Related Experiment Video
Updated: Jan 21, 2026

Molecular Evolution of the Tre Recombinase
Published on: May 29, 2008
Combining evolution and self-organization to find natural Boolean representations in unconventional computational
Matthew D Egbert1, Gerd Gruenert2, Bashar Ibrahim3
1Centre for Computational Evolution, University of Auckland, 1010 Auckland, New Zealand; Faculty of Mathematics and Computer Science, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
Abstract:
Designing novel unconventional computing systems often requires the selection of the computational structure as well as choosing the right symbol encoding. Several approaches apply heuristic search and evolutionary algorithms to find both computational structure and symbol encoding, which is time consuming because they depend on each other. Here, we present a novel approach that combines evolution with self-organization, in particular we evolve the computational structure but let the symbol encoding emerge through self-organization. This should not only be more efficient but should also lead to a more "natural" symbol encoding. We successfully demonstrate the potential of the technique, using an evolutionary algorithm to optimize the parameters of two non-linear media to perform as NAND-gates: a continuous-time recurrent neural network (CTRNN) and a computational model of BZ-droplet-based computing (DropSim). In both cases, the technique identified representations for TRUE and FALSE, and system configurations that performed successfully as NAND-gates. The effectiveness of the evolved NAND gates was further evaluated by their performance in half-adder networks, where again, both evolved systems performed correctly, producing the correct output for all possible inputs and for all possible transitions between inputs. We conclude that beyond the specific applications demonstrated here, combining evolution with self-organization could be a promising strategy widely applicable.
Related Concept Videos
The Evidence for Evolution
What is Natural Selection?
Convergent Evolution
Control Volume and System Representations
The control volume approach considers a stationary region in space through which fluid flows. This region is bounded by a control surface. For instance, in the case of water...
State Space Representation
Consider an RLC circuit, a...
Graphical and Analytic Representation of Sinusoids
The first step is measuring the peak-to-peak value, which is twice the amplitude of the sinusoid. This provides information about the maximum voltage swing of the waveform.
Secondly, the period and angular frequency are determined. The period is the time taken for one complete cycle of the waveform, while...

