Highlighted Article

Description: This new article by Whitacre and Atamas discusses the intimate relationship between cryptic genetic variation and degeneracy. The article hypothesizes that degeneracy plays an important role in resolving conflicts between exploitation and exploration at many levels of biological organization and can be readily applied to resolve similar conflicts that arise in a number of disciplines outside of biology.

Whitacre JM, Atamas SP: The Diversity Paradox: How Nature Resolves an Evolutionary Dilemma. Biology Direct (in press).

Abstract

Background: Adaptation, through selection, to changing environments is a hallmark of biological systems. Diversity in traits is necessary for adaptation and can influence the survival of a population faced with environmental novelty. In habitats that remain stable over many generations, effective stabilizing selection removes trait diversity from populations and should limit adaptability to environmental change. Paradoxically, field studies have documented numerous populations under long periods of stabilizing selection and evolutionary stasis that can rapidly evolve within new environments.

Presentation of the hypothesis: Recent studies have indicated that cryptic genetic variation (CGV) may facilitate rapid evolution in response to environmental novelty. Here we propose that CGV also resolves the diversity paradox by allowing populations under stabilizing selection to gradually accumulate hidden genetic diversity that reveals itself through trait differences as environments change. CGV represents a broader phenomenon, degeneracy, known to support genetic and non-genetic adaptation at many levels of biological organization. By integrating these paradigms, we propose that degeneracy fundamentally underpins evolvability at multiple levels of biological organization.

Implications of the hypothesis: The conditions that facilitate environment-induced adaptation are of great importance to the preservation of species and the eradication of evolvable pathogens. In conservation biology for instance, CGV revealed under predicted stress conditions may provide a more adaptively significant measure of intraspecific biodiversity for conservation efforts. Similar exploration-exploitation conflicts arise throughout sociotechnical systems and we consider how degeneracy principles can be applied in these contexts to improve flexibility and resilience.

Testing the hypothesis: Instead of conflicting, this hypothesis suggests that environmental stasis supports CGV accumulation and actually enables adaptation in novel environments. Moreover, degeneracy theory describes a more general resolution between the conflicting forces of short-term exploitation and longer-term exploration. We discuss molecular-based experimental systems, simulation studies, principles from population genetics, and field experiments for exploring the validity of these claims.

Previous Article (July 2011)

Description: This new article by Ed Clark and colleagues introduces new measures of degeneracy and presents evidence within artificial chemistries that several properties related to complexity (hypercycles, parasitic evasion) are only observed when degeneracy is present in the chemical reaction system.

Ed Clark, Adam Nellis, Simon Hickinbotham, Susan Stepney, Tim Clarke, Mungo Pay, Peter Young. Degeneracy Enriches Artificial Chemistry Binding Systems. ECAL 11, Paris, France, August 2011. IN PRESS

Abstract:  We hypothesise that degeneracy in the components of an artificial chemistry (AChem) facilitates the complexity of the system as a whole. We introduce definitions of degeneracy and redundancy, and show how these quantities can be calculated for the binding system of an AChem. We present a case study using the AChem Stringmol, in order to support our hypothesis. We demonstrate that the binding system in Stringmol has degeneracy and we create a deliberately poor variant: ‘sticky-Stringmol’, that has a binding system with no degeneracy. Comparing sticky-Stringmol to Stringmol, we note the loss of many simulation artifacts that have been used as evidence of the complexity of Stringmol, including: emergent macro-mutations, hypercycles, sweeps and parasite evasion. These results are evidence that degeneracy in the components of an AChemfacilitates the complexity of the system as a whole.

Previous Article (June 2011)

Description: This new article by Paul H. Mason provides an interesting introduction to the concept of degeneracy and a thorough review of its historical origins.

Mason, P.H., Degeneracy at Multiple Levels of Complexity. Biological Theory, 2010. 5(3): p. 277-288.

Abstract: Degeneracy is a poorly understood process, essential to natural selection. In the 18th and 19th centuries, the concept of degeneracy was commandeered by the colonial imagination. A rigid understanding of species, race, and culture grew to dominate the normative thinking that persisted well into the burgeoning new industrial age. A 20th-century reconfiguration of the concept by George Gamow highlighted a form of intraorganismic variation that is still underexplored. Degeneracy exists in a population of variants where structurally different components perform a similar, but not necessarily identical, function with respect to context. The presence of degeneracy increases a system’s complexity and robustness against perturbations. The loss of a genetic component in biological systems, for example, can be compensated by redundant elements (the presence of isomorphic and isofunctional components), or by degenerate elements (heteromorphic variants that are isofunctional). A historical survey of the use of the term “degeneracy” reveals how and why the processes it once designated, and the mechanisms it now represents, have largely escaped the purview of contemporary science. Despite confusion and general oversight, degeneracy has been characterized by select researchers at the molecular, genetic, and neuronal levels. The concept is a potent analytical tool to understand selection, variation, and transmission.

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