Towards more biological mutation operators in models of gene regulation
James Watson1, Nicholas Geard2, Janet Wiles
1jwatson@itee.uq.edu.au, University of Queensland; 2nic@itee.uq.edu.au, University of Queensland
Gene regulation is often viewed as a complex system whose properties
emerge from interactions between regulatory genes. A primary method
for studying the complex dynamics of gene regulation uses directed
graphs to explore structure, behaviour and evolvability. Mutation operators in such studies typically involve the insertion and
deletion of nodes and links at the network level. Such network-level mutation operators are sufficient to allow the statistical analysis of network structure, but impose limitations on the way the networks are
evolved. There are a wide variety of mutations in DNA sequences that
are yet to be analysed for their network-level effects. By modelling an
artificial genome at the level of a nucleotide sequence and mapping it to
a regulatory network, biologically grounded mutations can be mapped to
network-level mutations.
The method of mapping from nucleotide sequences to regulatory networks
is presented, and the effects of three sequence-level mutations
(single-point mutation, transposition and duplication) are discussed.
In short, it is rarely the case that nodes and links are cleanly added
or deleted, with even the simplest nucleotide changes capable of causing
a wide variety of network-level modifications. The vast majority of
mutations are neutral, resulting in a neutral plateau from which a range
of functional behaviours can be reached. This work aims to stimulate
more careful consideration of mutation operators in gene regulation
models than has previously been given.