This review paper discusses the perspective of complex biological systems as applied to inheritance and ontogeny, focusing on the continuity of genetic, epigenetic and microbiotic inheritance. The informational processuality within this continuity can be used as to exemplify the insufficiency of hierarchical concepts in grasping the complex and integrated nature of biological processes. The argument follows Bruni and Giorgi in emphasizing that while structures and substrates are organized hierarchically, communicational processes are organized heterarchically. The essay also argues the insufficiency of (...) a single, basic, i.e. genetic level of description, which is the prevalent idea of twentieth century biology, to explain all phenotypic variation. I argue that inheritance and development cannot be fully explained by some sub- or super-ordination and that such descriptions are merely heuristic tools that do not reflect the nature of such processes. (shrink)

Post-translational histone modifications and their biological effects have been described as a ‘histone code’. Independently, Barbieri used the term ‘organic code’ to describe biological codes in addition to the genetic code. He also provided the defining criteria for an organic code, but to date the histone code has not been tested against these criteria. This paper therefore investigates whether the histone code is a bona fide organic code. After introducing the use of the term ‘code’ in biology, the criteria a (...) putative organic code such as the histone code must conform to in order to be recognised as an organic code are described. Our current knowledge of histones and their major post-translational modifications, and the specific protein binding domains that recognise and translate these into specific biological effects, is then reviewed in detail. The histone modification system is then placed in the context of an organic code and it is concluded that it fulfils all the requirements of an organic code. The marks produced on histones by processes such as acetylation and methylation act as organic signs that are translated into unique biological effects, their biological meanings. These translations are accomplished by effector proteins that consist of a binding domain that recognises a specific histone mark and a regulatory domain that mediates the biological effect. Crucially, these domains can be experimentally interchanged between different effector proteins, thus altering the rules that specify the relationships between sign and meaning. The effector proteins therefore fulfil the role of adaptor molecules. (shrink)