Yes — the peptidyl transferase center (PTC) contains RNA in its active site.
But my point concerned the ribosomes that we actually find in cells, and in mitochondria. All contain proteins as essential components. None function as stripped-down (i.e., RNA-only) ribozymes, and require very significant numbers of proteins to form properly in a pre-ribosomal assembly scaffold. In 2007, George Church made this point in a conversation with Craig Venter and Robert Shapiro:
CHURCH: But isn’t it the case that, if we take all the life forms we have so far, isn’t the minimum for the ribosome about 53 proteins and 3 polynucleotides? And hasn’t that kind of already reached a plateau where adding more genomes doesn’t reduce that number of proteins?
VENTER: Below ribosomes, yes: you certainly can’t get below that. But you have to have self-replication.
CHURCH: But that’s what we need to do — otherwise they’ll call it irreducible complexity. If you say you can’t get below a ribosome, we’re in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins.
VENTER: In the RNA world, you didn’t need ribosomes.
CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins.
VENTER: Yes.
SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously.
If you can spare the time (spring cleaning your garage, maybe?), I’d encourage you to listen to Williams’s talk. He tells a great story. I was amazed, for instance, about the increase in ribosomal size with organismal complexity (rough correlation, anyway – see his remarks starting around 23:00).
In any case, the co-dependency between rRNA and ribosomal proteins could easily be a byproduct of history, not to be taken as an indication for what the very earliest stages of the system looked like. The ribosomal RNA could have evolved to depend on synthesized proteins, which if they’re now removed, it no longer functions.
The context in which the earliest stages of ribosomal evolution took place may have been radically different in the same way that an animal functioning without central nervous system, or a “heart-powered” circulatory system, aka a sponge, is radically different from a mammal. Remove my heart, or my brain and central nervous system, and I will “stop functioning” and die. But I have ancestors that lacked both, and yet they “worked” just fine.
Indeed – if you watch Williams’s talk on YouTube, that’s exactly what he argues.
The problem is not with hypothesizing an earlier, simpler system (an inference necessitated by any undirected chemistry → life scenario). The problem is showing how that system arose, endured in its pre-biological form, and would have functioned. George Church’s point, in the excerpt from the roundtable conversation, above, turns on the difficulty of seeing past (or earlier than) extant biology, to the putative simpler systems from which extant biology arose.
True enough, the top-down approach cannot see much past the phylogenetic signal. It can give some small indications here and there, but nowhere enough to give a full picture of what the first stages in the origin of life process were like. A bottom-up approach is needed instead. This is very difficult to connect to extant biology ofc.
We might have to accept that we can only explain how some sort of life could have originated, but never be able to say with any appreciable certainty that this is how our kind of life did originate.
Yes, that was the principal finding of the Noller et al. (1992) paper, linked above by Art.
To my knowledge, no wild-type ribosome, however, in any of the three major domains, contains only RNA. If anyone knows differently, kindly post the reference here.
Wait, what? I was not aware it has been shown that a ribosome can still function entirely without any proteins. If that is so, then that throws the inference that they’re necessarily co-dependent into very serious doubt. Works less well =/= doesn’t work at all.
I saw your summary as attempting to minimize and disguise that finding. “the peptidyl transferase center (PTC) contains RNA in its active site” is far from saying that ribosomes can function without any protein. And now that we agree, isn’t that good evidence for the plausibility of an ancestral naked ribozyme?
I am reminded of the evolution of the vertebrate lower jaw. Originally, it consisted of one cartilage or cattilage-replacement bone, the mandibular. Over time, we can observe dermal bones arising that cover and supplement the mandibular, and then gradually replace it. First the mandibular retreats from the front of the jaw, eventually ending up forming the articular bone only, and then the articular leaves the jaw (in the mamal line) to take up a place in the middle ear. The mammal jaw is left as a single bone, the dentary, with no trace (except in the embryo) of the mandibular. The major difference between this transition and ribosomal evolution is that we have both fossils and living representatives of some of the transitional stages. Still, one might argue that the ability of the naked ribozyme to function is a sort of living fossil, don’t you think?
Read the Noller et al. 1992 paper, linked by Art. These are in vitro biochemical assays, looking for peptide bond formation.
Not real cells genuinely making real proteins. No ribosome functioning in an actual cell is only “naked ribozyme,” to borrow your term.
“Still, one might argue that the ability of the naked ribozyme to function is a sort of living fossil, don’t you think?”
This is the standard view of most workers who focus on ribosome origins, articulated most winningly by Loren Williams in the YouTube video I linked (but I’ve heard the Israeli Nobelist Ada Yonath explain the view with vigor as well). It is also, not surprisingly, the view of John Mercer and Art Hunt, contributing in this thread.
Not my view, for three reasons:
(1) the extreme fragility on RNA on the early Earth
(2) the implausibility of running any real cell simply on catalytic / enzymatic RNAs
(3) absence of evidence, in real-time experiments in vivo, of naked ribozymes functioning as ribosomes.
Any ribosome in any real cell is much more complicated than naked ribozyme. There are functional reasons for those complications, not simply the evolutionary accretion of extra parts the cell can do without.
So? None of your objections seem relevant to the question. #1 needs some kind of support. So does #2. #3 suggests an impossible and nonsensical test. You appear to be avoiding the evolutionary scenario, which is that the rRNAs and ribosomal proteins we see today have coevolved for billions of years. What you have is just the failed argument that IC systems can’t evolve.
I will have more later, but I am compelled (for various reasons) to remind @pnelson and other readers of viroids - naked RNAs that exist in the modern biosphere (which, by my estimation, is a much harsher place for naked RNAs than the early earth, owing to the fact that all living things make, and secrete, enzymes whose duty it is to degrade RNA).
It is common lab lore that the enemy of RNA in the lab is not storage, or buffers, or any of a number of alleged insults - rather, it is YOU, and all the nucleases that drip off YOUR skin. This is more than urban legend, it is pretty accurate.
(And then there are stories I could tell about how hardy tobacco mosaic virus is …)
