Michael’s vocabulary seems correct to me.
You have not answered my question: What would “life” look like in the RNA world, and would it be so different from what we now call “life” that it is questionable whether it’s the same thing? It would help if you would say what you mean by “life” and what, in your view, are the minimum characteristics required for saying something is “alive.” Does it have to breathe oxygen? Does it have to breathe at all? Must it have metabolism? Must it be in cellular form? Must it be able to reproduce itself? Does it have a desire to preserve itself? Etc.
I’m familiar with all of it. But I thought the RNA world hypothesis dispensed with most of what you are talking about. I thought it was postulating a world long before DNA and protein had the roles they currently have.
You are writing as if you are talking about cells pretty much as we know them, only with pure RNA in the ribosome instead of an RNA-protein complex. You sound as if you are still imagining a cell nucleus containing DNA, mRNA, a cell wall, and protein machines. I though the whole purpose of the RNA world hypothesis was to explain what life looked like before all of that structure was in place.
I don’t think you’ve been following the conversation.
Now they are. I really don’t think you’ve been following the conversation.
I have. No idea what Church was thinking.
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Yes, but if we’re talking about a ribosome, whose only function is to translate mRNA into protein, that must be pretty late in the RNA world.
The existence of a ribosome would presumably require the existence of DNA and protein in whatever sort of cell is involved. Wouldn’t you agree? There’s no point to a ribosome otherwise.
No nucleus is required. No cell wall is required. But there certainly must be DNA and proteins. If the RNA world is to progress to the current world, there must be intermediate states, and the RNA ribosome is one of them.
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Unfortunately, Meyer’s thesis is entirely wrong, and he wasn’t raising legitimate questions. He may be intelligent, but if he’s informed on any key issues he isn’t showing it, and he raises no good questions. You prefer reviews that lie about that?
Again I link to my review, which you will not like because I don’t say good things about the book. But is that a valid criterion?
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I hadn’t seen your review before. Great stuff. I was amused that you and I apparently share some affection for the old tale of bumblebee flight. You wrote:
Bumblebees can’t fly, so don’t bother pointing out that bee in the garden.
and I wrote:
In this respect Meyer’s argument is rather like the old tale (probably apocryphal) about the men who worked out the flight equations for the bumblebee and concluded, to a mathematical certainty, that it is impossible for the bumblebee to fly. A scientist who concludes that his theoretical work makes some routinely observable fact impossible has to sigh, return to work, and figure out what he has got wrong. If he will not do so, he is doomed to spend the rest of his life railing at the bees.
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No one knows exactly how “life” would have been billions of years ago, but by looking at clues today, we can fill in some details.
First, if one goes back in time by looking at the fossil record, organisms become relatively simpler. Not surprisingly, the oldest fossils are microbial, indicating life was simpler at the beginning.
Second, all modern life forms use ribosomes, indicating that the LUCA already had them before it split into the many branches of organisms we see today. This implies the ribosome evolved before the LUCA split. Since the peptidyl transferase activity of a ribosome is due to its ribosomal RNA alone, this suggests RNA was already involved in some form of catalysis, albeit in a primitive form. The proteins complexed with ribosomal RNA (rRNA) stabilize it and augment its catalytic ability, indicating they arose (probably as short polypeptides) at the same time or later than rRNA.
There was very little oxygen on prebiotic earth, indicating the earliest life forms were anaerobic. Aerobic organisms came much later.
You know Eddie, the questions you ask can be answered if you just pick up articles written on the subject and read
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I think I do. In a strictly RNA world, you wouldn’t have ribosomes but catalytic RNA molecules. In an RNA-Peptide world, then you would get something closely resembling modern-day ribosomes.
Certainly they are now, but it’s highly unlikely they existed in an RNA world. However, they would be begin to form as peptides and RNA began to interact.
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OK, I guess I misunderstood the phrase “RNA world” to refer only to what you are suggesting would be “the early stages of the RNA world.” Hence I could not follow you.
Yes, I understand that. But again, I thought that the idea was that if you go back far enough, life was based entirely on RNA, with DNA and proteins either not yet in existence, or, if in existence, playing much more limited roles. I thought the idea was that there were these RNA replicators running around, that were the core of what was then “life,” and that the whole “translation from DNA to protein” system came along later. It is this notion that I have been calling highly speculative. What you are talking about now seems to be just an immediate forerunner on the system we have now, and not differing much from that system, and my harsher comments were not addressed to it.
Not necessarily. Modern-day ribosomes are just nucleoprotein complexes, so if short polypeptides interacted with RNA molecules in prebiotic times they could form such complexes.
I agree. But its likely the formation of primitive membranes accelerated the transition to life as we know it.
I think RNA-peptide world intermediates fill in this gap.
I appreciate your taking the time to answer, Michael, but I hope that your answer won’t cause Rumraket not to answer, because my question was inspired by his particular remarks, and I want to get his response as well.
Yes, I know that I can read the speculations of others. But I wanted to hear Rumraket’s speculations specifically, because of certain things that he said.
And I was interested in more than the details of ribosomes and catalysis. I wanted Rumraket’s conception of the anatomy of the hypothetical RNA-based organisms, compared to our modern ones. And his definition of “life” – which is as much a philosophical as a biological question.
Did you recently change your “handle” to include the word “Agnostic”, or was that word always in there? For some reason, I thought you started here as a Christian. And you mention Nigeria. One of the big Christian churches there, I believe, is the Anglican. Was that your denomination? Is there any connection between that particular denomination’s teaching and your drift to agnosticism, or was the cause more general?
There are a couple of useful inferences to be drawn from the ribosomal core being RNA: first, it demonstrates the existence of ribozymes, which would be required in the pure RNA world. Second, it answers the creationist chicken/egg problem “How can you make proteins, when proteins are required for translation?”
It should be obvious that there is no use for a ribozyme that catalyzes peptide bonds unless peptides are of use. It’s conceivable that this arose before DNA, and mRNAs were originally transcribed from something else, perhaps RNA genomes.
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I was recently baptized by the Confessing Scientist of PS, and handed down the title.
No. I am Roman Catholic.
My church’s teachings had nothing to do with my agnosticism/atheism. I stopped seeing Christianity as true because it shared the same problems facing other religions.
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Are you claiming that ribosomes have nothing to do with my published research?
If you lack a Wikipedia-level understanding of fundamental cell biology, how can you have an accurate perception of fields of biology?
Why not read up on it for yourself?
It’s not a postulate, it’s a hypothesis. Why not learn about it for yourself?
The discovery that RNA is the enzymatic core of the ribosome supports the hypothesis. The hypothesis never predicted that modern rRNA would be sufficient. The total exclusion of protein from the active site was astounding because it was not expected.
What’s your ID explanation of it?
There’s no onus on us to provide a more elaborate hypothesis.
This is quite vague. Catalyze what of peptide bonds, condensation or hydrolysis?
Regardless of what you choose, this statement seems wrong. A ribozyme can catalyze peptide bond formation or disruption, even if it has no use. If it can launch a nucleophilic attack using its 2’ ribose group on a substrate, then it would catalyze the transformation of that substrate. Chemistry is blind.
Am I misreading you?
The official ID Creationist explanation is that the ribozyme is a protein, LOL.
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Of course catalysts can catalyze chemical reactions even if this is useless. I don’t think anyone is disputing that. But the question to be answered here which is relevant in an evolutionary context, is why a ribozyme capable catalyzing the formation of peptide bonds should evolve and persist, if it’s performing this function was not somehow advantageous? You might posit hypothetically that it did not, at first, evolve to catalyze peptide bond formation, but had some other catalytic role it got selected for, and that it’s ability to catalyze peptide bond formation was initially a byproduct of this other function.
Entirely possible, but either way, if translation is to eventually evolve it becomes difficult to see how this could occur without some eventual advantage to a developing repertoire of these produced peptides.
The most immediate advantage is of course to aid the proto-ribosome itself in performing it’s already existing functions(most obviously it would in some other way have to aid in self-replication of whatever system it was a part, which would give it a justification for persistence in the first place).
Supposing it had some alternative catalytic role that aided the system it was part of to reproduce, it’s side-ability to generate peptides that aided itself could produce a positive feedback-loop where, as soon as it started generating peptides that aided itself, it could then go on further improving it’s ability to keep generating more of these peptides, which would then make it even better at doing it’s other job. Eventually it’s ability to reliably generate peptides to itself also produced many other peptides, presumably with low fidelity, meaning lots of random mutant versions of different peptides, which could also have useful functions that aided other things in this system, and … on and on.
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I haven’t answered because it seems to me it’s not my job to answer these questions (it’s really nobody’s job).
I actually don’t have to make any such decision, because if life as we know it emerged from non-life by some sort of gradual process, such a distinction will be arbitrary. Does it then really matter to the reality or possibility of such a process, when I decide to call it one thing or another?
One might decide to call it life when one more macromolecule or function is added to some simpler chemical system, and the state immediately before that non-life, or “proto-life”. These sorts of issues of labeling and categorization isn’t really what is interesting or relevant here.
The question is if there was such a gradual process that led to life as we know it, and is there evidence for it? To make headway towards answering such questions is to find out if life as we know it can be made simpler (working backwards in time towards non-life), or to see if there are some environmental circumstances under which abiotic chemistry can develop systems that are more life-like, and with the capacity to develop further into life as we know it.
Whether those simpler systems would then qualify as “life” by whatever arbitrary delineation we decide upon is rather besides the point. What is important is that there is such evidence. Evidence that many of the systems we know of from life as we know it, have possible simpler antecedents. And evidence that some environmental circumstances appear to have the potential to give rise to more complex chemical systems. There is certainly still a large gap to be bridged there, but we also have to concede, then, that the demonstration of a purely ribozyme-catalyzed formation of peptide bonds is a step towards narrowing that gap.
Back when these simpler systems were “in operation”, would that have been in the context of a cellular life-form? I don’t know, I’m not sure it would have to be. There are other forms of “unit of identity”(by that I mean something that would correspond to an individual in a population of individuals) known that might not correspond to anything we would call a cell. Self-propagating surface-catalyzed chemical cycles, and inorganic compartments are proposed alternatives being investigated. Unfortunately it is not currently possible from species comparisons alone to elucidate the relative timing of the ultimate origins of the translation system, and bona fide cellularization.
I don’t much care how many of these we want to tick before we call it life. I’m much more interested in the physical and chemical process of emergence, than I am in when exactly we should deign to label or categorize the thing we’re looking at as belonging to some particular set.
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Stop with the quibbling. It should have been quite clear what we’re talking about, not just any ribozyme but the one at the heart of the ribosome. It catalyzes the formation of a peptide bond between two amino acids. It also holds a template in place for a tRNA to sit, moves the template along, and other such stuff necessary for translation. Are we arguing about anything here?
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