Selective pressures on genomes in molecular evolution

We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.Comment: 16 pages, 3 figures, to be published in J. theor. Biolog

Nontrivial quantum effects in biology: A skeptical physicists' view

Invited contribution to "Quantum Aspects of Life", D. Abbott Ed. (World Scientific, Singapore, 2007).Comment: 15 pages, minor typographical errors correcte

Exploiting the Use of Cooperation in Self-Organizing Reliable Multiagent Systems

In this paper, a novel and cooperative approach is exploited introducing a self-organizing engine to achieve high reliability and availability in multiagent systems. The Adaptive Multiagent Systems theory is applied to design adaptive groups of agents in order to build reliable multiagent systems. According to this theory, adaptiveness is achieved via the cooperative behaviors of agents and their ability to change the communication links autonomously. In this approach, there is not a centralized control mechanism in the multiagent system and there is no need of global knowledge of the system to achieve reliability. This approach was implemented to demonstrate its performance gain in a set of experiments performed under different operating conditions. The experimental results illustrate the effectiveness of this approach

Artificial life meets computational creativity?

I review the history of work in Artificial Life on the problem of the open-ended evolutionary growth of complexity in computational worlds. This is then put into the context of evolutionary epistemology and human creativity

A synthesis of logic and bio-inspired techniques in the design of dependable systems

Much of the development of model-based design and dependability analysis in the design of dependable systems, including software intensive systems, can be attributed to the application of advances in formal logic and its application to fault forecasting and verification of systems. In parallel, work on bio-inspired technologies has shown potential for the evolutionary design of engineering systems via automated exploration of potentially large design spaces. We have not yet seen the emergence of a design paradigm that effectively combines these two techniques, schematically founded on the two pillars of formal logic and biology, from the early stages of, and throughout, the design lifecycle. Such a design paradigm would apply these techniques synergistically and systematically to enable optimal refinement of new designs which can be driven effectively by dependability requirements. The paper sketches such a model-centric paradigm for the design of dependable systems, presented in the scope of the HiP-HOPS tool and technique, that brings these technologies together to realise their combined potential benefits. The paper begins by identifying current challenges in model-based safety assessment and then overviews the use of meta-heuristics at various stages of the design lifecycle covering topics that span from allocation of dependability requirements, through dependability analysis, to multi-objective optimisation of system architectures and maintenance schedules

A run time adaptive architecture to trade-off performance for fault tolerance applied to a DVB on-board processor

Reliability is one of the key issues in space applications. Although highly flexible and generally less expensive than predominantly used ASICs, SRAM-based FPGAs are very susceptible to radiation effects. Hence, various fault tolerant techniques have to be applied in order to handle faults and protect the design. This paper presents a reconfigurable on-board processor capable of run-time adaptation to harsh environmental conditions and different functional demands. Run-time reconfigurability is achieved applying two different reconfiguration methodologies. We propose a novel self-reconfigurable architecture able to on demand duplicate or triplicate part of the design in order to form DMR and TMR structures. Moreover, we introduce two different approaches for voting the correct output. The first one is a traditional voter that adapts to different DMR/TMR domain positions whereas the second implies comparing the captured flip-flop values directly from the configuration memory read through ICAP. The comparison is done periodically by an embedded processor thus completely excluding the voting mechanism in hardware. The proposed run-time reconfiguration methodology provides savings in terms of device utilization, reconfiguration time, power consumption and significant reductions in the amount of rad-hard memory used by partial configurations