Creation (17 page)

Our immune systems do have built-in defenses that counter the effects of radiation damage. We have these mechanisms in place to deal with the much weaker radiation—ultraviolet—that causes sunburn and other forms of DNA damage. When detected, the severed DNA switches on genes that produce small molecules called cytokines, which flit from cell to cell, triggering cascades of repair programs. But they have limited reach, especially in response to prolonged exposure to damaging radiation, and this is why cytokine therapies are sometimes used to enhance the body's natural response.

David Loftus and his team at NASA Ames are planning a designed synthetic program in which the input is a detection system for radiation or DNA damage, and the output is the controlled release of cytokines. This program is different from the cancer assassin in that the output is a molecule that stimulates the body's own natural immune system. Carrying the program in a virus that will infect a cell will not work; the production needs to be self-contained. Therefore, a bacteria is the most appropriate synthetic cellular manufactory. The question is how to introduce a bacteria safely into humans without provoking an immune response.

The circuit is not yet built, and this construction will face all of the same problems as any synthetic biology project. But Loftus and his team have made stunning advances in the construction of the capsule to contain the cells. As if the circuitry of synthetic biology was not impressive enough, the biocapsule is made from carbon nanofibers. A minuscule mold sits on top of a hypodermic needle, which is attached to a pump. This is submerged into a suspension containing the carbon nanofibers; they are literally sucked onto the mold to form a capsule. This tiny pellet is half a centimeter long and half a millimeter wide, not much bigger than this letter I. Although the capsule is tiny, bacteria are much smaller, so it is large enough to imprison tens of thousands of them.

It is also biologically neutral, which means the carbon nanofibers will not provoke an immune response and will cause no harm to the astronaut. But with serendipitous grace they bunch together in a porous tangled mesh, like a sheaf of frozen worms, visible only under electron microscopy. The gaps running through this mesh are too small to allow bacteria through, but big enough to let small molecules, such as the cytokines that tackle radiation damage, seep out. The idea is simple enough. The synthetic bacteria cells are placed within the capsule, and the capsule is implanted under the skin of the astronauts. The cells contain a program that produces and releases cytokines upon exposure to solar and cosmic radiation. It requires no diagnosis or intervention, and, elegantly, the treatment for the sickness is prompted by its cause.

Imagine this technology applied to less exotic practical human problems: a synthetic cellular circuit permanently implanted under the skin to deliver the treatment to a disease without the patient ever knowing. The potential is breathtaking. Diabetes sufferers stand out as being obvious benefactors. The cells in the pancreas that produce insulin could effectively be replaced with synthetic organisms that serve exactly the same purpose. Instead of injecting insulin, a synthetic circuit borne by bacteria hidden in a biocapsule shell would produce insulin according to the body's fluctuating needs. In principle, the patient would never even be aware that this process was going on.

As ever with brand-new, untested inventions, this exact mechanism may yet come to nothing. It may turn out to be impractical or too expensive to be of general use. At best, this system is a decade away: the capsule is still being developed, and the synthetic circuits themselves are years from being tested in animals, therefore years from being tested in humans. Yet this shows how the need for practical solutions to complex problems typifies the renaissance nature of synthetic biology.

Reality Check

What I've described above is the promise and the hope of this new engineering project. I've outlined some of the highlights of ambition and success of this emerging endeavor. Currently, there aren't that many more, though the volume of synthetic biology publications is rapidly increasing. It is easy to get swept up in the hype as the rigor of the lab is translated into terms aimed at nonexperts designed to inform, enthuse, or generate criticism. However, the comparison with electrical engineering is one that has been made by synthetic biologists themselves, in an attempt to standardize the parts of DNA into component parts in order to construct living machines.

Yet the reality is that referring to living things as machines glosses over the facts of life. Cells and organisms are machines whose complexity is many orders of magnitude greater than an engine, a production line, or even a computer. Engineering, like evolution, is an iterative process. The incomprehensibly deep time since the origin of life on Earth has made the number of tests, failures, rebuilds, and further tests undergone by the mechanisms of life an impossibly large number. Every organism that has ever existed was an incarnation in a perpetual test of engineering function, unguided and ruthless: will it live, and live to reproduce itself? This is true, naturally, of any species or organism, but the real selection under scrutiny in evolution is individual genes, the functional natural component parts of living things. These work in consort, in networks, in cascades, and in meandering dynamic pathways. The complexity of a living organism has billions of years of successful testing behind it, and that means that to simplify or design genetic circuits into simple (or even complicated) tools is tricky. Biotechnology expert Rob Carlson told
Nature
in 2009 that “there are very few molecular operations that you understand in the way that you understand a wrench or a screwdriver or a transistor.”

The test of design in engineering is “Does it work?” and, more precisely, “Does it work as we designed it to?” In this new discipline the answer for many of the several thousand parts and circuits currently available is a simple no. The complexity of biology in cells generates noise—unpredictable variation that masks or subverts the intended output. The so-called repressilator that marked the beginning of synthetic biology in 2001 by making bacteria blink glowing green worked impressively well. But the surprise was that not all cells worked the same. The pulse of the glow was nowhere near consistent: some cells were brighter than others, some were slower, and some skipped a beat. The reasons why are not impossible to understand, but complexity breeds inscrutability, and that makes the reductionist ethos of engineering harder to fulfill. Once again, the analogy with electrical engineering even holds true here. We already make digital logic boards so dense and so filled with software that we don't fully understand their behaviors. This is why computers crash. These systems are built for a purpose and are tested and retested to make sure they succeed at the tasks we design them for. Still, that does not mean that we know or predict all potential behaviors that they may express. In computer hardware design, failure analysis is critical, just as it has been in human genetics for a century. We have always discovered genes and their functions only after observing them fail, that is, when they cause disease. Well-designed hardware is built to cope with the unpredicted and unpredictable noise that inscrutable complexity may host.

The problems caused by mutated genes that result in disease have a clear origin if you know where and how to look for it. In the wishfully simplified programs of synthetic biology, it is the unforced errors that are problematic. Decoding the obvious faulty mechanisms of diseases and designing successful programs are certainly the aims of genetics and synthetic biology. Yet understanding noise and catering to it remains a puzzling obstacle. Because of this, the parts, the circuits, and the living hosts make the dream of a standardized DNA construction kit an unrealized one as of now. However, this is a young field, immature and full of hope. Typically insightful, Isaac Asimov, the doyen of twentieth-century science fiction, noted that the best moments in science are not when you exclaim “Eureka!” but when you say, “Hmmm, that's interesting.” That noise, the fact that these programs don't quite work as designed, is definitely a problem—but a most interesting one.

Nevertheless, parallels with computing are striking. The legends of the computer industry's roots describe future billionaires like Steve Jobs and Bill Gates tinkering with electronics in their garages, playing with components and code to make better hardware and better software. The results were Apple and Microsoft, a computer on every desktop, the Internet, Google, and a smartphone in every pocket.

Whereas political revolutions tend to be defined by events, such as the storming of the Bastille or the execution of a head of state, the cultural revolution of computing was not triggered by any single act. Similarly, workers in nineteenth-century Europe were aware that newfangled technologies such as looms and spinning jennies were driving significant changes to their working lives, and those changes were happening at a fast pace. But the aggregation of that change and its significance were unknown at the time, and the term
industrial revolution
was introduced much later. The practitioners of synthetic biology are creating in a way that is novel for biology and for science, all within one decade. This manipulation of four billion years of evolution, specifically for the creation of unnatural biological tools, is potentially a revolution, one that is occurring right now.

Richard Feynman's aphorism is crucial: to understand something you must first be able to build it. The terms, the language used, and the techniques are all borrowed from the problem-solving ethos of engineers, a reductionist view of function through design. The extension of natural processes to serve humankind's desires is not new, but has rarely been approached with such a clear sense of built-in construction. Though the founders of synthetic biology had electrical engineering in mind, the metaphor that has stuck most is a well-known toy. Just like DNA, a Lego brick is universally adaptable, designed to fit with other pieces from other sets. Similarly, synthetic biologists have tried to make the individual components of their circuits interchangeable, so that construction of novel circuits is not hindered by the natural noise of biology. With that in mind, the spirit of invention, engineering, and creativity have been built into synthetic biology in a unique way. Yet as this revolution unfolds, questions of ownership, legality, and ethics press urgently upon us.

Remix and Revolution

“Rien ne se perd, rien ne se crée, tout se transforme.”

Antoine-Laurent Lavoisier

E
volution is the most creative enterprise that has ever existed. Nothing comes close to the diversity, sophistication, and beauty that have transpired at the hands of DNA and natural selection. At its heart are two words that carry a potential derogatory sense:
imperfect copying
. In another sense, evolution is the ultimate exemplar of that maxim made famous by Isaac Newton—“If I have seen further it was by standing on the shoulders of giants”—which neatly describes the derivative nature of creativity while exemplifying it, as he was borrowing and adapting the same idea from twelfth-century philosopher Bernard of Chartres, who was in turn probably referring to ancient Greek versions of the same idea. The French chemist Antoine-Laurent Lavoisier's version in the epigraph above was a comment on the nature of matter, but works equally well for energy, biology, and ideas: “Nothing is lost, nothing is created, everything is transformed.”

It's easy to apply a similar principle to culture, that while there may be nothing completely new under the sun, the creation of new ideas is still born of copying, adapting, and transforming what has come before. In music, for example, it's not too difficult to trace an evolutionary path of influence through several centuries of creativity, from Bach to Haydn to Mozart to Beethoven to Mendelssohn (or, in modern times, from Chuck Berry to the Beatles to Bowie to punk to Joy Division to the Smiths to the Stone Roses and on and on).

The nature of copying in music changed in the 1960s when a new method of musical creation emerged that was unlike anything that had come before. Technology enabled musicians not merely to copy and modify what had come before, but to directly borrow, co-opt, and lift it. The sampler allowed music producers to take the drums from one existing track, the horn section from another track, and the vocals from a third and mix them together with any other elements to create a new sound.
¹
As a technique for creating new sounds, sampling really took off on the streets of New York with the emerging hip-hop scene (then referred to as rap) of the 1970s. DJs in the Bronx would simultaneously entertain crowds, pay homage to their musical forefathers, and create radical new sounds by mixing records together on twin turntables. They would take the beat or riff from one record and drop rhythm or lyrics on top from another, often using soul records as their licks. In live performances at clubs, and later in recordings, they were not playing new music but creating it by adapting and remixing existing sounds. By the early 1980s, sampling machines were being used to record short extracts from a record so that they could be integrated into a new tune. It could be slowed down, speeded up, looped, or stretched to help create a brand-new sound that was derived from and built on the shoulders of previous works.

Synthetic biology is remixing. The ethos of this emergent scene is one of unprecedented and unbridled creativity that is a remix culture. DJs did not have to be virtuoso players of specific instruments in order to create new sounds. In synthetic biology, the creators do not need to be geneticists, DNA technicians, or even biologists to build new organisms. The principle is simply to create.

Since inception many of the pioneers of synthetic biology have strived to build a movement of open, democratic science, where there is a free exchange of ideas, techniques, and materials. If year zero of this new industrial revolution was the repressilator and the toggle switch in 2001, the first big inroads were made a couple of years later. The transition from tinkering in labs to a movement in science occurred during 2003 and 2004, with the emergence of two phenomena that became emblematic of the spirit of synthetic biology.

One was the founding of the Registry of Standard Biological Parts. For all the talk about the wonder of the interchangeable genetic alphabet, it takes a lot of code to make a life-form. That means there is a lot to play around with, and more important, to get wrong when remixing your code. Ironically, for something to be open and free for everyone to use, it needs to be codified and standardized. Think how annoying it is that electrical plugs are different in different countries, or phone chargers change from one model to the next. The language of music is universal, but you need a whole battery of adapters and plugs to perform it in different countries. Yet nuts and bolts are standardized, so that thread size or screw dimensions don't have to be reinvented every time you want to assemble a piece of furniture.

Transfer that to the unlimited amount of coded information contained in the new circuits of synthetic biological components. Dozens, and then hundreds, of labs started building their own gadgets and devices, all of which only work in circuits built into genomes of living things (or, in some cases, near-living viruses). Without standardization, useful sharing is hamstrung. Thus, in 2003, the BioBrick project was conceived by Drew Endy at Stanford, Tom Knight (then at MIT), and Christopher Voigt at University of California, San Francisco (UCSF). The BioBrick part is a useful and simplified way of plugging in bits and components so that everyone who signs up doesn't have to redesign each idea and each part for him- or herself. BioBrick parts are to genetics what the sampler is to music—a system for freeing up the elements of the rich biological past and the ingenuity of others' designs in order to foster extreme forms of creativity by standardizing the assembly of DNA components so that they don't need to be redesigned every time. This is where the comparison with Lego holds some weight. Lego bricks are beautifully designed to connect with any other Lego brick; there is a universal fit to the pieces, and they can be assembled regardless of their original kit. At the time of this writing, the BioBrick catalog contains more than ten thousand parts. Each one is a piece of DNA and is delivered in the mail as a dot on some blotting paper. Drop it into a solution, and the DNA floats off the paper, ready for assembly. Some BioBrick parts are genes, some are regulatory instructions, and some are combinations of both, already assembled to be integrated into new circuits. All have been standardized so they can be knitted together for new creations.

The other transformation that occurred at this time was the inception of the International Genetically Engineered Machine (iGEM) competition in 2003 and 2004. Each year, teams of undergraduate students devise a problem and design and build their proposed solution using only the components available in the Registry of Standard Biological Parts. Students compete to get into their college teams and spend weeks researching, designing, and enacting their solutions to their chosen problems. It is a talent competition for the brainy, and the excitement is palpable. Each team receives a kit consisting of a thousand BioBricks from the registry.

After rounds of regional selection, the finalists meet up at MIT in November for the annual jamboree. The teams show off and celebrate their creations, and synthetic biology pioneers and leaders decide a range of prizes. The grand prize is emblematic of the construction mindset: an oversize aluminum Lego brick.
²

The democratic principle is built into the registry and the iGEM competition, too. The resources are all free, but the expectation is that all players will contribute. The registry website declares that users “get some, give some.” All teams compile their notes and projects, successes and failures on open wiki pages designed to encourage sharing and standing on the shoulders of peers.

Although few of the iGEM projects have come to fruition yet, there is a kind of vibrancy about this endeavor that is unlike any science meeting I have seen before. Many undergraduate students do summer projects in their tutors' laboratories, where they often do menial or slavish jobs, part of the grind of data production that science is based on, and in so doing gain experience of the reality of lab life.
³
At the same time, iGEM teams create new and potentially important projects and solutions with a zest that is thrilling. They spend their summers inventing solutions to global problems. They are combining brand-new, often untested tools, and in so doing are building new ones using the most advanced biotechnology available. They then present their work to the judging panel, which is made up of a hefty proportion of the most significant synthetic biologists working today.

Hello World

In 2004, a striking entry came from a team-up between the University of Texas at Austin and UCSF. They designed a circuit and successfully integrated it into bacteria, which then acted as a photographic plate. One component was a light-sensitive protein, which would perform its function when stimulated by a beam of light. They linked this protein to a standard pigment-producing gene called lacZ. When they grew the synthetic bacteria on a flat clear plate and shone an image onto it, the bacteria processed the light and the dark at the resolution of one hundred megapixels per square inch. The work was published in the journal
Nature
, and the components developed into a new synthetic biology device: an edge detector. The projected image was a text message, which appropriately enough announced the arrival of this new field, but was also an in-joke displaying synthetic biology's computing roots. The phrase is the output of a standard test that programmers use to check that their coding language is functioning correctly. It simply read, “Hello World.”

The grand prize winners in 2009 were from Cambridge University: they extended the use of green fluorescent proteins (GFP) and designed a system for bacteria to produce multicolored dyes as a tunable detection tool. These are known as biosensors; they already exist for such purposes as detecting blood glucose levels. However, every biosensor so far has had to be designed from scratch and built specifically to detect just one target. The Cambridge iGEM team aimed to build a generic biosensor that could be tailored to multiple uses. For example, the engineered bacteria could be tuned and used as a detector of a specific toxic chemical in the environment, and produce a color-coded pigment in response to its concentration. They also eschewed the use of GFP, as this requires a fluorescence kit to see it; their aim was to make a biosensor that could be seen with the naked eye. The parts of the circuit are the sensor, a sensitivity tuner, and the pigment generator, six of which are new parts, and were submitted back into the registry for others to use.

Washington University took the grand prize in 2011 with a circuit that produces forms of fossil fuels. The runners-up, from Imperial College London, attempted to fight desertification—the gradual erosion of fertile ground into agriculturally and therefore economically useless land. By 2025, some estimates predict that as much as two-thirds of Africa's arable land will be rendered barren by this phenomenon. The Imperial team has engineered genetic circuits in cells that will nurture roots, which in turn shields fertile topsoil from the eroding elements. Seeds are coated in the synthetic bacteria, and once they germinate, the cells inveigle their way into the infant roots; the program they bear produces the plant hormone auxin, which accelerates growth into the topsoil.

The Slovenian national team appears to win the iGEM grand prize in even-numbered years, claiming the prize brick in 2006, 2008, and most recently in 2010, when they eschewed the language of DNA altogether. Instead of manipulating the code embedded in the
A, T, C,
and
G
bases of DNA to create a new function in translation, they used the simple fact that we can put those letters in a specific order to build a miniature production line. Living things are full of such production lines: one gene produces a protein that triggers another reaction, which triggers another gene, and so on. Unlike the ordered machinery of a factory, however, the inside of a cell is a busy milieu, with all the code and proteins effectively free-floating in the gooey plasma. Real factories would be disastrously unproductive if each part was allowed to randomly drift to the next step on the production line. Slovenia's team designed a sequence of DNA that organized the unsecured mess into a neat line by using DNA as a production-line scaffold. Instead of having proteins free-floating in the cell, they figured that they could tether them to a unique sequence of DNA. Many proteins bind to DNA anyway, so much is known about how to get a protein to clamp onto a specific sequence of DNA. With the right stretch of DNA each protein in a pathway can be pulled out of the cellular soup and tethered sequentially, resulting in a biological production line. The primary aim is that this scaffold will radically increase the efficiency of synthetic biology pathways. It also opens up the possibility of more tightly controlled oscillator switches or other standardized devices in the synthetic biology tool kit.

Careful Packing

Almost all of the iGEM teams come from universities. As described in the previous chapter, though, NASA has been quick to identify synthetic biology as a discipline that will enable its continuing mission: to boldly go. One of the more fanciful ideas NASA is exploring is synthetic bacteria that make bricks.

This challenge was taken up by students in the iGEM competition in 2011. An hour from San Francisco, Stanford University collaborated with nearby NASA Ames as well as Brown University to figure out how synthetic biology could help us build colonies on other planets. Led by Lynn Rothschild, they have asked how synthetic circuits can contribute to terraforming. As mentioned earlier, the issue of weight is absolutely critical in space travel. It is estimated that the act of launching a thing beyond the earth's gravitational pull costs around $5,000 per pound. The mass of
Saturn V,
carrying all the modules to get the three crew members of Apollo 11 to the moon, enable them to have a stroll for a few hours, and come back home, was around 3,000 tons. The lunar module itself, the
Eagle
that landed, was 17 tons. Estimates of a round-trip to Mars include consumables and life support of 200 tons alone. Much like packing for vacations, minimizing what you take with you and using what you find when you get there is the best way to do it. In situ resource utilization (ISRU) is Nasa's official name for this method, but I prefer to call it careful packing.