Just a clarification. John Koza wrote the possibly expired patent code. Their also seems to be a lot of interest in patents recently as witnessed in this Economist article and story on Planet Money. http://www.economist.com/blogs/democracyinamerica/2011/08/intellectual-property?fsrc=scn/tw/te/bl/patentsagainstprosperity

I work with genetic algorithms and genetic programming (GP), which is what the code in question is used for. John Koza once used the GP code to evolve a circuit that designed around an existing Wi-Fi patent. http://ipbiz.blogspot.com/2007/10/evolutionary-approach-to-design-around.html. I find it ironic that the current question is how to write code that designs around the original GP code. Technically you could use the GP code to evolve code that didn't infringe on the copyright or patent of the GP code.