framework, and use selections from our earlier work to suggest how this framework can provide new opportunities in the design of digital work materials. (shrink)

Many explanations in molecular biology, neuroscience, and other fields of experimental biology describe mechanisms underlying phenomena of interest. These mechanistic explanations account for higher-level phenomena in terms of causally active parts and their spatiotemporal organization. What makes such a mechanistic description explanatory? The best-developed answer, Craver's causal-mechanical account, has several weaknesses. It does not fully explicate the target of explanation, interlevel relation, or interactive nonmodular character of many biological mechanisms as we understand them. An alternative account of MEx, emphasizing interdependence (...) among a mechanism's components, remedies these difficulties. (shrink)

This paper starts by looking at the coincidence of surprising behavior on the nanolevel in both matter and simulation. It uses this coincidence to argue that the simulation approach opens up a pragmatic mode of understanding oriented toward design rules and based on a new instrumental access to complex models. Calculations, and their variation by means of explorative numerical experimentation and visualization, can give a feeling for a model's behavior and the ability to control phenomena, even if the model itself (...) remains epistemically opaque. Thus, the investigation of simulation in nanoscience provides a good example of how science is adapting to a new instrument: computer simulation. (shrink)

Systems biology is largely tributary to genomics and other “omic” disciplines that generate vast amounts of structural data. “Omics”, however, lack a theoretical framework that would allow using these data sets as such (rather than just tiny bits that are extracted by advanced data-mining techniques) to build explanatory models that help understand physiological processes. Systems biology provides such a framework by adding a dynamic dimension to merely structural “omics”. It makes use of bottom-up and top-down models. The former are based (...) on data about systems components, the latter on systems-level data. We trace back both modeling strategies (which are often used to delineate two branches of the field) to the modeling of metabolic and signaling pathways in the bottom-up case, and to biological cybernetics and systems theory in the top-down case. We then argue that three roots of systems biology must be discerned to account adequately for the structure of the field: pathway modeling, biological cybernetics, and “omics”. We regard systems biology as merging modeling strategies (supplemented by new mathematical procedures) from data-poor fields with data supply from a field that is quite deficient in explanatory modeling. After characterizing the structure of the field, we address some epistemological and ontological issues regarding concepts on which the top-down approach relies and that seem to us to require clarification. This includes the consequences of identifying modules in large networks without relying on functional considerations, the question of the “holism” of systems biology, and the epistemic value of the “systeome” project that aspires to become the cutting edge of the field. (shrink)

Simulations (both digital and analog) and experiments share many features. But what essential features distinguish them? I discuss two proposals in the literature. On one proposal, experiments investigate nature directly, while simulations merely investigate models. On another proposal, simulations differ from experiments in that simulationists manipulate objects that bear only a formal (rather than material) similarity to the targets of their investigations. Both of these proposals are rejected. I argue that simulations fundamentally differ from experiments with regard to the background (...) knowledge that is invoked to argue for the “external validity” of the investigation. (shrink)