how much more information is required to encode a given improvement in function. The formalism also points to strategies, such as increasing the concentration and/or diversity of molecular agents, that might maximize the effectiveness of chemical experiments that attempt to replicate steps in the origin of life.
Determination of the computational properties of a randomly generated instruction sequence is accomplished within Avida’s analyze mode. The trace feature in analyze mode generates detailed information on the state of the virtual computer at each step in the processing of a genome, including a notation of when a recognized function has been executed. An automated script parsed these logs to collect all of the data necessary to determine the functional properties of each sequence and cataloged the genomes found to be functional to permit later study. Detailed documentation of the Avida software, including descriptions of the trace function and analyze mode, can be found online at the Digital Evolution Laboratory at Michigan State University web site (http://devolab.cse.msu.edu/software/avida/doc).
We thank John Avise and Francisco Ayala for organizing this Sackler Colloquium; H. J. Cleaves, K. Esler, R. Lenski, H. Morowitz, C. Ofria, and D. Sverjensky for valuable comments and suggestions. This work was supported in part by the National Aeronautics and Space Administration Astrobiology Institute, the National Science Foundation, and the Carnegie Institution. J.W.S. is an Investigator of the Howard Hughes Medical Institute.