Researchers in the biological and biomedical sciences, particularly those working in laboratories, use a variety of artifacts to help them perform their cognitive tasks. This paper analyses the relationship between researchers and cognitive artifacts in terms of integration. It first distinguishes different categories of cognitive artifacts used in biological practice on the basis of their informational properties. This results in a novel classification of scientific instruments, conducive to an analysis of the cognitive interactions between researchers and artifacts. It then uses (...) a multidimensional framework in line with complementarity-based extended and distributed cognition theory to conceptualize how deeply instruments in different informational categories are integrated into the cognitive systems of their users. The paper concludes that the degree of integration depends on various factors, including the amount of informational malleability, the intensity and kind of information flow between agent and artifact, the trustworthiness of the information, the procedural and informational transparency, and the degree of individualisation. (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)

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)

Many philosophers of science follow Hempel in embracing both substantive and methodological anti-psychologism regarding the study of explanation. The former thesis denies that explanations are constituted by psychological events, and the latter denies that psychological research can contribute much to the philosophical investigation of the nature of explanation. Substantive anti-psychologism is commonly defended by citing cases, such as hyper-complex descriptions or vast computer simulations, which are reputedly generally agreed to constitute explanations but which defy human comprehension and, as a result, (...) fail to engender any relevant psychological events. It is commonly held that the truth of the substantive thesis would lend support to the methodological thesis. However, the standard argument for the substantive thesis presumes that philosophers’ own judgments about the aforementioned cases issues from mastery of the lay or scientific norms regarding the use of ‘explanation.’ Here we challenge this presumption with a series of experiments indicating that both lay and scientific populations require of explanations that they actually render their targets intelligible. This research not only undermines a standard line of argument for substantive anti-psychologism, it demonstrates the utility of psychological research methods for answering meta-questions about the norms regarding the use of ‘explanation.’. (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)

A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) scientists integrate the cognitive, social, material, and cultural dimensions of practice. Her findings and conclusions have broad implications for researchers in philosophy, science studies, cognitive science, and interdisciplinary studies, as well as scientists, educators, policy makers, and funding agencies. In studying the epistemic practices of scientists, Nersessian pushes the boundaries of the philosophy of science and cognitive science into areas not ventured before. She recounts a decades-long, wide-ranging, and richly detailed investigation of the innovative interdisciplinary modeling practices of bioengineering researchers in four university laboratories. She argues and demonstrates that the methods of cognitive ethnography and qualitative data analysis, placed in the framework of distributed cognition, provide the tools for a philosophical analysis of how scientific discoveries arise from complex systems in which the cognitive, social, material, and cultural dimensions of problem-solving are integrated into the epistemic practices of scientists. Specifically, she looks at how interdisciplinary environments shape problem-solving. Although Nersessian’s case material is drawn from the bioengineering sciences, her analytic framework and methodological approach are directly applicable to scientific research in a broader, more general sense, as well. (shrink)

We lay groundwork for applying ethnographic methods in philosophy of science. We frame our analysis in terms of two tasks: to identify the benefits of an ethnographic approach in philosophy of science and to structure an ethnographic approach for philosophical investigation best adapted to provide information relevant to philosophical interests and epistemic values. To this end, we advocate for a purpose-guided form of cognitive ethnography that mediates between the explanatory and normative interests of philosophy of science, while maintaining openness and (...) independence when framing such an investigation to achieve robust unbiased results. (shrink)

The purpose of this article is to develop an epistemology of scientific models in scientific research practices, and to show that disciplinary perspectives have crucial role in such an epistemology. A transcendental approach is taken, aimed at explanations of the kinds of questions relevant to the intended epistemology, such as “How is it possible that models provide knowledge about aspects of reality?” The approach is also pragmatic in the sense that the questions and explanations must be adequate and relevant to (...) concrete scientific practice. First it is explained why the idea of models as representations in terms of similarity or isomorphism between a model and its target is too limited as a basis for this epistemology. An important finding is that the target-phenomenon is usually not something that can be observed in a straightforward manner, but requires both characterization in terms of measurable variables and subsumption under concepts. The loss of this basis leads to a number of issues, such as: how can models be interpreted as representations if models also include conceptually meaningful linguistic content; how can researchers identify non-observable real-world target-phenomena that are then represented in the model; how do models enable inferential reasoning in performing epistemic tasks by researchers; and, how to justify scientific models. My proposal is to deal with these issues by analyzing how models are constructed, rather than by looking at ready-made models. Based on this analysis, I claim that the identification of phenomena and the construction of scientific models is guided and also confined by the disciplinary perspective within which researchers in a scientific discipline have learned to work. I propose a Kuhnian framework by which the disciplinary perspective can be systematically articulated. Finally, I argue that harmful forms of subjectivism, due to the loss of the belief that models objectively represent aspects of reality, can be overcome by making the disciplinary perspective in a research project explicit, thereby enabling its critical assessment, for which the proposed Kuhnian framework provides a tool. (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)

The contributions to this special issue on cognitive development collectively propose ways in which learning involves developing constraints that shape subsequent learning. A learning system must be constrained to learn efficiently, but some of these constraints are themselves learnable. To know how something will behave, a learner must know what kind of thing it is. Although this has led previous researchers to argue for domain-specific constraints that are tied to different kinds/domains, an exciting possibility is that kinds/domains themselves can be (...) learned. General cognitive constraints, when combined with rich inputs, can establish domains, rather than these domains necessarily preexisting prior to learning. Knowledge is structured and richly differentiated, but its “skeleton” must not always be preestablished. Instead, the skeleton may be adapted to fit patterns of co-occurrence, task requirements, and goals. Finally, we argue that for models of development to demonstrate genuine cognitive novelty, it will be helpful for them to move beyond highly preprocessed and symbolic encodings that limit flexibility. We consider two physical models that learn to make tone discriminations. They are mechanistic models that preserve rich spatial, perceptual, dynamic, and concrete information, allowing them to form surprising new classes of hypotheses and encodings. (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)

If folk science means individuals having well worked out mechanistic theories of the workings of the world, then it is not feasible. Laypeople’s explanatory understandings are remarkably coarse, full of gaps, and often full of inconsistencies. Even worse, most people overestimate their own understandings. Yet recent views suggest that formal scientists may not be so different. In spite of these limitations, science somehow works and its success offers hope for the feasibility of folk science as well. The success of science (...) arises from the ways in which scientists learn to leverage understandings in other minds and to outsource explanatory work through sophisticated methods of deference and simplification of complex systems. Three studies ask whether analogous processes might be present not only in laypeople but also in young children and thereby form a foundation for supplementing explanatory understandings almost from the start of our first attempts to make sense of the world. (shrink)

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)

The complex societal challenges of the twenty-first Century require scientific researchers and academically educated professionals capable of conducting scientific research in complex problem contexts. Our central claim is that educational approaches inspired by a traditional empiricist epistemology insufficiently foster the required deep conceptual understanding and higher-order thinking skills necessary for epistemic tasks in scientific research. Conversely, we argue that constructivist epistemologies provide better guidance to educational approaches to promote research skills. We also argue that teachers adopting a constructivist learning theory (...) do not necessarily embrace a constructivist epistemology. On the contrary, in educational practice, novel educational approaches that adopt constructivist learning theories often maintain traditional empiricist epistemologies. Philosophers of science can help develop educational designs focused on learning to conduct scientific research, combining constructivist learning theory with constructivist epistemology. We illustrate this by an example from a bachelor’s program in Biomedical Engineering, where we introduce conceptual models and modeling as an alternative to the traditional focus on hypothesis testing in conducting scientific research. This educational approach includes the so-called B&K method for constructing scientific models to scaffold teaching and learning conceptual modeling. (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)