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On evolvability and robustness in the matrix-GRT model

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Abstract

Quantifying evolution and understanding robustness are best done with a system that is both rich enough to frustrate rigging of the answer and simple enough to permit comparison against either existing systems or absolute measures. Such a system is provided by the self-referential model matrix-genome, replication and translation, based on the concept of operators, which is introduced here. Ideas are also taken from the evolving micro-controller research. This new model replaces micro-controllers by simple matrix operations. These matrices, seen as abstract proteins, work on abstract genomes, peptides or other proteins. Studying the evolutionary properties shows that the protein-only hypothesis (proteins as active elements) shows poor evolvability and the RNA-before-protein hypothesis (genomes controlling) exhibits similar intricate evolutionary dynamics as in the micro-controller model. A simple possible explanation for this surprising difference in behavior is presented. In addition to existing evolutionary models, dynamical and organizational changes or transitions occurring late in long-term experiments are demonstrated.

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Notes

  1. Of course, there are more properties of a molecule which can hit a threshold, e.g. energy or age [40].

  2. Software source available at http://www.biomip.de/Uwe/projects/mGRT.

  3. Perhaps the term Mergerase would be more appropriate.

  4. A reviewer suggested to look more into the sequences in the evolved systems which gave lots of further insight and possible explanations for the observed different systems phases.

  5. Compare this behavior to the movie accompanying [37], which also shows a phase 0 system behavior.

  6. Thanks to one reviewer who made me aware of this work.

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Acknowledgments

Many thanks to Peter Wills and Norman Packard for encouraging me to write this paper and to John McCaskill for providing the infrastructure. Reviewers made an excellent job and hopefully helped to improve the paper. Many thanks to Lee Altenberg and his help to improve the readability of the paper, in addition I am grateful for Charles Stewart helping to improve the English. This research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under Grant Agreement 318671 (MICREAgents). I am also indebted to Brigitte Hantsche-Tangen for her support, patience and love.

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  1. BioMIP, Organic Chemistry I, Ruhr-Universität Bochum, Bochum, 44780, Germany

    Uwe Tangen

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Correspondence to Uwe Tangen.

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Tangen, U. On evolvability and robustness in the matrix-GRT model. Genet Program Evolvable Mach 15, 343–374 (2014). https://doi.org/10.1007/s10710-014-9221-5

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