Stanley Miller synthesised amino acids, formaldehyde and HCN in an electric discharge tube that simulated a highly reducing atmosphere of NH3 and CH4 (Miller, 1953).
Butlerov discovered the Formose cycle in 1861 (Butlerov, 1861), which used formaldehyde as its input, and produced a vaste range of sugers, including ribose.
Authors assumed there was a reducing atmosphere composed of CH4, CO, CO2, NH3, N2, and H2O, with UV light, heat, and electric discharges, that water was the main solvent, that there were moderate pHs (7-9), that drying could occur by evaporation, that pressures and temperatures were similar to those now (Orgel and Lohrmann, 1974).
The Evolution of Biosphere Metabolism.
The Evolution of Autocatalytic Metabolic Cycles.
The Evolution of Metabolism on Surfaces.
The Chemical Evolution of Nucleic Acids: The RNA World Hypothesis.
Having considered chemical evolution of intermediate metabolism, let us move to the question of the origin of the precursors required for template replication.
The RNA world hypothesis was an answer to the chicken and egg question, "What came first, proteins or nucleic acids?" The question was raised because no evolvable minimal self-replicating system could be envisaged or produced with either of these substrates alone. Woese (1967), Crick (1968) and Orgel (1968) initiated a research program to demonstrate how non-enzymatic template replication would be possible. The discovery of ribozymes lead to a renewed interest in the importance of RNA, as both genotype and powerful phenotype.
Orgel and others hypothesised in the 1970s that pyrimidines, purines and pentose sugers (the components of nucleic acids) formed in a "prebiotic soup", that they combined with inorganic phosphate to form activated monomers, that these polymerized to form oligonucleotides, and that these oligonucleotides replicated by complementary base pairing (Orgel and Lohrmann, 1974).The fundemental assumption that underlies these earlier versions of the RNA world hypothesis seems to be that significant quantities of evolution did not take place before RNA template replication existed. This strong version of the RNA world can be rejected. No-one has explained satisfactorily how RNA template replication could arise spontaneously without some prior evolution.
Now Orgel writes that "I believe it is very unlikely that RNA did arise prebiotically on the primitive earth. Ribonucleotides are such complicated molecules that they are not likely to have formed in sufficient amounts and with sufficient purity on the primitive earth to permit the formation of even the simplest self-replicating RNA molecule. Consequently, we will now assume that 'organisms' based on some more easily synthesized polymeric, genetic material preceeded the RNA world." (Orgel, 2003). One reason for this change of heart is presumably the several decades of research that have shown how difficult it is, even using chemists, to produce a non-enzymatic template replication system from formaldehyde and hydrogen cyanide under prebiotic conditions. [These expriments are reviewed below.] Orgel now accepts the need for an 'informational chemistry' that preceeded the RNA world. Orgel supports chemoton theory saying that "pre-RNA organisms must at least have been able to produce ribose and make phosphoester bonds." However, his view differs from chemoton theory because he claims that these pre-RNA organisms must have had fairly sophisticated 'enzymes' (ibid p213). Such enzymes would have been of a non-protein substrate, (unless protein replication would have been possible before RNA), perhaps mineral as suggested by Cairns-Smith's theory of 'genetic takeover' (Cairns-Smith and Davies, 1977). Orgel distinguishes two types of takeover, discontinuous and continuous. In discontinuous, sequence information from the 1st system is not directly present in the second system, whereas in continuous takeover, monomers of the new genetic system substitute 1:1 the monomers of the 1st system. An example of the continuous type of takeover may be the transition from RNA to DNA. The importance of dual inheritance systems will be considered in due course. First we consider the problem of the origin of template replicating precursors.
The Prebiotic Formation of Nucleotides is Unexplained.
The Formose cycle is the primary candidate for the production of ribose and its phosphates, perhaps in Metal-Hydroxide Minerals (Orgel, 2004). Oro (1960) discovered the synthesis of adenine (a base component of nucleic acids) from very high concentrations of ammonium cyanide (ref), although it is difficult to imagine a prebiotic circumstance in which such a synthesis could occur. Orgel later discovered a more plausible prebiotic syntheis route for purines (ref), from a cold concentrated solution of HCN, suggesting a cold phase in the origin of life. No prebiotic route for pyrimidine synthesis is known. Nucleosides (combinations of the purine or pyrimidine base and the ribose suger) the have been difficult to produce under prebiotic conditions. Selective phosphorylation of nucleosides is not possible with inorganic phosphates, but is better with trimetaphosphates. Due to the lack of specificity of phosphorylation reactions, It is likely that early on, a mixture of polyphosphates existed, high energy molecules, with the capacity for a very wide range of reactions.
In conclusion, complex racemic mixtures of activated monomers would be expected in any early system. What mechanisms could explain the conversion of this messy system, consisting of non-specific reactions, and non-replicating polymers, into the precise set of replicatable nucleotides that exist in all extant living systems?
Orgel rejects the possibility of self-organization biochemical cycles without RNA templates as suggested by Weschtershauser (considered above) due to the lack of evidence that such self-organization can take place, and suggets that a template replicating polymer system is necessary (Orgel, 2000). It is one of the aims of this thesis to consider what self-organizing principles exist in metabolic systems, that can account for the origin of the RNA world.
The Prebiotic Polymerization of Nucleotides is Unexplained.
Nucleoside 2'-3'-phosphates, and activated nucleoside 5'-phosphates were used by Orgel et al to make oligomers, but their reactions were slow. Later, phosphoramidates were produced that could polymerize more rapidly. Kanavarioti et al, 2001 used ionic catalysts to synthesise 16-mers from Nucleoside 5'-phosphorimidazoles (Kanavarioti, 2001). Early experiments produced many 2'-5' isomers, or random mixtures of isomers. Ferris et al (2003) used monomeric 5'-phosphoroimidazolide nucleoside bulding blocks and a montmorillonite clay catalyst to produce 55-mers after 14 days. Encouragingly, 80% of the product was 3'-5'. Neither of these two reaction methods are prebiotically plausible.
Another theory was that of Oparin's coacervate droplets, positively charged droplets in the atmosphere. (Oparin ref). However, no evidence exists for their catalytic effects on nucleic acid polymerization.
The Origin of Prebiotic Template-Directed Synthesis is Unexplained.
Once polymers have formed, one must explain how these polymers can be replicated by catalysing the formation of complementary 3'-5' linked nucleotides, irrespective of sequence.
Early attempts to produce template-directed oligonucleotides used poly(U) templates to condense A with A, but could not attach A to C, U or G, evidence that Watson-Crick base pairing was responsible for the attachment of monomers to poly(U). Poly(C) was shown to catalyse the condensation of G with G, but not G with U, C, or A. However, the products were both 2'-5' and 5'-5' linked, not generally 3'-5' linked as in biological nucleic acids. The choice of metal iron was shown to effect the type of isomer, Mg++ and Pb++ produced 2'-5' bonds, whereas Mg++ and Zn++ produced 3'-5' bonds. Different activating agents were used to try to obtain isomer specificity, and sequence independence. Further details of experiments on template directed synthesis are found in the background chapter section "Non-Enzymatic Template Replication".
Evidence that RNA is Ancient.
Orgel claims that the existence of ribosomal peptide synthesis makes the RNA world almost certain (Orgel, 2004). Several authors have argued that NAD may be a molecular fossil from the RNA World (Orgel, 2003). [Discuss the evidence for this, and whether it is consistant with RNA in Protocells, or RNA outside protocells. At first glance it seems to be consistant with RNA in protocells, and not with RNA outside protocells. Orgal quotes.. Woese, 1967. Orgel, 1968. Orgal and Sulston, 1971. White, 1976.].
Coupled Inheritance Systems.
Cairns-Smith claims that a linear clay polymer must have evolved before RNA, because RNA is too complex to have arisen spontaneously. Unfortunately there is no demonstration of evolution in clay.
In opposition to Cairns-Smith's clays, Segre and Lancet have suggested that a lipid world could be a precursor to the RNA world. They propose that membrane lipid composition can act as an inheritance system.
Are any traces of earlier genetic systems retained in extant organisms?
The Thermodynamics and Kinetics of Living Systems.
A large literature exists on this subject. It is clearly the case that living systems are kinetically stable, but thermodynamically unstable. Several authors have written about how living systems have evolved to utilize energy to preserve themselves in a high free energy state. For example, Szoke et al (2003) describe how a motief of living systems is the presence of 'energy converters' that use drive reactions to convert themselves into a higher energy state from where they can then partake in other reactions, so reducing the heat wasted in the drive reaction. They give the example of membrane bound pyrophosphatases that can pump protons across the membrane. Their figure 1. is shown below.
Szoke et al claim that Catalysts of type 1 are more typical of living systems, since D is a kinetically stable product of food molecule B, but not a thermodynamically stable product compared with C. But why should living systems be selected for this sort of catalysis? One possibility is that a living system with a higher free energy is easier to recycle back into its food molecules once it degenerates.
Bibliography
Eschenmoser, A. Chemical Etiology of Nucleic Acids (2000) Pure Appl chem, 72, 343-345. Download pdf.
Szoke, A. William G. Scottc, Janos Hajdua. Catalysis, evolution and life. FEBS Letters 553 (2003) 18-20. Download pdf.
Orgel, L.E. Lohrmann, R. Prebiotic Chemistry and Nucleic Acid Replication. (1974). Accounts of Chemical Research, 7, 368-
Orgel, L.E. Some consequences of the RNA World Hypothesis. (2003) Origins of Life and Evolution of the Biosphere. 33, 211-218.
Orgel, L.E. Prebiotic Chemistry and the Origin of the RNA World. (2004) Critical Essays in Biochemistry and Molecular Biology.