Design by homologous recombination

Engineers have frequently used random mutations as a means of optimizing a protein or genetically engineered network. However, I don't think this is an effective optimization or design process. Planned mutations, such as the one used by the immune system, rely on homologous recombination rather than random mutations. Using recombination, we can plan the mutation events, therefore perform a much more predictable optimization. The optimization process can even be simulated computationally.