Programming Life

Densmore says the three parts necessary for any engineering project, be it computer chips or living cells, are clear: Figure out what you’re trying to build; the specific parts you need to build it; and your constraints. Once you’ve broken down a system like that, “you can actually look at each of those pieces in a very systematic way,” says Christopher Voigt, an associate professor of biological engineering at MIT.

In synthetic biology, those standardized pieces come in the form of DNA snippets, coded in strings of letters, each one representing a nucleotide in the alphabet of the molecule itself. Engineers’ design challenge is to build genomes from scratch by combining these small but specific pieces of genetic material. For each snippet, scientists have to figure out how it functions on its own and how that function changes when combined with other pieces.

When Voigt started engineering biology a decade ago, he was literally cutting and pasting strings of letters in Microsoft Word. He memorized the functions for each particular sequence of DNA and tried to assemble them into working genomes. This method was time-consuming, and the outcomes were riddled with error.

Today, scientists are starting to piece together possible genomes using complex computer algorithms that do the sequence- and rule-memorizing for them. In many ways, writing DNA code is becoming like writing computer code, but instead of ones and zeros, it’s written in As, Cs, Ts and Gs — abbreviations for the four interconnecting nucleotides that form DNA’s ladderlike structure. This four-letter language of life allows scientists to see inside biological systems and attempt to reprogram them.

Programming is what drew Densmore into the field of synthetic biology in the first place. A few years ago, Densmore was doing postdoctoral research at Berkeley when Voigt commissioned him to make a prototype computer system that streamlined biological engineering’s testing process to avoid redundancy. “Right now, we have the DNA, we build things, we learn, we feed that back into the algorithms, and we keep doing that loop,” Densmore says. Ever the analogist, he compares it to building cars. We don’t have to crash-test every single car to know how it will hold up. We test a few to determine what does and doesn’t work and then input those findings into a growing database to inform future designs.

The ultimate goal, of course, is to build designs with predictable outcomes. Want to make a plant that glows green when it’s lacking nitrogen? Densmore envisions a day when you can type such an outcome into a computer, whose algorithms will sift through the databases of known functions and find the specific DNA sequence necessary to achieve such a goal.

From Lab to Living Room

At this point, synthetic biology takes place mainly at lab benches, but this technology is aimed at mainstream uses and is becoming more accessible to mainstream users. (See “Biological Engineering in the Basement,” page 3). The applications for biological engineering, then, are limited only by our collective imagination.

“Because you’re treating it like engineering, the kinds of things you can do are much more substantial,” Keasling says. “You can do synthetic biology to produce a product, and they tend to be products either that evolution would not have selected for — like a fuel, for instance — or that evolution would not select to produce enough of — engineering microbes to produce artemisinin.”

Twelve years ago in his Berkeley lab, Keasling figured out how to program baker’s yeast to produce a chemical precursor to artemisinin, the world’s most potent anti-malarial drug. “We took the genes out of the [wormwood] plant and put them into a yeast,” Keasling explains. The yeast eats sugar and, using the genetic code from the wormwood as a blueprint, spits out artemisinic acid, a precursor to the drug. “It’s a process that’s just like brewing beer,” Keasling says. 

A quick chemical conversion turns the acid into a semi-synthetic version of the drug that hit the market in April. The pharmaceutical company that has licensed the technology plans to produce 100 million malaria treatments a year, covering between 25 and 33 percent of the global need. (See “Brewing Better Malaria Drugs,” page 3).

Giving Fossil Fuels the Boot

Keasling also sees these microbial factories as a solution to the energy crisis. “In fact, artemisinin is not too far off of a good diesel fuel,” he says. Gasoline, diesel and jet fuel are extracted and refined from crude oil. What was once organic material has been subjected to millions of years of pressure, which yields energy-rich organic molecules called hydrocarbons. But Keasling and his colleagues at the U.S. Department of Energy’s Joint BioEnergy Institute think there is a better (not to mention faster) way to turn the energy in organic materials into hydrocarbons. 

Keasling’s method feeds agricultural waste such as cornstalks and wheat straw to E. coli bacteria engineered to break down the sugars and produce biologically synthesized hydrocarbons that burn and function just like those in fossil fuels. In addition to improved efficiency, these fuels can work within our existing transportation infrastructure, so there’s no need to engineer new cars or gas stations.

“We have a billion tons of biomass that go unutilized in the U.S. on an annual basis, and if we could turn that into fuel, we could roughly produce a third of the need in the U.S.,” Keasling says. Since the fuels wouldn’t rely on burning petroleum products, it would also decrease the U.S. carbon footprint by roughly 80 percent.

Replacing Petroleum

The importance of petroleum isn’t limited to the stuff we pump into our gas tanks, either. It also comprises much of the manufactured world around us. Keasling uses the chair he’s sitting in as an example. The seat is upholstered in a petroleum-based fabric and stuffed with petroleum-based filler. The wooden frame is coated in a petroleum-based varnish. The linoleum floor? Petroleum as well. And that polyester shirt, too.

Keasling says the ubiquity of petroleum and the chemical products derived from it mask the fact that they are not the best materials for their respective jobs. For example, why is carpet made of nylon? “It’s not because that’s the best molecule for a fiber,” Keasling says. “It’s what you can get from petroleum.” Since we extract and refine copious amounts of crude oil these days for fossil fuels, it makes sense to use the nonfuel portions as well.

If scientists can replace petroleum-based fuels with ones derived from sugars, Keasling posits, then we ought to be able to use the same fermentation process to derive petroleum’s other chemicals from sugars as well. Keasling thinks it is only a matter of time before manufacturers phase out petroleum products in favor of more profitable and sustainable biosynthetic versions. A key component in Keasling’s work, be it anti-malarial drugs or biofuels, is the fact that the methods are open source and the technology can be produced on a large scale.

Promises and Implications 

Synthetic biologists are acutely aware that reengineering nature comes with risk. Never-before-seen genomes could destabilize a species as well as entire ecosystems. The fallout from unintentional gene transfer could be decades away, but stalling on decisions that tackle issues like climate change and habitat loss also carries enormous risks, says George Church, the unofficial godfather of biological engineering.

As a graduate student in the 1980s, Church developed one of the first methods for direct genome sequencing, determining the exact order of DNA’s base pairs, which led to the first commercial genome sequence. Church now directs PersonalGenomes.org, the only company that provides open-access genetic information. As a genetics professor at Harvard, he thinks synthetic biology should have the same safety features as other, more mainstream branches of engineering. Maybe more. 

Just like testing cars requires airbags and crash-test dummies in a controlled environment, Church says, genome testing should be done with ecosystems that are brought into a realistically complex but physically isolated space. When synthesizing DNA, safety measures could come in the form of DNA that can’t replicate outside of a defined environment, or genetic code that has been altered to prevent the exchange of functional genes between organisms.

The Right Reasons

“We have an obligation to do it right,” Church says. Synthesizing biology for the sake of curiosity alone isn’t enough. Nor is reviving species we drove to extinction just because we can. The reasons for synthesizing biology need to be clearly articulated, questioned and cross-examined from the beginning. 

Church says reviving an extinct species like the woolly mammoth might be more justified if it also addresses an issue like habitat preservation in the face of climate change. He illustrates the idea with a telling, if somewhat impractical example: “The permafrost, which has more carbon than all the rainforests put together, is at risk just by simple thawing, and a large herbivore like a mammoth could maintain it for another few decades against global warming,” Church says. 

A massive mammoth could punch through the insulating snow to allow ice-cold air to reach the soil and keep it cold. The herbivorous beast would also eat dead grass, allowing new grass to send its roots deeper into the ground to prevent erosion. And by knocking down trees, which absorb sunlight, a mammoth could cause more sun to be reflected, increasing the cooling albedo effect on the permafrost.

Like Church, other synthetic biologists are willing to take some risks for the sake of moving the field forward. “The world is a broken place,” says Laurie Zoloth, professor of bioethics at Northwestern University. She says our responsibility, and obligation, is to fix it. The key is to create a transparent framework that allows scientific experimentation to flourish — one that both governmental regulators and nongovernmental organizations can use to pursue projects that are good and sustainable and just, she says.

If synthetic biology is really the start of a revolution, Zoloth wants to see a world that takes into account the fact that that revolution might benefit some but be disastrous for others. In the case of treating malaria, semi-synthetic artemisinin may prevent millions of deaths from malaria while also throwing off the wormwood market for farmers of the herb.

Zoloth is especially intrigued by the kinds of internal moral choices synthetic biologists must make. “How [do] you create scientists who aren’t only good at all these different technical skills, but are very good at asking and thinking seriously about ethical questions, about moral questions, and coming to terms with the ramifications of their work?”

Fine-Tuned Tests

Drew Endy considers such questions when running Stanford’s genetic engineering lab. “The things I need and the things I want to do and the problems I might cause, directly or indirectly, are all going to involve many other people,” Endy says. “We operate today still largely in a regime of ignorance, with respect to details of the living world.” But having unknowns does not preclude biological engineers’ ability to experiment in these areas, he says. 

“We make living matter programmable,” Endy says. This means amassing the data and writing the code necessary to engineer the cells, organisms and systems that can address global problems. Once synthetic biologists have come up with the algorithms, living things like yeast, bacteria and even grass can pump out products and solutions. “Biology is the ultimate distributed manufacturing platform,” Endy says.

Over the next few decades, Endy anticipates seeing fine-tuned biologically engineered systems integrated into everyday lives, all over the planet. This could come in the form of bread machines that crank out loaves raised with yeast-based medications. Or personal manufacturing plants that turn yard waste into fuel. Endy imagines a world in which “humanity figures out how to reinvent the manufacturing of the things we need, so that we can do it in partnership with nature. Not to replace nature but to dance better with it.”

Biological Engineering in the Basement

Synberc director Jay Keasling warns that it takes a long time to engineer biology to be industrial strength, but the technology is becoming increasingly accessible. “The cheaper it becomes and the easier it becomes to engineer biology, the more it democratizes the field,” he says. 

“The idea that you could get a very large number of complex genes synthesized and delivered in a FedEx package is something that was not practical just a decade ago,” says Steve Evans of Dow AgroSciences. But today, many synthetic biology labs do just that. They outsource their DNA synthesis and have it delivered to their doors in days. The price of synthesis is dropping, too, which makes the idea of citizen scientists doing synthetic biology in home labs more feasible. One synthesis company’s website boasts it can synthesize up to 500 DNA base pairs for only $99 and ship the sequence in four to seven business days.

At this point, though, Evans says most do-it-yourself projects are still attempting to do pretty basic stuff. Take the Kickstarter project to engineer a plant that glows green, for example, or Keasling’s idea of making yeasts that will convert sugars into brand-new beer flavors.

While they seem simple, such feats of engineering still require a sophisticated understanding of biology — something Keasling says should not be underestimated. It’s not as easy as picking up an electronics kit or an Erector set, but Keasling anticipates that in a few years, toy stores may riff off the old-fashioned chemistry set he played with as a kid by coming out with a DIY biology version.

Brewing Better Malaria Drugs

The anti-malarial drug artemisinin is normally derived from a Chinese herb called sweet wormwood (Artemesia annua L.) and is toxic to the malaria parasite Plasmodium falciparum. Demand for this plant-based version of the drug has been high since 2005 when the World Health Organization officially recommended it, combined with other anti-malarial drugs, as a first-line treatment for malaria. 

But the price and availability of the commercially grown plant are often unstable, says Synberc director Jay Keasling, and the compound is too complicated to synthesize chemically, so he looked to biology to find a better way to get it.

Keasling took genes from wormwood and put them into baker’s yeast. These single-celled organisms use the instructions from the wormwood to produce artemisinic acid, a precursor to the drug. This acid still needs to be converted into artemisinin before it can be used as a drug, yet researchers have found no enzyme that triggers such a change. Instead, some scientists speculate that sunlight may transform the acid in wormwood into artemisinin, so they mimic that action in the lab, using a photocatalytic reaction to get the drug ready for anti-malarial action.

Keasling and colleagues also published a method for chemical conversion of the acid in Nature in April; the article is free to read, without a subscription. They also licensed the production to pharmaceutical manufacturer Sanofi royalty-free, so it can pump out a consistent, large-scale supply of the drug and sell it at cost to treat those with the disease around the world.

[Watch video of the event and read about the panelists at DiscoverMagazine.com/synbio.]