Organisms≠Machines

Nicholson, Daniel J.

doi:10.1016/j.shpsc.2013.05.014

Cited by 140 publications

(77 citation statements)

References 45 publications

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“…However, it is debated whether methodological reduction can lead to oversimplified ontological accounts of living systems (cf. Green 2015;Nicholson 2013). In spite of their success in 20th Century biology, it has been argued that reductionist strategies are inherently limited and lead to partial or incomplete accounts of living phenomena, either because some organizational features of biological systems are irreducible to the lower level (e.g.…”

Section: Reductionism and Its Limits In Molecular Biologymentioning

confidence: 99%

The Sum of the Parts: Large-Scale Modeling in Systems Biology

Groß¹,

Green²

2017

Philosophy, Theory, and Practice in Biology

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Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems "as a whole." Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call "modular reductionism" and "bottom-up reductionism." Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood "bottom-up." Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. Editorial introduction: This contribution from Fridolin Gross and Sara Green focuses on the promises and possible pitfalls of large-scale modelling in systems biology, from both a practical and a theoretical point of view. As readers will be aware, molecular biology has often been accused of being "reductionist." Systems biology has been presented as a potential response to this reductionism. Gross and Green distinguish two types of reductionisms: "modular reductionism" (the claim that living systems consist of individual functional subunits) and "bottom-up reductionism" (the claim that biological phenomena can and should be studied at the molecular level, understood as the "fundamental" biological level). They show how systems biology questions both forms of reductionism. To this end, they use two examples: whole-cell modelling of a very "simple" bacterium (from a piece published in 2012), and multi-scale computer modelling of the human heart. Without masking the limitations of these models, Gross and Green show the insights they can yield for anyone interested in ontologies of the living world. KeywordsAs with some of the other contributions in this special issue (e.g. Fagan's, and Kendig and Eckdahl's), a virtue of this paper is to illustrate how research strategies-particularly modelling strategies-can in...

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Section: Reductionism and Its Limits In Molecular Biologymentioning

confidence: 99%

The Sum of the Parts: Large-Scale Modeling in Systems Biology

Groß¹,

Green²

2017

Philosophy, Theory, and Practice in Biology

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“…One argument could be that a loss of intrinsic value stems from the way in which GM crops are (legally) perceived as human inventions rather than living organisms. While living organisms may have natural value and be granted intrinsic or inherent worth on the basis of having their own ends/telos (Taylor 1986;Sandler 2012), human inventions, machines and bio-artefacts may not (Nicholson 2013). Furthermore, if the telos of an organism is seen to be encoded in its genes as some have suggested (Rolston III 1991), then the moral status of a GMO could also be brought into question (Attfield 2012).…”

Section: Gm Crops Have Conservation Value For Instrumental Purposes Bmentioning

confidence: 99%

Do We Care About Synbiodiversity? Questions Arising from an Investigation into Whether There are GM Crops in the Svalbard Global Seed Vault

Wickson

2016

J Agric Environ Ethics

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The Svalbard Global Seed Vault provides a backup of seed collections from genebanks around the world. It's unique character has made it iconic in the public imagination as a 'Noah's Ark' for crop plants. Its remote location and strict controls on access have, however, also lent it an air of mystery, swirling with conspiracy theories. In this paper, I first clarify the aims of the Vault, the history of its development and the policies and practices of its current operation. Given concerns around its potential links to the biotechnology industry, I go on to ask whether GM crops are currently stored in the Vault. Presenting several reasons for why GM crops are formally excluded, while indicating the potential for both change and unintentional contamination, I am compelled to question whether GM crops should be excluded. Answering this requires an interrogation of their potential conservation value as modern contributors to crop biodiversity. In exploring this issue, I suggest that there has been surprisingly little discussion of the moral status and conservation value of bio-technological crop plants and indeed, of how we care for all the techno-lifeforms we are currently engaged in co-creating. I suggest that these are becoming important issues as biotechnological techniques and applications begin to rapidly evolve and diversify (e.g. through genome editing and synthetic biology). Emphasizing the scope for a refreshed interdisciplinary research agenda exploring the interface between biotechnology and biodiversity conservation, I conclude the article by proposing new concepts of synbiodiversity and symbiodiversity to encourage further debate.

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“…Although design principles and organizing principles are often used interchangeably, the preferences for one of these terms also reflect a concern with possible limitations of an engineering approach to biological systems. This question was already a theme in the early work of Bertalanffy and Mesarović (Drack, Chapter 7;Green and Wolkenhauer 2013), but it has regained its relevance in contemporary discussions about research methodologies in systems biology and about the fundamental question of what life is (Boogerd, Chapter 4;Braillard 2015;Boudry and Pigliucci 2013;Calcott et al 2015;Nicholson 2013). Is there something fundamental and distinct about living systems?…”

Section: Explanations and Design Principlesmentioning

confidence: 99%

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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Organisms≠Machines

Cited by 140 publications

References 45 publications

The Sum of the Parts: Large-Scale Modeling in Systems Biology

The Sum of the Parts: Large-Scale Modeling in Systems Biology

Do We Care About Synbiodiversity? Questions Arising from an Investigation into Whether There are GM Crops in the Svalbard Global Seed Vault

Introduction to Philosophy of Systems Biology

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