New Millennium Evol'n

Here an interesting older review that I stumbled across: James A Shapiro: A 21st Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering. It describes new ways of thinking "about genomes as sophisticated informatic storage systems and about evolution as a systems engineering process"

From an organizational point of view, distant effects of repetitive element dosage tell us that the whole genome is a single integrated system, regulated both in cis- and trans- by networks employing DNA repeats.

The emphasis here on repetitive DNA means to take into account centromeric and telomeric regions, and other dispersed repeats (which contain signals for transcription, chromatin organization and nuclear localization of DNA itself. That's a big portion of the genome that is included in this. While a number isn't given for this classification, transposable elements, which are most likely included here, comprise 40% of the human genome (and more of the mouse) alone. In other words, we are talking about a huge amount of the genome that has a role in regulation. Regulatory evolution just got a whole lot bigger- and messier.


Another interesting point:
...bioinformatics is far more than the application of contemporary technology to large data bases. Bioinformatics has the potential to lead us to novel computing paradigms that may prove far more powerful than the Turing machine-based digital concepts we now use.

There are many different analogies people have tried to use to make sense of biological systems. At the end of the day they all fall somewhat short. One of the things this statement is eluding to is that thinking about biological systems on their own terms is the best way to understand them. There is not analogy that can summerize fundamental biological processes.

The most exciting point for me is:
Significant evolutionary changes can result form altering the repetitive elements formatting genome system architecture, not just from altering protein and RNA coding sequences.

In other words, understanding genome architecture is fundamental to understanding Evolutionary changes and part of the key lies in repetitive elements. This and many papers that have been published since point to the declining emphasis of SNPs in evolutionary study and a shift to other sources of (random) variation.