An ID hypothesis: Front-loaded Evolution

Given that the PAM matrix more accurately portrays amino acid similarity from an evolutionary perspective (that is, the PAM matrix shows amino acid similarities based on what amino acid substitutions have been accepted by natural selection over evolutionary time)

Massimo Di Giulio (2001) argues that this actually makes approaches such as Freeland's tautological since the nature of the genetic code has had a significant effect on the distribution of amino acid substitutions making it far from an independent measure of the optimisation of that code.

TTFN,

WK

I'm not quite sure what you are asking about here Jar. The question of universality which your quote from Freeland addressed is pretty clear, there is no 'Universal' genetic code but there is one that is by far the most prevalent standard.

That is a very distinct question to the one the paper I referenced addressed towards the optimality of the standard genetic code. In fact the Freeland paper you referenced doesn't really say much about code optimisation at all.

TTFN,

WK

I just performed the same search, on the NCBI site limiting the search to the Prokaryota, and there were indeed hits below the 1e-05 level, a grand total of three of them and all from the same thing, a putative paired box domain protein from the protobacteria Methylocystis. I imagine that the sequence similarity is why this is identified as a putative paired box domain protein in the first place.

The region that comes up only covers 23% of the submitted amino acid sequence and has a maximum identity of 30% and less than 50% for positive (BLOSUM62 compatible) sites. If this was what he got then I'm not surprised Genomicus didn't want to go into any more detail about the results since they are so weak.

Perhaps more relevantly all of the lower hits are from tranposon and insertion sequences, suggesting that what we are seeing is a convergent signature for DNA binding interacting activity rather than an ancestral relic of a front loaded primeval PAX gene lineage. To support this the SMART database of protein architecture identifies 3 bacterial hits for the PAX domain and all 3 are from transposase sequences.

TTFN,

WK

Edited by Wounded King, : No reason given.

On another related point, if you take the mRNA coding for the sequence that Genomicus chose and blast that against the Prokaryota then you get no significant hits. As with the prestin gene the convergence at the amino acid sequence level does not extend to the DNA sequence, rather undecutting the contention that these reflect a deep ancestral genetic sequence.

In fact I was surprised not to get any significant hits since you would expect the selection for the similar amino acid sequences to produce some convergence, as there was some evidence for in the prestin paper, then again that similarity itself is so low that once the degeneracy of the genetic code is factored in perhaps there is no reason to expect any significant similarity at the DNA level.

And I'm not even going to start pointing out how massively unlikely such a handful of hits, especially ones so minimally below the significance level, is to support the sort of scenario Genomicus outlines when the sequences seem to be missing from the vast majority of all other prokaryotes.

Once again as with the prestin example if you take out virtually all the other context and cherry pick your organisms you can produce what look like highly unlikely convergences. But if you look below the amino acid level and include a wider panel of organisms the proposed examples of some sort of programmed genetic response become nothing but smoke on the wind.

TTFN,

WK

Fair enough, I'll admit that my experience is mostly based around comparative genetics amongst metazoans. The only bacterial sequences I generally encounter are in plasmids.

TTFN,

WK