Proposals for assembling molecular machine systems from parts based on biopolymers usually take the approach of computationally designing proteins, RNA, or DNA molecules to serve as devices or as components of supramolecular systems. An alternative approach that has also been pursued is directed evolution in the laboratory (for example, this post from April, 2011 “Much faster directed evolution of proteins could speed development of molecular machine systems“). Two years ago Harvard Medical School geneticist George Church and his colleagues introduced a multiplex automated genome engineering (MAGE) system for the large-scale evolution of not just one or a few genes, but of whole genomes via the simultaneous modification of many genes (“Programming cells by multiplex genome engineering and accelerated evolution” abstract, PDF). The goal of the project was to evolve organisms with improved properties, and it has since been adapted by at least one biofuels company that hopes to engineer bacteria to produce renewable fuels. One can also imagine using this approach to simultaneously engineer groups of genes to produce parts that work together to produce some complex result. New Scientist featured an update on this work. From “Evolution machine: Genetic engineering on fast forward“, by Jo Marchant:
…Say hello to the evolution machine. It can achieve in days what takes genetic engineers years. So far it is just a prototype, but if its proponents are to be believed, future versions could revolutionise biology, allowing us to evolve new organisms or rewrite whole genomes with ease. It might even transform humanity itself. …
Church calls this bold approach multiplex automated genome engineering, or MAGE. In essence, he has applied the key principles that have led to the astonishing advances in DNA sequencing – parallel processing and automation – to genetic engineering. And since Church was one of the founders of the human genome project and helped develop modern sequencing methods, he knows what he is doing.
Just as labs all over the world now buy thousands of automated DNA sequencing machines, so Church envisions them buying automated evolution machines. He hopes to sell them relatively cheaply, at around $90,000 apiece. “We’re dedicated to bringing the price down for everybody, rather than doing some really big project that nobody can repeat,” Church says.
Church’s stated focus is modifying organisms, but if the machines are inexpensive they might find use in modifying biomolecular machine systems to develop productive nanosystems.