Scott Minnich at U. Idaho sends this along:
This paper published online his summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.
The paper by Muskhelishvili and Travers, titled “Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information”, makes several very interesting points. First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary—much like Karl Drlica proposed years ago as we were obtaining the first bacterial genome sequences. In other words, DNA topology (due to supercoiling and histone-like protein binding), Transcription, and Metabolic energy (ATP levels influence DNA gyrase activity, which affects supercoiling, which affects transcription) are all keying off each other and thus there is an overall order to the positioning of anabolic and catabolic genes relative to the origin of replication. In short, I think this is a fascinating review looking at DNA organization and function which, in the authors words, are irreducibly complex.