A Philosophical Perspective on Evolutionary Systems Biology

O’Malley, Maureen A.; Soyer, Orkun S.; Siegal, Mark L.

doi:10.1007/s13752-015-0202-6

Cited by 7 publications

(4 citation statements)

References 69 publications

(84 reference statements)

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“…Systems biology, despite its remarkable advances in recent years, is still awaiting key theoretical insights to unveil the general principles of organization behind life's complexity (beyond the non-reductionist philosophy and methods developed from network theory and the sciences of self-organization). In addition, several authors have suggested that a new synthesis is required, and has already begun, in which systems and evolutionary theory merge (Soyer and O'Malley, 2013;O'Malley et al, 2015). Investigations on the origins of life, especially if they contemplate the actual interbreeding between organizational and evolutionary aspects of the problem (e.g., working with various kinds of protocell families, but including in the study short-/long-term effects coming from their population dynamics), could constitute very fertile ground for this ambitious project of bringing together two major traditions in the life sciences (the physiological and evolutionary traditions), and try to generalize, thereafter, biological theory.…”

Section: Final Remarks: Exploring the Principles Of Evolutionary Systmentioning

confidence: 99%

The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution

et al. 2020

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The concept of identity is used both (i) to distinguish a system as a particular material entity that is conserved as such in a given environment (token-identity: i.e., identity as permanence or endurance over time), and (ii) to relate a system with other members of a set (type-identity: i.e., identity as an equivalence relationship). Biological systems are characterized, in a minimal and universal sense, by a highly complex and dynamic, far-from-equilibrium organization of very diverse molecular components and transformation processes (i.e., 'genetically instructed cellular metabolisms') that maintain themselves in constant interaction with their corresponding environments, including other systems of similar nature. More precisely, all living entities depend on a deeply convoluted organization of molecules and processes (a naturalized von Neumann constructor architecture) that subsumes, in the form of current individuals (autonomous cells), a history of ecological and evolutionary interactions (across cell populations). So one can defend, on those grounds, that living beings have an identity of their own from both approximations: (i) and (ii). These transversal and trans-generational dimensions of biological phenomena, which unfold together with the actual process of biogenesis, must be carefully considered in order to understand the intricacies and metabolic robustness of the first living cells, their underlying uniformity (i.e., their common biochemical core) and the eradication of previous-or alternative-forms of complex natural phenomena. Therefore, a comprehensive approach to the origins of life requires conjugating the actual properties of the developing complex individuals (fusing and dividing protocells, at various stages) with other, population-level features, linked to their collective-evolutionary behavior, under much wider and longer-term parameters. On these lines, we will argue that life, in its most basic sense, here on Earth or anywhere else, demands crossing a high complexity threshold and that the concept of 'interidentity' can help us realize the different aspects involved in the process. The article concludes by pointing out some of the challenges ahead if we are to integrate the corresponding explanatory frameworks, physiological and evolutionary, in the hope that a more general theory of biology is on its way.

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Section: Final Remarks: Exploring the Principles Of Evolutionary Systmentioning

confidence: 99%

The Construction of Biological ‘Inter-Identity’ as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution

et al. 2020

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“…Enhancing network-based evolutionary analyses, beyond the now classic research program of phylogenetic networks, could consolidate comparative analyses in the nascent field of evolutionary systems biology [ 129 , 130 ], as illustrated by examples based on molecular networks. Network construction/gathering constitutes the first step of such analyses.…”

Section: Concrete Strategies To Enhance Network-based Evolutionary Anmentioning

confidence: 99%

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

Bapteste

Huneman

2018

BMC Biol

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The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

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“…Philosophers of science who adopt a system-biological approach to biology, and the biology of microorganisms in particular, or highlight processes rather than structures, share a similar view while complicating the distinction between life/non-life in viruses (Soyer and O'Malley 2013;O'Malley et al 2015). As Stephan Guttinger and John Dupré have argued, viruses "are not living things certainly, but they are stages of living processes" (Guttinger and Dupré 2016).…”

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confidence: 99%