"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Simulating the evolution of recruitment behavior in foraging Ants

Spatial heterogeneity in the distribution of food is an important determinant of species\u27 optimal foraging strategies, and of the dynamics of populations and communities. In order to explore the interaction of food heterogeneity and colony size in their effects on the behavior of foraging ant colonies, we built agent-based models of the foraging and recruitment behavior of harvester ants of the genus Pogonomyrmex. We optimized the behavior of these models using genetic algorithms over a variety of food distributions and colony sizes, and validated their behavior by comparison with data collected on harvester ants foraging for seeds in the field. We compared two models: one in which ants lay a pheromone trail each time they return to the nest with food; and another in which ants lay pheromone trails selectively, depending on the density of other food available in the area where food was found. We found that the density-dependent trail-laying model fit the field data better. We found that in this density-dependent recruitment model, colonies of all sizes evolved intense recruitment behavior, even when optimized for environments in which the majority of foods are distributed homogeneously. We discuss the implications of these models to the understanding of optimal foraging strategy and community dynamics among ants, and potential for application to ACO and other distributed problem-solving systems

Grand Challenge 7: Journeys in Non-Classical Computation

We review progress in Grand Challenge 7 : Journeys in Non-Classical Computation. We overview GC7-related events, review some background work in certain aspects of GC7 (hypercomputation, bio-inspired computation, and embodied computation) and identify some of the unifying challenges. We review the progress in implementations of one class of non-classical computers: reaction-diffusion systems. We conclude with warnings about “regression to the classical”

A Practical Investigation into Achieving Bio-Plausibility in Evo-Devo Neural Microcircuits Feasible in an FPGA

Many researchers has conjectured, argued, or in some cases demonstrated, that bio-plausibility can bring about emergent properties such as adaptability, scalability, fault-tolerance, self-repair, reliability, and autonomy to bio-inspired intelligent systems. Evolutionary-developmental (evo-devo) spiking neural networks are a very bio-plausible mixture of such bio-inspired intelligent systems that have been proposed and studied by a few researchers. However, the general trend is that the complexity and thus the computational cost grow with the bio-plausibility of the system. FPGAs (Field- Programmable Gate Arrays) have been used and proved to be one of the flexible and cost efficient hardware platforms for research' and development of such evo-devo systems. However, mapping a bio-plausible evo-devo spiking neural network to an FPGA is a daunting task full of different constraints and trade-offs that makes it, if not infeasible, very challenging. This thesis explores the challenges, trade-offs, constraints, practical issues, and some possible approaches in achieving bio-plausibility in creating evolutionary developmental spiking neural microcircuits in an FPGA through a practical investigation along with a series of case studies. In this study, the system performance, cost, reliability, scalability, availability, and design and testing time and complexity are defined as measures for feasibility of a system and structural accuracy and consistency with the current knowledge in biology as measures for bio-plausibility. Investigation of the challenges starts with the hardware platform selection and then neuron, cortex, and evo-devo models and integration of these models into a whole bio-inspired intelligent system are examined one by one. For further practical investigation, a new PLAQIF Digital Neuron model, a novel Cortex model, and a new multicellular LGRN evo-devo model are designed, implemented and tested as case studies. Results and their implications for the researchers, designers of such systems, and FPGA manufacturers are discussed and concluded in form of general trends, trade-offs, suggestions, and recommendations