Scuba Search : when selection meets innovation

We proposed a new search heuristic using the scuba diving metaphor. This approach is based on the concept of evolvability and tends to exploit neutrality in fitness landscape. Despite the fact that natural evolution does not directly select for evolvability, the basic idea behind the scuba search heuristic is to explicitly push the evolvability to increase. The search process switches between two phases: Conquest-of-the-Waters and Invasion-of-the-Land. A comparative study of the new algorithm and standard local search heuristics on the NKq-landscapes has shown advantage and limit of the scuba search. To enlighten qualitative differences between neutral search processes, the space is changed into a connected graph to visualize the pathways that the search is likely to follow

Fitness landscape of the cellular automata majority problem: View from the Olympus

In this paper we study cellular automata (CAs) that perform the computational Majority task. This task is a good example of what the phenomenon of emergence in complex systems is. We take an interest in the reasons that make this particular fitness landscape a difficult one. The first goal is to study the landscape as such, and thus it is ideally independent from the actual heuristics used to search the space. However, a second goal is to understand the features a good search technique for this particular problem space should possess. We statistically quantify in various ways the degree of difficulty of searching this landscape. Due to neutrality, investigations based on sampling techniques on the whole landscape are difficult to conduct. So, we go exploring the landscape from the top. Although it has been proved that no CA can perform the task perfectly, several efficient CAs for this task have been found. Exploiting similarities between these CAs and symmetries in the landscape, we define the Olympus landscape which is regarded as the ''heavenly home'' of the best local optima known (blok). Then we measure several properties of this subspace. Although it is easier to find relevant CAs in this subspace than in the overall landscape, there are structural reasons that prevent a searcher from finding overfitted CAs in the Olympus. Finally, we study dynamics and performance of genetic algorithms on the Olympus in order to confirm our analysis and to find efficient CAs for the Majority problem with low computational cost

Artificial evolution with Binary Decision Diagrams: a study in evolvability in neutral spaces

This thesis develops a new approach to evolving Binary Decision Diagrams, and uses it to study evolvability issues. For reasons that are not yet fully understood, current approaches to artificial evolution fail to exhibit the evolvability so readily exhibited in nature. To be able to apply evolvability to artificial evolution the field must first understand and characterise it; this will then lead to systems which are much more capable than they are currently. An experimental approach is taken. Carefully crafted, controlled experiments elucidate the mechanisms and properties that facilitate evolvability, focusing on the roles and interplay between neutrality, modularity, gradualism, robustness and diversity. Evolvability is found to emerge under gradual evolution as a biased distribution of functionality within the genotype-phenotype map, which serves to direct phenotypic variation. Neutrality facilitates fitness-conserving exploration, completely alleviating local optima. Population diversity, in conjunction with neutrality, is shown to facilitate the evolution of evolvability. The search is robust, scalable, and insensitive to the absence of initial diversity. The thesis concludes that gradual evolution in a search space that is free of local optima by way of neutrality can be a viable alternative to problematic evolution on multi-modal landscapes

Degeneracy: a link between evolvability, robustness and complexity in biological systems

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles

Origin of life in a digital microcosm

While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). We generated the exhaustive set of minimal-genome self-replicators and analyzed the network structure of this fitness landscape. We further examined the evolvability of these self-replicators and found that the evolvability of a self-replicator is dependent on its genomic architecture. We studied the differential ability of replicators to take over the population when competed against each other (akin to a primordial-soup model of biogenesis) and found that the probability of a self-replicator out-competing the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life.Comment: 20 pages, 7 figures. To appear in special issue of Philosophical Transactions of the Royal Society A: Re-Conceptualizing the Origins of Life from a Physical Sciences Perspectiv

Degenerate neutrality creates evolvable fitness landscapes

Understanding how systems can be designed to be evolvable is fundamental to research in optimization, evolution, and complex systems science. Many researchers have thus recognized the importance of evolvability, i.e. the ability to find new variants of higher fitness, in the fields of biological evolution and evolutionary computation. Recent studies by Ciliberti et al (Proc. Nat. Acad. Sci., 2007) and Wagner (Proc. R. Soc. B., 2008) propose a potentially important link between the robustness and the evolvability of a system. In particular, it has been suggested that robustness may actually lead to the emergence of evolvability. Here we study two design principles, redundancy and degeneracy, for achieving robustness and we show that they have a dramatically different impact on the evolvability of the system. In particular, purely redundant systems are found to have very little evolvability while systems with degeneracy, i.e. distributed robustness, can be orders of magnitude more evolvable. These results offer insights into the general principles for achieving evolvability and may prove to be an important step forward in the pursuit of evolvable representations in evolutionary computation