My question is : Does a cellular process exist which deliberately alters the structure of the genome?
Depending on what exactly structure of DNA means in this sentence, yes, definitely - as an absolute fundamental part of Eukaryotic biology.
Simplifying a little: DNA is a long thin molecule, in normal cells it is wrapped and coiled up with proteins into chromatin. How loosely or tightly this chromatin is packaged is a fundamental part of gene regulation. In fact, it's coming to be seen as the major unsolved part of how gene regulation works, probably as important as transcription factor regulation.
What's more a significant part of the control of how chromatin is arranged is through DNA modification via methylation (a semi-heritable form of epigenetic control).
So, yeah, cells modify the structure of their DNA both chemically and physically.
In any case, this:
quote:
Thus the cell is no longer a Cartesian duality, meaning separate molecules as information carriers, and a separate set up for carrying out that information. Or the whole cell participates in the cellular process.
is wrong anyway. Early work on DNA may have thought that, but it's well understood that the idea of passive DNA is wrong although unfortunately widely spread through poor analogies such as "DNA is the blueprint for life". DNA has a key role to play in the ongoing control of biological activity, it is not a passive molecule that simply make things that then go do their stuff.
edit
Oh, and - of course - transposons. There are parasitic* elements called transposons that exist within the genome that code for proteins that will cut them out of the gene and re-insert them elsewhere or make copies of themselves. These can occasionally also move other bits of DNA around.
* - some thing that transposons have an adaptive purpose, I think they're merely parasites. I think my view is probably more common.
Edited by Mr Jack, : Added transposons