We investigate fundamental decisions in the design of instruction set
architectures for linear genetic programs that are used as both model systems
in evolutionary biology and underlying solution representations in evolutionary
computation. We subjected digital organisms with each tested architecture to
seven different computational environments designed to present a range of
evolutionary challenges. Our goal was to engineer a general purpose
architecture that would be effective under a broad range of evolutionary
conditions. We evaluated six different types of architectural features for the
virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more
precisely modify the function of genetic instructions, (2) memory: we provided
an increased number of registers in the virtual CPUs, (3) decoupled sensors and
actuators: we separated input and output operations to enable greater control
over data flow. We also tested a variety of methods to regulate expression: (4)
explicit labels that allow programs to dynamically refer to specific genome
positions, (5) position-relative search instructions, and (6) multiple new flow
control instructions, including conditionals and jumps. Each of these features
also adds complication to the instruction set and risks slowing evolution due
to epistatic interactions. Two features (multiple argument specification and
separated I/O) demonstrated substantial improvements int the majority of test
environments. Some of the remaining tested modifications were detrimental,
thought most exhibit no systematic effects on evolutionary potential,
highlighting the robustness of digital evolution. Combined, these observations
enhance our understanding of how instruction architecture impacts evolutionary
potential, enabling the creation of architectures that support more rapid
evolution of complex solutions to a broad range of challenges
