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


Message 16 of 50 (64167)
11-03-2003 12:46 PM


I think what is missing here is the size of the pre-biotic "test tube" or reaction chamber, as such. 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. Second, no one knows the precise sequence or length of the first peptide/protein or the first RNA/DNA sequence. So before anyone can call something impossible, I think they should take these into account.
Replies to this message:
 Message 18 by DNAunion, posted 11-03-2003 11:49 PM Loudmouth has responded

  
Rei
Member (Idle past 5090 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 responded

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

    
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 responded

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

  
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 responded

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

  
Loudmouth
Inactive Member


Message 20 of 50 (64435)
11-04-2003 6:54 PM
Reply to: Message 18 by DNAunion
11-03-2003 11:49 PM


/*DNAunion*/ The paper I was addressing gave us this. But, the value it gave was overstated (as I already pointed out).

Sorry, I must have missed something. Did the paper limit the OoL to specific conditions or rule out others? What I am trying to get at is that Earth is a pretty big place, we're not talking about someone's backyard pool here.

*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.

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*/ 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.

RNA as the catalyst for life is still a theory, although it has good backing it seems. The question is could a RNA 20mer plus a peptide 20mer be involved? How specific does the sequence have to be? The fact that pseudo self-replicating RNA has been observed at 180mers does not rule out anything.


This message is a reply to:
 Message 18 by DNAunion, posted 11-03-2003 11:49 PM DNAunion has responded

Replies to this message:
 Message 21 by DNAunion, posted 11-05-2003 9:16 PM Loudmouth has responded

  
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 responded

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

  
Loudmouth
Inactive Member


Message 22 of 50 (65020)
11-07-2003 6:41 PM
Reply to: Message 21 by DNAunion
11-05-2003 9:16 PM


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.

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.

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?


This message is a reply to:
 Message 21 by DNAunion, posted 11-05-2003 9:16 PM DNAunion has responded

Replies to this message:
 Message 24 by DNAunion, posted 11-08-2003 1:55 AM Loudmouth has not yet responded
 Message 25 by DNAunion, posted 11-08-2003 12:29 PM Loudmouth has not yet responded

  
Rei
Member (Idle past 5090 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 responded

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

    
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 yet responded

  
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 yet responded

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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. (www.evcforum.net/cgi-bin/dm.cgi?action=page&f=13&t=25&p=18 -->www.evcforum.net/cgi-bin/dm.cgi?action=page&f=13&t=25&p=18">http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=13&t=25&p=18 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 is…is 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 (<-pun wasn't originally intended!) problem that needs addressing.

[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 yet responded

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

  
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 yet responded

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

  
Rei
Member (Idle past 5090 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 responded

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

    
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 yet responded

  
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 yet responded

  
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