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Author Topic:   Excellent paper-peptide self assembly
DNAunion
Inactive Member


Message 5 of 50 (63762)
11-01-2003 12:04 AM
Reply to: Message 4 by Rei
09-18-2003 8:32 PM


Re: Peptide self-assembly is one thing...
quote:
Rei: Isn't the left-handed molecule simply named as the left-handed molecule because it is the first one discovered, and then the inherent mirror to that molecule around a given point would be the right-handed molecule?
/*DNAunion*/ No.
quote:
Rei: Otherwise, how would one decide, given a previously never-witnessed molecule, that it was left or right handed?
/*DNAunion*/ Two methods (simplified here). One deals with rotation of light - either to the left or to the right - when passed through a sample of molecules. The other is based on a standardized method of orienting a molecule in three-dimensional space and then noting which side a certain molecular group is found on: the left or the right.

This message is a reply to:
 Message 4 by Rei, posted 09-18-2003 8:32 PM Rei has not replied

  
DNAunion
Inactive Member


Message 6 of 50 (63763)
11-01-2003 12:11 AM
Reply to: Message 3 by Percy
08-23-2003 11:36 AM


Re: Peptide self-assembly is one thing...
quote:
Persipient: You [note, not me] describe chirality as a problem for abiogenesis, but your example has to do with protein size. I must be missing your point, because I don't see what one has to do with the other in relation to abiogenesis.
/*DNAunion*/ Probability. If there is some mechanism directing the selection of amino acid enantiomers - ensuring that the L form is always picked - then length is irrelevant. But when the process occurs by undirected, non-biological processes, an easily made assumption is that both chiral forms - being present in equal quantities and being chemically equivalent - would be incorporated at random in a growing chain. Thus, the longer the chain, the less likely it would be to have all left-handed amino acids. It's like flipping a fair coin: it's not that hard to flip 4 consecutive heads, but try flipping 40 heads in a row.

This message is a reply to:
 Message 3 by Percy, posted 08-23-2003 11:36 AM Percy has replied

Replies to this message:
 Message 7 by Rei, posted 11-01-2003 12:57 AM DNAunion has replied
 Message 12 by Percy, posted 11-02-2003 9:01 AM DNAunion has not replied

  
DNAunion
Inactive Member


Message 8 of 50 (63777)
11-01-2003 2:21 AM
Reply to: Message 7 by Rei
11-01-2003 12:57 AM


Re: Peptide self-assembly is one thing...
quote:
Rei: And what evidence do you have that amino acids of different chiralities join readily?
/*DNAunion*/ And what evidence do you have that they don't?
*******************************
The following will suffice (at least for those who aren't arguing just to argue).
quote:
Reactions can proceed enantio-selectively if chiral reactants or catalysts are involved, or if some external chiral influence is present. But because chiral reactants and catalysts themselves require an enantioselective production process, efforts to understand the homochirality of life have focussed on external chiral influences. (G. L. J. A. Rikken & E. Raupach, Enatioselective Magnetochiral Photochemistry, Nature, vol 405, June 22 2000, p932-935)
For those that the above quote does not convince, then just use simple logic. If both enantiomers of amino acids would not be incorporated into polypeptides produced by undirected, non-biological processes alone, then why are OOL researchers searching for a solution for homochirality?

This message is a reply to:
 Message 7 by Rei, posted 11-01-2003 12:57 AM Rei has replied

Replies to this message:
 Message 9 by Rei, posted 11-01-2003 1:04 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 10 of 50 (63812)
11-01-2003 1:21 PM
Reply to: Message 9 by Rei
11-01-2003 1:04 PM


Re: Peptide self-assembly is one thing...
quote:
Rei: 2) The body of the summary undercuts your position
/*DNAunion*/ Nope, it supports my position.
Your further statements, however, expose your lack of knowledge of the topic.
quote:
Rei: ... it states that for opposite chiralities to bond, there would need to be a production process which creates a mix of chiral forms, and as a consequence, researchers are only concerned with the production process (i.e., it doesn't seem realistic that there would be a production process that would create such a mix)
/*DNAunion*/ Wrong. The rule is that undirected, non-biological processes produce racemic mixtures of the amino acid enantiomers (i.e., mixtures in which both enantiomers are present in equal number). The problem facing OOL researchers is trying to get a chirally pure solution by undirected, non-biological processes.
quote:
"Prebiotic syntheses of amino acids either on Earth or elsewhere would be expected to produce racemic mixtures (equal amounts of the L and D enantiomers, or D/L = 1.0). (Jeffrey L. Bada, Enhanced: Extraterrestrial Handedness?, Science, Volume 275, Number 5302 Issue of 14 Feb 1997, pp. 943)
And the one you didn't understand the first time...
quote:
Reactions can proceed enantio-selectively if chiral reactants or catalysts are involved, or if some external chiral influence is present. But because chiral reactants and catalysts themselves require an enantioselective production process, efforts to understand the homochirality of life have focussed on external chiral influences. (G. L. J. A. Rikken & E. Raupach, Enatioselective Magnetochiral Photochemistry, Nature, vol 405, June 22 2000, p932-935)
/*DNAunion*/ Some processes have been found that result in slight enantiomeric excesses (for example, CPL , circularly polarized light, can preferentially destroy one enantiomer over the other), but they are far short of producing a enantiomerically pure product under prebiotically plausible conditions.
PS: If anyone has any recent findings on homochirality I'd be interested. I stopped keeping up with the topic a couple of years ago.
[This message has been edited by DNAunion, 11-17-2003]

This message is a reply to:
 Message 9 by Rei, posted 11-01-2003 1:04 PM Rei has replied

Replies to this message:
 Message 11 by Rei, posted 11-01-2003 1:56 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 13 of 50 (63980)
11-02-2003 3:30 PM
Reply to: Message 11 by Rei
11-01-2003 1:56 PM


Re: Peptide self-assembly is one thing...
quote:
/*DNAunion*/ The problem facing OOL researchers is trying to get a chirally pure solution by undirected, non-biological processes. Some processes have been found that result in slight enantiomeric excesses (for example, CPL , circularly polarized light, can preferentially destroy one enantiomer over the other), but they are far short of producing a chrirally pure product.
quote:
Rei: Are you unfamiliar with the Murray and Murchison meteorites? Of course, that is just one possibility. Would you, perchance, happen to have the ratios of chiralities in the aforementioned meteorites on hand? I'm having trouble tracking it down.
/*DNAunion*/ I am familiar with the Murchison one, which involved CPL (a mechanism I mentioned originally). The enantiomeric excesses were small. Here are some personal notes I still have on CPL, which reference the Murchison meteorite.
CPL (Circularly Polarized Light)
It has been suggested that CPL (circularly polarized light) may have caused a ratio in chirality different than 50/50 for an amino acid contained in a meteorite that was studied. However, there are a few issues that cast some degree of doubt upon this explanation, at least if it is intended to explain biological homochirality.
(1) The amino acid that was examined is not one of the 20 biological amino acids
quote:
The reported L amino acid excesses are very small and would need to be amplified by some process in order to generate homochirality. Even if this did take place, the L amino acid homochirality would be associated with alpha-dialkyl amino acids, which are not major players in modern protein biochemistry. (Jeffrey L. Bada, Enhanced: Extraterrestrial Handedness?, Science, Volume 275, Number 5302 Issue of 14 Feb 1997, pp. 942 — 943)
(2) There was only a 2% to 9% difference between the two optical isomers
quote:
as reported by Cronin and Pizzarello on page 951 of this issue, some unusual amino acids present in the Murchison meteorite apparently do have small excesses of the L enantiomers (that is, D/L < 1.0). These measurements have minimized the contamination problem by focusing on amino acids that either are extremely rare or have never been reported in terrestrial organisms or the geosphere.
Four alpha-dialkyl amino acids--alpha-methylisoleucine and alpha-methylalloisoleucine (2-amino-2,3-dimethylpentanoic acid), alpha-methylnorvaline (2-amino-2-methylpentanoic acid), and isovaline (2-amino-2-methylbutanoic acid)--are reported to have an L enantiomeric excess of 2 to 9%. Only isovaline has been reported in some microbial peptides, where it is present as either the L or D enantiomer. The alpha-hydrogen analogs of two of these alpha-dialkyl amino acids, norvaline and alpha-amino-n-butamoic acid, are racemic, suggesting that enantiomeric excess is only preserved in amino acids that are resistant to racemization (Jeffrey L. Bada, Enhanced: Extraterrestrial Handedness?, Science, Volume 275, Number 5302 Issue of 14 Feb 1997, pp. 942—943)
quote:
Then, in 1996, John Cronin and Sandra Pizzarello at Arizona State University found that some unusual nonprotein amino acids in the Murchison meteorite show a small excess of the L-isomer (on the order of a few percent). (Christopher Wills and Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p120-121)
quote:
Recently, a new approach to this problem has been taken that is not subject to some of the criticisms of the earlier work (Cronin and Pizzarello). In these studies, the targets for analysis were Murhcison amino acids that (1) either have no known terrestrial source or are very restricted in occurrence in the biosphere, and (2) have chiral centers that are resistant to racemization (epimerization). Consequently, it is likely that the chiral centers of these amino acids retained their original configuration through the aqueous and mild thermal processing experienced in the meteorite parent body and that the original enantiomer ratios were not compromised by terrestrial contamination. An L-enantiomeric excess was observed in each case: [alpha]-methylisoleucine (7.0%), [alpha]-methylalloisoleucine (9.1%), isovaline (8.4%), and [alpha]-methylnorvaline (2.8%). Interestingly, the [alpha]-H analogues of these last two amino acids, that is, [alpha]-amino-n-butyric acid and [alpha]-aminopentanoic acid, were found to be racemates. (John R. Cronin, Clues from the Origin of the Solar System: Meteorites, chapter 6 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, 1998, Cambridge University Press, p134)
(3) CPL produces the slight deviation from equality by preferentially breaking down one form — that is, CPL-produced variance from a 50/50 ratio is a destructive process.
quote:
Although very small enantiomeric excesses (~2%) have been generated from racemic leucine irradiated with circularly polarized ultraviolet light, there was extensive decomposition (59 to 75%) during the experiment. This implies that amino acid survival during this type of enantiomeric enrichment process would be extremely poor. (Jeffrey L. Bada, Enhanced:Extraterrestrial Handedness?, Science, Volume 275, Number 5302 Issue of 14 Feb 1997, pp. 942 — 943)
quote:
A circularly polarized light wave has an electric field that rotates either clockwise or counterclockwise about the wave’s direction of motion. Ultraviolet light with these types of polarization are absorbed unequally by right-handed and left-handed molecules and can break down or destroy one form more easily than the other, creating an asymmetry in the relative populations of the two forms. (Ron Cowen, Starlight Shows Life the Right Path, Science News, August 1, 1998 v154 n5 p68(1))
With these objections in mind, it is not without reason to state that this kind of light does not yet hold the complete answer.
One final note. The enantiomeric excesses of the chiral biological amino acids in the Murchison meteorite have changed over the years due to terrestrial contamination. Consequently, one needs to be wary not to consider numbers for such amino acids when looking for non-biological causes of enantiomeric excesses.
quote:
If the amino acids detected in Nakhla had been formed by abiotic processes on Mars, they would originally have been racemic (D/L ~1). Contamination of the meteorite by terrestrial L-amino acids after it fell to Earth could have significantly lowered the initial D/L ratios of any endogenous amino acids, perhaps to values close to those we measured. We have observed a similar lowering of D/L ratios in an interior sample of Murchison during its residence on Earth. In measurements carried out in 1970, soon after Murchison fell, the D/L ratios for alanine, aspartic acid, and glutamic acid were close to 1.0. Analyses of the same Murchison sample today yielded D/L ratios in the range of 0.3 to 0.5 for aspartic acid, 0.7 to 0.9 for glutamic acid, and 0.7 to 1.0 for alanine. Concentrations of the abiotic nonprotein amino acids in Murchison, such as AIB and racemic isovaline, were found to be similar in both the 1970 and 1998 analyses, indicating that these amino acids have not been affected by terrestrial contamination. (Daniel P. Glavin, Jeffrey L. Bada, Karen L. F. Brinton, & Gene D. McDonald, Amino Acids in the Martian Meteorite Nakhla, Proceedings of the National Academy of Sciences, Vol. 96, Issue 16, August 3, 1999, p8835-8838)

This message is a reply to:
 Message 11 by Rei, posted 11-01-2003 1:56 PM Rei has replied

Replies to this message:
 Message 14 by Rei, posted 11-02-2003 4:41 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 15 of 50 (64038)
11-02-2003 8:45 PM
Reply to: Message 14 by Rei
11-02-2003 4:41 PM


Re: Peptide self-assembly is one thing...
quote:
Rei: You didn't address the key points of my posts (and I would be interested in your response).
/*DNAunion*/ No, I have addressed your key points. I showed at least one to be wrong and have addressed the others, just not to your satisfaction.
quote:
Rei: 1) The same point that I've brought up from the beginning that you haven't addressed: How readily enantioisomers react; I presented evidence that suggests that they don't react as readily.
/*DNAunion*/ You keep missing the point, or slightly altering it. The point is that long polymers are required for complex life functions, such as self-replication, and that undirected, non-biological processes are not likely to form them, one reason being that homochirality is needed.
Since you now reference enentiomers in general, that is what I will respond to.
Here is a reference to the first paper on the problem of enantiomeric cross inhibition: note what happens when both enantiomers are present and undirected, non-biological processes are used to try to form polymers.
quote:
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)
/*DNAunion*/ Here’s some others on the need for homochirality.
quote:
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)
quote:
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)
quote:
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)
quote:
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)
quote:
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'.
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)
quote:
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)
quote:
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. Morever, 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)
quote:
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)

This message is a reply to:
 Message 14 by Rei, posted 11-02-2003 4:41 PM Rei has replied

Replies to this message:
 Message 17 by Rei, posted 11-03-2003 2:03 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 18 of 50 (64289)
11-03-2003 11:49 PM
Reply to: Message 16 by Loudmouth
11-03-2003 12:46 PM


quote:
Loudmouth: I think what is missing here is the size of the pre-biotic "test tube" or reaction chamber, as such.
/*DNAunion*/ The paper I was addressing gave us this. But, the value it gave was overstated (as I already pointed out).
quote:
Loudmouth: We are talking about the rise of life, perhaps only once, on the Earth, a pretty big place, in the span of millions of years. Looking at things from a molecular perspective, large numbers appear quite quickly. Avagadro's number for example is in the 10^22 range
/*DNAunion*/ The two key things are (1) how improbable an event is, and (2) how many shots are available to hit the target. "Large numbers" of attempts don't do too much for us if the inverse of the probability is an even larger number.
Also, the number of shots are frequently based on unreasonable assumptions, such as the ignoring of side reactions, starting with "The Molecular Biologist's Dream: 'Once upon a time there was a prebiotic pool full of [beta]-D-nucleotides...'"*, and so on.
quote:
Loudmouth: Second, no one knows the precise sequence or length of the first peptide/protein or the first RNA/DNA sequence.
/*DNAunion*/ But they do have fairly good ideas how long an RNA molecule would have to be in order to self-replicate. Orgel and Joyce estimated that it would have to be at least 40 monomers in length in order to be able to fold up into a complex enough shape to perform the required function. Experiments since have found that such is probably far too low: the closed thing yet to a self-replicator that has been designed was about 180 nucleotides long.
***********************************
Short quote from "Prospects for Understanding the Origin of the RNA World", Gerald F Joyce & Leslie E Orgel, Chapter 2 of The RNA World: Second Edition, Cold Springs Harbor Laboratory Press, 1999, p50
[This message has been edited by DNAunion, 11-03-2003]

This message is a reply to:
 Message 16 by Loudmouth, posted 11-03-2003 12:46 PM Loudmouth has replied

Replies to this message:
 Message 20 by Loudmouth, posted 11-04-2003 6:54 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 19 of 50 (64292)
11-04-2003 12:01 AM
Reply to: Message 17 by Rei
11-03-2003 2:03 PM


Re: Peptide self-assembly is one thing...
quote:
/*DNAunion*/ You keep missing the point, or slightly altering it. The point is that long polymers are required for complex life functions, such as self-replication, and that undirected, non-biological processes are not likely to form them, one reason being that homochirality is needed.
quote:
Rei: If your claim about that is due to inhibitory effects exhibited in racemic mixtures, you're ignoring the fact that, given a chiral "seed" or reactant - any sort of chemical, in fact, which favors one isomer over another - racemic mixtures can readily be separated.
/*DNAunion*/ Gee, don't you think the dozen origin of life scientists I quoted would have already thought about that? Don't you think that if it were that easy, they would not even be worrying about how to get homochirality? Use some common sense, okay?
quote:
Rei: Do a search for the word "stereoselective" (or "enantioselective") and "synthesis" - I get 26,200 hits on google for the former, and 23,000 for the later - almost all papers and books on various reactions.
/*DNAunion*/ Now all you have to do is to try find one that shows that the simple method you proposed actually would work for the experiments being discussed. Looks like you have some work cut out for you.
quote:
Rei: Also, all of your posts argued in favor of my initial point: that reactants of different chiralities do not readily react with each other.
/*DNAunion*/ No they don't...you simply don't understand them.
They argue that the two enantiomeric forms DO readily react and that when they do, they poison the ability of the chain to grow any longer.
Try some simple logic again...if the two enantiomeric forms didn't react readily, then what's this enantiomeric cross inhibition problem all of those OOL authors are referring to? Why worry about it? The left handed molecules would react with other left handed molecules, and the right handed molecules would react with other right handed molecules: there would be no problem.
quote:
Rei: That is the very claim that I made that started off this discussion here - check the history.
/*DNAunion*/ No need to...you were wrong then, and are still wrong.
quote:
Rei: Finally, you're still dodging #2: That once a hypercycle begins with a certain chirality, it is effectively "locked in".
/*DNAunion*/ I haven't dodged the general question. In fact, I already posted a quote - way back in post 8 of this thread - that showed that PREEXISTING homochirality can produce homochirality (after all, that's what happens in cells). Remember that quote I posted twice and you just couldn't understand? Hopefully you've learned enough from me in the past couple of days to understand it now...
quote:
Reactions can proceed enantio-selectively if chiral reactants or catalysts are involved, or if some external chiral influence is present. But because chiral reactants and catalysts themselves require an enantioselective production process, efforts to understand the homochirality of life have focussed on external chiral influences. (G. L. J. A. Rikken & E. Raupach, Enatioselective Magnetochiral Photochemistry, Nature, vol 405, June 22 2000, p932-935)
/*DNAUnion*/ See, that was sufficient to address your general point and there was no need for me to restate it a third time. But, since you somehow think you've got me backed into a corner, yeah, I guess I'll spend the time to spoon feed it to you again.
[This message has been edited by DNAunion, 11-04-2003]

This message is a reply to:
 Message 17 by Rei, posted 11-03-2003 2:03 PM Rei has replied

Replies to this message:
 Message 23 by Rei, posted 11-07-2003 7:27 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 21 of 50 (64636)
11-05-2003 9:16 PM
Reply to: Message 20 by Loudmouth
11-04-2003 6:54 PM


quote:
/*DNAunion*/ The paper I was addressing gave us this. But, the value it gave was overstated (as I already pointed out).
quote:
Loudmouth: Sorry, I must have missed something. Did the paper limit the OoL to specific conditions or rule out others?
/*DNAunion*/ The paper assumed the entire volume of the ocean as the reaction vessel. Since the more-contemporary theories don’t posit the entire ocean as a prebiotic soup where life could have arisen within it anywhere — for example, one of the main current theories being restricted to areas immediately surrounding deep-sea hydrothermal vents - the calculation overestimates the number of chances per unit time.
quote:
/*DNAunion*/ The two key things are (1) how improbable an event is, and (2) how many shots are available to hit the target. "Large numbers" of attempts don't do too much for us if the inverse of the probability is an even larger number.
Also, the number of shots are frequently based on unreasonable assumptions, such as the ignoring of side reactions, starting with "The Molecular Biologist's Dream: 'Once upon a time there was a prebiotic pool full of [beta]-D-nucleotides...'"*, and so on.
quote:
Loudmouth: Unless you can quantitate the chances over say a 50 million year timespan you can't claim that the odds are against it. So, how does the inverse of the probability outweigh the chances? How many chances were there? Why do you feel they are unreasonable?
/*DNAunion*/ As I pointed out before, Orgel and Joyce estimated that a self-replicating RNA would have to be at least 40 monomers in length in order to be able to fold into a complex-enough shape to be able to perform such a complex function. Starting with The Molecular Biologist’s Dream: ‘Once upon a time there was a prebiotic pool full of [beta]-D-nucleotides’ and temporarily ignoring other problems (enantiomeric cross inhibition, side reactions, etc.), their calculation goes like this:
quote:
It is difficult to state with certainty the minimum possible size of an RNA replicase ribozyme. An RNA consisting of a single secondary structural element, that is, a small stem-loop containing 12-17 nucleotides, would not be expected to have replicase activity. A triple stem-loop structure, containing 40-60 nucleotides, offers a reasonable hope of functioning as a replicase ribozyme. One could, for example, imagine a molecule consisting of a pseudoknot and a pendant stem-loop that forms a cleft for template-dependent replication.
Would such a [40-monomer self-replicating] molecule be expected to occur within a population of random RNAs? A complete library consisting of one copy each of all 10^24 possible 40-mers would weigh about one kilogram. Furthermore, there may be many such 40-mers, encompassing both distinct structural motifs, and more importantly, a large number of equivalent representations of each motif. As a result, even a small fraction of the total library, consisting of perhaps 10^20 sequences and weighing about one gram, might be expected to contain at least one self-replicating RNA with the requisite properties. The above calculations assume that a self-replicating RNA can copy itself (or that a fully complementary sequence is automatically available; see below). If two or more copies of the same 40-mer RNA are needed, then a much larger library, consisting of 10^48 RNAs and weighing 10^28 grams, would be required. This amount is comparable to the mass of the Earth. (Prospects for Understanding the Origin of the RNA World, Gerald R Joyce and Leslie E Orgel, Chapter 2 of The RNA World: Second Edition, Cold Spring Harbor Laboratory Press, 1999, p60-61)
/*DNAunion*/ As far as how many chances there were, Werner Loewenstein has made an educated guess/calculation that resulted in approximately 10^48.
quote:
Thus, allowing for some cooling time of the planet, there were, at most, 0.9 billion years (4.5 x 1014 minutes) available for the development of the basic macromolecular hardware. And this is a generous estimate — if anything, it stretches the window of [molecular] evolutionary opportunity.
Now, to weigh those odds, we need to translate this window of time into an evolutionary trial number. For this we make a generous allowance about the trial space: we assume that the primeval evolutionary laboratory occupied the entire surface of the earth — a surface covered by an ocean 10 kilometers deep, with chemical building blocks in abundance everywhere. If we divide that maximized space then into compartments of cell size, 10 cubic micrometers, and grant a trial speed of 1 per minute — a super speed — we obtain a number of possible trials of the order of 10^48 [4.5 x 10^14 x 5 x 10^33 ]. (The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life, Werner R. Loewenstein, Oxford University Press, NY, 1999, p52).
/*DNAunion*/ Note that his calculation uses the entire volume of the ocean too, which is not in keeping with the main theories these days.
So not getting too technical, in order for two RNA replicases to exist simultaneously (one to copy the other to get things started) Joyce and Orgel calculate that there would need to be a library of about 10^48 unique RNAs, all existing at the same time. But Loewenstein calculates that there were only 10^48 total chemical trials over a 900 million year time span.
Of course there is more to be said, but that’s a lot to digest so perhaps I should refrain from going farther at this point.
[This message has been edited by DNAunion, 11-05-2003]

This message is a reply to:
 Message 20 by Loudmouth, posted 11-04-2003 6:54 PM Loudmouth has replied

Replies to this message:
 Message 22 by Loudmouth, posted 11-07-2003 6:41 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 24 of 50 (65087)
11-08-2003 1:55 AM
Reply to: Message 22 by Loudmouth
11-07-2003 6:41 PM


quote:
So not getting too technical, in order for two RNA replicases to exist simultaneously (one to copy the other to get things started) Joyce and Orgel calculate that there would need to be a library of about 10^48 unique RNAs, all existing at the same time. But Loewenstein calculates that there were only 10^48 total chemical trials over a 900 million year time span.
quote:
I don't see why the whole library has to be existant at the same time, maybe you could fill me in. I understood it to be a 1 in 10^48 chance so that all is needed is 10^48 tries for a decent chance of the correct ribozyme to come about by chance.
Let me start by trying to explain why two 40-mers might be needed - one to copy the other to get things started. I will use an analogy, replacing a ribozyme with an enzyme, and then using another analogy. Enzyme are biocatalysts (substances that accelerate biochemical reactions by lowering the activation energy and without being permanently altered in the process) that have a specific conformation: most are globular proteins. Think about a three-dimensional PacMan, the arcade man shaped like a circle with a triangular mouth. Globular enzymes have a cleft or pocket where other molecules (called substrates) dock and get worked on (split or joined, for example). This active area, analogous to PacMan's mouth, is called the active site and is the portion of the protein directly involved in catalysis (again, let's not get too technical). Now suppose that this PacMan protein attempted to copy itself, and that it is extremely flexible. It could reach around and nibble here and there, copying this and that segment. But how would the PacMan protein copy its own active site???? PacMan, no matter how flexible, can't bite his own mouth (imagine a dog chasing its tail trying to bite it: now imagine that dog chasing his own mouth...think he'll ever succeed?). Assuming that a ribozyme would suffer a similar problem, one solution would be to have another replicator on hand nearby to make a copy of the first.
Now, about the probability. Suppose a self-replicator is represented by a 6 on a fair die and you are given two dice. You need to get two 6's - one to replicate the other one to get things going. What is the probability of throwing a 6 on die 1 and a 6 on die 2 on the first roll of each? 1/6 x 1/6 = 1/36. So we can say that the probability of success is about 0.0278 (1 in 36). But we can't then reinterpret that probability by saying that we can just roll a single die 36 times (or what have you) and expect success. It's more than just a probability number; we also need two sixes to exist, one on each die, and to exist at the same time.
The way the authors explain it (though it is not meant to be taken too literally) is that one library ("die") consists of 10^24 unique sequences. Pick a single molecule from that library and consider it to a replicator. To have a match for that molecule you have to have a second library ("die") also consisting of 10^24 unique sequences (technically, the second library could have just a single molecule in it, but relying on just one molecule being the right one is almost like requiring a near miracle. To be sure you'd find the match, you'd need all 10^24 unique sequences in library 2).
That may not be the most accurate explanation, but maybe it helps.
One thing that has to kept in mind is that 10^48 40-mers existing at one time would have a mass comparable to the Earth's. Let's not focus on the "weight" but rather on the distribution of so many molecules - or even a fraction of them. For one 40-mer to replicate the other, the molecules can't arise one in "the Pacific Ocean" and the other in "the Indian Ocean": they'd never meet. Even if both arose on opposite shores of "the Indian Ocean" they'd never encounter one another. In fact, even if they sprung up just a mile apart the probability that they would meet is close to 0. And although it gets harder to "calculate", even if two partners arose just 10 yards away from each other it seems unlikely that one would happen to come into contact with the other.
And let's not forget that polymers tend to hydrolyze in water (we could get more technical, but that's the general idea). So there is a time limit on how long they have to wonder about looking for their partner. One's arising at time X and the other's arising at the same spot at time X + 10,000 years is going to do no good at all.
So not only would a pair of replicators have to arise in almost the same exact microscopic volume, but they would also have to arise at almost exactly the same time.
***********************
PS: Came back to make a quick comment. It's too late at night (well, early in the morning) for me to work anything up now, but I think I have a way of better explaining the two libraries probability thing (I am conceptually using arrays - multi-value data structures that store homogeneous data-type values in logically contiguous memory locations - but I should be able to explain it using an analogy of boxes of some kind). But it will take some time to work up.
***********************
quote:
This is an interesting debate, plan to read up and get back to it. Ribozymes and hypercycles aren't especially my specialty, but it does interest me. Any suggestions for online sources?
Sorry, I get most of my info from books on the subject.
[This message has been edited by DNAunion, 11-08-2003]

This message is a reply to:
 Message 22 by Loudmouth, posted 11-07-2003 6:41 PM Loudmouth has not replied

  
DNAunion
Inactive Member


Message 25 of 50 (65132)
11-08-2003 12:29 PM
Reply to: Message 22 by Loudmouth
11-07-2003 6:41 PM


Loudmouth, I came up with a much better way of explaining the probability for 2 RNA replicases arising together. And yeah, I was wrong to say that all 10^48 would have to exist at the same time: it might be "only" something like 10^28 40-mers that need to created at the same time.
quote:
So not getting too technical, in order for two RNA replicases to exist simultaneously (one to copy the other to get things started) Joyce and Orgel calculate that there would need to be a library of about 10^48 unique RNAs, all existing at the same time. But Loewenstein calculates that there were only 10^48 total chemical trials over a 900 million year time span.
quote:
I don't see why the whole library has to be existant at the same time, maybe you could fill me in. I understood it to be a 1 in 10^48 chance so that all is needed is 10^48 tries for a decent chance of the correct ribozyme to come about by chance.
BEGIN: REPEATED FROM LAST EXPLANATION
Let me start by trying to explain why two 40-mers might be needed - one to copy the other to get things started. I will use an analogy, replacing a ribozyme with an enzyme, and then using another analogy. Enzyme are biocatalysts (substances that accelerate biochemical reactions by lowering the activation energy and without being permanently altered in the process) that have a specific conformation: most are globular proteins. Think about a three-dimensional PacMan, the arcade man shaped like a circle with a triangular mouth. Globular enzymes have a cleft or pocket where other molecules (called substrates) dock and get worked on (split or joined, for example). This active area, analogous to PacMan's mouth, is called the active site and is the portion of the protein directly involved in catalysis (again, let's not get too technical). Now suppose that this PacMan protein attempted to copy itself, and that it is extremely flexible. It could reach around and nibble here and there, copying this and that segment. But how would the PacMan protein copy its own active site???? PacMan, no matter how flexible, can't bite his own mouth (imagine a dog chasing its tail trying to bite it: now imagine that dog chasing his own mouth...think he'll ever succeed?). Assuming that a ribozyme would suffer a similar problem, one solution would be to have another replicator on hand nearby to make a copy of the first.
END: REPEATED FROM LAST EXPLANATION
Now, about the probability associated with getting 2 replicases.
Suppose you are given two fair dice. What is the probability of throwing a 6 on die 1 and a 6 on die 2 on the first roll of each? 1/6 x 1/6 = 1/36. So we can say that the probability of success is about 0.0278 (1 in 36). Now let’s carry this over to the replicases, thinking of a replicase as a 6, but on a die with 10^24 faces. But first, let me explain something about the model chosen.
BEGIN: REPEATED FROM LAST EXPLANATION
One thing that has to kept in mind is that 10^48 40-mers existing at one time would have a mass comparable to the Earth's. Let's not focus on the "weight" right now (or the amount of resources that would go into making such a library) but rather on the distribution of so many molecules - or even a fraction of them. For one 40-mer to replicate the other, the molecules can't arise one in "the Pacific Ocean" and the other in "the Indian Ocean": they'd never meet. Even if both arose on opposite shores of "the Indian Ocean" they'd never encounter one another. In fact, even if they sprung up just a mile apart the probability that they would meet is close to 0. And although it gets harder to "calculate", even if two partners arose just 10 yards away from each other it seems very unlikely that one would happen to come into contact with the other. Further, let's not forget that polymers tend to hydrolyze in water (we could get more technical, but that's the general idea). So there is a time limit on how long they have to wonder about looking for their partner. One's arising at time X and the other's arising at time X + 10,000 years (even if in the exact same spot where the other’s ghost would be) is going to do no good at all. So not only would a pair of RNA replicases have to arise in almost the same exact microscopic volume, but they would also have to arise at almost exactly the same time.
END: REPEATED FROM LAST EXPLANATION
Now, take a pencil and draw a little dot, like the period at the end of a sentence. Now suppose that in that tiny volume (it does actually have three dimensions) there is some mechanism that spits out a pair 40-mers each second, with the nucleotide sequence of each molecule being determined by chance alone. What is the probability that the same sequence, capable of performing the replicase function, will appear together — in the same attempt - in that tiny volume? Let’s look at this from a reference frame centered on the left molecule of the pair. Well, there are 10^24 possible sequences 40 nucleotides long (sticking to just the four nucleotides found in extant RNA) and the authors assume that 10,000 or so of those will be capable of replicase activity: so 1 in about 10^20 random 40-mers counts as a success for the left hand molecule. Roughly speaking, then, for every 10^20 random 40-mers the mechanism spits out for the left hand molecule, one will be a replicase. But getting a single replicase will do no good if two are needed (one to copy the other to get things going). So now suppose a replicase appears as the left member of a pair (after some 10^20 attempts). What is the probability that the right member of that pair will match the left member? Since the sequences are being produced randomly, the two sequences are independent of each other. Therefore, the probability of getting the same sequence on the right is 1 in 10^24. Combining those two events (event X has to occur AND event Y has to occur, simultaneously) we multiply the two probabilities: 10^-20 x 10^-24 = 10^-44. Thus there would be about a 1 in 10^44 chance of two RNA replicases arising simultaneously in the same microscopic volume if some mechanism was producing a pair of random 40-mers per second, and 1 in 10^20 40-mers was capable of replicase activity. (NOTE: I am not exactly sure how the authors came up with 10^48 instead of 10^44 - looks like they simply multiplied 10^24 x 10^24 instead of 10^20 x 10^24).
The next question is, should we expect a single microscopic dot to produce the two needed RNA replicases given, say, 100 million years? No. There would nowhere near enough attempts to saturate the possibilities. The number of attempts (production of one pair counting as one attempt) would be as follows:
(1 attempt / sec) x (3600 sec / 1 hr) x (24 hr / 1 day) x (365 days / 1 year) x 100 million years = 3.15 x 10^15 attempts
Very roughly speaking, we’d need something like ten thousand trillion trillion microscopic RNA factories, each working around the clock pumping out 2 random 40-mers every second of every day of every year for 100,000,000 years straight before the number of attempts reaches 10^44.
10^44 / (3 x 10^15) = 3.33 x 10^28
Is it reasonable to assume so many RNA factories into existence at one time, and for that many to remain active (apparently RNA factories can be immediately replaced if they stop functioning), for that long of a period?
Note also that this model doesn’t take into account several obstacles that would greatly hinder the chances of success: for example, enantiomeric cross inhibition and side reactions, nor the very real possibility that an RNA replicase would have to be longer than 40 nucleotides.
[This message has been edited by DNAunion, 11-08-2003]

This message is a reply to:
 Message 22 by Loudmouth, posted 11-07-2003 6:41 PM Loudmouth has not replied

Replies to this message:
 Message 34 by Tokyojim, posted 11-16-2003 3:00 AM DNAunion has not replied

  
DNAunion
Inactive Member


Message 26 of 50 (65149)
11-08-2003 3:59 PM
Reply to: Message 23 by Rei
11-07-2003 7:27 PM


Re: Peptide self-assembly is one thing...
Oh geez, Rei's trying to peddle himself as some kind of expert on stereochemistry.
quote:
The process is known as "resolution" of the mixtures, and there's nothing secret about it; I'm surprised that you're even trying to debate about the topic without any sort of familiarity with how racemic mixtures are separated in the lab (to know how it applies to nature). The traditional method is the introduction of a chiral reactant or catylist (which need not be complex at all). Chiral reactants only react with one chiral form; the result is a diastereomer (look up the term yourself). The diastereomer and the desired chiral form are then separated via fractional crystallization (which itself can occasionally be used to separate chiral forms on its own, such as in racemic acid, an isomer of tartaric acid). How familiar are you with fractional crystallization, BTW?
Gee, I guess Rei is a real expert on stereochemistry, huh? Sure pretends to be one. But wait a tick, what is this from right here at the EvC forum?
quote:
--------------------------------------------------------------------------------
Rei: Isn't the left-handed molecule simply named as the left-handed molecule because it is the first one discovered, and then the inherent mirror to that molecule around a given point would be the right-handed molecule?
--------------------------------------------------------------------------------
/*DNAunion*/ No.
--------------------------------------------------------------------------------
Rei: Otherwise, how would one decide, given a previously never-witnessed molecule, that it was left or right handed?
--------------------------------------------------------------------------------
/*DNAunion*/ Two methods (simplified here). One deals with rotation of light - either to the left or to the right - when passed through a sample of molecules. The other is based on a standardized method of orienting a molecule in three-dimensional space and then noting which side a certain molecular group is found on: the left or the right. (http://EvC Forum: Excellent paper-peptide self assembly -->EvC Forum: Excellent paper-peptide self assembly message #5)
That’s a very good indication that Rei isn’t what he’s trying to come off as here - an expert on the subject. (I'm just glad I was able each him something about chirality).
Now, is there anything problematic about his proposed method of achieving homochirality as far as OOL is concerned? Yes. First of all, relating to the latter part of this statement:
quote:
The diastereomer and the desired chiral form are then separated via fractional crystallization (which itself can occasionally be used to separate chiral forms on its own, such as in racemic acid, an isomer of tartaric acid)
note that, as Rei correctly points out with his qualifying word occasionally, most racemic mixtures can’t be resolved by crystallization alone.
quote:
Unfortunately, few racemic compounds crystallize as separate enantiomers, and other methods of separation are required. (Organic Chemistry: Fourth Edition, L. G. Wade, Jr., Prentice Hall, 1999, p213)
So let’s not get carried away and think that just crystallizing ribose or amino acids is going to resolve racemates into two separate, chirally pure mixtures.
Second, let’s look at this statement by Rei:
quote:
The process is known as "resolution" of the mixtures, and there's nothing secret about it; I'm surprised that you're even trying to debate about the topic without any sort of familiarity with how racemic mixtures are separated in the lab (to know how it applies to nature).
Ignoring Rei relentless posturing, the question isis the method Rei discusses for resolution in the lab plausible for a prebiotic origin of homochirality? No.
First, his following statements do not agree with my college organic chemistry text on two points.
quote:
The traditional method is the introduction of a chiral reactant or catylist (which need not be complex at all). Chiral reactants only react with one chiral form; the result is a diastereomer (look up the term yourself).
Ignoring more of Rei’s relentless posturing, what he states in his first sentence differs from my college text which indicates that the method doesn’t involve introduction of just a chiral reactant or catalyst, but rather introduction of a CHIRALLY PURE reactant or catalyst.
quote:
The most common method of resolving a racemic mixture into its enantiomers is to use an enatiomerically pure natural product that bonds with the compound to be resolved. When the enatiomers of the racemic compound bond to the pure resolving agent, a pair of diastereomers is formed. (bold added, Organic Chemistry: Fourth Edition, L. G. Wade, Jr., Prentice Hall, 1999, p213)
The author goes on to illustrate the generalization with an actual example, and along the way, states:
quote:
We need a resolving agent that reacts with an alcohol and that is readily available in an enantiomerically pure state. (bold added, Organic Chemistry: Fourth Edition, L. G. Wade, Jr., Prentice Hall, 1999, p213 - 214)
Thus, according to the organic chemistry text, the method relies upon preexisting homochirality (of some other substance) to separate the molecules of interest into their enantiomers.
Also, Rei's second sentence from above "Chiral reactants only react with one chiral form; the result is a diastereomer (look up the term yourself)" does not agree with my organic chemistry text. In it, the resolving agent reacts with both enantiomers of the racemate.
I should point out, though, that my organic chemistry text devotes only a few pages to resolving racemic mixtures and so could easily not be comprehensive.
Anyway, based on what that college text states, I'll just outline the general procedure and follow up with a question about the prebiotic plausibility.
1) Obtain an appropriate and chirally pure resolving agent (which itself needs to be resolved somehow)
2) Add chirally pure resolving agent to racemic mixture to be resolved
3) Physically separate the two resulting diastereoisomers (using recrystallization, chromatography, etc.)
4) Store and maintain the two disatereoisomeric mixtures separate from each other
5) Chemically cleave the resolving agent from the desired diastereoisomer to yield the desired enantiomer
Sure that can all be done in the lab with direction and forethought, but is it plausible for those steps to occur by undirected, non-biological processes alone in order to resolve mixtures of ribose and amino acids? Call me a skeptic, but I’d said NOPE. And apparently OOL researchers agree with me. Otherwise, they would have a solution in hand and wouldn't still consider the origin of homochirality to be an unresolved ([This message has been edited by DNAunion, 11-09-2003]

This message is a reply to:
 Message 23 by Rei, posted 11-07-2003 7:27 PM Rei has not replied

Replies to this message:
 Message 27 by DNAunion, posted 11-14-2003 10:51 PM DNAunion has not replied

  
DNAunion
Inactive Member


Message 27 of 50 (66573)
11-14-2003 10:51 PM
Reply to: Message 26 by DNAunion
11-08-2003 3:59 PM


Re: Peptide self-assembly is one thing...
Found more than my college organic chemistry text that states resolving agents are enantiomerically pure.
quote:
7-3 CHEMICAL SEPARATION OF ENANTIOMERS VIA DIASTEREOMERS
a. Formation and Separation of Diastereomers. Resolving Agents
The largest number of recorded resolutions has been effected by conversion of a racemate to a mixture of diastereomers. In this type of reaction, the substrate to be resolved is treated with one enantiomer of a chiral substance (the resolvng agent)." (bold added, Ernest L. Eliel & Samuel H. Wilson, Stereochemistry of Organic Compounds, John Wiley & Sons, 1994, p322)
quote:
"The desirable characteristics of a good resolving agent are (Wilen, 1971):
(a) Ready availability
...
(g) Availability in high enantiomeric purity
..." (Ernest L. Eliel & Samuel H. Wilson, Stereochemistry of Organic Compounds, John Wiley & Sons, 1994, p323)
***************************
As a side note, the book being quoted from is devoted to stereochemistry of organic compounds and a whole chapter (pages 297 - 464) is dedicated to resolving racemates and the spontaneous, reverse process: racemization. Yet with all of the techniques the author knows of and discusses for resolving racemic mixtures, we see him stating the following:
quote:
"While nonracemic and enantiomerically pure compounds found in Nature are understood to arise mainly from chemical reactions catalyzed by enantioselective catalysts (i.e., enzymes), the original source of the latter and of their components, enantiomerically pure amino acids, eludes us. This mystery is a fascinating aspect of science that lends itself to much speculation ..." (Ernest L. Eliel & Samuel H. Wilson, Stereochemistry of Organic Compounds, John Wiley & Sons, 1994, p209)
[This message has been edited by DNAunion, 11-14-2003]

This message is a reply to:
 Message 26 by DNAunion, posted 11-08-2003 3:59 PM DNAunion has not replied

Replies to this message:
 Message 28 by Rei, posted 11-15-2003 5:56 PM DNAunion has replied

  
DNAunion
Inactive Member


Message 29 of 50 (66747)
11-15-2003 9:26 PM
Reply to: Message 28 by Rei
11-15-2003 5:56 PM


Re: Peptide self-assembly is one thing...
quote:
They argue that the two enantiomeric forms DO readily react and that when they do, they poison the ability of the chain to grow any longer.
Try some simple logic again...if the two enantiomeric forms didn't react readily, then what's this enantiomeric cross inhibition problem all of those OOL authors are referring to? Why worry about it? The left handed molecules would react with other left handed molecules, and the right handed molecules would react with other right handed molecules: there would be no problem.
quote:
It depends on what you're building. Clearly some chemicals have absolutely no problem with cross inhibition (such as quartz), It is an example of one of many cases where cross inhibition is limited due to the reduced "reactivity" of one "reactant" with another.
Varying levels of inhibition are widely recognized in organic chemistry
Why on earth would you expect all cross-inhibition rates to be the same? Please answer these questions before you continue.
...
1) Why would you expect all cross-inhibition rates to be the same?
I did not respond to your question originally because I figured I had already pointed out people stuffing words into my mouth too many times, so I just let this instance slide. But now you’ve countered me in a manner that at least somewhat implicitly stuffs the same claim into my mouth again.
quote:
Secondly, I've already shown that not every reaction is heavily cross-inhibited, and gave an example of one reaction (which took just a matter of minutes to find) which shows *no* cross inhibition.
You’ve apparently convinced yourself that the position you’ve stuffed into my mouth ("all reactions show the same rate of cross-inhibition")actually came from me instead of you.
So now I will respond. Please support your assertion by showing us where I stated that cross-inhibition rates are the same for all reactions/substances!
PS: Here's a hint: you can't.
[This message has been edited by DNAunion, 11-16-2003]

This message is a reply to:
 Message 28 by Rei, posted 11-15-2003 5:56 PM Rei has not replied

  
DNAunion
Inactive Member


Message 30 of 50 (66749)
11-15-2003 9:45 PM
Reply to: Message 23 by Rei
11-07-2003 7:27 PM


Re: Peptide self-assembly is one thing...
quote:
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).".
Which, despite all of the intellectual sounding statements, basically means nothing in regards to our discussion.
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:
quote:
Both homochiral and heterochiral products were produced at the same rate, indicating that the ligation chemistry [itself — in the absence of templates] was not inherently diasteroselective.
In the experiments discussed in the paper, homochirality does not get established in the absence of preexisting homochirality: all four possible outcomes were present in equal amounts.
2) The two "halves" were synthesized in the lab, not in nature. Directed processes can achieve things that undirected processes alone cannot be expected to (think about the computer you are typing on). Thus, the fact that some copies of the "halves" contained both enantiomers does not demonstrate that those non-enantiomerically pure peptides could have arisen by undirected, non-biological processes alone.
[This message has been edited by DNAunion, 11-16-2003]

This message is a reply to:
 Message 23 by Rei, posted 11-07-2003 7:27 PM Rei has not replied

  
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