LABORATORY SIMULATIONS

Appreciating contemporary life is one thing, but understanding how it might have arisen from nonliving matter billons of years ago is quite another. Can we be sure that the basic ingredients for life were present, or would have naturally emerged, on primordial Earth? Furthermore, is it likely that those nonliving building blocks could have fashioned a simple living cell given the harsh conditions on our planet billions of years ago? These questions can be studied in the laboratory, for the atmosphere and surface of today’s Earth differ greatly from those of the early Earth. Results of modern chemical experiments that mimic the geophysical environment on our young planet imply affirmative answers to these questions.

First, imagine again the setting on primeval Earth nearly 4 billion years ago. Physics had done its job to form the planet, geology was reshaping it boldly, and chemistry was altering the air, land and sea, but biology had yet to begin. As noted in the previous PLANETARY EPOCH, terrestrial gases interacted with one another, as well as with energy, thereby synthesizing bigger molecules. Nothing magical causes this rise in complexity, which would have occurred naturally provided the environmental conditions weren’t overly adverse and energy's intensity wasn't too low or high. Chemistry in action within optimal ranges—popularly known as obeying optimum Goldilocks principles ("not too hot, and not too cold, but just right")—can naturally yield the building blocks of life.

Simple Experiments With a test-tube-like contraption capable of holding water and some gases, much like that in Figure 5.14, laboratory gear can be used to simulate Earth’s early ocean and atmosphere. The gases in the bulb at upper left —usually a mixture of ammonia (NH3), methane (CH4), hydrogen (H), and sometimes carbon dioxide (CO2)—are meant to match the composition of the secondary atmosphere. Though toxic to present-day life, some blend of this gas was apparently optimum for the origin of life. Likewise, a flask of liquid at lower right is meant to resemble the primordial seas or some such pool of water. Upon heating this “ocean,” its water vapor rises to mix with the other gases in the “atmosphere,” whereupon it eventually condenses and “rains” back down with any newly formed chemicals—all of it reminiscent of the familiar evaporation-condensation-precipitation sequence happening every day now on Earth.

When the equipment is shut tight, allowing the gases to cycle endlessly without escaping—an “isolated system”—nothing much happens. In the absence of energy, these gases just cycle through the machine unchanged, refusing to react spontaneously with one another. For example, molecules of methane and water vapor, even upon direct contact, don't react chemically—unless they have a little help. And that help, that catalyst of sorts, is energy. When energy enters the experiment—making it an “open system”, that is, open to the environment—it breaks some of the bonds within each of the small molecules, allowing the liberated atoms and molecules to reform as larger, more complex molecules.

FIGURE 5.14 FIGURE 5.14 — This laboratory apparatus is designed to simulate the chemical activity in the ocean and atmosphere of primordial Earth. Water is heated (bottom right) and cycled around while mixing with simple gases and the all-important energy (top left). The result is the darkish, soupy organic matter collected in the trap below. (Lola Chaisson)

In order to hasten the reactions, chemists often employ gas abundances higher than those thought present on Earth long ago. Or they sometimes alter the quality of the energy from the amount presumed present billions of years ago. In this way, the molecules’ likelihood of colliding and reacting with one another improves greatly, allowing the experimental simulations to be completed in a few weeks. This sometimes introduces some unrealism and hence some controversy, but quite frankly, researchers with finite careers and one-year grants cannot afford to wait several hundred million years to determine the outcome of their experiments.

After several days of energizing the gases, a thick, brownish, soupy material collects in the trap at the bottom of the apparatus. Chemical analyses show this slimy product—called “gunk” by some, “pond scum” by others—to contain molecules indeed more complex than the initial reactants at the start of the test. Be assured, no worms or maggots crawl out of this primordial soup—not yet anyway. Nor has a simple cell, or even a single strand of DNA, been made under test-tube conditions. But many of the molecular products that are made are among the known precursors of life. They include several of the amino acids and nucleotide bases comprising the building blocks of all modern life. Chemicals such as formaldehyde (H2CO) are also produced, as well as other molecules (e.g., hydrogen cyanide, HCN, and formic acid, H2CO2) that are known to be among the basic ingredients of life as we know it. Although not all the acids and bases common to terrestrial life have yet been identified in the gunk, this “warm little pond,” much as theorized for life's origin by Charles Darwin in the mid-19th century, is regarded as a pretty good approximation of Earth’s early ocean into which heavy atmospheric molecules would have fallen, pulled down by relentless gravity.

The recipe for the successful construction of pre-life acids and bases isn’t a very stringent one. This experiment could successfully be done in a household kitchen or bathtub, though it makes one helluva mess and is not recommended. The gas mixtures, energy sources, and “cooking recipes” have been widely varied by chemists throughout the past few decades. The result is invariably the synthesis of complex organic molecules, provided no free oxygen (O2) is present. With even small doses of oxygen in the test tube, the gases oxidize, the concoction destabilizes, and no organic molecules are produced. Ironically, although much of Earth’s established life today requires oxygen, this gas was apparently toxic during the formative stages of that very same life. This is why we see no new acids and bases floating in the oceans or backyard streams of today’s planet; there’s too much oxygen around now.

A critical concern here is the amount and kind of energy used to power these experimental tests. Is it reasonable to suppose that enough of the right type of energy was present on the early Earth? As shown in Figure 5.14, the laboratory simulations are usually driven by energy provided by electrodes sparking the gases in the test tube. In reality eons ago, those electrical flashes would have been provided by prehistoric lightning storms. Spark discharges can also mimic several other types of energy undoubtedly present on Earth long ago. Besides lightning, plenty of volcanic activity and natural radioactivity were surely present, both of which produce heat. Cosmic rays, fast-moving particles probably among the debris of distant supernovae, also would have energetically belted our planet then much as they do now. Even the sound of thunder (in the absence of lightning) yields enough energy to have powered, in Earth’s early atmosphere, some of the chemical reactions known to occur in the laboratory experiments; if thunder can shatter windows in our homes, it can also break (and help reform) chemical bonds. Meteoritic bombardment is a further source of energy; as huge rocks plow through the atmosphere, their friction often generates enough heat to ignite chemical reactions, and their crash landings even more so.

Most of these energy sources are localized, hence were sufficiently intense to make or break molecular bonds only at isolated places on early Earth. Solar energy, however, was widespread, reaching nearly every nook and cranny on the surface of our planet. While ordinary sunlight isn’t energetic enough to trigger many chemical reactions, solar ultraviolet radiation is. And without oxygen on pre-life Earth, an ozone layer would not have surrounded our young planet, thus allowing plentiful ultraviolet radiation to have easily reached Earth’s surface. Apparently, much the same solar energy that clearly sustains life now was also active in helping to create life billions of years ago.

More Steps Toward Life Laboratory experiments like these are significant because they demonstrate conclusively that the molecular building blocks of life could have been made by strictly non-biological (i.e., chemical) means in any one of many different ways using raw materials readily present during the early history of planet Earth. These basic ingredients, however, are not life itself. To repeat, the organic molecules found in the gunk are still much simpler than a single cell. The synthesized amino acids and nucleotide bases are in fact much less complex than even the proteins and nucleic acids essential to contemporary life. How, then, were the acids, bases, sugars, and salts in this primordial soup initially assembled into proteins and nucleic acids? The answer is that this dilute organic slime must have been further concentrated so as to permit stronger and drier interactions.

As noted earlier (Figure 5.6), two amino acids can be linked to reach the next stage of complexity, provided a water molecule is removed. Such a dehydration condensation of many amino acids can then build up chain molecules into complex proteins. Successive linkages of nucleotide bases and energy-rich sugars can likewise produce lengthy nucleic acids.

Heat, for example, could have evaporated some water from clusters of acids and bases, especially along the shoreline of an ancient ocean or a lagoon inlet. Repeated in-and-out sloshing of tides in shallow waters might have led to a daily cycle of solar desiccation of molecules in a temporarily dried tributary during low tide, followed by further interaction among those molecules when washed into the open ocean at high tide.

The opposite condition—cold—can also disable water molecules from an organic mixture. The freezing of water transforms it from liquid to ice, thus allowing the acids and bases to better concentrate and hence link together. Regular freezing and thawing cycles could have enhanced the buildup of progressively larger chain molecules.

A third mechanism can effectively remove water while still in the presence of water. This might sound impossible, but it happens all the time in present-day life forms; even though composed mostly of liquid, the cells in our bodies routinely manufacture protein. They do it by using catalysts—third-party molecules that act like brokers by speeding up the process. Although the catalysts that now promote condensation reactions in today’s life forms were probably absent in the primordial ocean, chemists speculate that other catalysts likely existed 4 billion years ago. Certain kinds of clay commonly made by the weathering of rocks, for example, are thought by many researchers to have been the scaffolding needed to make larger organic molecules along the edges of oceans, lakes, and rivers. Clays, having layered, charged surfaces, could have potentially acted not only as tiny compartments to shelter acids and bases, but also as templates to assemble them into long, stringy substances.

Chemists are unsure if the first complex proteins and nucleic acids really did originate in any of these ways. The fossil record will probably never show the precise path whereby pre-life molecules gradually coalesced into something that might be genuinely called life. Nonetheless, heating, freezing, and catalyzing are all plausible agents for the assembly of small amino acids and nucleotide bases into larger proteins and nucleic acids. Some of these, in turn, owing to their hydrophilic (water-loving) and hydrophobic (water-repelling) properties, coiled up and folded over. As such, they became microscopic bags of chemicals enclosed by thin membranes. Somehow—and here admittedly there is a gap in our detailed understanding—they assumed forms that look like cells.

Advanced Experiments A single cell is astonishingly more complex than any of these pre-life molecules. To reach this very root of the evolutionary tree, biochemists currently seek to understand how proteins and nucleic acids were able to forge more intricate combinations of biological significance. Understanding in this area is limited, however. Researchers have only been able to surmise that persistent interactions among the many molecules on early Earth could have eventually produced something resembling today’s proteins, DNA, and simple cells.

More advanced laboratory experiments of recent years support this view. Repeated energizing and dehydrating the simulated environment of primordial Earth produce organic molecules more complex than amino acids and nucleotide bases. Of special interest are minute clusters of up to a billion amino acids united under the influence of heat. These proteinoid microspheres (also called “coacervate droplets”) do resemble protein-like substances that resist dissolution in water. Only ~0.01 mm (or 10 microns) across and hence requiring a microscope for observation, these are not well-known proteins such as insulin or hemoglobin, but simpler, protein-like compounds whose relevance to the origin of life is unclear. Chemical analysis confirms these microspheres to be dense little sacks of organic matter floating in a watery, mostly inorganic fluid. A view through a microscope, such as in Figure 5.15, shows them shimmering like globs of oil on the surface of water, or grease that bonds together as droplets on the surface of cooled chicken broth. Some chemists regard such microspheres as bona fide proteins; others aren’t so sure.

FIGURE 5.15 FIGURE 5.15 — Proteinoid microspheres are made by repeated energizing and dehydrating the primordial soup. The essence of this experiment can also be simulated by shaking a mixture of oil and water and watching globs of oil cluster on the surface of the water. Seen here through a microscope, each microsphere contains a large concentration of amino acids and measures a few microns across (1 micron = 10-4 cm.) (Sidney Fox)

Remarkably, the proteinoid microspheres made in laboratory experiments behave to some extent like true biological cells, "eating, growing, and excreting" in ways that resemble a primitive metabolism . The microspheres have semi-permeable membranes through which small molecules can enter from the outside as a kind of “food,” but through which most larger molecules created within cannot get out. Some discharge of “waste” is noticeable through a microscope but, by and large, these proteinoids display a net intake of matter, in some ways mimicking today’s biochemical cells. Indeed, these curious little bags of chemicals are actually observed to become larger in the process.

Not only that, these proteinoids often display a primitive form of replication. When the experimental gear is jostled to create some turbulence in the fluid—the analog of early oceanic wave action—some of the larger microspheres fragment into smaller ones, especially where "buds" appear at their interfaces as shown in areas marked A, B, and C of Figure 5.15. Some of these smaller, second-generation microspheres disperse, an apparent “death.” Others enlarge like their “parents,” only to be ruptured by another act of “replication” (although these microspheres likely lack enough information to direct their own replication from the basic building blocks). Environmental selection is underway, or so it seems.

In all, these fascinating proteinoid microspheres roughly approximate simple bacterial cells, especially the most ancient cells found in the fossil record, which is examined more closely in the next BIOLOOGICAL EPOCH. Some of the microspheres “eat,” some “grow,” some “reproduce,” and some “die.” Can they be called life? Most researchers reply almost certainly not since the microspheres lack nucleic acid or genetic coding. Yet who is to say what the first cells favored—protein metabolism or genetic reproduction? Or that protocells even remotely resembled modern cells? The distinction between matter and life is not clear-cut. And life itself, as noted earlier, is hard to define.

The great majority of biologists argue that amoebas are definitely alive, but that the molecular contents of the organic soup are not. Proteinoid microspheres apparently lie somewhere in between. But if they aren’t at least progenitors of Earth’s living systems—a kind of protolife—then Nature seems to have played a malicious joke on modern science.

Viruses The fuzzy interval between life and non-life often troubles scientists and laypersons alike. The central idea of chemical evolution is straightforward enough: Life evolved from non-life. But aside from biochemical intuition and laboratory simulations of some likely events on primordial Earth, do we have any direct evidence for naturally occurring complex systems within that blurred realm between living organisms and nonliving molecules? Fortunately, the answer is yes.

Virus particles are the smallest and simplest entities that sometimes appear to be alive—“sometimes” because viruses seem to display attributes of both non-living molecules and living cells. Derived from a Latin word for “poison,” viruses are of course a common cause of disease, but they may also hold clues to the origin of life. Although they come in many microscopic sizes and shapes, all viruses are smaller than a typical, modern cell; some contain only a few thousand atoms and span hardly 1 micron across, or a millionth of a meter. At least in terms of dimensions, viruses seem to bridge the gap between cells that are alive and molecules that are not. Figure 5.16 shows an example of one of the best known viruses, polio, here greatly magnified under a microscope.

Figure 5.16 FIGURE 5.16 — This photograph, taken through a high-powered microscope and magnified 300,000 times, shows a polio virus—a concentration of chemicals within the gray and uncertain area spanning the living and the non-living. (Harvard Medical School)

Viruses contain both protein and DNA (or RNA), though not much else—no unattached amino acids or nucleotide bases by means of which living organisms normally grow and reproduce. How, then, can a virus be considered alive? When alone, it’s not; a virus is absolutely lifeless when isolated from living organisms. But when inside a living system, a virus has all the properties of life. Viruses liven by injecting their DNA (or RNA) into cells of healthy living organisms, after which the virus’ genes seize control of the cells and establish themselves as the new master of chemical activity. Viruses then grow and reproduce copies of themselves by using the free amino acids of an invaded cell, often robbing the cell of its usual function. Some viruses multiply rapidly and wildly, spreading the disease and, if unchecked, eventually killing the invaded organism.

Biochemists are therefore unable to classify viruses as either living or non-living. Their status depends on their environmental circumstances. Even in the modern world, life seems to shade imperceptibly into non-life. Viruses apparently exist within that gray, uncertain realm.

Undersea Vents One of the strongest criticisms of the laboratory simulations of life’s origin concerns the energy needed to drive the experiments. This is especially problematic for the proteinoid microspheres, which do require much heat to form, so much so that only seething volcanoes could have likely provided it. That said, ancient volcanoes might well have been helpful in exactly this way, for they surely must have been frequent, widespread, and probably more intense during Earth’s youth.

If we are willing to relax the notion that life formed on the surface of the primordial sea, the submerged tectonic cracks and oceanic ridges noted in the PLANETARY EPOCH might be even better candidate sites for life’s origin. For there, plenty of concentrated energy and little free oxygen prevailed. Recent exploration by miniature submarines has made underwater, hydrothermal vents increasingly popular places to postulate life’s emergence on Earth. At places such as along the Mid-Atlantic Ridge and near the Galapagos Islands, complex ecosystems harboring many diverse life forms are known to exist, indeed to thrive, all of them powered by suboceanic heat engines, quite independent of the Sun.

Called “black smokers” (owing to their iron and sulfur outgassing), submarine vents are narrow crevices in the seafloor through which pressurized hot water (up to ~500 K) squirts like a Roman fountain. Figure 5.17 is a photo of one, taken underwater. The heated water rich in metals leached from molten rocks below interacts with the much colder seawater above, creating strong thermal gradients that enhance energy flow. The hot fluids actually rise within mineral-laden “chimneys” perched atop the suboceanic crust astride oozing magma, driving and sustaining much biological activity in, or at least near, the vents—but not conventional life forms familiar to us elsewhere in the (surface) biosphere. Often called “extremophiles” or “thermophiles” given their surprisingly high-temperature environment, heat-loving bacteria among other peculiar vent life is dependent neither on oxygen nor on sunlight. Among them are the so-called archaeabacteria, a relatively newly discovered domain of life that harks back to some of the most ancient life forms and that currently coexists within a remarkable underwater community of 2-meter-long (six-foot) worms, 10-kilogram (twenty-pound) clams, and idiosyncratic microbes thriving in what we at the surface would call decidedly uncomfortable conditions.

Figure 5.17 FIGURE 5.17 — A small, two-person submarine (called Alvin, partly seen at bottom) took this picture of a hydrothermal vent, or “black smoker”—one of many along an underwater ridge in the eastern Pacific Ocean. As scalding hot water pours from the top of the vent’s tube (near center), black clouds rich in sulfur billow forth, providing a strange environment for many odd life forms that manage to thrive under totally dark and oxygen-free conditions near the vent. (Woods Hole Oceanographic Institute)

Undersea hydrothermal vents could well have been the natural engines that drove the early emergence of biology several billion years ago. They do have some advantages over the formation of life on or near Earth’s surface, providing areas abundant in heat, lacking free oxygen, and clearly protected from the harsh realities of incoming ultraviolet radiation and asteroid bombardment that presumably made early surface conditions a Puritanical hell on Earth. Environments near such vents could have conceivably fashioned biology out of a geological setting, even if only at a single locale that successfully bridged the PLANETARY and BIOLOGICAL EPOCHS.

Exogenesis Another dissenting viewpoint about life’s origin either on or under the surface of Earth has gained strength in recent years, reinforcing the honest uncertainties plaguing the CHEMICAL EPOCH. Here the question concerns a possibly wider venue for life’s origin: Did it occur terrestrially anywhere on Earth or extraterrestrially someplace beyond? Endogenesis or exogenesis? Some astrobiologists feel that none of Earth’s land, sea or air might have been particularly well suited for the initial production of organic molecules. Not even the undersea vents are viable, they say, as the heat there may have been too great for the survival of acids and bases—in effect, even harsher than early conditions on Earth’s surface or in its atmosphere.

At issue once again is energy, that is, whether proper amounts of it—optimum values, neither too much nor too little—were available to power chemical reactions. Moreover, Earth’s early atmosphere might not have contained enough raw material for the reactions to have become important in any case. A minority of researchers argue that much, if not all, of the organic matter that combined to form the first living cells was more likely made in interstellar space and thereafter arrived on Earth embedded in comets, meteors, and interplanetary dust, parts of which managed to avoid burning up during their violent descent through the atmosphere.

Several pieces of evidence support this idea, considered by some to be a kind of weak panspermia whereby the molecular ingredients for life were brought intact to Earth, but not necessarily already formed life itself. First, there are the interstellar molecules noted in the STELLAR EPOCH, many of which contain carbon and at least one of them reported (yet unconfirmed) to be the amino acid, glycine. Second, laboratory experiments demonstrate that when icy mixtures of water, methane, ammonia, and carbon monoxide—precisely what’s found in the near-vacuum of interstellar space—are exposed to ultraviolet radiation like that from a newborn star, the result is intriguing and perhaps more realistic than some of the earlier simulations of chemistry on the young Earth. When the irradiated ice is later placed in water, oily, hollow droplets form with cell-like dimensions and obvious membranes made of organic matter; Figure 5.18 shows an example. As with the proteiniod microspheres noted earlier, these interstellar globules contain neither proteins nor DNA per se, but the results clearly show that even the alien, cold, virtual vacuum of galactic space is an apparently suitable place where simple protocellular structures can form—especially when they splash into a receptive ocean. And third, comets and meteorites are known to harbor organic matter; comets especially, often called “dirty snowballs,” are made mostly of the icy interstellar mixture just described. Since cometary impacts are thought to have provided much of Earth’s water, it’s perhaps only a small step to imagine that this incoming water already contained the building blocks of life.

Figure 5.18 FIGURE 5.18 — These oily, hollow droplets rich in organic molecules were made by exposing a freezing mixture of primordial matter to harsh ultraviolet radiation. When immersed in water, these curious little blobs display cell-like structure; most span ~10 microns across (or ~10-3 cm). Although not alive, they bolster the idea that at least life’s building blocks could have come from space. (NASA)

The idea that organic matter constantly rains down on Earth from space in the form of interplanetary debris is certainly plausible. The cratering record on the Moon shows that Earth experienced a period of late heavy bombardment ~3.8 billion years ago, just a bit earlier than when the oldest life forms appear in the fossil record (~3.5 billion years ago). Tens of thousands of tons of extraterrestrial matter do fall to Earth annually, even now. And the notion that chemical evolution occurs in space seems certain. Analyses of comets, meteorites and interstellar gas during the past two decades have proved beyond doubt that organic chemistry is widespread in the Universe. However, whether or not exogenesis was the primary means by which complex molecules first appeared in Earth’s oceans remains unclear. The origin of life, along with the origin of galaxies, represent the two chief missing links in all of cosmic evolution.


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