The sequence of nucleotide bases occurring in an organism’s DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of construction. In reality, any biochemical machine for which a DNA codescript is efficacious is itself produced through the mechanical interpretation of an identical or very similar codescript. In these (...) terms the origin of life can be described as a bootstrap process involving the simultaneous accumulation of genetic information and the generation of a machine that interprets it as instructions for its own construction. This problem is discussed within the theoretical frameworks of thermodynamics, informatics and self-reproducing automata, paying special attention to the physico-chemical origin of genetic coding and the conditions, both thermodynamic and informatic, that a system must fulfil in order for it to sustain semiosis. The origin of life is equated with biosemiosis. (shrink)

Molecular codes can be considered a special type of mapping among molecular species in biochemical systems. The formalization of molecular codes allows to identify these in network models of real world systems. Analyzing algorithmically identified codes leads to the observation that codes does not necessarily stand alone, but that we can identify certain relations among codes. In this paper I will define two types of relations that can occur among codes, code linkage and code nesting, and will discuss implications of (...) this finding. (shrink)

All information results from a process, intrinsic to living beings, of info-autopoiesis or information self-production; a sensory commensurable, self-referential feedback process immanent to Bateson’s ‘difference which makes a difference’. To highlight and illustrate the fundamental nature of the info-autopoietic process, initially, two simulations based on one-parameter feedback are presented. The first, simulates a homeostatic control mechanism (thermostat) which is representative of a mechanistic, cybernetic system with very predictable dynamics, fully dependent on an external referent. The second, simulates a homeorhetic process, (...) inherent to biological systems, illustrating a self-referenced, autonomous system. Further, the active incorporation/interference of viral particles by prokaryotic cells and the activation of CRISPR-Cas can be understood as info-autopoiesis at the most fundamental cellular level, as well as constituting a planetary network of self-referenced information. Moreover, other examples of the info-autopoietic nature of information are presented to show the generality of its applicability. In short, info-autopoiesis is a recursive process that is sufficiently generic to be the only basis for information in nature: from the single cell, to multi-cellular organisms, to consideration of all types of natural and non-natural phenomena, including tools and artificial constructions. (shrink)

Barbieri introduced and developed the concept of organic codes. The most basic of them is the genetic code, a set of correspondence rules between otherwise unrelated sequences: strings of nucleotides on the one hand, polypeptidic chains on the other hand. Barbieri noticed that it implies ‘coding by convention’ as arbitrary as the semantic relations a language establishes between words and outer objects. Moreover, the major transitions in life evolution originated in new organic codes similarly involving conventional rules. Independently, dealing with (...) heredity as communication over time and relying on information theory, we asserted that the conservation of genomes over the ages demands that error-correcting codes make them resilient to casual errors. Moreover, the better conservation of very old parts of the genome demands that they result from combining successively established nested codes such that the older an information, the more numerous component codes protect it. Barbieri’s concept of organic code and that of genomic error-correcting code may seem unrelated. We show however that organic codes actually entail error-correcting properties. Error-correcting, in general, results from constraints being imposed on a set of sequences. Mathematical equalities are conveniently used in communication engineering for expressing constraints but error correction only needs that constraints exist. Biological sequences are similarly endowed with error-correcting ability by physical-chemical or linguistic constraints, thus defining ‘soft codes’. These constraints are moreover presumably efficient for correcting errors. Insofar as biological sequences are subjected to constraints, organic codes necessarily involve soft codes, and their successive onset results in the nested structure we hypothesized. Organic codes are generated and maintained by means of molecular ‘semantic feedback loops’. Each of these loops involves genes which code for proteins, the enzymatic action of which controls a function needed for the protein assembly. Taken together, thus, they control the assembly of their own structure as instructed by the genome and, once closed, these loops ensure their own conservation. However, the semantic feedback loops do not prevent the genome lengthening. It increases both the redundancy of the genome and the information quantity it bears, thus improving the genome reliability and the specificity of the enzymes, which enables further evolution. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...) not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)