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  Topic: The Canonical Genetic Code, Resources & arguments< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 26 2002,00:55   

Ooh, another great opportunity for collaboration.  This is a huge topic with a lot of literature, so unless one happens to be a biochemist who did their PhD. on the topic it is hard for one person to scrape together the diverse information & references that are necessary to explain the problems with Paul Nelson's pseudoargument to the public.  I think Ken Miller's replies had some difficulty in this regard (and I don't even recall the statement "universal genetic code" being in the actual Evolution series -- is this just me missing it or is it actually there?)

The most complete presentation of Nelson v. common descent that I can recall was a longish talk that I recall listening to online -- but I can't find it at the moment.  Is there a good online essay where Paul Nelson actually lays out the argument from "the genetic code isn't quite universal" to the conclusion "common descent is false [to some unspecified degree]"?

Anyhow, Nelson's argument went like this:

- the code was thought to be universal, and this was crowning evidence for common descent because the code couldn't change because intermediate stages are fatal so it must have come from a common ancestor

[actually, it was just one of many pieces of evidence, but whatever]


- but it's not quite universal, therefore either:

(a) the code can change after all
(b) common descent is false

- Nelson doesn't like (a), citing a (single) paper that criticizes another (single) scientist's proposal about how a codon assignment could change.

- therefore evolutionists are dogmatically clinging to an auxilliary hypothesis that is shielding their main theory from rigorous testing.

I'm sure I'm oversimplifying, I heard the talk last year, but that's basically it.


However, I recall doing some digging on these arguments for an ARN post or two, I will see if I can find them...

Hmm, as usual the ARN UBB search engine is proving useless.  Well, here's some general points regarding "deviant/noncanonical genetic codes":

(1) Deviant genetic codes are most common in critters/organelles with small or otherwise weird genomes, e.g. ciliates (which Nelson specifically mentions IIRC):

Quote

Pubmed link

The molecular basis of nuclear genetic code change in ciliates

Quote: "Most changes in the genetic code involve termination: this may be because stop codons are rare, occurring only once per gene, and so changes in termination are likely to be less deleterious than change in sense codons. This would be particularly true for those species of ciliates whose genes reside on gene-sized chromosomes and/or have short 3' untranslated regions. In addition, termination is a competition for stop-codon-containing ribosomal A sites between release factors and tRNAs. Consequently, relatively small changes either in the tRNAs or in eRF1 may shift this balance toward partial or complete readthrough in some cases. For instance, Bacillus subtilis uses in-frame UGA codons extensively to encode tryptophan; however, this readthrough is inefficient, and UGA is also used as a stop codon [33, 34] . The abundance of stop codon reassignments relative to amino acid codon reassignment, however, could also be an observer bias. In-frame stop codons are much easier to detect in protein coding sequences than amino acid replacements, especially if the latter have similar properties."



(2) Some organisms, extant today, have ambiguous codon assignments (i.e. one codon codes for both an amino acid and 'stop' at the same time, proving that this is not necessarily a fatal situation, contra Paul Nelson.

[I've seen this stated in an article somewheres, if anyone else finds examples they might post them.  They pretty clearly refute the "transitional stages impossible" contention.]


(3) Deciding whether or not the code is optimal, how optimal, and how much a potential "frozen accident" is by no means a simple question as Nelson seems to assume.

The below paper argues for optimality in at least one sense, but note the back-and-forth, and how what constitutes "optimal" may be different for different organisms at different times (& which may thus result in the evolution of code deviants).

Quote

Pubmed link -- free online BTW

Mol Biol Evol 2000 Apr;17(4):511-8

Early fixation of an optimal genetic code.

Freeland SJ, Knight RD, Landweber LF, Hurst LD.

Department of Ecology, Princeton University, University of Bath, Bath, England.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible. Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space. This result is robust to variation in the methods and assumptions of the analysis. Although significantly better codes do exist under some assumptions, they are extremely rare and thus consistent with reports of an adaptive code: previous analyses which suggest otherwise derive from a misleading metric. However, all extant, naturally occurring, secondarily derived, nonstandard genetic codes do appear less adaptive. The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error. Potential criticisms of previous analyses appear to be without substance. That known variants of the standard genetic code appear less adaptive suggests that different evolutionary factors predominated before and after fixation of the canonical code. While the evidence for an adaptive code is clear, the process by which the code achieved this optimization requires further attention.


...and also note the rather unambiguous first sentence of the introduction of this article:

Quote

All known nonstandard genetic codes appear to be secondarily derived minor modifications of the canonical code (Osawa 1995).


Here is their conclusion FYI:

Quote

The Mechanism of Adaptive Code Evolution

This leads to the question of the evolutionary mechanisms responsible for an adaptive canonical code. The many models of precanonical code evolution, reviewed extensively elsewhere (Knight, Freeland, and Landweber 1999 ), permit two major possibilities: that an adaptive code was selected from a large pool of variants, or that an adaptive code arose de novo by code expansion (or simplification) within adaptive, error-minimizing constraints. Individual codon reassignments, necessary for adaptive code shuffling, are certainly possible, but the question remains unresolved, and two lines of evidence increasingly favor the latter explanation.

First, the notion of code expansion from a simpler primordial form, although still lacking in detail, is now associated with a diverse body of empirical and phylogenetic evidence (Knight, Freeland, and Landweber 1999 ). It seems unlikely that clear patterns of biosynthetic relatedness would be found in a code which had undergone extensive codon assignment shuffling. Additionally, while adaptive code structure is unlikely to be an artifact of a stereochemically determined code, empirical evidence suggests that stereochemistry is not without a role. For example, RNA molecules artificially selected to bind Arginine contain disproportionately many CGN/AGR codons (Knight and Landweber 1998 ). If all or most amino acids show stereochemical affinities for their corresponding codons, this would suggest that natural selection worked in concert with stereochemical interactions and biosynthetic expansion to produce the canonical code de novo, "choosing" the current 20 amino acids as those that satisfied criteria for both stereochemical affinity and error minimization. This interpretation would thus offer a novel insight into the selection of the proteinaceous amino acids from the near-infinite possibilities of both prebiotic syntheses and biosynthetic modification.

Conclusions

We have presented comprehensive evidence that the standard genetic code is a product of natural selection to minimize the phenotypic impact of genetic error; the arrangement of codon assignments meets, to an extraordinary degree, the predictions of the adaptive hypothesis and cannot be explained as an artifact of stereochemistry, biosynthetically mediated code expansion, or analytical methodology. However, the process by which an adaptive code evolved at present remains unclear, and yet its resolution may be of key importance to our understanding of the amino acid components universal to life.


This is the Osawa reference which looks to be key:

Osawa, S. 1995. The evolution of the genetic code. Oxford University Press, Oxford, England.


Anyhow, as usual when one begins to investigate the actual biology of an ID argument, one finds that the IDists are taking a thoroughly myopic view instead of looking at the broad range of evidence that is necessary.

Thanks, nic

  
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