Imagination is necessary for scientific practice, yet there are no in vivo sociological studies on the ways that imagination is taught, thought of, or evaluated by scientists. This article begins to remedy this by presenting the results of a qualitative study performed on two systems biology laboratories. I found that the more advanced a participant was in their scientific career, the more they valued imagination. Further, positive attitudes toward imagination were primarily due to the perceived role of imagination in problem-solving. (...) But not all problem-solving episodes involved clear appeals to imagination, only maximally specific problems did. This pattern is explained by the presence of an implicit norm governing imagination use in the two labs: only use imagination on maximally specific problems, and only when all other available methods have failed. This norm was confirmed by the participants, and I argue that it has epistemological reasons in its favour. I also found that its strength varies inversely with career stage, such that more advanced scientists do (and should) occasionally bring their imaginations to bear on more general problems. A story about scientific pedagogy explains the trend away from (and back to) imagination over the course of a scientific career. Finally, some positive recommendations are given for a more imagination-friendly scientific pedagogy. (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)

Manipulation of physical models such as tangrams and tiles is a popular approach to teaching early mathematics concepts. This pedagogical approach is extended by new computational media, where mathematical entities such as equations and vectors can be virtually manipulated. The cognitive and neural mechanisms supporting such manipulation-based learning—particularly how actions generate new internal structures that support problem-solving—are not understood. We develop a model of the way manipulations generate internal traces embedding actions, and how these action-traces recombine during problem-solving. This model (...) is based on a study of two groups of sixth-grade students solving area problems. Before problem-solving, one group manipulated a tangram, the other group answered a descriptive test. Eye-movement trajectories during problem-solving were different between the groups. A second study showed that this difference required the tangram's geometrical structure, just manipulation was not enough. We propose a theoretical model accounting for these results, and discuss its implications. (shrink)

This paper takes an embodied and extended cognition perspective to ER integration – a cognitive process through which a learner integrates external representations in a domain, with her internal model, as she interacts with, uses, understands and transforms between those ERs. In the paper, I argue for a theoretical as well as empirical shift in future investigations of ER integration, by proposing a model of cognitive mechanisms underlying the process, based on recent advances in extended and embodied cognition. I present (...) this new model in contrast to the still dominant classical cognitivist approaches to ER integration, and the educational technology intervention designs such approaches inspire. I then exemplify this distinction between the information processing model and the new model through a case of arithmetic problem solving. Corroborative neuroscience evidence presented in relation to this case provides empirical support for the new model by showing how bodily actions are critical to ER integration and learning. Finally, as educational implications of the new model, I demonstrate the need for: re-viewing the development of ER integration and expertise as fine-tuning of the learner's action or sensorimotor system, and a shift of focus in new-media intervention design principles based on this newer understanding of ER integration in science, technology, engineering and mathematics. (shrink)

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 (hybridization) and integrative systems biology (collaborative interdependence). 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)

Modelers are tackling ever more complex systems with the aid of computation. Model-based inferences can play a key role in their ability to handle complexity and produce reliable or informative models. We study here the role of model-based inference in the modern field of computational systems biology. We illustrate how these inferences operate and analyze the material and theoretical bases or conditions underlying their effectiveness. Our investigation reiterates the significance and centrality of model-based reasoning in day-to-day problem-solving practices, and the (...) role that debugging processes of partial or incomplete models can play in scientific inference and scientific discovery, particularly with respect to complex systems. We present several deeper implications such an analysis has for philosophy of science regarding the role of models in scientific practice. (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)

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)

In spite of the relevance of a scientific representation of the world for naturalism, it is surprising that philosophy of science is less involved in the debate on naturalism than expected. Had the viewpoint of philosophy of science been duly considered, naturalism could not have overlooked the established lesson, according to which there is no well-defined recipe for what science must or must not be. In the present paper I address some implications of this lesson for naturalism, arguing that a (...) radically naturalistic outlook fails to pay sufficient attention to some of the main lessons that philosophy of science has taught us concerning the nature of scientific theories. One of these lessons is that real scientific theories are far more normative than ordinary scientific naturalism is ready to accept, a circumstance that at a minimum is bound to force most naturalization strategies to re-define their significance. (shrink)

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production (IEP). I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under (...) study; ‘intervention systems’, which are measurement/experimental systems; and new technological systems. (shrink)

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production. I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under study; (...) ‘intervention systems’, which are measurement/experimental systems; and new technological systems. (shrink)

Studies of scientific practice demonstrate that the development of scientific models is an enactive and emergent process. Scientists make meaning through processes such as perspective taking, finding patterns, and following intuitions. In this paper, we focus on how a group of fourth grade learners and their teacher engaged in interpretation in ways that align with core ideas and practices in kinematics and computing. Cycles of measuring and modeling––including computer programming––helped to support classroom interactions that highlighted the interpretive nature of modeling (...) and participation in model construction as a knowledge-building process. We draw on literature from the history and philosophy of science in order to analyze the students’ interpretive actions as forms of epistemic and representational agency, constituting a construct we term disciplined interpretation. We demonstrate how students’ disciplined interpretative moves help to position them as owners of their own design decisions and their rights to interpret the phenomena they were modeling, data collected from those phenomena, and the scientific and computational models themselves. We present four extended episodes that characterize the nature of activity in the classroom and the development of students’ disciplined interpretations in terms of learning to recognize scientific patterns amid complex perceptual fields, and to represent them in ways that support sensemaking. (shrink)

Building computational models of engineered exemplars, or prototypes, is a common practice in the bioengineering sciences. Computational models in this domain are often built in a patchwork fashion, drawing on data and bits of theory from many different domains, and in tandem with actual physical models, as the key objective is to engineer these prototypes of natural phenomena. Interestingly, such patchy model building, often combined with visualizations, whose format is open to a wide range of choice, leads to the discovery (...) of new concepts and control structures. Two key questions are raised by this practice: how could discoveries arise from building external representations for which there is wide latitude in choice of the components from which they are built, and thus can be considered significantly arbitrary, and how could such discoveries allow engineering a real-world prototype system. To examine these questions, we present two case studies of discoveries that emerged from the building of such computational models in the bioengineering sciences. We then develop a process model that accounts for the discovery and transfer problems raised by both these cases, focusing on the process of building the model. Specifically, to account for the discovery problem, we propose that the process of building such models gradually leads to a close coupling between the modeler’s internal processes and the external dynamic model. To account for the transfer problem, we propose that the process of building the model leads to the creation of an enactive model that is generic, which closely enacts, and thus reveals, the way the system-level behavior of the engineered prototype emerges in time through the interaction of its parts. This enactive replication process leads to the model and the prototype forming a new class, which allows concepts and control structures developed for the computational model to be transfered to the real-world prototype. We argue that this account requires rethinking correspondence in engineering sciences as a plastic and enactive relation. A closer focus on the process of building models is required to develop a general account of this emerging approach to discovery. (shrink)

Inspired by Ronald Giere’s cognitive approach to scientific models, Cognitive Structural Realism has presented a naturalist account of scientific representation. CSR characterises the structure of theories in terms of cognitive structures. These are informational structures embodied in the brains of scientists. CSR accounts for scientific representation in terms of the dynamical relationship between the organism and its environment. The proposal has been criticised on account of its negligence of social aspects of scientific practice. The present paper aims to chart out (...) a reply to the objection. It shows that cognitive structures do not need to be put inside the brains of single individuals. Cognitive structures are redefined as extended structures in distributed cognitive systems under Free Energy Principle. (shrink)