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.