Primordial Puddles

In a dilute soup, amino acids are not likely to link together into proteins, simply because their polymerization is a dehydration reaction (the amine portion of one molecule attaches to the acid portion of the next molecule, with the loss of one water molecule ). For thermodynamic reasons, that means that protein formation will happen spontaneously only at very dense concentrations, unless there is a source of energy to drive the reaction. The same thermodynamic considerations also apply to RNA, DNA and many other organic polymers— they can form in a concentrated solution, but they will break up in the dilute, open ocean. So the first place we will look for early chemical evolution is in the tidal pools, puddles and lagoons in the shorelines that bordered the early oceans. These small pockets of water offer two very important features that are lacking in the open ocean— concentration, and isolation. Primordial Shorelines How much shoreline was there? If the continents and oceans of 4 billion years ago were about the same size as today, then we can guess that the coastlines were also approximately the same length— perhaps 1.6 million kilometers or 1.6 billion meters long, when measured at a walking scale. Because the continental rock of that time was younger and mostly igneous, the coast was probably more rugged than current coastlines— think Maine, California or Iceland, with many fresh volcanic rocks, and fewer sandy beaches or mud flats than modern coastlines. Rocky shorelines frequently contain tidal pools of varying sizes— and they may have provided some conditions that would have made biogenesis much more possible, 4 billion years ago. Let’s take a closer look at them now. Concentrating Pools To start with, let’s look at what we’ll call ‘concentrating pools’-- puddles, pockets and pools along the shoreline where the ocean’s content would have concentrated into a much thicker solution. Since NSF grants are not available for time machines that go back 4 billion years, we’ll look at some modern shorelines, and then draw conclusions about prebiotic conditions. Modern Pools and Puddles If you examine rocky shorelines such as in California or Maine, you’ll nearly always find many depressions above the high tide line where sea water can collect and evaporate. These concentrating pools might be anywhere from one to fifty meters from the high tide line, depending on the shoreline topography and the size of incoming waves (the pools need to be close enough to receive some wave splash or spray, but not so close that they are washed clean by waves). An informal survey by the author showed the presence of about 15 concentrating pools and puddles per meter of shoreline along a random sampling of rocky Maine coast . These pools ranged in size from shallow coin-sized puddles containing one or two cubic centimeters of water, all the way up to aquarium-sized pools holding dozens of liters. Under modern conditions, many of the smaller concentrating pools are filled with salt deposits or solidified organic crud, indicating that they have been filled many times and that their contents have evaporated and concentrated . Larger pools are often filled with brine, brackish water or fresh water, depending on recent weather. Most of the deeper pools contain sand, gravel or silt at the bottom. Ancient Pools and Puddles 4 billion years ago, shorelines probably had the same kinds and quantities of concentrating pools as today. If most of the shoreline along the early Earth was equally rocky, that means that it contained more than 20 billion concentrating pools and puddles. They would have contained a great variety of conditions, and would have been a great place to find denser concentrations of materials, and chemical reactions that couldn’t take place in the open ocean. The only real difference back then is that there was no life yet— so there were no gastropods or seagulls to eat any organic material that might have accumulated. Solar Concentration To get an idea of the extent of concentration possible via shoreline evaporation, let’s imagine a shallow one-liter depression, just above the high tide line in an arid climate, 4 billion years ago. About three times a day , wave splash would fill the pool with a dilute oceanic soup (possibly about 1 milligram per liter density). During low tides, the pool would evaporate dry. At each cycle, about a milligram of organic compounds would enter the pool. After about a month (100 cycles) there would be approximately 100 milligrams of material in the pool. That may not seem like a huge amount, but it would have contained about 4 x 1020 (400 quintillion) organic molecules, most likely including a few quadrillion amino acids. Of course the early seas also contained salt, and that would have also built up in the concentrating pools. If the seas back then had a salt content similar to today’s oceans, then a month’s evaporation in our one-liter pool would produce enough sodium chloride and other salts to fill the depression completely. Just before the end of each evaporation cycle, there would be a period when the puddle contained an extremely concentrated brine with hardly any water. Under those conditions, many organic compounds would polymerize via a dehydration reaction-- so there would be the potential for the formation of protein-like compounds, and possibly long chains of RNA. We’ll talk more about that later. Drainage and Selection Many concentrating pools would have been close enough to the water’s edge to be washed clean during heavy seas or very high tides. In addition, all of the tidal puddles and pools would have filled with fresh water whenever it rained. When that happened, the excess water would have dissolved any soluble materials and washed away any loose materials, leaving behind anything that was both insoluble and solidly attached to the rocks. Lipids and hydrophobic amino acids are water-repellent, so they would have been more likely to bind to the substrate and remain behind under those conditions. After a few years or a few centuries of evaporation, concentration and washing, some of the tidal puddles and pools would have developed quite an accumulation of insoluble organic material, possibly in the form of a tar, film or gelatin on the surface of the rocks. The many repeat cycles of wetting and drying would have also led to other interesting chemical effects— perhaps crystallization of some organic compounds, or formation of long polymer chains that couldn’t have developed in a single condensation. Mixing Pools Closer to the water’s edge there are pools and puddles that receive more constant wave action— they are located just above the high tide line. These ‘mixing pools’ are washed clean by large waves often enough that their contents don’t become concentrated. Modern Mixing Pools Modern mixing pools are nearly always filled with standing water and some forms of life— protozoa, algae, gastropods, crustaceans or other organisms, depending on climate and conditions. An informal survey by the author found approximately 10 mixing pools per meter of shoreline along a random sampling of rocky Maine coast. Ancient Mixing Pools 4 billion years ago, it seems likely that shorelines would have contained the same kinds and quantities of mixing pools as today. Of course 4 billion years ago, there were no life forms inhabiting them. Some of the mixing pools may have included globs of organic gels or tars that had washed down from the nearby concentrating pools and then attached to the rocks lining the mixed pools. Other insoluble organic material may have splashed into the mixing pools along with the sand or gravel to which it was attached. The mixing pools would not have offered any chemical concentration, since they were filled with water too frequently. But they would have been a great place where many chemical reactions could have occurred, once self-replication started. Many of the events that we’ll talk about later would have taken place in the mixing pools. Pool and Puddle Drainage In the networks of modern tidal puddles and pools, wave splash helps to mix the contents of different pools, and spread them to other pools. A particularly violent wave might sploosh the contents of a pool into several surrounding ones. After each wave passes there is usually further mixing as excess sea water drains off the rocks and back into the ocean. Usually the mixing pools and puddles exhibit complex drainage patterns— overflow from one depression seeps into another depression further down, and an errant raindrop may travel through a dozen pools before it reaches the open water. During the prebiotic world, the mixing and drainage between shoreline pools and puddles would have been almost like a chemical assembly line in a factory— ‘interesting’ chemicals from one pool would wander to another one, and a puddle near the shoreline might receive ‘interesting’ chemicals from several sources that were further upslope. Micropuddles Tidal pools are easy to visualize on a human scale, but in fact much of the chemical evolution that we’ll describe later probably happened in much smaller volumes of water. As rocky puddles and pools evaporate and become shallow, they usually break up into smaller micropuddles within the rough surfaces of the stone. A typical tidal puddle might contain 10 to 100 micropuddles when close to evaporating dry. Even the smallest of those volumes would still contain enough organic material to have significant chemical activity. For example, a micropuddle one cubic millimeter in volume (about the size of a mustard seed) holds about 1/100 gram of water, which contains a bit more than 1/100 microgram of organic material at our calculated soup density. That is a teensy dollop of material, but it is still about 500 billion organic molecules of average size , even in a dilute soup. That is plenty enough room for all sorts of interesting chemistry to occur. Of course, if the puddle’s contents were concentrated, there would be even more organic material to work with. Similar micropuddles might occur in the gaps and voids between the stones in a gravely shoreline (or in a tidal pool that was filled with gravel). Evaporation and concentration could still have taken place there, and the gravel would have provided an abundance of surfaces where larger compounds could attach, along with better protection from UV. Even the small spaces between sand grains, or the microscopic cavities in silt or clay, would have been roomy enough for chemical evolution to occur. For example: • An average gap between sand grains (about .1 mm) would contain about 5 million organic molecules if filled with dilute soup, and 5 billion molecules if filled with moderately concentrated soup. • An average gap between silt particles (20 microns) would contain 40,000 organic molecules in a dilute soup, or 40 million molecules in a moderately concentrated soup. • An average gap between clay particles (2 microns) would contain 40 organic molecules within its 4 picograms of dilute soup, or 40,000 molecules in a moderately concentrated solution. When we consider the number of possible ‘evolutionary pools’, focusing on micropuddles greatly increases the potential number of locations where the first life reactions could have occurred. Instead of tens of billions of pools and puddles in the centimeter-to-meter size range, there would have been many trillions or quadrillions of smaller pools in the micron-to-millimeter size range. A Matter of Scale We humans visualize best in the dimensions that are about our size— so in this book we’ll talk about evolution occurring in tidal pools and puddles that are at least a centimeter or two in size. It’s something that anyone can imagine putting their toes into . Even today, tidal pools are home to a great variety of life, and it sure makes a better story if we assume that the same could have happened 4 billion years ago. However if you want to be literal when visualizing early chemical evolution, it might be best to grab a microscope and consider teensier bodies of water that are closer to the molecular scale. Concentration Chemistry When concentrating pools were almost entirely dry, they would have contained an extremely thick solution of salts and organic chemicals with very low water content. Those conditions would have encouraged dehydration reactions (chemical reactions that result in the loss of water molecules). Let’s take a closer look at some possible results. Polypeptides One common dehydration reaction is the merging of amino acids into long-chain polypeptides—particularly when in the presence of sodium chloride and other salts . The amine (NH3+) branch of one molecule links to the acid (COO-) branch of the next, which creates a nitrogen-carbon bond with the loss of one water molecule. This reaction can continue almost indefinitely, and form amino acid chains which are hundreds or thousands of molecules long (called polypeptides or proteins, depending on their length). Prebiotic polypeptides would have been more random than modern proteins. For example, they probably had many cross-links, didn’t always connect neatly by the alpha carbons, and likely contained other organic compounds bound into the polymer. They would have included both levo- and dextro- amino acids, and they would also have contained a much wider assortment of different amino acids than is found in modern proteins. Though they would have been very different from today’s proteins, the resulting ‘proteinoid’ polymers would still have been relatively large and stable compounds, with many properties similar to modern proteins. Depending on conditions, some of the condensing pools may have produced a high density gel of such compounds, or even ‘primordial jerky’ when the pools dried completely. Chain Molecules There is another class of molecules that can form long chains. Those are small organic compounds such as the purines and pyrimidines, which contain aromatic rings. The rings consist of five or six molecules of carbon and/or nitrogen, linked by a ‘cloud’ of pi electrons which move freely between the different ring molecules. Aromatic rings are flat, and hydrophobic (water repelling), though they often have side chains that are polar (water attracting). These ‘chain molecules’ form polymers with the rings stacked in parallel, sort of like a pile of coins or plates. It makes for a fairly rigid structure that is moderately stable in water, thanks to the hydrophobic attraction between the aromatic rings. DNA and RNA are the most common modern examples of this sort of polymer. By some odd coincidence of chemistry, it’s certainly possible that some chains of RNA or DNA formed in concentrating pools, However, that would first require the assembly of nucleotides-- a combination of a purine or pyrimidine with a ribose sugar and some phosphates. And then those nucleotides would need to stack properly in a chain. Even if all that did manage to happen, it would still have been very different from modern DNA. For example, the chains would not be composed solely of the modern combination of just four nucleic acids. There would have been many other possible chain molecules in the soup, and they would have joined the chain just as readily as the ‘standard’ molecules. That means that any chains would not be a double helix, since they would lack the modern system of complementary base pairs, which allows two chains to link up like a spiral zipper. In the early chapters of this book, we are not going to assume that RNA or DNA was present at all in the soup. What we will assume is that there were some chains composed of purines, pyrimidines or similar compounds. However, they would have been much more random than modern chains, which much less predictable chemistry. Other Reactions Of course the aggregates in evaporating pools would have contained many other compounds as well as amino acids. At least in the early days of the soup, they’d generally be a random combination of whatever happened to form synthetically in the soup and condense there. In some cases, repeated cycles of immersion and drying might have produced crystallization or other forms of organization. During storms or very high tides, splashing waves may have detached the concentrated masses of organic materials and moved them to a different pool (or the open ocean). They might also have remained attached to their home puddle and then interacted with fresh soup splashed there by wave action. Concentration Synthesis The highly concentrated contents of a condensing puddle would also allow for general chemical synthesis of compounds that may not have formed in the raw soup. For example, most ‘primordial soup’ synthesis experiments do not show creation of pyrimidines (including guanine, thymine and uracil, all important constituents of RNA or DNA). However in dryer, more concentrated conditions the pyrimidines are frequently created in prebiotic simulations . The constant bombardment by UV (at least during the daytime) would have provided the energy for many chemical reactions that require an energy input. So we can expect that the tidal puddles and pools would have contained much more ‘interesting’ chemicals than were found in the open ocean. Pool Variations With a huge number of tidal pools and puddles spanning a geographically wide area, we can expect that a wide variety of conditions would have occurred. For example, some pools may have been located near geothermal features, with temperatures close to or above the boiling point of water, and high concentrations of sulfur and related compounds. Others might be located in Arctic reasons and be below freezing for part or all of the year. And of course other puddles would have been at every possible temperature in between. If the early earth started out with significant hydrocarbons, some puddles and rocks might be tar-covered, not unlike many present day beaches and rocky shorelines. In fact in the days before bacteria, oily deposits would have lasted much longer since there was nothing to eat them. We can also expect a wide range of salinity and pH values in the pools, depending on concentration levels, rainfall, local water contents and substrates. Given the wide range of conditions, within some of the tidal pools we might expect synthesis of some rarer organic compounds that might not be synthesized in the soup itself. Most likely, a few pools and puddles would have had conditions ideal for the life-forming sequences that we’ll talk about later. Clay and Minerals Clays are of particular interest when we look at pre-biotic conditions, since they are capable of catalytic activity. For example, montmorillonite clay can increase the formation of RNA chains by acting as a ‘template’ for their bonding (although the nucleosides generally bond by the ‘wrong’ carbons as compared to modern RNA). Phosphates are also extremely important in early biochemistry— phosphate bonds link the ribose sugars in the backbone of DNA and RNA, and they are part of the energy equation in most biological reactions (usually in the transition between ATP and ADP). Some of the puddles and pools would have contained phosphate-rich sediments or be lined with phosphate-rich rock, some of which would have dissolved. Such phospho-puddles may have been extremely important for life’s origins. Hydrophobic & Polar Compounds Another piece of chemistry that may have played a role in the organization of early chemical aggregates is the simple fact that oil and water don’t mix. On a molecular level, this means that hydrophilic (ionic) compounds tend to mix into a polar solution with the available water, and hydrophobic (non-polar) compounds group together, held together by weak van der Waals forces. Some compounds are amphiphilic, with a hydrophobic portion and a hydrophobic portion. They tend to congregate at the junction between oil and water, with their non-polar end embedded in the oil and their polar end in the water. Phospholipids are a common amphiphilic substance in modern living membranes. Many proteins are also amphiphilic, since some of the amino acids are hydrophobic (valine, leucine, tryptophan, phenylalanine etc) and some are hydrophilic (arginine, lysine, glutamine, etc). These properties would have helped the soup molecules to bind together in ‘interesting’ clumps. Hydrophobic bonding would have helped aggregates to remain attached to their substrates in the wetter concentration pools and mixing pools. The Puddle Laboratory In general, prebiotic rocky shores would have been an extremely interesting place, at least from a organic chemistry point of view. If there was a specific set of conditions that could cause the synthesis of a particular compound, then it was probably present in quantity, somewhere in the world. Think of the prebiotic coastline as a few trillion small petrie dishes with varying sizes, immersion frequencies, temperatures and substrates, with random connections between them. It’s a pretty decent organic laboratory where interesting reactions would have developed, spreading interesting compounds to their neighboring pools. Isolation One other feature of shoreline pools that is worth considering is the high degree of isolation that they provided. Confinement On a chemical level, the ingredients in a small puddle were confined into a relatively small volume, so they were more likely to react with each other instead of drifting away on the currents. That means that slow-moving, multi-stage and low-probability reactions could eventually take place there, simply because the ingredients would have stayed close to each other for long periods of time. The pores between grains of sand or silt would have been particularly good at confining organic chemicals into a restricted volume, especially if some of the molecules adsorbed onto the surface of the mineral grains, or if drying reduced the water content down to a thin film. Evolutionary Role of Isolation On an evolutionary level, having small isolated populations in multiple puddles increases the amount of selection and evolution that can take place. It increases the number of distinct populations on which natural selection can occur, and it exaggerates the effects of small variations so deleterious properties can die out more quickly. There is a good reason why Darwin discovered the basic theory of evolution after researching species in the Galapagos Islands-- a chain of small islands off the coast of South America. Evolution and speciation happens more easily in partially isolated places, where populations have time enough to diverge in relative isolation, and then occasionally invade neighboring islands to extend the range of a new species. Something similar would have happened on a chemical level in the pools— this ‘puddle evolution’ would have provided a big assistance to the development of early almost-life forms, even before true Darwinian evolution was possible. Later on, we’ll look more specifically at the results of evolution in multiple puddles, as we look at the early steps in the evolution of DNA and life. Puddle Alternatives Although we will focus on shoreline puddles and pools as the primary location for the evolution of DNA and early life forms, it is not the only possible location where life could have begun. In fact, it’s possible that this story should really happen in an entirely different environment. Since there are many competing theories for the location of life’s origin, let’s take a brief look at some of the alternatives. Micelles and Vesicles Many experimental setups have shown that naturally occurring lipids can form membranes spontaneously. In some situations they form micelles (hydrocarbons surrounded by a layer of amphiphilic molecules) or vesicles (cell-like spheres with a surrounding bilayer membrane that is remarkably similar to the membrane in modern cells). Membranes are particularly interesting, since they isolate the interior contents from the outside world, just as we have suggested for isolated puddles. Early vesicles probably would have merged with each other and split into smaller blobs on occasion, so the mixing that occurred in our ‘tidal puddle’ model could also have occurred that way. Some theorists claim that the lipids in micelles could themselves have contained reproductive information , but in this book we will only consider them as possible containers for a more traditional biochemistry based on proteins and RNA. Membranes definitely became important some time during early evolution. We’ll talk about them in later chapters, though only as an adjunct to the formation of cells. If you think that membranes predate the formation of proteins and DNA, then simply consider the next few chapters as happening inside oily blobs instead of in shoreline puddles. Hydrothermal Vents Hydrothermal vents lie deep in the oceans, at locations where magma (molten rock) lies close to the ocean floor. Water that has seeped close to the heated rocks is ejected from the vents, carrying a rich mix of materials. The hot water includes methane, hydrogen sulfide and ammonia— all prime ingredients for early formation of organic raw materials. Many Archaea (heat-loving bacteria) currently live in this extreme environment, frequently using sulfur compounds as an energy source. Several researchers have proposed the vents as a possible location for the origins of early life forms (they also suggest that the Archaea were the earliest life forms ). The vents themselves are hot enough (300° C) to decompose most organic compounds, but life may have developed in fissures near the vents. Although we won’t consider deep-sea locations any further, the concentration and mixing that we’ll talk about later may have occurred in sediments and cracks near thermal vents, instead. It would have been similar chemistry, just in a different container. Ice Caps Because solar output was probably about 25% lower 4 billion years ago, it is possible that the Earth was ice-covered back then, similar to the modern moons of Jupiter and Saturn. If that were the case, early evolution may have taken place within amorphous ice , or possibly in the oceans under cover of thick ice caps . Obviously any chemical action taking place in ice would have proceeded much more slowly. On the other hand, organic reactions under a protective cover of ice would have been possible even with an oxidizing atmosphere, and an icy world may have suffered less destruction when comets or other large bodies impacted the surface. If icy biogenesis is possible, it may also have occurred on other members of the Solar System— particularly on icy moons such as Ganymede, Europa and Titan. Again, we’ll assume a warmer sort of evolution in this book, but it may have occurred in a colder place. Just much more sloooowly. Clays RNA and DNA bind readily to the surface of clay particles , which can also act as a ‘template’ to form longer chains of RNA. It is possible that early chemical evolution took place deep within the nooks and crannies of silts and clays, where they would be relatively protected from hazards such as UV and a possible oxidizing atmosphere. Some researchers have even proposed that early chemical forms of life were based on self-replicating organization of clay or other mineral particles . Of course a carbon-based explanation for life’s origins is more plausible, particularly because the transition to real life would have been easier if the compounds didn’t have to change much. We’ll stick with surface puddles in future chapters, but there’s no reason why similar events couldn’t have occurred below the ground instead. Deep Subsurface The ‘deep hot biosphere’ theory looks at modern Bacteria and Archaea living far below the surface. Many of them use very simple chemical reactions involving sulfur, iron oxide and methane as an energy source. It is possible that they were the first forms of life, in which case the first chemical evolution may have happened deep under the Earth’s surface. It is a place that would have been relatively immune to damage from impacts, and relatively impervious to whatever was in the atmosphere and oceans. If the early Earth was as rich in deep organic compounds as the theory predicts, high concentrations of organic compounds would have already been present in some locations, similar to the kerogen and oil deposits found beneath the surface today. Presumably that catalysis and the other life-forming events that we’ll talk about later could have also happened in isolated cracks and crannies deep in the earth. In that case, eddies and pockets in the underground circulation would replace the tidal pools that we’ll use in the rest of this book. Panspermia The theories of panspermia (life everywhere) and exogensis (life from elsewhere) predict that life on Earth started from bacteria or other living cells that arrived on comets or in other forms from outside the Earth. Neither theory solves the problem of where life originated in the first place, but at least they allow it to have happened at some other location that may have had conditions that were more favorable for biogenesis. In the remainder of this book we’ll stick with biochemistry on Earth rather than elsewhere. There’s no way we’ll ever be able to prove that life started here, but it makes a more interesting story if it happened in our backyard! Previous Home Next