A review paper worth checking out in Molecular Ecology, Variation within and among species in gene expression: raw material for evolution. The salient bit:
We find: (i) microarray-based measures of gene expression are precise given appropriate experimental design; (ii) there is large inter-individual variation, which is composed of a minor nongenetic component and a large heritable component; (iii) variation among populations and species appears to be affected primarily by neutral drift and stabilizing selection, and to a lesser degree by directional selection; and (iv) neutral evolutionary divergence in gene expression becomes nonlinear with greater divergence times due to functional constraint.
In Darwin's Dangerous Idea Daniel Dennett contended that selection is "substrate neutral." If that is so than the wide open realm of gene regulation and differential expression is going to be a twist on a familiar theme.
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I agree with Dennett. It's the code that's important. Gene expression became easy to understand when I started thinking of it in terms of programming conditional statements: IF (foo) THEN {bar}. (Or for loops, while loops, etc.) Just like in any program you can also have nested conditionals, where activation of one gene causes a cascade of expression in numerous others. So mutation/selection for gene expression is just mutation/selection on the conditional portion of the code rather than the corresponding commands. In this light there's nothing novel or surprising about it.
Also demystifies a lot of the nonsense about "humans and chimps (or whatever) share 90-howevermuch % of their genes in common! How can they be so different?" A small change in the "if"s can make a huge diff.
Bingo, Agnostic!