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1. Abiogenesis and the monochiral problem - impossible for evolutionists to deny."
Bob, you have been repeatedly shown that common catalysts can yield the pure stereoisomers that you seem to have a problem with.
Did you know that under certain conditions, chemical reactions that yield amino acids and other organic compounds no longer produce racemic yields?
First example. Organic molecules from space tend to have an abundance of left handed isomers. Why? Well it has been found that circularly polarized light will tend to push reactions to favor the left handed variety of the organic isomer. The products need not be racemic.
But there is a far more important effect to be seen. Catalyst. There are a number of possible pathways. Let's examine a few, shall we.
Please take a look at the following paper.
http://www3.interscience.wiley.com/cgi-bin/fulltext/109082709/HTMLSTART
If you read it, you will find that amino acids themselves can catalyze the formation of more lefthanded amino acids. An amino acid acts as a catalyst to produce a enantiomeric excess of an isomer. As this happens, the reaction is in effect making more of the catalyst. It leads to an autoinductive process which becomes autocatalytic.
The area of amino acid catalysis may hold significant clues to the evolution of prebiotic chemistry. That prebiotic building blocks such as sugars can be formed asymmetrically from such reactions has recently led to speculation about the evolution of biological homochirality through such routes.[4] We report herein a proline-mediated reaction exhibiting an accelerating reaction rate and an amplified, temporally increasing enantiomeric excess of the product. Thus, catalysis with amino acids is implicated in an autoinductive, selectivity-enhancing process, providing the first general chemical strategy for the evolution of biological homochirality from a purely organic origin.
You might want to look up the following papers
Pizzarello, Sandra, Arthur L. Weber. 2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661, 1151, 20 February 2004
This one shows how the lefthanded amino acids autocatalyze the formation of the right handed sugars found
in DNA and RNA.
Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.. 2004 “Borate Minerals Stabilize Ribose” Science January 9; 303: 196
THis paper shows how borate will catalyze the formation of right handed sugars, also.
Which leads into my other cataylst. Minerals.
As shown by the above paper, minerals that have catalytic properties can also lead to an enantiomeric excess of a particular isomer.
You should now see that racemic mixtures need not be hypothesized. Circularly polarized light, organic catalysts and inorganic catalysts can all lead to reactions that favor one isomer. So your claims that lab experiments always lead to a racemic mixture are false. Even better,the organic catalyst make more of themselves giving higher and higher yields.
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I have more to add. I previously gave you a reference to the following.
Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.. 2004 “Borate Minerals Stabilize Ribose” Science January 9; 303: 196
Now the paper tells us that borate will both catalyze the formation of the correct right handed ribose sugars and will stabilize the sugars, protecting them from degredation. The same chemicals that react to form the ribose will also react to form adenine, cytosine, guanine and uracil, the four nucleobases.
If you add a little phosphate to the mix, the ribose sugars and the nucleobases will combine to form nucleotides. Now, as it turns out, in the presence of clay (specifically montmorillonite) these nucleotides will begin to polymerize and make RNA.
But there is another important aspect of the clay. Fatty acids are delived to earth from space and are also made on earth, hydrothermal vents being an example location. This same clay that will catalyze the formation of RNA will also lead to a spontaneous process in which small vesicles are formed with the fatty acid making a wall and trapping water and the RNA molecules inside.
So we see that two ubiquitous substances such as borate and clay can catalyze the reactions and processes that lead towards something resembling a cell. But there is one more key peice to this puzzle.
In the 1980s it was discovered that RNA could act as something more than a messenger. RNA can perform biological functions similar to proteins. (The first such discovery came when Tetrahymena, a single celled organism, was found to use some RNA as enzymes.) RNA can both replicate itself and perform protein-like functions such as acting like an enzyme. In these forms, they are known as ribozymes. The RNA can store genetic information, copy that information, and carryout protein-like cellular functions. So once we have the RNA inside the fatty acid walls, it is possible that they could perform life functions without the need for DNA and proteins. In this scenario, they would evolve later.
So you see that there is a solution, with lab support and evidence in extant life, that shows your racemized amino acids "problem" to not be a problem. So why don't you accept the evidence.
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Your assertion is that amino acids are formed in racemized mixtures and therefore proteins could not be formed that were using solely one isomer. Yet I have given you references that show you how catalyst can result in an enantioselective reaction. Here is another. "Physical and Chemical Rationalization for Asymmetric Amplification in Autocatalytic Reactions," Angew. Chemie, in press (with F.G. Buono and H. Iwamura). So, if catalyst can give us reactions that favor a given isomer, then you no longer have a racemic mixture. YOur problem goes away.
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I think I have already shown you why your supposed problems are not problems. YOu say "In fact I show that NO experiment in the lab has as its products - ONLY mono-chiral amino acids that are then used to form viable proteins as building blocks for a living system." Now, what I have shown you is that we can make all right handed ribose sugars that can then be polymerized into RNA all of the appropriate isomer. That sounds pretty close to the mark to me. Further, I have shown that these RNA strands can perform all of the processes needed for simple life such as storing genetic information and catalyzing reactions. Now you see, here is where you get into trouble. I have shown you repeatedly that catalyst are capable of making one isomer. I have shown you that RNA can act as a catalyst and still does in extant life. I think you already know about RNA's role in making proteins. Put it all together and you have RNA catalyzing the correct amino acids and then putting it together into working proteins. What? You do not take my word for it? Well...
Bailey, JM 1998 “RNA-directed amino acid homochirality” FASEB Journal 12:503-507
The phenomenon of L-amino acid homochirality was analyzed on the basis that protein synthesis evolved in an environment in which ribose nucleic acids preceded proteins, so that selection of L-amino acids may have arisen as a consequence of the properties of the RNA molecule. Aminoacylation of RNA is the primary mechanism for selection of amino acids for protein synthesis, and models of this reaction with both D- and L-amino acids have been constructed. It was confirmed, as observed by others, that the aminoacylation of RNA by amino acids in free solution is not predictably stereoselective. However, when the RNA molecule is constrained on a surface (mimicking prebiotic surface monolayers), it becomes automatically selective for the L-enantiomers. Conversely, L-ribose RNA would have been selective for the D-isomers. Only the 2' aminoacylation of surface-bound RNA would have been stereoselective. This finding may explain the origin of the redundant 2' aminoacylation still undergone by a majority of today's amino acids before conversion to the 3' species required for protein synthesis. It is concluded that L-amino acid homochirality was predetermined by the prior evolution of D-ribose RNA and probably was chirally directed by the orientation of early RNA molecules in surface monolayers.
Remember how we talked about the surfaces of borax and clays acting as catalyst. Well they found that RNA makes the left handed proteins even from a mixture of amino acids when on such a surface. SO that gives us three possible cases. The catalysts make the left handed amino acids. The catalyst makes the right handed ribose which then makes RNA which then serves as a catalyst for the left handed amino acids and puts them into proteins. Or RNA on a catalyst makes proteins using only lefthanded amino acids from a mix of amino acids.
How about one more catalyst to throw in the mix? This time another very common material: calcite.
Hazen RM, Filley TR, Goodfriend GA, 2001, "Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality" PNAS 98:5487-5490
The emergence of biochemical homochirality was a key step in the origin of life, yet prebiotic mechanisms for chiral separation are not well constrained. Here we demonstrate a geochemically plausible scenario for chiral separation of amino acids by adsorption on mineral surfaces. Crystals of the common rock-forming mineral calcite (CaCO3), when immersed in a racemic aspartic acid solution, display significant adsorption and chiral selectivity of D- and L-enantiomers on pairs of mirror-related crystal-growth surfaces. This selective adsorption is greater on crystals with terraced surface textures, which indicates that D- and L-aspartic acid concentrate along step-like linear growth features. Thus, selective adsorption of linear arrays of D- and L-amino acids on calcite, with subsequent condensation polymerization, represents a plausible geochemical mechanism for the production of homochiral polypeptides on the prebiotic Earth.
You might want to study up on the general concepts of that one. How catalyst can arrange molecules in specific ways on their surfaces such that two things can happen. Either reactants that would normally make a racemic mixture can come together in such a way that only one isomer will be made. Or, if you have a randon mix of isomers, that one one will fit on the surface in the right way for a reaction to take place and therefore you can selectively pick out one isomer from a mix.
