Regenesis (2 page)

In 2003 DuPont trademarked the name Bio-PDO and started producing the substance in quantity. The company claimed that this was the first time a genetically engineered organism had been utilized to transform a naturally occurring renewable resource into an industrial chemical at high volumes. The US Environmental Protection Agency, which regarded Bio-PDO as a triumph of green chemistry, gave DuPont the 2003 Greener Reaction Conditions Award (a part of the Presidential Green Chemistry Challenge). And why not? The biofiber used greener feedstocks and
reagents, and its synthesis required fewer and less expensive process steps than were involved in manufacturing other fibers. The production of Sorona consumed 30 percent less energy than was used to produce an equal amount of nylon, for example, and reduced greenhouse gas emissions by 63 percent. For its part, Mohawk touted its Sorona carpeting as environmentally friendly: “Every seven yards of SmartStrand with DuPont Sorona saves enough energy and resources to equal one gallon of gasoline—that's 10 million gallons of gasoline a year!” Here it was, finally: the politically correct carpet.

What these examples hinted at, however, was something far more important than mere political correctness, namely, that biological organisms could be viewed as a kind of high technology, as nature's own versatile engines of creation. Just as computers were universal machines in the sense that given the appropriate programming they could simulate the activities of any other machine, so biological organisms approached the condition of being universal constructors in the sense that with appropriate changes to their genetic programming, they could be made to produce practically any imaginable artifact. A living organism, after all, was a ready-made, prefabricated production system that, like a computer, was governed by a program, its genome. Synthetic biology and synthetic genomics, the large-scale remaking of a genome, were attempts to capitalize on the facts that biological organisms are programmable manufacturing systems, and that by making small changes in their genetic software a bioengineer can effect big changes in their output. Of course, organisms cannot manufacture just anything, for like all material objects and processes they are limited and circumscribed by the laws of nature. Microbes cannot convert lead into gold, for example. But they can convert sewage into electricity.

This astonishing capacity was first demonstrated in 2003 by a Penn State team headed by researcher Bruce Logan. He knew that in the United States alone, more than 126 billion liters of wastewater was treated every day at an annual cost of $25 billion, much of it spent on energy. Such costs, he thought, “cannot be borne by a global population of six billion people, particularly in developing countries.” It was widely known that bacteria could treat wastewater. Separately, microbiologists had known for years
that bacteria could also generate electricity. So far, nobody had put those two talents together. But what if microbes could be made to do both things simultaneously, treating wastewater while producing electrical energy?

Key to the enterprise would be the microbial fuel cell—a sort of biological battery. In ordinary metabolism, bacteria produce free electrons. A microbial fuel cell (MFC) consists of two electrodes—an anode and a cathode. A current is set up between them by the release of electrons from bacteria in a liquid medium. Electrons pass from the bacteria to the anode, which is connected to the cathode by a wire.

Logan and his colleagues constructed a cylindrical microbial fuel cell, filled it with wastewater from the Penn State water treatment plant, and then inoculated it with a pure culture of the bacterium
Geobacter metal-lireducens
. Lo and behold, in a matter of hours the microbe had begun purifying the sewage while at the same time producing measurable amounts of electricity. These results “demonstrate for the first time electricity generation accompanied by wastewater treatment,” Logan said. “If power generation in these systems can be increased, MFC technology may provide a new method to offset wastewater treatment operating costs, making advanced wastewater treatment more affordable for both developing and industrialized nations.”

The general setup wasn't difficult to replicate and within a few years a sophomore at Stuyvesant High School in New York City, Timothy Z. Chang, was designing, building, and operating microbial fuel cells at home and in his high school lab. He had experimented with some forty different strains of bacteria to discover which was best suited to maximum electricity production. “It may be possible to achieve even higher power yields through active manipulation of the microbial population,” he wrote in a formal report on the project.

By 2010 several teams of researchers were working on scaling up bacterial electricity production from sewage to make it into a practical, working, real-world option. By this time, synthetic biologists had gotten microbes to perform so many different feats of creation that it was clear that many of nature's basic units of life—microbes—were undergoing an extreme DNA makeover, a major course of redesign from the ground up.
Engineered microbes produced diesel oil, gasoline, and jet fuel. Microbes were made to detect arsenic in drinking water at extremely low concentrations (as low as 5 parts per billion) and report the fact by changing color. There were microbes that could be spread out into a biofilm. By producing a black pigment in response to selective illumination, they could copy superimposed patterns and projected images—in effect, microbial Xerox machines.

A student project reprogrammed
E. coli
bacteria to produce hemoglobin (“bactoblood”), which could be freeze-dried and then reconstituted in the field and used for emergency blood transfusions. In 2006, just for fun, five MIT undergrads successfully reprogrammed
E. coli
(which as a resident of the intestinal tract smelled like human waste) to smell like either bananas or wintergreen.

E. coli
was so supple, pliable, and yielding that it seemed to be the perfect biological platform for countless bioengineering applications. One of its greatest virtues was that the
E. coli
bacterium (and cousins, the Vibrio) are the world's fastest machines at doubling, small or large.
*
It reproduced itself every twenty minutes, so that theoretically, given enough simple food and stirring, a single particle of
E. coli
could multiply itself exponentially into a mass greater than the earth in less than two days.

Still, as malleable as it was, University of Wisconsin geneticist Fred Blattner decided he could materially improve the workhouse K-12 strain of the microbe to make it an even better chassis for synthetic biology engineering projects. The microbe had some 4,000 genes; many had no known function, while others were nonessential, redundant, or toxic. So Blattner stripped 15 percent of its natural genes from the K-12 genome, making it a sort of reduced instruction set organism, a streamlined, purer version of the microbe. Blattner described it as “rationally designed” and said that his genetic reduction “optimizes the
E. coli
strain as a biological factory, providing enhanced genetic stability and improved metabolic efficiency.” With forty genome changes, he had pre-engineered the microbe in order to make it easier to engineer.

In 2002 Blattner founded Scarab Genomics to sell his new and improved organism, now billing it as “Clean Genome
E. coli”
and marketing it under the slogan “Less is better and safer!” Researchers can buy quantities of the microbe, online or by fax, for as little as $89 a shot (plus a $50 shipping fee).

The upshot of all this is that, at least at the microbial level, nature has been redesigned and recoded in significant ways. Genomic engineering will become more common, less expensive, and more ambitious and radical in the future as we become more adept at reprogramming living organisms, as the cost of the lab machinery drops while its efficiency rises, and as we are motivated to maximize the use of green technologies.

Given the profusion and variety of biological organisms, plus the ability to reengineer them for a multiplicity of purposes, the question was not so much what they can be made to do but what they can't be made to do, in principle. After all, tiny life forms, driven solely by their own natural DNA, have, just by themselves, produced large, complex objects: elephants, whales, dinosaurs. A minuscule fertilized whale egg produces an object as big as a house. So maybe one day we can program an organism, or a batch of them, to produce not the whale but the actual house. We already have bio-plastics that can be made into PVC plumbing pipes; biofibers for carpeting; lumber, nature's own building material; microbe-made electricity to provide power and lighting; biodiesel to power the construction machinery. Why can't other microbes be made to produce whatever else we need?

In 2009 Sidney Perkowitz, a physicist at Emory University in Atlanta with a special interest in materials science, was asked to speculate about the future of building materials. “Think about the science-fictionish possibility of bioengineering plants to produce plastic exactly in a desired shape, from a drinking cup to a house,” he said. “Current biotechnology is far short of this possibility, but science fiction has a way of pointing to the future. If bioplastics are the materials breakthrough of the 21st century, houses grown from seeds may be the breakthrough of the 22nd.”

Similar proposals have been made by others, and they may be much closer than the twenty-second century; for example, using modified gourds and trees to grow a primitive, arboreal house (
inhabitat.com/grow-your-own-treehouse
). The technology of determining the shape and chemical
properties of plants by making them sensitive to simple cues of light and scaffolding is improving rapidly.

This focus on microbes and plants—especially on the overworked
E. coli
bacterium—may give rise to the impression that synthetic biology and genomic engineering have little to offer the charismatic megafauna—the higher organisms such as people. Nothing could be further from the truth. In fact these technologies have the power to improve human and animal health, extend our life span, increase our intelligence, and enhance our memory, among other things.

The idea of improving the human species has always had an enormously bad press, stemming largely from the errors and excesses associated with the eugenics movements of the past. Historically, eugenics has covered everything from selective breeding for the purpose of upgrading the human gene pool to massive human rights violations against classes of people regarded as undesirable, degenerate, or unfit because of traits such as religion, sexual preference, handicap, and so on, culminating, in the extreme case, in the Nazi extermination program.

Some proposals for enhancing the human body have had a harebrained ring to them, as for example the idea of equipping people with gills so that they could live in the sea alongside sharks. Burdened with past evils and silliness, any new proposal for changing human beings through genomic engineering faces an uphill battle. But consider this modest proposal: What if it were possible to make human beings immune to all viruses, known or unknown, natural or artificial? No more viral epidemics, influenza pandemics, or AIDS infections.

Viruses do their damage by entering the cells of the host organism and then using the cellular machinery to replicate themselves, often killing the host cells in the process. This leads to the release of new viruses that proceed to infect other cells, which in turn produce yet more virus particles, and so on. Viruses can take control of a cell's genetic machinery because both the virus and the cell share the same genetic code. However, changing
the genetic code of the host cell, as well as that of the cellular machinery that reads and expresses the viral genome, could thwart the virus's ability to infect cells (see Chapter 5).

All this may sound wildly ambitious, but there is little doubt that the technology of genome engineering is in principle up to the task. An additional benefit of engineering a sweeping multivirus resistance into the body is that it would alleviate a common fear concerning synthetic biology—the accidental creation of an artificial supervirus to which humans would have no natural immunity.

Genomic technologies can actually allow us to raise the dead. Back in 1996, when the sheep Dolly was the first mammal cloned into existence, she was not cloned from the cells of a live animal. Instead, she was produced from the frozen udder cell of a six-year-old ewe that had died some three years prior to Dolly's birth. Dolly was a product of nuclear transfer cloning, a process in which a cell nucleus of the animal to be cloned is physically transferred into an egg cell whose nucleus had previously been removed. The new egg cell is then implanted into the uterus of an animal of the same species, where it gestates and develops into the fully formed, live clone.