Universal Molecular Computation in Ciliates

How do cells and nature \compute"? They read and \rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a seven-city Directed Hamiltonian Path problem using DNA 1] launched the new eld of DNA computing, which in a few years has grown to international scope. However, unknown to this eld, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this \problem", which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. Here we develop a a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform at least any computation carried out by an electronic computer. 1 Gene unscrambling as computation Ciliates are a diverse group of 8000 or more unicellular eukaryotes (nucleated cells) named for their wisp-like covering of cilia. They possess two types of nuclei: an active macronucleus (soma) and a functionally inert micronucleus (germline) which contributes only to sexual reproduction. The somatically active macronucleus forms from the germline micronucleus after sexual reproduction , during the course of development. The genomic copies of some protein-coding genes in the micronucleus of hypotrichous ciliates are obscured by the presence of intervening non-protein-coding DNA sequence elements (internally eliminated sequences, or IESs). These must be removed before the assembly