Excellent paper-peptide self assembly

You gave three links, one of which you yourself seemed hesistant about. So I looked at the other two.One, about polar bears (http://www.springerlink.com/app/home/main.asp?wasp=6a86b7...), led to a site where one must pay to access the articles. I am not going to pay to look for your evidence: that’s your responsibility.The second link, about "various possibilities" (http://www.endeav.org/evolut/chiral/chiralit.htm) had an interesting abstract about the the Coriolis force, but the actual article didn’t seem to say what you think it might have. Here’s a quote, with emphasis added.

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1. The model
Let's assume that selection of the left or the right can go on the level of formation of cells and biotissue of plants or Protozos, as well as of inorganic structures due to selection between the left and the right forms of large supermolecular structures or formations.

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Let's postulate also, that asymmetry in the bioworld can be caused by the existence of oriented hydrodynamic flows of matter in a rotating medium.

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Prior to getting down to quantitative estimations, let's show that such a model is close to reality. To explain the point, it should be noted, that we, actually, postulate the fact that D and L molecular form selection in the course of living matter evolution on Earth have been caused by thermodynamics (naturally, with kinetic contribution to the process), and on levels of structures of higher hierarchies. We can assume that certain chiral chemical composition of organisms was maintained under juvenile Earth conditions at one of the hemispheres due to mechanisms related, basically, to the planet rotation around its own axis. In other words, Earth rotation direction (combined with gradients of the chemical potential determining fluid flow direction in plants and Protozoa and related to solar radiation flux gradients and gravitation) determined the dominating selection of asymmetric forms of large-scale superstructures and cells and, subsequently, of macromolecules, L-amino acids, D-sugars as the building material for living organisms.

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The evidence of asymmetry transition from lower hierarchical levels to the higher ones makes it possible to postulate a reverse phenomenon determined by evolutional selection and seemingly related to transition of asymmetry from the higher structures to the lower ones.

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The impression I get from skimming the article is that the authors are claiming that AFTER LIFE WAS ALREADY WELL ESTABLISHED AND EVOLVED TO THE LEVEL OF PLANTS AND PROTOZOA, rotation of the Earth could have influenced chirality of LARGE-SCALE SUPERSTRUCTURES, which could have then, the postulate, been backfed down the chain of hierarchical structures to ultimately influence the selection of monomer chirality.One problem with this theory is that it goes against the mainstream view which holds that homochirality is required for life to arise.Also, the article (which appears to be written by a foreigner who doesn’t speak English exceptionally well) doesn’t seem to have actually demonstrated the reverse flow of chirality it proposes (though I admit I didn’t carefully read it - but their use of the word postulate in terms of this part does indicate the lack of experimental support).[This message has been edited by DNAunion, 11-16-2003]

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First off, I stated that a *chiral* catalyst is used to separate them - but that means that a very small amount of imbalance in the catalyst will have dramatic effects in the overall isomer makeup of the solution.

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1) It does not mean that it WILL HAVE dramatic effects. Maybe the effects would be dramatic, maybe the effects would be slight, maybe the effects would be negligible.2) Exactly what chiral catalyst are you proposing for generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery catalyst?3) How did your as-of-yet unidentified chiral catalyst come to be present preferentially in one chiral form?4) How did your as-of-yet unidentified chiral catalyst maintain its chiral preference over an extended period of time? Was there some other chiral catalyst making it?

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If a small imbalance in an initial catalyst leads to a larger imbalance in the solution as a whole, can you see how that would easily amplify itself further?

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Can you see how, since racemization is a spontaneous process — which leads away from enantiomerically pure mixtures and towards racemic ones — a slight excess of one enantiomer could be lost?Can you see how enantiomeric cross inhibition could result in the locking up of some of the slight enatiomeric excess in molecules whose growth was still poisoned by inclusion of both enantiomers?

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Any new catalysts that develop in the system are going to have this greater imbalance, and will in turn amplify the imbalance.

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Aren’t you forgetting about enantiomeric cross-inhibition? That phenomenon deals with polymerization, not monomer formation, so your catalyst is helpless here.Just having a slight excess of one chiral form of a monomer does not mean that only that one enantiomer would be incorporated into growing polymers: the probability for both enantiomers being incorporated at some point would still be high and enantiomeric cross inhibition would greatly retard the production of polymers.Or does your mystery catalyst not only preferentially make one chiral form of monomers, but also, as if by magic, also serve as a polymerase, and one that ensures that only one chiral form gets incorporated into growing polymer chains? That would be one fantatstic catalyst!Leaving out magical molecules, we are still left with enantiomeric cross inhibition and the associated difficulty of polymer formation (and the locking up of some of the slight enantiomeric excess in growth-stunted molecules). With a low production rate of polymers (and a non-zero background rate of hydrolysis), the chances of hitting upon a useful catalyst is greatly reduced, and the chances of the amplification you are hoping for follow along.

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In the end, you can expect very few stereoisomers of the same chemicals.

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If everything you presented was unavoidable and non-problematic, sure. But mostly what you’ve done is paint an oversimplified, rosy picture; it’s devoid of nasty details (like spontaneous racemization, poisoning of polymer formation by enantiomeric cross inhibition, and the locking up of some of the enantiomeric excess in growth-stunted molecules) that always seem to get in the way of such speculations; it relies upon unidentified, mysterious catalysts; and it has not been demonstrated experimentally.

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Why would you expect differences in ratios not to amplify themselves in a prebiotic earth? Please explain.

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In a non-biological and undirected setting? Because having an enantiomeric excess of amino acids and/or nucleotides (the sugar moieties) is not the equilibrium state, and therefore, undirected processes will tend to bring any discrepancies back in line — back towards equilibrium. After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.Sure, if one ASSUMES into existence some somehow-enantiomerically enriched catalyst that can be maintained, somehow, in its enantiomerically enriched state over some extended period, and that can generate enantiomeric excesses in amino acids and/or ribose, and one also assumes into existence some other unidentified polymerase catalyst that preferentially selects the enantiomer that is present in slightly greater quantity (and also assumes anything else I’ve forgotten here), then sure, one can imagine an increase towards homochirality could occur. But even given all of that, homochirality is not assured.

First of all, I think Rei is being disingenuous.What I have been discussing in this thread has clearly been nucleotides, amino acids, and their polymers — the main molecules involved in OOL discussions. The first 14 posts in this thread, by everyone, were limited to amino acids/peptides: because Rei, in an OOL-related thread, spoke of enantiomers in general (step one in her plan to divert the topic?), at post 15 I replied and started discussing nucleotides also.But based on Rei’s statements lately, apparently Rei has been trying to slip her own ideas into the discussions without actually saying so, with her hidden agenda causing confusion.For example, I’ve pointed out and fully supported enantiomeric cross inhibition numerous times in relation to nucleotides and amino acids: the molecules being discussed. But Rei keeps acting like, and indeed stating that, enantiomeric cross inhibition isn’t a problem. Is she deaf, dumb, and blind? Well, if we assume she’s not, our options are limited. One of them is that Rei, unlike me, has stopped talking about just amino acids, nucleotides, and their polymers and has implicitly injected in some other molecules (what, quartz?) into the discussion, without actually mentioning them.I think it only fair that Rei stick to the topic others are discussing and stop trying to change them. Or at the very least, Rei should stop playing games and actually state what she is talking about.*********************************

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under which the pathway works in a chirally pure solution but has inhibition in a chirally imbalanced solution.

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Please learn to use appropriate terms: it helps communication.Chirally imbalanced? Do you mean a solution with an enantiomeric excess? Such a solution would be out of equilibrium and thus imbalanced. Or do you mean a racemic mixture, even though a racemic mixture is just about perfectly balanced, with 50% L and 50% D?Does your term chirally pure mean that it is a pure solution containing just the two chiral forms? If on the other hand you mean that only one enantiomer is present you should use the term enantiomerically pure. You see, an enantiomer is ONE of TWO chiral forms of a molecule, so if you mean only ONE enantiomer is present, then enantiomer is the correct word to convert into an adverb.***********************************

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Are you familiar with a Wimshurst Machine?

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No, and I don’t need to be, since a Wimshurst Machine isn’t a nucleotide or an amino acid or polymers made of these monomers.

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That is exactly what I am suggesting in this case. A slight imbalance of one catalyst, over long-term iterative processes, leads to a major imbalance of end products.

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And yet you’ve failed to answer any of these questions, as well as others:

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2) Exactly what chiral catalyst are you proposing for generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery catalyst?

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3) How did your as-of-yet unidentified chiral catalyst come to be present preferentially in one chiral form?

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4) How did your as-of-yet unidentified chiral catalyst maintain its chiral preference over an extended period of time? Was there some other chiral catalyst making it?

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All you are offering is speculation: you have no catalyst in hand and you have no experimental confirmation either.PS: Wimshurst Machines don’t count.

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If a small imbalance in an initial catalyst leads to a larger imbalance in the solution as a whole, can you see how that would easily amplify itself further?

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Can you see how, since racemization is a spontaneous process which leads away from enantiomerically pure mixtures and towards racemic ones a slight excess of one enantiomer could be lost?

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To lend some support to my last statement there, I’ll quote from an OOL book.

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It has been argued (Bada and Miller 1987) that racemization of amino acids is too rapid to permit amplification (by as yet unspecified reactions) to give rise to homochirality. Carbohydrates are more resistant to racemization than are amino acids. However, they are also chemically less stable, a factor that could equally defeat an amplification cycle. (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p247)

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Looks like Rei is facing a bigger problem than she thinks.

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Can you see how enantiomeric cross inhibition could result in the locking up of some of the slight enatiomeric excess in molecules whose growth was still poisoned by inclusion of both enantiomers?

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As I pointed out and referenced earlier, only certain types of chemical synthesis suffer from cross-inhibition.

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Yeah, and those being discussed being among them!!! So don’t pretend that what you said earlier, or now, has countered my last point — it still stands.

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Any new catalysts that develop in the system are going to have this greater imbalance, and will in turn amplify the imbalance.

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Arent you forgetting about enantiomeric cross-inhibition?

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Aren't you forgetting my reference?

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Nope, because you’ve given none that are relevant. You’ve provided no reference that shows that enantiomeric cross inhibition would not be a problem for nucleotides and/or amino acids, whereas I supplied what, a dozen, that showed it would be.

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Furthermore, I should add, cross-inhibition is only a problem when you're trying to build a *specific* chemical,

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Yeah, like the ones believed to have been involved in the OOL, like amino acids and nucleotides. Please don’t change the subject.

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... With a low production rate of polymers ..

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Where do you get a low production rate of polymers from?

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ENANTIOMERIC CROSS-INHIBITIONIt is a problem that prebiotic syntheses of polynucleotides and polypeptides would face, stunting the growth of chains and leading to low production rate of polymers.

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In the end, you can expect very few stereoisomers of the same chemicals.

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If everything you presented was unavoidable and non-problematic, sure. But mostly what youve done is paint an oversimplified, rosy picture; its devoid of nasty details (like spontaneous racemization,

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Why do you expect spontaneous racemization when you're using chiral reactants?

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Why do you expect chiral reactants in the first place?(That’s poor terminology, but I stuck with your phrasing)And why do you expect a small presence of a chiral catalyst to stop a spontaneous process like racemization from occurring?

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poisoning of polymer formation by enantiomeric cross inhibition,

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A non-issue - see above.

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A real issue for nucleotides and amino acidssee above and the dozen or so quotes I provided from OOL researchers.Please stick to the subject being discussed.

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You can poison specific polymers in a laboratory style environment, but you have yet to evidence that it poisons polymer formation in general.

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Go back and read the quotes I posted and/or research it yourselfI think you’re confused.

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and the locking up of some of the enantiomeric excess in growth-stunted molecules)

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How do you conclude that this would occur?

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Simple reasoning. Let’s look at the general idea of enantiomeric cross inhibition in nucleotides while looking at an average chain.Under racemic conditions (D/L = 1.0), the average chain starts to elongate but by the third monomer it has both enantiomers in it and so stops growing. Being so short, it won’t likely have any complex, useful function. Thus, the nucleotides in that chain are basically locked up in a useless molecule.Having a slight enantiomeric excess (instead of D/L = 1.0) might cause the average chain to incorporate one or two additional monomers, but would still quickly end up with both enantiomers. That chain too (being something like 4 or 5 monomers in length) is also not likely to be able to carry out any complex, useful function and so the nucleotides in it — which include the slight enantiomeric excess - are basically locked up in a useless molecule.Thus, enantiomeric cross inhibition would/could lock up some of the enantiomeric excess in growth-stunted molecules.

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Why would you expect differences in ratios not to amplify themselves in a prebiotic earth? Please explain.

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In a non-biological and undirected setting? Because having an enantiomeric excess of amino acids and/or nucleotides (the sugar moieties) is not the equilibrium state, and therefore, undirected processes will tend to bring any discrepancies back in line back towards equilibrium.

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One could apply that exact same argument toward the weather. Having turbulence in the atmosphere is not an equilibrium state, and so the world should balance itself out toward a simple constant atmospheric Coriolis flow. Does it?

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Too bad for you that we’re not talking about weather.What we are talking about is amino acids and nucleotides, and there is a thermodynamically spontaneous process, called racemization, that leads towards the equilibrium state of a racemic mixture.Here, I’ll repeat a quote form you.

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It has been argued (Bada and Miller 1987) that racemization of amino acids is too rapid to permit amplification (by as yet unspecified reactions) to give rise to homochirality. Carbohydrates are more resistant to racemization than are amino acids. However, they are also chemically less stable, a factor that could equally defeat an amplification cycle. (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p247)

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Please stick to the subject.

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Part of the nature of iterative processes is that errors magnify themselves tremendously.

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Your posts are evidence of that! :-)

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Take a class on chaos theory some time, then get back to me.

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Take a class on biochemistry some time, then get back to me.

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After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.

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Explain?

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The driving force behind racemization - towards equilibrium/racemic mixtures - is entropic (enthalpy remains constant). Going in the opposite direction — towards homochirality — has a positive delta G associated with it (because of the decrease in entropy) and thus is not spontaneous.

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Let me put it another way.

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Please don’t, you’ve gotten too far off topic already.[This message has been edited by DNAunion, 11-16-2003]

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1) The GL is itself homochiral, and it is the GL that "amplified" homochirality in the experiment. Take away the homochiral GL's influence and the various products appear in equal quantities:

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Now we're back to the GL? Nice try at a dodge there, but this conversation wasn't on the subject of the GL.

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Are you really that dense? Or are you just being dishonest? I just don't know anymore.YOU were the one who referenced the GL: it was YOUR statement I was replying to. Here, look at the actual exchange.

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Varying levels of inhibition are widely recognized in organic chemistry; for example, when studying a chiroselective peptide replicator, chemists at Skaggs found that "TLL autocatalytically accelerates its own production in reaction mixtures containing equimolar amounts of NL and EL (reaction 1; Fig. 3c), and adding TDD, TDL or TLD individually did not have any observable influence on the rate of TLL production. Indeed, reactions between NL and EL in the presence of equimolar amounts of all four templates, TLL, TDD, TDL and TDL (reaction 2), displayed a similar rate of product formation to that of the reaction where TLL was the only template present (Fig. 3c). These experiments suggest that TLL is the only active template involved in the ligation of EL and NL, and that all the other templates (enantiomer and diastereomers) act only as spectators during the formation of TLL (Fig. 3c).".

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Which, despite all of the intellectual sounding statements, basically means nothing in regards to our discussion.

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1) The GL is itself homochiral, and it is the GL that "amplified" homochirality in the experiment. Take away the homochiral GL's influence and the various products appear in equal quantities:

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The quote you posted is from a paper on the Ghadiri Ligase...the "GL".[This message has been edited by DNAunion, 11-17-2003]

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One, about polar bears (http://www.springerlink.com/app/home/main.asp?wasp=6a86b7...), led to a site where one must pay to access the articles. I am not going to pay to look for your evidence: thats your responsibility.

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It must have changed since I looked at it then, because I was able to access the full text the other day for free. I'll summarize: the distribution of a number of organic pesticides has been found to be chirally imbalanced in the world's oceans, leading to a chiral imbalance in wildlife.

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Sorry, but considering your general ad hom attitude and propensity for dishonesty, I am not about to take your word for it. If you've got the actual goods, present them.[This message has been edited by DNAunion, 11-17-2003]

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The second link, about "various possibilities" (http://www.endeav.org/evolut/chiral/chiralit.htm) had an interesting abstract about the the Coriolis force, but the actual article didnt seem to say what you think it might have. Heres a quote, with emphasis added.

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And here's a quite with my emphasis added

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Let's assume that selection of the left or the right can go on the level of formation of cells and biotissue of plants or Protozos, as well as of inorganic structures due to selection between the left and the right forms of large supermolecular structures or formations.
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You continually ignore the frequent use of the word "and" in the text, taking only from one side. The model seems to postulate both on the level of lifeforms *and* on biochemistry itself.

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So are you claiming that inorganic structures are biochemistry? YOU did highlight that part.Or are you referring to the supermolecular structures and formations? That doesn't work. First, those shouldn't be considered to be discussing biochemistry - carefully reread the clause you highlighted (of course you will disingenuous and stretch things beyond reason to try to make it somehow biochemical). Second, I already discussed superstructures in the following, which you so dishonestly omitted.

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The impression I get from skimming the article is that the authors are claiming that AFTER LIFE WAS ALREADY WELL ESTABLISHED AND EVOLVED TO THE LEVEL OF PLANTS AND PROTOZOA, rotation of the Earth could have influenced chirality of LARGE-SCALE SUPERSTRUCTURES, which could have then, the postulate, been backfed down the chain of hierarchical structures to ultimately influence the selection of monomer chirality.

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So in other words, you have absolutely no point. You just PRETEND to have a point hoping to score some cheap rhetoric points.[This message has been edited by DNAunion, 11-17-2003]

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For example, Ive pointed out and fully supported enantiomeric cross inhibition numerous times in relation to nucleotides and amino acids:

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In limited cases; it takes about 5 minutes of searching to dig up a process in which there is *no* or *minimal* cross inhibition.

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Gee, if it’s so simple, then why haven’t you done so already?Let me try to head off ANOTHER of your predictable tricks. My statements, which you claim to be countering and therefore should stick to discussing, deal with prebiotically plausible methods of creating templated polymers from monomer additions, and with the pools of monomers being racemic.

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And, as I've mentioned several times, that's only relevant for a particular route of creating a particular molecule - neither of which we are discussing when talking about abiogenesis.

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Wrong, on both counts. Enantiomeric cross inhibition is a problem for prebiotic polymerization of nucleotides. If that has nothing to do with abiogenesis, then what does? And, what are all of those OOL researchers I quoted talking about if not abiogenesis?Here, let me present those quotes to you again...why not try reading them this time?

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The aforementioned studies of the selectivities and limitations of template-directed oigomerization of oligonucleotides have been conducted under carefully controlled conditions using templates, as well as monomers, whose structural and chiral purity were rigorously controlled. In an experiment designed to test the requirement for chiral purity, it was demonstrated that incorporation of even a single mononucleotide of opposite chirality into the end of a growing chain in template-directed oligomerization is sufficient to terminate the reaction (Joyce et al., 1984). This observation (the phenomenon is referred to as enantiomeric cross-inhibition) has had serious consequences for theories of the origin of life (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, Cambridge University Press, 1998, p247)

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The chirality problem of the template-directed reaction was circumvented (and postponed) by the use of homochiral nucleotides. Based on laboratory experiments, it has been established that nucleotides synthesized by prebiotic reactions are always racemic — that is, they contain equal concentrations of D and L enantiomers. Thus a better simulated prebiotic experiment should use D and L ribose rather than D-ribose alone. When the same kind of experiment was carried out with the racemic mixture of activated ribonucleotides, the template-directed reaction did not proceed, because of enantiomeric cross-inhibition (Joyce et al, 1984). (Biogenesis: Theories of Life’s Origin, Noam Lahav, Oxford University Press, 1999, p207)

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Considerable effort has been directed toward finding an amplification mechanism by which a homochiral polynucleotide template, however produced originally, might selectively catalyze the oligomerization of like-handed monomers. This hope has been frustrated by the phenomenon of ‘enantiomeric cross-inhibition’ — the inhibition of template-directed oligomerization of activated mononucleotides when both D- and L- enantiomers are present in the reaction mixture. (Alan W. Schwartz, Selecting for Homochirality before RNA, Current Biology, Vol. 7 No. 8, August 1 1997, r477-r479)

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Laboratory experiments with nonenzymatic replication of RNA strands (see Joyce 1987, 1989, for a review) pointed out to the problem of enantiomeric cross-inhibition, the poisoning of chain growth on a template following the addition of building blocks with enantiomers of ribose. The chiral purity of the building blocks of RNA, the sugar moiety, is crucial for their participation in the self-replication reactions and hence in the establishment of the RNA World. (Biogenesis: Theories of Life’s Origin, Noam Lahav, Oxford University Press, 1999, p201—202)

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Why are chiral molecules in a state of absolute chiral purity so essential to the existence of life? The synthesis of specific proteins within living cells, mediated by DNA and RNA, as well as the replication of DNAs to pass on genetic information, all depend on an extremely precise ‘fitting together’ (complementarity) of the polymeric molecular chains involved. It was suggested early on that replicating double-stranded nucleic acid polymers would be impossible with a mixture of D- and L-monomer subunits. This has since been confirmed experimentally in studies which showed inhibition of nucleotide polymerization with chirally impure monomers. Similarly, molecular models have shown that the presence of ‘unnatural’ L-sugars in nucleotide polymers prevents them from adopting the complementary double-stranded helical structures necessary for self-replication. Thus, it is now generally accepted that the absolute homochirality for enantiomeric purity of biopolymer subunits are essential for self-replication and, by implication, for the origin of life. (William A. Bonner, Chirality Cosmochemistry and Life, Chemistry and Industry, n17, September 7 1992, p640-645)

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The origin of homochiral structures between the chemical and biological evolution on the Early Earth is a missing link in the process of the origin of life. Therefore the 'first asymmetric synthesis' continues to receive considerable scientific attention in biology, chemistry, as well as in physics. Recent experiments gave evidence for the feasibility of prebiotic polymerization reactions: The growth of chain length of special chiral molecules could be simulated successfully in the laboratory to reach the size of biopolymers. But for these "artificial" polymerization reactions monomers of the same handedness were required. The insertion of a "wrong" stereochemical configuration of only one enantiomer inhibits the whole polymerization process immediately. This has been well known state of the art and is defined as 'enantiomeric cross inhibition'.

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Because of the phenomenon of the 'enantiomeric cross inhibition' we assume, that life could only arise in an environment, in which a certain enantiomeric excess already came to existence. The origin of this enantiomeric excess is still unknown. (Uwe J. Mejerhenrich and Wolfram H. P. Thiemann [both from the University of Bremen], Enantiomer Separations Planned in Cometary Matter in Situ, Page not found - Astrobiology PS: Old link, may not still be present)

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Finally, there are no efficient prebiotic syntheses that produce purine ribosides or pyrimidine nucleosides. Added to this are the problems with the synthesis of ribose or nucleosides in that any prebiotic synthesis would generate racemic mixtures. Any template polymerization with such mixtures would show enantiomeric cross inhibition. Enantiomeric inhibition occurs if an activated L-nucleoside is polymerized into a template polymerization of activated D-nucleosides. Experimental evidence has clearly demonstrated that such conditions cause complete chain termination during polymerization. (http://campus.arbor.edu:8880/~michaelb/orglif.htm PS: Old link, may not still be present)

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Nucleosides are assembled from the ribose and bases, nucleotides are formed from nucleosides and phosphates, and oligonucleotides are chains of nucleotides. The hypothetical formation of the oligonucleotide components was described above; however, the locations for formation of these components are separate, so the components must be transported to a common location. Moreover, for ribose and the bases, they must be separated from complex witches’ brews of sugar enantiomers and similar compounds, many of which would have hindered nucleotide and oligonucleotide formation (Joyce, 1989). In particular, Joyce et al. (1994) found that template-directed oligomerization reactions are inhibited in racemic mixtures by molecules of opposite-handedness. (italic emphasis in original, John Washington, The Possible Role of Volcanic Aquifers in Prebiologic Genesis of Organic Compounds and RNA, Origins of Life and Evolution of the Biosphere, Vol. 30 No. 1, February 2000, p72)

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Since the template directed polymerization of one enantiomer is likely to be inhibited strongly by the presence of the other (enantiomeric cross-inhibition), it is hard to see how replication could get started, even from a racemic solution of pure beta-DL-nucleosides. (Byron Wingerd, RNA as a Prebiotic Precursor, 4/27/1997, http://www.msu.edu/user/wingerdb/rna.htm)

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[This message has been edited by DNAunion, 11-17-2003]

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Youve provided no reference that shows that enantiomeric cross inhibition would not be a problem for nucleotides and/or amino acids, whereas I supplied what, a dozen, that showed it would be.

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Again, why are you insistant that DNA and/or RNA had to be first?

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Rei, can you read? Look back at my statement you are replying to.

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Under racemic conditions (D/L = 1.0), the average chain starts to elongate but by the third monomer it has both enantiomers in it and so stops growing. Being so short, it wont likely have any complex, useful function. Thus, the nucleotides in that chain are basically locked up in a useless molecule.

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Wrong. In a laboratory environment, that may happen when you're dealing with a very limited set of very pure reactants, but in the real world, those chemicals are not going to stay short for long. There are too many things that could possibly react with them to either tear them apart or attach new things to them.

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And you thing ripping molecules apart and somehow attaching various other things to them is beneficial? Do those things happen to your hypothetical catatlysts that arise? Are they torn apart? Do they get inactivated by having various other things attached to them?

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You're dealing with your directed, single pathway logic again. That's not at all what is proposed with abiogenesis.

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Wrong. I am dealing with experiments conducted by scientists attempting to explain abiogenesis.[This message has been edited by DNAunion, 11-17-2003]

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After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.

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Explain?

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The driving force behind racemization - towards equilibrium/racemic mixtures - is entropic (enthalpy remains constant). Going in the opposite direction towards homochirality has a positive delta G associated with it (because of the decrease in entropy) and thus is not spontaneous.

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How is there a decrease in entropy?

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It's not my job to educate you. If you don't understand something, try reading a book.

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And need I mention that the trend of increasing entropy only is law inside closed systems?

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Wrong. It is possible for entropy to decrease in a closed system. However, total entropy cannot decrease in an isolated system.[This message has been edited by DNAunion, 11-18-2003]

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If all of these scientists are so sure that there's some sort of problem with abiogenesis, why do they believe in it?

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What would you suggest as an alternative?[This message has been edited by DNAunion, 11-18-2003]

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Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule

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THE homochirality of natural amino acids and sugars remains a puzzle for theories of the chemical origin of life1-18. In 1953 Frank7 proposed a reaction scheme by which a combination of autocatalysis and inhibition in a system of replicating chiral molecules can allow small random fluctuations in an initially racemic mixture to tip the balance to yield almost exclusively one enantiomer. Here we show experimentally that autocatalysis in a chemical reaction can indeed enhance a small initial enantiomeric excess of a chiral molecule. When a 5-pyrimidyl alkanol with a small (2%) enantiomeric excess is treated with diisopropylzinc and pyrimidine-5-car-boxaldehyde, it undergoes an autocatalytic reaction to generate more of the alkanol. Because the reaction involves a chiral catalyst generated from the initial alkanol, and because the catalytic step is enantioselective, the enantiomeric excess of the product is enhanced. This process provides a mechanism by which a small initial imbalance in chirality can become overwhelming.
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First of all, this experiment involved neither amino acids nor nucleotides (nor ribose).Second, no mention is made of whether or not all of the compounds involved are prebiotically plausible. If they aren’t, this paper has no direct bearing on the origin of life.Third, as always, we have to remember that this occurred in a lab. That is, what steps were taken to prevent unwanted side reactions? Were any other goal-oriented steps used? If so, how prebiotically plausible were those steps? If they rise to the level of illegitimate investigator interference then this paper has no direct bearing on the origin of life.However, I must admit, I am quite intrigued. I would like to see the experiment performed on amino acids and nucleotides, using prebiotically plausible molecules and conditions.[This message has been edited by DNAunion, 11-18-2003]

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Look, do you see me making fun of you?

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Uhm, yeah, I do. In fact, in addition to your doing that, I also see you repeatedly taking jabs at me personally, and being condescending - instead of sticking to the discussion - and I also see you stuffing words about religion into my mouth.All of these come from page 3 of this thread.

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DNAunion, prophet of the God of the Gaps.

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Play "God of the Gaps" all you want, but don't fail to address the meat of the issue.

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I could likewise start sentences with, "Does your invisible friend in the sky ... ".

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DNA, don't be a pain: you know very well that if we knew the exact route that abiogenesis took (even if it were your "poof, here's life!" method), there would be nothing to discuss.

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We're here to discuss theories as to what could lead to enantioselective properties, not trade insults over the gaps in our knowledge.

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Once again, introducing the "God of the Gaps!"

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I can just picture creationists in the 1800s now... "You say that the earth is billions of years old... and yet, we know of no way that the sun could be more than a few millions of years old - the best that you can come up with for its energy is "gravitational collapse". What, is there some "mystery, magical energy source" powering it that we don't know of? That has not been demonstrated experimentally.".

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The God of the Gaps is continually being forced to move into a new gap. Are you sure you want him in this one?

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That is why we discuss possibilities, not absolutes, when we're discussing gaps in scientific knowledge. Shoving a God wherever you see a gap is not a good plan for advancing human knowlege.

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Take a class on chaos theory some time, then get back to me.

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Next week I'll look to see if I can find any studies on the subject; you do your research as well.

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You're back to your old habits of A) splitting up individual posts into multiple, making it very hard to reply to, and B) focusing on personal attacks. If you keep this up, I will cease to respond in this thread. You have been warned; don't expect another warning

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Now we're back to the GL? Nice try at a dodge there

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since you seem to have this huge problem with the concept of how much of a sample size has been observed:

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You have a very serious problem with the concept of the percentage of total sample size observed that you have displayed again and again, and it gets very frustrating. Please quit pretending that we have observed even a tiny, remotely statistically significant percentage of total possibilities.

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Of course, knowing your love of quotes, you'd probably just ignore the article and extract an out of context quote,

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Thank you for being so mature Do most people you debate with end up getting sick of you in the process and leaving? If so, you shouldn't be surprised.

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Do you realize how bullheaded you look when you deliberately ignore what a person is saying?

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2) Exactly what method are you proposing for your deity generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery god-magic?

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3) How did your as-of-yet unidentified god-magic come to create preferentially one chiral form?

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4) How did your as-of-yet unidentified god-magic maintain the chiral preference over an extended period of time? Was there some other chiral catalyst making it?

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Yes, I know, you have far more time for this than I do. Is that something to really be proud of?

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Take a class on chaos theory some time, then get back to me.

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Take a class on biochemistry some time, then get back to me.
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So typical. You respond to a point with offhand dismissal

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So don't try to pretend that only I am to blame. If you start sticking to the discussion, I'll mirror that.[This message has been edited by DNAunion, 11-18-2003]

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After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.

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Explain?

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The driving force behind racemization - towards equilibrium/racemic mixtures - is entropic (enthalpy remains constant). Going in the opposite direction — towards homochirality — has a positive delta G associated with it (because of the decrease in entropy) and thus is not spontaneous.

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How is there a decrease in entropy?

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Okay, for any other people who were interested in the answer.

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A racemic modification has already been defined as an assembly of equal numbers of enantiomeric molecules, i.e., dextrorotary (+) and levorotary (-) molecules of the same substance. It might be noted that a racemic modification (or racemic form) with equal numbers of two types of molecules corresponds to a more random or disorderly state of affairs than a pure enantiomer (one single type of molecule), therefore there is an increase of randomness and therefore an increase in entropy as one passes from one enantiomer or other to a racemic modification. This process called racemization is thus thermodynamically favorable and may be brought about in a number of ways (e.g., by heat, or by treatment with acid, base, metal catalysts). (Elements of Stereochemistry, Ernest L. Eliel, John Wily & Sons, 1969, p16)

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Racemization is an energetically favored process since the concentration of the starting enantiomer is reduced by one-half during its operation. Since [delta]Ho = 0 for the enantiomers undergoing racemization (assuming no intermolecular interactions), it follows that the driving force for racemization is entirely entropic. (Stereochemistry of Organic Compounds, Ernest L. Eliel & Samual H. Wilen, John Wiley & Sons, 1994, p 425)

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Racemization is the process of producing a racemic modification [i.e., a racemic mixture] stating with one of the pure enantiomers. Since the two enatiomers have the same free energy, the equilibrium mixture will correspond to a 50-50 composition, i.e., it will be a racemic modification. Since the concentration of the pure enantiomer is reduced to one-half of its original value when racemization occurs, the free energy change associated with racemization is [delta]F = RT ln = -RT ln 2. (Stereochemistry of Carbon Compounds, Ernest L. Eliel, McGraw-Hill, 1962, p33)

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[This message has been edited by DNAunion, 11-19-2003]

Some things I forgot to point out earlier.

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Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule
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THE homochirality of natural amino acids and sugars remains a puzzle for theories of the chemical origin of life1-18. In 1953 Frank7 proposed a reaction scheme by which a combination of autocatalysis and inhibition in a system of replicating chiral molecules can allow small random fluctuations in an initially racemic mixture to tip the balance to yield almost exclusively one enantiomer. Here we show experimentally that autocatalysis in a chemical reaction can indeed enhance a small initial enantiomeric excess of a chiral molecule. When a 5-pyrimidyl alkanol with a small (2%) enantiomeric excess is treated with diisopropylzinc and pyrimidine-5-car-boxaldehyde, it undergoes an autocatalytic reaction to generate more of the alkanol. Because the reaction involves a chiral catalyst generated from the initial alkanol, and because the catalytic step is enantioselective, the enantiomeric excess of the product is enhanced. This process provides a mechanism by which a small initial imbalance in chirality can become overwhelming.
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First of all, this experiment involved neither amino acids nor nucleotides (nor ribose).

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Second, no mention is made of whether or not all of the compounds involved are prebiotically plausible. If they aren’t, this paper has no direct bearing on the origin of life.

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Third, as always, we have to remember that this occurred in a lab. That is, what steps were taken to prevent unwanted side reactions? Were any other goal-oriented steps used? If so, how prebiotically plausible were those steps? If they rise to the level of illegitimate investigator interference then this paper has no direct bearing on the origin of life.

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However, I must admit, I am quite intrigued. I would like to see the experiment performed on amino acids and nucleotides, using prebiotically plausible molecules and conditions.

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First, another of Rei’s claims is false/dishonest. Here’s the context.

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Can you see how, since racemization is a spontaneous process which leads away from enantiomerically pure mixtures and towards racemic ones a slight excess of one enantiomer could be lost?
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To lend some support to my last statement there, I’ll quote from an OOL book.

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It has been argued (Bada and Miller 1987) that racemization of amino acids is too rapid to permit amplification (by as yet unspecified reactions) to give rise to homochirality. Carbohydrates are more resistant to racemization than are amino acids. However, they are also chemically less stable, a factor that could equally defeat an amplification cycle. (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p247)
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Looks like Rei is facing a bigger problem than she thinks.

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Ah, finally an applicable quote. And my response? It's already been shown to occur. Sorry, there!

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And as I’ve shown, Rei’s offered support falls flat on its face. Rei’s doesn’t address amino acids, unlike the quote I presented. Rei’s doesn’t address nucleotides, unlike the quote I presented. In other words, Rei is again pretending to counter me and hoping no one notices. But he failed. Sorry, there!The second point is, where are the follow up publications that worked with amino acids and/or nucleotides? Since the researchers state that their method could be involved in the origin of homochirality associated with the OOL, then why didn’t they use one of the two main molecules believed to be associated with OOL: amino acids and nucleotides? Okay, well, maybe they got it work with something easier first, something not directly related to the origin of life. But the letter Rei posted is from 1995: that’s 8 years ago. The researchers — and the scientific community at large - have had 8 years to get this to work with amino acids and nucleotides...so where are the publications? I didn't find any and Rei apparently doesn't have one or he would have posted it, instead of the one he did. Evidence of those papers is absent...evidence of absence!? :-)[This message has been edited by DNAunion, 11-19-2003]