Critique on Calilasseia's "The Emergence Of Life On Earth"

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Critique on Calilasseia's "The Emergence Of Life On Earth"

#1  Postby rainbow » Mar 04, 2010 8:13 am

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)

[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[/i] 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)
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#2  Postby Mazille » Mar 04, 2010 8:38 am

So, where is your critique?
- Pam.
- Yes?
- Get off the Pope.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#3  Postby Spearthrower » Mar 04, 2010 8:40 am

Mazille wrote:So, where is your critique?


It's better than expected! :cheers:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#4  Postby rainbow » Mar 04, 2010 8:46 am

There are a couple of initial points to make.

1) The entire paper has been copied to the beginning of the thread, so that easy reference can be made.

2) Therefore when I extract a portion for discussion, there can be no possibility of quote mining.

3) As a general point wrt. the use of references, while important in an acedemic discussion - is only useful if the Entire Paper is reproduced, or if there is a link to the Entire Paper. We do not all have free access to scientific papers.

4) I will discuss the paper in block areas as they appear in the article, in a number of postings. As I'm sure this will lead to a number of side discussions - we made need to split the thread.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#5  Postby rainbow » Mar 04, 2010 9:03 am

Mazille wrote:So, where is your critique?

What's the hurry?

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.


There is no evidence to support the conclusion that there was no life during the bolide impact period, it is pure speculation.
What is clear is that the bolide impacts would have removed any evidence of life before this period.
...so we simply don't know.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#6  Postby josephchoi » Mar 04, 2010 9:06 am

Burden of proof is on you to substantiate the claim that there WAS life. We just look at the evidence, and find the evidence for life before the bolide impact period lacking...
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#8  Postby rainbow » Mar 04, 2010 9:13 am

Spearthrower wrote:
Mazille wrote:So, where is your critique?


It's better than expected! :cheers:


...and it will only get better, promise!

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 idea that life will be based on organic Chemistry is rather stating the obvious, though it doesn't follow at all that a reducing atmosphere is a requirement for the existence of life.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#9  Postby natselrox » Mar 04, 2010 9:13 am

:coffee:
When in perplexity, read on.

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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#10  Postby rainbow » Mar 04, 2010 9:18 am

josephchoi wrote:Burden of proof is on you to substantiate the claim that there WAS life. We just look at the evidence, and find the evidence for life before the bolide impact period lacking...

Not. I've made no proposition to that effect.
You really have to get your head around my statement that there is no evidence either way:
...so we simply don't know.


Cali made a proposition that there wasn't life, and there is no substantiation of this. Cali's fail, but not a big one.
Last edited by rainbow on Mar 04, 2010 9:19 am, edited 1 time in total.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#11  Postby Hey Zeus! » Mar 04, 2010 9:19 am

You might want to consider writing the critique first and posting it in its entirety rather than dishing it out piece by piece. It's a bit confusing to have a post called Critique on... then post the entire work you're critiquing without any commentary. I would suggest deleting this (is that possible on this board?), writing your critique and then posting it all at once. I think it would be better if the critique came first, followed by Calilasseia's essay but if you want to post it with his essay first, that works as well. I would just suggest having everything prepared before you do that.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#12  Postby rainbow » Mar 04, 2010 9:30 am

natselrox wrote::coffee:

I assume that since you have nothing to say, you agree with my comments so far.
Good!

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].

Now this gets more interesting. The GCMS reveals that indeed some of the more exotic amino acids are formed, but at concentrations of a millionth or less of the concentration of lysine.
...so the more sensitive analysis isn't really such good news, since it does show that certain amino acids weren't produced in sufficient quantity for further reaction.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#13  Postby rainbow » Mar 04, 2010 9:37 am

Hey Zeus! wrote:You might want to consider writing the critique first and posting it in its entirety rather than dishing it out piece by piece. It's a bit confusing to have a post called Critique on... then post the entire work you're critiquing without any commentary. I would suggest deleting this (is that possible on this board?), writing your critique and then posting it all at once. I think it would be better if the critique came first, followed by Calilasseia's essay but if you want to post it with his essay first, that works as well. I would just suggest having everything prepared before you do that.

Sorry if you find it confusing, but this is the way I choose to do so. I suggest that you wait until all the bits are in, and then merge it into one document, if that's what you want. You will find that it's a bit unwieldy, so I suggest that you look at the blocks as I've broken them.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#14  Postby rainbow » Mar 04, 2010 9:46 am

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].

What this does illustrate is that simple organic compounds, including amino acids - are indeed quite easily formed under quite a range of conditions, as long as the elements carbon, hydrogen, oxygen and nitrogen are present - in approximately the right ratios.
Nothing really surprising about that if you understand the Chemistry.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#15  Postby natselrox » Mar 04, 2010 9:50 am

Just a reminder, rainbow. You aren't refuting Calilasseia here. You are refuting those bracketed numbers.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#16  Postby 95Theses » Mar 04, 2010 9:53 am

rainbow wrote:I suggest that you wait until all the bits are in, and then merge it into one document, if that's what you want.


Personally I have no need to do that, as I am quite certain a certain blue butterfly will be along to do that fairly quickly after you finish.

i'm just bookmarking so I can watch the resulting carpet bombing.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#17  Postby tnjrp » Mar 04, 2010 9:59 am

95Theses wrote:I am quite certain a certain blue butterfly will be along to do that fairly quickly after you finish
Indeed with the subject like that I'm pretty sure he'll show up eventually (or someone will "rat this out" to him, in the worst case). So I'm bookmarking this as well in expectations of being able to brush up my knowledge about abiogenesis on the side.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#18  Postby hackenslash » Mar 04, 2010 10:10 am

I would say that it's really poor form, bordering on rude, to critique a piece written for a science writing competition when said competition hasn't been completed and is currently in abeyance.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#19  Postby rainbow » Mar 04, 2010 10:22 am

natselrox wrote:Just a reminder, rainbow. You aren't refuting Calilasseia here. You are refuting those bracketed numbers.


It is a Critique, not a Refutation. Please be aware of the difference.

Here is where it gets a bit wobbly:
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.

There is no explanation as to why the formation of amino acids should be 'an important step in any naturalistic origin of life', nor is it stated why they would need to be formed into peptide molecules. I can't find a single paper of any serious current researcher into Abiogenesis that still supports the Protein First Model.

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.

A bit of a confused statement if ever there was one. If Miller had included COS in his experiments, he might have made some polypeptides, but he didn't.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#20  Postby rainbow » Mar 04, 2010 10:51 am

tnjrp wrote:
95Theses wrote:I am quite certain a certain blue butterfly will be along to do that fairly quickly after you finish
Indeed with the subject like that I'm pretty sure he'll show up eventually (or someone will "rat this out" to him, in the worst case). So I'm bookmarking this as well in expectations of being able to brush up my knowledge about abiogenesis on the side.
:popcorn:


Of course, that is why we're here isn't it?

This bit though:
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].

This is quite a vast subject, and it would be difficult to do justice to it here. I can however find no papers that show that 'chiral catalysts' exist in nature outside of living systems.
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