Re: Genetic Code Evolution Paper

I made several errors due to sloppy reading in my comments about this
paper. They are corrected below.

"Perplexed in Peoria" <jimmenegay@xxxxxxxxxxxxx> wrote in message news:dh1iel$2krb$1@xxxxxxxxxxxxxxxxxxxxxx
> I came across this paper which is quite similar to the postings I
> made on this subject a few months ago.
> http://www.pnas.org/cgi/content/abstract/102/12/4442
>
> The big difference is that they postulate a set of two-nucleotide
> 'adapter' molecules (much like Crick's hypothesis) that functioned
> like tRNAs before ribosomal translation got started.

My bad. The two nucleotide entities that they postulate do not work
like Crick's adapters. They play no role in coded peptide/protein
synthesis. Instead, they are involved in organizing a 'metabolic
code'. In this regard, they are more similar to my pre-translation
ideas than I realized.

> They even suggest, as I did, that alpha-keto acids were the molecules
> charged onto the adapters and that they were reductively aminated there.
>
> One of the authors - Morowitz - has written much that I admire
> regarding the priority of membranes in the OOL and the plausibility
> of an autotrophic origin. This is the first time, AFAIK, that he
> has written anything specifically about the code.
>
> One of the other authors is from the Santa Fe Institute, so I will
> blame him for the mistakes and faulty logic that appear in the paper.
> ;-)

Morowitz and the SFI author - Eric Smith - coauthored another PNAS
paper that is worth a look. In it, they promote the reductive
citric acid cycle as the first network autocatalytic metabolic cycle.
However, unlike Wachtershauser, they think it can be done without
mineral catalysts. They even bring in an argument remarkably like
that of Dewar (discussed here in the MaxEP threads) which they claim
might be used to show that there cycle is the most likely possible
cycle that might arise.

> One example of this may be found in the first paragraph, where they
> write:
> ...codons for Glu and Pro both begin with C, and those for Cys and
> Leu begin with U. Codons beginning with G encode amino acids that
> can be formed by direct reductive amination of a simple alpha-keto acid.
> These include glycine, alanine, aspartate, and glutamate, which can
> be formed by reductive amination of glyoxalate, pyruvate, OAA, and
> alpha-KG, respectively.
>
> Well, I'm pretty sure that codons for Glu don't begin with C. Perhaps
> they meant Gln. And ALL amino acids except proline can be (and are)
> formed by reductive amination of simple alpha-keto acid. The ones
> they list are merely the best known alpha-keto acids.
>
> While their theory is quite similar to mine regarding code evolution,
> it is dramatically different regarding the origin of ribosomal
> translation. They have mRNAs before ribosomes. I don't. Their
> theory means that some coded proteins would have been available
> when ribosomes and tRNAs were inventing modern translation. But
> it makes it incomprehensible why modern translation would be so
> mechanically different from primitive translation. And why it makes
> so little use of coded proteins.

My bad again. They don't talk about translation using their scheme
at all. They talk very little about a transition from their metabolic
scheme to real translation using tRNAs and ribosomes.

[snip remainder of my review - which was mistake free ;-) ]


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