Eddie and ID books

That’s what I would expect from you.

Then let’s look at the paper together instead of arguing.

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Straw man alert…

I’ve already put it into everyday English:

If you don’t understand my everyday English, quote the parts you don’t understand and ask intelligent questions. Your straw-man tactic is banal and tedious.

Eddie, that’s truly pathetic. If you don’t even know for a fact that all living things have (highly homologous) ribosomes, you have absolutely no business arguing about this.

You’re just digging yourself in deeper.

Take a break and have a happy Thanksgiving. Read the cited papers. Try to have at least a Wikipedia level of knowledge before pretending to understand these things better than biologists do.


Thank you. I assumed this, whereas Mercer seemed to be silently denying it.

“A naked RNA ribosome doesn’t function as well as one with its proteins intact, but the point is that it does function, making an ancestral ribosome consisting solely of RNA entirely plausible,”

So your view, or at least the view of the RNA world people, is: some form of life existed that managed entirely with RNA, and then, by accident some proteins got associated with the RNA, forming our modern ribosome, and they happened to increase its stability, so they continued in that association, due to selection?

I think it needs to be stated that no-one has yet to show a protein-free ribosome capable of peptide bond formation. The paper @Mercer linked doesn’t show that there are no proteins in the ribosomes they treat with SDS and proteinase K, and subsequent experiments have shown that there are still some deeply buried proteins in the ribosome’s structure that aren’t digested by the proteases used in the assay. Attempts to more thoroughly rid the ribosome of it’s protein components haven’t yielded functional ribosomes.

However, @John_Harshman hits the nail on the head, as such a result cannot be said to be a conclusive argument that catalyzing peptide bond formation by a ribozyme requires help from proteins. The co-dependence of protein and RNA in the contemporary ribosome is just as likely to be a consequence of them evolving to depend on each other in a classic example of the Mullerian two-step, like proteins evolving to be dependent on chaperones to fold correctly.

In any case, fully protein-free peptide bond formation by ribozymes partially evolved by directed selection has been demonstrated. So RNA is, in point of fact, fully capable of catalyzing the formation of peptide bonds:

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Just being cautious, knowing your pedantic habits. If there happened to be one freak case that I didn’t know about, you’d be sure to hammer me for making the generalization. In any case, my use of the words “I assume” conveyed clearly that I accepted the standard view.

If you want a reason for caution on such things, how about the recent discovery of an animal that does not breathe oxygen? See:

If I had said, in another post, “and I assume all animals need to breathe oxygen,” and you knew about this exception, you’d have been sure to ram the error down my throat, as is your wont. So I was just protecting myself against potential aggression on your part – I was not indicating any practical doubt on my part that ribosomes are found in all living things.

Your desire to “catch people out” on side points that don’t affect the main point being made is puerile. If you were in the humanities rather than the sciences, this habit would mark you as intellectually boorish by both professors and fellow grad students alike. But apparently it’s encouraged in the life sciences, if the sort of life scientist who posts on these web sites is any indication, since a lot of them behave in that way, though few display the behavior to the extent that you do.

From this article

We get this:

The removal of the 59 elements identified by the analysis described above eliminated 93% of the original 23S rRNA. The remaining part, which consists of 220 nucleotides, is located in domain V (Figure 3). The central region of this 220-nucleotide fragment forms the peptidyltransferase center. Recently, it was observed that this fragment has a symmetric structure (Agmon-2005). The symmetry is clearly seen on the levels of both secondary and tertiary structure (blue and red regions, Figure 3B). One half of this symmetric structure corresponds to the P site (blue), the other half to the A site (red). Moreover, there is a close correspondence between the positions of the nucleotides of the two halves that are involved in the fixation of the equivalent elements of the tRNAs in A and P sites (Samaha-1995, Nissen-2000, Kim-1999, Hansen-2002). In the polynucleotide chain of the remaining part, the P-site half precedes the A-site half. The similarity between the two halves is so high that it is logical to suggest that they originated by a duplication of the same RNA fragment (Agmon-2005). From this point of view, the evolution of 23S rRNA started with an initial fragment of about 110 nucleotides, which presumably was able to bind the CCA terminus of what would later become tRNA. The duplication of this fragment allowed the resulting molecule to bind two CCA termini simultaneously. Within this arrangement, the two CCA termini associated with the two halves are juxtaposed in space to allow for the transpeptidation reaction. Most probably, this dimer was already able to synthesize oligopeptides with random amino acid sequences, hence the designation proto-ribosome. This view is supported by the fact that in-vitro-selected small RNA molecules resembling the peptidyl-transferase center were able to perform transpeptidation (Zhang-1997, Zhang-1998), thus demonstrating that this reaction does not require any other element of the ribosome structure.

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And that person is … (drum roll)?

Thank you for this qualification. I suspected that this would be the case.

And also fully capable of putting out all the proteins necessary for life?

I don’t know, does it have to be able to do that and how do you know? I am not aware that proteins are necessary for life. How did you arrive at that conclusion?

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It seemed that way only to you, I’m afraid.

That’s a really silly way to say it. But the scenario isn’t entirely different: start with an RNA ribosome. At various times, various proteins are introduced into the system. If they improve function in some way, they’re both retained and improved by selection. Does that for some reason seem implausible to you?

What, beyond the ability to catalyze peptide bonds, would be necessary in order to make a ribosome “fully capable”?


And Abzymes (catalytic antibodies) too.

Vague. “Are introduced” is a passive verb, with no agent. What is the means by which they are “introduced”? We know how proteins are formed now. How would they be formed in the world you are envisioning? What would be the steps?

If you can clearly answer my first question, you will probably have answered my second. I need a scenario. In the modern case, I have a scenario: DNA, messenger RNA, codons and the ribosome, amino acid chains emerging, folding, etc. I need a picture painted of the earlier scenario. Maybe this already exists. If you can point me to a source with diagrams comprehensible to a layman, with, say, a left-to-right flow as is often used to show the DNA to RNA to protein process we have today, that would be helpful. I tire of merely verbal narratives.

They’re necessary for life as we know it. If you postulate that there was an earlier era of “life” on earth (and when it was, you would have to specify) that required no proteins, the onus would be on you to describe the features of this different kind of “life” and show how it could work. You would probably need to include your working definition of “life” as well.

In the same way they’re formed now. I do not understand the source of your confusion. Proteins result from translation of mRNAs transcribed from DNA sequences. DNA sequences are subject to mutations. Some mutations can result in increased transcription of sequences or new open reading frames. Existing proteins can acquire new functions. Are you unfamiliar with any of this?

It’s the same scenario. The only differences is a ribosome composed entirely of RNAs. I’m not understanding your confusion here.

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That doesn’t pass the smell test. This shows that ID books do not inform their readers on the basics.

The enzyme at the center of life is not a side point.

You’re still digging, Eddie. Your ad hominems are silly diversions.

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Diffusion, most likely. Membrane proteins diffuse along the plane of the lipid bilayer in many extant organisms. Cytosolic proteins too are not left out, as they can sometimes diffuse through the intracellular aqueous milieu.

So if we had a prebiotic, membrane-bound “organism”, diffusion could account for the movement of proteins and other substances across its membrane and within its intracellular space.

The odds of extant proteins originating in prebiotic times are staggeringly low, so its logical to assume they were a lot simpler, maybe 7 - 30 amino acids long. Prebiotic chemical reactions could easily have synthesized these short peptides.

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I’ll take that as a no, you have no idea whatsoever whether proteins are required for life. All you know is they perform critical roles in life as we know it, that’s it.

Of course, there’s a long history of things one could have imagined were necessary to do all sorts of things, but turned out weren’t. Just up above we discovered that proteins aren’t required to catalyze peptide bond formation.

Just to pick a few other examples, it is now known that enzymes aren’t required to catalyze the reductive Kreb’s cycle, it is known that membrane transport proteins aren’t required to transport small molecules across a lipid bilayer, and that amino acid homochirality isn’t required for functional protein structures.


I don’t think this is accurate. Proteins in extant life forms are synthesized via the translation of mRNAs at ribosomes. Its extremely unlikely there were ribosomes in prebiotic times.

Then they won’t be ribosomes. Ribosomes are nucleoprotein complexes. “Pre-ribosomal RNA” would be a better descriptor.

See the latest breakthrough on the prebiotic synthesis of peptides:

Actual paper:

It turns out large proteins could have been synthesized in prebiotic times.

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