Theories on the Origin of Life

The leading theories on the origin of life could be divided into three main groups:
1) the RNA world
2) under high temperature and pressure
3) extraterrestrial origin

Some background information

The subject matter is generally divided into five stages:

• synthesis of organic compounds
• synthesis of biochemical substances (experiments mainly reports on the production of amino acids under presumed prebiological conditions).
• having to do with the production of large molecules such as proteins.
• having to do with organized cellular structures.
• concerns the evolution of macromolecules and metabolism.

The macromolecules of life:

• amino acids are the building blocks of proteins, which are synthesized at one of many small cellular bodies called ribosomes. In meteorites we can detect over 70 amino acids, but human bodies only make use of 20 amino acids.
• proteins are organic compounds, which are essential biomolecules of all living organisms. Their elements are: hygrogen, carbon, oxygen, notrogen and sulphur. They are made up of a series of amino acids
• the nitrogeneous base compounds U, C, G, A and T are ring compunds which are constituents of nucleic acids.
• nucleic acids are organic molecular structures consisting of five-carbon sugars, a phosphate and mainly one of the five bases
• lipids are a wide group of organic compounds having in common their solubility in organic solvents, such as alcohols. They are the constituents of cell membrane and have a multitude of other important roles.

Somethings that I have read up on:

1. To create macromolecules of life
2. When can earliest life form?
3. Prebiotic Earth
4. The nonenzymatic synthesis of biological monomers in an atmosphere of methane, nitrogen, ammonia, and water
5. The RNA world
6. Life originated from extreme conditions and its relation to minerals
7. Why extraterrestrial origin of life?

When can earliest life form?

• The Earth was thought to coalesce about 4.5 billion years ago.
• Microfossils found in ancient rocks from Australia and South Africa demonstrate that terrestrial life was flourishig by 3.5 billion years ago. Even older rocks from Greenland, 3.9 billion years old, contain isotopic fingerprints of carbon that could have belonged to a living organism. In other words, only 100 million years or so after the earliest possible point when Earth could have supported life, organisms were already well enough established that evidence of them remains today.
• 'Zircon' are minerals of great resistance to high temperature and pressure. Specific analysis of the isotopes of elements (uranium and lead) present in a grain of zircon from the Narryer Gneiss Complex in Western Australia are consistent with the presence of continental crust and even liquid water between 4.4 and 4.3 billions years ago. It is known that heavy oxygen is produced by the interaction between rock and liquid water, a process that should occur at sufficiently low temperatures. The presence of the heavy isotope of oxygen in the zircons from the sample mentioned above suggest that magma had been produced by an episode of high temperature (or heavy pressure) on the surface of the early Earth, on which there was liquid water.

Prebiotic Earth:

• According to the accretion model, several lunar-(0.01 Earth mass) to Mars-sized (0.1 Earth mass) objects would have impacted the Earth. The number, size and position of the terrestrial planets are partly a consequence of the randomness associated with the small number of these bodies. The conditions associted with a very large impactor of lunar or Martian size are extreme and would have wiped out much of the earlier structure of the planet to depth of many kilometers. Any life forms that may have existed at the time would not have survived.So, the question is when could the last impact be? It is estimated to be 4.5 billion years ago, the age of the oldest moon rock.
• The size distribution and the flux of the objects that formed the Earth in the first 10 years are important. With a continual flux of smaller objects, water would have been kept in the atmosphere and hydrogen would have been lost to space at a significant rate. The water that dissolved in the molten rock would have been transported to the interior by convection. Below about 100km depth, the water would have been lost by reaction with metallic iron to form iron hydride in solution in the iron phase and ferrous oxide in silicates. Carbon as CO, CO₂, or CH₄ is not readily lost to space, but carbon is soluble in iron and some should have entered the core.
• Accretion and the formation of the Earth's core are thought to have occurred simultaneously. Giant impacts supplied their already differentiated cores to the Earth. Enormous amounts of heat were added to the Earth by the processes. Most of this heat had to escape to space for the Earth to cool below the melting point. Plate tectonics is much too slow to release this heat. A more likely form of convection is by total melting of material at depth and eruption of the material to the surface. As a result, preexsting metallic iron carried by accreting bodies would have been removed from near-surfaced regions.
• If segregation of iron into the core was inefficient and metal remained in the upper mantle to buffer the redox state of magmas, or if the metallic core, mantle, and outgassed volatiles were all in thermodynamic equilibrium during the period of rapid heat loss, CO and CH₄ would have been the predominant thermodynamically stable forms of carbon injected into the atmosphere form the interior. The primitive atmposphere would have been rich in H₂, CO, CH₄, NH₃ and H₂S. Furthermore, the impacts of large iron-bearing asteroids comparable in mass to that of the oceans may have yielded pulses of highly reduced gases as a result of equilibration between vaporized iron and elemental hydrogen, carbon, nitrogen and sulphur.
• In the absence of metal, the composition of the atmosphere would have been determined by the redox state of the near-surface metal-free silicate melts. Under this circumstance (neutral redox composition), CO₂ would have been the predominant carbon-bearing gas; other major atmospheric constituents would have been N₂ and H₂O; sulphur would have emerged from hydrothermal vents as H₂S; and CH₄. CO and H₂ would have occured at trace amounts at best.

The nonenzymatic synthesis of biological monomers in an atmosphere of methane, nitrogen, ammonia, and water (a portion in 1981 report of Space Studies Board):
[There are] many observations that gaseous mixtures, for example, methane, nitrogen, ammonia, and water, if supplied if energy such as spark discharges, produce amino acids including those found regularly in proteins. The distribution if monomers so produced is qualitatively and quantitatively similar to that found in carbonaceous meteorites. In addtion, most protein amino acids may be produced nonenzymatically starting with simple organic compounds such sa formaldehyde and hydroxylamine.

Furthermore, the abiotic routes of formation of all the components of DNA and RNA are known. Sugars easily form spontaneously from formaldehyde; polymerization occurs under alkaline conditions. The condensation of hydrogen cyanide in the presence of ammonia produces amino acids as well as the purine nucleotide bases, adenine and guanine, components of all nucleic acids. Cytosine, a base found in nucleic acids, can be readily synthesized from cyanoacetylene. By deamination, cytosine yields another major base of RNA, uracil. Thymine, a major base of DNA, which in today's genetic code is informationally equivalent to uracil, can be formed from the condensation of uracil with formaldehyde. In the presence of phosphate the phosphorylated forms of the nucleotides of these bases can be produced nonenzymatically. Fatty acids may be formed from carbon monoxide and hydrogen in the presence of nickel-iron catalysts, catalysts that might have been brought in by meteorites. Glycerol is a component of fats that has also been obtained nonenzymatically in the laboratory by reduction if glyceraldehyde. Glyceraldehyde itself, a common intermediate in cell energy-yielding reactions, may be formed by condensation of formaldehyde under alkaline conditions.
Top

The RNA world:

• Darwin's theory on natural selection implied that all current life-forms could have evolved from a single, simple progenitor which is referred to as the 'last' common ancestor. By identifying the commonalities in contemporary organisms, we can infer that intricate features present in all modern varieties of life also appeared in the common ancestor because it is next to impossible for such universal traits to have evolved separately. One feature is the presence of genetic information and the means to replicate and carry out those heritable instructions for functioning and reproducing. In addtion, the system for replicating genetic material had to allow for some random variation in the heritable characteristics of the offspring so that new traits could be selected and lead to the creation of diverse species.
• Another commonality is that all living things consist of similar organic (carbon-rich) compounds. Also, the proteins found in present-day organisms are fashioned from one set of 20 standard amino acids. Furthermore, all contemporary organisms carry their genetic information in nucleic acids - RNA and DNA - and use essentially the same genetic code. From these findings, we can infer that the last common ancestor stored genetic information in nucleic acids that specified the composition of all needed proteins. It also relied on proteins to direct many of the reactions required for self perpetuation. The question now becomes where does the proteins and nucleic acids come from?
• The Chicken and Egg problem (nucleic acids and proteins):Nowadays nucleic acids are synthesized only with the help of proteins, and proteins are synthesized only if their corresponding nucleotide sequence is present. It is extremely improbable that proteins and nucleic acids, both of which are structurally complex, arose spontaneously in the same place at the same time. Yet it also seems impossible to have one without the other. The paradox is resolved by the RNA world - a world in which RNA catalyzed all the reactions necessary for the precursor of life's last common ancestor to survive and replicate. The RNA could subsequently have developed the ability to link the amino acids together into prteins. For the RNA world to exist, RNA needs the capacity to replicate without the help of proteins and an ability to catalyze every step of protein synthesis.
• Why RNA is favored over DNA as the originator of the genetic system: The ribonucleotides in RNA are more readily synthesized than are the deoxyribonucleotides in DNA. It is easy to envision ways that DNA could evolve from RNA and then, being more stable, take over RNA's role as the guardian of heredity. Researchers suspect that RNA came before proteins because they face difficulty composing any scenario in which proteins could replicate in the absence of nucleic acids.
• In 1983, Thomas R. Cech and Sidney Altman independently discovered the first known ribozymes, enzymes made of RNA, indicating that the ancient RNA may have been catalytic. However, no RNA molecules that direct the replication of other RNA molecules have been identified in nature. In the mean time, Cech and Jack W. Szostak have modified naturally occurring ribozymes so that they can carry out some of the most important subreactions of RNA replication, such as stringing together nucleotides or oligonucleotides.
• In an experiment, Szostak created a pool of random oligonucleotides to approximate the random production presumed to have occurred some 4 billion years ago. From that pool, he was able to isolate a catalyst that could join together oligonucleotides. Also, the catalyst could draw energy for the reaction from a triphosphate group, the very same group that now fuels most biochemical reactions in living systems.
• Another piece of supporting evidence that RNA could have created protein synthesis is that Harry F. Noller, Jr. discovered that it is RNA in ribosomes, not proteins, that catalyzes formation of the peptide bonds.
• To explain how self-replicating RNA was created from its constituents, it is hypothesized that the nucleotides in RNA formed when direct chemical reactions led to joining of the sugar ribose with nucleic acid bases and phosphate. Then, these ribonucleotides spontaneously joined to form polymers, at least one of which happened to be capable of engineering its own reproduction.
• First problem with the above hypothesis: in the absence of enzymes, workers have difficulty synthesizing ribose in adequate quantity and purity. It has long been known that ribose can be produced easily through a series of reactions between molecules of formaldehyde. Yet when such reactions occur, they yield a mixture of sugars in which ribose is always a minor product. The relative paucity of ribose would militate against development of an RNA world, because the other sugars would combine with nucleic acid bases to form products that inhibit RNA synthesis and replication. No one has yet discovered a simple, complete chain of reactions that ends with ribose as the main products.
• Second problem: Attempts to synthesize nucleotides directly from their components under preiotic conditions have met with only modest success. One series of experiments has yielded purine nucleosides - units consisting of ribose and a purine base but excluding the phosphate group. Investigators are unable to produce pyrimidine nucleosides efficiently without the aid of enzymes.
• Third proble: formation of nucleotides by combining phosphate with nucleosides has been achieved by simple prebiotic reactions, but the kinds of nucleotides that occur in nature arose along with related molecules having incorrect structures. If such mixtures were produced on the young earth, the abnormal nucleotides would have interacted with the normal ones to interfere with catalysts and RNA replication. It is thus not easy to see how prebiotic reactions could have led to the development of the ribonucleotides needed for producing self-replicating RNA. This problem might be solved by the presence of inorganic catalysts or the existence of nonenzymatic reactions leading to efficient synthesis of pure ribonucleotides that scientists have not yet identified.
• Fourth problem: the condensation of ribose with bases would give complex mixtures of products, including L- as well as D-nucleosides, and nucleosides with alpha- as well as those with beta-glycosidic linkages.
• Fifth problem: Assuming that ribonucleotides were able to emerge nonenzymatically, we still have to demonstrate that the nucleotides could assemble into polymers and that polymers could replicate without the assistance from proteins. Again, the reactions might be catalyzed by minerals. Experiments were conducted to investigate the replication of RNA. In the experiments, scientists synthesized oligonucleotides and mixed them with free nucleotides. The nucleotides lined up on the oligonucleotides and combined with one another to form new oligonucleotides. Forming such complements from an original template - "copying" - would be the first step in prebiotic replication of a selected strand of RNA. Then the strands would have to separate, and a complement of the complemet (a replica of the original strand) would have to be constructed. In practical, scientists were unable to achieve the second step of replication - copying of the complement - without help from protein enzymes. Also, they can induce copying of the original template only when experiments were run with nucleotides having right-handed configuration (all nucleotides synthesized biologically today are right-handed). Since on the primitive earth, equal numbers of both kinds of nucleotides would have been present, scientists put equal numbers of both kinds of nucleotides in the reaction mixtures, but copying was inhabited. The problem may be solved if copying without replication have produced a pair of complementary strands and one of the strands happened to be a ribozyme that could copy its complement and thus duplicate itself.
• First alternative self-replicating molecule: Eschenmoser proposed a molecule called pyranosol RNA (pRNA) that is closely related to RNA but with an extra carbon atom in the ring. Eschemoser finds that complementary strands of pRNA can combine by standard Watson-Crick pairing to give double-strand units that permit fewer unwanted variations in structure than are possible with normal RNA. Also, pRNA strands do not twist around each other. In a world without protein enzymes, twisting could prevent the strands from separating cleanly in preparation for replication. The molecule has not been found yet.
• Second alternative self-replicating molecule: Peter E. Nielsen used computer-assited model building to design a polymer that combines a protein-like backbone with nucleic acid bases for side chains. One strand of this polymer or peptide nucleic acid (PNA), can combine stably with a complementary strand. This implies that peptide RNA may be able to serve as a template for the construction of its complement.

Life originated from extreme conditions and its relation to minerals

• Earth's microbial ecosystems revealed that in 3.5 billion-year-old sediments from Western Australia appear to have occupied shallow marine hydrothermal environments dominated by island volcanism. In addtion, the contemporary microorganisms with the most ancient lineages based on molecular phylogenies are anaerobic, thermophilic, sulphur-metabolizing archaebacteria. These organisms were isolated from hot springs and hydrothermal vents where they thrive up to 105^oC
• Minerals as containers: Some rocks, like gray volcanic pumice, are laced with air pockets created when gases expanded inside the rock while it was still molten. Many common minerals, such as feldspar, develop microscopic pits during weathering. Each tiny chamber in each rock on the early earth could have housed a separate experiment in molecular self-organisation. The hydrothermal origins hypothesis was rejected because amino acids decompose rapidly when they are heated. In 1998, Jay A. Brandes conducted an experiment in which the amino acid leucine broke down within a matter of minutes in pressurised water at 200^oC. But when Brandes added to the mix an iron sulphide mineral of the type commonly found in and around hydrothermal vents, the amino acid stayed intact for days.
• Minerals as scaffold: Clays are made up of various ions embedded in a two-dimensional silicate lattice. The elements involved are mainly silicon, oxygen, aluminium, iron and magnesium. Clays are formed when water causes the chemical weathering of rocks. The concentration of ions in clays is extremely variable; the surfaces of clays usually have a net negative charge that is neutralised by a positive counter-ion (e.g. Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺, Fe²⁺). These charges might be able to attract organic molecules and hold them in place. In the late 1970s an Israeli research group demonstrated that amino acids can concentrate on clay surfaces and then link up into short chains that resemble biological proteins. These chemical reactions occurred when the investigators evaporated a water-based solution containing amino acids from a vessel containing clays. Separate research teams led by James P. Ferris of the Rensselaer Polytechnic Institute and by Gustaf Arrhenius of the Scripps Institution of Oceanography demonstrated that clays and other layered minerals can attract and assemble a variety of organic molecules. The team at Rensselaer also found that clays can act as scaffolds for the building blocks of RNA.
• Minerals as templates: The chemical structure of calcite in many mollusk shells bonds strongly to amino acids. With the help of his colleages, Robert M. Hazen ran experiments to immerse well-formed, fist-size crystal of calcite into a 50-50 solution of aspartic acid. They observed that calcite's "left-handed" faces selected L-amino acids, and vice versa, with excesses approaching 40% in some cases. Also, calcite faces with finely terraced surfaces displayed the greatest selectivity. Thus, the researchers speculate that these terraced edges might force the L and D amino acids to line up in neat rows on their respective faces. Under the right environmental conditions, these organised rows of amino acids might chemically join to form protein-like molecules - some entirely of L amino acids, others entirely of D.
• Minerals as catalysts: When Brandes and his colleague subjected hydrogen, nitrogen and the iron oxide mineral magnetite to the pressures and temperatures characteristics of a seafloor vent, the mineral catalysed the formation of ammonia, which is required in biological reactions. In 1988 Wachtershauser proposed that minerals - mostly iron and nickel sulphides that abound at deep seafloor vent - could have served as the template, the catalyst and the energy source that drove the formation of biological molecules. Researchers at Carnegie placed ingredients known to be available to the young earth in capsules and placed the capsules in a massive steel pressure chamber that squeezes the tiny capsules to pressures approaching 2000 atmospheres and heats them to about 250^oC. It is found that many common minerals, including most oxides and sulphides of iron, copper and zinc, promote carbon addition by a routine industrial process known as Fischer-Tropsch(F-T) synthesis. This process can build chainlike organic molecules from CO and hydrogen. It was also demonstrated that F-T reactions can build molecules with 30 or more carbon atoms under some hydrothermal-vent conditions in less than a day.
• Minerals as reactants: In the catalysis experiments mentioned above, significant quantities of elemental sulphur, organic sulphides, methyl thiol and other sulphur compounds appeared as well. The sulphur in the compounds must have been liberated from the iron sulphide mineral. Liberation of iron was also found. This suggested that iron and sulphur, the elements that form the active center of certain biological enzymes such as aconitase, can be dissolved from iron sulphide minerals under extreme heat and pressure.

Why extraterrestrial origin of life?

• Scientists suspect that the early days were hot, dry and sterile. It is now clear that space debris bombarded the young planet, creating cataclysms equivalent to the detonation of countless atomic bombs. Impact of this kind, common until 4.0 billions years ago, surely aborted any fledgling life struggling to exist before that time. The short time span for life to emerge implies that the process might have required help from space molecules.
• Since his first report in 1993, John R. Cronin of Arizona State University has demonstrated a slight surplus of left-handed-ness in several amino acids extracted from two different meteorites. Some believe life's left-handedness is by chance, but extraterrestrial starting ingredients may have predetermined this molecular peculiarity
• Astronomers see signatures of a range of organic compounds throughout the universe, especially among the clouds. For example, a decade of research conducted by Allamandola and others has revealed that polycyclic aromatic hydrocarbons are the most abundant class of carbon-bearing compounds in the universe, trapping as much as 20 percent of the total galactic carbon in their molecular lattices.
• Experiments revealed that even at the extremely low temperatures and pressure of space, the UV radiation can break chemical bonds. When the atoms are locked in ice, this bond-breaking process can make molecular fragments recombine into unusually complex structures that would not be possible if these fragments were free to drift apart. Bertein started with a simple ice of frozen water, methanol and ammonia - in the same proportions seen in space ice - the experiment yielded complex compounds such as the ketones, nitriles, ethers and alcohols found in carbon-rich meteorites. They also created hexamethylenetetramine, or HMT, a six-carbon molecule known to produce amino acids in warm, acidic water. David W. Deamer found that some of the molecules in the cloud-chamber ice grains form capsulelike droplets in water. These capsules are strikingly similar to extracts of meteorites from Murchison.
• Researchers found that interstellat amorphous ice when exposed to radiation such as that found in deep space, it too can flow. Thus, it could be an explanation of how organic molecules may endure and react within the ice.
• Emerging consensus in planetary science agree that the early prebiotic atmosphere is a neutral one rich in carbon dioxide and molecular nitrogen. Early CO₂-rich atmospheres are implied by "hot" accretion scenarios for Earth, in which core formation takes place quickly, leaving the upper mantle in an oxidized state. The short photodissociation lifetimes of CH₄ and NH₃ in model paleoatmospheres reinforce this conclusion. There is a dense, 10- to 20-bar CO₂ early terrestrial atmosphere, consistent with the early faint sun "paradox". Synthesis of key prebiotic molecules such as hydrogen cyanide and formaldehye would have been much more difficult in CO₂ atmospheres than in reducing ones.
• A long standing objection to extraterrestrial origin is that the organic compounds would be totally dissociated by the heat of cometary atmosphere passage and the ensuing impact. However, researchers speculated that aerobraking (slowing by atmospheric drag) and uneven distribution of shock energy throughout theimpacting projectile will conspire to yield some region of the comet for which temperatures remain low enough to allow at least the hardier organics to survive. Because gas-phase results on shock pyrolysis are not available, it is estimated that alanine could withstand temperatures of ~700K for 1s, whereas other amino acids should withstand temperaturesin the range of 600 to 800K. Through modelling, it is shown that dense CO₂ atmospheres allow intact cometary organics to be delivered in large amounts. (this part i don't really understand all the equations)