Newman, M. E. J., & Engelhardt, R. (1998). Effects of neutral selection on the evolution of molecular species. Working papers 98-01-001, Sante Fe Institute.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....previously unencountered phenotypes. Moreover, a selection induced transition can occur where two neutral networks are close at the genotypic level. Their study concluded that the success of the evolutionary search in such a space is less dependent on the initial conditions. In a different work, [14] shows directly that the maximum fitness obtainable during the adaptive walk of a population increases with increasing degree of neutrality. Barnett extended the NK fitness landscape model to include neutrality where he observed that the constant innovation property helped to escape local ....

Newman, M. E. J., and R. Engelhardt, R., Effects of neutral selection on the evolution of molecular species", Proc. Roy. Soc. London Series B Vol. 265 (1998) 1333-1338.

....in relation to biological modelling. Several models of neutrality have been proposed that generalise Kauffman s NK landscape model by adding a tuneable level of neutrality. These include the NKp ( probabilistic NK) model developed by Barnett [1] and another model developed by Newman Engelhardt [10], which we term, analogously, NKq ( quantised NK) The NKp and NKq models, while both based on the NK landscape model, employ distinctly different approaches to modelling neutrality. Due to these differences, the fitness landscapes generated by the two neutral models should be expected to display ....

....genes [8] By altering the level of epistatic interaction, it is possible to generate a range of landscapes from a smooth peak with a single optimum to a rugged terrain with many local optima. The basic NK model was further developed into models incorporating neutrality by Newman Engelhardt [10] and independently by Barnett [1] These models have been used to investigate the biological phenomenon of neutrality and to explore the potential of neutrality to improve the efficiency of evolutionary algorithms as a search and optimisation technique [13] III. LANDSCAPE MODELS Landscapes in ....

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Newman, M. & Engelhardt, R., Effect of neutral selection on the evolution of molecular species. Proc. R. Soc. London B., 256, 13331338, 1998.

....on a neutral landscape. In this study, neutrality per se is not central to the phenomena of interest, but it does enable the change in diversity to be demonstrated very clearly. The critical feature is the punctuated equilibria dynamic displayed by populations evolving on neutral landscapes [1, 6, 8]. II. METHODOLOGY AND RESULTS The Royal Staircase model [12] a variation of the wellknown Royal Road functions [7] is a simple landscape with clearly defined neutral layers. Genotypes are specified by binary strings consisting of N blocks of length K. Each genotype has a base fitness of 1, to ....

.... an integer in the range [1, N 1] For the simulations described here, a Royal Staircase landscape with N = 4 and K = 8 was used (i.e. 4 blocks of 8 bits each = genotype of length 32 bits) In order to provide the clearest demonstration of the phenomena, the methodology of Newman and Engelhardt [8] was followed and a population of size 100 was used, initially converged upon a random genotype. Trial simulations with a nonconverged initial population were also run and similar phenomena were observed. The reason for this similarity is that, after a block has been discovered and the population ....

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Newman, M. & Engelhardt, R., Effect of neutral selection on the evolution of molecular species, Proc. R. Soc. London B., Vol. 256, pp. 1333-1338, 1998.

....structures without the need for specially engineered genetic operators functional diversity of proteins. 5. Degenerate Encodings efficiency gains in terms of evolutionary search, e.g. through the use of neutral mutations and their corresponding neutral networks, for example see [Barnett 97] [Newman Engelhardt 1998]. 6. Compression of representation large structures represented with a relatively small genotype. 7. Alternative implementation of functions, for example, through the use of the operon model. 8. Positional Independence this amounts to the position (locus) of a gene on the chromosome bearing ....

Newman, M.E.J., Engelhardt, Robin. Effects of neutral selection on the evolution of molecular species. Proc. R. Soc. London B, 1998.

....has been developed. A neutral network is comprised of individuals in the search space which are separated by single point neutral mutations. It has been shown that within such a fitness landscape with increasing degrees of neutrality the maximum fitness attainable in a population increases [6]. The implications for GE have yet to be empirically investigated, however the suggestion is that by increasing the degeneracy in the code, the maximum obtainable fitness should rise. During the mapping process it is possible to generate invalid (incompletely mapped) individuals, and so to ....

Newman M.E.J., Engelhardt Robin. 1998. Effects of neutral selection on the evolution of molecular species. In Proc. R. Soc. London B 265, pages 1333-1338.

....the basis for this theory within our artificial population, which is occurring due to the genetic code degeneracy which is part of the genotype to phenotype mapping process. Following on from Kimura, others have noted the benefits that neutral evolution can bring to the evolutionary process [8] [6]. In particular in [6] it has been suggested that the maximum fitness attainable on a fitness landscape with a degree of neutrality increases as the degree of neutrality increases. Further investigation is required to determine the ramifications, if any, for GE based on these and other ....

....within our artificial population, which is occurring due to the genetic code degeneracy which is part of the genotype to phenotype mapping process. Following on from Kimura, others have noted the benefits that neutral evolution can bring to the evolutionary process [8] 6] In particular in [6] it has been suggested that the maximum fitness attainable on a fitness landscape with a degree of neutrality increases as the degree of neutrality increases. Further investigation is required to determine the ramifications, if any, for GE based on these and other observations. 6 Conclusions The ....

Newman M.E.J., Engelhardt Robin. Effects of neutral selection on the evolution of molecular species. In Proc.R.Soc.London B, 265 pages 1333-1338.

.... general that it occurs in artificial evolutionary systems, such as evolving cellular automata [10,34] and populations of competing self replicating computer programs [1] In addition to the increasing attention paid to this type of epochal evolution in the theoretical biology community [18,21,26,35,41,49], recently there has also been an increased interest by evolutionary search theorists [5,25] More directly, Chen et al. recently proposed to test our original theoretical predictions in an experimental realization of a genetic algorithm that exhibits epochal evolution [9] 4 James P. ....

....allowed to be set in any arbitrary order. The architectural approach we have taken here should be contrasted with the use of randomized fitness functions that have been modified to have neutral networks. These include the NKp landscapes of Ref. 5] and the discretized NK fitness functions of Ref. [35]. The popularity of random fitness functions seems motivated by the idea that something as complicated as a biological genotype phenotype mapping can only be statistically described using a randomized structure. Although this seems sensible in general, the results tend to be strongly dependent on ....

M. Newman and R. Engelhardt. Effect of neutral selection on the evolution of molecular species. Proc. R. Soc. London B., 256:1333--1338, 1998.

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Newman, M. E. J., & Engelhardt, R. (1998). Effects of neutral selection on the evolution of molecular species. Working papers 98-01-001, Sante Fe Institute.

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