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)

Change and necessity is a statement of Darwinian natural selection as a process driven by chance necessity, devoid of purpose or intent.

This is a wide ranging and deeply learned examination of evolutionary developmental biology, and the foundations of life from the perspective of information theory. Hermeneutics was a method developed in the humanities to achieve understanding, in a given context, of texts, history, and artwork. In Readers of the Book of Life, the author shows that living beings are also hermeneutical interpreters of genetics texts saved in DNA; an interpretation based on the past experience of the cell (cell lineage, species), confronted (...) with and incorporating present environmental clues. This approach stresses the history, not only of the digital record saved in the DNA, but also of the flesh - the cellular organization which has a direct time-continuity with the very origins of life. This book is aimed at reconciling two opposite approaches to life. The first strictly sticking to a belief that all phenomena observed in the realm of the living can be explained from laws of physics. The opposite stressing the importance of features characteristic for a given level of description. To bring both views into a common understanding, the first part gives a comparison of the two problem solving strategies. The second part surveys the development of 20th century biology, bringing to light branches that never became part of the research mainstream. The third section of the book reviews a large body of recent evidence that can be interpreted in favor of the hermeneutic arguments. (shrink)

Open peer commentary on the article “A Critique of Barbieri’s Code Biology” by Alexander V. Kravchenko.: One of the main problems of biosemiotics, i.e., the distinction between code-based artifacts and life itself, does not seem to be resolved yet. Semiosis requires codes but it cannot be based on a single code. I sketch a model that demonstrates the role of codes in semiosis and helps to see correspondences between the models of Peirce and Saussure.

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)

Life appears to be a natural property of matter, but the problem of its origin only arose after early scientists refuted continuous spontaneous generation. There is no chance of life arising ‘all at once’, we need the standard scientific incremental explanation with large numbers of small steps, an approach used in both physical and evolutionary sciences. The necessity for considering both theoretical and experimental approaches is emphasized. After describing basic principles that are available (including the Darwin-Eigen cycle), the search for (...) origins is considered under four main themes. These are the RNA-world hypothesis; potential intermediates between an RNA-world and a modern world via the evolution of protein synthesis and then of DNA; possible alternatives to an RNA-world; and finally the earliest stages from the simple prebiotic systems to RNA. The triplicase/proto-ribosome theory for the origin of the ribosome is discussed where triples of nucleotides are added to a replicating RNA, with the origin of a triplet code well-before protein synthesis begins. The length of the code is suggested to arise from the early development of a ratchet mechanism that overcomes the problem of continued processivity of an RNA-based RNA-polymerase. It is probable that there were precursor stages to RNA with simpler sugars, or just two nucleotides, but we do not yet know of any better alternatives to RNA that were likely to arise naturally. For prebiotic stages (before RNA) a flow-reactor model is suggested to solve metabolism, energy gradients, and compartmentation simultaneously – thus the intense interest in some form of flow reactor. If an autocatalytic cycle could arise in such a system we would be major steps ahead. The most likely physical conditions for the origin of life require further clarification and it is still unclear whether the origin of life is more of an entropy (information) problem (and therefore high temperatures would be detrimental), rather than a kinetic problem (where high temperatures may be advantageous). (shrink)

New discoveries in the life sciences have affirmed that the virtual script as well as its context-dependent reading and interpretation determine the final living creature. An extended understanding of Darwinian Theory is crucial for understanding life as semiosis in terms of Peirce and Eco’s semiotic models. The semiosis of living systems is potentially unlimited. Genes are not static and unchangeable scripts, but can always be reinterpreted by new interpretants that illuminate them from different points of view, depending on which properties (...) are relevant in a particular context. The encyclopedia is a term, in Umberto Eco’s semiotics, which represents the multidimensional space of semiosis that is governed by a self-sustaining production of interpretants. The paper will present the idea of understanding the Extended Synthesis in terms of a biosemiotic enyclopedia. (shrink)

Progress in molecular biology has revealed profound relations between linguistic and genomic sciences, mainly through advances in bioinformatics. The structural symmetries between biochemical and verbal syntaxes raise the question of their origins: did they emerge independently, or did one arise from the other? Does the genetic code contain the traces of a protolanguage, a universal grammar whose gradual evolution and successive mutations progressively led to the polymorphism of natural languages? To explore this question, we review the isomorphism of the genetic (...) code and verbal codes from lexical, syntactic, semantic and pragmatic standpoints. We discuss the limits of these symmetries and their anthropomorphic connotations. We observe the gradual evolution of species and languages according to parallel mechanisms, and the genetic roots of the physiology of language. In conclusion, we hypothesize that human observers may not be projecting linguistic frameworks onto genomic structures. Rather, it could be their linguistic faculties that reflect the grammatical structure of genetic code. (shrink)