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. I assure those of you reading this that through this entire discussion, I have tried to be very honest. I started posting hoping to have a real discussion about science. I came ready to listen to whatever DNAUnion or anyone else had to say. I was (and still am) ready to change my mind about anything that I am wrong about--if I really am wrong about them.
Did I really come across as dishonest? Did anyone besides DNA think so? If so, than I apologize. In the future I will try to be more clear about what I write. I'm new around here so please bear with me. Perhaps I am not as polished in my writing skills as others, but I assure you I am not dishonest.
Now, I will get back to my discussion with DNAUnion. I will start again from the beginning so everyone will see I am not trying to set up strawmen or be dishonest in any way.
Oh, before we start. I will freely admit that abiogenesis has NOT been observed. I believe that this is perhaps one of DNAUnion's problems, s/he thinks I am trying to prove that it has been observed. That is not my intention. All I am saying is the evidence we have indicates that it is possible and probably happened.
So let us start with what I originally posted.
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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
Lets start with #1. This was the one point that DNAUnion did not dispute.
However, some others on this forum have questioned this statement:
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Really? I would like to see the support of this. I was under the impression that any amino acids formed naturally would be oxidized by oxygen in the atmosphere.
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I would like to know your sources of this information.
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It is really the evolutionists job to do the speculation, since I don't think that life arose in this manner.
Simply speculating is not science. I would have great doubts about evolution if all scientists did was speculate. However, that is not all they do--they also search for facts which help them determine the truth.
For example, one way to tell if there was oxygen in the past is by checking for branded iron formations. Banded iron formations are layers of hematite (Fe2O3) and other iron oxides deposited in the ocean 2.5 to 1.8 billion years ago. Most scientists believe that oxygen was introduced into the atmosphere, for the first time in significant quantities, beginning about 2.5 billion years ago when photosynthesis evolved. This caused the free iron dissolved in the ocean water to oxidize and precipitate. Thus the banded iron formations mark the transition from an early earth with little free oxygen and much dissolved iron in water to present conditions with lots of free oxygen and little dissolved iron. This is one of the ways we can tell there was very little oxygen in the early atmosphere.
Now, let us move on to #2. 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?
DNAUnion, apparently thought that there was no evidence to support my statement, and concluded that I was wrong. I believe there is evidence. Let me try to explain once again.
First let me explain why self-replicating peptides were a prediction of most abiogenesis theories. We have established that amino acids can be formed naturally. But amino acids are not life. Just a bunch of amino acids floating around would do no good. 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.
As you can see self-replicating peptides have much to do with abiogenesis theories.
Now, do these self-replicating peptides exist? Yes. The first one to be discovered was the GL peptide. I described it before but I will review again:
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There have been several self-replicating peptides discovered. The one I referenced was a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4, can auto-catalyze its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution.
It uses a single-stranded DNA hexamer and its two trimer fragments) are based on a polymer catalyzing its own formation from two fragments.
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A 32-residue alpha-helical peptide based on the leucine zipper motif of GCN4 is shown to act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide bond condensation of a 15-residue and 17-residue constitutional peptide fragments in neutral and dilute aqueous solutions.
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.
The point I was trying to make by discussing this peptide was that self-replicating peptides are possible. 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.
However, this peptide does demonstrate that my statement #2 is true. The 3 peptides required could, in theory, have synthesized naturally. Please do not misunderstand me. I am not saying that this is what happened. I am saying that the existence of this peptides and what we know about peptide synthesis does technically prove that my statement #2 is correct.
But now, perhaps you asking, if this peptide was not the first one, what was? Are we any closer to finding it? The answer is yes.
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.
Something interesting about probabilities:
http://www.talkorigins.org/origins/postmonth/apr98.html.
Something else interesting. The Chmielewski group has discovered how to convert a sixteen amino acid peptide into an eighty amino acid protein in one step. I don't know much about this yet. I'll try to post more about it.
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:
discover: To learn about for the first time in one's experience: discovered a new restaurant on the west side.
I kind of feel silly arguing about this though since it is only a game of words.
Now let us move on to #3. DNAUnion also challenged this. I will admit that this has not been observed. However, the evidence once again indicates that it is possible. I said previously that I meant peptide nucleic acid, not amino acids. I have edited my first post to reflect that.
The evidence supports that peptide nucleic acid can form naturally:
Peptide nucleic acid (PNA) consists of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. AEG can be produced directly in electric discharge reactions from CH4, N2, NH3, and H2O. Electric discharges also produce ethylenediamine, as do NH4CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH4CN polymerization in the presence of glycine leads to the adenine and guanine-N9-acetic acids, and the cytosine and uracil-N1-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine. The difference is that it has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides based on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides. However, RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa.
DNAUnion has recently posted this:
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You still haven’t supported your (3) - either the original or your altered version.
Unfortunately I cannot respond to this because I am not sure what s/he is talking about. What altered version?? What have not I supported?
Perhaps if s/he will clarify this we will be able to discuss it better.
Now we will move on to #4. DNAUnion once again disputed this.
I will bring out the dictionary again.
autocatalysis: Catalysis of a chemical reaction by one of the products of the reaction.
replication: The process by which genetic material, a single-celled organism, or a virus reproduces or makes a copy of itself
So auto-catalysis is replication because one of the products of it is the catalyzer--it has made a copy of itself. I described one such auto-catalyzer. Let me review it again:
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what was originally thought was that "DNA makes RNA makes protein." Obviously, if all three of these are needed at the same time for life, it causes problems for abiogenesis. However, we now know that certain things do not need DNA but instead reverse transcribe their RNA. So we can illiminate DNA from that formula. Can we also illiminate proteins? Well, we also now know that RNA can do the function of proteins and act as an enzyme
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Hammerhead ribozymes are small, catalytic RNAs that undergo self-cleavage of their own backbone to produce two RNA products. All hammerhead ribozymes contain three base-paired stems and a highly conserved core of residues required for cleavage. The cleavage reaction proceeds by an attack of a 2' hydroxyl oxygen of a catalytic site cytosine on the phosphorus atom attached to the 3' carbon of the same residue, breaking the sugar phosphate backbone and producing a 2', 3' cyclic phosphate. As for protein ribonucleases, a metal ion bound in the active site (Mg++) stabilizes the ionized form of the 2' hydroxyl oxygen, promoting the catalytic attack.
The hammerhead ribozyme coordinates Mg++ in the proper geometry to stabilize the trigonal bipyramid intermediate formed by attack of the 2-OH on the phosphate. The end products are a 2,3 cyclic phosphate and a 5-OH.
In conclusion, I still believe that all four of my statements were correct.
However, before ending, I would like to directly address a few of the comment DNAUnion made on his most recent postings:
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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.
DNA, I explained what I said earlier in this post. I assure you I am honest.
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Black stuffed words in my mouth, setup a strawman, then knocked it down, then pathetically pretended he didn't do any of it. The best explanations involve an act of stupidity and/or dishonesty: you got a better explanation?
I apologize if you got that impression, but I did not stuff words in your mouth or set up a strawman. Perhaps I am not as intelligent as some people, but I am not dishonest.
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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.
Peptidyl transferase is catalyzing RNA, which is exactly what I was talking about. It is very revelent. I was not trying to point out a shortcoming in your knowledge (nor was I changing the subject).
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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.
Correct. You misunderstood what I was saying. I did not mean to say that this exact peptide was the first one. It is simply a self-replicating peptide. I explained about this above.
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And the 32-aa peptide we’ve been discussing has no relevance to abiogenesis since it cannot actually self-replicate.
self-replication: Replicating oneself or itself
What does the GL peptide do (and Chmielewski's peptide)? It replicates itself (I put the definition of replicate somewhere above).
So yes it is self-replication.
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That’s wrong: RNA is not even made of amino acid chains.
I said earlier that I wrote the wrong thing (didn't you read my post?). I meant nucleic acids not amino acids. I will edit my post to let people know I made that mistake.
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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.
What kind of RNA polymer are you looking for?
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Those are the piececs of the puzzle? What happened to your original list?
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Did you drop it because 3 out of 4 hadn’t been demonstrated?
No, I did not drop anything.
I have explained what I said before. As you can see I did not try to be dishonest at anytime. As you can also (hopefully) see, I have supported my statements, and my conclusion remains the same. I believe anyone looking at the facts should come to the same conclusion. Do you disagree? If you would like to discuss more about this, let me know.
--Black
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