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 All currently known organisms rely on DNA to replicate and proteins to run cellular machinery, but these large molecules—intricate weaves of thousands of atoms—are not likely to have been around for the first organisms to use. "Life could have started up from the small molecules that nature provided," says Robert Shapiro,a chemist from New York University. Shapiro and others insist that the first life forms were self-contained chemistry experiments that grew, reproduced and even evolved without needing the complicated molecules that define biology as we now know it. Primordial Soup An often-told origin-of-life story is that complex biological compounds assembled by chance out of an organic broth on the early Earth's surface. This pre-biotic synthesis culminated in one of these bio-molecules being able to make copies of itself. The first support for this idea of life arising out of the primordial soup came from the famous 1953 experiment by Stanley Miller and Harold Urey, in which they made amino acids—the building blocks of proteins—by applying sparks to a test tube of hydrogen, methane, ammonia, and water.
But were the first complex molecules proteins or DNA or something else? Biologists face a chicken-and-egg problem in that proteins are needed to replicate DNA, but DNA is necessary to instruct the building of proteins. Many researchers, therefore, think that RNA—a cousin of DNA—may have been the first complex molecule on which life was based. RNA carries genetic information like DNA, but it can also direct chemical reactions as proteins do.
Shapiro, however, thinks this so-called "RNA world" is still too complex to be the origin of life. Information-carrying molecules like RNA are sequences of molecular "bits." The primordial soup would be full of things that would terminate these sequences before they grew long enough to be useful, Shapiro says. "In the very beginning, you couldn't have genetic material that could copy itself unless you had chemists back then doing it for you," says Shapiro. Instead of complex molecules, life started with small molecules interacting through a closed cycle of reactions. These reactions would produce compounds that would feed back into the cycle, creating an ever-growing reaction network. All the interrelated chemistry might be contained in simple membranes, or what physicist Freeman Dyson calls "garbage bags." These might divide just like cells do, with each new bag carrying the chemicals to restart—or replicate—the original cycle. In this way, "genetic" information could be passed down. Moreover, the system could evolve by creating more complicated molecules that would perform the reactions better than the small molecules. "The system would learn to make slightly larger molecules," Shapiro says. This origin of life based on small molecules is sometimes called "metabolism first" (to contrast it with the "genes first" RNA world). To answer critics who say that small-molecule chemistry is not organized enough to produce life, Shapiro introduces the concept of an energetically favorable "driver reaction" that would act as a constant engine to run the various cycles. Driving the First Step in Evolution A possible candidate for Shapiro's driver reaction might have been recently discovered in an undersea microbe, Methanosarcina acetivorans, which eats carbon monoxide and expels methane and acetate (related to vinegar). Biologist James Ferry and geochemist Christopher House from Penn State University found that this primitive organism can get energy from a reaction between acetate and the mineral iron sulfide. Compared to other energy-harnessing processes that require dozens of proteins, this acetate-based reaction runs with the help of just two very simple proteins. The researchers propose in this month's issue of Molecular Biology and Evolution that this stripped-down geochemical cycle was what the first organisms used to power their growth. "This cycle is where all evolution emanated from," Ferry says. "It is the father of all life." Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says. 
How the primitive Earth cooked up proteins is a chemical mystery. These molecules – vital to biological functions – are made of long strands of hundreds of amino acids, but researchers are unclear how even some of the shortest amino acid chains, called peptides, formed prior to the dawn of living organisms.
Recent experiments have demonstrated how a volcanic gas, carbonyl sulfide (COS), may have been instrumental in the "prebiotic" build-up of peptides. There are several mechanisms for connecting amino acids. Organisms use enzymes, and chemists have identified other catalysts that can do the job. However, Leslie Orgel from the Salk Institute points out that few of these things were ingredients of Earth’s environment billions of years ago. "With carbonyl sulfide, we have a very realistic agent," Orgel said. This gas is known to fume out of volcanoes today and was likely present in the planet’s fiery past. Orgel and colleagues formed peptides by adding COS to a watery solution containing various amino acids at room temperature. About 7 percent of the amino acids formed pairs and triplets. This peptide yield increased to as high as 80 percent when the researchers added metal ions to the solution. The results, published in the Oct. 2004 issue of the journal Science, lend credence to a theory that life arose near underwater volcanic vents, which to this day support thriving, self-contained ecosystems. Because carbonyl sulfide breaks down quickly in water, the researchers speculate that chains of amino acids most likely formed on rocks near the COS source. Whether life could have blossomed on this ocean bed of peptides is not yet known. Interestingly, the amino acid building blocks may not have formed at the vents but instead may have rained down in comets and meteorites. Astronomers have identified many small organic molecules in space, which opens the possibility of peptide factories being seeded on places besides Earth. "I think it likely that other planets with volcanic activity might have this sort of chemistry," Orgel said. Over the past 20 years scientists have warmed up to the idea that the majority of life on our planet lives not on Earth's surface but beneath its crust. The theory has spurred new ideas about life's origins on Earth and where to look for life on other planets. Earth's crust gets warmer the closer it is to the molten iron-nickel believed to be at our planet's core. One question that scientists who study life beneath Earth's crust face is, at what temperature is it too hot for life to survive? Since scientists believe Earth at one point was mostly molten, the answer to the question may shed light on how early life could have first evolved on our planet.
Much of this life beneath the crust, which scientists refer to as biomass, are microbes that use hydrogen and minerals like iron to get energy from food sources in the same way that humans use oxygen to obtain energy from our food. Lovley is at the forefront of research into such microbes. He has discovered dozens of different species, including Strain 121, a microbe that grows at 121° Celsius (250° Fahrenheit)—the highest temperature currently known for life. The ability to grow at 121° Celsius is significant because for over a century it has been the temperature used to sterilize medical equipment. Scientists thought that such temperatures would kill all life-forms. "It's kind of a benchmark," Lovley said. "This is like breaking the four-minute mile." Strain 121, which goes dormant at temperatures below 80° Celsius (176° Fahrenheit), lives in environments known as hydrothermal vents on the ocean floor. The vents spew hydrogen- and mineral-rich hot water from deep in the Earth's crust to the surface. For several years scientists have known that other microbes survive in and around hydrothermal vents at temperatures above 100° Celsius (212° Fahrenheit). Strain 121 just "opens that window where life can exist a little bit wider," Lovley said. Jack Farmer, an astrobiologist at Arizona State University in Tempe, said that opening this window for life on Earth expands the potential for life to develop and persist elsewhere in the solar system and beyond. "As the upper temperature limit for life has increased, new opportunities for habitable environments have opened up, and subsurface hydrothermal environments are among the most important," Farmer said. "Poor Man's Drill" John Delaney, a marine geologist at the University of Washington in Seattle, led the expedition that brought to the surface the chunk of hydrothermal vent from which Strain 121 was isolated. Delaney said that examining such environments gives researchers a snapshot of what life is like deeper in the Earth's crust, where temperatures are higher. "Our way of doing it was a 'poor man's drilling program," he said. The expedition team used a remotely operated submarine to cut out and bring to the surface a chunk of hydrothermal vent from the Juan de Fuca Ridge, which lies about 200 miles (322 kilometers) offshore from Washington's Puget Sound and nearly 1.5 miles (2.4 kilometers) deep in the Pacific Ocean. The seafloor at the Juan de Fuca Ridge is cold, about 2° Celsius (36° Fahrenheit). But down beneath the seafloor the temperature warms gradually until, eventually, it is scalding hot.
A chunk of one of these chimneys, or hydrothermal vents, is what Delaney and his team brought to the surface. "We figured we would see different kinds of microbes in the wall as it got to hotter and hotter temperatures, and [that] pretty soon microbes wouldn't be there … [which would] indicate a limit to life under those conditions," he said. Limits and Origins Microbes like Strain 121 that live in environments lacking organic carbon are known as archaea, which literally means "ancient." Archaea are genetically different from seemingly similar bacteria, which need organic matter and photosynthesis to survive. The discovery of Strain 121 bolsters the theory held by some scientists that Earth's first life-forms were archaea that could thrive at high temperature via chemical reactions with hydrogen and iron. "They appear to be the branches closest to what is the last common ancestor of existing life," Lovley said. "All are hyperthermophiles that live at high temperatures." Early in Earth's history, according to Delaney, volcanic eruptions occurred on the ocean floor as the planet's core separated from its crust. These eruptions could have allowed the mixing of hydrogen and minerals like iron and sulfur, upon which microbes could thrive. "That may be one of the paths the origins of life takes," Delaney said. If that's the case, he added, then studying hydrothermal vents is a step in the process of understanding how the dynamics of such a system might work. And understanding how such a system works on Earth may help in the search for life on other planets.Farmer, the Arizona State University astrobiologist, said, "At the bottom line, hydrothermal systems were widespread in the early solar system and are thought to still be present in the subsurface of many other solar system objects, like Mars, Europa, and even the interiors of large asteroids." So perhaps the question for scientists isn't is there life on other planets, but is there life inside them.  Long ago, before microbial organisms first took shape as organic cells and began to colonize the biosphere, naked living processes may have commenced within the confines of hollow bubbles of deep-sea rock. This take on the origins and early stages of biochemistry, laid out in a bold new scientific treatise, could dramatically rewrite the opening chapters of the story of life on Earth. It also implies that extraterrestrial life might exist in much greater abundance that has been traditionally presumed.
If Martin, a biochemist, and Russell, a geologist, are right, then traditional hypotheses about how the Earth's earliest forms of life evolved are due for a rewrite. The pair has published their far-reaching theory in Philosophical Transactions: Biological Sciences, a journal of the Royal Society of London. The document, at 24 pages, is a hefty and exhaustive tome by the standards of scientific publishing, which can usually pack any idea into six pages or less. But that's because describing early life—like developing it—requires a bit of time and effort. A Rocky Start All living organisms are made up of cells—membrane-enclosed organic sacks—that contain proteins and strands of genetic material. Without the biological machinery inside, cellular membranes couldn't grow, multiply, or even repair themselves. The most fundamental of life's processes, reproduction, would be inconceivable. Without the membrane that encloses its fragile components, the molecular machinery of life would be unshielded from the harsh forces of its surrounding environment and would be torn apart before it could do its work. "Life starts with a cell wall or a membrane," Russell said. "Otherwise, it bleeds to death." What scientists have so far lacked is a convincing explanation for how an organic cell wall could have developed before there was the biological apparatus to build it. And thus arises a vexing microcosmic variation on the chicken-and-egg riddle: Which came first, the apparatus inside, or the membrane that holds each bundle of life together? Martin and Russell believe they've solved the conundrum by thinking outside the biological box. The first containers of life, they suggest, were themselves neither products nor producers of biochemistry. They were tiny, hollow chambers—enveloped by rock. Buried, Alive Cavity-riddled masses of iron sulfide formed naturally where hydrothermal vents spewed warm, compound-rich fluids into deep-sea waters, explains geologist Russell. These "culture chambers" provided just the sort of incubator that the chemical ingredients of life needed to initiate biochemistry. "These inorganic compartments were the precursors of cell walls and membranes found in free-living (cells)," Martin and Russell wrote. Trapped within their inorganic incubators, "the first cell couldn't feed itself," said Russell. "Like a child in the womb, it had to be fed, to be nurtured" by the stream of nutrients and energy that continued to bubble up from the hydrothermal vents beneath them, he said. It doesn't sound like an easy way to live, but there must have been multiple ways to pull it off, Martin and Russell argue, because there are three fundamentally different forms of life. Two of them—the eubacteria and their simple cousins, the archaebacteria—diverged evolutionarily even at this early stage in the history of life, they suspect. From these humble beginnings, however, life would soon burst forth into a new and exciting world—the juvenile Earth. First, the researchers hypothesized, biological processes produced and deposited fatty molecules along the inner surfaces of the iron sulfide cavities. Eventually, these fats formed into cohesive membranes that fully enclosed the biological activity inside. Archaebacteria and eubacteria arose independently from parallel occurrences of this series of events, Martin and Russell proposed. That landmark development rendered obsolete the original, inorganic compartments, and the first true cellular life was ready to emerge. When the first of these organisms broke free from the confines of their iron sulfide cocoons, said Martin, "they were all alone in an uninhabited planet." "This lonely little spot" of life might have evolved quickly, Martin hypothesized, because virtually every adaptation that arose opened up whole new classes of untapped chemical resources in the organisms' submarine world. "It's as if you went into a bank (for the first time), and they gave you all the money." The Whole Trinity Eventually, organisms became numerous enough that competition among them ensued. That, Martin and Russell suggested, may have been when some eubacteria and archaebacteria hit on the strategy of joining forces, thereby forming the third class of life, the eukaryotes. These organisms, composed of complex cells with complete, organ-like internal structures, include all multi-cellular life forms such as plants and animals. The ancient strategic merger that created them explains why most eukaryotes resemble eubacteria in certain biochemical respects but depend on archaebacteria-like internal organelles such as mitochondria or chloroplasts, Martin and Russell asserted. That argument, like many the pair of researchers has made in their new model of life's origins, broadsides conventional wisdom. Martin and Russell fully expect their theory to be held to the fire that burns in the crucible of rigorous scientific discourse. |