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Author | Topic: Abiogenesis | |||||||||||||||||||||||||||||||||||||||||||||||||||
NosyNed Member Posts: 9004 From: Canada Joined: |
Also, If there was no or little oxygen in the early Earth atmosphere, then what would protect the amino acids and the potential proteins from UV light (oxygen produces ozone)? Some questions should be left up to the reader, so to speak. This one is definitly not "rocket science". Why don't you think it over for a few minutes and suggest a couple of reasonable answers for yourself?
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JonF Member (Idle past 197 days) Posts: 6174 Joined: |
DNA, is there really a need for the ad hominems? Nitpicking, those aren't ad hominems, they're just insults.
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DNAunion Inactive Member |
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?
[This message has been edited by DNAunion, 04-08-2004]
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DNAunion Inactive Member |
quote: quote: 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.
quote: 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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DNAunion Inactive Member |
quote: quote: quote: 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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DNAunion Inactive Member |
quote: quote: 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?
quote: 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.
quote: 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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DNAunion Inactive Member |
quote: Which time? Your original?
quote: That’s wrong: RNA is not even made of amino acid chains.
quote: You still haven’t supported your (3) - either the original or your altered version.
quote: Agreed...still.
quote: That’s the theory: where’s your support that such could occur naturally?
quote: Who said PNA actually was the precursor to RNA? Again, theory, not fact.
quote: Yes, RNA can store genetic information.
quote: Yes, it can (although the ribozymes that spliced out internal sequences — those originally discovered by Cech — are not technically catalysts).
quote: 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.
quote: Those are the piececs of the puzzle? What happened to your original list?
quote: 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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Muhd Inactive Member |
Well, I would say that their was a big slab of rock or something that blocked the UV light from the "chemical soup", but this is also a problem since it is generally thought that lightning was involved in the formation of amino acids.
It is really the evolutionists job to do the speculation, since I don't think that life arose in this manner.
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JonF Member (Idle past 197 days) Posts: 6174 Joined: |
Well, I would say that their was a big slab of rock or something that blocked the UV light from the "chemical soup", but this is also a problem since it is generally thought that lightning was involved in the formation of amino acids. Ever considered how well UV light penetrates water?
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RAZD Member (Idle past 1434 days) Posts: 20714 From: the other end of the sidewalk Joined: |
ever consider how UV penetrates the atmospheres of venus and jupiter?
the whole atmosphere was different. we are limited in our ability to understand by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}
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Black Member (Idle past 5213 days) Posts: 77 Joined: |
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.
quote: Lets start with #1. This was the one point that DNAUnion did not dispute. However, some others on this forum have questioned this statement:
quote: 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:
quote: 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:
quote: 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:
quote: 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:
quote: 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:
quote: DNA, I explained what I said earlier in this post. I assure you I am honest.
quote: 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.
quote: 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).
quote: 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.
quote: 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.
quote: 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.
quote: What kind of RNA polymer are you looking for?
quote: 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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DNAunion Inactive Member |
quote: 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.
quote: 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?
quote: Not really. The RNA World theory doesn’t require self-replicating peptides at all.
quote: That peptide cannot self-replicate. Put it in a pool of free amino acids and it cannot construct a copy of itself.
quote: So it has no direct relevance to abiogenesis.
quote: It is not a self-replicating peptide: it cannot build a copy of itself from its monomers.
quote: 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.
quote: No, it doesn’t support your #2 because the peptide cannot self-replicate.
quote: 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]
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DNAunion Inactive Member |
For some odd reason (muddy the waters?) Black mixed in link to RNA probability calcultaion with his discussion of peptides.
quote: Here’s what Black is apparently referring to from that link.
quote: 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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DNAunion Inactive Member |
quote: 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:
quote:
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DNAunion Inactive Member |
quote: Then perhaps you need to rephrase another part of your original post so that it is not misleading.
quote: Maybe the part about we would expect to observe certain things should be taken out or rephrased.
quote: 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.
quote: 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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