The BioLogos website’s Open Forum includes a thread, “A plethora of thoughts on Intelligent Design,” which is aptly titled. It is loooong, highlighted by musings from ID critic and computer science Josh Swamidass of Washington University, last seen attempting to show how cancer disproves intelligent design. BioLogos includes a helpful feature that gives a current approximate reading time to peruse the whole discussion — 85 minutes. Yikes.

With other business to attend to, we won’t claim to have read the whole thing, but one comment by a BioLogos reader, going by the name Benjamin Kirk, or “benkirk,” was noted by an email correspondent who asked about it. Kirk thinks he has caught Stephen Meyer in a damning error in Signature in the Cell:

Meyer simply makes the false claim that peptidyl transferase is a protein. So despite an entire chapter devoted to the RNA World hypothesis, he just happens to characterize the single strongest evidence for the hypothesis in a completely false way. Ignorance cannot be an excuse, as Meyer even cited Wally Gilbert’s single-page News&Views paper in which this prediction was clearly stated (Nature 319:618, 1986)!

“But a few RNA enzymic activities still exist, the two described recently, and possibly others in the role of ribosomal RNA or in the splicing of eukaryotic messenger RNA.”

Meyer has neither acknowledged nor corrected the false claim.

Our correspondent, with no expertise in transcription/translation or peptidyl transferase, wants to know if Meyer has been caught out. No, he hasn’t. The story is a bit complicated so here’s a quick summary, followed by an elaboration.

There has been a longstanding debate over the nature of the peptidyl transferase, but we now know it’s made of RNA. Meyer mentions “peptidyl transferase” in two places in Signature in the Cell: Chapter 5 and Chapter 14. In Chapter 5, he calls it a “protein.” This is indeed mistaken, as peptidyl transferase is really RNA.

But it doesn’t affect his argument in any way whatsoever. In Chapter 5, he’s just explaining and describing the numerous “integrated” parts and processes involved in transcription and translation.

In Chapter 14, Meyer notes that peptidyl transferase is now known to be semi-accomplishable via engineered ribozymes using RNA alone — not just RNA plus protein! [Note: The term “peptidyl transferase” is interesting in that it can be used to refer both to a biological molecule and to a biological process. See Wikipedia, which states, “Peptidyl transferase is an aminoacyltransferase (EC 2.3.2.12) as well as the primary enzymatic function of the ribosome.”] Judging from the literature, this seems to be correct. So Kirk’s complaint that Meyer ignores evidence for the RNA World (i.e., that peptidyl transferase can be accomplished using RNA) is false.

In other words, in the place where Meyer erroneously calls it a “protein,” the error doesn’t affect his argument. In the place where it matters, Meyer correctly notes that peptidyl transferase can be accomplished with RNA and shows how this still doesn’t support the RNA World. So he addressed the core of Kirk’s complaint, and in the one place where it could have affected Meyer’s argument he gets it right. The whole complaint reduces to nitpicking. What else is new?

If this satisfies you, you can stop reading here. Want to know more? Then proceed.

As Benjamin Kirk points out about peptidyl transferase, Meyer in Signature in the Cell calls it a “protein,” writing: “A protein within the ribosome known as a peptidyl transferase then catalyzes a polymerization (linking) reaction involving the two (tRNA-borne) amino acids” (p. 128).

As noted, we now know that the peptidyl transferase center, where the active site is, is RNA. See Figure 2A here. Note that while the peptidyl transferase center itself is composed of a lot of RNA, surrounding it are some interwoven proteins.

So let’s look briefly now at Meyer’s Chapter 5 and Chapter 14.

In Chapter 5, “The Molecular Labyrinth,” he discusses many of the numerous components that are necessary for transcription and translation. Some of these components Meyer recognizes are RNAs, while some of these Meyer recognizes are proteins. His point is that a whole suite of components are necessary and thus the process shows “integrated complexity” (p. 132) or “functional integration” (p. 132) where many parts of both RNA and protein are necessary. Here’s the thrust of his argument:

These and other developments in molecular biology since the 1960s have shown that the information-processing system of the cell depends on a “tightly integrated” system of components-indeed, a system of systems. Both the transcription and translation systems depend upon numerous proteins, many of which are jointly necessary for protein synthesis to occur at all. Yet all of these proteins are made by this very process. Proteins involved in transcription such as RNA polymerases, for example, are built from instructions carried on an RNA transcript. Translation of the RNA transcript depends upon other specialized enzymes such as synthetases, yet the information to build these enzymes is translated during the translation process that synthetases themselves facilitate. (p. 133)

As far as this argument goes, if the peptidyl transferase enzyme is made of protein, RNA, or both really doesn’t matter. There are so many parts he discusses — some protein, some RNA, some both — that if one happens to be “both” rather than just “protein” it does nothing to change the vast number of parts and the integrated complexity necessary for transcription and translation.

If you read Meyer carefully, it’s easy to see that he acknowledges that translation involve both RNA and protein. Here’s what he writes in Chapter 5:

For their part, ribosomes must also perform many functions’ These include : (l) enhancing the accuracy of codon-anticodon pairing between the mRNA transcript and the aminoacyl-tRNAs, (2) polymerizing (via peptidyl transferase) the growing peptide chain… (p. 130)

The overall description is correct. And if you read what Meyer writes in Chapter 14, you’ll see that he qualifies the nature of peptidyl transferase and greatly mitigates the error in Chapter 5. In Chapter 14, “The RNA World,” Meyer critiques the RNA World hypothesis. He goes into more detail about the irreducible complexity of the protein-production process, and argues that it could not have evolved from an RNA World precursor:

In short, the evolving RNA world would need to develop a coding and translation system based entirely on RNA and also generate the information necessary to build the proteins that later would be needed to replace it. This is a tall order. The cell builds proteins from the information stored on the mRNA transcript (i.e., the copy) of the original DNA molecule. To do this, a bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). (p. 305)

As you see, Meyer explicitly acknowledges that coding, transcription, and translation involve both proteins and RNAs.

RNA World proponents get excited when we find cellular components that use RNA because they claim these are relics from the RNA World. Kirk insinuates that when Meyer claims that peptidyl transferase is a “protein,” he’s trying to hide the fact that peptidyl transferase is made of RNA, which would point to an RNA World origin.

But in Chapter 14, when he discusses the RNA World, Meyer doesn’t claim that peptidyl transferase can only be accomplished via protein. So it’s not as if he is trying to hide anything. He writes:

Advocates of the RNA-world hypothesis have defended the possibility because of the demonstrated catalytic properties of some RNA molecules. Eugene Koonin and Yuri wolf, two prominent scientists at the National Center for Biotechnology Information, recently reviewed the results of research on the capacities of RNA catalysts in an important article assessing the plausibility of an RNA-based translation system. They note that in the last twenty years, molecular biologists have documented, or engineered, ribozymes that can catalyze “all three elementary reactions” required for translation, including aminoacylation (the formation of a bond between an amino acid and an RNA), the peptidyl-transferase reaction (which forms the peptide bond between amino acids), and amino-acid activation (in which adenosine monophosphate is attached to an amino acid). (p. 306)

Meyer then goes on to offer strong critiques of the argument from the catalytic ability of ribozymes. Suffice to say engineered ribozymes can’t do nearly what real biological systems do:

At first glance, these results may seem to support the feasibility of an RNA-based translation system. Nevertheless, significant reasons to doubt this aspect of the RNA-world hypothesis remain, as Koonin and Yuri note. First, though ribozymes have demonstrated the capacity to catalyze representative examples of the three main types of chemical reactions involved in translation, they have not demonstrated the ability to catalyze anywhere near all the necessary reactions that fall within these general classifications. … Thus, even in the one case where ribozyme engineers have produced an RNA-aminoacyl catalyst, the ribozyme in question will not produce a molecule with a functional specificity or capacity to perform coordinated reactions, equivalent to that of the synthetases used in modern cells. Yet without this specificity and capacity to coordinate reactions, translation — the construction of a sequence-specific arrangement of amino acids from the specific RNA transcript — will not occur. Similar limitations affect the RNA catalysts that have been shown to be capable of peptidyl-transferase activity (i.e., catalyzing peptide bonds between amino acids). These ribozymes (made of free-standing ribosomal RNA) compare quite unfavorably with the capacities of the protein-dominated ribosomes that perform this function in extant cells. For example, researchers have found that free-standing ribosomal RNA can only catalyze peptide-bond formation in the presence of another catalyst. More important, apart from the proteins of the ribosome, freestanding ribosomal RNA does not force amino acids to link together into linear chains, which is essential to protein function. (p. 306)

Finally, what about Kirk’s claim that RNA usage in peptidyl transferase is some amazing prediction made by RNA World proponent Walter Gilbert in his famous 1986 paper that coined the term “RNA World” (Nature, 319:618, 1986)? Kirk offers this quote from the paper:

But a few RNA enzymic activities still exist, the two described recently, and possibly others in the role of ribosomal RNA or in the splicing of eukaryotic messenger RNA.

Though this was in truth a far-sighted prediction, it is only more after-the-fact circumstantial evidence for the RNA World — the kind they almost always offer.

In Signature in the Cell, Meyer acknowledges that RNA is used all over the cell, and in Chapter 14 he points out that peptidyl transferase activity can be carried out directly by designed ribozymes. This indicates there was no attempt to deceive, which is the heart of the charge advanced by Benjamin Kirk. So what’s the big deal? There isn’t one.

There are, however, numerous unresolved problems for the RNA World thesis (for instance, see here and here). Meyer mentions many of them in the book. Kirk is invited to read a little more carefully next time.