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  Topic: Evolution of Genetic Code, Addendum< Next Oldest | Next Newest >  
JxD



Posts: 16
Joined: Dec. 2002

(Permalink) Posted: Dec. 30 2002,21:53   

David Ardell has several papers he authored on this subject, linked on his website at Stanford.

There is also The Coevolution of Genes and the Genetic Code, put up at the Santa Fe site.

Other interesting papers:
Shigehiko Kanaya, Yuko Yamada, Makoto Kinouchi, Yoshihiro Kudo, Toshimichi Ikemura:
Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis
J Mol Evol 53 (2001) 4, 290-298

Robin D. Knight, Laura F. Landweber, Michael Yarus:
How Mitochondria Redefine the Code
J Mol Evol 53 (2001) 4, 299-313

Shin-ichi Yokobori, Tsutomu Suzuki, Kimitsuna Watanabe:
Genetic Code Variations in Mitochondria: tRNA as a Major Determinant of Genetic Code Plasticity
J Mol Evol 53 (2001) 4, 314-326

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 31 2002,12:52   

Thanks!

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 31 2002,17:16   

If I had a month or two, I would review the literature on the question of "optimality" of the genetic code.  It seems to me that there are many different ways that the code could be optimal, and other variations which might not make any difference.

E.g., if every amino acid kept the same number of codons, etc., but the standard table was simply "flipped" right-to-left, would this make any difference?

I have no idea myself, but such things are important to think about.  Wes had some pretty good stuff on this posted somewhere at one point...

  
Wesley R. Elsberry



Posts: 4807
Joined: May 2002

(Permalink) Posted: Jan. 01 2003,01:59   

You might be thinking of this thread.

Basically, I took up the question of how many different codes could be constructed with the same statistical properties as the canonical genetic code, and found the number to be very large indeed, around 2.3e69.

Wesley

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Jan. 03 2003,20:59   

Quote (Wesley R. Elsberry @ Jan. 01 2003,01:59)

Ah, that's it.  Lots of good material there.

Briefly, here is an important argument rarely made:

1) Number of combinatorially possible codes:
Lots and lots and lots

2) Number of "optimal" codes:
A lot less, but probably still lots

If #2 is true, then the argument for the monophyly of extant life based simply on the canonical code (leaving aside all of the other evidence for the monophyly of life) remains strong, because there would be no reason for independent origination events to land on one or the other of the equally optimal codes.

E.g., if n = # of equally optimal codes = 10, then the random probability of (say) the three domains of life landing on the same code is p = 1*1/10*1/10, or 1/100.  This is already quite a coincidence on the independent origins hypothesis.  The probability of (say) 20-odd animal phyla landing choosing the same code out of a range of 10 equally optimal codes would be 1/10^20, already quite astronomical.

And of course if there were more like 1000 or 1 million equally optimal codes, then the random probability of independent origins hitting on the same code goes up exponentially factor.

Note that these results hold even if the canonical code is literally "one in a million", since there are many more combinatorially possible codes than a mere million.

The only way for the independent design hypothesis to produce nonrelated organisms with the same code is to postulate some motive for the IDer to design things this way on purpose -- but postulating motives is something that IDists refuse to do, at least officially.

nic

  
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