The Origin Of Life With Recent Updates

Since the usual canards about the origin of life have been resurrected elsewhere on this forum by at least one of the usual suspects, I thought it apposite to reprise an article I wrote originally for another forum way back in 2010, with some recent additions to include more recent work. Note that full references to relevant peer reviewed scientific papers are provided (superscript numbers in the main text match numbers in the reference list at the end of this article).

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].

As part of the foundational work allowing the RNA World hypothesis to be placed upon a firm footing, work on the synthesis of nucleotides was conducted, and while several problems arose early in said research, these problems have now been solved, largely due to some impressive research by John D. Sutherland, who provided neat solutions to the nucleotide formation problem in several papers75-82.

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].

More recent work includes experiments with synthetics model protocells, including several papers that can be found in the following collections provided by the peer reviewed scientific journal Nature:

Collection #1

Collection #2

Collection #3

Additionally, more recently, a team of Japanese scientists have published four papers, establishing not only that RNA molecules can exhibit self-replication when provided with a source of nucleotides, but that those RNA molecules generate a molecular ecosystem through Darwinian evolution71-74. This of course couples with the previous work on Darwinian evolution of RNA replicators by Joyce covered in reference [48] below, and numerous similar papers by other scientists in the same vein.

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)

[7] A Hydrogen Rich Early Earth Atmosphere by Feng Tian, Owen B. Toon, Alexander A. Pavlov and H. de Sterck, Science, 308: 1014-1017 (13th May 2005)

[8] A Rigorous Attempt To Verify Interstellar Glycine by I. E. Snyder, F. J. Lovas, J. M. Hollis, D. N. Friedel, P. R. Jewell, A. Remijan, V. V. Ilyushin, E. A. Alekseev and S. F. Dyubko, The Astrophysical Journal, 619(2): 914-930 (1st February 2005)

[9] Interstellar Glycine by Yi-Jehng Kuan, Steven B. Charnley, Hui-Chun Huang, Wei-Ling Tseng, and Zbigniew Kisiel, The Astrophysical Journal, 593: 848-867 (20th August 2003)

[10] Prebiotic Materials From On And Off The Early Earth by Max Bernstein, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)

[11] Racemic Amino Acids From The Ultraviolet Photolysis Of Interstellar Ice Analogues by Max P. Bernstein, Jason P. Dworkin, Scott A. Sandford, George W. Copoper and Louis J. Allamandola, Nature, 416: 401-403

[12] A Combined Experimental And Theoretical Study On The Formation Of The Amino Acid Glycine And Its Isomer In Extraterrestrial Ices by Philip D. Holtom, Chris J. Bennett, Yoshihiro Osamura, Nigel J Mason and Ralf. I Kaiser, The Astrophysical Journal, 626: 940-952 (20th June 2005)

[13] The Lifetimes Of Nitriles (CN) And Acids (COOH) During Ultraviolet Photolysis And Their Survival In Space by Max P. Bernstein, Samantha F. M. Ashbourne, Scott A. Sandford and Louis J. Allamandola, The Astrophysical Journal, 601: 3650270 (20th January 2004)

[14] The Prebiotic Molecules Observed In The Interstellar Gas by P. Thaddeus, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (7th September 2006)

[15] Molecular Asymmetry In Extraterrestrial Chemistry: Insights From A Pristine Meteorite by Sandra Pizzarello, Yongsong Huang and Marcelo R. Alexandre, Proceeding of the National Academy of Sciences of the USA, 105(10): 3700-3704 (11th March 2008)

[16] Organic Compounds In Carbonaceous Meteorites by Mark A. Sephton, Natural Products Reports (Royal Society of Chemistry), 19: 292-311 (2002)

[17] Peptides By Activation Of Amino Acids With CO On (Ni,Fe)S Surfaces: Implications For The Origin Of Life by Claudia Huber and Günter Wächtershäuser, Science, 281: 670-672 (31st July 1998)

[18] Carbonyl Sulphide-Mediated Prebiotic Formation Of Peptides by Luke Leman, Leslie Orgel and M. Reza Ghadiri, Science, 306: 283-286 (8th October 2004)

[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

[20] Homogeneous Catalysis In The Decomposition Of Diazo Compounds By Copper Chelates: Asymmetric Carbenoid Reactions[/i] by H. Nozaki, H. Takaya, S. Moriuti and R. Noyori, Tetrahedron, 24(9): 3655-2669 (1968)

[21] Prebiotic Amino Acids As Asymmetric Catalysts by Sandra Pizzarello and Arthur L. Weber, Science, 303: 1151 (20 February 2004)

[22] Homochiral Selection In The Montmorillonite-Catalysed And Uncatalysed Prebiotic Synthesis Of RNA by Prakash C. Joshi, Stefan Pitsch and James P. Ferris, Chemical Communications (Royal Society of Chemistry), 2497-2498 (2000) [DOI: 10.1039/b007444f]

[23] RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998)

[24] Catalysis In Prebiotic Chemistry: Application To The Synthesis Of RNA Oligomers by James P. Ferris, Prakash C. Joshi, K-J Wang, S. Miyakawa and W. Huang, Advances in Space Research, 33: 100-105 (2004)

[25] Cations As Mediators Of The Adsorption Of Nucleic Acids On Clay Surfaces In Prebiotic Environments by Marco Franchi, James P. Ferris and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 33: 1-16 (2003)

[26] Ligation Of The Hairpin Ribozyme In cis Induced By Freezing And Dehydration by Sergei A. Kazakov, Svetlana V. Balatskaya and Brian H. Johnston, The RNA Journal, 12: 446-456 (2006)

[27] Mineral Catalysis And Prebiotic Synthesis: Montmorillonite-Catalysed Formation Of RNA by James P. Ferris, Elements, 1: 145-149 (June 2005)

[28] Montmorillonite Catalysis Of 30-50 Mer Oligonucleotides: Laboratory Demonstration Of Potential Steps In The Origin Of The RNA World by James P. Ferris, Origins of Life and Evolution of the biosphere, 32: 311-332 (2002)

[29] Montmorillonite Catalysis Of RNA Oligomer Formation In Aqueous Solution: A Model For The Prebiotic Formation Of RNA by James P. Ferris and Gözen Ertem, Journal of the American Chemical Society, 115: 12270-12275 (1993)

[30] Nucelotide Synthetase Ribozymes May Have Emerged First In The RNA World by Wentao Ma, Chunwu Yu, Wentao Zhang and Jiming Hu, The RNA Journal, 13: 2012-2019, 18th September 2007

[31] Prebiotic Chemistry And The Origin Of The RNA World by Leslie E. Orgel, Critical Reviews in Biochemistry and Molecular Biology, 39: 99-123 (2004)

[32] Prebiotic Synthesis On Minerals: Bridging The Prebiotic And RNA Worlds by James P. Ferris, Biological Bulletin, 196: 311-314 (June 1999)

[33] RNA Catalysis In Model Protocell Vesicles by Irene A Chen, Kourosh Salehi-Ashtiani and Jack W Szostak, Journal of the American Chemical Society, 127: 13213-13219 (2005)

[34] RNA-Catalysed Nucleotide Synthesis by Peter J. Unrau and David P. Bartel, Nature, 395: 260-263 (17th September 1998)

[35] RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension by Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret E. Glasner and David P. Bartel, Science, 292: 1319-1325, 18th May 2001

[36] RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998)

[37] RNA Evolution And The Origin Of Life by Gerald F. Joyce, Nature, 338: 217-224 (16th March 1989)

[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)

[40] Synthesis Of Long Prebiotic Oligomers On Mineral Surfaces by James P. Ferris, Aubrey R. Hill Jr, Rihe Liu and Leslie E. Orgel, Nature, 381: 59-61 (2nd May 1996)

[41] The Antiquity Of RNA-Based Evolution by Gerald F. Joyce, Nature, 418: 214-221, 11th July 2002

[42] The Roads To And From The RNA World by Jason P. Dworkin, Antonio Lazcano and Stanley L. Miller, Journal of Theoretical Biology, 222: 127-134 (2003)

[43] A Self-Replicating Ligase Ribozyme by Natasha Paul & Gerald F. Joyce, Proc. Natl. Acad. Sci. USA., 99(20): 12733-12740 (1st October 2002)

[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)

[45] Ribozymes: Building The RNA World by Gerald F. Joyce, Current Biology, 6(8): 965-967, 1996

[46] Self-Sustained Replication Of An RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce, ScienceExpress, DOI: 10.1126/science.1167856 (8th January 2009)

[47] The Origin Of Replicators And Reproducers by Eörs Szathmáry, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)

[48] Darwinian Evolution On A Chip by Brian M. Paegel and Gerald F. Joyce, Public Library of Science Biology, 6(4): e85 (April 2008)

[49] Formation Of Bimolecular Membranes From Lipid Monolayers And A Study Of Their Electrical Properties by M. Montal and P. Mueller, Proceedings of the National Academy of Sciences of the USA, 69(12): 3561-3566 (December 1972)

[50] Lipid Bilayer Fibres From Diastereomeric And Enantiomeric N-Octylaldonamides by Jürgen-Hinrich Fuhrhop, Peter Schneider, Egbert Boekema and Wolfgang Helfrich, Journal of the American Chemical Society, 110: 2861-2867 (1988)

[51] Molecular Dynamics Simulation Of The Formation, Structure, And Dynamics Of Small Phospholipid Vesicles by Siewert J. Marrink and Alan E. Mark, Journal of the American Chemical Society, 125: 15233-15242 (2003)

[52] Simulation Of The Spontaneous Aggregation Of Phospholipids Into Bilayers by Siewert J. Marrink, Eric Lindahl, Olle Edholm and Alan E. Mark, Journal of the American Chemical Society, 123: 8638-8639 (2001)

[53] The Lipid World by Daniel Segré, Dafna Ben-Eli, David W. Deamer and Doron Lancet, Origins of Life And Evolution of the Biosphere, 31: 119-145, 2001

[54] Replicating Vesicles As Models Of Primitive Cell Growth And Division by Martin M. Hanczyc and Jack W. Szostak, Current Opinion In Chemical Biology, 8: 660-664 (22nd October 2004)

[55] RNA Catalysis In Model Protocell Vesicles by Irene A Chen, Kourosh Salehi-Ashtiani and Jack W Szostak, Journal of the American Chemical Society, 127: 13213-13219 (2005)

[56] Coevolution Of Compositional Protocells And Their Environment by Barak Shenhav, Aia Oz and Doron Lancet, Philosophical Transactions of the Royal Society Part B, 362: 1813-1819 (9th May 2007)

[57] Computational Models For The Formation Of Protocell Structures by Linglan Edwards, Yun Peng and James A. Reggia, Artificial Life, 4(1): 61-77 (1998)

[58] Coupled Growth And Division Of Model Protocell Membranes by Ting F. Zhu and Jack W. Szostak, Journal of the American Chemical Society, 131: 5705-5713 (2009)

[59] Evolution And Self-Assembly Of Protocells by Ricard V. Solé, The International Journal of Biochemistry & Cell Biology, 41: 274-284 (2009)

[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)

[61] Formation Of Protocell-Like Vesicles In A Thermal Diffusion Column by Itay Budin, Raphael J. Bruckner and Jack W. Szostak, Journal of the American Chemical Society, 131: 9628-9629 (2009)

[62] Generic Darwinian Selection In Catalytic Protocell Assemblies by Andreea Munteanu, Camille Stephan-Otto Attolini, Steen Rasmussen, Hans Ziock and Ricard V. Solé, Philosophical Transactions of the Royal Society Part B, 362: 1847-1855 (2007)

[63] Kin Selection And Virulence In The Evolution Of Protocells And Parasites by Steven A. Frank, Proceedings of the Royal Society of London Part B, 258: 153-161 (1994)

[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)

[66] Synchronisation Phenomena In Protocell Models by Alessandro Filisetti, Roberto Serra, Timoteo Carletti, Irene Poli and Marco Villani, Biophysical Reviews and Letters, 3(1-2): 325-342 (2008)

[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)

[71] Darwinian Evolution In A Translation-Coupled RNA Replication System Within A Cell-Like Compartment by Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Takeshi Sunami, Tomoaki Matsuura & Tetsuya Yomo, Nature Communications, 4: 2494 (3rd October 2013)

[72] Emergence And Diversification Of A Host-Parasite RNA Ecosystem Through Darwinian Evolution by Taro Furubayashi, Kensuke Ueda, Yohsuke Bansho, Daisuke Motooka, Shota Nakamura, Ryo Mizuuchi and Norikazu Ichihashi, eLife, 2020;9: e56038 (21st July 2020)

[73] Host–Parasite Oscillation Dynamics And Evolution In A Compartmentalized RNA Replication System by Yohsuke Bansho, Taro Furubayashi, Norikazu Ichihashi and Tetsuya Yomo, Proceedings of the National Academy of Sciences of the USA, 113(15): 4045-4050 (March 28th 2016)

[74] Evolutionary Transition From A Single RNA Replicator To A Multiple Replicator Network by Ryo Mizuuchi, Taro Furubayashi & Norikazu Ichihashi, Nature Communications, 13: 1460 (2022)

[75] Synthesis Of Activated Pyrimidine Ribonucleotides In Prebiotically Plausible Conditions by Matthew W. Powner, Béatrice Gerland and John D. Sutherland, Nature, [b]459:[b] 239-242 (14th May 2009)

[76] Two Step Potentially Prebiotic Synthesis Of α-D-Cystidine-5’-Phosphate From D-Glyceraldehyde-3-Phosphate by Carole Anastasi, Michael A. Crowe and John D. Sutherland, Journal of the American Chemical Society (Communications), 129: 24-24 (2007)

[77] Chemoselective Multicomponent One-Pot Assembly Of Purine Precursors In Water by Matthew W Powner, John D Sutherland and Jack W Szostak, Journal of the American Chemical Society, 132(46): 16677-16688 (24th November 2010)

[78] Synthesis Of Aldehydic Ribonucleotide And Amino Acid Precursors By Photoredox Chemistry by Dougal J Ritson and John D Sutherland, Angewandte Chemie International Edition, 52(22): 5845-5847 (27th May 2013)

[79] A Prebiotically Plausible Synthesis Of Pyrimidine β-Ribonucleosides And Their Phosphate Derivatives Involving Photoanomerization by Jianfeng Xu, Maria Tsanakopoulou, Christopher J Magnani, Rafał Szabla, Judit E Šponer, Jiří Šponer, Robert W Góra and John D Sutherland, Nature Chemistry, 9(4): 303-309 (April 2017)

[80] Prebiotically Plausible Oligoribonucleotide Ligation Facilitated By Chemoselective Acetylation by Frank R Bowler, Christopher KW Chan, Colm D Duffy, Béatrice Gerland, Saidul Islam, Matthew W Powner, John D Sutherland and Jianfeng Xu, Nature Chemistry, 5(5): 383-389 (May 2013)

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Thanks Callissea for introducing me to the joys of plagiarism!!! I rip so much of your stuff when encountering the ignorance of YECs.

3 Likes

Was this a relay synthesis?

The problem this faces is Eigen’s Paradox. If you have self-replicating RNA and if on average you have more than one change every generation you’re going to lose a lot of information. So that’s a big problem because the way cells deal with this problem is they’ve got error correction mechanisms. The problem is any origin of life scenario is before the cell has enough information to provide those error correcting mechanisms. It needs those error correcting mechanisms. So Eigen’s paradox kills self-replication long before a cell is large enough to have the error correcting mechanisms to correct the errors of high Fidelity Levels.

The scientific papers I referenced in my article all say you’re wrong. Read them and find out why.

1 Like

I told you on the original thread to read the papers and essay that Calli presented here. But no, You just had to display your lack of comprehension, rushing in to make your facile comment before READING.

Learned your lesson yet?

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A more detailed response to the asinine objection above …

Item one: if the error rate in replication is small enough, then it won’t adversely affect a population of replicators. Especially if that population consists of several million replicators, and only one or two replicators in that population is affected at any one time.

Item two: this is merely a rehash of that other favourite creationist fallacy, the “one true sequence” fallacy. What matters isn’t exact sequence, but function. If a mutation doesn’t affect function, then your objection is rendered null and void. Indeed, given that many different RNA sequences have been demonstrated experimentally to exhibit self-replication capability, we can also toss this objection into the bin on that basis.

Item three: given that the authors of the scientific papers I cited in my article were able to maintain populations of functioning RNA replicators over periods of several years (indeed, the Japanese team I mentioned ran their experiments over a four year period, with no observed collapse of their populations), I think you have to ask yourself the elementary question of how this is possible, if your objection is something other than an exercise in smoke blowing.

And since you’ve resurrected the fallacy in question, it’s time to deal with it:

The “One True Sequence” Fallacy

A number of fallacies are in circulation amongs the enthusiasts for reality denial, and one that I wish to highlight here is known in scientific circles as “The Error of the One True Sequence”. This fallacy asserts that one, and ONLY one, DNA sequence can code for a protein that performs a specific task. This is usually erected alonside assorted bogus “probability” calculations that purport to demonstrate that evolutionary processes cannot achieve what they plainly do achieve in the real world, but those other probability fallacies will be the subject of other posts. Here I want to destroy the myth that one, and ONLY one, sequence can ever work in a given situation.

Insulin provides an excellent example for my purposes, because insulin is critical to the health and well being of just about every vertebrate organism on the planet. When a vertebrate organism is unable to produce insulin, the well-known condition of diabetes mellitus, then the ability to regulate blood sugar is seriously disrupted, and in the case of Type 1 diabetes mellitus, in which the beta-cells of the Islets of Langerhans in the pancreas are destroyed by an autoimmune reaction, the result is likely to be fatal in the medium to long term due to diabetic nephropathy resulting in renal failure.

Consequently, the insulin molecule is critical to healthy functioning of vertebrate animals. The gene that codes for insulin is well known, and has been mapped in a multiplicity of organisms, including organisms whose entire genomes have been sequenced, ranging from the pufferfish Tetraodon nigroviridis through to Homo sapiens. There is demonstrable variability in insulin molecules (and the genes coding for them) across the entire panoply of vertebrate taxa. Bovine insulin, for example, is not identical to human insulin. I refer everyone to the following gene sequences, all of which have been obtained from publicly searchable online gene databases:

[1] Human insulin gene on Chromosome 11, which is as follows:

atg gcc ctg tgg atg cgc ctc ctg ccc ctg ctg gcg ctg ctg gcc ctc tgg gga cct gac
cca gcc gca gcc ttt gtg aac caa cac ctg tgc ggc tca cac ctg gtg gaa gct ctc tac
cta gtg tgc ggg gaa cga ggc ttc ttc tac aca ccc aag acc cgc cgg gag gca gag gac
ctg cag gtg ggg cag gtg gag ctg ggc ggg ggc cct ggt gca ggc agc ctg cag ccc ttg
gcc ctg gag ggg tcc ctg cag aag cgt ggc att gtg gaa caa tgc tgt acc agc atc tgc
tcc ctc tac cag ctg gag aac tac tgc aac tag

which codes for the following protein sequence (using the standard single letter mnemonics for individual amino acids, which I have colour coded to match the colour coding in this diagram of the insulin synthesis pathway in humans):

MALWMRLLPLLALLALWGPDPAAA
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
RR
EAEDLQVGQVELGGGPGAGSLQPLALEGSLQ
KR
GIVEQCCTSICSLY
QLENYCN

Now, I refer everyone to this data, which is the coding sequence for insulin in the Lowland Gorilla (differences are highlighted in boldface):

atg gcc ctg tgg atg cgc ctc ctg ccc ctg ctg gcg ctg ctg gcc ctc tgg gga cct gac
cca gcc gcg gcc ttt gtg aac caa cac ctg tgc ggc tcc cac ctg gtg gaa gct ctc tac
cta gtg tgc ggg gaa cga ggc ttc ttc tac aca ccc aag acc cgc cgg gag gca gag gac
ctg cag gtg ggg cag gtg gag ctg ggc ggg ggc cct ggt gca ggc agc ctg cag ccc ttg
gcc ctg gag ggg tcc ctg cag aag cgt ggc atc gtg gaa cag tgc tgt acc agc atc tgc
tcc ctc tac cag ctg gag aac tac tgc aac tag

this codes for the protein sequence:

MALWMRLLPLLALLALWGPDPAAA
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
RR
EAEDLQVGQVELGGGPGAGSLQPLALEGSLQ
KR
GIVEQCCTSICSLY
QLENYCN

which so happens to be the same precursor protein. However, Gorillas are closely related to humans. Let’s move a little further away, to the domestic cow, Bos taurus (whose sequence is found here):

atg gcc ctg tgg aca cgc ctg cgg ccc ctg ctg gcc ctg ctg gcg ctc tgg ccc ccc ccc
ccg gcc cgc gcc ttc gtc aac cag cat ctg tgt ggc tcc cac ctg gtg gag gcg ctg tac
ctg gtg tgc gga gag cgc ggc ttc ttc tac acg ccc aag gcc cgc cgg gag gtg gag ggc
ccg cag gtg ggg gcg ctg gag ctg gcc gga ggc ccg ggc gcg ggc ggc ctg gag ggg ccc
ccg cag aag cgt ggc atc gtg gag cag tgc tgt gcc agc gtc tgc tcg ctc tac cag ctg
gag aac tac tgt aac tag

Already this is a smaller sequence - 318 codons instead of 333 - so we KNOW we’re going to get a different insulin molecule with this species … which is as follows:

MALWTRLRPLLALLALWPPPPARA
FVNQHLCGSHLVEALYLVCGERGFFYTPK
AR
REVEGPQVGALELAGGPGAGGLEGPPQKRGI
VE
QCCASVCSLYQLENYCN

clearly a different protein, but one which still functions as an insulin precursor and results in a mature insulin molecule in cows, one which differs in exact sequence from that in humans. Indeed, prior to the advent of transgenic bacteria, into which human insulin genes had been transplanted for the purpose of harnessing those bacteria to produce human insulin for medical use, bovine insulin harvested from the pancreases of slaughtered beef cows was used to treat diabetes mellitus in humans. Now, of course, with the advent of transgenically manufactured true human insulin, from a sterile source, bovine insulin is no longer needed, much to the relief of those who are aware of the risk from BSE.

Moving on again, we have a different coding sequence from the tropical Zebrafish, Danio rerio, (sequence to be found here) which is as follows:

atg gca gtg tgg ctt cag gct ggt gct ctg ttg gtc ctg ttg gtc gtg tcc agt gta agc
act aac cca ggc aca ccg cag cac ctg tgt gga tct cat ctg gtc gat gcc ctt tat ctg
gtc tgt ggc cca aca ggc ttc ttc tac aac ccc aag aga gac gtt gag ccc ctt ctg ggt
ttc ctt cct cct aaa tct gcc cag gaa act gag gtg gct gac ttt gca ttt aaa gat cat
gcc gag ctg ata agg aag aga ggc att gta gag cag tgc tgc cac aaa ccc tgc agc atc
ttt gag ctg cag aac tac tgt aac tga

And this sequence codes for the following protein:

MAVWLQAGALLVLLVVSSVSTNPG
TPQHLCGSHLVDALYLVCGPTFTGFFYNP
KR
DVEPLLGFLPPKSAQETEVADFAFKDHAELI
RK
RGIVEQCCHKPCSI
FELQNYCN

so again we have a different insulin precursor protein that is ultimately converted into a different insulin molecule within the Zebra Fish.

I could go on and extract more sequences, but I think the point has already been established, namely that there are a multiplicity of possible insulin molecules in existence, and consequently, the idea that there can only be ONE sequence for a functional protein, even one as critically important to life as insulin, is DEAD FLAT WRONG. Now, if this is true for a protein as crucial to the functioning of vertebrate life as insulin, you can be sure that the same applies to other proteins, including various enzymes, and therefore, whenever the “One True Sequence” fallacy rears its ugly head in various places, the above provides the refutation thereof.

Needless to say, the above remarks also apply to self-replicating RNAs in prebiotic chemistry experiments, as documented in those scientific papers you manifestly never bothered to read.

Oh, and one final note … in case you never learned this, the smallest RNA strand demonstrated to possess self-replicating capabililty is just FIVE NUCLEOTIDES LONG. The paper documenting this is the following:

Multiple Translational Products From A Five-Nucleotide Ribozyme by Rebecca M. Turk, Natalya V. Chumachenko and Michael Yarus, Proceedings of the National Academy of Sciences of the USA, 107(10):, 4585-4589 (9th March 2010)

From that paper:

I think this covers relevant bases.

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Excellent article, as always. Thank you!

However, the link to the diagram you referenced is dead. The closest diagram I could find, based on file name, is this (in SVG format), but I have no idea if it’s the correct one. And, I might have missed something here, but are your protein sequences supposed to be colour coded to match the diagram? If so, the colours have not carried over to the forum.

Had to remove the colour codes because this forum doesn’t support them. Forgot to edit the article to take account of this. :slight_smile:

But the principle still remains, namely that those insulin sequences I dig out of the ExPasy database years ago destroy the “one true sequence” fallacy wholesale. :slight_smile:

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Suspected that was the case. No problem for me, just thought I’d let you know :slight_smile:

I know. You don’t need to convince me. It’s just a matter of nitpicking details in form, not in content.

Is that a band? :woman_shrugging:t6:

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