RNA World
by Bradford1989 Nobel Laureate in Chemistry Sidney Altman authored 'The RNA World.' The opening paragraphs:
The phrase "The RNA World" was coined by Walter Gilbert in 1986 in a commentary on the then recent observations of the catalytic properties of various RNAs. The RNA World referred to an hypothetical stage in the origin of life on Earth. During this stage, proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task of genetic information and the full range of catalytic roles necessary in a very primitive self-replicating system. Gilbert pointed out that neither DNA nor protein were required in such a primitive system if RNA could perform as a catalyst. At that time, it had only been demonstrated that RNA could cleave or ligate phosphodiester bonds. Nevertheless, as is a frequent occurrence in science, a general hypothesis was constructed from a few specific instances of a phenomenon. This hypothesis proved to be very effective in stimulating thought about the origin of life on Earth. Ensuing discoveries of other natural catalytic RNAs that could cleave and ligate phosphodiester bonds, and the very recent observation that the region surrounding the peptidyl transferase center of a bacterial 50S ribosomal subunit contains RNA and no protein, further buttress the hypothesis. Finally, the so-called "evolution in vitro" methodology, which is able to scan an enormous number of nucleic acid sequences in vitro for any given function, has revealed that RNA, indeed, can have many different catalytic functions as so can, presumably, DNA.
DNA and RNA also carry information. How did the described catalytic function create information? If it did not then how did the information originate.
Smokey offered references. The abstract of one follows:
Would the existence of ribozymes having "substrate recognition, product formation, rate acceleration, and turnover" answer the information question. We know the end of this story- a cell. Is this the type of specificity required to fill in details like the generation of information rich DNA? If not where are they? Back to Altman.
On further reflection, many doubts have been raised about whether or not the original genetic/catalytic material could have been RNA as we know it today because extreme conditions on the primitive Earth might have led to the rapid chemical degradation of RNA. Nevertheless, even if the precise chemical nature of the early genetic/catalytic material differed from present-day RNA, it seems reasonable to conclude that the RNA World did exist at some time. If very primitive life on Earth did not arise until about 3.5 billion years ago, there was, perhaps, a period of 0.5 billion years in which to sample many polymer sequences that originally arose through non-biochemical mechanisms and that ultimately evolved directed the first self-replicating systems.
What was the nature of these self-replicating systems? Is there a pathway to cellular systems containing enough descriptive information to evaluate?
October 17th, 2006 at 2:56 pm
The existence? No. The ability to derive such ribozymes from random sequences by selection answers your "information question."
Collections of RNAs, of course. What do you think "The RNA World" means?
Comment by Smokey — October 17, 2006 @ 2:56 pm
October 17th, 2006 at 3:08 pm
Why would selection favor sequences leading to protein synthesis?
What was the nature of these self-replicating systems?
Collections of RNAs, of course, as described in Altman's Nobel lecture.
That's what I thought. Is there a pathway to cellular systems containing enough descriptive information to evaluate?
Comment by Bradford — October 17, 2006 @ 3:08 pm
October 17th, 2006 at 3:34 pm
RNA is more labile than protein.
That required thinking on your part? It wasn't clear from the text you cited?
Yes. In fact, it has orders of magnitude more descriptive information than anything advanced by an ID advocate.
Please don't cite Dembski, as he's never had the courage to use any of his mathematical descriptions to evaluate a biological system or to make an experimental prediction.
Comment by Smokey — October 17, 2006 @ 3:34 pm
October 17th, 2006 at 3:57 pm
Bradford, I don't know if it was explained to you when you joined our illustrious crew, but YOU have the power in your own threads to govern the discussion as you will.
That means you may make use of that "Move to Memory Hole" button at the bottom of posts whenever you like. §;o)
Comment by Joy — October 17, 2006 @ 3:57 pm
October 17th, 2006 at 4:03 pm
To Joy and Bradford,
For what it is worth, I agree that Daniel's post is worthy of going to the memory hole.
Please feel free to put this one there too.
Comment by Thought Provoker — October 17, 2006 @ 4:03 pm
October 17th, 2006 at 4:24 pm
So you think they'd stoop to dodging such a simple, albeit inconvenient, question like "how do you know it looks designed"?
Comment by Daniel — October 17, 2006 @ 4:24 pm
October 17th, 2006 at 4:31 pm
Hey Smokey and Bradford,
It seems that this paper is relevant to your discussion. They discuss the RNA world as well as SELEX. It is available at Science Direct. Could you consider to read it and provide some comments?
Self-organization vs. self-ordering events in life-origin models
David L. Abel, , and Jack T. Trevors, 1,
Comment by Albert Voie — October 17, 2006 @ 4:31 pm
October 17th, 2006 at 4:48 pm
Albert,
Why does it seem to be relevant?
Does the paper contain any new data? If not, why would it be worth $30?
Comment by Smokey — October 17, 2006 @ 4:48 pm
October 17th, 2006 at 4:57 pm
Albert,
It looks like an interesting paper - too bad it's only out in advanced press, and not available through my institution till december. But I checked out the previous two papers by Abel and Trevors - in particular, "Chance and necessity do not explain the origin of life" appears very critical about to-date explanations of abiogenesis and storage of hereditary material as nucleic acids. But, before you IDers go and get your hopes up, it's funded by the Gene Emergence Project, which is part of the Origin-of-Life Foundation. They describe themselves as follows:
Comment by Daniel — October 17, 2006 @ 4:57 pm
October 17th, 2006 at 6:40 pm
Is there a pathway to cellular systems containing enough descriptive information to evaluate?
Yes. In fact, it has orders of magnitude more descriptive information than anything advanced by an ID advocate.
That's not what I asked. Are there pathways. We know what real pathways look like. Identifiable enzymes and substrates related to real functions. Anything like this or is this where faith in the outcome takes over?
Comment by Bradford — October 17, 2006 @ 6:40 pm
October 17th, 2006 at 6:46 pm
Thanks Joy. It gets personal when I'm misquoted with it is designed "because it looks designed."
Comment by Bradford — October 17, 2006 @ 6:46 pm
October 17th, 2006 at 6:56 pm
Why would selection favor sequences leading to protein synthesis?
RNA is more labile than protein.
That's a comparative description not an answer as to why sequences enabling protein synthesis would be favored by a selection process.
Comment by Bradford — October 17, 2006 @ 6:56 pm
October 17th, 2006 at 7:03 pm
No, it's a contrast that explains why organisms that use proteins for enzymes would have an advantage over those that use RNA.
It's a succinct answer to your question. I also answered your question above.
Are there any pathways with identifiable enzymes and substrates related to real functions for which you can describe their design?
And why would "pathways" necessarily involve enzymes and substrates? Aren't there signal transduction pathways that involve things like receptors and ligands and ions?
Comment by Smokey — October 17, 2006 @ 7:03 pm
October 17th, 2006 at 7:08 pm
LOL I didn't know that was getting personal, but let's see what you actually said:
Sorry, but I thought you said even a bushman could tell, by looking at it, that certain biological features were designed. I asked how could he, or anyone, tell. You haven't answered. I guess it was too tough a question.
Comment by Daniel — October 17, 2006 @ 7:08 pm
October 17th, 2006 at 7:12 pm
That answers a different question than the one I posed. Before a protein can benefit an organism it must be synthesized. What is the selective value of a single tRNA aminoacyl synthetase? How does this system evolve incrementally?
Comment by Bradford — October 17, 2006 @ 7:12 pm
October 17th, 2006 at 7:18 pm
I said the bushman "could utilize his analytical skills to distinguish an object that had changed or evolved from one that resulted from intelligent input." Using analytical skills does not equate to it is designed because it looks designed. Your questions are fashioned on your deliberate misunderstanding. If you can't control it then find something else to do.
Comment by Bradford — October 17, 2006 @ 7:18 pm
October 17th, 2006 at 7:22 pm
You're the one endorsing a catalytic jump start for OOL but again are there identifiable pathways?
Comment by Bradford — October 17, 2006 @ 7:22 pm
October 17th, 2006 at 7:25 pm
Amino acids, peptides, oligopeptides are all cofactors and chaperones for RNAs and RNA-catalyzed processes. The selective value of an RNA system that can string together small peptides is obvious.
As for increments, Yarus et al. touch on that (albeit perhaps by implication).
Contrary to the proclamations of almost everyone here, Darwinian forces were most certainly in play from the very get-go in the prebiotic world. That's why RNA degradation (not uncatalyzed breakdown, mind you, but biotic nucleolytic activity) is so close to the heart of the extant RNA World, and why proteolysis factors so heavily in life as we know it (as well as Life before there was LAWKI). Understand this and lots of other misconceptions fall by the wayside.
Comment by Art — October 17, 2006 @ 7:25 pm
October 17th, 2006 at 7:51 pm
OOL "explanations" are a skip and jump game. Reference processses and systems without providing real descriptions of how they were generated and then use them to explain selective value. This becomes real when you can reference experiments showing actual rather than imaginary functional precursor cells with actual rather than imaginary processes consisting of interacting RNAs.
Contrary to the proclamations of almost everyone here, Darwinian forces were most certainly in play from the very get-go in the prebiotic world. That's why RNA degradation (not uncatalyzed breakdown, mind you, but biotic nucleolytic activity) is so close to the heart of the extant RNA World, and why proteolysis factors so heavily in life as we know it (as well as Life before there was LAWKI). Understand this and lots of other misconceptions fall by the wayside.
Proteolysis factors are sufficiently explained by metabolic selection. The RNA world take is convenient but unnecessary speculation.
Comment by Bradford — October 17, 2006 @ 7:51 pm
October 17th, 2006 at 7:51 pm
Bradford :
So how do your "analytical skills" arrive at such conclusions? (i.e. my still unanswered question, how can you tell?)
Comment by Daniel — October 17, 2006 @ 7:51 pm
October 17th, 2006 at 8:01 pm
So how do your "analytical skills" arrive at such conclusions? (i.e. my still unanswered question, how can you tell?)
As I've repeatedly explained a rational conclusion that natural forces alone are insufficient to generate a complex and specified outcome x is an indicator of intelligent causality. This message is both complex and specified. So are the symbolic sequences of the Rosetta Stone. So too are the nucleotide sequences in a functional genome. Scramble the sequences and you retain complexity while losing specificity and function.
Comment by Bradford — October 17, 2006 @ 8:01 pm
October 17th, 2006 at 8:11 pm
Bradford:
Ok, natural forces insufficient. Got it. You've tested natural forces then, and have found them insufficient? I only know of one study that tested that, Behe and Snokes (2004), and they found it sufficient in their case.
So, who's tested natural forces and found them insufficient?
Comment by Daniel — October 17, 2006 @ 8:11 pm
October 17th, 2006 at 8:22 pm
Insufficient to generate life. That's the contention which contrasts with abiogenesis. The jury may be out for both sides although we clearly lean in different directions.
Comment by Bradford — October 17, 2006 @ 8:22 pm
October 17th, 2006 at 8:36 pm
I told you before not to misquote me.
Yes, who's found natural forces insufficient to generate life?,
Who has found otherwise? As I said the jury is out.
Comment by Bradford — October 17, 2006 @ 8:36 pm
October 17th, 2006 at 8:46 pm
Seriously, just answer the question. Please.
Comment by Daniel — October 17, 2006 @ 8:46 pm
October 17th, 2006 at 8:53 pm
Bradford:
So, your stance seems to be "the experiment has not been done, thus design".
You'll fit right in at TelicThoughts.
In the meantime, the process of HTR will continue to tell us just how life arose.
So, if I understand you correctly, Bradford, you're claiming that an understanding of the origins of the central core processes of life on earth is unnecessary.
Um, OK.
Comment by Art — October 17, 2006 @ 8:53 pm
October 17th, 2006 at 8:54 pm
Why are you avoiding the question?
Comment by Daniel — October 17, 2006 @ 8:54 pm
October 17th, 2006 at 9:03 pm
So, your stance seems to be "the experiment has not been done, thus design".
Experiments have been done and results do not explain how information arises or how biological systems arise to say nothing of generating putative precursor cells.
In the meantime, the process of HTR will continue to tell us just how life arose.
The process will give you just enough upon which to extrapolate mightily.
Proteolysis factors are sufficiently explained by metabolic selection. The RNA world take is convenient but unnecessary speculation.
So, if I understand you correctly, Bradford, you're claiming that an understanding of the origins of the central core processes of life on earth is unnecessary.
No. I'm asking you to acknowledge the insufficiency of evidence supporting your claims.
Comment by Bradford — October 17, 2006 @ 9:03 pm
October 17th, 2006 at 9:24 pm
Too much "reality-based" reasoning?
Comment by Daniel — October 17, 2006 @ 9:24 pm
October 17th, 2006 at 9:26 pm
Too much "reality-based" reasoning?
Too much immaturity on your part. Take the night off.
Comment by Bradford — October 17, 2006 @ 9:26 pm
October 17th, 2006 at 9:27 pm
Bradford:
Um, with due respect, Bradford, you're the one who's insisting that others here accompany you in denying any and all experimental evidence that confounds your claims, that contradicts your creed. We don't have unedited slow-motion video of each and every nanosecond since the beginning of time - the only evidence that teleologists will accept. But the results that have been generated by HTR point pretty clearly in one direction. There's nothing we can do for those who are offended by the directions that research take.
You are welcome to deny the facts (such as those of Yarus et al. - studies, not a study, that you have tried to bluff your way around) - after all, it's your blog. And you're free to insist that others toe your line. But I don't think you should expect others to accept any of this.
Comment by Art — October 17, 2006 @ 9:27 pm
October 17th, 2006 at 9:29 pm
Immaturity? I'm not the one deleting non-insulting comments. Where did I utter a profanity, or insinuate anything inappropriate.
Ok, I'm sorry that you deleted my comments. Oh, wait…
Comment by Daniel — October 17, 2006 @ 9:29 pm
October 17th, 2006 at 9:39 pm
Untrue. I state my view and insist on nothing from you other than civility.
We don't have unedited slow-motion video of each and every nanosecond since the beginning of time - the only evidence that teleologists will accept.
I'll accept data that lives up to its billing. There's a long way between what you have introduced and a cell.
But the results that have been generated by HTR point pretty clearly in one direction. There's nothing we can do for those who are offended by the directions that research take.
I'm not offended Art. I'm just not going to go along with your insistence as to the only legitimate interpretation.
You are welcome to deny the facts (such as those of Yarus et al. - studies, not a study, that you have tried to bluff your way around) - after all, it's your blog.
I do not deny the facts of Yarus only their restrictive interpretation.
And you're free to insist that others toe your line. But I don't think you should expect others to accept any of this.
Art you are free to believe whatever you wish. I would not have it any other way. That's a part of the American cultural heritage I value greatly; having lived in countries where it is not valued.
Comment by Bradford — October 17, 2006 @ 9:39 pm
October 17th, 2006 at 9:46 pm
Bradford,
How is asking simple questions uncivil? Please, now will you answer why you think ribozymes or nucleic acids look too complicated to have been generated by natural forces?
Comment by Daniel — October 17, 2006 @ 9:46 pm
October 17th, 2006 at 9:50 pm
And sorry Art, I know you're trying to rationalize with Bradford and I'm jumping in. But really, I just want to ask simple, polite questions, that appear to induce severe cognitive dissonance for some reason.
Comment by Daniel — October 17, 2006 @ 9:50 pm
October 17th, 2006 at 9:54 pm
Please, now will you answer why you think ribozymes or nucleic acids look too complicated to have been generated by natural forces?
Why can't you cease asking leading questions? I'm not claiming that natural forces could not generate nucleic acids. What I have maintained is that more than nucleic acids are needed. A minimal genome requires functional sequence specificity. That is what has not been demonstrated.
Comment by Bradford — October 17, 2006 @ 9:54 pm
October 17th, 2006 at 9:55 pm
Bradford
Seriously, Bradford. It's pretty clear that you have not an inkling of what Yarus did. It's both annoying and revealing that you continue to comment on this area of research.
It's also revealing that you cannot bring yourself to admit what is undeniable - that the occurrence of codons/anticodons in amino acid-binding RNAs is evidence for a stereochemical basis for the genetic code - evidence that supports the hypothesis that physical associations between RNA and amino acid lie at the heart of the genetic code. There is no question that these results are evidence for these things, and to deny this very modest statement is to resort to stonewalling.
The civil thing to do would be to acknowledge that the discussion has gone beyond your familiarity with the subject and to sit back and strive to learn some new things. Better yet, ask some questions that flow from the items being mentioned (rather than insist that the facts do not exist).
Comment by Art — October 17, 2006 @ 9:55 pm
October 17th, 2006 at 10:00 pm
Finally! We're getting somewhere!!!!
Before you said that natural forces were insufficient to generate such biological features. Now you're saying that natural forces haven't been shown to be sufficient for such features thus far. There's a huge difference there, and I'll agree totally with that.
Of course that only implies that "we don't know how the OOL happened, but you think it was designed." I disagree, and I'm curious as to why you think that, but if you'd prefer I'll leave it at that.
Comment by Daniel — October 17, 2006 @ 10:00 pm
October 17th, 2006 at 10:16 pm
Bradford: "You're the one endorsing a catalytic jump start for OOL but again are there identifiable pathways?"
Where did I endorse a "catalytic jump start for OOL," Bradford? Have you considered asking questions before jumping to absurd conclusions?
"That's a comparative description not an answer as to why sequences enabling protein synthesis would be favored by a selection process."
No, it was a contrast, and a direct answer to your question.
"This becomes real when you can reference experiments showing actual rather than imaginary functional precursor cells with actual rather than imaginary processes consisting of interacting RNAs."
And your position must therefore be entirely fake, since you don't do experiments? In what way is the derivation of ribozymes by selection of random polynucleotides "imaginary"
"Proteolysis factors are sufficiently explained by metabolic selection."
Really? What's your explanation, then?
"As I've repeatedly explained a rational conclusion that natural forces alone are insufficient to generate a complex and specified outcome x is an indicator of intelligent causality."
But you haven't offered any rationality to support your conclusion. Mostly, you've denied/ignored the existence of much of the most basic, relevant data.
"Scramble the sequences and you retain complexity while losing specificity and function."
Selection makes scrambled sequences into specific, functional ones. That's reality.
"Insufficient to generate life. That's the contention which contrasts with abiogenesis. The jury may be out for both sides although we clearly lean in different directions."
But your leaning is associated with ignorance and/or blatant misrepresentation of the relevant data.
"Who has found otherwise? As I said the jury is out."
You've said very different things elsewhere, like "Nucleic acids are functional based on their codon specificity."
"Experiments have been done and results do not explain how information arises or how biological systems arise to say nothing of generating putative precursor cells."
Which experiments, exactly? Are you familiar with all the relevant ones? I ask because you were trying to claim that the RNA in the RNA World hypothesis coded for something else.
"I'll accept data that lives up to its billing. There's a long way between what you have introduced and a cell."
Why didn't you accept that the function of RNAs isn't dependent upon codons?
"I'm not offended Art. I'm just not going to go along with your insistence as to the only legitimate interpretation."
There's a big difference between interpretation and ignoring/fudging the evidence.
"I do not deny the facts of Yarus only their restrictive interpretation."
Which facts (from which papers) and which interpretation?
Comment by Smokey — October 17, 2006 @ 10:16 pm
October 17th, 2006 at 10:17 pm
It's also revealing that you cannot bring yourself to admit what is undeniable - that the occurrence of codons/anticodons in amino acid-binding RNAs is evidence for a stereochemical basis for the genetic code - evidence that supports the hypothesis that physical associations between RNA and amino acid lie at the heart of the genetic code. There is no question that these results are evidence for these things, and to deny this very modest statement is to resort to stonewalling.
Art, I'm not denying that Yarus can be presented as evidence. I'm denying the sufficiency of the evidence. There is a very tried and true way to overcome doubters. A study that goes beyond Yarus and demonstrates a system coming together. You want me to conclude that we have sufficient evidence for a synthesis mechanism that includes the code and the tRNAs, tRNA aminoacyl synthetases, ribosomes et. al. You and the others would not be spending the time and effort were the evidence that convincing. It is simply not.
Comment by Bradford — October 17, 2006 @ 10:17 pm
October 17th, 2006 at 10:25 pm
"Scramble the sequences and you retain complexity while losing specificity and function."
Selection makes scrambled sequences into specific, functional ones. That's reality.
Selection enables changes in an existing, functional genome that favor the survival of an organism. That's reality. Selection from ribozymes to cells is the stuff of science fiction until and unless demonstrated otherwise.
Comment by Bradford — October 17, 2006 @ 10:25 pm
October 17th, 2006 at 10:41 pm
Bradford:
Huh?
You are now claimimg that the data that tells us that the RNA World is at the core of life as we know it in unconvincing? Do you really know what you are claiming? Do you know how wrong you are?
Beyind the most recent Nobel Prize in Medicine, are you aware of what processes and constituents make up by far the bulk of stuff in a cell? Do you know what a cell devotes a majority of its energetic resources to?
"The RNA World lies at the core of life" is not an assertion that is lacking for support. Rather, it is probably the most correct way to view life. The data tell us as much.
And I have found that it is a good jumping off point for tying together numerous biological phenomena. Such as the OOL. There is no escaping the fact that, somehow and somewhere, the OOL involved the origination of an RNA World. To deny this is to in essence deny that RNA exists and has central functions in LAWKI.
Comment by Art — October 17, 2006 @ 10:41 pm
October 17th, 2006 at 10:47 pm
C,mon Art. Denying the sufficiency of evidence indicating that ribozymes lead to cells equate to denying RNA? I'm far from the only one doubting OOL paradigms.
Comment by Bradford — October 17, 2006 @ 10:47 pm
October 17th, 2006 at 10:51 pm
Just to interject another comment - Josh Rosenau quoted a slide from a talk Dawkins gave at Kansas University, and whatever you may think of Dawkins, this slide really very accurately portrays the discussion going on here:
It's too bad, but science and deductive reasoning simply don't work like that. Yet, that's the state of the argument between IDers (including this discussion) and biologists.
Comment by Daniel — October 17, 2006 @ 10:51 pm
October 17th, 2006 at 10:55 pm
4. I can't understand how Theory A explains X
Only in the matter of OOL there is no explaining x.
Comment by Bradford — October 17, 2006 @ 10:55 pm
October 17th, 2006 at 10:57 pm
Hello All,
I feel a little like Eris with a Golden Apple.
I am interested in seeing the reaction to this chapter of RNA World I found a link to…
http://rna.cshl.edu/content/fr...
Comment by Thought Provoker — October 17, 2006 @ 10:57 pm
October 17th, 2006 at 11:15 pm
Bradford, one more thing: why do you refer to Yarus singularly when Art pointed you to "Yarus et al."
Do you know what "et al." means?
Comment by Smokey — October 17, 2006 @ 11:15 pm
October 17th, 2006 at 11:18 pm
Bradford: "Selection enables changes in an existing, functional genome that favor the survival of an organism. That's reality."
Bradford, you cited selection in vitro that produced functional enzymes and pasted the abstract. No genomes were involved in this bit of reality.
Do you even bother read the stuff you cut and paste?
Comment by Smokey — October 17, 2006 @ 11:18 pm
October 17th, 2006 at 11:26 pm
Hi Smokey,
I hadn't thought of that one. Then again, I haven't had as much experience debating with Bradford as you have.
Frankly, I would be extremely impressed if you two could agree with the bulk of what is said in these few pages of Yarus' work.
Check that, "extremely impressed" is putting it way too mildly. More like knock-me-over-with-a-feather-shock. Having Bradford say "is that all?" would be an implicit agreement with what was said. That would be impressive enough.
Comment by Thought Provoker — October 17, 2006 @ 11:26 pm
October 17th, 2006 at 11:39 pm
Bradford: "Selection enables changes in an existing, functional genome that favor the survival of an organism. That's reality."
Bradford, you cited selection in vitro that produced functional enzymes and pasted the abstract. No genomes were involved in this bit of reality.
Smokey you observed machine parts strewn on the ground. They need to be assembled and working in concert. If selection is analogous to the assembler you still have workable parts on the ground but no machine to show for it.
Do you know what "et al." means?
Get a life Smoke. Do you know what Halt die Klappe means?
Comment by Bradford — October 17, 2006 @ 11:39 pm
October 18th, 2006 at 12:15 am
Here is the "et al." and most of the chapters in RNA World…
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
http://rna.cshl.edu/content/fr...
A bushel of Golden Apples from Eris?
Comment by Thought Provoker — October 18, 2006 @ 12:15 am
October 18th, 2006 at 12:27 am
Bradford:
Um, denying that the origins of the RNA World are not central to the OOL is pretty much denying RNA and it's central role in life.
If you are of a mind that the RNA World is irrelevant, then whence the extant RNA World? Support your assertions with positive experimental results, if you would.
You, like these other occasional "skeptics", offer nary an iota of positive experimental evidence to support your doubts.
What's up with that anyway?
Comment by Art — October 18, 2006 @ 12:27 am
October 18th, 2006 at 1:33 am
"Smokey you observed machine parts strewn on the ground. They need to be assembled and working in concert. If selection is analogous to the assembler you still have workable parts on the ground but no machine to show for it."
Bradford, I didn't observe any "machine parts strewn on the ground." I am referring to using variation and selection to transform random sequences into functional enzymes in vitro, things I suspect that in vivo you would characterize as machines to make a vapid argument for design.
Analogies are great explanatory devices, but analogies aren't arguments. Moreover, you are just avoiding confronting the data you claim are insufficient but haven't bothered to examine.
BTW, you didn't answer my question. To which specific papers and conclusions of Yarus et al. were you referring?
"Do you know what Halt die Klappe means?"
Yes. Do you know what "Que porra é essa?" means? This question comes to mind when you claim that "Nucleic acids are functional based on their codon specificity," right after we were discussing nucleic acids whose function has nothing to do with codons.
I asked whether you knew what "et al." means because you were portraying the massive amount of work by Yarus et al. as a single study with a single conclusion by Yarus alone.
To which specific papers and conclusions of Yarus et al. were you referring?
TP: "Frankly, I would be extremely impressed if you two could agree with the bulk of what is said in these few pages of Yarus' work."
I agree with it. Why would that impress you?
As for Bradford, he's already on the record:
"The enzymatic qualities alluded to are limited and have not been found to catalyze the synthesis of proteins from nucleic acid templates in theorized prebiotic environments. "
"Catalytic RNA does not catalyze the synthesis of proteins. That is the function of tRNA amino acyl synthetases."
I'm sure he came to that conclusion after careful study of all the relevant evidence, aren't you?
Comment by Smokey — October 18, 2006 @ 1:33 am
October 18th, 2006 at 7:13 am
Um, denying that the origins of the RNA World are not central to the OOL is pretty much denying RNA and it's central role in life.
I do not deny that the RNA world is the centerpiece of OOL.
You, like these other occasional "skeptics", offer nary an iota of positive experimental evidence to support your doubts.
In this case you have it reversed. If you wish to support your own centerpiece then the burden is on you and don't blame others for pointing out where OOL falls short.
Comment by Bradford — October 18, 2006 @ 7:13 am
October 18th, 2006 at 7:19 am
Analogies are great explanatory devices, but analogies aren't arguments. Moreover, you are just avoiding confronting the data you claim are insufficient but haven't bothered to examine.
Bull. The data falls far short of what it needs to indicate to show life arises Smoke. You can assert otherwise all day long and it won't change that.
I asked whether you knew what "et al." means because you were portraying the massive amount of work by Yarus et al. as a single study with a single conclusion by Yarus alone.
Truncated phrases and abbreviations are common in informal forums like this. Your complaint like your attitude is petty.
Comment by Bradford — October 18, 2006 @ 7:19 am
October 18th, 2006 at 10:28 am
Bradford,
If you want to be credible in leveling that criticism against anyone, you should start with yourself. Yet, you were the one taking it "personally" last night when I asked simple questions like "why do you think that."
But at least you are following the gameplan for ID/Creationists:
Comment by Daniel — October 18, 2006 @ 10:28 am
October 18th, 2006 at 11:37 am
How could you possibly know, Bradford? You lack even superficial familiarity with the data. You can't even get the RNA World hypothesis right when you claim that the RNAs in it are coding for something else.
That's precisely my point! When Art wrote "Yarus et al.," he was referring to a huge body of work, using "et al." in its most literal sense. You assumed that he was using a more formal reference to a single paper, and tried to bluff your way through.
Pointing out your ignorance of the vast majority of relevant data when you globally claim them be insufficient is the antithesis of pettiness. Also, for the record, I'm not complaining. Your arrogance is very entertaining.
Daniel, in all fairness to Bradford, he's using a far more refined version of the gameplan:
4. Claim that the data are insufficient to support X
4a. Misunderstand and misrepresent the most fundamental aspect of X (i.e., claim that the RNA World includes RNAs that code for something else)
4b. refuse to look at the data, but pretend to be familiar with them
5. Therefore Initial Assumption B must be right
Comment by Smokey — October 18, 2006 @ 11:37 am
October 18th, 2006 at 11:48 am
Smokey,
Oh of course he is. But that's just a permutation of the same basic gameplan, right? The failure of deductive reasoning is of the same kind, so I go with the simpler statement to try and get my point across.
Comment by Daniel — October 18, 2006 @ 11:48 am
October 18th, 2006 at 12:13 pm
Hi Guys,
May I offer the following paragraph from RNA World Chapter 3?
As I stumbled my way through it, this appeared to be a key point.
To me it provides for some specific questions.
Bradford, are you familiar with the 1987 Weiner and Maisel proposal concerning early RNA reproduction?
If you are familiar with it, I take it you disagree with it. In your opinion is this the fundamental leap in logic you disagree with?
While I suspect you disagree with this 1987 proposal, if it did turn out to be correct, wouldn't the "genomic tag hypothesis" be an natural outgrowth of the 1987 proposal?
What experimental data can you point to that would contradict the statement "As genomic tags enter a second decade, no evidence has appeared that contradicts the hypothesis…"
Smokey, are you familiar with the 1987 Weiner and Maisel proposal concerning early RNA reproduction?
If you are familiar with it, I take it you agree with it. In your opinion is this a fundamental assumption to the RNA World?
While I suspect you agree with this 1987 proposal, if it did turn out to be incorrect, wouldn't the "genomic tag hypothesis" become vacuous?
What experimental data can you point to the supports the statement "As genomic tags enter a second decade… experimental support continues to mount."
Comment by Thought Provoker — October 18, 2006 @ 12:13 pm
October 18th, 2006 at 2:40 pm
HA! Is that all you think you do? Find your comments/responses, Daniel, have someone else read them and have them tell you if you think you're being civil.
If anyone should be making the comment you just did…. it's not you.
Comment by Doug — October 18, 2006 @ 2:40 pm
October 18th, 2006 at 3:00 pm
Doug,
Could you give me an example of something that I said which was uncivil? I asked critical questions, sure, and in past conversations perhaps I said something that I regret, but I don't recall name-calling or using profanity in my comments anytime recently..
But if there's something that was offensive to Bradford or others, other than asking "why life looks designed," please let me know so I can apologize. Otherwise, I'll call your bluff.
Comment by Daniel — October 18, 2006 @ 3:00 pm
October 18th, 2006 at 4:36 pm
Daniel,
Your post about the "It looks designed crap" was clearly uncivil.
Asking "How is asking simple questions uncivil?" was insincere, provocative and distracting.
If you want to debate, please debate. This topic provides ample opportunaty to make your points without trying to trap Bradford. Point to the evidence. Quotes from Yarus, Weiner, Maisel "et al" will go a lot further towards making your point than trying to get a quote from Bradford.
Bradford,
Please feel free to move this post to the memory hole in an effort to get back on subject.
I would really be interested in hearing people's opinions on the RNA World. I already know what the different sides think of each other.
Comment by Thought Provoker — October 18, 2006 @ 4:36 pm
October 18th, 2006 at 4:43 pm
If you can't see it for yourself…. then please call it.
Comment by Doug — October 18, 2006 @ 4:43 pm
October 18th, 2006 at 5:10 pm
TP,
How? Do you really think that the equivalent of "it looks designed" is a legitimate agrument??? Such arguments are vacuous, are they not?
Which part wasn't sincere? I was honestly interested in exploring Bradford's deductive reasoning process, and straighforward questions like "so why do you think that" were too personal for him, so he started playing the delete game. Up until that point, I was seriously hoping for interesting and stimulating responses from him, or for him to say that his views were not, in fact, based on science. Yes, though, I admit that I found it hilarious that he got offended by my inquiries. It was funny, afterall.
But for being curious about Bradford's methods of logical deduction, I hereby apologize.
Yes, I was not being topical. My sincere apologies for staying on the sidelines for the Yarus et al. discussion, which I found very informative (I hadn't seen most of Yarus's works, nor had I read any of his book).
I didn't realize that not being topical was such an offense - so, for not being topical, I apologize.
Anything else?
Comment by Daniel — October 18, 2006 @ 5:10 pm
October 18th, 2006 at 5:13 pm
1) I'm familiar with it.
2) Not necessarily. It clearly would be tough to replace if it failed to be supported by the data.
3) Probably, at least in the short term.
4) The data are cited in the chapter.
I'd also like to know how any intelligent design can be inferred from the use of an exonuclease to chew back the 3' end of tRNAs, only to have ATP(CTP):tRNA
nucleotidyltransferase add back CCA to the end. This makes sense as a holdover from the RNA world, but it would be far more intelligent just to include the proper 3' end in the gene encoding the tRNA.
Comment by Smokey — October 18, 2006 @ 5:13 pm
October 18th, 2006 at 5:34 pm
To Daniel,
You may notice a link above where you type your posts. It says "Comment Guidelines".
Here is an excerpt…
Now, that we have that cleared up…
Bradford, please feel free to delete this post along with the other non-topical posts.
Comment by Thought Provoker — October 18, 2006 @ 5:34 pm
October 18th, 2006 at 5:59 pm
Ok, one more parting question, that I will try to make specifically inclusive of the RNA World discussion, yet continuing my earlier line of thought, directed at Bradford, who I've been trying to gain some level of understanding with regards to:
Bradford,
(1) you clearly think that natural forces are inadequate to explain aspects in the work of Yarus, Weiner, Maisel, et al.
(2) so you argue that the first replicting biomolecules or cells must have been assembled de novo by a "designer."
Now my question(s): On what basis do you think that RNA was assembled into its current structure for a greater purpose? You've said the alternative (natural forces) is insufficient, yet no one has determined this to be the case. You've said that your analytical skills enable you to arrive at the conclusion that RNA was designed. Could you explain your analysis methodology? (Some of my own thoughts as to how a scientific mind would approach these questions, in my opinion, in the next paragraph)
If RNA's structure is suited to mere functionality, i.e. because it works, wouldn't that suggest a natural mechanism? (selection involves conservation of what works, and discarding of what doesn't) Alternatively, does RNA bear some hallmark or signature, left over by its "designer" that biologists have by chance overlooked? (if so, what?; if not, why would you still think RNA is designed?)
These are questions that I hope all of us should be asking each other.
Comment by Daniel — October 18, 2006 @ 5:59 pm
October 18th, 2006 at 6:21 pm
Hi Smokey,
I asked…
What experimental data can you point to the supports the statement "As genomic tags enter a second decade"¦ experimental support continues to mount."
You answered…
Do you mean the 114 references at the end of the chapter?
Ok, I should have noticed that. But that was still too easy. Could you highlight some of the more outstanding references while I continue to struggle my way through this?
Comment by Thought Provoker — October 18, 2006 @ 6:21 pm
October 18th, 2006 at 6:30 pm
I'm not an expert on any of this, and don't plan to become one. But I do have a few questions I hope someone will answer so I'll at least be able to follow the assertions and counter-assertions…
1. Does RNA spontaneously generate in hypothetical pre-biotic earth conditions?
2. If so, what are those conditions?
3. How stable are these loose RNA molecules in those conditions (how long do they last)?
Thanks.
Comment by Joy — October 18, 2006 @ 6:30 pm
October 18th, 2006 at 6:47 pm
TP:
"Do you mean the 114 references at the end of the chapter?"
Not all of them. Start with the ones they cited on page 82.
"Ok, I should have noticed that. But that was still too easy. Could you highlight some of the more outstanding references while I continue to struggle my way through this?"
Sorry, probably not. I'm going to be struggling my own way through a meeting that is slightly removed from my field. I feel your pain.
Comment by Smokey — October 18, 2006 @ 6:47 pm
October 18th, 2006 at 6:56 pm
Joy,
I'm not a chemist, so I can't answer all your questions. However, you should keep in mind that the energetic barrier isn't the polymerization of nucleotides into RNA, but the charging of the nucleotides with the three phosphates. The enzymes in your body promote the polymerization by speeding up hydrolysis. Remember that enzymes, like all catalysts, speed up reactions–they don't reverse the arrows.
As for #3, that's very hard to measure, because all living things spew ribonuclease into their environment. We go to ridiculous lengths to inhibit ribonuclease when preparing RNA. It's so prevalent that touching your finger to the surface of a solution containing RNA will degrade it all (except for the double-stranded parts) within seconds.
Also, generating a few RNAs in prebiotic soup is trivial relative to the pathways that are being filled in supporting the RNA World hypothesis. I predict that you'll be disappointed if you move the bar that low.
Comment by Smokey — October 18, 2006 @ 6:56 pm
October 18th, 2006 at 7:58 pm
Daniel Says:
Daniel, whining about how a blog is being run, because his posts were deleted?
Now that is rich!
Comment by RogerRabbitt — October 18, 2006 @ 7:58 pm
October 18th, 2006 at 9:06 pm
Smokey
I don't follow OOL research, but I do seem to recall that the RNA-World hypothesis was invented to get around the little problem of spontaneously generating cellular life forms. Because we know that in a biotic world, cellular life forms do not spontaneously generate.
So I just wanted to know if RNA is observed to spontaneously generate, in what conditions it is observed to spontaneously generate, and how that process is expected to work in pre-biotic conditions.
Thought you might know, since you seem pretty convinced of the hypothesis.
Comment by Joy — October 18, 2006 @ 9:06 pm
October 18th, 2006 at 9:31 pm
Joy,
One of the things I have noticed in a couple of places. The OOL transition between chemicals and RNA is a no man's land. The biologists actually say "let the chemists figure that part out". While I haven't seen a quote from a chemist, I can easily understand why they wouldn't be all that interested. If they wanted to study biology, they would have become biologists. A catch-22.
Comment by Thought Provoker — October 18, 2006 @ 9:31 pm
October 18th, 2006 at 10:12 pm
Joy:
"I don't follow OOL research, but I do seem to recall that the RNA-World hypothesis was invented to get around the little problem of spontaneously generating cellular life forms."
Regardless of its "invention," I seem to recall that it wasn't well known until the ribozyme and ribosome data supported it in spades while amazing virtually everyone. Arguments aren't very persuasive without new data.
"Because we know that in a biotic world, cellular life forms do not spontaneously generate."
Yes, but that has little to do with the RNA World hypothesis, because it would work with or without enclosure in cells.
About #3, my response wasn't clear. I mean that modern measures of RNA stability aren't very relevant to pre- or peri-biotic scenarios, because they wouldn't be inundated with ribonuclease.
Comment by Smokey — October 18, 2006 @ 10:12 pm
October 19th, 2006 at 10:46 am
Thanks TP and Smokey. I googled around a bit and see that chemists aren't overly taken with the idea because RNA is unstable even when there's no ribonuclease around.
Sidney Altman does say that if the RNA in the RNA World were chemically different from the RNA in our world, then an RNA World (or, a Not-RNA RNA World) makes perfect sense. But according to Leslie Orgel, uncomtaminated strands of RNA of "any size" are unlikely to form in nature. More precisely, "…the direct synthesis of nucleotides from prebiotic precursors in reasonable yield and unaccompanied by larger amounts of unrelated molecules could not be achieved by presently known chemical reactions."
But don't let that discourage anyone. All we need is some unknown and heretofore unimagined chemical reaction that constructs practically indestructible not-RNA RNA, and poof! Molecular proto-life is born, starts constructing proteins and proceeds to build itself an incredibly complex isolating environment (cell). At which point the not-RNA becomes real RNA, constructs a permanent record of proteins it's found useful (DNA), and immediately learns how to reproduce the whole sheebang in one fell swoop.
I suppose the spontaneous generation of clever, free-living, reproducing not-RNA molecules is no more of a stretch than the spontaneous generation of clever, free-living, reproducing cells. And it all goes back to the spontaneous generation of matter and energy, so something from nothing has an illustrious scientific history despite the fact that no one's ever observed spontaneous generation of nucleic acids or life or universes.
Belief-in spontaneous generation apparently comes naturally and easily to human beings. Guess that means it has to be true…
Comment by Joy — October 19, 2006 @ 10:46 am
October 19th, 2006 at 12:54 pm
Hi Joy,
While I think the closing statement was a little too sarcastic, I thought your post on the whole was very good. I would encourage everyone to look at the links you provided. Sidney Altman had a more positive spin than the other link. BTW, your quote is actually from the RNA World book that I managed to find several links to. Unfortunately, I couldn't find Chapter 2 which is where the quote came from. I would have liked to have seen the quote in context.
The latter link included an interesting list of other hypotheses that included…
It looks like it is possible Leslie Orgel is just doing the RNA World one better. This coincides with my guess about a "no man's land" between chemists and biologists.
Comment by Thought Provoker — October 19, 2006 @ 12:54 pm
October 19th, 2006 at 1:50 pm
Moi? Too sarcastic? Au contraire, mon ami! It does appear that human beings apprehend the situation innately - everything just poofed into existence at some point in time (including time itself). I'd strongly suspect that innate apprehension of this situation means it's gotta be true. It's our differing guesses about HOW and WHY things just poofed into existence in time that are unfortunately limited by the very fact that we're humans living and dying here inside the bubble instead of viewing it from the outside.
Most people have an innate propensity to assign an intelligible universe to an intelligent agent that *is not* the intelligible universe. Others presume the intelligible universe *is* the causal agency. Still others assume there's no causal agency at all. Everybody believes their assumptions are the only true Truth, and insist that everybody else bow down to it.
It has always been thus. I call it "Dueling Metaphysics," a perennial pastime.
Comment by Joy — October 19, 2006 @ 1:50 pm
October 19th, 2006 at 3:42 pm
RNA Disney World…
Bradford over at TT has posted an interesting thread on RNA World. Bradford, like a typical IDiot is looking for empirical and detail testable pathways. The sophisticated and intellectually superior Darwinists on the thread is befuddled by Bradford's…
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