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major form of pollution from farms is the phosphates—compounds of phosphorus and oxygen—concentrated in fertilizer. When fertilizer washes out into rivers and oceans, the phosphates cause algae blooms and other ecological upheavals that eventually create vast dead zones where nothing can survive. One reason for the high levels of phosphates in fertilizer is that much of it comes from the manure of livestock such as pigs and chickens. These animals cannot break down the phosphates in their food, so it just goes straight through their digestive systems. E. coli, among other bacteria, make enzymes that can break down those phosphate-bearing molecules. When researchers insert E. coli’s genes in pigs, the animals produce manure that has only a quarter of the normal level of phosphates.

It’s chimeric turnaround: thirty years ago scientists were putting animal genes into E. coli. Now they are giving animals the genes of E. coli.

EXPANDING LIFE’S ALPHABET

Herbert Boyer used his intimate knowledge of E. coli’s biology to help create genetic engineering. Today scientists are using his tools to learn more about E. coli itself. In the process, they’re answering some of the most fundamental questions about life.

Scientists have long debated why life on Earth, with almost no exception, uses only twenty amino acids to build proteins. (E. coli is unusual in its ability to make a twenty-first amino acid, called selenocysteine.) There are hundreds of perfectly respectable kinds of amino acids life could have chosen from. To join the Amino Acid Club, a molecule needs only the proper ends. It must have a cluster of nitrogen and hydrogen atoms at one end (an amine) and a cluster of carbon, hydrogen, and oxygen on the other (a carboxyl group). An amine from one amino acid snaps onto the carboxyl group of another like LEGO pieces. It matters little what lies in between. A chemist can synthesize hundreds of different amino acids, and so can the chemistry of outer space. In 1969, a meteorite coated with tarry goo fell to Earth. Scientists found seventy-nine kinds of amino acids lurking inside it.

So why do we have just twenty? One way to investigate the question is to try to produce an organism that can make more. In 2001, Peter G. Schultz of Scripps Research Institute in La Jolla, California, and his colleagues did just that, by engineering E. coli. Like other living things, E. coli uses a genetic code in which three bases of DNA translate into one amino acid. There are sixty-four possible codons in E. coli’s genetic code, most of which it uses regularly. Schultz and his colleagues identified one that it uses only rarely. They engineered E. coli so that this neglected codon now instructed the microbe to add an unnatural amino acid to a protein.

Science magazine hailed the achievement as “the first synthetic life form with a chemistry unlike anything found in nature.” In the years since, scientists have added over thirty more unnatural acids to E. coli’s repertoire. Originally E. coli could make these new proteins only if it was supplied with the unnatural amino acids. Recently scientists have begun engineering E. coli to make unnatural amino acids from its natural food.

This research has pushed the debate over the genetic code to new ground. No one can argue that life’s twenty amino acids are the only ones that can make life possible. Some scientists now argue that the genetic code is just a historical artifact. Early life built its proteins with the most abundant amino acids on the planet, and that unconscious choice was frozen in place. Other scientists argue that the genetic code is actually the best of all possible codes. It offers the biggest range of potential proteins with the fewest genes. And still other scientists argue that natural selection produced the genetic code because it is robust, with the least risk of producing a lethally deformed protein if a mutation strikes a gene.

In our hands, however, the rules of the genetic code have changed. Schultz and other researchers are looking for practical applications for E. coli