I want to catch up with a couple of stories that are a couple of months old; they got lost in the crush of the holidays. The stories are from the frontiers of artificial life. You might have heard of a man called Craig Venter. He got exasperated with the slow pace of the federally funded effort to sequence the human genome, so he founded his own institute and private company to do it, using his own DNA, and he forced the government pace. In the end the race was declared an honorable but the competition greatly accelerated the process of genetic engineering.

Back in 1995, Venter led an effort to make the first genetic sequence of a living organism, and since then he’s been trying to make the first world’s artificial organism from scratch. In the journal Science he reports the replication of the genome of Mycoplasma genitalium, the species that was the subject of their original sequencing effort. It’s not actually life, but it’s getting very close. Venter is an interesting man. He has a fancy yacht called The Sorcerer II, and he goes on trips each year across the oceans, not just to enjoy himself, but also to sample the microbial diversity of the oceans and use it to fuel his research.

Sequencing an organism is one thing. Building it from scratch is entirely different. It’s a formidable task. Perhaps most noteworthy about what he’s done is that the starting point was not the raw nucleotides, or the chemical layers that DNA is made of, but a set of preassembled cassettes of DNA that the team had ordered from commercial suppliers. This means that almost anyone with a reasonably well-equipped genetics lab could do what they did. Mycoplasma genitalium’s genome is a single circular chromosome that’s 580,076 base pair letters long and contains 485 protein-coating genes. The team divided it on paper into a hundred and one units. Those are the cassettes, each containing four or five genes.

They also took the precaution of editing one gene in particular so that it would not work. The gene in question is crucial to the organism’s ability to stick to mammal cells and thus become infectious. Disrupting it forestalled the risk of anything too nasty happening. You can think of this as the kill gene. All that remains to create what most researchers in the field would be willing to recognize as an artificial organism is to insert such a chromosome into a bacterial cell that has had its own chromosome removed. At the moment no one is clever enough to make all the cellular machinery that translates genes into the stuff of life, so they use this shortcut. But if the newly constituted cell were able to grow and reproduce, the nature of its progeny would be dictated by the implanted chromosome, and they would have made artificial life.

Craig Venter wants to understand how life works. One way to do this is to discover what he calls the minimal genome. This is a platonic idea of life that would contain only the genes necessary for survival and reproduction, and it would shed light on the nature of what’s called LUCA, the last universal common ancestor of life on Earth. In practice that ideal is very difficult to reach since many genes cover for each other. Venter knows that about one hundred of Mycoplasma genitalium’s five hundred genes could be eliminated individually without killing it. But eliminate all of them and it dies. Assembling “mix and match” genomes with a lot of different combinations of cassettes that each contain a handful of genes might be the way to figure out what’s going on.

Venter also has practical goals. He hopes to use modified bacteria to make fuels. Natural bugs can turn out both hydrogen and methane. There’s talk of modifying them to produce high value liquid fuel for jets for example, and there are other companies seeking to do the same thing. Either way the field of artificial life is going to be fueled by commercial objectives and not just simple curiosity.

The second part of this story is an event that took place at Berkeley at the end of last year. Fifty-six teams from twenty countries convened in an event called the Genetically Engineered Machine competition, popularly known as iGEM. The underlying goal of the competition is to figure out whether biological organisms and devices can be built from a collection of standard “off the shelf” parts just as someone might build a plane or a car from a kit. The people taking part were students, undergraduates. For them it’s an amazing opportunity to construct whatever they can imagine: living organisms that crank out biofuel, detect and remove pollutants, or even gauge the purity of olive oil.

These students are helping to build a new field called synthetic biology. To solve the problems of synthetic biology, iGEM has an annual competition, and they hope to develop a library of DNA snippets, each with a specific function, that have been engineered to snap together with other library parts like genetic legos. These are called biobricks, and they’re created according to strict guidelines so that each one is compatible with the others in the collection, which officially is the Register of Standard Biological Parts. The registry contains about 2000 different biobricks. With the biobricks, the competition’s founders want to eliminate much of the drudgery and unpredictability of genetic engineering and give students the freedom to do invent new biological functions.

Here’s an example. Austin Day, who’s a senior at UC Berkeley, holds up an IV bag filled up with a brown-red liquid resembling Bloody Mary mix. The unsavory concoction is Berkeley’s entry into the genetic engineering competition, a blood substitute called bactoblood made from modified bacteria. Spurred by a worldwide shortage of human blood for transfusions, the Berkeley team developed a synthetic version by tinkering with the DNA of the common bacterium E. coli. The young biologist and his team added a collection of genes to produce hemoglobin, the molecule in red blood cells that carries oxygen around our bodies. Then they inserted more genes to create BactoBlood suitable for freeze-drying. For safety, like Craig Venter, they installed a genetic kill switch to destroy the E. coli DNA, leaving essentially just a bag of hemoglobin. It’s a disease-free, self-replicating, and universally compatible substance. Not too bad for ten weeks of work by a group of undergraduates.

This is the future of biology, and Craig Venter says this: “The way biology is normally taught, it comes across as pretty dismal. You memorize a lot of facts, and then you regurgitate them to people.” He thinks that the approach of biobricks and involving undergraduates is the best way forward. The grand prize winner at the Berkeley competition was a first-time team from Beijing University. Yifan Yang, a fourth year biology major, built a bacterial assembly line in which a task is divided amongst genetically identical cells that have specialized but are able to cooperate. This division of labor mimics the human body, where genetically identical cells differentiate into heart, liver, and muscle cells for example. This is the divide-and-conquer strategy used by all multicellular organisms. Representing his team, Yang proudly hoisted iGEM’s trophy over his head: a gigantic silver Lego brick.

The greatest legacy of all from the students in this competition will be the new biobricks they build. The newly formed Biobricks Foundation is drafting a public license that will ensure that the DNA bricks are freely available to all researchers and that they remain open source. Eventually the library of biobricks will reach a critical mass that will enable people to build sophisticated organisms that can carry out useful functions. This is a very exciting prospect; it’s the maturation of the new field of synthetic biology. The biology that results might not look anything like terrestrial biology, and it could have capabilities undreamt of presently. Perhaps some of those capabilities already exist somewhere in the universe.

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We don’t know exactly how life started on Earth. It’s one of the biggest questions in science, and we may never know exactly because much of the evidence has been lost with time. But in the lab scientists are trying to create artificial life to show the possible pathways by which simple chemicals could have arranged themselves into the first cells. Around the world, a handful of bold scientists are trying to create life from scratch, and they’re getting closer. Experts expect an announcement within three to ten years from someone in the little known field of “wet” artificial life.

Listen to Mark Bedau, chief operating officer of a company called ProtoLife based in Venice, Italy. “It’s going to be a big deal, and everyone’s going to know about it,” he said. We’re talking about a technology that could change the world in pretty fundamental ways, in fact, in ways that are impossible to predict.” That first cell of synthetic life made from the basic chemicals in DNA might not seem like much to non-scientists. For one thing, you’ll need a microscope to see it.

Creating proto-cells does have the potential to shed new light on our place in the universe because it will remove one of the few fundamental mysteries about the creation of our role in the universe. Several scientists believe that man-made life forms will one day offer the potential for solving a variety of problems from fighting diseases, to locking up greenhouse gases, to eating toxic waste. Bedau figures there are three major hurdles to creating synthetic life. First, you need a container or membrane for the cell to keep bad molecules out, allow good ones in, and the ability to multiply. Each cell is like a tiny chemical factory. Although the nutrients necessary for life exist in sea water or in a pond, they’re not concentrated sufficiently for the vital chemical reactions to take place with sufficient speed.

Second, you need a genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes. That’s tricky because this has to occur naturally. Scientists don’t believe that an intelligent designer created the genetic system. They believe that it occurred by chance in a process of unguided evolution. In the lab, scientists will have to simulate this type of unguided process and yet produce an outcome that has function and form built into a biological system.

The third requirement is a metabolism that can extract raw materials from the environment as food and change it into energy. That’s key, although it’s not the hardest part actually, because in nature there are many ways that energy changes hands, and there is much raw available energy in the environment. So the energy requirement for life is easy to meet, and life on Earth has found many different ways to harness energy from the environment.

One of the leaders in this field, Jack Szostak, who works at the Harvard Medical School, predicts that within the next six months scientists will report evidence of success in the first step, creating a cell membrane, since that is, as he puts it “Not a big problem.” Scientists are using fatty acids in that effort, and in fact Szostak, who’s usually modest about his efforts, is perhaps the world leader in creating a cell in the laboratory. He’s been working more than ten years at it, and he’s made major strides towards concentrating the nutrients in naturally occurring containers or vesicles.

Szostak’s also optimistic about the next step, getting nucleotides, the building blocks of DNA, to form a working genetic system. His idea is that once the container is made, if scientists add nucleotides in the right proportions, then Darwinian evolution could simply take over. The question is how did nature add nucleotides in those right proportions? Perhaps if it did happen by chance and Darwinian evolution takes over, the correct proportions of nucleotides would come to dominate all the other proportions, thereby explaining how life came to be the way it is. Szostak says, “We aren’t smart enough to design these things. We let evolution do the hard work, and then we figure out what happens.”

In Gainesville, Florida, Steve Benner, a biological chemist at the Foundation for Applied Molecular Evolution, is attacking that problem by going outside of natural genetics. Normal DNA consists of four bases, adenine, cytosine, guanine, and thymine, known as A, C, G, and T, molecules that spell out the genetic code in pairs. Benner is now trying to add eight new bases to the genetic alphabet. Bedau says there are legitimate worries about creating life that could run amok, but there are ways of addressing it, and it will be a very long time before that is a problem. As he says, “When these things are created, they are going to be so weak. It’ll be a huge achievement if you can keep them alive for an hour in the lab. But the idea of them getting out and taking over, never in our imagination could this happen.”

It’s a good cautionary note to end on because many things that couldn’t occur in the imagination of scientists actually do end up happening. So as artificial life moves from hypothesis to reality, scientists will have enormous pressure to be cautious about what happens with their creations.

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Back in the mid-1970s a group of MIT undergraduates walked into the office of a mid-level NASA administrator. They managed to talk their way into a meeting with a pretty high level NASA official with a very weird idea. They wanted to send a set of robotic ants to the planet Mars. The ants would spill out of a lander and, connected by a neural net, would explore the surface, roaming over its terrain. These students excitedly explained how with a neural net and a lot of redundancy it didn’t matter if some of the ants fell into crevasses or their sensors failed to work. Overall, with hundreds or thousands of these little ants crawling over the surface a large amount of data would be contained and sent back to the spacecraft. It was a cheap and clever way of doing a mission.

I have a feeling they were laughed out of the office. Anyway, nothing came of it. At the time in the 1970s, computers were new, so the students were projecting towards a level of miniaturization and computer power that did not yet exist. However, now it does exist, and NASA is once again taking seriously the idea of using miniaturized probes rather than the large spacecraft we’re used to. These are called nanonauts. Engineers are now designing a new breed of planetary explorer. They’re tiny, shape shifting devices that can be carried on the wind like dust but can also communicate, fly in formation, and take scientific measurements. One name for them is smart dust and they may one day provide a unique method of studying locations interesting to astrobiology such as Mars and Venus.

This technology is already in use in various places. Geologists use smart motes or smart dust to go into volcanoes and places that are impossible for humans to reach. There is very strong evidence that security agencies are already using smart dust, perhaps even with tiny cameras onboard, to spy on us or for espionage purposes. It’s better not to think about that. Let’s just think about the scientific applications. Engineers at the University of Glasgow are designing some new nanobots, smart dust particles consisting of a computer chip about a millimeter in size surrounded by a polymer sheath that can be made to wrinkle or smooth out by applying a small voltage. Roughening the surface of the polymer means the drag on the smart dust particle increases, and it floats higher in the air. Conversely, smoothing out the surface causes the particle to sink. Simulations show that by switching between rough and smooth modes, the smart dust particles can gradually hop towards a target even in swirling winds. It’s a very clever idea.

Dr. John Barker from the University of Glasgow described applications of smart dust at the Royal Astronomical Society’s national meeting in Preston just a week ago. He said the concept of using smart dust swarms for planetary exploration has been talked about for some time, but this is the first time anyone has looked at how it could actually be achieved. Computer chips of the size and sophistication needed to make smart dust particles now exist, and scientists are looking through the range of polymers available to find one that matches a requirement for high deformation using minimum voltages.

Smart dust particles would use wireless networking to communicate with each other and form swarms. Dr. Barker explains, “We envisage that most of the particles can only talk to their nearest neighbors, but a few can communicate at much longer distances. In our simulations we’ve shown that to fly a swarm of fifty dust particles would organize them into a star formation, even in turbulent wind. The ability to fly in formation means the smart dust could form a phased array. Then it would be possible to process information between the distributed computer chips and collectively beam a signal back to an orbiting spacecraft.”

For the smart dust to be useful in planetary exploration, they would have to carry sensors. With current technology chemical sensors tend to be rather large for the sand grain-sized particles that would be carried in the thin Martian atmosphere. However, the atmosphere of Venus is much denser and could carry smart sensors up to a few centimeters in size. Dr. Barker says that scientific studies can be carried out on Venus using technology we have now, but with the speed of miniaturization, within ten years we should have chips that have components which are only a few nanometers across which means our smart particles would behave more like macromolecules diffusing through an atmosphere than dust grains. That means Mars is within reach too. This is a new and exciting way to do planetary exploration, and I’m sure we’ll be hearing more about it in the years to come.

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