Of Codes and RNA — August 26th, 2011 by Ann Gauger
Origin of life research has problems, and here’s why. DNA carries the information necessary to build proteins. It performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins. But there is no direct way to convert a given DNA sequence into a protein sequence—no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.
That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how this process has been discovered, see Stephen C. Meyer’s Signature in the Cell [1].)
The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. Building the machinery that translates DNA into protein requires the prior existence of DNA, RNA and protein, all three. This should give us pause, because we have no naturalistic explanation for problems involving causal circularity.
So when it was discovered that some RNAs could carry out (very limited!) chemical reactions, scientists seeking a purely materialistic explanation for life’s origin were thrilled. Perhaps here was the solution to the conundrum. Perhaps RNAs could be both catalysts and information carriers. Perhaps the first living world was RNA-based.
Fast forward to now. Researchers continue to try to design RNAs that can copy themselves, and try to expand the range of chemistries they can carry out. The RNA world, if it ever existed, though, would be a very impoverished place, based on what human designers have been able to produce so far. And the problem of how an RNA world could become a DNA/RNA/protein world would remain.
Enter the Direct RNA Templating (DRT) model of Michael Yarus et al. [2]. The hypothesis was originally based on the discovery that the activity of one RNA catalyst could be blocked by the presence of the amino acid arginine. From this result Yarus hypothesized that perhaps other RNAs would show an affinity for particular amino acids. In a series of papers he and his coworkers identified other such RNAs and, based on statistical analysis, they argued that these RNAs contained a higher than expected frequency of triplets corresponding to the particular codons or anticodons now used to specify that amino acid in the modern genetic code [3].
But is their analysis correct? In a peer-reviewed paper published this week in BIO-Complexity, Stephen C. Meyer and Paul Nelson take on the DRT model [4]. They carefully examine the claims of Yarus et al. and find them wanting. Inadequate null hypotheses, arbitrary selection of data for analysis, and unrealistic assumptions about prebiotic chemistry are just a few of the problems. Rather than go through their arguments here, I encourage you to read their paper yourself.
Why does it matter? Critics of intelligent design have advanced the DRT model as the answer to the sequencing problem—how genetic information in RNA (in the hypothetical RNA world) eventually could have been translated into more stable and versatile proteins. Based on the analysis in this paper, however, the sequencing problem has not been solved, even partially. There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.
[2] doi:10.1126/science.3381099