Response to commentaries on our paper gene and genon concept: coding versus regulation

We have been glad to see that our paper (Scherrer and Jost 2007) solicited such insightful or supportive commentaries as those of Noble, of Gros, of Prohaska and Stadler, of Forsdyke, and Billeter, as well as the alternative proposal of Stadler et al., and we hope that this will trigger further conceptual discussions about the definition of the gene and inspire further research about programs of gene expression, in the light of recent advances in molecular biology and bioinformatics (Billeter 2009; Forsdyke 2009; Gros 2009; Noble 2009; Prohaska and Stadler 2008; Stadler et al. 2009). The commentaries raise some important issues. We agree with some of them, but disagree with others, whereas still others reflect terminological decisions that could be taken so or otherwise. In the sequel, we shall try to address these issues in a systematic manner and motivate the terminological decisions that we have taken. This will also give us the opportunity to emphasize some points that were not explicitly laid out in our original paper.