The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or (...) conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics. (shrink)

This article presents an update on known and unknown biological codes. While the genetic code has been recognized as a code for decades, most other codes were hidden in the shadow of this hallmark discovery. It was the dawn of the new millennium when the histone language and code were proclaimed in the years 2000 and 2001, respectively, marking the start of an explosion in the number of published codes across all biological disciplines since then. Actually, there are hundreds to (...) thousands of biological codes, but only a fraction—although still a substantial number—have been explicitly described as such. A first assessment of those codes allows for a simple categorization into structural and regulatory codes, at the same time maintaining Marcello Barbieri´s initial differentiation of organic versus neural codes. The article reviews prominent codes and showcases restriction-modification and toxin-antitoxin systems as code systems that have gone unrecognized until today. This article should read as a motivation for all those who want to discover ever more new codes—from literature or in the field. (shrink)

In hybrid nature that results from a random mix of technological infrastructures and natural ecosystems, environmental fundamentals are modified producing dramatic effects on the semiosis of several species. Human intrusion in ecosystems creates new spatial configurations that have a reduced ecological complexity when compared with systems less affected by human manipulation. This causes cascading effects on other environmental fundamentals. F.i., systems that face a low complexity, are more exposed to changes that in turn can reduce the performances of individual species (...) due to a higher level of uncertainty. The flux of information could be apparently maintained in hybrid nature when some natural patterns and processes are replaced by human artifacts and associated dynamics, but the process of signification could be strongly modified. The strict contact between people and wild organisms in hybrid nature requires new types of strategies to guarantee the continuation of the natural dynamic of populations and communities. Rural sanctuaries are proposed as one of the possible models on which to invest in order to harmonize the technological and natural processes with the goal to assure a multiscale sustainability. (shrink)

The fossil record shows that the stromatolites built by cyanobacteria 2 and 3 billion years ago are virtually identical to those built by their modern descendants, which is just a part of much evidence revealing that bacteria have barely changed in billions of years. They appeared very early in the history of life and have conserved their complexity ever since. The eukaryotes, however, did the opposite. They repeatedly increased the complexity of their cells and eventually broke the cellular barrier and (...) gave origin to all living creatures that we see around us. This gives us one of the major problems in evolution: why have the prokaryotes maintained the same complexity throughout the history of life while the eukaryotes have become increasingly more complex? Here it is shown that a solution does exist, but it is based on experimental data that so far have largely been ignored. It is based on the discovery that, in addition to the genetic code, many other organic codes exist in living systems. The potential to generate organic codes was already present in the common ancestor but was not transmitted indefinitely to all its descendants. After the genetic code and the signal transduction codes that gave origin to the first cells, the prokaryotes evolved no other organic code, whereas the ancestors of the eukaryotes continued to explore the coding space and gave origin to splicing codes, histone code, cytoskeleton codes, tubulin code, compartment codes, and sequence codes. This experimental fact suggests that the prokaryotes did not increase their complexity because they did not evolve new organic codes, whereas the eukaryotes became increasingly more complex because they maintained the potential to bring new codes into existence. (shrink)