Evolution has been Disproven

I hate being out of contact so long. I always miss the good threads... Okay, fair question. Try this on for size: Bailey, JM 1998 RNA-directed amino acid homochirality FASEB Journal 12:503-507

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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. (emphasis added)

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Just to preclude an argument, Bailey's idea about surface constraint of RNA is also supported. See, for example 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

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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.

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Does this answer your question?

Yoo-hoo, Defender? Was your question on homochirality sufficiently answered? (Post #48)

Yeah. Except that homochirality isn't a problem. Try this on for size:Bailey JM, 1998, "RNA-directed amino acid homochirality", FASEB J 12:503-507

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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- ibose 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.

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Let me know if there's something you don't get from the article.You should also look at Ghadiri MR et al, 2001, A chiroselective peptide replicator, Nature 409:797-801.

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The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules1, but none of the possible physiochemical processes considered can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material1 or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature. Here we report that a 32-residue peptide replicator, designed according to our earlier principles, is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical 'editing' function; in contrast to the previously observed error correction, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.(references in original deleted for clarity).

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Obviously, you are apparently one of the few that still thinks the homochirality problem is an insoluable issue. You really ought to get out more.edited to fix url problemsThis message has been edited by Quetzal, 02-09-2005 09:27 AM

In discussion board parlance, this is called "moving the goalposts". Your first argument raised the homochirality problem. That was addressed. As far as chicken and egg issues, the Ghadiri article addressed this fairly succinctly, perhaps you missed it? However, since you insist on claiming we're dodging the issue, how about:Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP, 2001, "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension", Science 292:1319-25

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The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

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Okay, so RNA can polymerize RNA using only base nucleosides and a primer. Still not satisfied? How about we build the RNA in the lab? Zhang B, Cech TR, 1997 "Peptide bond formation by in vitro selected ribozymes", Nature 390:96-100

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An attractive solution to the problem of the origin of protein synthesis in an evolving 'RNA world' involves catalysis by nucleic acid without assistance from proteins. Indeed, even the modern ribosome has been considered to be fundamentally an RNA machine, and the large ribosomal subunit can carry out peptidyl transfer in the absence of most of its protein subunits. Successive cycles of in vitro selection and amplification have been used to find RNAs that perform many biochemical reactions, including transfer of an RNA-linked amino acid to their own 5'-amino-modified terminus. Here we demonstrate the in vitro selection of ribozymes (196 nucleotides) that perform the same peptidyl transferase reaction as the ribosome: that is, they can join amino acids by a peptide bond. Like ribosome substrates, one amino acid (N-blocked methionine) is esterified to the 3'(2')-O of adenosine, whereas the acceptor amino acid (phenylalanine) has a free amino group. Our best characterized ribozyme recognizes the amino-acid ester substrate by binding its adenosine moiety, and is therefore capable of utilizing Leu- and Phe- as well as Met-derived substrates. Such lack of specificity with respect to the amino acid is a feature necessary for a generalized protein-synthesizing enzyme.

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Still too complicated? How about the formation of a ribozyme ligase using only two nucleotides? Reader JS, Joyce GF, 2002, "A ribozyme composed of only two different nucleotides", Nature 420:841-4

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RNA molecules are thought to have been prominent in the early history of life on Earth because of their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, owing to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unit. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyse the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalysed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

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Keep 'em coming. I've got a million of them. Ummm, what IS the problem of "folding" and "oxidation" you mention? Replication I already covered.

Ya know, it's been my experience that when someone's cornered, they resort to insult. Your stridency betrays your lack of a coherent argument rebutting what I posted. Especially since the posts quite thoroughly rebut your initial question concerning homochirality. Moving the goalposts doesn't help - I can keep pushing you back into a corner until you exit from the sidereal universe somewhere below the Higgs boson.However, in the interests of keeping this "discussion" moving, I'll ignore your insulting tone. After all, there might be someone reading this that could learn something. I have a feeling either you don't understand the articles I posted, or you're deliberately being obtuse. Let me know which is which - I'd be happy to go into detail on the articles if there's something you don't understand.For example, when you say: You are apparently not realizing that the Ghadiri article answers this question.Here, I'll quote the relevant portions for you again:

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From Ghadiri et al 2001:

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Here we report that a 32-residue peptide replicator, designed according to our earlier principles, is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical 'editing' function; in contrast to the previously observed error correction, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product.

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Note the emphasized bits:
a) the RNA is naturally self-catalyzing
b) it makes use of simple molecules to build itself
c) it has a dynamic (built-in) error correction system that is simply an expression of its chemical compositionYour next bit (right after implying I was a liar, which was uncalled for) states a brand spanking new question (moving the goalposts again): Since you hadn't asked this question before, I find it difficult to understand why you are complaining I hadn't answered it. OTOH, if you had read the remaining articles I gave you, you would have noted that they provide some clues as to the answer. For example:

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From Cech 1997:

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Successive cycles of in vitro selection and amplification have been used to find RNAs that perform many biochemical reactions, including transfer of an RNA-linked amino acid to their own 5'-amino-modified terminus

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This is called autocatalysis. IOW, the RNA (only 196 nucleotides long, btw), is building itself, simply through its own chemical composition and reactions with surrounding molecules. Interesting, no?Of course the second article was even more interesting: a simple binary molecule capable of catalyzing the formation of RNA. The relevant portion:

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Reader 2002

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Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyse the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalysed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

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Umm, you must have missed the sentence immediately following the part you quoted from the article. Here, let me refresh your memory:

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From Johnston, et al 2001:

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The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. (This is the bit you quoted). In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication.

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IOW, in the very next sentence, they state unequivocally that they discovered evidence to support the "premise" you singled out for criticism. You really need to read the articles I post if you're going to criticize them. I didn't read it? Lol. Bare assertion. What is "information" in this context? For that matter, what is "coding" except for a convenient analogy? If you've read the articles posted thus far, you'll note that all of them point to the fact that the sequences are determined by the simple chemical rules that govern how organic compounds form. The fact that some of these compounds are autocatalytic is a feature of their chemical properties. It's got nothing to do with "coding" except by way of analogy. IOW, the "code" wasn't "determined" in any way. It's just the way the molecules formed through basic chemical reaction. Nice try.Beyond that, if you want to talk about "information" and all that, please find an appropriate thread. I just told you - its a basic property of the way certain molecules interact. Maybe you should take a course in organic chemistry. Amazing stuff, carbon. However, for those interested, there is a great deal of experimental work being conducted. One I happen to like quite a bit is: Landweber LF, Pokrovskaya ID, 1999, Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution., PNAS 96:173-178

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In vitro selection, or directed molecular evolution, allows the isolation and amplification of rare sequences that satisfy a functional-selection criterion. This technique can be used to isolate novel ribozymes (RNA enzymes) from large pools of random sequences. We used in vitro evolution to select a ribozyme that catalyzes a novel template-directed RNA ligation that requires surprisingly few nucleotides for catalytic activity. With the exception of two nucleotides, most of the ribozyme contributes to a template, suggesting that it is a general prebiotic ligase. More surprisingly, the catalytic core built from randomized sequences actually contains a 7-nt manganese-dependent self-cleavage motif originally discovered in the Tetrahymena group I intron. Further experiments revealed that we have selected a dual-catalytic RNA from random sequences: the RNA promotes both cleavage at one site and ligation at another site, suggesting two conformations surrounding at least one divalent metal ion-binding site. Together, these results imply that similar catalytic RNA motifs can arise under fairly simple conditions and that multiple catalytic structures, including bifunctional ligases, can evolve from very small preexisting parts. By breaking apart and joining different RNA strands, such ribozymes could have led to the production of longer and more complex RNA polymers in prebiotic evolution. (emphasis added for J)

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I like this article because it specifies that RNA catalysts can form from simpler precursors - answering J's question concerning how RNA arose in the first place.But wait, there's more. J wants to know how this molecule developed its capabilities. Some very interesting work is being done on precisely this issue. Here's an article that specifies how one of the key reactions arose: Lee N, Bessho Y, Wei K, Szostak JW, Suga H, 2000, "Ribozyme-catalyzed tRNA aminoacylation", Nat Struct Biol 7:28-33

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The RNA world hypothesis implies that coded protein synthesis evolved from a set of ribozyme catalyzed acyl-transfer reactions, including those of aminoacyl-tRNA synthetase ribozymes. We report here that a bifunctional ribozyme generated by directed in vitro evolution can specifically recognize an activated glutaminyl ester and aminoacylate a targeted tRNA, via a covalent aminoacyl-ribozyme intermediate. The ribozyme consists of two distinct catalytic domains; one domain recognizes the glutamine substrate and self-aminoacylates its own 5'-hydroxyl group, and the other recognizes the tRNA and transfers the aminoacyl group to the 3'-end. The interaction of these domains results in a unique pseudoknotted structure, and the ribozyme requires a change in conformation to perform the sequential aminoacylation reactions. Our result supports the idea that aminoacyl-tRNA synthetase ribozymes could have played a key role in the evolution of the genetic code and RNA-directed translation. (emphasis added for J's benefit)

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Your point being you don't have the first clue what you're talking about? You brought it up. You tell me what the "problem" is. Learn the subject matter? Lol. Talk about weak arguments. You post the issue or question, I'll let you know when it covers something I "have no idea" about. As for wasting time, I would agree that someone's wasting their time. It's not immediately obvious that person is you, however.edited to fix hanging sentenceThis message has been edited by Quetzal, 02-10-2005 10:51 AM

You're accusing me of cut-and-paste because I posted the abstracts of the articles I referenced? Fine. From now on, I'll simply post the reference without any further notation and let the interested reader dig through the literature to find the information. I post the abstracts as a courtesy. It's unnecessary to the argument. From now on, I'll simply state something along the lines of "RNA is capable of self-catalysis. Here are 25 references you can check to verify I'm not making it up." ALL of the abstracts are available through PubMed if anyone's interested. On the other hand, anyone who actually bothers to read the abstracts can certainly see where they support my assertions.Of course, the likelihood of a creationist actually bothering to dig up the reference is slim. However you want it Percy.

For reference, PS isn't disagreeing with me. Cech used the term "molecular machine" in his article. I personally don't like the machine analogy any better than I like semantically confusing terms like "coding". However, everyone but you seems to realize that these are analogies used to illustrate an idea or concept (in this case, input-process-output similar to a machine) - not that Cech or anyone else thinks they're "machines" in the sense of a mechanical device, let alone the implication that they were manufactured or designed with a purpose. I'll be happy to say I agree with Cech's experiment - it's not controversial. He was reporting the results of an experiment, after all. I'll also be happy to say I don't necessarily agree with his terminology, although I certainly understand what he meant by it. Does that clear things up?

Thanks for your input. However, in point of fact Juhranimo expended a fair amount of electrons accusing me of not only cut-and-paste, but not actually reading the articles I posted. When Percy not only agrees with him, but uses the exact same terminology (i.e., cut-and-paste), it is obvious the Admin/Board Owner agrees.To me, the abstracts are not only self-explanatory in most cases, but directly refuted the contentions they were designed to address. If anyone had questions about the details, a simple "what does this mean" would have sufficed to generate as much explanation as one could wish. However, Percy has stated his preferences, so be it. Actually makes my life easier. It's a hell of a lot less time consuming to post "Shapiro R. "Prebiotic ribose synthesis: a critical analysis" Orig Life Evol Biosph. 1988;18(1-2):71-85" refutes your assertion that RNA couldn't form naturally."This message has been edited by Quetzal, 02-10-2005 11:34 AM

This has to be one of the single most brilliant refutations of scientific evidence ever encountered on EvCForum. Congratulations.

Thank you Sylas.My apologies to Ned and Admin, as well. I obviously over-reacted. I admit to be a bit irritated at J for his insulting broadsides - especially the one about cut-and-paste - so I was probably a bit over-sensitive.

Hmmm, looks like J has, like Elvis, left the building. Pity, it was starting to get interesting...