Course Description
With the increasing use of computers in modeling of complex systems, evolutionary algorithms have become a useful tool in exploring questions in evolutionary biology. This course introduces students to evolutionary algorithms -- computer models of evolutionary processes. Through readings, lectures, guided exercises and independent projects, students will gain familiarity with the advantages and disadvantages of using computer models to explore questions in evolutionary biology. Primary focus will be on one research platform, Avida, and on its strengths and limitations as a research tool to study fundamental principles of evolution. Issues accessible to study using Avida include the topography of fitness landscapes and selective environments, the relative effects of mutations of various kinds and rates, the emergence of complexity in evolving populations and the 'transfer' of complexity from environment to genome via evolutionary processes, the effects of resource limitations, and so on.
Assigned readings will be from the professional literature of both evolutionary algorithms and evolutionary biology and from web resources, with substantial in-class time devoted to discussion of the readings. Class time will also be spent on familiarization with the research platform, its control files and operation, and on designing projects using that platform to approach issues of interest in evolution.
Prerequisite: Junior or senior with at least one biology course at the 200 level. No particular computer expertise is required.