I have located my reference on the "universal" genetic code.
Graur and Li, 2000, Fundamentals of Molecular Evolution
2nd ed. References below are from their discussion.
In any one genome, there are typically only a few
departures from the universal code. No one organism has
all the exceptions. For example, vertebrate mitochondrial
genomes have four exceptions. Departures from the
universal code typically occur in reduced genomes (e.g.,
mitochondria) with GC mutational biases. Actually, Graur
and Li claim that they are always associated with such
conditions, but I do not know myself whether there might be
some exceptions, e.g. some Paramecium species have
non-standard codes coupled with inordinate amounts of
DNA. At any rate, these nonstandard genetic codes
typically occur in those situations where evolutionary
pressures might be expected to favor them. This is not
evdence against evolution.
Jukes, 1985 proposed the codon-capture hypothesis to
explain departures from the universal genetic code.
Castresana et al., 1998 provide an example in which two
steps in the process can actually be seen in living
AAA normally codes for lysine. In hemichordate
mitochondria, it is unassigned. In echinoderm
mitochondria, it is asparagine. The evolutionary process
starts with the replacement of AAA in the genome with AAG,
which also codes for lysine, due to mutational pressures
favoring G. Next, the tRNA that carries lysine mutates its
anticodon from UUU, which paired with AAA or AAG, to
CUU, which only pairs with AAG. AAA becomes unused.
This is the condition in hemichordates (which appear from
18S to be the sister taxon to echinoderms). The next step
is a mutation in the asparagine tRNA. By changing the
adjacent U to a C, the GUU of the asparagine tRNA
becomes capable of recognizing AAA as well as its usual
AAU and AAC. At this point, AAA can reappear as a
functional codon if some of the AAU or AAC codons for
asparagine mutate to AAA. This is the condition in
echinoderms. Throughout all this, the translation of a
particular gene would remain unchanges as long as the
mutations kept pace with each other.
Codon usage is highly uneven, so the loss of rare codons
and capture by other tRNAs can occur with minmal impact
on the genome.
There is some evidence for a very different genetic code
before the origin of any modern lineage of organisms.
Inconveniently for the Discovery Institute, this consists of
evidence for the evolution of a complex system (the modern
universal code) rather than casting doubt on the
evolutionary connectedness of organisms. Several tRNAs
appear to represent ancient duplications of other tRNAs.
This implies that the common ancestor of all living
organisms was getting along with a greatly reduced
version of the present system until gene duplication
provided the opportunity to specialize into the modern level
Dr. David Campbell
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