Bioattractors: dynamical systems theory and the evolution of regulatory processes

Abstract

In this paper, we illustrate how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems. Our argument is that the genotype-phenotype map can be characterized by the phase portrait of the underlying regulatory process. The features of this portrait -such as attractors with associated basins and their bifurcations -define the regulatory and evolutionary potential of a system. We show how the geometric analysis of phase space connects Waddington's epigenetic landscape to recent computational approaches for the study of robustness and evolvability in network evolution. We discuss how the geometry of phase space determines the probability of possible phenotypic transitions. Finally, we demonstrate how the active, self-organizing role of the environment in phenotypic evolution can be understood in terms of dynamical systems concepts. This approach yields mechanistic explanations that go beyond insights based on the simulation of evolving regulatory networks alone. Its predictions can now be tested by studying specific, experimentally tractable regulatory systems using the tools of modern systems biology. A systematic exploration of such systems will enable us to understand better the nature and origin of the phenotypic variability, which provides the substrate for evolution by natural selection.

Parameter asymmetry and time‐scale separation in core genetic commitment circuits

“…This aspect was recently reviewed by Jaeger and Monk [4]. Thus, mathematics underpins the process of not only understanding "how" living systems work, but much more interestingly, "why" they do so in particular ways, rather than others.…”

The number of cell types, information content, and the evolution of complex multicellularity

“…The traditionally accepted mechanism for cell fate specification relies on the inherent multi-stability of gene regulatory networks (e.g., [39][40][41]). Each stable state provides the conditions that specify a cell type that can be "fixed" in a developmental repertoire ad hoc by natural selection as an organism adapts to its different environmental conditions.…”

Aristotelian essentialism: essence in the age of evolution

“…49 If, as Rosenberg (2001) argues, the process of natural selection operates on function, and is rather "blind" to structure, we shouldn"t expect the essence of a natural kind, being so central to the process of ontogenic development, to be necessarily tied-up to a particular material realisation base. 50 Jaeger & Monk (2014), Dupré (2013), Rosa & Exteberria (2011), Gilbert & Bolker (2001) been refined by the selective pressures of the conceptual challenges of contemporary biology, an evolved essentialism is at hand.…”

“…37 This fact brings with it two important points, the first being that a common set of modules possessed by the members of a single species is able to ground a wealth of their morphological variationfor one and the same developmental module can be responsible for a wide variety of phenotypic variation in a particular structure as a result of (broadly construed) environmental influences: as described above, alterations in upstream signalling are interpreted by these modules into downstream regulatory control 31 Thus, in the context of dynamical systems theory, the morphological structures associated with these modules are often characterised as "attractor-states" which shape the "valleys" of an organisms" epigenetic landscape, resulting in many distinct developmental pathways leading to the same end-state. See Monk (2014), andStriedter (1998). 32 See Amundson (2005) for an excellent in-depth discussion of the "structuralist" paradigm and its relation to that of the Modern Synthesis.…”