Creation (16 page)

Clocks and Waves

The first forays into the creation of biological components occurred in 2000 with two papers in the journal
Nature
merrily breaching the barrier between biology and electronics. One was the creation of a biological clock in the bacteria
E. coli
. By piecing together three sections of DNA that naturally prevent other genes from producing their proteins, Michael Elowitz and Stanislas Leibler at Princeton University constructed a circuit that dictates not merely that a gene is
ON
or
OFF
, but is
ON
and
OFF
in an oscillating wave. The wave continues as each gene inverts the output of the next: one switches the next
OFF
, which switches the next
ON
, et cetera. Cells have a natural cycle as they reproduce and grow, but this circuit was unlinked to that. The output of the circuit was the expression of the gene for green fluorescent protein (GFP), and so the cells would glow green in slow waves.

The second component part was made by a team from Boston University led by Timothy Gardner. They built a genetic version of a type of electric component known as a bistable, or more evocatively, a flip-flop. These types of switches flip between two states, but each of these positions has a function. You push the button on a CD player to turn it on, and again to turn it off, but in the off position, the player is actually on standby, rather than cut off from the main supply. It has two states,
ON
and
ON STANDBY
, and flipping between the two is fully reversible.

Both these engineering projects adopted not only the language of life to build unnatural gadgets, but also the language of electronics to convey the functional design ethos these gadgets were bringing to biology. They were given names that could be straight out of the lexicon of electronics (or possibly science fiction): the glowing wave circuit gained a new electronics-sounding moniker, the repressilator; the bistable flip-flop device borrowed from an existing electrical part, a toggle switch.

These two inventions are rightly seen as the first synthetic biology parts: microscopic tools designed to enact a program but built from DNA. The synthetic biology workshop opened with these first parts built, and what followed was a cascade of other mechanisms, tools, parts, and pieces, all made out of DNA, taken, modified, fused, and redesigned from evolution's toolbox. In the last ten years we have gone from the species-barrier-breaking insertions of genetic engineering to an ever-expanding toolbox packed with widgets. There are now switches, pulse generators, timers, oscillators, counters, and logic calculators. The combinations of these and many other components have extended our control of living systems to genes, protein function, cell growth and reproduction, metabolism, and the ways cells talk to one another.

Less obviously practical than the cancer assassin program, but no less complicated, was a circuit built in 2009 by Jeff Hasty and his colleagues at the University of California. Timekeeping cycles are fundamental to most living things. They are known as circadian rhythms and determine all sorts of patterns of behavior in relation to the flow of time through our lives, such as the passing of day and night. We rely on cells to regulate our own metabolisms, such as in the rhythmic release of insulin or in the orchestration of sleep cycles, both of which are disrupted in people who regularly work night shifts. How these timers work is only partially understood, but they use similar mechanisms to the artificial biological clocks built in these synthetic circuits. Hasty wanted to design synthetic circuits that created a regular pulse of activity, like the ticking of a clock. These so-called oscillators work as cellular timekeepers, determined by the careful design of a loop of genetic activity within a bacteria, three genes following a circular set of instructions. Imagine three friends standing on the corners of a triangle, sixty feet apart, all facing inward. Each has a chair but only stands if the friend to his or her right is seated. When the first stands, the second sits and the third stands. The first then sits, the second stands, and so on. This continuous response is called a negative feedback loop, and the reaction time of the three creates a clock of activity. It won't work with four people, as the flow will end as the fourth person will be seated after one round, and that will not prompt the first to sit down again.

As it is, this circuit will continue as long as the people can manage it. There is no output, though. Now imagine that, as well as standing and sitting, the first person alone also has to sing a note, but only while standing. As long as the game continues along those rules, he or she will be singing every other complete circuit. If you close your eyes and only observe the output, you would hear a regular burst of song. This is a basic biological oscillator.

In a synthetic biology oscillator, when gene A is active, it shuts down gene B, which activates gene C, which completes the circuit by shutting down gene A. The program is constructed from those three component parts—genes and their activation sequences—and imported into the guts of a bacteria. In the version involving people, the frequency of the burst of song is determined by the speed at which each of the friends reacts to his or her neighbor. In the cell, it is the speed at which the protein is produced. Gene A is translated into a working protein, which binds to the
ON/OFF
switch for Gene B, and so on, but each step takes time. The clock function is a result of this delay. As with the note being sung, the output of the circuit in bacteria might be the expression of a fluorescent protein, which will slowly come on and off with a regular pulse. In synthetic biology, the aim is to elicit control from these DNA circuits, so the ability to fine-tune is desirable. Adding other loops and other mechanisms can introduce further control to the frequency and strength of the output, adding to the complexity of the logic.

One limitation of this basic biological clock is that the simple oscillator circuit is self-contained. In clock terms, this would be as if all wristwatches kept time perfectly, but everyone's was set to a different time. Time is most useful as a commodity only if we all synchronize our watches; otherwise, watching
The
Ten O'Clock News
would be a lottery. In bacteria, engineering a single cell to produce a regular pulse is one thing, but to turn that pulse into a synchronized wave in a population of bacteria is entirely more difficult.
E. coli
reproduce every twenty minutes or so; it's a busy crowd to exert military control over.

In Jeff Hasty's program, though, the circuit also sends out a signal to all neighbors, which syncs the beginning of the loop. Rather than three people in a triangle, it becomes a wave in a football stadium. You still stand when your neighbor sits, but it happens in banks of people at the same time. The pulse, the output of a hearty cheer, is bellowed not by one person but by thousands. The bacteria, speeded up in time-lapse video, pulse with glowing green, like a luminous ripple. Anyone who has ever been part of a decent wave will know that it's impressive enough. But the size of these bacterial populations is far greater than any stadium capacity. The act of inducing perfect synchronicity in these synthetic bacteria is the equivalent of making every traffic light in the world turn green at exactly the same time.

That's a neat trick indeed, and shows the level of control these new synthetic circuits give us. But it also has valuable potential as a tool for synchronizing the output of a population of synthetic cells.

Insulin's job is to tell the body how and when to process carbohydrates and fats after you've eaten some roast potatoes. Glucose is the fuel that powers cells (and by extension, organisms), but the concentration of this simple sugar in your blood is a delicate balance: too much or too little is deadly poisonous. We take in glucose directly in our diets, and other foodstuffs get converted to glucose in our muscles and liver where it is stored in other forms such as fat. We have evolved all sorts of mechanisms and biological cheat sheets to make sure our cells are fueled by a constant supply of glucose, regardless of whether you have just scoffed a chocolate bar or not eaten for hours. Insulin is an integral hormone to maintaining glucose levels and it does so by instructing cells in various tissues to collect glucose from the bloodstream. In doing so, glucose levels in the blood are reduced, and the production of glucose from stored fat is turned off. The production of insulin is prompted by high blood glucose, and shuts down when it reaches a threshold, so is in itself part of a feedback loop. Importantly, the curiousness of insulin production in the body is that, even when we are at rest, the level of insulin is not still. It oscillates gently at a rate of between three to six minutes regardless of blood glucose, like an idling car. When this process malfunctions, diabetes is the result. A hypothetical, synthetic circuit with the ability to oscillate in its production of insulin (or anything) in a whole population of cells, rather than in an individual one, would be of enormous benefit in mimicking the natural pulse and ultimately be a potential therapy for diabetes patients.

As with Ron Weiss's cancer assassin program, these engineered biological circuits are not nearly ready for clinical use. That program is carried in a modified virus, unable to reproduce and unable to enact its software without the machinery of existing living cells. The virus has to infect the cell before it can enact its diagnosis and sentence. Most of the circuits of synthetic biology are integrated into the genomes of bacteria, but as of now we are unable to test synthetic circuitry in humans. A long time before we reach that point, there is the not insignificant problem of delivering the software and its packaging to the place where it's needed. The bacteria themselves are merely vessels that carry the software and provide the mechanics of producing that circuit's output. Humans are covered in, and full of, bacteria, which are much smaller than human cells, and so we can carry maybe ten times more bacterial cells than our own. Almost all are benign or beneficial, especially in our guts, where billions of bacteria—our microbiome—provide digestive functions we don't inherently possess. However, our bodies are good at detecting and destroying invasive species, so genetically enhanced bacteria would need to be undetectable to the immune system, coated in a molecular invisibility cloak in such a way that the legions of intruder alarm cells patrolling our bodies simply fail to identify the synthetic cell. Yet our immune systems have had billions of years to evolve the ability to detect foreign invaders, and free-roaming synthetic bacteria would be policed harshly. An alternative could be to package the bacteria and hide them from the immune system. Unlikely though it sounds, NASA is working on precisely that problem.

Under the Skin

NASA's base at Ames resembles a archetypal small American town, just off at Californian freeway, with wide roads, grassy squares, faux stucco buildings, and acres of blue, blue sky. Except that in between these blocks of normality, there are colossal paeans to the grandstanding 1950s optimism that science would deliver the future. The biggest wind tunnel in the world occupies several blocks, its interior roomy enough to accommodate a full-size airplane. The air intake is a giant black rectangular grille so large that it's difficult to gauge its colossal scale, until I spy some NASA scientists playing street hockey, dwarfed at its base. Four blocks to the north is a gargantuan hangar built in the 1930s to house the building of dirigibles, short-lived rigid airships. In a clean room (i.e., a room free of dust and dirt) around the corner, the next Moon-bound spaceship, LADEE, hovers as its carbon dioxide–based levitating propulsion engine is tested by technicians.

Naturally, NASA exists to explore space. On the corner of a spacious crossroads there is a building whose concrete facade is pockmarked with casts from meteorite impacts. Inside, the researchers in NASA's synthetic biology program are using the microscopically small to solve some of the biggest problems that lie between us and our desire to explore strange new worlds.

The sun beats down at Ames; while being the bringer of energy and life on Earth, it is far less charitable off-world. Sporadically and unpredictably, our star will blast out a shot of extremely high-energy particles with enough clout to disrupt power supplies on Earth. Similarly, other stars in the universe eject a continuous bombardment of high-energy particles from deep space that bathes the galaxy in radiation. Beyond the protective blanket of our atmosphere solar flares and galactic cosmic rays combine to be one of the most restrictive dangers for human space exploration. Radiation, including in these interstellar forms, has the effect of slicing up DNA randomly. Often that is not a problem: DNA repair is a major industry within our cells, with legions of copyediting proteins beavering away to make sure that errors in the code, or mismatches in the two strands of the double helix, are identified and patched up. Occasionally, the damage may occur in one of the many genes that control cell division; if that happens in a gene whose purpose is to instruct a cell to stop duplicating itself, then you have the beginnings of a cancer—uncontrolled and unrestricted cellular growth. Conversely, breaking up the many genes necessary for the cell's continued existence can result in the inception of a natural cell suicide program.
⁴
Unrestrained cell death or cell growth is equally bad for an organism's well-being. We are constantly exposed to damaging radiation, but mostly in small doses or infrequently. This is why, when you have an X-ray in a hospital, the technician stands behind a protective screen. It's a rare event for you, but unshielded, technicians are exposed dozens of times every day, with potentially deadly consequences. In outer space, the exposure is continuous.

In 2005, the U.S. Federal Aviation Administration set off on a virtual round-trip to Mars, including a fourteen-month stopover on the red planet. They calculated the amount of exposure to space radiation astronauts would receive, and deduced that astronauts would suffer a significantly increased lifetime risk of cancer (as well as a host of other conditions, including cataracts and sterility) as a result of exposure to cosmic rays and a bout of radiation from a solar flare. The safety limit was a journey of around fifty million miles—just short of halfway to the sun. Shielding on the spacecraft prevents radiation exposure to humans, but it is heavy, and weight is a critical issue when calculating the propulsion and cost of lifting off of our planet. The hostility of space means that our biology is just as limiting as our engineering when it comes to exploring the heavens.