“Insights” are a dime a dozen. A detailed explanation is what is wanted. Tour shows the difficulties which stand in the way of any such detailed explanation.
No, I don’t. I live in a protein-DNA world in which RNA plays an important ancillary role. You need to learn the terminology. “RNA world” refers to a hypothetical world, allegedly prior to ours, in which RNA, not DNA, was the key player.
And yet you have beliefs on how the first life came about, correct?
Eddie, you can say this over and over, all you want. Your ill-informed assertions do not change the fact that you live in an RNA World. The raison d’être for protein and DNA is to make RNA, specifically to make ribosomal RNA. RNA sits at the center of the goings on in the cell - the most important catalysts, the most important regulators, the most important communicators, are all RNA, or they derive directly from primordial mechanisms that center on RNA.
I disagree. The raison d’etre for DNA and RNA is to make proteins. RNA is a means to that end.
In any case, you are gloriously missing the point, which is that I am not denying an important role to RNA, but pointing out that you are misusing the term “RNA world” as it is used in origin-of-life discussions. My complaint is about your misleading use of the phrase in the context of “how did life begin?” discussions. “RNA World” does not mean “any world, including today’s, in which RNA is an important part of life”; it means “a hypothetical earlier state of organic life, in which the modern DNA-protein system had not yet evolved, and RNA ran the whole show.” But since you seem obtuse on this point, I will let it go. You can read the origin of life literature, or you can ignore it, as you please.
Many, perhaps most, functional RNAs are never translated into proteins.
With all due respect, @Eddie, I am much more familiar with the OOL literature than you. The fact that you cling to assertions and ideas that ignore the fundamental nature of life - today and at the beginnings of life - tells me that 'tis you who are ignoring things.
Getting back to the matter of Tour’s ill-conceived assertions in this regard - in ignoring that RNA even exists, Tour misses out on the identity of the central player, the key onto which any and all OOL scenarios must converge. No matter how one may spin things, the identification of the central feature of life (an accomplishment that is firmly grounded in the RNA World hypothesis) constitutes a huge achievement, one that puts the lie to Tour’s claims about the supposed futility of OOL research.
For the ID community, I believe their perverse denial of all this has caused them to miss an interesting opportunity. One can summarize the molecular biology research program of the DI pretty simply - biochemical function, in general, is so rare in sequence space that it cannot “evolve”. Even before Behe’s first book, we knew that this is wrong, and we know so with more certainty today.
However, what is not known is whether there may be a magic bullet, as it were, a single function that in fact fits this bill. The problem is, how does one identify this, and then study it to confirm some design-related hypotheses? Well, a good place to look for such an entity would be at the origins of life. The RNA World hypothesis has taken us there. We already know one possible subject of study. But, because the ID community is divorced from science, and can only dig in their heels when faced with the abundance of evidence that tells us that the first ID models are wrong, they are unable to move on, to follow new leads and directions, to, as it were, go where the evidence leads.
How can you possibly know that? Have you seen my library?
Certainly, if you aren’t aware of how the phrase “RNA world” is generally used, I would say that you aren’t familiar with the OOL literature at all.
Which would make sense, as your field is plant biology, not origin of life.
Most of your reply has nothing to do with the point at issue, which is how the phrase “RNA world” is generally used in origin of life discussions. If you could just admit that you were stretching the phrase beyond its normal meaning, we might be able to get along, but since you are digging in your heels on a point you could easily concede (without surrendering anything of your views on ID or on origins), it’s evident that you have some sort of aversion to peace-making, no-cost verbal adjustments. So I have to leave it at that.
Fair enough. I was thinking of mRNA and tRNA and their role in protein synthesis. I would say the raison d’etre of RNA in that context is to make proteins. I have no interest in denying other functions to RNA. In any case, it should be easy enough for Art Hunt to see that I am disputing his use of a phrase, i.e., “RNA world,” which has acquired a specialized meaning in origin of life discussions. He is using the phrase in a general way which ignores that specialized meaning, and since the context here (Tour’s work) is origin of life discussions, I think it’s downright misleading to depart from the common usage in OOL discussions.
Slow down, Eddie. I strongly suspect @Art was exactly familiar with how the term was used over 30 years ago after Altman and Cech. The term isn’t very popular anymore because it tends to ignore the central role of RNA in living organisms today. You are fighting an irrelevant fight with someone that outclasses you in this particular area. Please give it a break.
LOL. @Eddie dreams he is more an authority than say, Tom Cech:
There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today’s biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNA world to infer what the primordial RNA world might have looked like.
My usage of the term is well, well within its normal meaning.
I’m sure @Eddie can find, in his library, the following:
The term “RNA world” was first coined by Gilbert (1986), who was mainly interested in how catalytic RNA might have given rise to the exon–intron structure of genes. But the concept of RNA as a primordial molecule is older, hypothesized by Crick (1968), Orgel (1968), and Woese (1967). Noller subsequently provided evidence that ribosomal RNA is more important than ribosomal proteins for the function of the ribosome, giving experimental support to these earlier speculations (Noller and Chaires 1972; Noller 1993). The discovery of RNA catalysis (Kruger et al. 1982; Guerrier-Takada et al. 1983) provided a much firmer basis for the plausibility of an RNA world, and speculation was rekindled. The ability to find a broad range of RNA catalysts by selection of RNAs from large random-sequence libraries (SELEX) (Ellington and Szostak 1990; Tuerk and Gold 1990; Wright and Joyce 1997) fueled the enthusiasm, and made it possible to conceive of a ribo-organism that carried out complex metabolism (Benner et al. 1989). The widely accepted order of events for the evolution of an RNA world and from the RNA world to contemporary biology is summarized in Figure 1.
Did an RNA world exist? Some of the most persuasive arguments in favor of an RNA world are as follows. First, RNA is both an informational molecule and a biocatalyst—both genotype and phenotype—whereas protein has extremely limited ability to transmit information (as with prions). Thus, RNA should be capable of replicating itself, and indeed RNA can perform the sort of chemistry required for RNA replication (Cech 1986). Second, it is more parsimonious to conceive of a single type of molecule replicating itself than to posit that two different molecules (such as a nucleic acid and a protein capable of replicating that nucleic acid) were synthesized by random chemical reactions in the same place at the same time. Third, the ribosome uses RNA catalysis to perform the key activity of protein synthesis in all extant organisms, so it must have done so in the Last Universal Common Ancestor (LUCA). Fourth, other catalytic activities of RNA—activities that RNA would need in an RNA world but that have not been found in contemporary RNAs—are generally already present in large combinatorial libraries of RNA sequences and can be discovered by SELEX. Fifth, RNA clearly preceded DNA, because multiple enzymes are dedicated to the biosynthesis of the ribonucleotide precursors of RNA, whereas deoxyribonucleotide biosynthesis is derivative of ribonucleotide synthesis, requiring only two additional enzymatic activities (thymidylate synthase and ribonucleotide reductase.) Finally, a primordial RNA world has the attractive feature of continuity; it could evolve into contemporary biology by the sort of events that are well precedented, whereas it is unclear how a self-replicating system based on completely unrelated chemistry could have been supplanted by RNA.
Opinions vary, however, as to whether RNA comprised the first autonomous self-replicating system or was a derivative of an earlier system. Benner et al. (2010) and Robertson and Joyce (2010) are circumspect, noting that the complexity and the chiral purity of modern RNA create challenges for thinking about it arising de novo. On the other hand, the recent finding that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions (Powner et al. 2009) means that it is premature to dismiss the RNA-first scenarios. Yarus (2010), an unabashed enthusiast for an RNA world, argues for a closely related replicative precursor. In vitro evolution studies directed towards an RNA replicase ribozyme continue apace and are of great importance in establishing the biochemical plausibility of RNA-catalyzed RNA replication (Johnston et al. 2001; Zaher and Unrau 2007; Lincoln and Joyce 2009; Shechner et al. 2009).
What might the first ribo-organism have looked like? Schrum et al. (2010) describe progress in achieving replication of simple nucleic acid-like polymers within lipid envelopes, thereby constituting “protocells.” These liposomes can grow and upon agitation can divide to give daughter protocells, carrying newly replicated nucleic acids. Whether by lipids or other means, some form of encapsulation must have been a key early step in life. Encapsulation can protect the genome from degradation and predation, allows useful small molecules to be concentrated for the cell’s use, and enables natural selection by ensuring that the benefit of newly derived functions accrues to the organism that stumbled across them.
The question remains - how can Tour be praised for dismissing this, and much, much more?
Art Hunt has no publications whatsoever in the origin of life area. He is a plant biologist. You are making an argument from authority, i.e., that I should defer to Art because he is a biologist and I am not – which has nothing to do with the point in dispute. I am making a statement about how the phrase “RNA world” is used in OOL discussions. Neither you nor Art has provided any textual evidence from the literature that I am incorrect. Until you do, I will maintain my position.
What about RNA? That’s what we are talking about - the RNA World.
Art:
Your long list of passages from biologists (and by the way, I’m quite familiar with the sort of discussion contained in those passages) proves exactly my point, which is that when the subject is the origin of life, “RNA world” is used as I have said. You shifted the meaning of the term in the midst of a discussion of Tour regarding the origin of life. I was objecting to your attempt to deflect my point by shifting the frame of reference. Such shifts lead to lack of clarity in discussion.
Give us a list of your publications regarding the role of RNA in the origin of life.
I don’t believe you. Your prior comments on this board show someone utterly unfamiliar with “the sort of discussion” that pertains to Tour’s uninformed comments about OOL research.
I don’t care whether you believe me or not.
This comment suggests that you were unfamiliar with the double meaning of “RNA World” that Art made clear with his quote from Tom Cech:
There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today’s biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNA world to infer what the primordial RNA world might have looked like.
There are actually fascinating connections between the focus of my research and the primordial RNA World.
Yes, I read the passage from Tom Cech. It begins:
Which is a slightly more expansive version of how I defined “RNA world” for Art Hunt.
Now, the context of my original discussion was the origin of life, and that is why only Cech’s first definition is relevant to my discussion. I was not denying that the phrase could be used in English in more than one way. But it should have been very obvious from context that I was referring to the phrase in Cech’s first sense, i.e., pertaining to a hypothetical era back near the origin of life. When I mocked the “RNA world” hypothesis, I was mocking a particular account of the origin of life, not the statement that RNA is very important in modern living systems.
There is no reason why Art Hunt should not have picked that up. He claims great familiarity with ID people – he debates them, publicly and privately. He is surely aware of the extended treatment of “RNA World” origins speculation in many ID writings. So his attempt to “correct” me by telling me that I live in an RNA world, whether I admit it or not, when he should have known that I was talking about 4 billion years ago, not today, was combative for no reason. And this is not the first time I’ve had this experience with Art. I found he behaved the same way on BioLogos, when I tried to make statements about Behe. No matter how carefully I qualified the statements, he would would come back at me, ignoring all the context I had provided, charging me with erroneously interpreting Behe.
We philosophers are used to saying things like “in this respect” or “as far as this particular point is concerned,” and it’s just standard in philosophy (and in the humanities generally) for conversation partners to respect the caveats and qualifications offered by a speaker, rather than ignore them and “correct” the speaker as if he never offered them. I’ve repeatedly said here that I’m talking about the way the phrase is used with respect to the origin of life. Art has chosen to ignore that. Well, if he wants to waste his own time by holding out for his “correction,” he can do so. He won’t waste any more of mine.
LOL. When exactly was this?
You need to take a break, @Eddie.