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Author | Topic: Abiogenesis - Or Better Living Through Chemistry | |||||||||||||||||||||||
DNAunion Inactive Member |
quote: /*DNAunion*/ But (besides other potential problems) we are no longer dealing with the complete volume of an ocean: as Rei points out.
quote: /*DNAunion*/ Under that current most likely scenario the Talk Origins' calculation becomes invalid.
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DNAunion Inactive Member |
quote: /*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]
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DNAunion Inactive Member |
quote: quote: /*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]
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DNAunion Inactive Member |
/*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-LM (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-LM 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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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-LM-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 checkdoes 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: 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]
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DNAunion Inactive Member |
quote: /*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: /*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: /*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]
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DNAunion Inactive Member |
quote: /*DNAunion*/ Uhm, no we won't. You've asserted that as fact...you have an obligation to support your claim or withdraw it.
quote: /*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: /*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]
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DNAunion Inactive Member |
quote: /*DNAunion*/ First, it was THE ONLY paper you gave as support.
quote: /*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.
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DNAunion Inactive Member |
quote: /*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: /*DNAunion*/ So who’s doing that?
quote: /*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]
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DNAunion Inactive Member |
quote: quote: /*DNAunion*/ Nope, 100% correct.
quote: /*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]
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DNAunion Inactive Member |
quote: /*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 meand 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 natureGet 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]
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DNAunion Inactive Member |
quote: quote: quote: 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: So go ahead show that already.
quote: Hmmmm...makes one wonder why you picked that one paper specifically?!?!?!
quote: quote: 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: quote: 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: quote: Uhm, sound logic, supported by a detailed explanation.
quote: Yeah, yeah..."nanny nanny boo boo, DNAunion stick your head in doo doo"...we get it already.
quote: 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: quote: 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: quote: 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]
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DNAunion Inactive Member |
/*Rrhain response to me*/
quote: quote: 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: 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: quote: 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: 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: [This message has been edited by DNAunion, 11-11-2003]
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DNAunion Inactive Member |
/*Rrhain responds to me*/
quote: 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]
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DNAunion Inactive Member |
quote: 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: quote: quote: [This message has been edited by DNAunion, 11-15-2003]
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DNAunion Inactive Member |
quote: quote: Wrong. The problem I pointed out, and that Rrhain's allegedly countered, was the ORIGIN of HOMOchirality.
quote: Given preexisting homochirality, yes, homochirality can be maintained. I didn't argue against that...becuase that's not the point being discussed.
quote: Yep, given preexisting homochirality they showed that homochirality could be maintained. Quite irrelevant.
quote: 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]
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