Over the last couple of years, several people have referred me to the following paper:
Yarus M, Caporaso JG, Knight R. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem. 2005;74:179-98.
I have often been told that this review outlines very powerful evidence that shows the genetic code gradually evolved over time and sometimes been challenged to respond. The basic hypothesis is a stereochemical origin for the genetic code. The authors summarize this as follows:
It states that there is specific affinity between codons or anticodons and amino acids.and
Triplet codon and anticodon sequences from amino acid-binding structures made of something very like RNA were used to build the genetic code.
Essentially, a specific class of RNA molecules, approximately 70-80 nucleotides in length, will bind specific amino acids if the codon (or anticodon) for that amino acid is found in the binding site.
The authors summarize the experimental evidence for such codon/anticodon binding for eight amino acids: phenylalanine (F), isoleucine (I), histidine (H), leucine (L), glutamine (Q), arginine (R), tryptophan (W), and tyrosine (Y):
5. There are true negatives, such a glutamine anticodons and hisidine codons, indicating that the technique does not unexpectedly force a positive result. 6. Only one amino acid, glutamine, shows no significant association with either codons or anticodons. Stereochemical associations seem the rule raher than the exeption. 7. The amno acid sites showing strong association with cognate triplets are chemically varied: basic, polar, aliphatic, and aromatic sidechains are detected.and
It is intriguing that the one exception to stereochemical origin is glutamine, an amino acid for evidence of coevolution (see above) is among the strongest.
Yet could this be an example of something I discuss in my book? “The Duck causes us to see more ducks?”
One thing that seemed rather obvious to me was that this list of eight amino acids could have been more varied. So to follow-up my hunch, I quickly and easily located a page that describes the properties of amino acids.
If you scroll down slightly, you will find a figure that is introduced as follows:
The figure below Venn diagram grouping amino acids according to their properties. This was adapted from Livingstone & Barton, CABIOS, 9, 745-756, 1993 (PubMed), and is just one of many classifications that are possible, but is probably that which most people would agree covers the most protein contexts.
Check out the figure:
Figure 1. Amino acids grouped by properties.
Now consider what happens when we score the amino acids from the Yarus et al. review:
Figure 2. Amino acids that bind codons or anticodons in red; non-binder in blue.
It looks like it could be more varied to me. It is not clear that we should conclude “stereochemical associations seem the rule.” From these data alone, we might alternatively conclude that stereochemical associations occur among a distinct and clustered subset of amino acids. Hmmm.
What’s more, consider what happens when we next include the amino acids that were generated by the Miller-Urey experiments:
Figure 3. Amino acids that bind codon/anticodons in red; amino acid that doen't bind codons/anticodons in blue/ amino acids recovered from Miller-Urey experiment in yellow; amino acids recovered in Miller-Urey experiment and that bind their codons/anticodons in orange.
Like I said, could the Duck being causing us to see more ducks?
More later……