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Author Topic:   Abiogenesis - Or Better Living Through Chemistry
DNAunion
Inactive Member


Message 49 of 85 (63761)
10-31-2003 11:58 PM
Reply to: Message 48 by Rei
09-24-2003 2:16 PM


quote:
Going back to our primitive ocean of 1 x 10^24 litres and assuming a nucleotide concentration of 1 x 10^-7 M [23], then there are roughly 1 x 10^49 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 10^34) could be produced in a year, let alone a million years. (from Talk Origins article)

/*DNAunion*/ But (besides other potential problems) we are no longer dealing with the complete volume of an ocean: as Rei points out.

quote:
Rei: BTW, most scientists don't believe that life developed in the exposed atmosphere; the current most likely accepted location is undersea thermal vents.

/*DNAunion*/ Under that “current most likely” scenario the Talk Origins' calculation becomes invalid.


This message is a reply to:
 Message 48 by Rei, posted 09-24-2003 2:16 PM Rei has not yet responded

  
DNAunion
Inactive Member


Message 51 of 85 (64032)
11-02-2003 8:13 PM
Reply to: Message 47 by Omega Red
09-24-2003 6:29 AM


Re: sadistics
quote:
From the article:
"Going back to our primitive ocean of 1 x 10^24 litres and assuming a nucleotide concentration of 1 x 10^-7 M [23], then there are roughly 1 x 10^49 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 10^34) could be produced in a year, let alone a million years." (from Talk Origins article)

/*DNAunion*/ I already pointed out one problem with the calculation...here's a second.

The calculation implicitly relies upon homochirality. If both enantiomeric forms of the bases (actually, the sugar moieties of the bases) were present, enantiomeric cross inhibition would hinder the formation of long polymers needed for replication or other complex function.

[This message has been edited by DNAunion, 11-02-2003]


This message is a reply to:
 Message 47 by Omega Red, posted 09-24-2003 6:29 AM Omega Red has not yet responded

Replies to this message:
 Message 52 by Rrhain, posted 11-03-2003 7:09 AM DNAunion has responded

  
DNAunion
Inactive Member


Message 53 of 85 (64118)
11-03-2003 8:49 AM
Reply to: Message 52 by Rrhain
11-03-2003 7:09 AM


Re: sadistics
quote:
/*DNAunion*/ The calculation implicitly relies upon homochirality.

quote:
Rrhain: But achieving homochirality isn't a problem:

/*DNAunion*/ Wrong. That article does not demonstrate how homochirality can originate...the "self-replicating" molecules themsevles start out chirally pure: they then select the correct enantiomeric forms. In other words, it uses preexisting homochirality to "create" homochirality.

Also, the calculation I was referencing dealt with polynucleotides, not peptides.

By the way, there are other problems with using that paper to support origin of life, as in, "See, this is how life arose". For example, despite the misleading term used by the authors and others, the peptides do not self-replicate.

[This message has been edited by DNAunion, 11-03-2003]


This message is a reply to:
 Message 52 by Rrhain, posted 11-03-2003 7:09 AM Rrhain has responded

Replies to this message:
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DNAunion
Inactive Member


Message 54 of 85 (64156)
11-03-2003 12:19 PM
Reply to: Message 53 by DNAunion
11-03-2003 8:49 AM


Re: sadistics
/*DNAunion*/ My internet playtime will be short for a few days, so I figured I'd go ahead and follow up what I said in my last post. The following is from my personal notes.

Ghadiri Ligase is not a True Self-Replicator

First, I will use an analogy that employs the letters of the English alphabet and a short sentence in order to demonstrate why the Ghadiri ligase is not a true self-replicator.

For this analogy, I will equate the 23-character “sentence” METHINKSITISLIKEAWEASEL with the 32-amino-acid Ghadiri ligase. Each of the letters represents an amino acid residue along the length of the GL (my abbreviation for the Ghadiri ligase) where each of the individual “letters” is covalently bonded to its nearest neighbor(s) on the same strand (analogous to the same physical sentence, when there are two). The covalent bonds between the units will be represented with dashes (-) between the “letters” (M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L).

A true self-replicator can extract its individual building blocks (monomers/letters) one at a time from its surroundings (a pool of monomers/letters) and construct a functional copy of itself using itself as a template for the sequencing of the units, followed by release of the copy. In order to allow them to separate from each other but to not decompose, the template and the copy should not be covalently bonded together but both the template and the copy should be covalently bonded internally. Note that the letters can’t simply line up according to the template’s sequence and be done with it; they also have to be covalently linked to their nearest neighbors in the growing copy after being non-covalently attached to the template. Forming this bond between units within the same strand requires either a catalyst or the pre-activation of each of the building blocks. And since we are looking for a true self-replicator, the sequence itself should be performing the function, whether it is catalyzing the bond directly or pre-activating incoming monomers. The process we will look at (the less involved of the two) involves two basic steps for each monomer added: first, the correct monomer is “chosen” from the stocked pool of monomers and lines up along the template, then the template sequence covalently bonds the new monomer to the elongating string.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M (correct monomer lines up non-covalently with template)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M E (correct monomer lines up non-covalently with template)
M-E (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E T (correct monomer lines up non-covalently with template)
M-E-T (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T H (correct monomer lines up non-covalently with template)
M-E-T-H (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H I (correct monomer lines up non-covalently with template)
M-E-T-H-I (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I N (correct monomer lines up non-covalently with template)
M-E-T-H-I-N (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N K (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K S (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S I (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S-I (template sequence covalently bonds new monomer to growing string)

[next 26 steps omitted to save space]

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E L (monomer lines up with template)
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L (final monomer covalently bonded to others)

So how does the actual Ghadiri ligase measure up (in a prebiotic context)? Not very well. Using the same analogy, here is how the GL functions.

The first PREEXISTING half of the sequence -- M-E-T-H-I-N-K-S-I-T, which for some unknown reason just happens to be floating around nearby, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T

The second PREEXISTING half of the sequence -- I-S-L-I-K-E-A-W-E-A-S-E-L, which is also just floating around nearby for some unknown reason, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T I-S-L-I-K-E-A-W-E-A-S-E-L

The two halves are covalently bonded together – BUT NOT BY ANY EXTRA ACTION PERFORMED BY THE TEMPLATE SEQUENCE ITSELF, BUT BY THE SEPARATE TWO HALVES THEMSELVES, BECAUSE ONE OF THEM WAS PRE-ACTIVATED BY SOME OTHER PROCESS.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L

How is it that the needed halves just happen to be floating around? Because the researchers intentionally synthesize those exact two sequences, preactivate the copies of one of the sequences, and then supply both for reaction.

This analogy points out some conceptual reasons why the Ghadiri ligase is not a true self-replicator: it absolutely requires (1) the correct 15- and 17-aa sequences already be available in the surroundings, (2) both halves to already be held together by covalent bonds, and (3) one of the two halves to already be activated. The Ghadiri ligages is powerless to recreate itself from the individual building blocks that make it up.

Let’s try looking at it with a second analogy.

What do we know that truly self-replicates? The most obvious answer is, life. To make sure that we are not throwing in excess complexity, what is the simplest form of life known? A bacterium (or to be a bit more precise, the bacterium Mycoplasma genitalium). Let’s double check…does a bacterium self-replicate? Yes. Okay, how?

In very simple terms, a bacterium takes in simple, raw materials from its surroundings and then the bacterium uses those simpler precursors to construct extra copies of its own constituents – such as DNA, proteins, mRNA, etc. – and then divides to form two bacteria, each like the original.

Now, is this similar to the way the GL “self-replicates”? No, not at all. If the GL were a bacterium, it would require two preexisting halves of another bacterium that would then simply line up with it and join together to form a whole bacterium. In the real world, a bacterium is given only simple raw materials such as inorganic substances and sugars, that it uses to build a complete copy of itself from scratch; whereas in the “GL world” the bacterium has to be handed EVERYTHING already setup, for free, and just joins the two preexisting halves together.

Okay, let’s try looking at this from an informational point of view.

A true self-replicating protein would not need any help by being supplied large amounts of very specific, external information; the needed information for self-replication would be contained in the self-replicator itself. But for the GL, it requires being handed approximately 130 bits of information*. How much is that? Suppose a random process were used to select a single number between 1 and 429,000,000,000,000,000,000,000,000,000,000,000,000,000, and that you know nothing other than the range and that the integer was chosen randomly, with each integer in that range being just as likely to have been selected as any other. Would you be willing to bet your life that you could guess the single number selected given just a single try? Of course not – that would be suicide. But, handed 130 bits of information, you’d be able to correctly pick that one integer in one try. And even if the rough calculation is too high by 10 orders of magnitude, or even 20 orders of magnitude, the fact still remains that the GL requires an enormous amount of preexisting information to be handed to it, for free, in order for it to “self-replicate”.

Where does that information come from? Some other process, which is doing “99.99…%” of the work. The GL absolutely relies upon some unknown, informationally rich, external process to build the parts of the GL. Just as a printed page cannot self-replicate – it requires a vastly more complex, external object (a photocopier) to do nearly all of the work – neither can the GL.

And here’s the kicker. The GL would need to be handed that much information for free to create just ONE copy of itself. In order to create a second copy, it would need to be handed, for free, ANOTHER 130* bits of information! Need a third copy? That requires yet ANOTHER 130* bits of information, and so on, and so on, and so on.

However you slice it, the GL is not a true self-replicator. And others have pointed this out.

quote:
”David Lee and his colleagues at the Scripps Research Institute in La Jolla, California, have now shown that autocatalytic capabilities are not confined to RNA or DNA or even PNA. They isolated a small peptide, part of a protein made by yeast, and showed that it could catalyze the joining together of two fragments of itself to make more copies of the complete peptide.

Here again, of course, the result is far from a completely self-replicating molecule. Such a molecule would have to start not with two pieces of itself but with a set of building blocks – in this
case amino acids – and make a copy of itself from scratch.” (Christopher Wills & Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p136)


So is the GL a catalyst? Yes – it accelerates the rate of the two halves joining without itself being altered in the process. It has been shown that even in the absence of the GL, the preexisting, pre-activated 15-aa and 17-aa fragments will bond together to form the full 32-aa GL. In the presence of the full GL, this rate of combination of the halves to form the full template is increased, and after doing so, the original template is ready to align another set of two halves so that they too will bond together. What the GL does is to orient two preexisting, pre-activated, specific sequences in the correct manner so that they can interact more readily (of course the probability of two halves finding each other and being properly oriented in order to link up is much greater when they are aligned linearly in tandem on a template than when colliding randomly in a solution). So yes, the GL is a true catalyst.

So does the term autocatalytic fit the GL? Yes – it is a catalyst whose product is itself.

Is the GL a true self-replicator? No.

*******************************************
* The information calculation was done very quickly in “back-of-the-napkin” fashion. The complete peptide is 32 amino acids long, and the rule is that living cells use 20 amino acids in the production of peptides. Since we are not looking at preexisting life or evolution in order to generate the correct sequence, and since intelligent direction is not involved either, the sequence of monomers would be generated by undirected, non-biological process alone. So, using the simplifying assumption that each amino acid is just as likely as any other to be incorporated at position X, we have 20 equally likely possibilities for each of 32 positions. That gives a total of 20^32, or about 4.29 x 10^41, possible unique sequences. On a piece of paper, in just four lines of “code”, I calculated 4.29 x 10^41 to be about 2^130 (the first number is actually almost 1,000 times greater than the second, but I was trying to avoid doing a complicated calculation and also didn’t want to overestimate). With 2^130 equally likely possibilities, you need, on average, 130 bits of information to find the one correct outcome in one shot. Also, note that I mention above in the actual discussion that the information calculation’s being too high by even 20 orders of magnitude would not alleviate the problem with the GL. That is, if a more detailed calculation came out to 10^21, it would still require about 70 bits of information be handed to it for free, which is still probably enough to win a state lottery, twice in a row. And the GL would need that huge amount of information for each copy of itself it was to make.

[This message has been edited by DNAunion, 11-03-2003]


This message is a reply to:
 Message 53 by DNAunion, posted 11-03-2003 8:49 AM DNAunion has not yet responded

Replies to this message:
 Message 55 by Rei, posted 11-03-2003 12:51 PM DNAunion has responded

  
DNAunion
Inactive Member


Message 57 of 85 (64294)
11-04-2003 12:22 AM
Reply to: Message 55 by Rei
11-03-2003 12:51 PM


Re: sadistics
quote:
Rei: First off, the Ghadiri self-replicator is just a single example;

/*DNAunion*/ It was THE ONE example that was offered, and I showed it didn't work. I did my job, now its your turn (see below).

quote:
Rei: there are countless possibilities (I could equally, say, go into the SunY self-replicator, the hexanucleotide self-replicator, Eckland's RNA polymerase self replicator, etc).

/*DNAunion*/ But since you have asserted as fact that the SunY ribozyme and Eckland's RNA polymerase are self-replicators, you have a position to back up. So you now need to post quotes from the papers for the experiments that show those molecules actually self-replicate.

quote:
Rei: In reality, there are going to be millions of possible simple self-replicators,

/*DNAunion*/ Gee, then why in the world are OOL researchers still looking, considering that they've conducted numerous experiments that start with pools consisting of trillions of random sequences? And why is the closest thing to a self-replicating RNA designed so far around 180 nucleotides long?

I guess all the OOL researchers just don't know what they're doing. Tell you what...why don't you become one and solve the riddles for them. You just might get a Nobel Prize.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 55 by Rei, posted 11-03-2003 12:51 PM Rei has not yet responded

Replies to this message:
 Message 78 by DNAunion, posted 11-29-2003 3:10 PM DNAunion has responded

  
DNAunion
Inactive Member


Message 58 of 85 (64296)
11-04-2003 12:32 AM
Reply to: Message 55 by Rei
11-03-2003 12:51 PM


Re: sadistics
quote:
Rei: Just assuming that the Ghadiri peptide is randomly pieced together (just coincidentally, it is of a form that is ideally suited to be formed by abiotic peptide synthesis, but we'll ignore that)

/*DNAunion*/ Uhm, no we won't. You've asserted that as fact...you have an obligation to support your claim or withdraw it.

quote:
Rei: ... you would have odds of 4.29e41 for producing it. However, its subunits 6.655e20 - 6.655e20 times as common as the original self-replicating peptide. If the Ghadiri ligase was formed in an environment that tends to form peptides like itself, then its subunits are quite likely to occur there as well.

/*DNAunion*/ So show that such is the case: show us an experiment where the Ghadiri ligase halves were formed under prebiotically plausible conditions. Of course, you can't. More of your unsupported speculation.

quote:
Rei: Furthermore, I might ask: when given partial subunits, will the replicator assemble a partial copy of itself? If so, then its odds of survival just vastly increased, because the partial copy is well on its way to becoming a full copy, or even a deformed copy that itself makes partial copies.

/*DNAunion*/ Actually, under the conditions used in the experiment, if some partial subunits were added and they ended up binding to the template or the "halves", they would hinder "self-replication".

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 55 by Rei, posted 11-03-2003 12:51 PM Rei has not yet responded

  
DNAunion
Inactive Member


Message 60 of 85 (64299)
11-04-2003 12:46 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
Rrhain: First, it was a start to more research. Not the sole piece of information.

/*DNAunion*/ First, it was THE ONLY paper you gave as support.

quote:
Rrhain: Second, you're ignoring an important point in the paper: [“enantiomeric”] Mutations get corrected:

/*DNAunion*/ Ignoring something completely irrelevant to the discussion does not make one guilty of “ignoring” something, despite your insinuation.

That such “mutations” are corrected is completely irrelevant as to the ORIGIN of homochirality (which was your point, wasn’t it), and also completely irrelevant to whether or not the GL is a self-replicator (which was my point). So why should I need to address such an irrelevant point? Fact is, there is no reason.


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has responded

Replies to this message:
 Message 64 by Rrhain, posted 11-07-2003 5:59 AM DNAunion has responded

  
DNAunion
Inactive Member


Message 61 of 85 (64301)
11-04-2003 12:57 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
Rrhain: The point is that there are ways to achieve homochirality.

/*DNAunion*/ So show us the experiment that started with racemic mixtures of ribonucleotides and produced homochirality in polynucleotides under prebiotically plausible conditions. “In principle” is one thing, experimental support is another.

quote:
Rrhain: We should not simply claim that because something is difficult for us right now means that it will never be possible to figure out.

/*DNAunion*/ So who’s doing that?

quote:
Rrhain: Too many times we have claimed something to be impossible (like the synthesis of organic compounds from inorganic reagents) only to find out that it is quite possible.

/*DNAunion*/ Not the most parallel analogy. What you bring up was stated to be literally impossible and was based on a philosophical world view. What I am pointing out is very different.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has not yet responded

Replies to this message:
 Message 69 by MarkAustin, posted 11-14-2003 8:28 AM DNAunion has responded

  
DNAunion
Inactive Member


Message 62 of 85 (64302)
11-04-2003 1:05 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
/*DNAunion*/ For example, despite the misleading term used by the authors and others, the peptides do not self-replicate.

quote:
Rrhain: Incorrect.

/*DNAunion*/ Nope, 100% correct.

quote:
Rrahin: Did you read the article?

/*DNAunion*/ Yes, I did. The real question is, did you read my post??

NosyNed obviously did, because unlike you, he saw my points. One of them, simply put, is as follows:

If object A requires some other, external process P to do “99.99..%” of the work involved in making a copy of A, then A is NOT a SELF-replicator.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has not yet responded

  
DNAunion
Inactive Member


Message 63 of 85 (64306)
11-04-2003 1:32 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
Rrahin [quoting material]: “Synthetic polymers are simpler than biological systems and provide a model for understanding the origin of homochirality in biomolecules. One proposal stems from observations that polymers made from building blocks of random handedness will contain mixtures of right- and left-handed blocks so complex that no two polymers will have identical stereochemistry. All the polymers will be chiral, but if one exists, it is unlikely that its mirror image will too. For small polymers consisting of only a few building blocks, the number of possible combinations of right- and left-handed blocks is small, and the mirror images are easily formed. However, for a polymer comprising 20 building blocks there are almost a million possibilities, and an enormous number of blocks would be required to build all the possible mirror images. Biological molecules often have over 100 building blocks, pushing the limits of available materials and making it extremely unlikely that a molecule and its mirror image can be prepared in the same batch. If the sample of polymers contained some that were self-replicating, it is reasonable that the most efficient one will emerge, and only this homochiral polymer will exist.”

/*DNAunion*/ sigh…. I’ve been typing away and posting at this site for 5 hours now and still haven’t managed to address all replies to me…and I have to get up in 5 hours to go to my two jobs. I’ll have to make this less in depth than normal.

First, the author seems to lose track of his own point. He/she starts by relying upon both enantiomers being randomly incorporated into polymers in order to produce such a wide range of differing molecules that the mirror images would not likely exist (note that 2^20 = 1,048,576; with two possibilities for each position – a right-handed and a left-handed enantiomer – and 20 building blocks in the polymer, the author says there are nearly one million possibilities). Yet at the end, without explanation, he says that the self-replicating molecule would be homochiral!? Looks like the author magically pulled a rabbit out his hat!

Second, his use of probability almost sounds “Creationist” in nature…”Get polymers at least this long and the probability of hitting a particular one drops to zero”. Not that he/she is wrong, but isn't turn about fair play? Shouldn't we reject his probability argument?

Third, that author assumes that some hypothetical concentrated monomer broth (in which side reactions obviously don’t occur) would produce MORE THAN ONE self-replicator. His experimental support???

Fourth, not only does the author assume more than one self-replicator would arise, but that the most efficient one would be homochiral. Why?

Fifth, the author is apparently not aware of enantiomeric cross inhibition, which would poison chain growth when both enantiomers are incorporated into a single growing chain.

********************
That's it for me tonight. My fingers are beat and I am already going to have a hard time getting up and lasting all day at work(s). I will probably be short on time tomorrow so may not get a chance to respond.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has not yet responded

  
DNAunion
Inactive Member


Message 65 of 85 (65086)
11-08-2003 12:56 AM
Reply to: Message 64 by Rrhain
11-07-2003 5:59 AM


Re: sadistics
quote:
First, it was a start to more research. Not the sole piece of information.

quote:
First, it was THE ONLY paper you gave as support.

quote:
That's because I am not here to do your homework for you.

Ah, so your argument has already run out of steam and you are reduced to mere rhetoric. Not a speck of science in your whole post: it's little more than "nanny nanny boo boo, stick your head in doo doo"-type argumentation.

Anyway, you do realize that it was you who made a claim and it was you who offered only one paper as support; and that that one paper did not support your "contradiction" of me. One failed paper...if anyone has more homework to do on this, it would be you.

quote:
Since you seem to be stating that something is a physical problem on a fundamental basis, the response is merely to show you that it isn't a fundamental problem.

So go ahead show that already.

quote:
It may be a specific problem for a specific proposed method, but that is a separate question.

Hmmmm...makes one wonder why you picked that one paper specifically?!?!?!

quote:
Ignoring something completely irrelevant to the discussion does not make one guilty of “ignoring” something, despite your insinuation.

quote:
What makes you think it is irrelevant? Do you not think that a process that actively suppresses non-homochiral molecules is important to the question of how homochirality came about?

Nope, because the experiment uses preexisting homochirality to then merely propagate homochirality. That doesn’t even attempt to explain how homochirality could have come about. See, it is irrelevant.

quote:
That such “mutations” are corrected is completely irrelevant as to the ORIGIN of homochirality

quote:
Why? Other than your say so, why?

Uhm...simple logic. The experiment required preexisting homchirality. Thus, it does not even attempt to explain the origin of homochirality. Is that really so difficult to grasp???

quote:
also completely irrelevant to whether or not the GL is a self-replicator (which was my point).

quote:
And what evidence, other than your say so, shows that it is not a self-replicator?

Uhm, sound logic, supported by a detailed explanation.

quote:
You seem to be playing a game.

Yeah, yeah..."nanny nanny boo boo, DNAunion stick your head in doo doo"...we get it already.

quote:
You claim that X is not seen. When shown an example of X, you then claim that it isn't an example of Y and hope to high heaven that nobody notices that you didn't ask for Y in the first place.

Now who’s playing games! Why the use of variables instead of actual words? So tell us, exactly what did I claim is not seen? Exactly what example of that did you present? Exactly what did I supposedly change the requirement into in order to avoid being shown to be wrong?

Until you do attempt to tell us, here’s a brief review of the original exchanges between us on this.

quote:
The calculation implicitly relies upon homochirality. If both enantiomeric forms of the bases (actually, the sugar moieties of the bases) were present, enantiomeric cross inhibition would hinder the formation of long polymers needed for replication or other complex function.

quote:
But achieving homochirality isn't a problem:

[link - NAI News Article: One-Handed Life – link]


Now your paper did not demonstrate any prebiotically plausible mechanism that would explain the origin of homochirality. Nothing that contradicts or counters my original statements, despite what your “But...” (and the rest) indicates.

quote:
So why should I need to address such an irrelevant point?

quote:
Because your mere assertion that it is irrelevant is not sufficient to show that it is.

Uhm, I explained why it was irrelevant; it didn't deal with the ORIGIN of homochirality, nor did it have anything to do with whether or not the GL was capable of self-replication.

[This message has been edited by DNAunion, 11-08-2003]


This message is a reply to:
 Message 64 by Rrhain, posted 11-07-2003 5:59 AM Rrhain has responded

Replies to this message:
 Message 66 by Rrhain, posted 11-10-2003 9:03 PM DNAunion has responded
 Message 80 by DNAunion, posted 11-29-2003 3:16 PM DNAunion has not yet responded

  
DNAunion
Inactive Member


Message 68 of 85 (65939)
11-11-2003 11:03 PM
Reply to: Message 66 by Rrhain
11-10-2003 9:03 PM


Re: sadistics
/*Rrhain response to me*/

quote:
Ah, so your argument has already run out of steam.

quote:
Incorrect.

No, correct. You haven't even tried to add support for your position in the last couple of posts. You've basically been just ignoring the reasoning I have already presented, pretending it doesn't exist, and sneaking in opponent-bashing rhetoric. If you still had steam left, you'd be supporting your position.

quote:
The argument is still there. I, however, do not wish to do all the heavy lifting. If you cannot be bothered to get off your ass, then you shouldn't be surprised to find that you don't have all the information.

You still don’t understand how things work. YOU make a claim, YOU back it up. It’s not my job to run around looking for YOUR evidence to support YOUR position. Simple enough?

quote:
and that that one paper did not support your "contradiction" of me.

quote:
You claimed it didn't support self-replication, despite the fact that the paper directly talks about the molecules self-replicating.

Wrong, what I said was that the GL cannot actually self-replicate. What I said is pretty clear cut, and can be demonstrated. What you claim I said is ambiguous and one could always try to assert that at least in some sense the paper did support self-replication. So let's stick to facts so the debates doesn't go off in directions it shouldn't.

Now, about the GL's inability to self-replicate...I covered that on “day one”, remember? Here, Let me point it out to you again.

quote:
For example, despite the misleading term used by the authors and others, the peptides do not self-replicate.

See? As I pointed out way back then, at the very start... sure, the authors use the term self-replication, but the molecules are not actually capable of self-replication. You can point out that the authors label the GL as self-replicating until you turn blue in the face, but it won't change the fact that it can't.

And all you have to do is actually read my detailed explanation of why the GL can’t self-replicate. It’s should be sufficient to convince any reasonable and objective person.

Here's one for the road.

quote:
”David Lee and his colleagues at the Scripps Research Institute in La Jolla, California, have now shown that autocatalytic capabilities are not confined to RNA or DNA or even PNA. They isolated a small peptide, part of a protein made by yeast, and showed that it could catalyze the joining together of two fragments of itself to make more copies of the complete peptide.

Here again, of course, the result is far from a completely self-replicating molecule. Such a molecule would have to start not with two pieces of itself but with a set of building blocks – in this
case amino acids – and make a copy of itself from scratch.” (Christopher Wills & Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p136)


[This message has been edited by DNAunion, 11-11-2003]


This message is a reply to:
 Message 66 by Rrhain, posted 11-10-2003 9:03 PM Rrhain has responded

Replies to this message:
 Message 70 by Rrhain, posted 11-14-2003 5:06 PM DNAunion has responded

  
DNAunion
Inactive Member


Message 71 of 85 (66571)
11-14-2003 10:36 PM
Reply to: Message 70 by Rrhain
11-14-2003 5:06 PM


Re: sadistics
/*Rrhain responds to me*/

quote:
You can whine that the GL isn't self-replicating until you turn blue in the face, but it won't change the fact that it does.

If that's your position, then surely you can explain in detail exactly how the GL actually self-replicates. You can start by explaining exactly how the GL itself produces its own constituents: the two "halves" that are joined to form the full template.

[This message has been edited by DNAunion, 11-14-2003]


This message is a reply to:
 Message 70 by Rrhain, posted 11-14-2003 5:06 PM Rrhain has not yet responded

Replies to this message:
 Message 72 by NosyNed, posted 11-15-2003 1:12 AM DNAunion has responded

  
DNAunion
Inactive Member


Message 73 of 85 (66629)
11-15-2003 11:48 AM
Reply to: Message 72 by NosyNed
11-15-2003 1:12 AM


Re: sadistics
quote:
If you'd all stop for a minute and define what you mean by self replication you'll note that you are using different meanings. Sort that out!

I’ve already given a working definition of self replication, and also pointed out qualities that exclude molecules from being classified as being able to actually self replicate.

quote:
A true self-replicator can extract its individual building blocks (monomers/letters) one at a time from its surroundings (a pool of monomers/letters) and construct a functional copy of itself using itself as a template for the sequencing of the units, followed by release of the copy. In order to allow them to separate from each other but to not decompose, the template and the copy should not be covalently bonded together but both the template and the copy should be covalently bonded internally. Note that the letters can’t simply line up according to the template’s sequence and be done with it; they also have to be covalently linked to their nearest neighbors in the growing copy after being non-covalently attached to the template. Forming this bond between units within the same strand requires either a catalyst or the pre-activation of each of the building blocks. And since we are looking for a true self-replicator, the sequence itself should be performing the function, whether it is catalyzing the bond directly or pre-activating incoming monomers. The process we will look at (the less involved of the two) involves two basic steps for each monomer added: first, the correct monomer is “chosen” from the stocked pool of monomers and lines up along the template, then the template sequence covalently bonds the new monomer to the elongating string.

[For the GL,] How is it that the needed halves just happen to be floating around? Because the researchers intentionally synthesize those exact two sequences, preactivate the copies of one of the sequences, and then supply both for reaction.

This analogy points out some conceptual reasons why the Ghadiri ligase is not a true self-replicator: it absolutely requires (1) the correct 15- and 17-aa sequences already be available in the surroundings, (2) both halves to already be held together by covalent bonds, and (3) one of the two halves to already be activated. The Ghadiri ligages is powerless to recreate itself from the individual building blocks that make it up.


quote:
What do we know that truly self-replicates? The most obvious answer is, life. To make sure that we are not throwing in excess complexity, what is the simplest form of life known? A bacterium (or to be a bit more precise, the bacterium Mycoplasma genitalium). Let’s double check…does a bacterium self-replicate? Yes. Okay, how?

In very simple terms, a bacterium takes in simple, raw materials from its surroundings and then the bacterium uses those simpler precursors to construct extra copies of its own constituents – such as DNA, proteins, mRNA, etc. – and then divides to form two bacteria, each like the original.

Now, is this similar to the way the GL “self-replicates”? No, not at all. If the GL were a bacterium, it would require two preexisting halves of another bacterium that would then simply line up with it and join together to form a whole bacterium. In the real world, a bacterium is given only simple raw materials such as inorganic substances and sugars, that it uses to build a complete copy of itself from scratch; whereas in the “GL world” the bacterium has to be handed EVERYTHING already setup, for free, and just joins the two preexisting halves together.


quote:
A true self-replicating protein would not need any help by being supplied large amounts of very specific, external information; the needed information for self-replication would be contained in the self-replicator itself. But for the GL, it requires being handed approximately 130 bits of information*. How much is that? Suppose a random process were used to select a single number between 1 and 429,000,000,000,000,000,000,000,000,000,000,000,000,000, and that you know nothing other than the range and that the integer was chosen randomly, with each integer in that range being just as likely to have been selected as any other. Would you be willing to bet your life that you could guess the single number selected given just a single try? Of course not – that would be suicide. But, handed 130 bits of information, you’d be able to correctly pick that one integer in one try. And even if the rough calculation is too high by 10 orders of magnitude, or even 20 orders of magnitude, the fact still remains that the GL requires an enormous amount of preexisting information to be handed to it, for free, in order for it to “self-replicate”.

Where does that information come from? Some other process, which is doing “99.99…%” of the work. The GL absolutely relies upon some unknown, informationally rich, external process to build the parts of the GL. Just as a printed page cannot self-replicate – it requires a vastly more complex, external object (a photocopier) to do nearly all of the work – neither can the GL.

However you slice it, the GL is not a true self-replicator. And others have pointed this out.

--------------------------------------------------------------------------------
”David Lee and his colleagues at the Scripps Research Institute in La Jolla, California, have now shown that autocatalytic capabilities are not confined to RNA or DNA or even PNA. They isolated a small peptide, part of a protein made by yeast, and showed that it could catalyze the joining together of two fragments of itself to make more copies of the complete peptide.

Here again, of course, the result is far from a completely self-replicating molecule. Such a molecule would have to start not with two pieces of itself but with a set of building blocks – in this case amino acids – and make a copy of itself from scratch.” (Christopher Wills & Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p136)
--------------------------------------------------------------------------------


[This message has been edited by DNAunion, 11-15-2003]


This message is a reply to:
 Message 72 by NosyNed, posted 11-15-2003 1:12 AM NosyNed has not yet responded

  
DNAunion
Inactive Member


Message 74 of 85 (66773)
11-16-2003 12:35 AM
Reply to: Message 69 by MarkAustin
11-14-2003 8:28 AM


Re: sadistics
quote:
The calculation implicitly relies upon homochirality. If both enantiomeric forms of the bases (actually, the sugar moieties of the bases) were present, enantiomeric cross inhibition would hinder the formation of long polymers needed for replication or other complex function.

quote:
Chirality was the question. Nothing else.

Wrong. The problem I pointed out, and that Rrhain's allegedly countered, was the ORIGIN of HOMOchirality.

quote:
It has been demonstrated that it is possible for molecules to selectively extract the correct handed molecules, indeed correct errors of chirality.

Given preexisting homochirality, yes, homochirality can be maintained. I didn't argue against that...becuase that's not the point being discussed.

quote:
As I read the article, the intent was to prove that molecules of the correct chirality could be selected. They did so.

Yep, given preexisting homochirality they showed that homochirality could be maintained. Quite irrelevant.

quote:
They have demonstrated that chiralirty need not be a problem.

They didn't show what Rrhain needs them to show in order to uphold his counter to me: that the ORIGIN of HOMOchirality isn't a problem.

[This message has been edited by DNAunion, 11-16-2003]


This message is a reply to:
 Message 69 by MarkAustin, posted 11-14-2003 8:28 AM MarkAustin has responded

Replies to this message:
 Message 75 by MarkAustin, posted 11-18-2003 9:29 AM DNAunion has responded

  
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