Tuesday, October 18, 2011

Two-Fold Fragile Codons and Amino Acids

If you read Brian Cusack’s paper (discussed here) you may have wondered why the evolutionists did not distinguish the two-fold fragile codons from the single-fold fragile codons. Perhaps I missed it, but I saw no mention of this distinction. The evolutionists define as “fragile” those codons that can be changed into a STOP codon with a single substitution. They are shaded gray in the table below (from Figure 1 in the paper):

For instance, TCG, which codes for the amino acid serine (Ser), becomes a STOP if the cytosine (C) at the second position is replaced with an adenine (A). As the table shows, there are 18 such codons (shaded in gray).

But of these 18 “fragile” codons, five of them are two-fold fragile. That is, there are two different substitutions that can change the codon into a STOP. The other 13 codons are single-fold fragile in that one and only one substitution can effect the change to a STOP.

The two-fold fragile codons are: TTA, TCA, TAT, TAC and TGG. The first two code for the amino acids leucine (Leu) and serine, respectively. The next two both code for tyrosine (Tyr), and the final one codes for tryptophan (Trp).

This leads to another distinction. The evolutionists also point out that there are six amino acids that are coded for exclusively by fragile codons. They are also shaded in gray in the figure (Tyr, Gln, Lys, Glu, Cys and Trp). These are the “fragile amino acids.”

But Tyr and Trp—both aromatic hydrophobics and the two largest amino acids—are coded for exclusively by two-fold fragile codons. We might call them the “two-fold fragile amino acids.”

The theme of the evolutionists’ paper is that these fragile codons appear less frequently where transcriptional error correction mechanisms are less effective. Fewer fragile codons means there will be fewer erroneous STOP signals in regions where they are more likely to go uncorrected.

All that makes sense, but why didn’t the evolutionists mention the two-fold fragile codons and the amino acids that are coded for exclusively by them? Would they not have expected the correlation with the correction mechanisms to be even stronger? Am I missing something, or could this be yet another case of evolutionary confirmation bias by the authors and reviewers?

1 comment:

  1. I see nothing in the paper indicating that the authors noticed "two-fold fragile codons." If they had, would it have altered their conclusions in any way?

    Was it an oversight or "evolutionary confirmation bias"? The data they used are available in publicly accessible databases (see Materials and Methods). Since your intellect is not clouded by evolutionary bias, why not test your hypothesis? There might be a paper in it!