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)

In this essay we argue for the possibility to describe the co-presence of species in a community as a consortium built by acoustic codes, using mainly the examples of bird choruses. In this particular case, the consortium is maintained via the sound-tope that different bird species create by singing in a chorus. More generally, the formation of acoustic codes as well as cohesive communicative systems (the consortia) can be seen as a result of plastic adaptational behaviour of the specimen who (...) can solve and avoid conflicts both with conspecifics and with other species in the vicinity. Thus, sign-relations appear to resolve potential conflicts, and as a foundation for symbiotic aggregations. The spatio-temporal configuration of consortia—their chronotope—includes several eco-fields as respective to different functions of the participating organisms. Biological study is combined with a semiotic approach that, as we suggest, should be more often used together to effectively describe ecological processes. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal (...) processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

Acoustic codes assure the intra and interspecific communication of vocal animals. They are composed by a sequence of nominal entities and by magnitude modulation confirming in such a way contemporarily a behavioural and ecological nature. The acoustic codes find evidence in the acoustic niche hypothesis by which species in order to reduce interspecific competition occupy a restricted portion of the available frequencies modulating very precise acoustic cues . Their evolution, like other aspect of biology, is under control of the environmental (...) conditions assuming the more favourable configurations. These nominal entities respond also to the amount of energy by which are emitted allowing to the eavesdropping individuals to range the distance at which a potential competitor is broadcasting a signal. Environmental alterations, especially if of anthropogenic origin, can produce severe consequence of the acoustic codes that in turn may affect the prey–predator balance and the complexity of communities. In fact acoustic codes under an environmental constraint like human noise intrusion can be modified in order to reduce a masking effect, demonstrating their phenological plasticity. The new ecological discipline of soundscape ecology offers the possibility to investigate the nature and the evolution of the acoustic codes in different environmental conditions. (shrink)

We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of codepoiesis introduced by Barbieri, a new idea of semio-poiesis is proposed. Semio-poiesis, a recursive auto-referential processing of semiotic system, becomes a form of organization of the bio-world when and while notions of meaning and aiming are introduced into it. The description of the genetic code as a semiotic system allows us to apply the method of internal reconstruction to (...) it: on the basis of heterogeneity and irregularity of the current state, to explicate possible previous states and various ways of forming mechanisms of coding and textualization. The revealed patterns are consistent with hypotheses about the origin and evolution of the genetic code. (shrink)