Abiogenesis

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The ribozymes that Cech discovered spliced segments out of themselves and did not have multiple turnover capabilities.

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But things have happened since that time.

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Who cares? Not me. I spoke specifically about the ribozymes Cech first discovered, the ones that spliced out internal sequences from themselves. Those are the ones I said weren't technically enzymes.

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Black: Ever here of peptidyl transferase?

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Sure. Have you ever heard of relevance? Seems not, since peptidyl transferase has zip to do with my statement.If you are trying to pretend you've pointed out a shortcoming in my knowledge by trying to slyly change the subject you are only showing more dishonesty and/or inability to understand simple exchanges.[This message has been edited by DNAunion, 04-08-2004]

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...discovered...

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No, synthesized.

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It was based on a protein found in nature, an alpha-helical coiled coil.

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And the authors stated they, with forethought, modified it in order for it to perform the desired function: a function the original peptide did not perform. It was designed, not discovered.[This message has been edited by DNAunion, 04-08-2004]

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... it absoluately requires researchers to synthesize all of its highly complex "halves" and preactivate them...

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... It's occuring in a lab with the researchers synthesizing all of 15-aa and 17-aa molecules, and preactivating them, with those presynthesized and preactivated halves being required for the full template - which the researchers designed - to then simply align them to help them bond - as intended - more readily.
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Definitely not applicable to abiogenesis. Unless you are suggesting that some intelligent researchers were around 3.5 - 4 billion years ago continuousaly synthesizing highly complex and specific 15-aa and 17-aa halves, preactivating them as required, and feeding them to the reaction.

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No, intelligent researchers are not needed 3.5-4 billion years ago. The reason is simple: the researchers were simulating natural processes.

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No they weren’t. Their setup does not model natural processes; natural processes would produce random amino acid sequences in the absence of any genetic system encoding peptides.The experiment required SPECIFIC 15-aa and SPECIFIC 17-aa sequences. And EACH copy of the full template to be made required its own set of one presynthesized 15-aa and one presynthesized 17-aa half, preactivated, of course.Where do you believe all of these SPECIFIC 15-aa and 17-aa "halves" came from in the absence of genetic encoding?

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Black: These peptides could have been synthesised naturally.

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How many? 1? So what? Since the peptide is completely incapable of replicating itself, there would be just 1 copy that would eventually hydrolyze — it’s existence would have been for naught.Even if 100 somehow happened to arise at the same time at the same place (stretching believability to its limits), that’s all there would be 100. They can’t replicate. Those 100 would sooner or later hydrolyze — their existence would have been for naught.What is needed is a polymer that can build a copy of itself from its monomers. The 32-aa peptide simply can't do that...not in the least.

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But self-replicating peptides do because they are kind of like one of the predictions of abiogenesis theories.

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And the 32-aa peptide we’ve been discussing has no relevance to abiogenesis since it cannot actually self-replicate. It would need researchers to presynthesize and preactivate its "halves", and to feed them to the reaction. And this would require CONTINUED intervention since the peptide can't actually self-replicate.

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Regarding RNA from peptide nucleic acids...I find that the evidence supports what I said before.

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Which time? Your original?

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(3) RNA could form from amino acid chains (peptides)

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That’s wrong: RNA is not even made of amino acid chains.

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RNA may be polymerized using the PNA as template accounts for enzymatic activities including PNA replication.

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You still haven’t supported your (3) - either the original or your altered version.

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So now let's review: Amino acids form naturally, as predicted by abiogenesis theories.

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Agreed...still.

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If synthesised correctly, peptides (chains of amino acids) can self-replicate, as predicted by abiogenesis theories.

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That’s the theory: where’s your support that such could occur naturally?

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The substances to create PNA (the precursor to RNA) form naturally, etc., as predicted by abiogenesis theories.

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Who said PNA actually was the precursor to RNA? Again, theory, not fact.

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RNA can do the function of DNA, as predicted by abiogenesis theories.

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Yes, RNA can store genetic information.

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RNA can act as a catalyst, as predicted by abiogenesis theories.

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Yes, it can (although the ribozymes that spliced out internal sequences — those originally discovered by Cech — are not technically catalysts).

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RNA can do auto-catalysis, as predicted by abiogenesis theories.

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Just so we are clear: no RNA polymer that could have kick started life has ever been discovered in experiments carried out under prebiotically plausible conditions.

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These things were required for abiogenesis...and now we know they are true. These are the pieces of the puzzel.

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Those are the piececs of the puzzle? What happened to your original list?

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(1) Amino acids could form naturally
(2) Amino acids could link together (as peptides) and reproduce naturally
(3) RNA could form from amino acid chains (peptides)
(4) RNA would need neither DNA nor protein to catalyze its own replication

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Did you drop it because 3 out of 4 hadn’t been demonstrated?[This message has been edited by DNAunion, 04-08-2004]

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Black: Now, let us move on to #2. [(2) Amino acids could link together (as peptides) and reproduce naturally] DNAUnion disputed this right away. Here is what DNAUnion has just posted regarding it:

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That’s the theory: where’s your support that such could occur naturally?
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DNAUnion, apparently thought that there was no evidence to support my statement, and concluded that I was wrong.

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No, if I had been claiming that your statement was wrong I would have shown reason why it was wrong. What I said was that what you stated is the theory; and asked you to provide experimental support for you statement.

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Black: First let me explain why self-replicating peptides were a prediction of most abiogenesis theories. However, amino acids can hook up together. So scientists predicted that if amino acids could hook up together in a certain way, the ones that had just hooked up would start hooking others up in the same way. If this were possible, it would be self-replication.

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How do you propose the individual amino acids would be linked up into polymers?What fraction of all possible polypeptides do you suppose can actually self-replicate? And what support do you have?

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Black: As you can see self-replicating peptides have much to do with abiogenesis theories.

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Not really. The RNA World theory doesn’t require self-replicating peptides at all.

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Black: Now, do these self-replicating peptides exist? Yes. The first one to be discovered was the GL peptide.

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That peptide cannot self-replicate. Put it in a pool of free amino acids and it cannot construct a copy of itself.

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Black: The objection that DNAUnion has raised to this is that it is unlikely that this peptide and the other peptides that it bonds together could synthesis naturally. I agree with him. I do not believe (nor does anyone else that I know) that it was this exact peptide that was the first self-replicating peptide.

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So it has no direct relevance to abiogenesis.

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Black: The point I was trying to make by discussing this peptide was that self-replicating peptides are possible.

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It is not a self-replicating peptide: it cannot build a copy of itself from its monomers.

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Black: I was not trying to say that this exact peptide was the first one. Perhaps DNAUnion misunderstood what I was trying to say here and that is the reason he thinks I am dishonest.

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No, you were dishonest for stuffing words into my mouth, and then for trying to justify your actions. That’s different from what is being discussed here.

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Black: However, this peptide does demonstrate that my statement #2 is true. The 3 peptides required could, in theory, have synthesized naturally.

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No, it doesn’t support your #2 because the peptide cannot self-replicate.

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Black: For example, the Chmielewski Group has synthesised another self-replicating peptide. Their peptide E1E2 contains an acidic 'stripe' of glutamic acid residues along one side of the helix. They shortened the peptide to a length of 26 residues. Studying the self-replicating capacity of the new peptide, called RI-26, they observed catalytic efficiency (catalyzed rate constant:uncatalyzed rate constant) of 100,000, which is more than 20 times higher than the previous record for self-replicating molecules. Their peptide also exhibited cross-catalysis as well as auto-catalysis.

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Still unsupported is your claim that it can self-replicate (in any way relevant to abiogenesis).[This message has been edited by DNAunion, 04-10-2004]

For some odd reason (muddy the waters?) Black mixed in link to RNA probability calcultaion with his discussion of peptides.

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Black: Something interesting about probabilities: http://www.talkorigins.org/origins/postmonth/apr98.html.

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Here’s what Black is apparently referring to from that link.

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[The chances are ] Quite good actually. There are 1.6 x 10^60 possible 100 nucleotide sequences. In a primordial ocean of 10^24 litres with a nucleotide concentration of 10^-6M (reasonably dilute), assembling a 100 nucleotides sequences on clay al la Ferris [3] and assuming it takes a week to make a full sequence, then you can have produced roughly 1 x 10^50 sequences in a year!

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Wrong.1) He limits assembly to just clay surfaces but uses the whole volume of the entire primordial ocean in his calculation, vastly overestimating the number of sequences that would be produced.2) RNA may not even be able to exist at depths anywhere near the ocean’s bottoms [A 10-meter water column equates to approximately 1 bar of pressure so, assuming Archean atmospheric pressure was at least 1 bar, this observation seems to impose a depth limit on origin of life at ‘deep-sea vents’ at about 30 meters or less, unless the theory does not require sugar formation from CH2O. (John Washington, The Possible Role of Volcanic Aquifers in Prebiological Genesis of Organic Compounds and RNA, p67)]3) What about unwanted cross reactions? What about enantiomeric cross inhibition? These would also drastically lower the number of RNA sequences that would actually be produced.4) What about release from the mineral surfaces of any long RNA polymers that formed?

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Black: DNAUnion attacked the use of the word 'discovered' instead of 'synthesized'. He is correct in saying that it was synthesized. However, in synthesizing it, they discovered it was possible, so I am also correct in saying it was discovered:

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discover: To learn about for the first time in one's experience: discovered a new restaurant on the west side.

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I kind of feel silly arguing about this though since it is only a game of words.

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Indeed, so why did you start it?Why did you select the misleading term DISCOVERED? Especially when the point your were trying to support was:

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Black: (2) Amino acids could link together (as peptides) and reproduce naturally

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Black: Now let us move on to #3. DNAUnion also challenged this. I will admit that this has not been observed.

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Then perhaps you need to rephrase another part of your original post so that it is not misleading.

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If abiogenesis were possible, we would expect to observe certain things.

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(3) RNA could form from amino acids

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Maybe the part about we would expect to observe certain things should be taken out or rephrased.

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Black: DNAUnion has recently posted this:

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You still haven’t supported your (3) - either the original or your altered version.
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Unfortunately I cannot respond to this because I am not sure what s/he is talking about.

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No, we aren’t sure what YOU are talking about because you keep changing things. First you had a list of 4 items, then a few posts ago you offered a different list of items, then you went back and changed one of the items in your original list. Stabilize your argument already.

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Black: What altered version??

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LOL! From the person who just admitted to going back and changing the very statement under discussion! You’re a hoot!

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Now we will move on to #4. DNAUnion once again disputed this.

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I will bring out the dictionary again.

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autocatalysis: Catalysis of a chemical reaction by one of the products of the reaction.

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replication: The process by which genetic material, a single-celled organism, or a virus reproduces or makes a copy of itself

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So auto-catalysis is replication because one of the products of it is the catalyzer--it has made a copy of itself.

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Autocatalysis and self-replication are not the same thing. For example:

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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.

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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)

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See, the 32-aa is autocatalytic, but it is not a self-replicator. Different things.In fact, you yourself refute your claim, as follows:

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I described one such auto-catalyzer. Let me review it again:

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Hammerhead ribozymes are small, catalytic RNAs that undergo self-cleavage of their own backbone to produce two RNA products. ...

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So by your stating that the hammerhead ribozymes are autocatalytic you are claiming that they replicate themselves, even though you say they undergo self-cleavage of their own backbone to produce two RNA products. But how can one be replicating itself if it cleaves its own backbone resulting in two RNA molecules that differ from the original?********************************
Just so that we are all clear on what I actually stated, here’s Black's original statement followed by my reply to it.

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Black: (4) RNA would need neither DNA nor protein to catalyze its own replication

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DNAunion: That's the theory. No prebiotically plausible experiment has accomplished this.

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[This message has been edited by DNAunion, 04-10-2004]

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In conclusion, I still believe that all four of my statements were correct.

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Only one has been confirmed by experimentation.

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DNAunion: The experiment required SPECIFIC 15-aa and SPECIFIC 17-aa sequences. And EACH copy of the full template to be made required its own set of one presynthesized 15-aa and one presynthesized 17-aa "half", preactivated, of course.

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And the 32-aa peptide we’ve been discussing has no relevance to abiogenesis since it cannot actually self-replicate.

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Black: self-replication: Replicating oneself or itself

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Too simplistic and not the one applicable to abiogenesis. More below.

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What does the GL peptide do (and Chmielewski's peptide)? It replicates itself (I put the definition of replicate somewhere above).

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So yes it is self-replication.

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No, it is not self-replication when discussing OOL. You are guilty of equivocation. The GL peptide simply does not self-replicate in any manner relevant to abiogenesis and your attempts to tie its activity to OOL is disingenuous.A self-replicator in the OOL sense cannot rely upon researchers to synthesize every one of its complex and highly improbably halves, preactivate them, and feed them to the reaction. That’s simply not what abiogenesis is about.If the peptide were placed in an amino acid solution and it could create copies of itself, then yes, it would be a self-replicator in a sense relevant to abiogenesis. But it can’t do that, not at all, so it’s not a self-replicator in the OOL sense.And it’s not just me saying this:

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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.

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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)

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Next topic:

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DNAunion: Just so we are clear: no RNA polymer that could have kick started life has ever been discovered in experiments carried out under prebiotically plausible conditions.

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Black: What kind of RNA polymer are you looking for?

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One that could have kick started life, of course. There are several criteria, and not all of them are self-evident. Some of them include:1) Must be able to make a complete (complementary) copy of itself from its constituent monomers - free riobnucleotides — under prebiotically plausible conditions.2) a) The complementary copy must be able to make a complete (complementary) copy of itself from its constituent monomers — free ribonucleotides — under prebiotically plausible conditions.ORb) The original must be able to make a complete (complementary) copy of its complementary molecule it produced, again from the constituent monomers - free ribonucleotides - under prebiotically plausible conditions.3) The molecule must be able to evolve.********************************
Edited to add 2b[This message has been edited by DNAunion, 04-11-2004]

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DNA, is there really a need for the ad hominems? Tone it down please.

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The attitude seems to be your modus operandi around here and if it is going to continue you'll be taking an extended break.

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And anyone who made it past elementary school can see that I didn't say it
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But since you seem incapable of grasping something so simple, let me explain it to you
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Did you lose your mind? Yep
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If you had half a brain and were honest you wouldn't be able to try to claim that two very different things you said were the same
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Odd, I didn't see a similar warning given to Mark24 for the following comments he made in another thread.

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Mark24: Good grief!!!

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Look, it is all VERY simple. That means it can't have been fucked about by liquefaction or hydrodyamic sorting, right? That means it was, whether you like it or not,

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DO YOU UNDERSTAND?

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Mark24: You mean your argument got whipped, six of the best trousers down, don't you?

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You can't help yourselves, can you? You are such a compartmentalised thinkers that you never cross-check one of your held beliefs against another for consistency. This is ALL creationism is, tiny factoids ripped from their context at the expense of all directly contradictory data.

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It was crashingly obvious to anyone who actually was a critical thinker that you were being a hypocritical creationist grasping at straws for something that would support your view. Typical.

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Mark24: But [you] hypocritically say:

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You now appear to be backtracking as hard as you can claiming that liquefaction actually eliminated any such artifact!

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Please can you reconcile your two contradictory statements, above. Was the Ce a genesis event recorded, or not. You can't have it both ways, mate.

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Good luck.

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Mark24: There are no coral reefs in the Precambrian, blowing that entire paragraph out of the water.

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Absolute & utter hypocrisy.

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So if you aren't going to be a hypocrite you have to drop the non-fossilisation argument, or withdraw the objection of "fully formed fossils" appearing in the GC. Which is it?

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And I redraw your attention to your missing fossil inconsistency.

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No, no, NO!!!! Why is this so hard for you to understand?

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No, no, NO!!!

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You really do have a comprehension problem, don't you?

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A complete non-answer.

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Crashfrog: For God's sake, DNA. Say it in one post or don't say it at all, you know? This is excessive badgering.

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Splitting up a reply into multiple posts that address individual topics is not only badgering, but excessive badgering??? Please Crashfrog, get a life!The one doing any badgering here is you Crashfrog.Of the dozens of points raised, addressed, and discussed, you did not reference any of them. All you did was begin waging another of your "badger DNA" campaigns.This is just the latest in your typical gorilla warfare tactics.If you have something of worth to contribute to the discussion, then by all means, please do so. If not, your "contributions" do no good, except to shows us your ability to hold a personal grudge indefinitely.[This message has been edited by DNAunion, 04-11-2004]

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Black: Well, before I start the message I would like to say a couple things. DNAUnion has make quite a lot of attacks on my character. He has repeatedly called me dishonest.

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That's pretty misleading, but I'll ignore that problem of yours for now.The thing is, I have also shown WHY your actions fit the actual "charges" I have made. They aren't empty charges I fabricated out of thin air, they're supported by facts.1) You stuffed words into my mouth that I absolutlely did not say and then you pretended to show me to be wrong by attacking your words instead of mine.2) I called you on it and explicitly stated that I did not say what you claimed I had.3) Instead of your simply admitting your error - as an honest person would do - you went further by tying to claim I had surely said it - even though I did not and I explicitly stated I did not.4) I pointed out the error in your "logic" that "showed" I had said it.5) I've even shown now that YOUR OWN STATEMENTS about autocatalysis and self-replication refute the logic you used.You did not have, and still do not have, any case for your stuffing words into my mouth, or your subsequent compounded disingenuousness.**********************************************Now, since YOUR OWN STATEMENTS refute your own offered logic for claiming I said what I clearly did not, the question remains: is your act of stuffing words into my mouth an act of dishonesty on your part, the result of a moment of stupidity on your part (since not even you can make your claim make sense), or some third, less obvious option? Just tell us and the matter will be settled.[This message has been edited by DNAunion, 04-11-2004]

EDITED: AbbyLeever moved his post so that it ended up below my reply to it: so I have moved my response so that it once again follows the statements it addresses.[This message has been edited by DNAunion, 04-11-2004]

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DNAunion: Odd, I didn't see a similar warning given to Mark24 for the following comments he made in another thread.

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Crashfrog: Interesting... do you truly believe that "somebody else did it too!" constitutes a mitigating circumstance?

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No, but I do think it is odd that some people can use obscenities - such as you calling me an asshole and Mark24 using "the 'F' word" - and no moderators object, and that some people can make aggressive statements about the inabilitiy of their opponents to understand simple matters ("Absolute & utter hypocrisy", "No, no, NO!!!! Why is this so hard for you to understand?", "You really do have a comprehension problem, don't you?", etc.) - and no moderators object: but when I say the kinds of things the moderator quoted above it must be pointed out and I must be warned.

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Crashfrog: Do you believe that's a mature response?

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No, I don't believe yours was a mature response! :-)In fact, I don't believe MOST of your responses to me are mature. You've taken up a badgering posture: you don't address any of the points I raise, you just hide in the shadows and sporadically snipe in a gorilla warfare-like manner.[This message has been edited by DNAunion, 04-11-2004]