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Welcome to the age of synthesized life, built from scratch. Soon, it may be so cheap and simple a teen hacker could do it. Or a terrorist.
It's 8 o'clock on a Wednesday night at the University of Toronto's medical sciences building, and Emanuel Nazareth holds a Petri dish up to the light. He squints at the clear, tiny bubbles dotting its amber surface, as though staring at it will make it grow.
It's three days till show time and their project looks like spit on a plate.
He pops it back in the incubator without saying a word.
Assistant engineering professor Stephen Davies trudges past, both hands buried deep in the pockets of his khakis, and sighs. He knows the score. With less than 48 hours of growing time left, "it's going to take a miracle" to make this project fly.
But Matt Scott, a 30-year-old mathematician pitching in from the University of Waterloo, is beaming. It's his first night.
Never before has he dirtied his hands in a "wet" lab, shifting from the cold world of manipulating numbers to manipulating life: "It's just really neat," he says, "fiddling with genetic components to get a certain behaviour."
Fiddling, indeed. Here in this fourth-floor lab, where a poster in a stairwell advertises a lecture titled "Does God exist?", these young minds are at serious play in the Lord's proverbial fields, transforming living things into toys of their choice.
E. coli, the common intestinal bug and scourge of undercooked hamburger, is being remade into a living Etch A Sketch that could say, "Hi Mom." Another batch is being reprogrammed to change colour, like a mood ring, at different temperatures. And, ready or not, their efforts have earned them an invite to one of the more ambitious science fairs ever held.
There will be no papier-mâché volcanoes, robots or homemade clocks at this competition. It's being held at the Massachusetts Institute of Technology, the planet's mecca of innovation. The exhibits will be lab-made life forms modified with genetic parts that were dreamed up, designed and constructed with computers and DNA.
If you think designing life is the sacred business of a divine executive, think again.
In the 21st century, this godlike power is shared by people who schlep backpacks and study for mid-terms, such as Mr. Nazareth, a 22-year-old, fourth-year engineering undergrad.
In reading DNA, science isn't much beyond the "See Dick run" stage. Yet a growing scientific movement is already afoot to rewrite it. The goal is audacious -- to make living things that behave like invented gadgets.
This emerging science is called synthetic biology, a term that confirms the profound, if eerie, fact that creating DNA -- the building block of life -- is no longer the sole domain of nature.
New and relatively cheap computing technology is allowing students and even non-scientists to assemble the chemical chains that encode genetic functions, making it possible to design and construct genes, and soon perhaps life itself, from scratch. At this very moment, in a lab outside Washington, D.C., scientist Craig Venter, famous for mapping a private version of the human genome in 2000, is leading efforts to create the world's first human-designed species.
Driving the field is a twin-engine philosophy: First is the idea that the best way truly to understand life is to build it. Second is the hope that these life forms could be harnessed to do human bidding. The genetic codes of organisms could be rewritten to produce hard-to-make drugs, gobble up pollution, pump out clean energy, kill cancer cells or simply grow flowers that bloom on your birthday.
"There is nothing mystical or spiritual about this. I don't have to invoke the gods," says Toronto researcher Andrew Hessel, raising his arms to the heavens one stormy morning. "DNA is the only language used to program life on this planet. . . . To change the organism, you change the instructions in the DNA program."
In the 19th century, chemists learned to synthesize organic compounds they once thought only nature could make. From there, they went on to invent a raft of things, from plastics to polyester, that nature never imagined.
Synthetic biology has similar dreams. Its proponents believe that it could fuel the next industrial revolution, in which manufacturing plants rely on the biological processes of cells instead of petroleum.
Scientists at DuPont have already redesigned E. coli (the bacterial equivalent of the lab rat) to produce a new, Spandex-like fibre by means of a fermentation process that relies on the glucose of cheap corn syrup. The company that made its name in chemicals is now building a $100-million (U.S.) biological factory in Tennessee.
As well, the Bill and Melinda Gates Foundation has handed a University of California at Berkeley team $42.6-million (U.S.) to rewire E. coli to help mass produce the malaria drug artemisinin. And in addition to building a new species, Dr. Venter has secured a multimillion-dollar grant from the U.S. Department of Energy to design a clean energy source from the genes of microbes.
Drew Endy is an articulate 35-year-old MIT professor who was one of the founders of the MIT science fair and has emerged as a leader in the field. As he puts it, "Whatever biological systems do, you can imagine programming them for the purposes of human intention and human needs."
Of course, humans don't always have the best intentions. Synthetic chemistry brought the world poisonous gases as well as pantyhose. So now, with companies that will mail tailor-made genes to your house, and with machines to manipulate DNA available on eBay, the field's own pioneers as well as the Pentagon are considering putting safeguards around synthetic biology.
After all, Prof. Endy recently received an e-mail message from someone interested in constructing his own genetic component -- someone in Grade 10. If even a high-school student can now experiment with the technology, could it be that designing life is little more than child's play?
By Thursday morning, it's clear to all at the U of T lab that the mood-ring-like temperature sensor will have to be abandoned.
They have managed to join only one of the genetic parts, needed to make the E. coli flash red in hot water or green in cold, to the bug's genome. They'll have to settle for taking to MIT the project's theoretical description, including Mr. Scott's predictive mathematical models of how it would work.
"Microbiology ain't easy -- it's a lot easier to solder wires together," Prof. Davies says glumly. But then he shrugs, reminding everyone within earshot that the fair is about learning first, and having fun most of all. "This," he says, "is a competition everyone will win."
At 46, he hardly looks older than the students he leads. An electrical engineer, Prof. Davies used to work on submarines, mapping sonar patterns, before the Cold War ended. But he switched specialties after U.S. researchers managed to construct engineering's Holy Grail devices -- the toggle switch and oscillator -- out of DNA chemicals. These genetic levers can be programmed to turn proteins off and on.
That idea sparked his interest in recruiting students to try their hands at building "circuits" with genes, and this year he found himself leading the first U of T team to enter the MIT fair. And despite mid-terms and little money, they are managing to redesign microbes in their spare time.
In all, 13 teams from universities around the world are vying for a prize, and competition is bound to be stiff. Last year, only five U.S. schools entered the intercollegiate Genetically Engineered Machines competition, or iGEM for short.
Students from the California Institute of Technology came second by creating a strain of yeast that can distinguish between decaf coffee, regular and espresso. The University of Texas team won with a casserole dish containing a miniature lawn of bacteria, genetically programmed to behave like Kodak film. The result produced the first biological photograph, flashing the simple message, "Hello World."
Ever since a trio of California scientists joined three E. coli genes to the genome of a monkey virus in 1972, researchers have had the ability to redesign DNA.
Thanks to this so-called recombinant DNA technology, labs the world over are teeming with creatures that carry the genes of other species, allowing the study of human diseases, such as cancer, in manageable models such as mice.
But using this method actually to compose DNA was for the most part impractical. Mr. Hessel, who works in computational biology at Toronto's Princess Margaret Hospital, likens it to the tedious process of writing a ransom note by cutting individual letters from magazines and pasting them together to spell out a sentence.
What's more, no one really knew what to write. Very few of the chemical sequences that make up DNA were known when this technology emerged 33 years ago. (Those chemicals are essentially sugars, known as nucleotides, represented by the letters A, C, G and T. In the twisted-ladder structure of DNA, there is a letter at the end of each rung, A joining to T, C joining to G, in a pattern called a base pair.) But in the tech boom of the late 1990s, new computers capable of cracking genetic code burst on to the biology scene. Most helped to sequence DNA in large-scale projects such as the human genome. Under the radar, however, a few companies were thinking small.
One of the major stumbling blocks to cooking up a genetic code from scratch had been the tiny volumes any recipe would demand. The chemistry of a cell is a million times smaller than the liquid dispensed by any eye dropper in a lab. In fact, Mr. Hessel says, to make a fragment of DNA requires droplets of nucleotides so minute, they evaporate before you have time to add the next ingredient.
A solution to the size problem came from a familiar gadget -- the ink-jet printer, the device that hooks up to home and office computers to lay down billions of minuscule ink dots that produce letters on a page. Why not fill the ink cartridge with nucleotides instead of ink -- with genetic As, Cs, Gs and Ts?
Mr. Hessel says this miniaturization of chemistry, known as micro-fluidics, is one of the key drivers of synthetic biology. It reduces the amount of nucleotide chemicals required for any experiment, their cost and the effort it takes to assemble them.
"DNA," he says, "is getting pretty freaking cheap to make."
Now, anyone interested in typing up genetic code can enter it with keystrokes and e-mail it to a commercial lab that will, in effect, hit a "print" button, spit the code out as chemical dots on a glass sheet, synthesize it and send a living version of it back to you, usually tucked inside bacteria for transport.
In the past few years, dozens of mail-order companies that synthesize DNA have appeared. When Blue Heron Biotechnology, the largest of these firms, launched in 2001, the unit cost of a DNA base pair was $15 to $20 (U.S.). Today, the price is no more than $1.60.
The aim, says Blue Heron CEO and founder John Mulligan, who once worked on the human genome project, is to make it faster and cheaper for researchers to outsource the assembly of DNA than to make it for themselves.
"We're going to build you exactly what you are looking for," Dr. Mulligan says. "Whole plasmids [the genetic material of a microbe], whole genes, gene fragments . . . and in one to two years, possibly a whole genome."
Sales at Blue Heron Bio have ballooned by 30 to 50 per cent every year, with one of its major growth markets being orders for genetic code designed from scratch. And unlike in the 1970s, the DNA sequences are now available by the metre to download. GenBank, the world's public on-line genome sequence repository, has amassed 40 billion bits of code from various species -- banana, human being and Ebola virus among them. And that number doubles every 18 months.
Today, Mr. Hessel says, "you don't need to be a genetics professor, you don't need to have a lab, you just need a laptop" to construct genetic code. "You can download a gene sequence from GenBank -- you can do it sitting in a Starbucks."
If the technology has evolved quickly, so has the culture.
"Fast-forward to the late 1990s and people started showing up who were half a generation younger," says Roger Brent, co-founder of the Molecular Sciences Institute in Berkeley, which has been a breeding ground of synthetic biology's key concepts. "To them, DNA was just a bunch of ones and zeroes, a digital language, a program."
Students are now flocking to synthetic biology from fields that have never before taken an interest in the life sciences. Blogs and websites draw them to the ideals of the new discipline as a universally accessible, democratic technology, and one with the potential to produce environmentally clean products, says 35-year-old Rob Carlson, a physicist at the University of Washington and another of the field's leading thinkers.
But Prof. Carlson, who once worked with Dr. Brent in Berkeley, acknowledges a less sober-minded element: "There's also the fact that it's just a new kind of Lego to play with. They're excited by the idea of dealing with molecules and building stuff out of life. . . . It's something new to hack."
Emanuel Nazareth began programming computers at the age of 10, not long after he and his family emigrated from Kenya to the Toronto suburb of Mississauga.
First, it was text-based, in BASIC. Then colour came along. For fun, he modelled worlds with Sim City. He would make games, animate the characters he created and compete with friends over e-mail in building fantasy lands.
"Too much!" his mother would say of his computer time. "Go out and play sports!"
After graduating from high school with a 93 per cent average, he secured a spot in biomedical engineering at U of T, one of the more competitive undergrad programs in the country. And so the slight, serious and extremely soft-spoken Mr. Nazareth comes at genetics like an engineer, describing it in mechanical terms. As he wrote in a school essay this spring, genes are to him components of a network powered by circuits. Biology is a system best manipulated when broken down into modules.
A few weeks before the iGEM competition, over a bowl of linguine at an Italian café near campus, Mr. Nazareth explains that he decided his future lay in bioengineering after seeing an artificial arm being controlled by the inputs and outputs of the nervous system.
So he volunteered to join this year's iGEM team and work with Prof. Davies and students such as Hannah Fong, the 21-year-old immunology student who came up with the Etch A Sketch idea.
Their bacterial machines, Mr. Nazareth realizes, are just dazzling gizmos to explore and demonstrate the potential of synthetic biology -- which, he says, is endless. One example he offers over lunch is a cell programmed to roam the body and chew up bad cholesterol.
"If you can take even the most rudimentary concepts of electrical engineering and can pull them off in a cell," Mr. Nazareth says, "the control that could give you and the applications are mind-boggling."
When genetic engineering first shifted from science fiction to reality in the 1970s, people feared Frankenstein creations would escape into the wild and alter the planet.
One scientist went so far in his attempt to allay public fears that he drank milk spiked with E. coli containing an oncogene, or cancer gene, added to its DNA. When the bug turned up later in his stools, he offered it as evidence that modified microbes could not even survive the digestive tract.
Paul Berg, who won a Nobel prize in chemistry for his work on 1970s recombinant DNA technology, says the fears of the day were largely misplaced: "An altered species doesn't survive easily in the wild. It was just silly.'' But such concerns triggered the historic 1975 Asilomar conference in California's Monterey Peninsula, where 140 of the world's biologists spent four days figuring out how to police themselves.
That conference set down rules of containment and safety regulations under which biologists still operate. The advent of synthetic biology, however, has led to calls to update these provisions, in light of contemporary fears -- namely, the threat of bioterrorism.
In 2002, for example, State University of New York scientists announced that they had built a functioning polio virus from scratch using mail-order DNA parts and a genome map freely available on the Internet.
That feat took three years. But a year later, genome scientist Dr. Venter reported it had taken his team only three weeks to assemble a virus that could infect bacteria.
Also in 2003, the U.S. Central Intelligence Agency released a report titled "The Darker Bioweapons Future," saying synthetic biology could lead to the construction of pathogens "worse than any disease known to man." It also noted that, with the technology broadly available through a home computer, it is a field tough to monitor by traditional means.
Anyone with a credit card can register on-line to a DNA synthesis company and e-mail in the genetic code they want. Dr. Mulligan says Blue Heron matches all the requests it receives with the genomes of pathogens specified by the U.S. Centers for Disease Control, to ensure no one is building anything destructive. But reports suggest that not all companies follow such rules.
Meanwhile, an amateur who lacks expertise in manipulating life forms can buy kits that include instructions for moving genes between organisms. In a recent paper on the proliferation of home-based biotechnology, Prof. Carlson wrote that this "process might be slightly more complicated than baking cookies, but it is for the most part less complicated than making wine or beer."
This summer, MIT, the J. Craig Venter Institute and the Center for Strategic and International Studies announced a joint project to investigate the benefits and risks of synthetic biology, with an eye to crafting safeguards to prevent abuse.
But Prof. Carlson feels that keeping the technology open is the best way to ensure that he world is prepared for the hazards it hypothetically could unleash. A black market of biotechnology, he argues, would just leave everyone in the dark.
Laurie Zoloth, a bioethicist at Northwestern University in Chicago, described the fears around this new field as a delicate balance. "There has to be an understanding," she says, "that this could really be used as a nasty weapon."
And while biologists of the 1970s tended to know each other and their work, much of science today is conducted behind the proprietary veils of corporations, whose "ethical overview may not be as rigorous or transparent."
On the other hand, Dr. Zoloth says, "it would also be worrisome to over-hype the fear." While the technology is freely available, she argues that it is still "exquisitely difficult" to pull off.
"It is far too early to say this is impermissible. . . . There is real value in it because it offers a creative way to look at the world's intractable problems, such as malaria, pollution and energy shortages."
Berkeley's Dr. Brent wants people to think big. Before dismissing this as risky business, he says, people should remember that the 1970s revolution in cutting and pasting DNA gave birth to biotechnology. Within a decade, researchers had figured out how to produce insulin using a human gene engineered into E. coli.
"You had guys in white jumpsuits climbing up and down catwalks fiddling with knobs on three-storey fermenters -- this was in full industrial swing in the 1980s."
He predicts that synthetic biology will revolutionize manufacturing the same way, so that glucose, the main energy source of a cell, will one day power industry.
"When the price of oil, which is rising, surpasses the cost of glucose, which is declining, one is likely to see a brisk conversion of the whole world's chemical industry," Dr. Brent says. "Synthetic biology needs to articulate some of these grand goals so that people can see its potential."
Drew Endy sits cross-legged in sneakers on a chair at Toronto's new Centre for Medical and Related Sciences, and fantasizes: "We should be able to combine a redwood and bamboo to quickly grow a mega-structure."
After all, why grow a tree if you can reprogram its genome to grow a table, or a bridge?
"I'm a structural engineer -- I get to retire when I can grow my own bridge," he says. "It is a fun fantasy, but if I could enable that, that would be cool."
Prof. Endy says nature's version of genetics is a lousy basis from which to build things. If there is a "deliberate design" to biology, he can't see it. Legions of researchers are studying it, but "in the meantime, let's invent our own."
The idea that humans could make new species that surpass nature's models with more intelligent designs sounds at first like stunning hubris. The goal -- to make life forms that are easier to manipulate and never mutate unless programmed to do so --sounds like the same brand of doomed cockiness that deemed the Titanic unsinkable.
Indeed, McGill University ethicist Margaret Somerville says the emergence of synthetic biology "should have us very concerned."
She describes the "unprecedented powers this new science gives us to alter the nature of nature" as part of a wider "post-human, post-nature revolution."
According to Prof. Somerville, the new technology is not like changing a river's course by building a dam -- it could give rise to creatures that ultimately prove beyond human control.
"Life is an enormously complex biological entity . . . and we have no idea what we might be affecting when we alter it in such a fundamental way," she says.
Prof. Endy fully supports the need to investigate safeguards, but he argues that necessity is the mother of invention -- and no disrespect, but she trumps mother nature.
Scientists cannot easily build useful biological machines from genetic code as nature made it. That model has evolved over billions of years, whereas human understanding of genomes now is so crude that it is more logical and far simpler to start from scratch.
This, he says, doesn't mean scientists are angling to play the role of creators. "For me, the difference between constructing and creating is this: God or gods create -- they have unlimited resources, perfect knowledge, and infinite abilities, so they create.
"Humans never have that, especially engineers. We have a budget, we've got finite resources. . . . We have an imperfect understanding of everything, and we have a very limited ability to do stuff."
Prof. Endy has no illusions that starting from scratch will be easy. "We don't know how to engineer replicating machines."
At the U of T lab, Prof. Davies has found simply trying to tweak natural life forms with lab-made parts is a humbling experience. There's no guide or blueprint to predict how an organism will behave when you flick one gene on or off, or add a new one -- not as there might be with a real machine.
"The students in my lab can take months to make a single [genetic] connection and measure the output," he says, "and then the thing goes and replicates and mutates, and you have to start all over again."
Neither are there standard tools or instruments to measure things, or easy formulas to create mathematical models that might predict biological behaviour.
For this reason, Prof. Endy is trying to bring such accoutrements to biology. Just as an engineer's tool box holds uniform items such as nuts, bolts, transistors or cables, a Registry of Standard Biological Parts has been created at MIT.
This registry now holds more than 1,500 fragments of DNA code dubbed "biobricks," genetic components that have each been designed from scratch and designated to perform a specific function. They include parts to turn genes off and on, to send signals between cells or to change their colours between red, green, yellow and cyan. All have been crucial parts for the iGEM teams. They are also freely available on-line to anyone interested.
Prof. Endy hopes that all universities will soon contribute to the registry and that it will one day include enough parts to construct the genome of an entire organism.
"Sure, why not?" he says. "We don't build computers out of random chunks of silicon and metal found lying about the Canadian countryside -- we refine and process that material in order to make it simpler."
But why do this with biological parts at all, if it would take a small fraction of the time and far fewer headaches to do it with plastic or silicon or some other artificial material?
The draw, Prof. Endy explains, is not what biological systems do, but where they do it. For example, he wants to build a biological version of a counter. "You can go to Staples and buy one of those simple counters that counts to 9,999 for five bucks. . . . But if you had a genetically encoded counter that counted up to 256, you could put it into a cell."
Once inside, the device could track the cell's age and how many times it divides. "I could hook it up to a suicide mechanism, and any cell that divides more than 200 times, it would say, 'Kill it, it's forming a tumour . . .' "I don't think I'm ever going to put silicon inside every cell of my body."
Whether synthetic biology's efforts succeed or fail, he says, researchers will end up understanding more than ever before about the components needed to build life.
A frisson of excitement runs through the U of T lab. It is a Friday morning in November, there has been growth overnight, and everyone is relieved. They will be able to write on their biological Etch A Sketch after all.
The part that would allow them to erase (in true Etch A Sketch form) didn't take. But still, as Prof. Davies says, "there may be something to show at the presentation."
They return the cells to the incubator while Hannah Fong works out the correct sugar formula to use as ink on their bacterial screen. But there is little time to grow a large plate of bugs or to see if the writing would actually be visible.
Prof. Davies suggests that "Hi Mom" be the message, but there may not be enough room. They decide to stick to straight-line letters, and go with "HI."
By 4:30 that afternoon, there is still nothing visible but, able to wait no longer, they pile into a rented Toyota Camry for the road trip to Boston. At 3:30 the next morning, they roll into their hotel and everyone checks in for a few hours' sleep -- everyone, that is, but Mr. Nazareth.
School work has left little time for him to practise his presentation. He had hoped to rehearse on the way down, but reading in the car made him nauseous. So here he is, before dawn, going over his lines in the hotel stairwell.
At 8 a.m., they lay eyes on MIT for the first time. Mr. Scott, the mathematician, has flown in to meet them. And soon after the iGEM jamboree begins, they realize they're not alone -- the challenges of the work have proved universal.
"None of this year's projects appear to have advanced to the level of a fully working prototype," Prof. Davies says.
The Texas team once again advances its biological-photograph capabilities. Cambridge University offers a method to control cell movement. The team from Zurich presents a primitive version of the kind of living counting machine Prof. Endy envisions.
Against the odds, U of T wins four prizes, including the Nothing Can Stop Us award and another for the Best Advice Given in a Presentation.
That advice was offered by Mr. Nazareth, who has learned the lesson that while his field is racing ahead, speed is not the key. After all, it took nature eons to evolve life forms. So when it comes to building living things in the lab, the undergraduate told the gathering, "You can never allocate enough time for assembly."
Carolyn Abraham is The Globe and Mail's medical reporter.
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