On the Advantages of Variable Length GRNs for the Evolution of Multicellular Developmental Systems

TY - JOUR

T1 - On the Advantages of Variable Length GRNs for the Evolution of Multicellular Developmental Systems

AU - Trefzer, Martin Albrecht

AU - Kuyucu, Tuze

AU - Miller, Julian Francis

AU - Tyrrell, Andy

PY - 2013/2

Y1 - 2013/2

N2 - Biological genomes have evolved over a period of millions of years and comprise thousands of genes, even for the simplest organisms. However, in nature, only 1–2% of the genes play an active role in creating and maintainingthe organism, while the majority are evolutionary fossils. This raises the question whether a considerably larger number of (partly redundant) genes are required in order to effectively build a functional developmental system, of which, in the final system only a fraction is required for the latter to function.This paper investigates different approaches to creating artificial developmental systems (ADSs) based on variable length gene regulatory networks (GRNs). The GRNs are optimised using an evolutionary algorithm (EA). A comparison is made between the different variable length representations and fixed length representations. It is shown that variable length GRNs can achieve both reducing computational effort during optimisation and increasing speed and compactness of the resulting ADS,despite the higher complexity of the encoding required. The results may also improve the understanding of how to effectively model GRN based developmental systems. Taking results of all experiments into account makes it possible to create an overall ranking of the different patterns used as a testbench in terms of their complexity. This ranking may aid to compare related work against. In addition this allows a detailed assessment of the ADSused and enables the identification of missing mechanisms.

AB - Biological genomes have evolved over a period of millions of years and comprise thousands of genes, even for the simplest organisms. However, in nature, only 1–2% of the genes play an active role in creating and maintainingthe organism, while the majority are evolutionary fossils. This raises the question whether a considerably larger number of (partly redundant) genes are required in order to effectively build a functional developmental system, of which, in the final system only a fraction is required for the latter to function.This paper investigates different approaches to creating artificial developmental systems (ADSs) based on variable length gene regulatory networks (GRNs). The GRNs are optimised using an evolutionary algorithm (EA). A comparison is made between the different variable length representations and fixed length representations. It is shown that variable length GRNs can achieve both reducing computational effort during optimisation and increasing speed and compactness of the resulting ADS,despite the higher complexity of the encoding required. The results may also improve the understanding of how to effectively model GRN based developmental systems. Taking results of all experiments into account makes it possible to create an overall ranking of the different patterns used as a testbench in terms of their complexity. This ranking may aid to compare related work against. In addition this allows a detailed assessment of the ADSused and enables the identification of missing mechanisms.

UR - http://www.scopus.com/inward/record.url?scp=84873305033&partnerID=8YFLogxK

U2 - 10.1109/TEVC.2012.2185848

DO - 10.1109/TEVC.2012.2185848

M3 - Article

VL - 17

SP - 100

EP - 121

JO - IEEE Transactions on Evolutionary Computation

JF - IEEE Transactions on Evolutionary Computation

SN - 1089-778X

IS - 1

M1 - 6151118

ER -