User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/18

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The Simulink version

 * I was working all the day in the Simulink version of the AKT model. It was an exhausting activity, because of the involved number of parameters and variables. I think that the experience was ggod, but the next time I would make first an sketch of the diagram by hand and the I will codify it.

The papers of Andreas Wagner on Robustness, Energy Consumption, and Robustness Evolvability
During the night I read the following papers:


 * 1) A. Wagner (2007): Energy Costs Constrain the Evolution of Gene Expression. Journal of Experimental Zoology (Mol dev Evol), 308B:322-324 (PDF file: [[Media:JEZ_MDE07_exprcost.pdf]]).
 * 2) * The paper argues about the energy cost associated to the synthesis of nucleotides, amino acids, as well as their polymerization into RNA and proteins. The author shows that changes in gene expression coming from mutations are not selectively neutral, i.e. the evolvability is reduced when the cost increases. The results are based on protein half-life information obtained at the genome scale. The paper shows a graphic with th einformation concerning the percentage of the cell energy budget associated with the simultaneous doubling of mRNA (in yeast) and protein expression of a single gene, as might occur after a gene duplication event. It seems that the average (median) yeast protein can change its expression only by 0.5% without a change in energy costs visible to natural selection. The paper does not explain what is understood by 'visible to natural selection', I must then check this concept somewhere else, in previous papers by the same author, I think.


 * 1) A. Wagner (2007): Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B, No. 275, pp. 91-100(PDF file: [[Media:PRS07_RobEvo_eprepub.pdf]]).


 * 1) S. Ciliberti, O. C. Martin, A. Wagner (2007): Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology. PLOS Computational Biology, Vol. 3, Issue 2, pp. 0164-0173(PDF file: [[Media:PlosCompBio07_Cili_main.pdf]]).
 * 2) A. Wagner: Energy Constraints on the Evolution of Gene Expression (2005). Mol. Biol. Evol. 22(6):1365-1374(PDF file: [[Media:MBE05_exprcost.pdf]]).

I think that it would be better if I read again the previous papers, to have in mind the arguments exposed there.


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