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Prebiotic Earth Scenarios Founded On Tarry Barbecue Mess


A Nature review that begins with the pronouncement that an experiment “has quashed” major objections to the RNA world of prebiotic origins (Ref 1) is bound to raise a few eye-brows.  It is a bold pronouncement indeed and one that must be accompanied by a water-tight set of evidences.  In his review of the work of John Sutherland and others at the University of Manchester, science writer Richard Van Noorden promised just that by declaring to his readers that these same scientists had achieved the ‘never-before-performed’ feat of making a ribonucleotide- one of the components of RNA- in the lab (Ref 1).  Key to the success of the experiment was the presence of a phosphate group that, in addition to serving as one of the final reactants in the ribonucleotide synthesis process, also functioned as a catalyst earlier on in the reaction (Refs 1-3).  This result was the culmination of twelve long years of laboratory-based research during which simple molecules had been shown to be the “unwitting choreographers” of ribonucleotide synthesis (Ref 1).

Sutherland’s work fell squarely within the boundaries of the popular ‘RNA world’ hypothesis which posits that RNA preceded DNA in the prebiotic processes that later brought about life. In contrast New York University chemist Robert Shapiro maintained his position on the ‘Non-RNA-World’ rostrum by voicing his concerns over the assertion that Sutherland’s laboratory experiment had really provided a justifiable representation of the chemical maelstrom of the early earth (Ref 1).  Ten years ago Shapiro laid out the ground work for what he saw as the implausible order of events that would have had to ensue if ribonucleotides were to have existed in sufficient quantities for the formation of RNA.  In Shapiro’s assessment
“An isolated lagoon or other body of sea water would have to undergo extreme concentration, to perhaps 10-5 of its initial volume. This reduction in volume would be needed to bring urea from a concentration of 10-4 to 10-5 M assumed for many substances in a prebiotic ocean to that necessary for the reaction. It would further be necessary that the residual liquid be held in an impermeable vessel……The concentration process would have to be interrupted for some decades (assuming a temperature near 25°C) with the urea concentration near saturation, to allow the reaction to occur. At this point, the reaction would require quenching (perhaps by evaporation to dryness) to prevent loss by deamination. At the end, one would have a batch of urea in solid form, containing some cytosine (and uracil). This sequence cannot be excluded as a rare event on early Earth, but it cannot be termed plausible.” (Ref 4)
University of California chemist David Deamer and colleagues likewise contended that conditions on early earth would have been “inconsistent with moving beyond the initial stages of generating monomers and perhaps random polymers” (Ref 5) while former Yale biochemist Harold Morowitz famously wrote of the RNA world as “an environment that is impossibly improbable”(Ref 6).  The rich specter of energy sources that would have decimated biologically-relevant molecules such as RNA led physicist Paul Davies to similarly question a naive reliance on prebiotic soup scenarios in general:
“A watery soup is a recipe for molecular disassembly, not self-assembly… The same energy sources that generate organic molecules also serve to destroy them.  To work constructively, the energy has to be targeted at the specific reaction required.  Uncontrolled energy input, such as simple heating, is far more likely to prove destructive than constructive.  The situation can be compared to a workman laboriously building a brick pillar by piling bricks one on top of another.  The higher the pillar goes, the more likely it is to wobble and collapse…As a general rule, if you simply heat organics willy-nilly, you end up not with delicate long chain molecules but with a tarry mess, as barbecue owners can testify.” (Ref 7, pp. 89-90).
To be sure, these same arguments ring as true today as they did when they were originally published regardless of which energy source is under study.  Several alternative ‘Origins’ hypotheses have of course been put forward (Ref 5-8).  Writing in the Proceedings of the National Academy of Sciences, the late Salk Institute biochemist and RNA World champion Leslie Orgel considered the notion of some self-organizational principle through which chemical cycles might have originated on the early earth (Ref 8).  As Orgel pointed out, organic chemists have been successful in generating very simple chemical cycles- that is cycles that include perhaps one or two intermediate stages.  Yet such an achievement is a far cry from the labyrinthine biochemical cycles that exist in even the simplest forms of life (Ref 8).  In Orgel’s own words,
“To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic.”  (Ref 8 )
With the prebiotic earth reduced to a tarry barbecue mess upon which magic is the best we can come up with for explaining the origin of life’s biochemistry, one may rightly ask how much of what is under discussion falls within contemporary limitations over what is definable as science.  As astronomer Guillermo Gonzalez and philosopher Jay Richards are quick to note, science today has become “applied naturalism” defined broadly as, “the conviction that the material world is all there is, and that chance and impersonal natural law alone explain, indeed must explain, its existence” (Ref 9, p.224).  In his review of Sutherland’s experiments, Access Research Network correspondent David Tyler re-instated intelligent design as a viable alternative for explaining the origins of information-rich molecules such as RNA (Ref 10). 
Literature Cited
1. Richard Van Noorden (2009), RNA world easier to make, Nature, 13 May 2009, See http://www.nature.com/news/2009/090513/full/news.2009.471.html
2. Matthew W. Powner, Béatrice Gerland & John D. Sutherland (2009), Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 459, 239-242 

3. Kate Ravilious (2009), Molecule of life emerges from laboratory slime, New Scientist, 13th May, 2009, Online Access http://www.newscientist.com/article/mg20227084.200-molecule-of-life-emerges-from-laboratory-slime.html                           

4. Robert Shapiro (1999), Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life, Proc Natl Acad Sci U S A. 1999 April 13; 96 (8): 4396-4401                                                            

5. David Deamer, Jason Dworkin, Scott Sandford, Max Bernstein, Louis Allamandola (2002), The First Cell Membranes, Astrobiology Volume 2 pp. 371-381
6. Richard Robinson (2005), Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks, PLoS Biol 3(11): e396
7. Paul Davies (1999) The Fifth, Miracle, The Search for the Origin and the Meaning of Life Published by Simon and Schuster, New York
8. Leslie E. Orgel (2000), Self-organizing biochemical cycles, PNAS Vol 97, pp. 12503-12507
9. Guillermo Gonzalez and Jay Richards (2004), The Privileged Planet, How Our Place In The Cosmos is designed for Discovery, Regnery Publishing Inc, Washington D.C, New York, p.39
10. David Tyler (2009), Ribonucleotides and the revival of the “warm little pond” scenario, ARN, 19th May, 2009, See  http://www.arn.org/blogs/index.php/literature/2009/05/19/ribonucleotides_and_the_revival_of_the_

TCS, thanks for the link. Mapou
herb, yes he has recovered, and his wife has also. He tells both stories in the audio. TCS
After studying the lives of more than a dozen of the world’s most influential atheists, Vitz discovered that they all had one thing in common: Defective relationships with their fathers. By defective, Vitz means the fathers were dead, abusive, weak, or abandoned their children.
One thing in common? I count four things not in common. Adel DiBagno
You might find this audio presentation of interest: The Psychology of Atheism.
Thanks---I'm going to give that a listen over the weekend. Sounds like he has some interesting theories. From a review of one of his books:
After studying the lives of more than a dozen of the world's most influential atheists, Vitz discovered that they all had one thing in common: Defective relationships with their fathers. By defective, Vitz means the fathers were dead, abusive, weak, or abandoned their children.
The only reservation I have is that he allegedly was an atheist himself until his 30's or so, but apparently he has recovered. herb
Mapou, You might find this audio presentation of interest: The Psychology of Atheism. TCS
Hate is very wasteful, I leave that to religion. Like atheism. tribune7
Mapou: "With the pre-biotic earth reduced to a tarry B-BQ mess upon which magic is the best we can come up with for explaining the origins of life's biochemistry, one might rightly ask how much of what is under discussion falls within contemporary limitations over what is definable as science." (Robert Deyes) This sounds remarkably like a person suggesting pre-biotic environments fall outside the area of the knowable. As to hate, if my hate is as you say, subconscious, then, thank you for the diagnosis. You'll be sure to inform me if my atheism is actually faith in a different guise won't you? rvb8
rvb8 @11:
Mapou; ‘full of hate’? Not really, merely skeptical that people suggesting it is impossible to know a pre-biotic past
See? There you go again. Your hate is subconscious. Who said that a prebiotic past is impossible to know? That is neither the point nor the argument. The argument is that a naturalistic origin of life comes face to face againt a wall of exponential and sequential complexity that no prebiotic soup can ever hope to breach. The absurdity is so blinding, it hurts just to think about it. Monkeys banging on typewriters do not do it justice.
Hate is very wasteful, I leave that to religion.
Your hate IS religious in nature. You are too blind to notice it. Mapou
Mapou; 'full of hate'? Not really, merely skeptical that people suggesting it is impossible to know a pre-biotic past are the most qualified to judge those who give plausible possibilities of this past, and then extrapolate from those possibilities a path for life to emerge. Hate is very wasteful, I leave that to religion. rvb8
Hmmm, that last hyperlink didn't work. Let's try one Bilboe
rvb8 @2:
That didn’t take long Mapou, christianity mentioned in the very first post.
Well, my hand is forced because all I hear from the other camp are cries that the creationists have taken over the schools and whatnot, when we all know that it's the materialists.
Therefore when a group of scientists establish it is possible to get to RNA by natural causes
See what I mean? You make might point for me. You are full of hate. Your hate is so thick, you invent impossible scenarios and see things that are not there. Mapou
From the article:
However, Robert Shapiro, professor emeritus of chemistry at New York University disagrees. 'Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever,' he says. According to Shapiro, it is hard to imagine RNA forming in a prebiotic world along the lines of Sutherland's synthesis. 'The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely,' argues Shapiro.
nullasalus already found Robert Shapiro's comments regarding "this particular pathway" of Sutherland's, here. Bilboe
The quoted Shapiro criticsm is of RNA world synthesis generally, and not this particular pathway that was recently reported. I recall reading that Miller had investigated eutectic freezing as a possible mechanism for meeting the challenges laid out by Shapiro. Freezing prifies water, thereby concentrating the residual chemicals in small pockets. The ice is the "impermeable barrier" Shapiro requires. Since the temperature would be closer to 0 than 25 C, the reactions would take centuries, perhaps, not decades. Finally, drying could be accomplished as the ice sublimated away into the air. My own speculation is that the metabolism first and the RNA first groups are going to have to realize that some of the products of each - amino acids, simple sugars, RNA bases, etc were all present at various times and places. They could then mix, brought together by ocean currents. There is often such a Hegelian synthesis of approaches in science. Nakashima
This is a very clever experiment and it is similar in objective to the Miller/Urey experiment which created some amino acids. This was a much more complex and non intuitive process but in the end it produced two of the initial building blocks for a RNA polymer. Barry introduced this topic a day or so after it was published and we discussed this last week. There are many issues and others may want to comment on additional issues: 1. This experiment only produced two of the four ribonucleotides so I assume work is on to produce the other two. 2. This is simpler than the Miller?Urey objectives which was to produce as many amino acids as possible. Here there are only 4 molecules needed but slightly more complex molecules than an amino acid. 3. The real problem lies ahead and it is two fold: first to see if these polymers can combine in any extensive way and second the heart of the problem is to form any polymer of interest. It is one thing to hypothesize an RNA world, it is quite another to actually arrive at a long useful polymer. We are talking about having two legos here and what we have to build out of these legos is an airplane that works by a random process once we got the other two legos. 4. The experimenters must show that the conditions that produced the two molecules is reasonable on a primitive earth. They claim they have and Shapiro says they haven't. I am sure there will be many he said/she said debates going on. The stakes to some are high. 5. The experimenters must also show that this reaction can take place in the presence of all the other molecules that may have been present in the prebiotic environment. In other words can the reactions take place if a whole host of competitors are present for their own chemical reactions. It is unlikely that sterile conditions of the laboratory were present in little pools of water in the distant past. 6. My guess is that deep intense heat vents are now out. No uv getting down there. Or is there a scenario for that too? jerry
rvb8--These vast improbables, (as they say at UD almost daily) we can’t possibly know by science :-) Therefore when a group of scientists establish it is possible to get to RNA by natural causes the howl goes up, What these fellows did was a wonderful achievement and the howls you might hearing have little to do with it but much to do with the interpretations and extrapolations that some with a certain philosophical bent are applying to it. For instance, they did not synthesize RNA, much less by "natural causes" as a careless reader might assume from your post. Actually, IIRC, they did not even manage to synthesize half the ribonucleotides required. So the problem comes down to some -- and they aren't the IDists -- demeaning a very good thing by overblowing it. What I would be interested in is some discussion as to the effect the natural forces expected to be found outside a pristine lab would have on this synthesis, and the reasonableness of the ribonucleotides self-sequencing in a chain to produce a protein, and the protein surviving much less replicating to evolve into something containing DNA code. tribune7
RVB: First, Mapou mentioned an issue of motivation that in the era of Lewontin and imposed philosophical materialism in the name of science, is a serious one. One that too often evolutionary materialism supporting commenters at UD duck or distract from rather than squarely face and cogently address. On the substantial issue, there is good reason to see that it is utterly improbable on the gamut of the observed cosmos, that relatively simple organic molecules in whatever prebiotic "soup" strikes your fancy, would spontaneously give rise to digitally coded, language based, algorithm-implementing homochiral molecular nanotechnology using information systems. Such chemical and thermodynamic constraints as are known to act will strongly push projected prebiotic systems to simpler, not more complex states, much less, information-rich, algorithm-processing ones. Indeed, Mr Shapiro's recent observations in Sci Am on the problems of RNA world hypotheses (which inadvertently apply to his own metabolism first model) bear noting:
RNA's building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . . The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life's building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry . . . some writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case. A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . . To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .
On the other hand, we do have a routinely observed source of such information systems. Namely, intelligent designers. In that context, it is fair to infer that a very viable -- indeed, arguably best -- current explanation for the information-rich algorithmic systems at the heart of cell based life is just that: intelligent designers. It is further fair comment to observe that one reason many stoutly resist such an inference is their a priori commitment to evolutionary materialism as a worldview and indeed quasi-religion. GEM of TKI kairosfocus
That didn't take long Mapou, christianity mentioned in the very first post. These vast improbables, (as they say at UD almost daily) we can't possibly know. Therefore when a group of scientists establish it is possible to get to RNA by natural causes the howl goes up, 'but you can't possibly know the environment'. Correct, they can't, but plod on doing science, these dogged scientists plod, despite nay sayers. Real science I suppose. rvb8
Great post. Why do materialists hold on to their worldview in the face of unsurmountable odds? Is it because of their fear and hatred of religion, especially of certain Christian doctrines or authority figure? I think so. It must be a deep seated fear, however, because it takes a lot of hate to maintain so much dishonesty within one's mind. Are there any psychologists on UD who might want to take a stab at this? Mapou

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