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THE ORIGIN OF LIFE
OCEAN

THE ORIGIN OF LIFE

      The idea that a living thing could arise from nonliving things is not only a very old idea, it was the predominant idea held in Western civilization prior to the mid-17th century.  It was commonly thought that flies would arise spontaneously from decaying garbage, mice would appear from wet sawdust, frogs would spring directly from mud, etc.  After Louis Pasteur demonstrated that living things, even microscopic living things, arose directly from prior living things, the question of the origin of the first living things became much more important.

    It is not known how life originated--there are no time machines and fossils of pre-cells either do not exist or are difficult to interpret.  Even if life is generated someday in a lab, there is no guarantee that the first living things developed through similar processes.  Is it possible that life developed naturally from a nonliving earth?  Charles Darwin suggested that life could have arisen chemically “in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc. present.” (He never made this suggestion publicly, perhaps for fear of the public reaction to it.) There is a great body of accumulating evidence which suggests that many of the steps thought to be important in the evolution of life in the early earth could have occurred through natural processes.   Although life has not been generated in a laboratory, it should be understood that it is unrealistic to expect that biochemists have succeeded in replicating all of the chemical reactions which could have occurred in all of the earth’s oceans over a period of 400 million years in the first fifty or so years of experimentation.  The discoveries which have already resulted from this research (such as the catalytic properties of RNA) have already made great contributions to the scientific understanding of the world.

 

1)     Is it possible that organic molecules (those complex molecules of living things) arose from simple inorganic molecules in the absence of life?  Yes.

ORGANIC

     Organic molecules were once thought to exist only in living things and to have possess an “animism” or a “vital force” which could not arise without life.  Many of those who thought so called themselves vitalists and argued that because life had properties outside the physical and chemical world, science would never be able to explain the origin of a living cell (or many other things for that matter, such as the digestion of food, the functioning of the nervous system, embryological development, etc.)  It was thought that an organic molecule could never be generated outside of living things. 

     It is now known that this view is incorrect: the organic molecules which form the building blocks of living things can be formed abiotically, without life.  Organic molecules even seem to form outside the planet earth. Simulations of conditions in space have generated a variety of organic molecules such as amino acids and nucleotides (Strazzulla, 2001; Simakov, 2002).    Solutions of NH4CN were frozen for 25 years (at -20 to -78oC) and the products of electrical discharges in reducing gases (like those of a reducing atmosphere) were frozen for 5 years in order to simulate the conditions which exist on Jupiter’s moon Europa.  Analysis of the results isolated substantial amounts of adenine, guanine, and amino acids (primarily glycine but also others such as alanine and aspartic acid) (Levy, 2000).

     More than 100 organic and inorganic molecules have been detected in the dust of the galaxy (Greenberg, 2002).  The Jupiter moons Callisto and Ganymede seem to organic molecules (McCord, 1997).  Meteorites can contain organic molecules such as nucleotides, amino acids, and amino acid precursors.  Analysis of Halley’s comet suggests that 14% of the comet is composed of organic carbon, including adenine and formaldehyde (the latter being a precursor for sugars in abiotic reactions).  Six studies of a famous meteorite (the Murchinson meteorite) have isolated the amino acids glutamic acid, aspartic acid, glycine, β-alanine, leucine, alanine, and the exotic amino acids α-aminoisobutyric acid and isovaline.  Additional amino acids were isolated in some (but not all) of the studies including praline, sarcosine, valine, and isoleucine (Engel, 2001; Simakov, 2002).   Nucleotides (purines and pyrimidines including uracil) are present in the Murchison meteorite (Martins, 2008).Organic molecules have been identified in Martian meteorites (Trevors, 2003b). Ribose can be made in large quantities through abiotic synthesis, especially in the presence of boron and calcium (Kirschvink, 2006).

     Organic molecules would also have reached the early earth from space since the earth lacked oxygen in its primitive atmosphere and matter falling from space would not have undergone combustion.  The early earth may have been bombarded with large quantities of extraterrestrial material, perhaps 1011 to 1012 kg per year (Trevors, 2003b; Martins, 2008). In the early earth, the bombardment of the planet by material from space would have created organic molecules at the impact sites in addition to those organic molecules originated from the extra-terrestrial objects themselves. Currently, about 320,000 kg of organic material fall to earth each year from space and around the time of the origin of life, this value may have been 100 million kg of organic material/year. The amount of organic material created at the sites of impacts could have been about 100 times greater than this, about 10 billion kg/year (Chyba, 1992). During the first 100 million years of earth’s history, the amount of energy created by high velocity meteorite impacts was probably double the amount of energy which reached earth from the sun. The energy from impacts was probably a significant source of organic compound synthesis in the early earth (Managadze, 2007).

Amino acids in addition to nucleic acid bases (adenine and guanine) have been isolated from meteorites.  Extraterrestrial amino acids have been isolated in the K/T rocks that mark the time when an extraterrestrial impact caused mass extinctions at the end of the Mesozoic Era.  Organic molecules would have been formed in comets and could have reached earth on impact (Dworkin, 2001).  Actually, meteorites and interplanetary dust continue to bring organic molecules formed in space to earth (Chyba, 1992). The amount of organic carbon that could have accumulated by 3.9 billion years ago by its spontaneous synthesis on earth and the arrival of organic molecules from space is estimated to be 100 to 10,000 times greater than the amount of organic matter currently in the biosphere (Deamer, 2003).

     Organic molecules can form without life on earth as well.  The Miller-Urey experiment (and subsequent experiments) demonstrated that all the building blocks of life can be synthesized using only the gases of the primitive earth's atmosphere and a source of energy (there would have been plenty of energy in a primitive earth—the heat of a semimolten planet, lightning, solar radiation unfiltered by an ozone layer, etc.).  By simply mixing inorganic molecules and energy, the following organic molecules have been produced: all the amino acids (the building blocks of proteins; the 4 most abundant amino acids in our bodies were the most easily formed), all essential sugars, triphosphate nucleotide precursors needed for the synthesis of the DNA and RNA (ATP, TTP, GTP, CTP, & UTP; adenine [A] is the most common base in living organisms & was the most easily formed), aldehydes, and carboxylic acids (Orgel, 1994; Oro, 1961; Miller, 1974; Julian, 2003; Saladino, 2001; Rode, 1999; Delaye, 2005). Miller found that up to 10% of all carbon atoms could be incorporated into organic molecules and up to 2% incorporated into amino acids (Miller, 1974).  An analysis of a meteorite supported the results of the Miller-Urey experiment: both the meteorite and the experiment produced some of the same amino acids and in the same relative quantities (Orgel, 1994).  The Salt-induced Peptide Formation (SIPF) reaction catalyzes the formation of all amino acids under the conditions thought to have existed in the early earth. Copper ions and sodium chlorine (salt) are required for this reaction (Li, 2008).

Although it is generally accepted that there was not free oxygen gas in the early atmosphere, there is disagreement as to whether the early atmosphere was strongly reducing (with methane, carbon dioxide, ammonia, nitrogen, and water) or neutral (with nitrogen, carbon dioxide, and water). If the atmosphere was not reducing, then the primary sources of organic molecules would have been underwater vents and the organic matter reaching earth from space (Lazcano, 1996). If the atmosphere was not reducing, then most of the synthesis of biomolecules would have occurred at hydrothermal vents on the ocean floor with additional organic molecules arriving from space (Delaye, 2005). Water brought to earth in the impacts of comets and carbonaceous asteroids resulted in the formation of oceans between (4.5 and 3.5 billion years ago); the same process was probably occurring on Mars and Venus as well (Chyba, 1990).The environment where seawater changed by subthermal vents mixed with normal seawater would have provided a chemical environment more conducive to some of the chemical steps thought to be important for the first steps in the origin of life (Martin, 2002a).IIn addition to the molecules named above, the Miller-Urey experiment produced an oily residue.  Similar reactions on a primitive earth would have produced an oily layer over the oceans which would have protected molecules from UV light and promoted polymerization (Bada, 2004). A hydrogel environment, with its retention of organic molecules, might have provided a suitable site for some of the events leading to life (Trevors, 2005).

     Methane-rich gases which have been shocked (by phenomena ranging from lightning and UV light to comet and meteorite impacts) can make organic molecules (McKay, 1997; Chyba, 1992).  Organic molecules would have formed in the primitive earth’s atmosphere if it were a reducing atmosphere (as are the atmospheres of the outer planets of the solar system).  Although the ancient atmosphere was probably not as reducing as the conditions in the original Miller-Urey experiment, such conditions would have existed in deep sea subthermal vents (Mather, 1988). The subsurface of the earth would have provided protection from harmful ultraviolet light  that the surface was exposed to and it is possible that life developed in deeper regions of the earth (Trevors, 2003b; Trevors, 2002).  It has been demonstrated that small organic molecules can form inside certain minerals (such as olivine and magnesium oxide); these organic molecules would be released when the minerals are weathered (Freund, 2001). 

     Thus, it has been shown that the small organic molecules which serve as building blocks of living things can be generated by inorganic molecules and energy, in the complete absence of life.  Oxygen and hydrogen are two of the three abundant elements in the universe and water is found throughout our solar system and in interstellar space. The majority of the early earth atmosphere would have been lost in dramatic events of the early solar system such as the formation of the sun and the impact which resulted in the formation of the earth’s moon. Most of earth’s surface water came from meteorites ad comets which subsequently impacted earth (Mottl, 2007). Oceans on earth may date from 4.0 to 4.4 billion years ago (Bada, 2004; Trevors, 2003b).  The high amount of deuterium present in modern seawater (160 ppm which is 8 times higher than its concentration in solar nebulae) is evidence of that the water on the surface of the earth originated from water ice in the comets which bombarded the early earth (Delsemme, 2000; Delaye, 2005).    

     Would the organic molecules which were accumulating in the earth’s oceans have been stable once they were generated?  Yes.  Because of the absence of microbes on the primitive earth to digest them and the lack free oxygen in the primitive earth’s atmosphere to react with them, these molecules would have been stable.  The early earth’s oceans would have gradually accumulated more and more of these molecules, becoming the “primordial soup”.  Certain metal oxides (such as zinc oxides) interact with ribose nucleotides and concentrate them from dilute solutions (Arora, 2006).

2)     Small organic molecules can form in the absence of life.  Could these small organic building blocks have joined to form larger biomolecules in the absence of life?  Yes.

POLYMER

     Amino acids can fuse when exposed to heat to produce protein-like substances (called proteinoids) which can have catalytic activities (Nashimoto, 2001).  Peptides form abiotically in modern subthermal vents (Bada, 2004).  It is possible that the early earth’s rotation and the nearness of the moon helped to form chains of organic molecules.  In modern biotechnology,  PCR (polymerase chain reactions),  is used to replicate small amounts of DNA.  DNA strands replicate at low temperature and then are dissociated at a high temperature so that they can then again replicate at low temperature.  These repeating cycles can generate 1015 copies of an original strand in 40 cycles.  Evidence from geological deposits and from the deposition of materials in stromatolites and shellfish indicate that the length of the day in early earth was less than it is now.  It is thought that the moon originated from an impact with the forming earth about 5 billion years ago.  By 3.9 billion years ago, it is thought that the moon was closer to earth than it is now (perhaps 200,000 km distant as opposed to modern 380,000 km) and that the earth’s rapid rotation produced days 2-6 hours in length.  These factors would have meant that the coastline experienced frequent large-scale tides which might have stretched 100 km inland.  Thus molecules would have experienced a continuous, rapid alteration of hot, dry conditions with more concentrated salts followed by dilute, cool, aqueous conditions.  Proteins can’t replicate well under these conditions but DNA would.  DNA and RNA strands would have associated in the presence of salts, especially on the surfaces of minerals, and dissociated when diluted (Lathe, 2004).  At high temperatures, amino acids form clusters and small peptides (Andras, 2005).

     Certain mineral surfaces (feldspar, calcite, zeolites, clays) provide sites where small organic molecules fuse to form larger ones.  Chains of the amino acid glycine have formed on clays.  A common clay, montmorillonite, catalyzes the union of RNA nucleotides.  The small molecules (RNA nucleotides, amino acids) absorb onto these surfaces, and since apparently they are in close enough proximity to each other and in the right orientation, they can bond to form chains.  Small proteins of over 200 amino acids have been produced and short strands of DNA and RNA (up to 50 nucleotides long).   In the case of RNA, the type of bond between nucleotides found in living organisms (3’ to 5’) is the predominant bond form rather than alternate bonds (such as 2’ to 5’) (Parsons, 1998; Sowerby, 2001; Saladino, 2001; Rode, 1999).  Clay minerals such as montmorillonite bind RNA, including ribozymes, and protect them from degradation from UV light and X rays (Biondi, 2007; Franchi, 2005).

      Living organisms use organic molecules which have incorporated metal ions for a variety of activities such as reactions involving energy storage molecules (such as pyruvic acid).  Such organometallic compounds can be synthesized without life (in conditions similar to those found in the ocean’s hydrothermal vents) and they in turn can synthesize pyruvic acid (Cody, 2000). 

 

 

 

3) Can molecules replicate themselves in the absence of life?  Yes.

REPLICATE

      Short RNA and DNA molecules can serve as templates and replicate themselves.  One RNA molecule has actually shown itself not only to be a template of its own replication, but a catalyst of the replication of other RNA molecules as well (Green, 1992; Doudna, 1991).   In 1996, a small protein (based on a protein found in yeast) was observed to replicate itself (Lee, 1996; Kauffman, 1996).  Self-replicating peptides based on coiled motifs have been observed (Ghosh, 2004).  Amines and esters can combine to form an amide which then serves as a template for other amines and esters to do the same.  There are a number of organic molecules which are not found in living things which have been shown to replicate (especially vinyl homopolymers and copolymers) (Orgel, 1992; Rebek, 1994).  Yeast, fungi, and mammals possess unrelated prion proteins which can generate fibers under certain conditions (Chernoff, 2004).

      Some experiments have tried to simulate “natural selection” acting on self-replicating molecules.  Molecules continue to replicate themselves but mutations occur as the rounds of replication continue.  Not only can the replication continue, apparently indefinitely in the right conditions, mutations arise which allow the molecules to replicate faster (so that they have an advantage over the original molecules used).


 

4) Living organisms use certain forms of molecules (stereoisomers) and not others.  Can this nonrandom selection of stereoisomers occur in the absence of life?  Yes.

STEREOISOMER STEREOISOMER

    When organic molecules form in the absence of life, alternate forms exist which differ in their “handedness” although they are identical in their chemical formula.  The two molecules given above are alternate forms of the same molecular structure (called D-stereoisomers and L-stereoisomers).  In living things, the vast majority of sugars are D-stereoisomers while the vast majority of amino acids are L-stereoisomers.        How could living things accumulate one specific stereoisomer from pools of building blocks composed of both stereoisomers?  There are a number of ways in which chains of molecules can with a predominance of one of the stereoisomers.   It is possible that the L stereoisomers of amino acids that are found in living things (as opposed to the D stereoisomers which are not) are more commonly formed under abiotic conditions.  The Murchison meteorite dates to about 4.5 bya, a time before the appearance of life on earth.  Not only were amino acids found inside this meteorite (including ones which are either very rare on earth or have never been isolated), there were excesses of the L-stereoisomers (Cronin, 1997; Bada, 1997; Chyba, 1997). Some amino acids isolated from meteors do exist with a predominance of L-isomers (Pizzarello, 2004). tRNA molecules are the first components of the translation apparatus to interact with amino acids. tRNA molecules preferentially interact with l-amino acids (rather than d-amino acids), suggesting that the structure of molecules in the RNA world determined the homochiral nature of proteins (Tamura, 2008).

     Mineral surfaces have been shown to provide sites where small organic molecules can join to form larger molecules.  Calcite separates different stereoisomers of organic molecules so that resulting chains contain only one stereoisomer (as in modern living things) rather than random mixtures of different stereoisomers (Hazen, 2001).  When serine amino acids form octamer clusters, there is a preference for clusters of the same stereoisomer.  Such clusters would determine the handedness of the molecules they interacted with (Schalley, 2002).  Analysis of the Murchison meteorite not only has isolated amino acids, but an excess of the L-amino acids.  Not only was there a non-random occurrence of the two stereoisomers of amino acids, the form most common in the meteorite is the form most common in living things today (Engel, 2001).  When peptide bonds are formed around a chlorocuprate salt complex, the central copper atom influences the selection of the amino acids forming new bonds based on handedness and favors the formation of chains of one stereoisomer (Plankensteiner, 2004; Plankensteiner, 2005). It is possible that homochirality is a requirement for self-replication and that the first self replicating molecule instituted homochiral biomolecules (Kuhn, 2008).

     A new protein called dirigent can maneuver reacting molecules so that only one stereoisomer is formed and these reactions can occur in the absence of life (Davin, 1997; Kaiser, 1997).  It has been demonstrated that in short nucleotide chains which are replicating in the absence of life will produce chains made of the same type of stereoisomer (Joyce, 1984).  Attaching amino acids to molecules similar to nucleotides can determine which stereoisomer is formed (for example, the L-form of the amino acid lysine attached to peptide nucleic acid [PNA] monomers can cause a chain in which only L-stereoisomers of these monomers are used).  Not only are chains using the same stereoisomer completed faster than those with the opposite form, the incorporation of opposite stereoisomers inhibits the replication of the strand (Wittung, 1994).  (Thus the first living things would have had an advantage if they evolved a mechanism to insure that only one stereoisomer was used.)   Other organic molecules (such as tetranucleotide cyclophosphates) can also form short chains with only one stereoisomer (Szathmary, 1997).

 

5)     Could organic molecules form membranous balls?  Could these precells perform some activities that cells perform? Yes.

MEMBRANE

  In the absence of cells, lipids in solution can form layers that are similar in structure and function to cell membranes.  Such lipid bound balls can be called micelles, coacervates, and microspheres and can be considered protocells (Conde-Frieboes, 2001; Simoneit, 2004; Trevors, 2003a). Lipid bilayer membranes can self-assemble from the organic molecules in meteorites (Deamer, 2003). New lipids can be synthesized from precursors in these micelles in the absence of life.  These vesicles can accumulate organic molecules inside, increase in size, and even split once they reach a certain size (Bachmann, 1992; Luisi, 1989; Morowitz, 1988; Luisi, 1999).).  If enzymes (proteins which speed chemical reactions) are in these droplets, chemical reactions can occur.  If they contain the enzyme RNA polymerase, RNA nucleotides are taken from the environment and assembled into RNA chains.  Organic molecules gathered from meteorites have been found to form these membranous balls in water. Proteins which existed before RNA could have stabilized protocells, facilitating the development of RNA (Andras, 2005).  Clays such as motmorillonite accelerate both the formation of RNA polymers and the formation of lipid vesicles (Delaye, 2005; Biondi, 2007).

     Organic molecules which can form membranes continue to be synthesized in modern times.  The Mid-Atlantic Ridge today possesses volcanic rock low in SiO2 (ultrafamic rock), a type of rock which was much more abundant in the early history of the earth.  This rock not only generates hydrogen gas (as iron is oxidized) which bacteria can use as an energy source, it also forms hydrocarbons (with chains up to 29 carbons).  Such molecules could have been important in the formation of the first membranes (Holm, 2001).  Simulations of the formation of organic molecules in the interstellar ices of comets (using UV light) form organic molecules that self-assemble into such vesicles (Dworkin, 2001).

     The surface between layers of water and lipid can also be important for assembly of these structures.  Liquid hydrocarbons could have developed on the early earth through chemical reactions occurring in anoxic conditions (as has been demonstrated in labs), through electrical activity in an atmosphere containing methane, in deep-sea vents, and in meteorites.  The surface between such liquid hydrocarbons and surrounding water could have provided a surface at which the first lipid membranes (which are nonpolar like the hydrocarbons) could have developed without the need of enzymes.  The diffusion of nonpolar hydrogen gas (which bacteria can use as an energy source) through this nonpolar material could have provided an early energy supply (Trevors, 2003a).  Lipids spontaneously form micelles, droplets, bilayers, and vesicles in water and on the surface of water (Trevors, 2003a)

 

THE LEAP TO THE RNA WORLD

     The next topic will describe the possibility of protocells whose metabolism and genetics was based on RNA.  Although RNA nucleotides can both form and assemble into chains in the absence of life, some feel that there might have been an important step which immediately preceded the wide usage of RNA (Luisi, 1999).  Peptide nucleic acid (PNA) is achiral and might have been an early predecessor to RNA.  Diamino acids which might have supported a chemistry of PNA have been found in meteorites Another possible predecessor of RNA which can be synthesized in the absence of life is tetrose nucleic acid TNA. TNA nucleotides form stable bonds with themselves and with RNA nucleotides (Joyce, 2002, Bada, 2004; Meierhenich, 2004). N-phosphoryl amino acids (PAA) can be synthesized abiotically.  They may be important in consideration of the origin of life because they can both self assemble into small peptides and add phosphates to nucleosides to form nucleotides.  It is possible that they formed early small proteins which helped to generate the precursors of the RNA world (Lehman, 2004). A number of sugar units can be used in nucleotide synthesis. A variety of pentopyranosyl sugars can generated oligonucleotides with stronger and more efficient base pairings than RNA. It is possible that the “RNA world” replaced a more primitive genetic system (Beier, 1999).Membranes are a site at which low levels of catalytic reactions can occur.  Peptide bonds can form between amino acids linked to fatty acids and alcohols.   This could have predated the RNA world  (Pflug, 2001).

Adenine is formed in prebiotic conditions.  Adenine can react with aldehydes to produce molecules which can function as nucleosides.  This might have predated the synthesis of ribose and more modern nucleosides (Vergne, 2000).  Ribose and other pentose sugars can be synthesized from formaldehyde and glycoaldehyde, two substances which are known from space and were probably present in the early earth. The presence of borate helps to stabilize ribose once it is formed (Ricardo, 2004).