Eluem Blyden wrote:
>> I am interested in codon bias as a combinatorial optimization
> problem...in some organisms, "optimal" codon usage appears to be
> correlated with the level of gene expression--highly expressed genes use
> the optimal codons whereas genes with lower expression use rare codons.
> Essentially, I am interested if this pattern results from a complex
> optimization process?
Well, my first response is to suggest that all evolutionary processes
are 'complex'. As for codon usage patterns in organisms that
preferentially use a particular subset of codons in their highly
expressed genes...well this is a result of selection, and selection is
at work in many, many ways, not just at the level of codon usage.
Q. Is it a complex optimization process, then?
A. No more so than the evolution of a particular gene (if a mutation
occurs and this mutation is selectively positive, then it has a good
chance of becoming fixed). In the case of codon usage, if a mutation
occurs (at a synonymously degenerate site) and it confers some selective
advantage, then it has a good chance of becoming fixed...and so on. The
net result is that some genes are more 'optimally' suited to life in a
particular organism, because of their codon usage. To me this seems
like any other type of evolution (a gene with an extra cysteine or
proline might be more stabe at higher temperatures and so might be more
suited to life in a thermophile than an ortholog without these amino
Hope I'm making sense.
> Does one need more proof of this than coming up with the question? I
> mean, how else could one possibly encode all the temporal and relational
> compexity of expressing the right genes at the right place, at the right
Read one of Richard Dawkins books.
> The problem with molecular biology is that it insists on having a
> central dogma and is actually PROUD of that!!! Codons are context
> sensitive, complex repositories of information about 3 different four
> dimensional molecules (DNA/RNA/Protein; 4th D = time). Gene expression
> is not only the basis of conciousness it is a kind of conciousness of
> its own.
>> Bias. What does that mean? How prejudicial can you get? the word you
> are looking for is ENTANGLEMENT. "NO DNA makes NO RNA makes NO PROTEIN"
> to paraphrase....
Now I'm lost.
> Nevertheless, I would be interested to know what references you do find
> if you are willing to share them. Thanks in advance.
> Eluemuno R. Blyden,PH.D. Khepera
I'm glad that you have put so much though into this and I'm sure we
would benefit by a more lengthy explanation of your hypotheses and
thoughts. For reading, try anything by:
Sharp, P., Lloyd, A.T., Ikemura, T., Grantham, R., Woulfe, K.,
Andersson, S.G.E., Bulmer, M., Shields, D.C. and so on.
James O. McInerney Phone/Voicemail: +44 171 938 9247
Senior Scientific Officer, email:j.mcinerney at nhm.ac.uk
The Natural History Museum,
London SW7 5BD
Whenever I think of the past, it brings back so many memories...