Prediction and control sufficient for reliable medical and other interventions are prominent aims of modeling in systems biology. The short-term attainment of these goals has played a strong role in projecting the importance and value of the field. In this paper I identify the standard models must meet to achieve these objectives as predictive robustness—predictive reliability over large domains. Drawing on the results of an ethnographic investigation and various studies in the systems biology literature, I explore four current obstacles to (...) achieving predictive robustness; data constraints, parameter uncertainty, collaborative constraints and system-scale requirements. I use a case study and the commentary of systems biologists themselves to show that current practices in the field, rather than pursuing these goals, frequently use models heuristically to investigate and build understanding of biological systems that do not meet standards of predictive robustness but are nonetheless effective uses of computation. A more heuristic conception of modeling allows us to interpret current practices as ways that manage these obstacles more effectively, particularly collaborative constraints, such that modelers can in the long-run at least work towards prediction and control. (shrink)

This paper explores the relation between scientific knowledge and common sense intuitions as a complement to Hoyningen-Huene’s account of systematicity. On one hand, Hoyningen-Huene embraces continuity between these in his characterization of scientific knowledge as an extension of everyday knowledge, distinguished by an increase in systematicity. On the other, he argues that scientific knowledge often comes to deviate from common sense as science develops. Specifically, he argues that a departure from common sense is a price we may have to pay (...) for increased systematicity. I argue that to clarify the relation between common sense and scientific reasoning, more attention to the cognitive aspects of learning and doing science is needed. As a step in this direction, I explore the potential for cross-fertilization between the discussions about conceptual change in science education and philosophy of science. Particularly, I examine debates on whether common sense intuitions facilitate or impede scientific reasoning. While contending that these debates can balance some of the assumptions made by Hoyningen-Huene, I suggest that a more contextualized version of systematicity theory could supplement cognitive analysis by clarifying important organizational aspects of science. (shrink)

It is a widespread assumption in philosophy of science that data is what is explained by theory—that data itself is not explanatory. I draw on instances of representational and explanatory practice from mammalian chronobiology to suggest that this assumption is unsustainable. In many instances, biologists employ representations of data in explanatory ways that are not reducible to constraints on or evidence for representations of mechanisms. Data graphs are used to exemplify relationships between quantities in the mechanism, and often these representations (...) are necessary for explaining particular aspects of the phenomena under study. I argue that this kind of representation is distinct from representing laws or generalizations, and its primary purpose is to convey particular types or patterns of quantitative relationships. The benefit of the analysis is two-fold. First, it provides a more accurate account of explanatory practice in broadly mechanistic analysis in biology. Second, it suggests that there is not an explanatory “fundamental” type of representation in biology. Rather, the practice of explanation consists in the construction of different types of representations and their employment for distinct explanatory purposes. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

In science policy, it is generally acknowledged that science-based problem-solving requires interdisciplinary research. For example, policy makers invest in funding programs such as Horizon 2020 that aim to stimulate interdisciplinary research. Yet the epistemological processes that lead to effective interdisciplinary research are poorly understood. This article aims at an epistemology for interdisciplinary research, in particular, IDR for solving ‘real-world’ problems. Focus is on the question why researchers experience cognitive and epistemic difficulties in conducting IDR. Based on a study of educational (...) literature it is concluded that higher-education is missing clear ideas on the epistemology of IDR, and as a consequence, on how to teach it. It is conjectured that the lack of philosophical interest in the epistemology of IDR is due to a philosophical paradigm of science, which prevents recognizing severe epistemological challenges of IDR, both in the philosophy of science as well as in science education and research. The proposed alternative philosophical paradigm entails alternative philosophical presuppositions regarding aspects such as the aim of science, the character of knowledge, the epistemic and pragmatic criteria for accepting knowledge, and the role of technological instruments. This alternative philosophical paradigm assume the production of knowledge for epistemic functions as the aim of science, and interprets ‘knowledge’ as epistemic tools that must allow for conducting epistemic tasks by epistemic agents, rather than interpreting knowledge as representations that objectively represent aspects of the world independent of the way in which it was constructed. The engineering paradigm of science involves that knowledge is indelibly shaped by how it is constructed. Additionally, the way in which scientific disciplines construct knowledge is guided by the specificities of the discipline, which can be analyzed in terms of disciplinary perspectives. This implies that knowledge and the epistemic uses of knowledge cannot be understood without at least some understanding of how the knowledge is constructed. Accordingly, scientific researchers need so-called metacognitive scaffolds to assist in analyzing and reconstructing how ‘knowledge’ is constructed and how different disciplines do this differently. In an engineering paradigm of science, these metacognitive scaffolds can also be interpreted as epistemic tools, but in this case as tools that guide, enable and constrain analyzing and articulating how knowledge is produced. In interdisciplinary research, metacognitive scaffolds assist interdisciplinary communication aiming to analyze and articulate how the discipline constructs knowledge. (shrink)