Here is an ID research paper published in PNAS. Note that some important principles of evolutionary theory are criticized in the abstract. This research shows how ID is capable of being applied in biology.
The regulatory utilization of genetic redundancy through responsive backup circuits
( evolution | gene duplications | modeling | systems biology | noise )
Ran Kafri *, Melissa Levy *, and Yitzhak Pilpel
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Communicated by Marc W. Kirschner, Harvard Medical School, Boston, MA, June 12, 2006 (received for review March 6, 2006)
Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such “responsive backup circuits” in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.
Author contributions: R.K., M.L., and Y.P. performed research.
Conflict of interest statement: No conflicts declared.
Freely available online through the PNAS open access option.
*R.K. and M.L. contributed equally to this work.