Biology of Applied Digital Ecosystems

A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research. Here, we discuss how biological properties contribute to the self-organising features of biological ecosystems, including population dynamics, evolution, a complex dynamic environment, and spatial distributions for generating local interactions. The potential for exploiting these properties in artificial systems is then considered. We suggest that several key features of biological ecosystems have not been fully explored in existing digital ecosystems, and discuss how mimicking these features may assist in developing robust, scalable self-organising architectures. An example architecture, the Digital Ecosystem, is considered in detail. The Digital Ecosystem is then measured experimentally through simulations, with measures originating from theoretical ecology, to confirm its likeness to a biological ecosystem. Including the responsiveness to requests for applications from the user base, as a measure of the 'ecological succession' (development).Comment: 9 pages, 4 figure, conferenc

Ecosystem-Oriented Distributed Evolutionary Computing

We create a novel optimisation technique inspired by natural ecosystems, where the optimisation works at two levels: a first optimisation, migration of genes which are distributed in a peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. We consider from the domain of computer science distributed evolutionary computing, with the relevant theory from the domain of theoretical biology, including the fields of evolutionary and ecological theory, the topological structure of ecosystems, and evolutionary processes within distributed environments. We then define ecosystem- oriented distributed evolutionary computing, imbibed with the properties of self-organisation, scalability and sustainability from natural ecosystems, including a novel form of distributed evolu- tionary computing. Finally, we conclude with a discussion of the apparent compromises resulting from the hybrid model created, such as the network topology.Comment: 8 pages, 5 figures. arXiv admin note: text overlap with arXiv:1112.0204, arXiv:0712.4159, arXiv:0712.4153, arXiv:0712.4102, arXiv:0910.067

CoBRA: A Coevolutionary Meta-heuristic for Bi-level Optimization

This article presents CoBRA, a new parallel coevolutionary algorithm for bi-level optimization. CoBRA is based on a coevolutionary scheme to solve bi-level optimization problems. It handles population-based meta-heuristics on each level, each one cooperating with the other to provide solutions for the overall problem. Moreover, in order to evaluate the relevance of CoBRA against more classical approaches, a new performance assessment methodology, based on rationality, is introduced. An experimental analysis is conducted on a bi-level distribution planning problem, where multiple manufacturing plants deliver items to depots, and where a distribution company controls several depots and distributes items from depots to retailers. The experimental results reveal significant enhancements with respect to a more classical approach, based on a hierarchical scheme.Cet article présente CoBRA, un nouvel algorithme paralléle et coévolutionnaire pour l'optimisation bi-niveau. CoBRA se base sur un modèle coévolutionnaire pour faire face aux problèmes d'optimisation bi-niveau. Il manipule une méta-heuristique à base de population sur chaque niveau, chacune coopérant avec l'autre de manière à garder une vue générale sur le problème complet. De plus, afin d'étudier la pertinence de CoBRA par rapport aux approches plus classique, une nouvelle méthodologie, basée sur la rationalité est introduite. Est conduite ensuite une étude expérimentale sur un problème bi-niveau de distribution-production, dans lequel des usines contrôlées par une entreprise produisent des marchandises pour des dépôts, et une autre entreprise contrôlant les dépôts se charge de livrer les marchandises à des clients. Cet article se conclut sur l'observation d'un réel gain de performance par rapport à une approche plus classique, basée sur un modèle hiérarchique

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

ABSTRACTS OF PAPERS Presented at the 16th International Pectinid Workshop Halifax, Nova Scotia, Canada May 11–18, 2007

VIMS Author Contributions: Scallop dredge selectivity: A review of sequential ring size increases from 1994 to 2003 in the US sea scallop fishery By: DuPaul, William D.; Rudders, David B. Pages: 1307-1308 Industry-based sea scallop dredge surveys in support of rotational area management By: Rudders, B.; DuPaul, William D. Pages: 1337-1338 Size-selectivity of the commercial northwest Atlantic sea scallop (Placopecten magellanicus) dredge By: Yochum, Noelle; DuPaul, William D. Pages: 1355-135

Evolutionary morphogenesis for multi-cellular systems

With a gene required for each phenotypic trait, direct genetic encodings may show poor scalability to increasing phenotype length. Developmental systems may alleviate this problem by providing more efficient indirect genotype to phenotype mappings. A novel classification of multi-cellular developmental systems in evolvable hardware is introduced. It shows a category of developmental systems that up to now has rarely been explored. We argue that this category is where most of the benefits of developmental systems lie (e.g. speed, scalability, robustness, inter-cellular and environmental interactions that allow fault-tolerance or adaptivity). This article describes a very simple genetic encoding and developmental system designed for multi-cellular circuits that belongs to this category. We refer to it as the morphogenetic system. The morphogenetic system is inspired by gene expression and cellular differentiation. It focuses on low computational requirements which allows fast execution and a compact hardware implementation. The morphogenetic system shows better scalability compared to a direct genetic encoding in the evolution of structures of differentiated cells, and its dynamics provides fault-tolerance up to high fault rates. It outperforms a direct genetic encoding when evolving spiking neural networks for pattern recognition and robot navigation. The results obtained with the morphogenetic system indicate that this "minimalist” approach to developmental systems merits further stud

Effect of Neuroactive Compounds on the Settlement of Mussel (Perna Canaliculus) Larvae

Herein, we present the first laboratory study on the effects of pharmacologically active compounds on larval settlement of the green-lipped mussel, Perna canaliculus. Competent hatchery-reared larvae were exposed to seawater containing excess K+ in the form of KCl and K2SO4 and the neurotransmitters -aminobutyric acid (GABA) and acetylcholine. Both KCl and K2SO4 were identified as active inducers of larval settlement with maximum inductions occurring after exposures to 10 and 7.5 mM, respectively. Peak settlement response to KCl was higher (>64%) than that achieved with K2SO4 (>41%). GABA did not induce larval settlement and displayed toxic and settlement inhibitive effects at 10-4 and 10-3 M. Acetylcholine induced larval settlement (>49%) at 10-4 M with minimal acute toxic effects (LC < 10%). To gain insight into the class of acetylcholine receptors involved, atropine was used to block the muscarinic-type receptors. Atropine treatment alone did not inhibit settlement compared to control assays, indicating that muscarinic-type receptors are not involved in settlement behavior. Furthermore, results showed that atropine did not significantly decrease acetylcholine induced settlement responses, which suggests an active role of the nicotinic-type receptors in the biochemical pathways of mussel settlement. Results of this study provide new insights on the mechanism of settlement behavior in P. canaliculus, which may have direct application to the growing New Zealand aquaculture industry