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)

PARTI The Philosophical Situation: A Critical Appraisal We must begin with the mistake and find out the truth in it. That is, we must uncover the source of ...

The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling (...) pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems. (shrink)

Computational systems biologists create and manipulate computational models of biological systems, but they do not always have straightforward epistemic access to the content and behavioural profile of such models because of their length, coding idiosyncrasies, and formal complexity. This creates difficulties both for modellers in their research groups and for their bioscience collaborators who rely on these models. In this paper we introduce a new kind of visualization that was developed to address just this sort of epistemic opacity. The visualization (...) is unusual in that it depicts the dynamics and structure of a computer model instead of that model’s target system, and because it is generated algorithmically. Using considerations from epistemology and aesthetics, we explore how this new kind of visualization increases scientific understanding of the content and function of computer models in systems biology to reduce epistemic opacity. (shrink)

Novel computational representations, such as simulation models of complex systems and video games for scientific discovery, are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a theoretical analysis of the cognitive roles such representations play, based on an ethnographic study of the building of computational models in a systems biology laboratory. Specifically, we focus on a case of model-building by an engineer that (...) led to a remarkable discovery in basic bioscience. Accounting for such discoveries requires a distributed cognition analysis, as DC focuses on the roles played by external representations in cognitive processes. However, DC analyses by and large have not examined scientific discovery, and they mostly focus on memory offloading, particularly how the use of existing external representations changes the nature of cognitive tasks. In contrast, we study discovery processes and argue that discoveries emerge from the processes of building the computational representation. The building process integrates manipulations in imagination and in the representation, creating a coupled cognitive system of model and modeler, where the model is incorporated into the modeler's imagination. This account extends DC significantly, and we present some of the theoretical and application implications of this extended account. (shrink)

Confronting any science studies or learning sciences researcher in the 21st century is the reality of interdisciplinary science. New hybrid fields1 collaboratively build new concepts, combine models from two or more disciplines and forge inter-reliant relationships among specialists with different skill sets to solve new problems. This paper emerges from our recognition that inescapable psychological factors, including identity dynamics, must be described and analyzed in order to better understand the social and cognitive practices specific to interdisciplinary science. In analysis of (...) the foundations and opportunities for an... (shrink)

Thought experiments have played a prominent role in numerous cases of conceptual change in science. I propose that research in cognitive psychology into the role of mental modeling in narrative comprehension can illuminate how and why thought experiments work. In thought experimenting a scientist constructs and manipulates a mental simulation of the experimental situation. During this process, she makes use of inferencing mechanisms, existing representations, and general world knowledge to make realistic transformations from one possible physical state to the next. (...) The simulation reveals the impossibility of integrating multiple constraints drawn from existing representations and the world and pinpoints the locus of the required conceptual reform. (shrink)

We begin our commentary by summarizing the commonalities and differences in cognitive phenomena across cultures, as found by the seven papers of this topic. We then assess the commonalities and differences in how our various authors have approached the study of cognitive diversity, and speculate on the need for, and potential of, cross-disciplinary collaboration.

The paper argues that the practice of thought experintenting enables scientists to follow through the implications of a way of representing nature by simulating an exemplary or representative situation that is feasible within that representation. What distinguishes thought experimenting from logical argument and other forms of propositional reasoning is that reasoning by means of a thought experiment involves constructing and simulating a mental model of a representative situation. Although thought experimenting is a creative part of scientific practice, it is a (...) highly refined extension of a mundane form of reasoning. It is not a mystery why scientific thought experiments are a reliable source of empirical insights. Thought experimenting uses and manipulates representations that derive from real-world experiences and our conceptualizations of them. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

There is substantial evidence that traditional instructional methods have not been successful in helping students to restructure their commonsense conceptions and learn the conceptual structures of scientific theories. This paper argues that the nature of the changes and the kinds of reasoning required in a major conceptual restructuring of a representation of a domain are fundamentally the same in the discovery and in the learning processes. Understanding conceptual change as it occurs in science and in learning science will require the (...) development of a common cognitive model of conceptual change. The historical construction of an inertial representation of motion is examined and the potential instructional implications of the case are explored. (shrink)

We historically and conceptually situate distributed cognition by drawing attention to important similarities in assumptions and methods with those of American ?functional psychology? as it emerged in contrast and complement to controlled laboratory study of the structural components and primitive ?elements? of consciousness. Functional psychology foregrounded the adaptive features of cognitive processes in environments, and adopted as a unit of analysis the overall situation of organism and environment. A methodological implication of this emphasis was, to the extent possible, the study (...) of cognitive and other processes in the natural (real world) contexts in which they occur. We therefore emphasize commonalities and differences between functional psychology and D-Cog. One purpose of the comparison is to consider the extent to which criticisms directed at functional psychology are relevant to D-Cog. We also examine the relation between functional psychology and philosophical pragmatism and conclude that D-Cog's conceptual framework would be strengthened through more explicit adoption of philosophical pragmatism, consistent with the eventual trajectory of functional psychology. (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)

This paper examines the nature of model-based reasoning in the interplay between theory and experiment in the context of biomedical engineering research laboratories, where problem solving involves using physical models. These "model systems" are sites of experimentation where in vitro models are used to screen, control, and simulate specific aspects of in vivo phenomena. As with all models, simulation devices are idealized representations, but they are also systems themselves, possessing engineering constraints. Drawing on research in contemporary cognitive science that construes (...) cognition as occurring in a complex distributed system comprising people and artifacts, I argue that reasoning with model systems is a constraint satisfaction process involving co-construction, manipulation, and revision of mental and physical models. (shrink)

' this volume will make a significant contribution to a more adequate understanding of the 'nature of scientific knowledge and inquiry' ' ISIS Vol.79,No.1,1988.

Cases where analogy has played a significant role in the formation of a new scientific concept are well-documented. Yet, how is it that genuinely new representations can be constructed from existing representations? It is argued that the process of ‘generic modeling’ enables abstraction of features common to both the domain of the source of the analogy and of the target phenomena. The analysis focuses on James Clerk Maxwell's construction of the electromagnetic field concept. The mathematical representation Maxwell constructed turned out (...) to be a system of abstract laws that when applied to electromagnetic systems yield laws of a dynamical system that will not map back onto the mechanicals domains used in their construction. (shrink)

This paper presents an analysis of emotional and affectively toned discourse in biomedical engineering researchers’ accounts of their problem solving practices. Drawing from our interviews with scientists in two laboratories, we examine three classes of expression: explicit, figurative and metaphorical, and attributions of emotion to objects and artifacts important to laboratory practice. We consider the overall function of expressions in the particular problem solving contexts described. We argue that affective processes are engaged in problem solving, not as simply tacked onto (...) reasoning but as integral to it. The examples we present illustrate the close relation of emotion to problem solving and experimentation; they also implicate social and cultural dimensions of emotion expression. The analysis underscores a need to consider emotional expression to be intimately and importantly tied to the cognitive achievements and social negotiations of laboratory practices. (shrink)

Concept formation in science is a reasoned process, commensurate with ordinary problem-solving processes. An account of how analogical reasoning and reasoning from imagistic representations generate new scientific concepts is presented. The account derives from case studies of concept formation in science and from computational theories of analogical problem solving in cognitive science. Concept formation by analogy is seen to be a process of increasing abstraction from existing conceptual structures.

The paper frames interdisciplinary research as creating complex, distributed cognitive-cultural systems. It introduces and elaborates on the method of cognitive ethnography as a primary means for investigating interdisciplinary cognitive and learning practices in situ. The analysis draws from findings of nearly 20 years of investigating such practices in research laboratories in pioneering bioengineering sciences. It examines goals and challenges of two quite different kinds of integrative problem-solving practices: biomedical engineering and integrative systems biology. Practical lessons for facilitating research and learning (...) in these specific fields are discussed and a preliminary set of interdisciplinary epistemic virtues are proposed as candidates for cultivation in interdisciplinary practices of these kinds more widely. (shrink)

The origins of the ‘ incommensurability problem’ and its central aspect, the ‘ meaning variance thesis’ are traced to the successive collapse of several distinctions maintained by the standard empiricist account of meaning in scientific theories. The crucial distinction is that between a conceptual structure and a theory. The ‘thesis’ and the ‘problem’ follow from critiques of this distinction by Duhem, Quine and Feyerabend. It is maintained that, rather than revealing the ‘problem’, the arguments leading to it simply show the (...) inadequacy of the reductionist theory of meaning. The genuine remaining problem is that of the development of a new theory of meaning in science. (shrink)

Visual analogy is believed to be important in human problem solving. Yet, there are few computational models of visual analogy. In this paper, we present a preliminary computational model of visual analogy in problem solving. The model is instantiated in a computer program, called Galatea, which uses a language for representing and transferring visual information called Privlan. We describe how the computational model can account for a small slice of a cognitive-historical analysis of Maxwell’s reasoning about electromagnetism.

Cases where analogy has played a significant role in the formation of a new scientific concept are well-documented. Yet, how is it that genuinely new representations can be constructed from existing representations? It is argued that the process of ‘generic modeling’ enables abstraction of features common to both the domain of the source of the analogy and of the target phenomena. The analysis focuses on James Clerk Maxwell's construction of the electromagnetic field concept. The mathematical representation Maxwell constructed turned out (...) to be a system of abstract laws that when applied to electromagnetic systems yield laws of a dynamical system that will not map back onto the mechanicals domains used in their construction. (shrink)

The notion of mutation is applicable to the generation of novel designs and solutions in engineering and science. This suggests that engineers and scientists have to work against the biases identified in counterfactual thinking. Therefore, imagination appears a lot less rational than claimed in the target article.

The claims of the epistemological 'anarchists' have their roots in the orthodox tradition as well as in the Popperian. In particular they follow from the work of Quine. Meaning variance and incommensurability follow directly from the holistic conception of meaning in his 'network' view. Quine's efforts to evade this conclusion fail. His attempt to develop a theory-neutral notion of observation sentence is shown (1) to be inconsistent with his previous claims since it involves the tacit acceptance of the 'dogma of (...) reductionism', (2) to involve the acceptance of a questionable 'third dogma', i.e. the stimulus-response theory of behaviorist psychology, and (3) ultimately to miss the point of the anarchists. In Quinian terms, in order for observation sentences to perform the function of intertheoretical 'arbiters', what is needed is 'similarity of assent', which is not a meaningful notion on an internetwork basis. (shrink)

In his article, "Is Essentialism Unscientific?" (1988), Jarrett Leplin claims that I do not have sufficient grounds for rejecting the customary "philosophical method of discovery" that allows for the direct transfer of theories developed in the philosophy of language to science. While admitting that all attempts at transfer thus far have failed, he still maintains that method is sound. I argue that the wholesale failure of these attempts is reason enough to suspect the method and to try to devise one (...) more suitable to fathoming how "meaning", "reference", and "meaning change" are to be understood for scientific theories. The method I have proposed in Nersessian (1984b), and subsequent work, demands that we learn how to incorporate the actual practices of meaning construction in science into our analyses. Leplin distorts my analysis and, thus, fails to understand the insights that study provides. (shrink)