Phylogeny Recapitulates Learning: Self-Optimization of Genetic Code
Autor: | Brian Sulkow, Chong Di, Oliver Attie, Wei-Gang Qiu |
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Jazyk: | angličtina |
Rok vydání: | 2018 |
Předmět: |
0106 biological sciences
0303 health sciences Theoretical computer science Natural selection Artificial neural network Phylogenetic tree Computer science Genetic code 010603 evolutionary biology 01 natural sciences Travelling salesman problem Hopfield network 03 medical and health sciences Hebbian theory Learning rule 030304 developmental biology |
DOI: | 10.1101/260877 |
Popis: | Learning algorithms have been proposed as a non-selective mechanism capable of creating complex adaptive systems in life. Evolutionary learning however has not been demonstrated to be a plausible cause for the origin of a specific molecular system. Here we show that genetic codes as optimal as the Standard Genetic Code (SGC) emerge readily by following a molecular analog of the Hebb’s rule (“neurons fire together, wire together”). Specifically, error-minimizing genetic codes are obtained by maximizing the number of physio-chemically similar amino acids assigned to evolutionarily similar codons. Formulating genetic code as a Traveling Salesman Problem (TSP) with amino acids as “cities” and codons as “tour positions” and implemented with a Hopfield neural network, the unsupervised learning algorithm efficiently finds an abundance of genetic codes that are more error-minimizing than SGC. Drawing evidence from molecular phylogenies of contemporary tRNAs and aminoacyl-tRNA synthetases, we show that co-diversification between gene sequences and gene functions, which cumulatively captures functional differences with sequence differences and creates a genomic “memory” of the living environment, provides the biological basis for the Hebbian learning algorithm. Like the Hebb’s rule, the locally acting phylogenetic learning rule, which may simply be stated as increasing phylogenetic divergence for increasing functional difference, could lead to complex and robust life systems. Natural selection, while essential for maintaining gene function, is not necessary to act at system levels. For molecular systems that are self-organizing through phylogenetic learning, the TSP model and its Hopfield network solution offer a promising framework for simulating emerging behavior, forecasting evolutionary trajectories, and designing optimal synthetic systems. |
Databáze: | OpenAIRE |
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