How to be wrong big time

I was just reading some feedback I gave after the EPSRC Systems Biology Meeting where I said that the Codon usage work of Prof. A. Carbone was not relevant to Systems Biology. I cannot think why I was so negative as I remember discussing her work with Prof. Johnjoe McFadden in the taxi and how important it could actually be. It might be very significant because it forces us to re-evaluate the Darwinian view of evolution as a universal tree of life. It makes it much more likely that the view of Manfred Eigen of an evolutionary Bramble Patch rather than a nicely branched tree is much more likely.

The key point is that codin usage amongst bacteria clusters them according to their lifestyles. These relationships are highly poly-phyletic - there is not a single ancestral line that can be traced between the organisms so this means there has to be considerable convergence in the evolution of lifestyle. This is actually a perfect example of how chemistry and physics constrain biology to end up with the same solution to solve the same problem but from many different directions. We see this in mass and flight speed in insects, birds and mammals - engineering defines the system.

The question is why is there a link between codon usage and life style? Here is a wild guess or two:

• Environmental availability of resources will be similar for similar lifestyles - chemical restrictions.
  
• Thermostability will be one of the driving factors.