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Author Topic:   Excellent paper-peptide self assembly
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 4 of 50 (56381)
09-18-2003 8:32 PM
Reply to: Message 3 by Percy
08-23-2003 11:36 AM


Re: Peptide self-assembly is one thing...
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? Otherwise, how would one decide, given a previously never-witnessed molecule, that it was left or right handed?
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 3 by Percy, posted 08-23-2003 11:36 AM Percy has not replied

Replies to this message:
 Message 5 by DNAunion, posted 11-01-2003 12:04 AM Rei has not replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 7 of 50 (63766)
11-01-2003 12:57 AM
Reply to: Message 6 by DNAunion
11-01-2003 12:11 AM


Re: Peptide self-assembly is one thing...
And what evidence do you have that amino acids of different chiralities join readily?
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 6 by DNAunion, posted 11-01-2003 12:11 AM DNAunion has replied

Replies to this message:
 Message 8 by DNAunion, posted 11-01-2003 2:21 AM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 9 of 50 (63809)
11-01-2003 1:04 PM
Reply to: Message 8 by DNAunion
11-01-2003 2:21 AM


Re: Peptide self-assembly is one thing...
1) This doesn't cover how readily opposite chiralities bond - it just briefly mentions that it's possible. Of course it's possible - the issue here is how readily they will. You can even cause xenon to bond in the right conditions Did you not read my post? I stated "readily".
2) The body of the summary undercuts your position - 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)
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 8 by DNAunion, posted 11-01-2003 2:21 AM DNAunion has replied

Replies to this message:
 Message 10 by DNAunion, posted 11-01-2003 1:21 PM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 11 of 50 (63816)
11-01-2003 1:56 PM
Reply to: Message 10 by DNAunion
11-01-2003 1:21 PM


Re: Peptide self-assembly is one thing...
quote:
*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).
My apologies, I misread your article summary as saying something to the opposite. However, you still have not answered part 1 - i.e., my initial question. Note that it is a question, not a statement, but I have yet to see a valid response to it. One would think that there is a difference in bonding affinities between different chiralities, because a common methods of separating racemic mixtures include seeding with a crystal of one enantiomer and chemical reaction with a chiral reactant. It would seem that once a hypercycle began with one chirality, that chirality would be locked in.
quote:
The problem facing OOL researchers is trying to get a chirally pure solution by undirected, non-biological processes.
Are you unfamiliar with the Murray and Murchison meteorites? Of course, that is just one possibility. I hope you're not playing a game of "God of the Gaps" here.
quote:
/*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 chrirally pure product.
Would you, perchance, happen to have the ratios of chiralities in the aforementioned meteorites on hand? I'm having trouble tracking it down.
This topic always reminds me of a quote by Albert Einstein, when asked about why there are more electrons than positrons in the universe:
"The electron got there first."
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 10 by DNAunion, posted 11-01-2003 1:21 PM DNAunion has replied

Replies to this message:
 Message 13 by DNAunion, posted 11-02-2003 3:30 PM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 14 of 50 (63999)
11-02-2003 4:41 PM
Reply to: Message 13 by DNAunion
11-02-2003 3:30 PM


Re: Peptide self-assembly is one thing...
Thanks for digging up the percentage on the Murchison meteorite. The Murray meteorite also had a non-racemic mixture, although I would imagine that the percentages were also not *too* high of a L/R ratio.
quote:
With these objections in mind, it is not without reason to state that this kind of light does not yet hold the complete answer.
As you'll notice from my post on this subject, however:
quote:
Of course, that is just one possibility.
You didn't address the key points of my posts (and I would be interested in your response).
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.
2) How once a hypercycle starts with a certain set of amino acids, it is effectively "locked in".
------------------
"Illuminant light,
illuminate me."
[This message has been edited by Rei, 11-02-2003]

This message is a reply to:
 Message 13 by DNAunion, posted 11-02-2003 3:30 PM DNAunion has replied

Replies to this message:
 Message 15 by DNAunion, posted 11-02-2003 8:45 PM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 17 of 50 (64178)
11-03-2003 2:03 PM
Reply to: Message 15 by DNAunion
11-02-2003 8:45 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.
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. 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.
Also, all of your posts argued in favor of my initial point: that reactants of different chiralities do not readily react with each other. That is the very claim that I made that started off this discussion here - check the history.
Finally, you're still dodging #2: That once a hypercycle begins with a certain chirality, it is effectively "locked in".
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 15 by DNAunion, posted 11-02-2003 8:45 PM DNAunion has replied

Replies to this message:
 Message 19 by DNAunion, posted 11-04-2003 12:01 AM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 23 of 50 (65028)
11-07-2003 7:27 PM
Reply to: Message 19 by DNAunion
11-04-2003 12:01 AM


Re: Peptide self-assembly is one thing...
quote:
/*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?
/*Pretentious Code Brackets*/ Hmm, I'm not familiar with this line of argument before. What is it, the "Don't you think someone would have thought of it before?" argument? Can you actually add any substantive backing, or are you going to leave it at that?
quote:
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.
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?
Everything keeps boiling down to the exact same point, DNAunion - my very first point: Different enatioisomers don't play well with each other; they much prefer to bond with their own types.
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.
It depends on what you're building. Clearly some chemicals have absolutely no problem with cross inhibition (such as quartz), despite racemic forms existing (quartz's lattice can spiral clockwise or counterclockwise (which effects the polarization of light), but rarely both in the same small area of a given crystal). 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; 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).".
Why on earth would you expect all cross-inhibition rates to be the same? Why would you expect no diastereomers? Please answer these questions before you continue.
quote:
/*DNAunion*/ No need to...you were wrong then, and are still wrong.
/*Pretentious Code Brackets*/ And you have yet to provide any evidence, despite being asked to multiple times. "Asserting" that someone is wrong without providing requested evidence merely makes you look inept at debating.
quote:
/*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...
/*Pretentious Code Brackets*/ So, then, my point stands in its original form, so I'll reiterate in boldface: Once a hypercycle begins with a particular chirality, that chirality is "locked in"..
quote:
/*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.
Still having fun with your cite? Unless by "external" they mean any sort of chiral reactant or catalyst (i.e., rather easy to come by), or unless by "if chiral reactants or catalysts are involved," they're not meaning homochiral (as would seem to be implied by the next line), then it's incorrect (I already cited an example with *zero* cross inhibition - I got tons of hits when searching, want more examples?). Or are you going to continue to harp on the fact that I misread it the first time you posted it (something that I acknowledged)?
Again, I refer you back to the two things you need to answer in your next post:
1) Why would you expect all cross-inhibition rates to be the same?
2) Why would you expect no diastereomer production (altering the isomer ratios)?
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 19 by DNAunion, posted 11-04-2003 12:01 AM DNAunion has replied

Replies to this message:
 Message 26 by DNAunion, posted 11-08-2003 3:59 PM Rei has not replied
 Message 30 by DNAunion, posted 11-15-2003 9:45 PM Rei has not replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 28 of 50 (66714)
11-15-2003 5:56 PM
Reply to: Message 27 by DNAunion
11-14-2003 10:51 PM


Re: Peptide self-assembly is one thing...
My apologies; I was rather busy for a while, and forgot about this thread. First off, I stated that a *chiral* catalyst is used to separate them - but that means that a very small amount of imbalance in the catalyst will have dramatic effects in the overall isomer makeup of the solution.
If a small imbalance in an initial catalyst leads to a larger imbalance in the solution as a whole, can you see how that would easily amplify itself further? Any new catalysts that develop in the system are going to have this greater imbalance, and will in turn amplify the imbalance. In the end, you can expect very few stereoisomers of the same chemicals. The only reason that it is a problem in laboratory synthesis is that we have relatively few (compared to nature) types of different catalytic reactions going on to amplify differences.
It's like doing laboratory synthesis of a chemical, using varying purity of reagents. If all of your reagents are 100% pure, your end product would be 100% pure (assuming that there's only one pathway the reactions can take, there's no rate of reaction problems, you can actually achieve 100% purity, etc). What if your reagents were 99% pure - will your end product be 99% pure? No - the impurities will help introduce alternative paths that the reaction can take; your end product will likely be notably less than 99% pure. What if you used 90% pure reactants? Depending on what you're synthesizing, you may not get much of it at all as an end product. It's part of nature: imbalances tend to amplify themselves in iterative environments (that's why we'll never be able to predict the weather very long range... well, that and quantum theory).
Why would you expect differences in ratios not to amplify themselves in a prebiotic earth? Please explain.
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. Why? Because of my initial point: That, depending on the situation, different stereoisomers may tend to bond preferentially with their own types. And, you have so far done not a thing to address that how, once a hypercycle begins with a given chirality, that chirality is "locked in".
I would like to add that you've been focusing on attacking my knowledge of the subject just because I was unaware of how they determine which molecule receives which name - in response to a post where you showed *your* lack of knowledge on other related subjects - and are avoiding my core points (listed above). I'm not trying to claim to be an expert on the subject. But I would like my points of contention addressed as much as any other poster.
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)
In a single reaction? Of course you're not going to get much of a ratio (although, there are some possibilities**). After 10,000 iterative reactions? You'd be lucky to have even a slightly racemic mixture.
Also, here's another interesting theory (genetic takeover). I wouldn't put any money on it yet, but it's an interesting concept.
** - In reference to the Coriolis Force method, there is already some good evidence to back this up; pollutant conentrations in polar bears, for example are sometimes heavily chiral, despite the original pollutants being a racemic mixture. How would you account for this? Clearly, there is *some* sort of natural enatioisomer-selective process going on, and it varies from location to location.
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 27 by DNAunion, posted 11-14-2003 10:51 PM DNAunion has replied

Replies to this message:
 Message 29 by DNAunion, posted 11-15-2003 9:26 PM Rei has not replied
 Message 31 by DNAunion, posted 11-15-2003 10:31 PM Rei has not replied
 Message 32 by DNAunion, posted 11-16-2003 12:03 AM Rei has replied

  
Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 33 of 50 (66775)
11-16-2003 1:57 AM
Reply to: Message 32 by DNAunion
11-16-2003 12:03 AM


Re: Peptide self-assembly is one thing...
quote:
1) It does not mean that it WILL HAVE dramatic effects. Maybe the effects would be dramatic, maybe the effects would be slight, maybe the effects would be negligible.
Fair enough.
quote:
2) Exactly what chiral catalyst are you proposing for generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery catalyst?
DNAunion, prophet of the God of the Gaps.
quote:
3) How did your as-of-yet unidentified chiral catalyst come to be present preferentially in one chiral form?
4) How did your as-of-yet unidentified chiral catalyst maintain its chiral preference over an extended period of time? Was there some other chiral catalyst making it?
Are you familiar with a Wimshurst Machine? It's a neat electrostatic generator that uses induction to generate power. That is, an imbalance in the charges of the plate is amplified by the process. A curious thing about it is which terminal ends up positively charged and which one ends up negatively charged: it's random. What happens is, it is essentially impossible to have the two disks have precisely the same charge on them. However minutely different the charge is, it gets amplified with each pass.
That is exactly what I am suggesting in this case. A slight imbalance of one catalyst, over long-term iterative processes, leads to a major imbalance of end products.
Play "God of the Gaps" all you want, but don't fail to address the meat of the issue.
quote:
quote:
If a small imbalance in an initial catalyst leads to a larger imbalance in the solution as a whole, can you see how that would easily amplify itself further?
Can you see how, since racemization is a spontaneous process which leads away from enantiomerically pure mixtures and towards racemic ones a slight excess of one enantiomer could be lost?
Only if you have a completely pure solution - i.e., free from chiral catalytic influences. When the catalysts are chiral, an imbalance in the ratios betwen catalysts will lead to an imbalance in the end products. When your next line of catalysts are the ones produced from the previous go-round, you get a further imbalance. And a further imbalance, and further, etc.
quote:
Can you see how enantiomeric cross inhibition could result in the locking up of some of the slight enatiomeric excess in molecules whose growth was still poisoned by inclusion of both enantiomers?
As I pointed out and referenced earlier, only certain types of chemical synthesis suffer from cross-inhibition.
quote:
Any new catalysts that develop in the system are going to have this greater imbalance, and will in turn amplify the imbalance.
Arent you forgetting about enantiomeric cross-inhibition?[/quote]
Aren't you forgetting my reference? Furthermore, I should add, cross-inhibition is only a problem when you're trying to build a *specific* chemical, through a *specific* pathway, under which the pathway works in a chirally pure solution but has inhibition in a chirally imbalanced solution. Here, we're talking about a near incomprehensive number of different chemicals in the same solution. This sort of pathway inhibition is virtually irrelevant.
Let me put it another way. You you're specifically trying to spell the word "AUSTRALOPITHECUS". However, so long as the K key exists, whenever you try to type O-P-I, the K attaches intstead of an I, inhibiting the process. Ok, but what if you first created AUSTRALOP, and ITHECUS, and then joined them? What if you created AUST, RALO, PITH, and ECUS, and joined them? What if HOMOHABILUS functioned the same or nearly the same as AUSTRALOPITHECUS? Etc. Your strict laboratory synthesis analogy is about as unlike a prebiotic earth as you can get, where you have countless different types of reactions going on at once. The more different routes something can take, the less relevant a certain route being inhibited is; in fact, for every route that you have inhibited, odds are you're creating a new possible route.
And, as I mentioned before, even in a laboratory synthesis environment, cross inhibition is not always an issue.
quote:
Or does your mystery catalyst
Look, do you see me making fun of you? I could likewise start sentences with, "Does your invisible friend in the sky ... ".
quote:
not only preferentially make one chiral form of monomers
That's a given, now isn't it, in most cases with a chiral catalyst?
quote:
but also, as if by magic,
You're one to speak.
quote:
also serve as a polymerase, and one that ensures that only one chiral form gets incorporated into growing polymer chains?
I'm not discussing a specific catalyst, just catalysts. DNA, don't be a pain: you know very well that if we knew the exact route that abiogenesis took (even if it were your "poof, here's life!" method), there would be nothing to discuss. We're here to discuss theories as to what could lead to enantioselective properties, not trade insults over the gaps in our knowledge.
quote:
With a low production rate of polymers
Where do you get a low production rate of polymers from?
quote:
(and a non-zero background rate of hydrolysis)
There have been a number of theories on the rates of hydrolysis versus polymerization, with varying "wet" and "dry" theories. One such theory involves an in-between, with early polymer forming in the gaps between clay particles.
quote:
quote:
In the end, you can expect very few stereoisomers of the same chemicals.
If everything you presented was unavoidable and non-problematic, sure. But mostly what youve done is paint an oversimplified, rosy picture; its devoid of nasty details (like spontaneous racemization,
Why do you expect spontaneous racemization when you're using chiral reactants?
quote:
poisoning of polymer formation by enantiomeric cross inhibition,
A non-issue - see above. You can poison specific polymers in a laboratory style environment, but you have yet to evidence that it poisons polymer formation in general.
quote:
and the locking up of some of the enantiomeric excess in growth-stunted molecules)
How do you conclude that this would occur?
quote:
it relies upon unidentified, mysterious catalysts; and it has not been demonstrated experimentally.
Once again, introducing the "God of the Gaps!"
I can just picture creationists in the 1800s now... "You say that the earth is billions of years old... and yet, we know of no way that the sun could be more than a few millions of years old - the best that you can come up with for its energy is "gravitational collapse". What, is there some "mystery, magical energy source" powering it that we don't know of? That has not been demonstrated experimentally.".
The God of the Gaps is continually being forced to move into a new gap. Are you sure you want him in this one?
That is why we discuss possibilities, not absolutes, when we're discussing gaps in scientific knowledge. Shoving a God wherever you see a gap is not a good plan for advancing human knowlege.
quote:
quote:
Why would you expect differences in ratios not to amplify themselves in a prebiotic earth? Please explain.
In a non-biological and undirected setting? Because having an enantiomeric excess of amino acids and/or nucleotides (the sugar moieties) is not the equilibrium state, and therefore, undirected processes will tend to bring any discrepancies back in line back towards equilibrium.
One could apply that exact same argument toward the weather. Having turbulence in the atmosphere is not an equilibrium state, and so the world should balance itself out toward a simple constant atmospheric Coriolis flow. Does it?
Part of the nature of iterative processes is that errors magnify themselves tremendously. Take a class on chaos theory some time, then get back to me.
quote:
After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.
Explain?
quote:
Sure, if one ASSUMES into existence some somehow-enantiomerically enriched catalyst that can be maintained,
It's a given. No mixture is ever exactly even.
quote:
somehow, in its enantiomerically enriched state over some extended period, and that can generate enantiomeric excesses in amino acids and/or ribose
Or whatever early life was based on, which may have nothing to do with life as we know it today.
quote:
and one also assumes into existence some other unidentified polymerase catalyst that preferentially selects the enantiomer that is present in slightly greater quantity
Why are you requiring two catalysts, again? And why must one of them be a polymerase (assuming that you mean according to current usage of the term, DNA and RNA polymerases, although you could be meaning it in a general sense)?
quote:
(and also assumes anything else Ive forgotten here), then sure, one can imagine an increase towards homochirality could occur. But even given all of that, homochirality is not assured.
Actually, given that, it is assured. Given that differences amplify themselves over time, as they are observed to do in many systems, then it is assured. The question is whether they amplify themselves in this particular system. Next week I'll look to see if I can find any studies on the subject; you do your research as well. Of course, remember, we're not talking about a laboratory synthesis environment with a single iteration. We're talking about an environment in which the products of the first reaction are involved in the second, and those products in the third, etc, for billions upon billions of iterations.
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 32 by DNAunion, posted 11-16-2003 12:03 AM DNAunion has replied

Replies to this message:
 Message 35 by DNAunion, posted 11-16-2003 10:28 PM Rei has not replied
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Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 36 of 50 (67080)
11-17-2003 1:28 PM


DNAunion:
You're back to your old habits of A) splitting up individual posts into multiple, making it very hard to reply to, and B) focusing on personal attacks. If you keep this up, I will cease to respond in this thread. You have been warned; don't expect another warning.
quote:
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.
It's implicit in your line of argument. Because, by your line of argument, if not every reaction receives a high degree (or any degree at all, in the case of many reactions) of cross inhibition, then it's not a problem: it only poses problems for *particular pathways* to develop early life. There are countless possible pathways. Your argument, unless all reactions have the same degree of inhibition, is thus near useless.
quote:
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:
Now we're back to the GL? Nice try at a dodge there, but this conversation wasn't on the subject of the GL. Let me ask you a question - since you seem to have this huge problem with the concept of how much of a sample size has been observed:
What percentage of possible proteins have we looked at that are the length of the GL to test to see whether they're ever self replicating? The ghadiri ligase is, what, 32 amino acids long? We're looking at 4.29e41 possible combinations here for a protein of that length.
You have a very serious problem with the concept of the percentage of total sample size observed that you have displayed again and again, and it gets very frustrating. Please quit pretending that we have observed even a tiny, remotely statistically significant percentage of total possibilities. Even in our proportionally tiny percentage of self replicators that we have observed, there are going to be countless different ways such a protein can be formed. Given this, the odds that there will be routes with no cross inhibition seem to be almost a given.
quote:
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)
You seem to accept evolution (just not abiogenesis), right? If that is the case, then look at what an undirected process has accomplished since then (or do you believe in "directed evolution"?) "Synthesized in the lab, not in nature". Ah. Just assuming that there are 10 tons of chemicals and solvents involved in brand new, documented organic chemistry expierments being conducted each year on the subject of abiogenesis (not likely, but let's be nice. ), Earth's oceans alone (0.04% of Earth's mass) have a mass of 1.35 quintillion metric tons (1,350,000,000,000,000,000 metric tons). Even assuming that only 0.1% of the oceans were involved (and that nothing on land was involved), that's still giving a volume of 1,350,000,000,000,000 metric tons of reactants operating for a billion years. That is *Far Better* than in a lab. Of course, you won't accept that, because in your worldview, only directed things achieve amazing results, right?
quote:
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.
Why? It has preposterously more possible chances in nature to occur. Unless you feel there is some sort of laboratory situation that cannot occur in nature - and if so, please name it.
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You gave three links, one of which you yourself seemed hesistant about. So I looked at the other two.
That one was about hijacking earlier, much simpler forms of life. The sample concept presented was in selective growth of clays, in which different types of crystals compete with each other for further mineral deposits. Deposits of organic material on the surface of the crystals could aid in such selection, and these deposits would likely be chiral (corresponding to the type of crystal substrate they're growing on). Eventually, with a much greater range of possible chemistry, the organic component took over.
Again, though, I think such a concept is still too speculative, and I'd like to see more research done on whether it is possible for different clays to have competitive selection.
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One, about polar bears (http://www.springerlink.com/app/home/main.asp?wasp=6a86b7...), led to a site where one must pay to access the articles. I am not going to pay to look for your evidence: thats your responsibility.
It must have changed since I looked at it then, because I was able to access the full text the other day for free. I'll summarize: the distribution of a number of organic pesticides has been found to be chirally imbalanced in the world's oceans, leading to a chiral imbalance in wildlife.
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The second link, about "various possibilities" (http://www.endeav.org/evolut/chiral/chiralit.htm) had an interesting abstract about the the Coriolis force, but the actual article didnt seem to say what you think it might have. Heres a quote, with emphasis added.
Let's assume that selection of the left or the right can go on the level of formation of cells and biotissue of plants or Protozos, as well as of inorganic structures due to selection between the left and the right forms of large supermolecular structures or formations.
And here's a quite with my emphasis added
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Let's assume that selection of the left or the right can go on the level of formation of cells and biotissue of plants or Protozos, as well as of inorganic structures due to selection between the left and the right forms of large supermolecular structures or formations.
You continually ignore the frequent use of the word "and" in the text, taking only from one side. The model seems to postulate both on the level of lifeforms *and* on biochemistry itself.
Let me add again that a chiral imbalance is not needed, as I have discussed in the first part of this post. But if it was, here's yet another way it could have occurred - a film at the surface of the water, which deals with the water/air border (how many possible methods do you need?)
Of course, knowing your love of quotes, you'd probably just ignore the article and extract an out of context quote, such as "Theories on the emergence of the homochiral biopolymers of life at prebiotic times suggest the involvement of enantioselective reactions starting from heterochiral mixtures of alpha-amino acid and nucleic acid precursors (1-7). Polymerization reactions of racemates in isotropic media would lead, however, to formation of polymers comprising a random sequence of left (S)- and right (R)-handed repeat units in a binomial distribution (8). Thus, the probability of obtaining oligomers with homochiral sequence will become negligible with increasing length (9-11)." to try and convince people who don't know better.
Almost any assembly that occurs on a two dimensional inorganic surface would be expected to be subject to the chiral influences of that surface. And, as I stated before, that is not even necessary, since any chiral imbalance or influence would be expected to imbalance the system as a whole, especially any that gets closer to self replication
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First of all, I think Rei is being disingenuous. .... apparently Rei has been trying to slip her own ideas into the discussions without actually saying so, with her hidden agenda causing confusion. .... Is she deaf, dumb, and blind? ...
Thank you for being so mature Do most people you debate with end up getting sick of you in the process and leaving? If so, you shouldn't be surprised.
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What I have been discussing in this thread has clearly been nucleotides, amino acids, and their polymers the main molecules involved in OOL discussions.
There is absolutely no necessity that the first forms of life had to have been based on what life currently is based on. That is why we need to discuss enantioisomers in general.
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For example, Ive pointed out and fully supported enantiomeric cross inhibition numerous times in relation to nucleotides and amino acids:
In limited cases; it takes about 5 minutes of searching to dig up a process in which there is *no* or *minimal* cross inhibition. And, as I've mentioned several times, that's only relevant for a particular route of creating a particular molecule - neither of which we are discussing when talking about abiogenesis. There are near countless possibilities under each category (routes and molecules) that can work just fine.
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Do you mean a solution with an enantiomeric excess?
Yes.
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Does your term chirally pure mean that it is a pure solution containing just the two chiral forms?
No. "chirally pure" - Google Search
If you'd rather I use the term enantiomerically pure, that's fine, so long as we're on the same page.
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No, and I dont need to be, since a Wimshurst Machine isnt a nucleotide or an amino acid or polymers made of these monomers.
Do you realize how bullheaded you look when you deliberately ignore what a person is saying? Did you even read the analogy?
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2) Exactly what chiral catalyst are you proposing for generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery catalyst?
3) How did your as-of-yet unidentified chiral catalyst come to be present preferentially in one chiral form?
4) How did your as-of-yet unidentified chiral catalyst maintain its chiral preference over an extended period of time? Was there some other chiral catalyst making it?
2) Exactly what method are you proposing for your deity generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery god-magic?
3) How did your as-of-yet unidentified god-magic come to create preferentially one chiral form?
4) How did your as-of-yet unidentified god-magic maintain the chiral preference over an extended period of time? Was there some other chiral catalyst making it?
That said (turning it back on yourself), and with me pointing out yet again that we have looked at such a tiny percentage of the sample size that it's about as deceptive as you can get to ask for an exact route, I will repeat what you quite obviously did not read in your skipping over my analogy (and my entire discussion about how synthesis of a product with varying purity of reactants generally has the production rate of the end product fall off faster than the purity of the reactants - why should I even bother when you don't read what I write?): There always is an imbalance, even if incredibly small. In most real-world applications, imbalances tend to magnify themselves when subjected to iterative processes instead of converging.
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Yeah, and those being discussed being among them!!! So dont pretend that what you said earlier, or now, has countered my last point it still stands.
And don't pretend that what *I* said - that the odds of it being a particular self replicator that we discover, and having been made through the exact process that we make it - are so small as to make them essentially zero. The number of possibilities out there makes it incredibly likely that the first self replicator is *not* something that we have ever observed, and that even if it was, it would *not* be produced through the route that we produced it.
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Youve provided no reference that shows that enantiomeric cross inhibition would not be a problem for nucleotides and/or amino acids, whereas I supplied what, a dozen, that showed it would be.
Yes, I know, you have far more time for this than I do. Is that something to really be proud of? Again, why are you insistant that DNA and/or RNA had to be first? I would expect the first life to be a simple ligase that makes broken copies of itself (anything that is "close" to itself increases the odds of random interactions producing another copy of itself). This would be replaced by a ligase that makes correct copies of itself with correct source material, and broken copies of itself with incorrect source materials. This would be replaced by a ligase that either itself can handle a wider range of source materials, or can also create another ligase that creates correct and/or broken copies of the source materials; etc. This progresses until you have a fairly stable hypercycle. DNA or RNA would be a later introduction to the system. "RNA world" is a fairly old concept (1967, I believe); it had some reinvigoration in the early 1980s with the discovery of catalytic RNA molecules, but is anything but universally accepted.
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... With a low production rate of polymers ..
Where do you get a low production rate of polymers from?
ENANTIOMERIC CROSS-INHIBITION
... which effects *some* pathways for *some* molecules, but not *other* pathways, and not on *other* molecules, out of tredecillions of possibilities molecules with, perhaps, quindecillions of possible assembly methods, for something merely as long as GL.
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Why do you expect chiral reactants in the first place?
1) Inorganic substrates (incuding the water/air boundary - any 2d substrate will do).
2) *Any* level of imbalance should get magnified.
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And why do you expect a small presence of a chiral catalyst to stop a spontaneous process like racemization from occurring?
Not stop. Produce a mixture with an enantiomeric excess.
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Go back and read the quotes I posted and/or research it yourselfI think youre confused.
You just claimed that you're not trying to state that all synthesis has enantiomeric cross inhibition. Are you saying that, now?
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Under racemic conditions (D/L = 1.0), the average chain starts to elongate but by the third monomer it has both enantiomers in it and so stops growing. Being so short, it wont likely have any complex, useful function. Thus, the nucleotides in that chain are basically locked up in a useless molecule.
Wrong. In a laboratory environment, that may happen when you're dealing with a very limited set of very pure reactants, but in the real world, those chemicals are not going to stay short for long. There are too many things that could possibly react with them to either tear them apart or attach new things to them. You're dealing with your directed, single pathway logic again. That's not at all what is proposed with abiogenesis.
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Too bad for you that were not talking about weather.
What we are talking about is amino acids and nucleotides, and there is a thermodynamically spontaneous process, called racemization, that leads towards the equilibrium state of a racemic mixture.
Racemization in peptide assembly when a ligase or the subunits has an enantioisomeric excess? How? Again, there will always be minute excesses, so you have to show that the ratios *converge* instead of *diverging* when there's an excess, in an iterative process (i.e., when the results of one process become the reactants in the next).
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It has been argued (Bada and Miller 1987) that racemization of amino acids is too rapid to permit amplification (by as yet unspecified reactions) to give rise to homochirality. Carbohydrates are more resistant to racemization than are amino acids. However, they are also chemically less stable, a factor that could equally defeat an amplification cycle. (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p247)
Ah, finally an applicable quote. And my response? It's already been shown to occur. Sorry, there!
Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule
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THE homochirality of natural amino acids and sugars remains a puzzle for theories of the chemical origin of life1-18. In 1953 Frank7 proposed a reaction scheme by which a combination of autocatalysis and inhibition in a system of replicating chiral molecules can allow small random fluctuations in an initially racemic mixture to tip the balance to yield almost exclusively one enantiomer. Here we show experimentally that autocatalysis in a chemical reaction can indeed enhance a small initial enantiomeric excess of a chiral molecule. When a 5-pyrimidyl alkanol with a small (2%) enantiomeric excess is treated with diisopropylzinc and pyrimidine-5-car-boxaldehyde, it undergoes an autocatalytic reaction to generate more of the alkanol. Because the reaction involves a chiral catalyst generated from the initial alkanol, and because the catalytic step is enantioselective, the enantiomeric excess of the product is enhanced. This process provides a mechanism by which a small initial imbalance in chirality can become overwhelming.
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Take a class on chaos theory some time, then get back to me.
Take a class on biochemistry some time, then get back to me.
So typical. You respond to a point with offhand dismissal. Here I am, trying to answer each and every one of your points, and you ignore me with a wave of your hand on 2/3 of the things that I write. By the way, I have taken classes on both. (Preparing for another insult from you...)
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The driving force behind racemization - towards equilibrium/racemic mixtures - is entropic (enthalpy remains constant). Going in the opposite direction towards homochirality has a positive delta G associated with it (because of the decrease in entropy) and thus is not spontaneous.
How is there a decrease in entropy? And need I mention that the trend of increasing entropy only is law inside closed systems?
P.S. - Seing as you're so fond of quotes, allow me to turn your favorite old argument back on yourself. If all of these scientists are so sure that there's some sort of problem with abiogenesis, why do they believe in it?
------------------
"Illuminant light,
illuminate me."

Replies to this message:
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Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 47 of 50 (67384)
11-18-2003 1:16 PM
Reply to: Message 46 by crashfrog
11-18-2003 8:46 AM


I've warned him about this - and now I'm going to live up to my word and not respond. I've never found a person with a more annoying "debate" style here - and that says a lot, seing as how we have teenage YECs at this site.
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 46 by crashfrog, posted 11-18-2003 8:46 AM crashfrog has not replied

  
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