The conclusion of the paper you cited is especially interesting. They see that epigentic inheritance seems especially transitory, yet conclude that the resulting major changes in body plan that can result could bring about major evolution once the different methylation pattern is established.
http://www.dbmi.columbia.edu/~xiw7002/xiaoyan_files/N_genetics.pdf
Because of the inherent instability of epigenetic inheritance, fixation of an epigenetically-determined phenotype is probably less stable than fixation through a genetic selection mechanism. Waddington, for example, was unable to reduce the frequency of the crossveinless phenotype in negative selection experiments once the phenotype was fixed17. In contrast, after only two or
three generations of negative selection, we observed a complete reversion to wild-type frequency of ectopic outgrowth in our sensitized iso-KrIf-1 strain in the geldanamycin selection experiment (data not shown). Similarly, epigenetic traits such as color
variegation or cold adaptation in plants are unstably inherited18,19. Therefore, a combination of both epigenetic and genetic mechanisms is probably required to explain the rapid changes in body plans that are observed in the fossil record20
Are we both agreed that this is where the next battleground will be fought between creationists and evolutionists? And it makes me wonder (to quote LedZep) about the citrate plus e.coli. Namely, what would happen if they removed the citrate diet? If after removing the citrate diet the e.cole reverted back to the original after X number of generations, then the so-called random mutations would not have been random at all, but rather epigenetic responses to environmental stresses (which has been my suspicion all along, btw).