Mini-Course on Modelling Micro-Evolution
Adam Prügel-Bennett, Nordita
28, 29 and 30 May from 9:15--11:00
Lecture Theatre B, NBI/Nordita
Micro-evolution describes the evolution of a population of gene
sequences which undergo selection, amplification, mutation and sexual
recombination, as well as other possible evolution operators. Although
originally motivated by biology it has also taken on an extra significance
as a description of Directed Molecular Evolution and Genetic
Algorithms. In the former evolution in a test tube is used to develop
new drugs and enzymes while in the latter an evolutionary strategy is used
to evolve good solutions to hard problems. This course introduces the
applications of micro-evolution and develops a theory for describing
micro-evolution based on statistical physics.
- Tuesday 28 May. Applications of Micro-Evolution.
- Directed Molecular Evolution.Some micro-biology,
DNA, RNA and proteins, overview of the techniques used in
directed molecular evolution.
- Genetic Algorithms. Optimization problems,
NP-completeness, hill-climbing techniques, simulated
annealing, description of GAs, selection, mutation and
crossover.
- Problems of Biology. Fitness landscapes, neutral
selection, locally distributed populations, co-evolution, why
is there sex?, why is there diploidy?, multiplicative fitness
landscapes, Muller's ratchet, evolution in noisy environments.
- Wednesday 29 May. Micro-Evolution as a Statistical Mechanics
Problem.
- The Statistical Mechanics Formalism. Phase space,
microscopic variables, order-parameters, cumulants,
correlations.
- Selection. Calculating selection, roulette wheel
selection, deterministic/Baker selection, scaling selection,
tournament selection, ranking selection, truncation
selection, Boltzmann selection, optimization, noise in
selection.
- Thursday 30 May. The Genetic Operators.
- Mutation. Calculating mutation, maximum entropy
techniques.
- Crossover/Sexual Recombination Uniform Crossover,
single-point cross\-over, interface energy, mixing, the
shuffling problem.
- The Benefits of Sexual Recombination. Trap functions,
stochastic hill-climbing, basin with a barrier.
Lecture notes
Last modified 15 May 1996
Adam Prügel-Bennett