History of development of evolutionary methods in St. Petersburg school of computer simulation in biology

The work presents a short history of development of evolutionary methods in the St. Petersburg school of computer simulation of biological processes. Several moments confirm priority of this school in modeling of micro- and macroevolutionary processes. A peculiarity of the school is a combination of the applied and theoretical study, penetration into the biological essence of phenomenon, consideration of real interrelationships of ecological and physiological parameters. The natural tendency for transition to modeling at the level of single individuals and then-to imitation of evolutionary processes on computer is traced. Paradoxically, such detalization sometimes does not worsen, but improves prognostic properties of models of populations, communities, and ecosystems, and besides, makes unnecessary monitoring of some variable characteristics, because the individual-based approach allows to direct account for adaptive processes and hidden evolutionary relationships between the life history parameters. Problems and perspectives of development of evolutionary methods of modeling are analyzed.     

Mathematical model for the ecosystem response of Lake Ladoga to phosphorus loading

The ecosystem response model described in this paper combines an ecosystem model and a three-dimensional circulation model of Lake Ladoga developed earlier by the authors. The ecosystem model describes the process of Lake Ladoga eutrophication, and its biological submodel describes changes in the phyto- and zooplankton. In the earlier model version, lake circulation was determined using a two-dimensional hydrodynamical model which was not completely adequate. The present model allows calculation of the distributions of phyto- and zooplankton and mineral phosphorus and nitrogen. One of its main advantages is that reliable computations of the ecosystem dynamics over an extended period of time are possible. The response of the ecosystem to different levels of phosphorus pollution loading and to weather conditions is studied.     

The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.     

Imitational modeling of process of evolution: From organic macromolecules to protocell and animal cell

A dynamic imitational model of initial stages of cell evolution has been developed based on role of environmental calcium concentration. The model is designed from our hypothesis about the medium of the appearance of protocells, which could be potassium water reservoirs rather than sea salt water with its predominance of sodium salts. The necessary elements of the appearance of the protocells served organic molecules, code of their synthesis, and formation of macromolecules under favorable ion concentration in environment: a high K⁺ and Mg²⁺ and a low Na⁺ concentration. The model is based on an assumption that one of the first stages in evolution of life was the appearance in the potassium-magnesium water reservoirs of organic molecules capable for self-replication on the basis of genetic code and formation of protocell with the potassium cytoplasm. The model has demonstrated necessity of formation of cell envelope for development of the protocell. Replacement of the dominant cation in water reservoirs—potassium by sodium—required the appearance of ion-transporting devices in plasma membrane and their participation in adaptation of cells to environment. This stage of evolution was accompanied by the most important morphofunctional event—formation of the plasma membrane instead of cell envelope. The membrane provided the ion asymmetry in the cell (preservation of K⁺ in it) relatively to the sodium external medium for maintaining optimal intracellular medium. In the model system, predecessors of animal cells elaborated mechanism of maintenance of the potassium cytoplasm with the sodium counterion dominating in the environment.