Life as We Grow It: The Promises and Perils of Synthetic Biology

A Discover event highlights how scientists are engineering DNA that may one day eliminate malaria, solve the energy crisis and feed the world.

By Breanna Draxler|Wednesday, December 11, 2013
DNAtree
DNAtree
wavebreakmedia / Shutterstock

What if you could turn a bread machine into your personal pharmacy? Or fill your gas tank with fuel made from grass clippings? Or light your home with glowing houseplants? While radical in concept, these ideas are startlingly practical and already in the works. 

Researchers are reimagining biology to turn the inherent productivity of living things into a whole new method of manufacturing solutions to real problems. These scientists say before long, synthetic biology will join the growing list of revolutionary technologies — like cars, smartphones and the Internet — that initially scared or surprised us, but have since become so pervasive and necessary in our daily lives that we take them for granted.

At its most basic, synthetic biology is about making DNA from scratch, on scales from individual molecules to cells, tissues and even entire organisms. The field’s raison d’être is to design and build brand-new biological systems to eradicate deadly diseases, manufacture better materials and reduce reliance on nonrenewable resources.

“It is difficult to imagine the transitions led by synthetic biology,” says Juan Enriquez, co-founder of Synthetic Genomics, a California-based company that commercializes genome-related technologies. “It may sound obscure and distant from what you’re doing,” Enriquez says, but the work of these scientists will ultimately affect every one of us. “This stuff will change your life.”

Evolution by Design

To explore this new frontier of science, Discover teamed up with Synberc, a research consortium of synthetic biologists and engineers from Stanford, Harvard, MIT, University of California in San Francisco and UC Berkeley. We gathered nine pioneering researchers on the red-roofed Berkeley campus to describe the tools, discuss the applications and deliberate the ethical ramifications of what it means to engineer life, in an event moderated by Discover editor-at-large Corey Powell.

“Think of these folks as explorers who are coming in to give reports of the edges of the known world,” says Enriquez, the keynote speaker. What they’re finding isn’t just new; it demonstrates possibilities we didn’t even know existed. Enriquez told the group he thinks the work of synthetic biologists could alter the future of the human species. “We are actually transitioning from a Homo sapiens into a Homo evolutis — a creature that begins to directly and deliberately engineer evolution to its own design.”

A Rich Legacy

The nascent field of synthetic biology sits squarely upon a solid scientific foundation built by decades of research in biotechnology and genetic engineering. In agriculture, for example, researchers transfer genes from other organisms into crops to get certain characteristics. “We insert insect-resistance traits and herbicide-tolerance traits,” says Steve Evans, who works at Dow AgroSciences. “For the most part, they come from either bacteria or from other plants.” The resulting crops have fundamentally changed how farmers grow our food.

Evans traces the past century of incremental progress in the field of biotechnology by using the example of the soil-dwelling bacterium Bacillus thuringiensis. Some strains of these bacteria produce a protein that paralyzes the digestive system of a specific group of insects so they starve to death. The bacterium targets agricultural pests, such as corn rootworm and Colorado potato beetle, but leaves pollinators like bees unharmed. 

Farmers began using the biological pesticide on their fields in the early 1900s. By midcentury, scientists had isolated the bacteria’s toxic protein and were able to manufacture it in large-enough quantities to commercialize it as a spray-on insecticide.

Then the scientists cranked the zoom lenses on their metaphorical microscopes even further to focus on the specific genes in the bacteria that coded for production of the toxic protein. When they inserted those genes into crop genomes, through a technique called recombinant DNA, the plants were able to produce the protein for bug resistance on their own, eliminating the need to spray insecticide. 

The first genetically engineered pest-resistant crop on the market was a potato whose genes were complemented by those of Bacillus thuringiensis. Since the EPA approved the Bt tuber in 1995, public reactions to this and other modified crops have been mixed. While the pioneering Bt potato did not prove a commercial success, genetically engineered corn, soybeans and cotton have become the norm for the vast majority of farmers in the United States today. Genetic engineering, though contentious, has transformed agriculture into a well-oiled and finely tuned biological machine that aims to feed the growing global population.

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Researching agricultural applications of biotechnology, Steve Evans (left) has helped develop a number of hybrid crop seeds that grow into plants resistant to insects and tolerant of herbicides. Virginia Ursin (center) has successfully produced and patented a number of genetic crop technologies, and she hopes to eventually engineer corn that can convert nitrogen from the air into usable ammonia. Jay Keasling (right) engineers microorganisms to produce life-saving drugs, energy-saving fuels and improved materials — work that earned him the title of Discover’s Scientist of the Year in 2006.

Martin Klimek

Biology, Reimagined

Finding such new and different uses for biology, then, is not conceptually novel. Taking genes out of one organism and inserting them into another has demonstrated the potential of biotechnology as well as its limits. With techniques such as recombinant DNA, finding the right genome sequence in one organism to trigger expression of particular proteins or traits in another requires as much luck as skill.

“We take a highly empirical approach,” says Virginia Ursin, a science fellow at Monsanto, the company that developed the beetle-resistant Bt potato. This approach requires tweaking and testing plant genomes over and over until researchers find a combination of genes that works. In the case of the Bt potato, they succeeded in finding and incorporating the right gene. In contrast, after more than 30 years of trying to create corn that can convert atmospheric nitrogen into usable ammonia instead of relying on fertilizers, Ursin says she is still far from finding a way. “One of the visions [of biotechnology] was making corn fix nitrogen,” Ursin says. “That was in 1982; it still hasn’t been done. It speaks to the complexity of it.”

Synthetic biology offers a more calculated approach to modifying genetics. It doesn’t rely on the trial and error of empirical methods. Nor is it limited to the extent of existing genomes. As the latest upgrade to biological engineering methods, synthetic biology enables researchers to come up with new and predictable genetic outcomes using mathematical and engineering principles. And these researchers can design, test, and build new genomes on a much shorter timescale.

Think of it this way: The automobile was a useful innovation, but until the advent of the assembly line, it wasn’t actually available to most people. After this critical block was overcome, the accessibility of cars has made them ubiquitous in much of the world. They have changed how (and where) we live. Likewise, living systems can be engineered to address all kinds of critical issues we face as a species, and then be manufactured for large-scale distribution. Biological engineering aims to design solutions with intention and precision rather than groping around in hopes of finding them, as was often the case with genetic engineering. 

“In genetic engineering, ‘engineering’ is really kind of a misnomer because there wasn’t a lot of engineering in there,” says Jay Keasling, director of Synberc. In contrast, synthetic biology offers sophisticated and fine-tuned control, with reliable, reproducible results. By fitting DNA into an engineering template, the messy field of biology emerges as a complex but somewhat predictable system — one that synthetic biologists have begun to maneuver in recent years.

Designing Living Solutions

Christina Smolke, an associate bioengineering professor at Stanford, describes the work of synthetic biologists in simple terms. “It’s basically encoding your program within DNA,” she says. In natural, unaltered organisms, she explains, each sequence of DNA in a genome codes for a particular outcome, expressed as a protein that determines a quality of the individual or even the species as a whole. When a synthetic biologist builds and inserts foreign DNA into a cell, that cell will read the code as if it were its own. Its cellular machinery will execute the program by producing the same protein as the native organism, taking on new qualities, just as in recombinant techniques. 

Synthetic engineers take it a step further, mixing and matching these pieces to come up with outputs that are altogether new. “I think for many people who wind up doing engineering, they’re motivated by design,” says Smolke. “They want to make and build things as opposed to just studying existing systems.” These particular biological systems can be custom designed to address real-world problems.

“If we look at all the global challenges we’re facing, whether it’s sickness or famine or having safe, clean, environmentally friendly materials, I think [synthetic biology] would be the natural place to gravitate for solutions,” says electrical engineer-turned-biological engineer Douglas Densmore, now an assistant professor in the department of electrical and computer engineering at Boston University. Solutions to these problems are not going to magically appear anytime soon via natural selection, so Densmore says we need to be proactive and engineer solutions instead. “We’ve gotten really good at engineering physical systems in the world. I’ve always thought of [engineering biological systems] as a natural next step.”

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.

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Trained as an electrical engineer, Douglas Densmore (left) gave up building video games to build biological circuits. Christopher Voigt’s dad told him there was no future in computers, so he opted for chemical engineering, which led him to synthetic biology. Christina Smolke (right) doesn’t just study biology; she pioneered the design and application of RNA molecules to reprogram it.

Martin Klimek

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.”

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Rather than contemplate the swiftly changing science of synthetic biology itself, bioethicist Laurie Zoloth (left) concerns herself with how this technology affects the moral compasses of the women and men who are developing it. On The Colbert Report last fall, George Church (center) had to stop the host from eating a DNA sample in which Church encoded the text from 20 million copies of his latest book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. Drew Endy (right) was named one of Esquire’s 75 most influential people of the 21st century and one of President Barack Obama’s 2013 Champions of Change for his work redesigning genomes and developing genetically encoded computers.

Martin Klimek

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.]

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