The artificial worlds approach to emergent evolution

Fishing forward and reverse: Advances in zebrafish phenomics

Understanding how the genome instructs the phenotypic characteristics of an organism is one of the major scientific endeavors of our time. Advances in genetics have progressively deciphered the inheritance, identity and biological relevance of genetically encoded information, contributing to the rise of several, complementary omic disciplines. One of them is phenomics, an emergent area of biology dedicated to the systematic multi-scale analysis of phenotypic traits. This discipline provides valuable gene function information to the rapidly evolving field of genetics. Current molecular tools enable genome-wide analyses that link gene sequence to function in multi-cellular organisms, illuminating the genome-phenome relationship. Among vertebrates, zebrafish has emerged as an outstanding model organism for high-throughput phenotyping and modeling of human disorders. Advances in both systematic mutagenesis and phenotypic analyses of embryonic and post-embryonic stages in zebrafish have revealed the function of a valuable collection of genes and the general structure of several complex traits. In this review, we summarize multiple large-scale genetic efforts addressing parental, embryonic, and adult phenotyping in the zebrafish. The genetic and quantitative tools available in the zebrafish model, coupled with the broad spectrum of phenotypes that can be assayed, make it a powerful model for phenomics, well suited for the dissection of genotype-phenotype associations in development, physiology, health and disease.

Phenomics of cardiac chloride channels

Forward genetic studies have identified several chloride (Cl-) channel genes, including CFTR, ClC-2, ClC-3, CLCA, Bestrophin, and Ano1, in the heart. Recent reverse genetic studies using gene targeting and transgenic techniques to delineate the functional role of cardiac Cl- channels have shown that Cl- channels may contribute to cardiac arrhythmogenesis, myocardial hypertrophy and heart failure, and cardioprotection against ischemia reperfusion. The study of physiological or pathophysiological phenotypes of cardiac Cl- channels, however, is complicated by the compensatory changes in the animals in response to the targeted genetic manipulation. Alternatively, tissue-specific conditional or inducible knockout or knockin animal models may be more valuable in the phenotypic studies of specific Cl- channels by limiting the effect of compensation on the phenotype. The integrated function of Cl- channels may involve multiprotein complexes of the Cl- channel subproteome. Similar phenotypes can be attained from alternative protein pathways within cellular networks, which are influenced by genetic and environmental factors. The phenomics approach, which characterizes phenotypes as a whole phenome and systematically studies the molecular changes that give rise to particular phenotypes achieved by modifying the genotype under the scope of genome/proteome/phenome, may provide more complete understanding of the integrated function of each cardiac Cl- channel in the context of health and disease.

The evolution of trophic structure

The trophic relationships of an ecological community were represented by digital individuals consuming resources or prey within a simulated ecosystem and producing offspring that may differ from their parents. When individuals meet, a few simple rules are used to decide the outcome of their interaction. Trophically complex systems persist for long periods of time even in finite communities, provided that the strength of predator-prey interaction is sufficient to repay the cost of maintenance. The topology of the food web and important system-level attributes such as overall productivity follow from the rules of engagement: that is, the macroscopic properties of the ecosystem follow from the microscopic attributes of individuals, without the need to invoke the emergence of novel processes at the level of the whole system. Evolutionarily stable webs exist only when the pool of available species is small. If the pool is large, or speciation is allowed, species composition changes continually, while overall community properties are maintained. Ecologically separate and topologically different source webs based on the same pool of resources usually coexist for long periods of time, through negative frequency-dependent selection at the level of the source web as a whole. Thus, the evolved food web of species-rich communities is a highly dynamic structure with continual species turnover. It both imposes selection on each species and itself responds to selection, but selection does not necessarily maximize stability, productivity or any other community property.

A rule-based approach to the modelling of bacterial ecosystems

This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.

The origins of Michael Conrad's research programs (1964-1979)

This paper summarizes Michael Conrad's academic and professional career from the time he began his Ph.D. studies in 1964 to his appointment at Wayne State University in 1979. It describes the origins of several of his major research interests and presents a personal evaluation of how this early work continues to be of fundamental importance.

Symbiotic interactions in the EVOLVE III ecosystem model

Parasitic feeding mechanisms were introduced into the EVOLVE III ecosystem model. The modified system exhibited a number of interesting behaviors, including obligative and facultative parasitism, transient facultative mutualism and nonsymbiotic feeding. Speciation and massive die-offs were also observed. The introduction of a symbiotic capability altered the co-evolutionary development of traits that exhibited an arms race when the symbiotic capability was not present. Stable mutualisms were not possible in the present version of the model due to the restriction that organisms were not allowed to feed both on other organisms and from the environment at the same time. The ecosystem biomass increased with increased symbiotic activity. Biomass was influenced by the balance of virulence and resistance traits in the population and decreased as these traits became more disparate.