Re: Is the paradigm of genetic code evolution wrong?

"William L Hunt" <wlhunt@xxxxxxxxxxxxx> wrote in message news:gpm3c6$c2p$1@xxxxxxxxxxxxxxxxxxxxxx
It is generally accepted that the early genetic code was simpler.
Hundreds of papers have been written attempting a glimpse of this
first simpler code.
This usually involves some smaller initial set of codons and/or a
smaller initial set of amino acids.
There have been many proposed initial simpler sets of codons and amino
acids for this first code.

Today, in every organism, the genetic code is the outcome of the
interaction of three structural units (tRNAs, aminoacylation sites and
ribosomes).

Those "aminoacylation sites" are today better known as aminoacyl-tRNA
synthases. But that mechanism for recharging the spent tRNAs could
not be the primitive mechanism (because the machinery is made of
protein). And, for that matter, the metabolic pathways for synthesizing
the amino acids are also probably not primitive (again because the
machinery is made of protein.

As I sketched here several years ago, I believe that both missing functions
(tRNA re-aminoacylation and amino acid synthesis) evolved together
with the genetic code. And that the relationship between biosynthetic
precursors and rows of the code is the essential clue.

But when I look at the result of this interaction, when each unit is
reduced to the simplest structure that is still functional, the result
is not a simpler genetic code but a much more complex code.
Everything seems turned a bit upside down. The simplest structures
produce the most complex code.

Could you expand upon this? I can easily imagine simplifications of the
machinery which would produce a simpler code. For example, it is
a simplification of both machinery and code to have a code in which
the third codon position NEVER matters (rather than the current
situation of sometimes mattering and sometimes not). And I can
imagine an earlier code which was ambiguous between valine and
isoleucine or between aspartate and glutamate. (Codon sharing).
Do you consider that kind of ambiguous code to be more complex?

As the structures evolve and become more complex, the code they
produce becomes incrementally simpler and simpler until we have the
standard code of today.

Could this view that the early code must have been simpler be
completely wrong?
I think it is.

The early code was more complex in that it coded for more specific
amino acids? More complex in that the codons were not neatly
arranged into blocks of 2 or 4? More complex in that some of the
things coded for were not amino acids?

Only the last of those sounds interesting to me.

.

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