What Is Life?
One
Birth of a Cell
MAY 2005. In a new industrial park at Porto Marghera, some four miles across the lagoon from Venice, an American physicist by the name of Norman Packard is staring at the enormous 30-inch-wide display screen of a Macintosh G5 computer. Floating around against a dark background is a dense assortment of red, green, and blue dots.
"Blue is water, the greens are hydrophobic molecules, which means they don't like water, and the reds are hydrophilic molecules, which do," Packard says.
The simulation begins with the dots spread out evenly across the screen in a relatively homogeneous mix. But then in the incremental time-steps of the particle dynamics program, a pattern emerges. The greens move toward one another and then converge and clump together, forming a spherical structure. The reds, meanwhile, follow the greens and arrange themselves on the outside of the mass, as if to protect it from intrusion. The result is a vesicle, a tiny bilayered fluid-filled sac. The vesicle has formed itself spontaneously, the result of a self-assembly process driven by Brownian motion (the random thermal movement of molecules in a fluid medium) and by various chemical reactions.
"We believe that this combination of chemical reactions and self-assembly is one of the crucial combinations that we need to understand to make these artificial cells," Packard says.
Artificial cells? Venice? A city of more than a hundred churches, miles of canals, and innumerable ancient palazzi, all of them suspended in time, a place where nothing fundamentally new has happened for hundreds of years? Somehow the location is strangely fitting. In its heyday, Venice was a world-class power and trading center as well as a realm of considerable intellectual freedom. The city was now and always had been home to a variety of creative spirits: composers, artists, and scientists, including Galileo. And its labyrinthine streets and alleys were bathed in the green waters of the Venetian lagoon—water just coincidentally being the medium in which, according to most theories, earthly life originally began. So why should it not begin again, here?
Norman Packard, for one, finds no incongruity in the prospect. Packard is the chairman, CEO, and scientific head of ProtoLife s.r.l., a Venetian start-up company located in Parco Vega, a technology park the regional government had created on the grounds of an old chemical factory.
"The city of Venice, but even more generally the region of Veneto, wants to diversify its portfolio of activities," Packard said. "Venice has this very strong component of tourism that dominates its economy in many ways, and so it's trying to create some economic diversity that can give a certain kind of life to the city, not related to tourism."
ProtoLife's business plan is founded on an attempt to start life over, to begin from the beginning. It's not their intention to redo Genesis, outdo Frankenstein, or to blaze a path of glory through one of the final frontiers of applied science—although, if they're successful, Packard and his crew will end up doing all those things. The company's motivation is far more prosaic, practical, and commercial: to create artificial cells. Made from scratch and called "protocells," they will be programmed to carry out useful tasks such as synthesizing vaccines and drugs, cleaning up toxic waste, scavenging excess CO2 from the atmosphere, and other such miracles, and earning the company a tidy profit in the process.
After watching his simulation run a few more times—"We've done between six and seven thousand runs so far," he says—Packard walks down a polished green marble hallway, turns right, unlocks a door, and enters the company's lab suite. This is the domain of ProtoLife's chief chemist, Martin Hanczyc, a postdoc Packard recently hired away from Jack Szostak's competing artificial cell project at Harvard. In fact, ProtoLife is only one of a half dozen or so scientific efforts bent on creating new life: in addition to the ProtoLife and Harvard projects, there are others at Rockefeller University in New York, the University of Nottingham in England, and the University of Osaka in Japan, among other places. All too obviously, creating life is an undertaking whose time has come.
Hanczyc's laboratory at ProtoLife boasts a full supply of chemical apparatus: the usual lab glassware, serological pipettes, fume hoods, scales, centrifuges, microscopes, plus heavier machinery. "This is one of our main analytic tools, a combination spectrophotometer and fluorometer," Packard says of a large piece of equipment. "You find this in practically every chemistry lab in Europe, so we have one too."
Hanczyc has been synthesizing and studying various types of vesicles, and today Packard wants to show me what they look like. Packard is a big man with shaggy blond hair, glasses, and a courtly manner. He has a slow and deliberate style of speech, which includes a precise, mellifluous Italian, courtesy of his wife, Grazia Peduzzi, who was born in Milan. He squints through a fluorescence microscope, adjusts the focus, and finally, there they are: the real-life correlates of the objects he had been simulating on the computer.
"Somewhat dried up," he says of the vesicles, which Hanczyc had prepared a while ago.
A vesicle is not a living thing. It's just a shell, a husk, the merest framework of the full artificial cell that's supposed to assemble itself on the premises and spring into life at some undefined point in the future. Nevertheless, what we have here on the microscope stage is something passably astonishing, slight and rudimentary though it might appear at first glance. For these filmy minute blobs are the first stirrings of an event that last took place billions of years ago: the genesis of life.
THE DREAM OF creating life has ancient roots in the human imagination. In Frankenstein, which Mary Shelley completed in 1817 at the age of nineteen, the scientist Victor Frankenstein cobbled together a creature from body parts he'd spirited away in the dead of night from graveyards, dissection rooms, and slaughterhouses. The resulting beast came to life when Dr. Frankenstein, by unspecified means, infused "a spark of being into the lifeless thing that lay at my feet."
Serious scientific attempts at infusing a "spark of life" into inanimate flesh go back at least to Luigi Galvani's discovery in 1771 that by applying electrical currents to a dissected frog's legs he could cause them to twitch as if alive. A hundred years later, in 1871, Darwin spoke of life as possibly having arisen "in some warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, &c., present."
As if following Darwin's recipe, when twentieth-century scientists approached the problem of understanding how life originally arose on earth, they attempted to re-create what they thought were the original prebiotic conditions. The canonical effort, now a cliché of twentieth-century science history, was the 1952 "Urey/Miller experiment," in which the chemists Harold Urey and Stanley Miller put ammonia, hydrogen, and methane inside a closed flask, circulated steam through this "atmosphere," and added bolts of "lightning" in the form of periodic electrical sparks. All they got for their trouble were some amino acids (building blocks of proteins) that were not in the mixture to begin with. The Urey/Miller experiment was once considered a very big deal, but it isn't by some of the protocell project's scientists: "We are not searching in the black and hoping that something happens," says the protocell researcher Uwe Tangen. "We're really trying to engineer these things."
Attempting to build an artificial cell is hardly a new idea in biology, but the specific protocell design Packard and Hanczyc are working on originated with Packard's longtime friend, the Los Alamos physicist Steen Rasmussen. Even as a boy in Denmark, Rasmussen liked to grapple with the big questions. He was by nature of a metaphysical turn of mind, and while still a kid he discussed subjects of cosmic import with his father, who was a bricklayer. Did the universe have a beginning—or an end? Where did it come from? Where was it going?
Later, in the 1980s, Rasmussen, together with Chris Langton, Norman Packard, and some others, became one of the founding fathers of the artificial life (ALife) movement. Launched at a Los Alamos workshop in 1987, artificial life was an attempt first to simulate and then actually to create a new life-form. Supposedly there was to be "soft," "wet," and "hard" artificial life, existing in the form of software, wet chemistry, and robotics, but the reality of the situation turned out to be quite different. "Most of the activities in the artificial life community have been with simulations," Rasmussen admits.
For a long time, that was true even of Rasmussen himself, who over the years had run countless computer simulations of various life-forms, modeling their possible self-assembly routes, evolutionary development pathways, and so on. But his abiding passion had always been to understand what life was and how it arose. At length he decided that the best way to understand life was to make some of it himself, ab initio.
In truth, he became obsessed with the idea. Although he lived in an adobe-style house surrounded by a number of natural life-forms, including his wife, Jenny, and three kids—not to mention horses, chickens, a parakeet, dog, and cat—he did most of his thinking at the Los Alamos lab and on his daily commute to and from, a route that took him past some of the most inhospitable, sun-blasted terrain imaginable: desiccated red cliffs, dry desert sands, and, occasionally, the whited bones of dead animals.
So daunting was the goal of creating new life, he realized, that only the simplest and most radically stripped-down design would have the remotest chance of actually working. Any given entity, in Rasmussen's view, had to have three main attributes in order to be considered alive: it had to take in nutrients and turn them into energy, meaning it had to have a metabolism; it had to reproduce itself; and its descendants had to be able to evolve by means of natural selection. A conventional biological cell, which did all that and more, was a masterpiece of complexity: it had an outer wall through which various essential substances were selectively transported in and out. It had an inner wall around the nucleus, which did the same. And both the nucleus and the cytoplasm surrounding it were brimming with all sorts of enzymes and other biochemicals, plus microstructures and organelles: the ribosomes, the mitochondria, the Golgi bodies, and all the rest. So very complex were even the simplest biological cells that it was a wonder they worked at all.
Rasmussen didn't want to get bogged down with all that incredible complication and detail, so he set about devising "the most lousy, simple, self-replicating, autonomous unit you can imagine," a cell so small it would be "the size of dust."
He got rid of the DNA, the nucleus, the organelles, and much of the rest of standard cell wetware. His protocell would be a minimal living entity, thousands of times smaller than a biological cell, and would be composed of three main structures: a container made of fatty acid molecules; a primitive metabolic system; and a new type of genetic material called PNA.
Fatty acids were also known as lipids, and their major attraction for Rasmussen was that "they make the containers for free. You put them in water and they make the containers. That's the state they want to be in. They want to join up and make these structures." The component molecules did this on account of their chemical polarity: one end of the molecule was hydrophobic (or water-avoiding), the other hydrophilic (or water-seeking), and so when placed in water the molecules naturally arranged themselves into little spongelike vesicles with the hydrophilic ends forming the outside surfaces and with the hydrophobic ends huddled together on the inside. (Many of the protocell's activities would be governed by the twin forces of hydrophobia and hydrophilia.)
For genes, Rasmussen needed a molecule that could both contain hereditary information in the manner of DNA or RNA, and could replicate, but without having to go through all the biochemical, biomechanical, and other enzymedriven contortions those molecules underwent in natural cells. What he needed, in short, was a coding molecule that could unzip and replicate in some quick and dirty, no-sweat, E-Z fashion. For this he chose PNA, peptide nucleic acid, a substance synthesized in 1991 by Peter Nielsen, the Danish biochemist. This was a double-stranded molecule that could split down the middle, just like DNA, uncovering its A, T, C, and G bases. Its advantage for Rasmussen, however, was the different ways in which the double-stranded and single-stranded versions of PNA behaved in the cell. A double-stranded stretch of it was hydrophobic and would sink down into the interior of the container and away from the water that surrounded the cell. At a preset temperature, the PNA molecule would spontaneously separate lengthwise inside the cell. The bases of the two single strands were hydrophilic and would therefore rise up to the cell's outer surface. There they would encounter matching PNA fragments that were also floating in the surrounding water, placed there with malice aforethought by the experimentalists. Those fragments would now attach themselves to the single strands, thereby forming new double-stranded molecules which, hydrophobic once again, would sink back down into the cell's innards. That took care of gene replication.
The protocell's metabolic, growth, and self-reproduction processes would be a product of light-sensitive lipid molecules being force-fed into the container. Light would activate the polarity of the molecules in such a way that their hydrophilic ends would rise to the container's surface and squeeze themselves in and among the other molecules that made up the cell's exterior. When the quantity of those surface molecules reached a certain critical mass, the forces holding them together would be overcome and the cell would split in half, reproducing itself.
Natural selection would come into the picture as the protocells reproduced: those that possessed some selective advantage in the speed or efficiency of replication would displace and ultimately wipe out those deficient in those qualities.
That was the basic design plan and operating formula of Steen Rasmussen's protocell. An ingenious design by any standard, especially if it worked. But in order to put his plan into effect, the wee matter of funding had to be addressed.
"I am doing this because I want to understand what life is," Rasmussen said. "That's the driver. Now that's not enough to get money, so the secondary driver is of course, Well, how can this be useful?"
From a practical point of view, there were three key benefits to Rasmussen's protocells. One was their relative safety: because artificial cells would be structurally and chemically alien to modern biology, they would be far less risky to experiment with than genetically engineered biological cells. As strictly nonbiological entities, "they'd have a much harder time interacting with modern life," Rasmussen said. "They'd be much less of an environmental or health hazard."
Second was their controllability: since they were designed to be programmable, the scientists ought to be able to coax the protocells to perform a larger range of tasks than was possible using ordinary cells and conventional biological engineering techniques. Suitably programmed protocells could unpollute the environment. They could act as "living pharmaceuticals," adapting themselves to a given individual's changing medical needs. They could produce new fuels, chemicals, structures, materials, and technologies.
Finally, because of the commercial value of those activities, they might even—unlike most other research projects financed by the government—make a profit.
AS IT TURNED OUT, money for such a far-fetched project was relatively easy to come by in Europe—provided that you and your organization were based there. Plus, office space for part of the effort was available for free in Venice, as Norman Packard learned while winding up his previous career in Santa Fe.
Norman was at this stage well into what might be called his Third Major Career Cycle (there were also smaller epicycles). Packard, who happened to be a cousin of David Packard, cofounder of Hewlett-Packard, had started out as a fairly conventional physicist, winning his Ph.D. at the University of California, Santa Cruz, in the late 1970s, after which he pursued a course of research into the main problem areas of the day: chaos theory, self-organizing systems, artificial life. That was his First Career Cycle. (As an epicycle to which, he and his friend Doyne Farmer designed and built miniaturized computer systems that were able to predict, fairly reliably, where a roulette ball would land after a spin of the disk. Never averse to making money with physics, Packard, together with Farmer and Mark Bedau, all of whom had been friends since their undergrad days at Reed College, secreted these devices on themselves and brought them into the casinos of Nevada—until they were busted by the gaming authorities.)
Later, Packard and Farmer founded the Prediction Company, a financial-markets consulting firm in Santa Fe. After several years of successfully modeling, anticipating, and forecasting the allegedly "unpredictable" behavior of the stock market, the business had made small fortunes for both of them. That was Packard's Second Career Cycle. At that point, "it seemed like the right time to try and break loose and pursue some other agendas," he said.
The agenda for his Third Career Cycle was established at a meeting with Rasmussen, Bedau, and their friend John McCaskill, a theoretical chemist from Sydney, Australia, who by that time had occupied several prestigious academic posts in Germany. The meeting was held at a villa in the Italian resort town of Cannobio, on Lago Maggiore, at the foot of the Swiss Alps. It was about a hundred miles from Lake Geneva, where Mary Shelley had gotten the idea for and started writing Frankenstein. The villa was owned by the family of Packard's wife, Grazia.
By the time of this gathering in the summer of 2002, these four researchers—Packard, Rasmussen, McCaskill, and Bedau—were old friends, and had closely shared scientific interests, orientations, and ambitions. Ever since a similar meeting two years before at Ghost Ranch in New Mexico (the former home of artist Georgia O'Keeffe, which was later made into a conference center), the four of them had become increasingly fixated on Steen Rasmussen's protocell design plan. Now, after a week's worth of discussions in Cannobio, the band of brothers decided that the time had come to implement Steen's design. They laid out an organizational plan, a timetable for action, and an informal division of labor, and then they mutually pledged themselves to actually building a protocell.
When they arrived in Cannobio, they were four investigators in search of a project. By the time they left they were the Four Protocell Musketeers. Then they disbanded, each to carry out his allotted part of their overall vision.
First, John McCaskill would apply to the European Union for a grant to establish an international consortium to be known as PACE, an acronym for Programmable Artificial Cell Evolution. Its primary and ultimate objective would be to exploit the programmability of protocells if and when they were brought into existence, but in the interim PACE would function as an umbrella organization that would provide guidance and research money to several European member institutions.
In the fall of 2003, PACE was funded by the European Commission (the executive branch of the European Union) in the amount of 6.6 million euros (about $8.6 million). Switzerland and Lithuania, which were not members of the EU but were nevertheless interested in the PACE project, kicked in with additional money. Soon John McCaskill acquired lab space at an outlying branch of the Fraunhofer Institute, a legendary organization with research centers spread out all over Germany, and gathered together a staff of eleven.
Second, Steen Rasmussen would apply to the Los Alamos lab for funding. In October 2004, his request was granted, and Los Alamos National Laboratory (LANL) appropriated $4.5 million for the Protocell Assembly project.
Third, Packard and Bedau would set up and run a profitmaking company that would finance future protocell research in the event that sufficient funding was not obtained through other channels. The company that emerged was ProtoLife s.r.l.,1 founded with $600,000 in seed money from private "angel investors," the major contributor being Norman Packard himself. The firm would be located at Parco Vega in the city of Marghera, across the lagoon from Venice, in the industrial park the Veneto Regional Government had created as a high-tech research heaven (and named it after a star).
Packard, Grazia, and their two children relocated to Venice, while renting out their Santa Fe house, and moved into a top-floor apartment in the tallest residential structure on the Grand Canal, the Palazzo Contarini degli Scrigni. Bedau, meanwhile, took a year's leave from Reed College, where he was a philosophy professor, and similarly moved himself and his family to Venice.
Fourth and finally, the protocell four would establish a "Center for Living Technology" as a conference, coordinating, training, and educational center—a place where the project's scientists could plot protocell construction strategies and from which the world at large could be informed of the "living technology" that a race of protocells would make possible. A living technology, they theorized, would be one that conferred many of the benefits of living systems—autonomy, robustness, adaptability to environmental changes, self-repairability, and so on—although it would be based not on machines but on programmable chemical cells.
The European Center for Living Technology (ECLT) was born in December 2004 at the Palazzo Giovanelli in Venice. The Palazzo Giovanelli was a three-story pink Gothic mansion that had been built in the first half of the fifteenth century. The place was on the Grand Canal, and the interior was fitted out with marble stairways, gilt-edged doors, mirrors, chandeliers, ballrooms with coffered ceilings, arched windows, and, on the top floor, a stained-glass skylight. The center had been established at Giovanelli not because of its opulence, but because the University of Venice, which had rights to the building, gave ECLT the run of the entire third floor for free.
Suddenly the Four Protocell Musketeers were awash in almost $14 million and flush with laboratories, equipment, simulation facilities, and scientific staff. All they needed now was to build their little organism.
BY MID-2005, all four protocell operations were up and running. At Los Alamos, Rasmussen's group had built containers. "We have pieces of the metabolism working too," Rasmussen said. "What we're working on right now is to integrate the metabolism with the gene."
In Venice, ProtoLife was trying to get its vesicles to perform functions that would create an initial earnings stream for the company.
"Long before ProtoLife is creating any revenue from freestanding, autonomous, self-reproducing artificial cells," Norman Packard said, "it will be producing revenue from much more primitive systems that will be engineered using some of the same tools that we're developing to take us along the path to the artificial cell."
For example, using a variety of hydrophobic-hydrophilic building blocks ("We have nineteen different kinds in our refrigerator," Packard said), ProtoLife chemists were customdesigning vesicles that could be used as targeted drug-delivery vehicles. These would be valuable commodities, especially if they had the ability to evade the human immune system. (Such structures were known within the drug industry as "stealth vesicles.")
None of the Protocell Four, Packard said, believed that their project would create freestanding, living, autonomous cells within the four-year duration of their EU and American funding, "but everybody hopes that it will produce some version of an artificial cell that can exist on technological life support."
Meaning what?
"You'd better ask John McCaskill," Packard said.
John McCaskill's lab was in the German town of Sankt Augustin, a few miles outside of Bonn. It was in a parkland setting, boasted its own castle (the Schloss Birlinghoven), and was a place where, in the early morning, it was not unusual to see people taking their exercise on horseback.
"Norman's lab is just getting started," McCaskill said in Sankt Augustin. "We've been doing this for a while."
That was evident from the quantity of their machinery and instrumentation. One room contained three generations of reconfigurable computers. There were chemical etching machines; supplies of dangerous chemicals; a laser lab; and, most important, a room where the scientists made their own three-dimensional, microfluidic chips.
Microfluidic chips were like computer chips except that fluids coursed through them along with the more usual electric current.
"A microfluidic system is a system which contains flows of material at the microscale, sub-nanometer scale," McCaskill said. "An example would be current tools for chemical diagnostics where one performs tests on chemicals in parallel by flowing the chemicals down these small channels and observing the reactions that take place in them."
A finely controlled fluidic environment was to be the protocell's birthplace, cradle, and life-support system.
"It's like an iron lung for artificial cells," McCaskill said.
Under the laser microscope that was necessary to observe it, McCaskill's microfluidic system looked like an ordinary computer chip: wires and channels running in a maze along precise, geometrical pathways. The important thing about those channels, however, was the variety of chemicals that could be made to flow through them at extremely slow and precise rates, while the microelectrodes could be made to deliver comparably minute electrical impulses, all of it under real-time direct observation and full computer control. Until it could exist on its own, that precisely controlled flow of chemical nutrients would constitute the cell's feeding system—a microscopic, mechanochemical womb.
In McCaskill's scenario, something like the first baby protocell, a bare five nanometers across, would be born inside such a microfluidic womb by 2008, and would be kept alive by deft manipulation of inputs and outputs until it could exist on its own.
"The task of reaching a freestanding artificial cell," he said, "then just becomes one of successively withdrawing the life support."
Once it had been withdrawn, would the independently existing protocell constitute a genuine life-form? The answer hinged on knowing what life, in essence, really was—a question that scientists and philosophers had contended with for decades, with scant success.
In 1943 Erwin Schrödinger, the quantum physicist, wrote what was destined to become a celebrated and highly influential book devoted to just that question, which he nevertheless discreetly refrained from answering.
Copyright © 2008 by Ed Regis
