Toy models for macroevolutionary patterns and trends

Alicea, Bradly; Gordon, Richard

doi:10.1016/j.biosystems.2014.09.007

Cited by 6 publications

(1 citation statement)

References 149 publications

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“…The first is that a general structuralist approach is a useful heuristic in dealing with the holistic nature of phenotypes (Emmeche, 2011). Additionally, emergentist approaches also help us understand emergent processes (Emmeche and Hoffmeyer, 1991) and act to countervail genecentric approaches (Alicea and Gordon, 2014). Along with these advantages, our approach provides a formal set of links between the evolution of development and regulatory mechanisms provided by the cybernetic embryo framework is a crucial component to reverse engineering the embryo defined as a multicausal, cascading, nested decision-making system (Gordon and Stone, 2017).…”

Section: Discussionmentioning

confidence: 99%

Origins of the Embryo: Self-organization through cybernetic regulation

et al. 2018

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Section: Discussionmentioning

confidence: 99%

Origins of the Embryo: Self-organization through cybernetic regulation

et al. 2018

Self Cite

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Macroevolution, differentiation trees, and the growth of coding systems

Igamberdiev,

Gordon

2023

Biosystems

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Punctuated equilibrium as an emergent process and its modified thermodynamic characterization

Wosniack

Luz

Schulman

2017

Journal of Theoretical Biology

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We address evolutionary dynamics and consider under which conditions the ecosystem interaction network allows punctuated equilibrium (i.e., alternation between hectic and quasi-stable phases). We focus on the links connecting various species and on the strength and sign of those links. For this study we consider the Tangled Nature model, which allows considerable flexibility and plasticity in the analysis of interspecies interactions. We find that it is necessary to have a proper balance of connectivity and interaction intensities so as to establish the kind of mutual cooperation and competition found in nature. It suggests evolutionary punctuated equilibrium as an emergent process, thus displaying features of complex systems. To explicitly demonstrate this fact we consider an extended form of thermodynamics, defining (for the present context) relevant out-of-equilibrium "collective" functions. We then show how to characterize the punctuated equilibrium through entropy-like and free energy-like quantities. Finally, from a close analogy to thermodynamic systems, we propose a protocol similar to simulated annealing. It is based on controlling the species' rate of mutation during the hectic periods, in this way enhancing the exploration of the genome space (similar to the known behavior of bacteria in stressful environments). This allows the system to more rapidly converge to long-duration quasi-stable phases.

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Toy models for macroevolutionary patterns and trends

Cited by 6 publications

References 149 publications

Origins of the Embryo: Self-organization through cybernetic regulation

Origins of the Embryo: Self-organization through cybernetic regulation

Macroevolution, differentiation trees, and the growth of coding systems

Punctuated equilibrium as an emergent process and its modified thermodynamic characterization

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