A Brief History of Creation

by Bill Mesler

  In 1978, Cech, a relatively young assistant professor at the University of Colorado, Boulder, began a series of experiments to isolate the protein that was responsible for the gene splicing that Gilbert had recently discovered, the removal of introns from RNA molecules. Cech imagined that the protein would be rather easy to find. He would simply take cell extracts and purify them until he found the culprit that was causing the splicing. But his research team was stymied. Even with samples they were sure were entirely free of proteins, the RNA still ended up being spliced. Eventually, they were able to prove that the RNA itself was responsible for its own splicing.

  Not long after Cech began his work, Altman, a researcher at the Medical Research Council Laboratory of Molecular Biology in Cambridge, then led by Sydney Brenner and Francis Crick, began his own study of a strange enzyme called ribonuclease P. Ribonuclease P was unusual because RNA seemed to make up about 80 percent of its mass, which scientists had always discounted as an unimportant anomaly. Altman kept up the work when he moved on to a professorship at Yale, and eventually he was able to conclude that RNA was, in fact, the critical catalytic component of ribonuclease P. RNA, not protein, was responsible for the observed reactions.

  Cech and Altman’s discoveries revolutionized our understanding of biochemistry. Some proteins catalyze chemical reactions. Some are motors. Still others, embedded in cell membranes, open and close channels that make it possible for the phenomena of consciousness to take place. Eating, digesting, moving, even thinking—all are, at their most basic level, functions of proteins. Proteins control the chemical processes responsible for virtually everything an organism does at the cellular level, and proteins had always been understood to be the sole cellular components carrying out these reactions. But Cech and Altman proved that some RNA molecules—which came to be called ribozymes—could also act as catalysts like proteins do. The discovery earned each a share of the 1986 Nobel Prize in Medicine.

  As Gilbert pointed out in his Nature article, the discovery of ribozymes had huge implications for the study of the origin of life. Here was a part of the cell that could accomplish both replication and metabolism. He argued that at some point very early in the history of evolution, the simple cells that populated the Earth merely contained RNA. “The first stage of evolution proceeds,” he wrote, “by RNA molecules performing the catalytic activities necessary to assemble themselves . . . [eventually] using recombination and mutation to explore new functions to adapt to new niches.” The theory came to be known by the phrase with which Gilbert had titled his influential article, “The RNA World.”

  BOTH CECH AND ALTMAN had come to their groundbreaking revelations about RNA while working with samples taken from a microscopic protozoan called Tetrahymena thermophila. Tetrahymena is a remarkable little creature, part of the ciliate family, eukaryotes first observed by Antonie van Leeuwenhoek and characterized by the stringy cilia that spring from them like clumps of hair. Tetrahymena comes in seven different “sexes” and is capable of thriving over a wide range of temperatures. But what particularly sets it apart from other single-celled organisms is the wide variety of biological processes it shares with more complex organisms. It has a primitive digestive system, with a mouth-like pore for ingesting food. Remarkably, the tiny organism contains about twenty-five thousand genes, nearly as many as human beings have. The presence of such a wide array of genes makes Tetrahymena useful for modern biological research, as does the ease with which it can be cultured.

  A Tetrahymena as seen by a scanning electron micrograph.

  Tetrahymena had already been at the center of an absurdly large number of important biological discoveries, including the identification of the first cytoskeleton-based motor protein (a primitive muscle-like protein) and the existence of lysosomes and peroxisomes, which are like the cell’s little wastebins. In fact, the very same sample of Tetrahymena used by Cech and Altman was also being used by a completely different group of researchers who would go on to win a Nobel Prize for a completely different discovery. One of those scientists, a young, mild-mannered Canadian named Jack Szostak, would go on to build upon the discovery of ribozymes to become one of the leading origin-of-life scientists of the twenty-first century, and the most famous of the modern scientists who actively study the RNA-world model.

  THE SON OF A PILOT in the Royal Canadian Air Force, Szostak was captivated by the Apollo missions during his childhood. But he had always been more interested in the experiments the astronauts would conduct on the moon than in space travel itself. Biology had been a particular area of interest. In school, he was a prodigy. He enrolled in McGill, Canada’s most prestigious university, when he was just fifteen years old.

  After joining Harvard Medical School as a professor of chemistry in 1982, at the age of twenty-seven, Szostak first turned to the subject of DNA repair in the yeast Saccharomyces cerevisiae, a model eukaryotic organism that had fascinated countless scientists since Pasteur’s time. Soon thereafter, he attended a lecture given by UC Berkeley molecular biologist Elizabeth Blackburn regarding the genetics of Tetrahymena. Szostak felt Blackburn’s advances could be brought to bear on work he was doing in his own lab that involved a long-standing problem in eukaryotic cell biology: Because the enzymes that copy DNA never quite reach the ends of chromosomes, scientists had always expected that part of the chromosome should remain uncopied at the end of each round of cell division. That this was not always true had long left scientists puzzled.

  Along with molecular biologist Carol Greider, Szostak and Blackburn devised a set of experiments to figure out what was happening. By making Saccharomyces-Tetrahymena hybrid chromosomes, they were able to show that tiny pieces of DNA called telomeres, Greek for “end part,” from the ends of Tetrahymena chromosomes could protect Saccharomyces chromosomes from being shortened, and vice versa. This finding not only explained the paradox; it had significant implications for understanding cellular aging and cancer. Szostak, Blackburn, and Greider’s work was published in 1982. In 2009, nearly three decades later, the three shared a Nobel Prize for the discovery.

  AFTER HIS WORK WITH telomeres, Szostak began looking for a new scientific challenge. Very early in his career, he had decided he wanted to work on what he considered the three big questions in science: the origin of the universe, the origin of consciousness, and the origin of life. He realized early on that his math wasn’t up to par to tackle the physics associated with the origin of the universe. And though, like Henry Bastian and Francis Crick, he was tremendously enticed by the idea of unraveling the phenomenon of consciousness, he felt the technology wasn’t yet there to make much of an impact. But after Cech and Altman’s discoveries about the nature of RNA, Szostak saw an opportunity to make important strides in understanding the origin of life.

  As early as 1984, Szostak had started to immerse himself in the study of ribozymes, trying to better understand what their roles might have been in the earliest cells. His goal switched to finding something that was held up as a kind of holy grail among those who subscribed to the RNA-world theory: an RNA molecule that could do the work of copying itself. Nothing like it existed, or had ever existed, as far as anyone could prove. But Szostak had new avenues to approach the problem that hadn’t been available to many of his predecessors.

  Since the Miller-Urey experiment, re-creating the chemical steps that would have led to FLO’s initial appearance had proved perplexingly difficult. Though some progress had been made, few scientists had had much success. But Szostak recognized that there might be another way of approaching the problem. By the 1990s, with advances in knowledge about the cell and the development of modern techniques to manipulate the cellular machinery, it became possible for scientists to consider building a cell from scratch. Instead of trying to re-create all the difficult chemical steps necessary for the emergence of the first life, Szostak was simply trying to create it in his laboratory.

  THE ERA OF completely synthetic life-forms began in 2002 when a research scientist at a labor
atory in Long Island injected the contents of a syringe into a small white mouse. Within minutes, the mouse was dead, its body frozen by paralysis, the telltale sign of the lethal dose of poliovirus it had just received. The poliovirus’s deceptively simple RNA-based replication cycle had gone into overdrive, hijacking the mouse’s cells into making countless copies of itself, until the host cells, each swollen with ten thousand new viruses, ruptured, releasing them to infect more host cells. But what made this particular poliovirus attack so remarkable was that it had been induced using viral DNA built from scratch in the laboratory, the brainchild of a Stony Brook University virologist named Eckard Wimmer. The poliovirus genome had been deciphered in the summer of 1981, and Wimmer’s team had only to download the genetic recipe—a simple string of about seventy-five hundred A’s, G’s, C’s, and U’s—off of the Internet.

  The technology for synthesizing DNA had been perfected in the previous decades. Building such molecules, while not exactly child’s play, was well within the repertoire of the modern molecular biologist by the turn of the millennium. Geneticist Craig Venter and his team started work on synthesizing an entire bacterial genome, a feat vastly more complex than Wimmer’s simple virus. Even the smallest and simplest cells consist of hundreds of highly evolved enzymes, as well as the genetic code and all the other trappings used by modern organisms. Though it took twenty-four scientists ten years and forty million dollars, they succeeded, via a complex series of laboratory manipulations, in synthesizing their bacterial genome in 2010. It contained a staggering 1,077,947 base pairs.*

  To make their bacteria, Venter and his team began by adding the synthetic chromosomes they had built to a culture of natural Mycoplasma that was subjected to an electric shock. The shock allowed the artificial chromosome to enter the host cell. Then, as the host’s cellular machinery went to work on the synthetic genome, daughter cells were produced containing only the artificial chromosome. This chromosome, having been endowed with all of the instructions for making all of the proteins needed to keep the cell running indefinitely, took over, and thus the first completely artificial organism came to life. They named it “Synthia.” It contained about eighty times as much genetic information as the poliovirus.

  The implications for the future of biotechnology were truly remarkable. The potential applications reached into fields as diverse as synthetic fuel production and medicine. But many scientists were quick to point out that Synthia did little to answer the question of where the information required to build a cell came from in the first place. Venter, like Wimmer before him, essentially copied the blueprint that nature had provided them after four billion years of molecular tinkering. It was an astonishing feat of engineering but proved nothing about how life began.

  SZOSTAK BEGAN CONTEMPLATING a synthetically engineered cell as far back as the mid-1990s. What set his vision apart from that of men like Venter and Wimmer was that he wanted to understand the origin of life, not merely copy the blueprint provided by nature. The key question for him was how the blueprint would arise from scratch. He had some clues to draw upon, provided by a remarkable set of experiments carried out all the way back in the 1960s by Sol Spiegelman, the biochemist who had originally recruited Carl Woese to the University of Illinois.

  Spiegelman and his colleagues performed a series of telling experiments that showed how RNA molecules might behave like organisms and evolve on their own—in a test tube—in a Darwinian fashion. Spiegelman started with a virus known as bacteriophage Qβ—pronounced “cue beta”—which infects the common gut bacterium Escherichia coli. They purified Qβ’s RNA genome and the protein that copies it, and then mixed these together in a test tube along with the precursors that the protein uses to construct a new Qβ RNA molecule. They let this mixture react for a little while and then transferred a few drops of the solution, now containing various imperfect copies of the original RNA molecule, to a new test tube that contained only the protein and precursors. They did this a total of seventy-four times, each time transferring a few drops from the last test tube to the next. In each exchange, a new population of mutant molecules was transferred, serving as the starting point for the “molecular evolution” that would take place in the next test tube.

  The end of this process revealed something remarkable: the starting RNA molecules were about 4,500 nucleotides long, but the ones present in the seventy-fifth test tube were only 218 nucleotides long. There appeared to be a sort of competition in which shorter molecules tended to win. This made perfect sense, since short molecules could be copied faster, and thus could exponentially outcompete longer molecules. In essence, Spiegelman had created a form of natural selection among naked strands of RNA in his test tubes. His colleagues dubbed his creations “Spiegelman’s monsters.”

  In 1975, two scientists in chemist Manfred Eigen’s lab performed a surprising experiment that built upon Spiegelman’s work. This time they simply mixed the precursors and the protein without the master RNA template. Astonishingly, they found that over time, molecules very similar to Spiegelman’s minimal RNA molecule appeared. This result showed that, given the right conditions, a meaningful information-containing molecule, like RNA, can spontaneously arise. The results obtained by Spiegelman and his colleagues became a touchstone for origin-of-life scientists in the RNA-world camp. The only problem was that the molecules were not truly self-replicating. They could make copies of themselves only in the presence of the copying protein, itself the complex product of a biological blueprint. Thus, the concept of a self-copying RNA molecule became the holy grail of RNA-world research.†

  Though various teams had tried to find such a self-replicating RNA molecule, Szostak envisioned taking the concept one step further by building a true RNA organism. Building on an idea he had come up with alongside Italian biochemist Pier Luigi Luisi in 2003, Szostak wanted to work on building an actual RNA-based cell, one in which the RNA was housed in a lipid membrane.

  According to Szostak’s model, the first living thing might have been a naked RNA molecule. But the first living cell—FLO—would have needed a membrane for early evolution. Szostak saw two good reasons for this requirement. The first was that molecules that stay together evolve together. It seems unlikely that a single strand of RNA could do all of the various functions needed to propagate a cell. A small family of molecules might have been required, held inside a small bubble that forced them to collaborate. These molecules would copy each other and influence each other’s evolution in mutually beneficial ways.

  The second, closely related reason was the problem of freeloaders. An RNA molecule that was generally good at copying other RNA molecules in its environment would be beset by parasitic RNA molecules, few of which might actually contribute to the welfare of the pack. Enclosing the copying ribozyme in a cell with only its collaborators—the freeloading viruslike RNA molecules locked safely outside—would make the encapsulated ensemble much more efficient.

  In all modern cells, membranes are composed of molecules known as amphiphiles. These molecules are made up of fats, like animal tallow and coconut oil, which form the basis of almost every soap and shampoo. When placed in water, under the right conditions, they have a natural tendency to spontaneously form bubbles ranging in size from the microscopic to the very large, which could have formed the basis of simple cell membranes. There may be good reason to suspect that such lipid bubbles were abundant on the primitive Earth, even before life had devised ways of making them. Meteorites like Murchison have been found to contain similar molecules, and small bubble-like structures form from the organic “goo” common in such meteorites. This goo could have spontaneously formed cell-like compartments in shallow pools on the Earth.

  To realize this vision of FLO, Szostak developed a novel approach harnessing the power of natural selection. Using billions of small random RNA molecules encased in tiny lipid bubbles, he simply lets them compete in test tubes just as Spiegelman’s monsters did. The ones that copy themselves well should grow at the expense o
f those that do not. Szostak hopes that, at some point, a set of these RNA molecules will spontaneously solve the problem of making each other and the membrane itself from simpler precursors that the scientists supply. The result will be a living, evolvable RNA-based organism: an RNA-world re-creation of FLO.

  A COUPLE OF BLOCKS from Boston’s Charles River, on the seventh floor of a research building owned by Harvard Medical School, a microscope sits in a room barely larger than a walk-in closet. On the door hangs an old photograph of Mahatma Gandhi. Dressed in traditional garb, the Hindu holy man and leader of India’s struggle for independence is bent over and peering into a small microscope. Inside, the room is barren except for a single chair and a small table upon which sits an actual microscope. Above it, a picture cut out of a magazine is taped to the wall. It is a picture of a protocell as imagined by Szostak, brightly colored and simple, devoid of all the typical machinery of the cell except for a single strand of RNA. Next to it are four simple words: “A Cell Is Born.”

  If Jack Szostak and his team are successful in their quest to create a living model of his vision of FLO, it is there, in that little room, that the first self-replicating RNA-based cell will be seen by a human being. It will be a species more primitive than any currently living on Earth, a monumental discovery. It will undoubtedly be greeted by a flood of sensational press coverage. In the eyes of many, the problem of the origin of life will have been largely solved.

  Yet history shows that a great enigma will likely remain. It will be the same dilemma embodied by the question once posed by the physicist Enrico Fermi to his old friend Harold Urey: Is this how it could have happened, or how it did happen?