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Adam and the Genome and the Evolution of the Genetic Code

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Much of biologist Dennis Venema’s book Adam and the Genome focuses on attempting to rebut arguments for intelligent design. This, as noted already in the present review series, may come as a surprise to the reader who was expecting a book all about Adam and Eve in light of genetic science. But it’s good to have substantive arguments from critics, including Dr. Venema of BioLogos, whatever the packaging may say.

Thus, after finishing his discussion of the evolution of new proteins, Venema asks: “So if there is good evidence that ‘complex, specified information’ can arise in sufficient quantity to account for the diversity of life, and that ‘irreducibly complex’ biochemical systems can indeed be built up over time, is there anything left to argue for within ID?” (p. 88)

We saw in the previous two installments (here and here) that Venema did not successfully show that new complex proteins can evolve, absent design. Undeterred, Venema turns to Stephen Meyer’s arguments against a naturalistic origin of the genetic code — i.e., the transcription-translation system that is used to generate proteins in every living organism. Venema cites the work of Michael Yarus, a biochemist who has investigated whether there is any biochemical basis for the origin of the genetic code. Venema states, “Some amino acids do, in fact, bind directly to their codons in the absence of tRNA molecules” and “This suggests that at least part of the genetic code passed through a stage where amino acids lined up directly on their codons rather than with the help of tRNA molecules.” (p. 87)

Venema is by no means the first person to brandish Yarus’s work in response to ID arguments. In fact, so frequent was Yarus’s work being cited after Meyer published Signature in the Cell in 2009, that in 2011 Meyer and Paul Nelson co-published a peer-reviewed technical paper responding to it in the journal BIO-Complexity.

Before discussing the problems with Yarus’s research in detail, it’s important to note what this paper does not claim to explain. It does not attempt to explain how RNA arose from simpler chemicals, nor how DNA evolved from RNA to become the information-carrying molecule of life. More importantly, it does not touch upon the central question addressed by Meyer’s book Signature in the Cell, namely, How do the nucleotide bases become properly ordered in the DNA to produce functional proteins? Even Venema admits that Yarus’s work “does not give a complete picture of how the code originated.” (p. 89)

That having been said, the arguments in Adam and the Genome about Yarus’s work were already addressed in detail by Meyer and Nelson in their technical paper. For example, Venema claims that “Some amino acids do, in fact, bind directly to their codons in the absence of tRNA molecules.” But Meyer and Nelson note multiple problems with Yarus’s claims:

  1. Yarus’s methods introduce a statistical bias that was designed to select RNAs, whether intentionally or unintentionally, that capture the relevant amino acids, even when these RNAs may have nothing to do with his direct templating hypothesis.
  2. Yarus’s work is plagued by negative results. He studied eight of the 20 or so amino acids used in living things, and claimed that out of their 48 possible codons and anti-codons, ten exhibited a statistically significant chemical attraction to their corresponding amino acid within the genetic code. Thus, Meyer and Nelson observe that “Yarus et al.’s experiments show no chemical affinity between specific triplets and their cognate amino acids in 79% of the RNA molecules they studied.”
  3. Even if there were amino acids with some affinity to RNA molecules, Yarus’s work provides no explanation for how or why those amino acids would be linked via peptide bonds, as they are in the ribosome today.
  4. Yarus has primarily studied the binding affinities of complex amino acids which require many enzymes for their production. Meyer and Nelson explain that this leads to “an acute chicken and egg problem. Which came first, the aptamer-amino acid affinities that Yarus et al. propose as the basis of the code and translation system, or the translation system that would have been necessary to produce those amino acids (and, thus aptamer-amino acid affinities) in the first place?”
  5. Meyer and Nelson explain: “[I]n addition to its other deficiencies it is important to point out that Yarus et al. do not solve the sequencing problem, although they do claim to address it indirectly. Instead, Yarus et al. attempt to explain the origin of the genetic code — or more precisely, one aspect of the translation system, the origin of the associations between certain RNA triplets and their cognate amino acids.”

Venema’s doesn’t even attempt to respond to Meyer and Nelson’s points (2), (3), (4), and (5). He does attempt to respond to point (1), but doesn’t provide the evidence to back up his response.

Venema cites the binding affinities of certain amino acids and states: “Like Behe’s, Meyer’s designer seems to choose designs that have the appearance of having evolved.” (p. 89) But if Meyer and Nelson’s arguments hold merit, then this system doesn’t look like it evolved at all, so this argument doesn’t hold up.

Indeed, Venema is aware of Meyer and Nelson’s technical paper. He doesn’t mention it in the body of Adam and the Genome, so most readers will have no idea that Meyer co-authored a detailed, technical rebuttal to the very evidence Venema is discussing. However, Venema does mention Meyer and Nelson’s paper in an endnote buried at the back of the book. There, he claims that Meyer and Nelson are wrong to argue that “the binding affinities observed between some amino acids and their codons or anticodons are merely an artifact of Yarus’s experimental design.” (p. 207) Venema writes: “This claim, however, is not supported by the evidence that Yarus and his colleagues present in their numerous publications.” But he provides no details or citations to Yarus’s other work to explain why Meyer and Nelson are wrong. At present, Venema’s counter-claim appears to be an unbacked assertion, and Meyer and Nelson’s concerns stand.

As a last point, there are some serious skeptics of the idea that the genetic code could evolve from an RNA world precursor. A recent paper in BioSystems finds the RNA world faces “insuperable” problems:

The preservation of encoded information processing during the historically necessary transition from any ribozymally operated code to the ancestral aaRS enzymes of molecular biology appears to be impossible, rendering the notion of an RNA Coding World scientifically superfluous.

(Peter R. Wills and Charles W. Carter, “Insuperable problems of the genetic code initially emerging in an RNA world,” BioSystems (2017))

In other words, the idea that an RNA-only based genetic code that uses chemistry to match amino acids to RNA (as what Yarus proposes) could transition to a genetic code that uses amino-acid based enzymes like aminoacyl-tRNA synthetases to match tRNAs with their proper amino acid (under the genetic code) “appears to be impossible, rendering the notion of an RNA Coding World scientifically superfluous.”

It seems that Yarus’s model, promoted by Venema in Adam and the Genome, has some very serious challenges yet to overcome.

Photo: Michael Yarus, by Emily Krauter via University of Colorado, Boulder.