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  launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, 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 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.
KeywordsTuring Machine State Symbol Circular Permutation Splice System Telomere Binding Protein
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