Explanatory Integration Challenges in Evolutionary Systems Biology

Green, Sara; Fagan, Melinda Bonnie; Jaeger, Johannes

doi:10.1007/s13752-014-0185-8

Cited by 32 publications

(29 citation statements)

References 82 publications

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“…Recent advances in panomics (e.g., genomics, epigenomics, proteomics, metabolomics) and systems biology are redefining our understanding of how gene networks are regulated and dynamically interact with each other and the environment, resulting in a new synthesis of biological systems development and functioning (Huang 2012;Forrest 2014;Davila-Velderrain et al 2015). Breakthroughs in understanding the relationships between evolutionary processes and biological development, and advances in the use of life history theory to explain how mismatches between biological propensities and modern environments influence the onset of disease, have also provided a new way of considering the relationship of an individual's or a population's genetic endowment and the phenotypes that emerge (Del Giudice et al 2015;Green et al 2015;Hanson and Gluckman 2014;Lieberman 2014;Gluckman and Hanson 2006a).…”

Section: Part 2: Emergence Of the Life Course Health Development Frammentioning

confidence: 99%

The Emerging Theoretical Framework of Life Course Health Development

Halfon

Forrest

2017

Handbook of Life Course Health Development

115

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Section: Part 2: Emergence Of the Life Course Health Development Frammentioning

confidence: 99%

The Emerging Theoretical Framework of Life Course Health Development

Halfon

Forrest

2017

Handbook of Life Course Health Development

115

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“…Aside from aiming to bridge between ideas from general systems theory and experimental approaches, structuralist theories of pattern formation may regain their relevance in systems biology (Green, Fagan and Jaeger 2015). According to structuralists, many patterns observed in nature are not only products of random genetic variation and natural selection, but result from more general constraints imposed by complexity (e.g., Goodwin, 1994).…”

Section: Functional and Evolutionary Systems Biologymentioning

confidence: 99%

“…While systems biology seems to offer new ways of providing mechanistic explanations, other aspects of systems biology may be better described as non-mechanistic approaches (Gross, Chapter 10; see also Jones 2014; Chapter 14). For instance, some scholars have argued that some practices of modeling and explanation are better described through appeals to law-like explanatory ideals (Fagan, 2016;Chapter 8;Green, Fagan and Jaeger 2015), topological explanations (Huneman 2010;Jones 2014), or design explanations (Braillard 2010;Boogerd, Chapter 4;Wouters 2007). The diversity of explanatory ideals in systems biology creates new venues for scientific and philosophical analysis but also poses challenges for interdisciplinary collaboration (see section below).…”

Section: Explanations and Design Principlesmentioning

confidence: 99%

“…In Fagan's view, the failure to communicate is at least partly due to the different standards of explanation held by the two groups, i.e. whether generalizable law-like principles or concrete mechanistic explanations are the end goal (see also Green, Fagan and Jaeger 2015).…”

Section: Interdisciplinary Collaboration and Science Educationmentioning

confidence: 99%

“…Against this background, many philosophers have been positively surprised by how many systems biologists are open to interactions. The number of joint publications by philosophers and practicing scientists is a positive indication of the mutual interest in philosophy of systems biology (e.g., Boogerd et al 2013;Calcott et al 2015;Carusi et al 2012;Drack and Wolkenhauer 2011;Green, Fagan and Jaeger 2015;O'Malley and Soyer 2012;Jones and Wolkenhauer 2012).…”

Section: Future Perspectives For Philosophy Of Systems Biologymentioning

confidence: 99%

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Introduction to Philosophy of Systems Biology

Green

2016

Philosophy of Systems Biology

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The intention with this volume is to provide a format for scholars to express their personal viewpoints and tell their story in response to the same set of questions (see Preface). Unlike many edited volumes, this book is therefore not divided into thematic sections. The aim of this introduction is to summarize core common themes among the contributor's chapters so as to guide readers interested in specific topics. Given the richness of the contributions that touch upon many diverse topics in response to the posed questions, I have not summarized each contribution separately. Rather, I focus on core questions and highlight where more information on common themes and novel insights can be found. I also hope that the introduction will provide some background for scientists, philosophers as well as other readers interested in discussing the philosophical implications of systems biology. What is systems biology?Broadly understood, systems biology aims to capture the dynamic complexity of living systems through the combination of mathematical, computational and experimental strategies (Kitano 2001). One overarching research question is how biological function emerges from the interactions of processes whose dynamics are nonlinear and constrained by the organization of the system as a whole (cf. Wolkenhauer, Chapter 24). Research in systems biology is driven by complex problems requiring interdisciplinary solutions, but there are different views on the most significant methods, values and aims of systems biology. Some scholars emphasize computational integration of big data from multiple sources as a characteristic feature of systems biology (Aderem 2005), whereas others stress that systems biology is a merger of systems theory with biology (Wolkenhauer and Mesarović 2005). Differences in theoretical and methodological standpoints are sometimes characterized by the differences between pragmatic and systems-theoretical systems biology: the former sees systems biology as a straightforward extension of genomics and molecular biology and the latter highlights the need for a formal systems theory of living systems (O'Malley and Dupré, 2005, for further reflections see Boogerd et al. 2007). In both cases, however, researchers must navigate in what Nersessian (Chapter 20) calls an adaptive problem space where knowledge and methods are continuously reconfigured and combined into new hybrid methods, concepts, and models. The combination of theoretical reflection and technologically mediated methodological innovations make systems biology particularly intriguing from a philosophical perspective.It is debatable whether systems biology brings something radically new to the life sciences. Systems biology has been described in terms as different as a new 'holistic paradigm' or 'revolution' in biology to being merely a 'buzzword' used for funding purposes (Kastenhofer 2013b). It is difficult to point to radical historical shifts or 'revolutions', but systems biology develops in a unique historical and technological context offering ...

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Systems science and the art of interdisciplinary integration

Green

Andersen

2019

Syst Res Behav Sci

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Systems sciences address issues that cross‐cut any single discipline and benefit from the synergy of combining several approaches. But interdisciplinary integration can be challenging to achieve in practice. Scientists with different disciplinary backgrounds often have different views on what count as good data, good evidence, a good model, or a good explanation. Accordingly, several scholars have reported on challenges encountered in interdisciplinary settings. This chapter outlines how some of the challenges play out in systems biology where disciplinary ideals and domainspecific practices sometime collide. We focus on tensions arising due to differences in epistemic standards between modellers with a background in physics or systems engineering, on one hand, and experimenters with a background in molecular biology on the other. We propose that part of the problem of interdisciplinary integration can be understood as the result of unfounded “disciplinary imperialism” on both sides, in which standards from one discipline are uncritically applied to new domains without recognition of other valid or complementary perspectives. Addressing and explicating the disciplinary background for the different views can help facilitate interdisciplinary collaboration in science and improve science education.

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Explanatory Integration Challenges in Evolutionary Systems Biology

Cited by 32 publications

References 82 publications

The Emerging Theoretical Framework of Life Course Health Development

The Emerging Theoretical Framework of Life Course Health Development

Introduction to Philosophy of Systems Biology

Systems science and the art of interdisciplinary integration

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