I now turn to some of the evidence for abiogenesis in more detail, though this article I wrote some time ago needs updating with new data, but it’s still sufficient to demonstrate that we have a large body of evidence supporting the relevant postulates.
The Emergence Of Life On Earth
In the earliest period of the history of the planet, it was a body devoid of life, and conditions on the planet were far from conducive to the appearance of life, particularly during the episode termed “The Late Heavy Bombardment”[1] by scientists, which saw intense bolide impact activity taking place on the planet’s surface. Once this episode, and subsequent episodes postulated to have taken place, were complete, the Earth cooled, a solid crust formed, and liquid water in quantity began to appear. Thus, the stage was set for the processes that were to result in the emergence of life.
It was Darwin himself who first speculated about the origins of life, with his short remarks about a “warm little pond”[2], but, in the middle of the 19th century, this would remain speculation, as the means to determine the mechanisms that might apply had not yet been developed. However, it made eminent sense to scientists following Darwin, to hypothesise that any natural mechanisms responsible for the origin of life would be based upon organic chemistry, since life itself is manifestly based thereupon - millions of organic reactions are taking place within your body as you read this, and indeed, the cessation of some of those reactions constitutes the end of life for any organisms affected.
Alexander Oparin, the Soviet biochemist, was the first to publish hypotheses about the chemical basis of the origin of life[3], and based his own hypotheses on the notion that a reducing atmosphere existed on the primordial Earth, facilitating the production of various organic compounds that would then react further, producing a cascade of escalating complexity that would ultimately result in self-replicating entities. Back in 1924, his hypotheses remained beyond the remit of scientists to test, but that would soon change.
The first indications that Oparin had alighted upon workable ideas came in 1953, with the celebrated Miller-Urey Experiment[4], in which electrical discharges in a reducing atmosphere composed of simple molecules produced measurable quantities of amino acids. Miller himself only cited the presence of five amino acids, as he was reliant at the time upon paper chromatography as his primary analytical tool, which was only sensitive enough to detect those five amino acids cited. However, Miller had been more successful than he originally claimed: after his death, preserved samples of his original reaction mixtures were subject to state-of-the-art analysis, using gas chromatograph mass spectrometry, a technique millions of times more sensitive, and regarded as the ‘gold standard’ in modern organic analysis. That subsequent analysis yielded not five, but twenty-two amino acids[5].
Early criticism of Miller’s work in the scientific community focused upon the requirement for a reducing atmosphere in accordance with the Oparin model. However, subsequent workers determined by repeat experimentation, that a range of atmospheric constitutions would be suitable for a Miller-Urey type synthesis on a prebiotic Earth[6], several of those constitutions being only mildly reducing, expanding the range of conditions for which the Oparin model would be viable. More recently, work has suggested that the prebiotic Earth could have developed an atmosphere containing considerably more hydrogen than originally thought[7], making the Oparin reducing atmosphere once again more plausible. Indeed, the range of conditions under which amino acids could be synthesised has since been expanded to include interstellar ice clouds, courtesy of more recent research[8 - 14], and the Murchison meteorite was found to contain no less than ninety amino acids, nineteen of which are found on Earth, which were obviously synthesised whilst that meteorite was still in space. Other data from meteorites adds to this body of evidence[10, 15, 16].
The formation of amino acids itself, whilst an important step in any naturalistic origin of life, would need to be accompanied by some means of linking those amino acids into peptide molecules[17] - the process by which proteins are formed. A significant step forward with respect to this, arose when researchers alighted upon the fact that carbonyl sulphide, a gas that is produced in quantity naturally by volcanoes, acts as a catalyst for the formation of peptides, increasing yields dramatically[18]. This would facilitate peptide formation not only in the vicinity of hydrothermal vents, but in the vicinity of terrestrial volcanoes close to bodies of open water. Indeed, Miller had produced the 22 amino acids found in some of his reaction mixtures by extending the synthesis to include volcanic input, though not carbonyl sulphide - the addition of carbonyl sulphide would, however, facilitate peptide formation rapidly once the amino acids themselves were formed.
One additional problem to be overcome was the ‘chirality problem’. Amino acids, with the exception of glycine, are chiral molecules, existing in two forms that are mirror images of each other in space (stereoisomers). Initially, methods for producing one form preferentially over another were something of a puzzle, but chemists working in an entirely different field established that a process called ‘chiral catalysis’ exists, indeed, this work led to a Nobel Prize for the researchers in question[19]. The demonstrated existence of working chiral catalysts[20] led abiogenesis researchers to seek such catalytic processes in their own field, and, in due course, these were alighted upon[15, 21- 24].
However, amino acids are not the only molecules required for life, important though they are. Some form of self-replicating molecule, providing the basis of an inheritance mechanism, is required. Given the difficulties involved in synthesising DNA as a total synthesis, researchers turned to RNA instead, a molecule that still forms the basis of the genomes of numerous extant taxonomic Families of viruses today. RNA, being easier to synthesise, was considered a natural first choice for the basis of primordial genomes, and thus, attention turned to the synthesis of RNA under prebiotic conditions. This was soon found not only to be possible, but to be readily achievable in the laboratory, and indeed, catalysis plays a role in these experiments. Natural clays formed from a mineral called montmorillonite provide a ready natural catalyst that would have been present in quantity on a prebiotic Earth, and the catalytic chemistry of RNA formation whilst adsorbed to such clays is now a standard part of the scientific literature[22- 42].
Having established that RNA was synthesisable under prebiotic conditions, researchers then turned to the matter of establishing the existence of self-replicating species of RNA molecules. This was duly successful[30, 43, 45 - 47], establishing that such species could have arisen among the extant RNA molecules being synthesised on a prebiotic Earth, and of course, once one self-replicating species exists, the process of evolution can begin, which has also since been demonstrated to apply to replicating RNAs in appropriate laboratory experiments[48].
Once a self-replicating molecule that can form the basis of an inheritance mechanism exists, the next stage scientists postulate to be required is encapsulation within some sort of selectively permeable membrane. The molecules of choice for these membrane are lipids, which have been demonstrated repeatedly in the laboratory to undergo spontaneous self-organisation into various structures, such as bilayer sheets, micelles and liposomes. Indeed, in the case of phospholipids, they can be stimulated to self-organise by the simple process of agitating the solution within which they are suspended - literally, shake the bottle[49 - 53].
Moreover, research has established that these lipids can encapsulate RNA molecules, and selectively admit the passage of base and sugar molecules to facilitate RNA replication[54, 55]. With the advent of this discovery in appropriate laboratory research, protocell formation is but a short step away, and indeed, the latest research is now actively concentrating upon the minimum components required in order for a viable, self-replicating protocell to exist. Prebiotic lipid formation is also a part of the repertoire of the literature in the field, and some papers now extant document the first experiments aimed at producing viable self-replicating protocells[55 - 70].
Whilst scientists naturally accept that ‘joining the dots’ between these individual steps is entirely proper, particularly on a body the size of a planet over a 100 million year period, the absence of experiments actively coupling these stages is a matter remaining to be addressed, though such experiments will be ambitious in scope indeed if they are to produce complete working protocells at the end of a long production line starting with a Miller-Urey synthesis.
A ‘grand synthesis’ of this sort in the laboratory is not high on the scientific agenda at the moment, which is more concerned with validating the individual hypothesised steps, but once those steps are accepted as valid in the field, doubtless one day a ‘grand synthesis’ will be attempted, and the success thereof will establish beyond serious doubt that our pale blue dot became our home courtesy of well-defined and testable chemical reactions. Even so, no one conversant with the literature seriously considers any more that magical forces are required to produce life: just as vitalism was refuted by Wöhler’s classic experiment, that gave rise to organic chemistry as an empirical science in the first place, so it is likely to be rendered ever more irrelevant in abiogenesis research, as the steps leading to life’s blossoming on our planet are traversed and studied in ever greater detail.
References:
[1] An apposite paper (among many) covering the Late Heavy Bombardment is:
Origin Of The Cataclysmic Late Heavy Bombardment Period Of The Terrestrial Planets by R. Gomes, H. F. Levison, K. Tsiganis and A. Morbidelli, Nature, 435: 466-469 (26th May 2005)
[2] Cited in The Life And Letters Of Charles Darwin, Including An Autobiographical Chapter, edited by Francis Darwin, 1887
[3] The Origin And Development Of Life by Alexander Oparin, 1924 (English translation: NASA TTF-488)
[4] A Production Of Amino Acids Under Possible Primitive Earth Conditions by Stanley L. Miller, Science, 117: 528-529 (15th May 1953)
[5] The Miller Volcanic Discharge Spark Experiment by Adam P. Johnson, H. James Cleaves, Jason P. Dworkin, Daniel P. Glavin, Antonio Lazcano and Jeffrey L. Bada, Science, 322:404 (17th Ocotber 2008)
[6] Amino Acid Synthesis From Hydrogen Cyanide Under Possible Primitive Earth Conditions[/i] by J. Oró and S. S.Kamat, Nature, 190: 442-443 (1961)
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[19] Nobel Prize for Chemistry, 2001, was awarded to William S. Knowles, Ryoji Noyori and K. Barry Sharpless, for their work establishing the existence of asymmetric catalysts and chiral catalysis - see the Nobel Lecture by William S. Knowles here
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[38] Sequence- And Regio-Selectivity In The Montmorillonite-Catalysed Synthesis Of RNA by Gözen Ertem and James P. Ferris, Origins of Life and Evolution of the Biosphere, 30: 411-422 (2000)
[39] Synthesis Of 35-40 Mers Of RNA Oligomers From Unblocked Monomers. A Simple Approach To The RNA World by Wenhua Huang and James P. Ferris, Chemical Communications of the Royal Society of Chemistry, 1458-1459 (2003)
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[44] Emergence Of A Replicating Species From An In Vitro RNA Evolution Reaction by Ronald R. Breaker and Gerald F. Joyce, Proceedings of the National Academy of Sciences of the USA, 91: 6093-6097 (June 1994)
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[60] Formation Of Protocell-Like Structures From Glycine And Formaldehyde In A Modified Sea Medium by Hiroshi Yanagawa and Fujio Egami, Proceedings of the Japan Academy, 53: 42-45 (12th January 1977)
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[64] Nutrient Uptake By Protocells: A Liposome Model System by Pierre-Alain Monnard and David W. Deamer, Origins of Life and Evolution of the Biosphere, 31: 147-155 (2001)
[65] Synchronisation Phenomena In Internal Reaction Models Of Protocells by Roberto Serra, Timoteo Carletti, Alessandro Filisetti and Irene Poli, Artificial life, 13: 123-128 (2007)
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[67] Synthetic Protocell Biology: From Reproduction To Computation by Ricard V. Solé, Andreea Munteanu, Carlos Rodriguez-Caso and Javier Macia, Philosophical Transactions of the Royal Society Part B, 362: 1727-1739 (October 2007)
[68] Template-Directed Synthesis Of A Genetic Polymer In A Model Protocell by Sheref S. Mansy, Jason P. Schrum, Mathangi Krisnamurthy, Sylvia Tobé, Douglas A. Treco and Jack W. Szostak, Nature, 454: 122-125 (4th June 2008)
[69] The Emergence Of Competition Between Model Protocells by Irene A Chen, Richard W. Roberts and Jack W. Szostak, Science, 305:1474-1476 (3rd September 2004)
[70] Thermostability Of Model Protocell Membranes by Sheref S. Mansy and Jack W. Szostak, Proceedings of the National Academy of Sciences of the USA, 105(36): 13351-13355 (9th September 2008)
Have fun wading through that list of scientific papers.
See what I’m saying yet? (Hmmm… Probably not.) Well, let’s try this…
… Something of a dilemma, huh? Yeah, those can be tricky sometimes… Gosh. What to do? 
Hey, I have an idea. Just whisper your question in my ear, and I’ll evaluate it and tell you whether or not you should ask it. If it’s a silly question, I promise I won’t tell anybody… (leaning in closer with hand cupped behind ear)…
