Saturday, May 05, 2018

The Guardian Sept, 2017

Ya-googly shows this criticisms of Urey Miller:

Source: https://evolutionnews.org/2014/06/squeezing_the_l/

(1) They still used the wrong gasses: methane, ammonia, and water vapor. For decades, geochemists have not considered it likely these gasses were abundant in the early Earth atmosphere.
(2) They still ignored the presence of oxygen, which destroys the desired products. Wells explained that oxygen was likely abundant due to photodissociation of water in the atmosphere. The oxygen would remain, while the hydrogen would quickly escape to space.
(3) Even if trace amounts of ammonia or methane and other reducing gasses were present, they would have been rapidly destroyed by ultraviolet radiation.
(4) No amino acids have been generated in spark-discharge experiments using a realistic atmosphere of nitrogen, carbon dioxide and water vapor, even in the absence of oxygen.
(5) The amino acids produced were racemic (mixtures of left- and right-handed forms). Except in rare exceptions, life uses only the left-handed form. Astrobiologists need to explain how the first replicator isolated one hand out of the mixture, or obtained function from mixed-form amino acids initially, then converted to single-handed forms later. Neither is plausible for unguided natural processes — especially when natural selection would be unavailable until accurate replication was achieved.
(6) Undesirable cross-reactions with other products would generate tar, destroying the amino acids. Only by isolating the desired products (a form of investigator interference — one might call it intelligent design) could they claim partial success.
(7) Amino acids tend to fall apart in water, not join. Under the best conditions with cyanamide, Bada and Parker only got dipeptides. Repeated cycles of wetting and drying would need to be imagined for polymerization, but many astrobiologists today think life originated at deep sea hydrothermal vents.
(8) The desired reagents would be extremely dilute in the oceans without plausible concentrating mechanisms. Even then, they would disperse without plausible vessels, like cell membranes, to keep them in proximity.
(9) Lifeless polypeptides would go nowhere without a genetic code to direct them.
(10) The Miller experiments cannot speak to the origin of other complex molecules needed by life: nucleic acids, sugars, and lipids. Some of these require vastly different conditions than pictured for amino acid synthesis: e.g., a desert environment with boron for the synthesis of ribose (essential for RNA).


Old news

I doubt all readers will have the chemistry background, but here are why these "criticisms" are bogus;
(I'll only cite one or two articles from the professional literature per false claim)
1) The Miller/Urey results were replicated with many gas mixes. Further, the early Earth atmosphere was highly reduced.
G. Schlesinger and S.L. Miller:
1983 "PREBIOTIC SYNTHESIS IN ATMOSPHERES CONTAINING CH4, CO, AND CO2. I. AMINO ACIDS" J Mol Evol 19:376

Zahnle, Kevin, Laura Schaefer and Bruce Fegley
2010 “Earth's Earliest Atmospheres” Cold Spring Harbor Perspectives in Biology

Holland, Heinrich D.
2006 “The oxygenation of the atmosphere and oceans” Phil. Trans. R. Soc. B 2006 361, 903-915 doi: 10.1098/rstb.2006.1838
(2) They still ignored the presence of oxygen, which destroys the desired products.
Cleaves, H. James, John H. Chalmers, Antonio Lazcano, Stanley L. Miller, Jeffrey L. Bada
2008 “A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres” Orig Life Evol Biosph 38:105–115

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196
(3) Even if trace amounts of ammonia or methane and other reducing gasses were present, they would have been rapidly destroyed by ultraviolet radiation.
Cleaves, H. James, Stanley L. Miller
1998 “Oceanic protection of prebiotic organic compounds from UV radiation” PNAS-USA v. 95, issue 13: 7260-7263

E. T. Wolf and O. B. Toon
2010 “Fractal Organic Hazes Provided an Ultraviolet Shield for Early Earth” Science 4 June 328: 1266-1268
(4) No amino acids have been generated in spark-discharge experiments using a realistic atmosphere of nitrogen, carbon dioxide and water vapor, even in the absence of oxygen.
Repeated variation of fake objection #2

Cleaves, H. James, John H. Chalmers, Antonio Lazcano, Stanley L. Miller, Jeffrey L. Bada
2008 “A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres” Orig Life Evol Biosph 38:105–115
(5) The amino acids produced were racemic (mixtures of left- and right-handed forms).
We find racemic peptides throughout life. We humans even have enzymes that are racemic, and those that convert amino acids to the opposite forms. So, while the statement of fact is correct, the reply is "So what."
(5 B) Astrobiologists need to explain how the first replicator isolated one hand out of the mixture, or obtained function from mixed-form amino acids initially, then converted to single-handed forms later."
Solved. Actually solved.
Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 "Enantiomeric cross-inhibition in the synthesis of oligonucleotides on a nonchiral template" J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K, Ghadiri MR, 2001 "A chiroselective peptide replicator" Nature 409: 797-51, Feb

Yao Shao, Ghosh I, Zutshi R, Chmielewski J. 1998 "Selective amplification by auto- and cross-catalysis in a replicating peptide system" Nature, Dec 3;396(6710):447-50

Hazen, R.M., T.R. Filley, and G.A. Goodfriend. 2001 "Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality" Proceedings of the National Academy of Sciences 98(May 8):5487
(5 C) Neither is plausible for unguided natural processes — especially when natural selection would be unavailable until accurate replication was achieved.
Wrong again. Just one example will do which also applies to fake objection #3;

Mulkidjanian, Armen Y., Dmitry A Cherepanov, Michael Y Galperin
2003 "Survival of the fittest before the beginning of life: Selection of the first oligonucleotide-like polymers by UV light" BMC Evolutionary Biology 2003 3:12

I see I am running out of time this morning. I'll do the last 5 later tonight, or perhaps tomorrow.

The source of these objections is a professional creationist, Jon Wells, in his book, "Icons of Evolution." The rest of the book is as full of falsehoods as these examples.

(6) Undesirable cross-reactions with other products would generate tar, destroying the amino acids.
Jon Wells loves this sort of claim because his followers lack the chemistry education to know he is bluffing. The solution to the solution is also joined in creationist bluff #7;
(7) Amino acids tend to fall apart in water, not join. Under the best conditions with cyanamide, Bada and Parker only got dipeptides. Repeated cycles of wetting and drying would need to be imagined for polymerization, but many astrobiologists today think life originated at deep sea hydrothermal vents.
So in fake objection #6 organic molecules make a dense cross-linked tar, and then in #7 are too dilute to ever find each other. Classic "Heads I win, Tails you lose" creationist double-think.
The actual scientific publication in fake objection #7 regarding cyanamide is;

Parker, E.T., Zhou, M., Burton, A.S., Glavin, D.P., Dworkin, J.P., Krishnamurthy, R., Fernández, F.M. and Bada, J.L.
2014 "A plausible simultaneous synthesis of amino acids and simple peptides on the primordial Earth" Angewandte Chemie International Edition, 53(31), pp.8132-8136.

It is a delightful paper that had slipped my notice until now. (Discussions even with creationists can be a learning opportunity). The basic result was that very simple conditions can produce more complex organic molecules than just Amino Acids (AAs). Rather than be a problem, it showed that under the same conditions known to produce AAs, they also spontaneously combined into small peptides. That is a solution, not a problem. The fake objection continues that, "Repeated cycles of wetting and drying would need to be imagined for polymerization."

My, my. Just imagine the repeated cycles of wetting and drying in tide pools, in stream side ponds, and any of the many other common locations for "wetting and drying." That was not difficult. However, the creationist twaddle tossed in a non-sequitur, "many astrobiologists today think life originated at deep sea hydrothermal vents."

I don't know if there are any recent polls of astrobiologists on the topic, but the hydrothermal vent hypothesis has been around since 1997;

Huber, Claudia, Gunter Wächtershäuser
1997 “Activated Acetic Acid by Carbon Fixation on (Fe,Ni)S Under Primordial Conditions” Science v. 276: 245-247

The advantages were that the hydrothermal vents eliminated the problem of bringing organic molecules into contact with minerals, and each other.

Huber, Claudia, Gunter Wächtershäuser
1998 “Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life” Science v.281: 670-672

Here are a few papers I suggest to expand your reading on hydrothermal vent chemistry;

Bernd R.T. Simoneit, Ahmed I. Rushdi and David W. Deamer
2007 “Abiotic formation of acylglycerols under simulated hydrothermal conditions and self-assembly properties of such lipid products” Advances in Space Research Volume 40, Issue 11, Pages 1649-1656

Philipp Baaske, Franz M. Weinert, Stefan Duhr, Kono H. Lemke, Michael J. Russell, and Dieter Braun
2007 "Extreme accumulation of nucleotides in simulated hydrothermal pore systems" PNAS | May 29, vol. 104 | no. 22 | 9346-9351

Again, creationists are using the ignorance of their followers to make money.

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