Marcello Barbieri

University of Ferrara | UNIFE · Department of Morphology, Surgery and Experimental Medicine

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These di...

The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the...

A Video on Code Biology Dear Colleagues, I have given an interview on Code Biology to João Carlos Major and he has turned it into a one-hour long video that you can see, if you wish, by clicking on this link https://youtu.be/9rYFUD3SRi0 All the best Marcello Barbieri

Updated List of Biological Codes (Organic codes and Neural codes) with References

The genetic code is the set of rules that all living cells use for the synthesis of proteins, and to this purpose they employ three different types of RNAs: the messenger-RNAs, the transfer-RNAs and the ribosomal-RNAs. The messenger-RNAs carry genetic information in the form of sequences of codons, where the codons are groups of three nucleotides....

In 1965 I was employed as a research assistant at the Institute of Histology and Embryology in the Medical Faculty of Bologna University and a few months later, in 1966, I read a paper by Breck Byers that described the results of a cooling treatment on one-day old chick embryos (Byers 1966). More precisely, Byers discovered that an incubation of th...

The idea that animals have feelings, emotions and minds has been a popular belief since time immemorial, but it has always been taken for granted that only man makes use of signs. All animals, for example, recognize a fruit when they see it, but only human beings recognize it when they hear its name.

Traditional linguistics was based on the idea that language is an activity that links sounds and meaning, an idea that has been referred to as 'the code view of language' because codes are the most familiar processes that generate meaning. Ever since the work of Noam Chomsky, however, this view has been increasingly replaced by 'the syntax view of...

The experimental evidence has shown that the genetic code is based on arbitrary, or conventional, rules, in the sense that any codon can be associated to any amino acid, and this means that there is no deterministic link between them. This is in sharp contrast with the traditional paradigm of the stereochemical theory, which claims that the rules o...

For a long time it has been assumed that the rules of the genetic code were determined by chemistry – either by stereochemical affinities or by metabolic reactions – but the experimental evidence has revealed a totally different reality; it has been shown that any codon can be associated to any amino acid, and this means that there is no determinis...

The classical theories of the genetic code (the stereochemical theory and the coevolution theory) 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 amin...

Various independent discoveries have shown that many organic codes exist in living systems, and this implies that they came into being during the history of life and contributed to that history. The genetic code appeared in a population of primitive systems that has been referred to as the common ancestor, and it has been proposed that three distin...

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 complexit...

The phylogenetic trees reconstructed from molecular data have led to the discovery that all living creatures belong to three primary kingdoms, or domains, because there are three types of cells in nature. The primary kingdoms are referred to as Archaea, Bacteria, and Eukaya, and their first representatives were the first modern cells that appeared...

Today there is a very wide consensus on the idea that embryonic development is the result of a genetic programme and of epigenetic processes. Many models have been proposed in this theoretical framework to account for the various aspects of development, and virtually all of them have one thing in common: they do not acknowledge the presence of orga...

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These di...

The discovery of the genetic code has revealed the existence of a deep parallel between protein synthesis and language. In both cases, a small set of units is used to create an unlimited variety of objects by arranging the units in countless different combinations. In technical terms this process is called recursion, and the presence of recursion a...

There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimiz...

An operative definition is one that allows us to make experimental tests that prove whether or not organic codes do exist in Nature. The starting point is the idea that a code is always a set of rules that establish a correspondence between two independent worlds (Barbieri 2003). The Morse code, for example, is a correspondence (or a mapping) betw...

Today there are two major theoretical frameworks in biology. One is the ‘chemical paradigm’, the idea that life is an extremely complex form of chemistry. The other is the ‘information paradigm’, the view that life is not just ‘chemistry’ but ‘chemistry-plus-information’. This implies the existence of a fundamental difference between information an...

The purpose of this chapter is to show that organic codes played a key role in the origin and the evolution of mind as they had in all other great events of macroevolution. The presence of molecular adaptors has shown that the genetic code was only the first of a long series of codes in the history of life, and it is possible therefore that the ori...

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)...

The discovery of the genetic code has shown that the origin of life has also been the origin of semiosis, and the discovery of many other organic codes has indicated that organic semiosis has been the sole form of semiosis present on Earth in the first three thousand million years of evolution. With the origin of animals and the evolution of the br...

The clear neotenic features of our anatomy and the details of our foetal development make it very likely that the preconditions for language were created by a fetalization process, more precisely by a process that produced an extrauterine phase of foetal development, and gradually extended it to the point that it became longer than the intrauterine...

Modern biology has not yet come to terms with the presence of many organic codes in Nature, despite the fact that we can prove their existence. As a result, it has not yet accepted the idea that the great events of macroevolution were associated with the origin of new organic codes, despite the fact that this is the most parsimonious and logical ex...

Thomas Sebeok and Noam Chomsky are the acknowledged founding fathers of two research fields which are known respectively as Biosemiotics and Biolinguistics and which have been developed in parallel during the past 50years. Both fields claim that language has biological roots and must be studied as a natural phenomenon, thus bringing to an end the o...

Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular e...

The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different...

The idea that life is based on signs and codes, i.e., that “Life is semiosis”, has been strongly suggested by the discovery of the genetic code, but so far it has made little impact, and is largely regarded as philosophy rather than science. The main reason for this is that there are at least three basic concepts in modern biology that keep semiosi...

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs...

The mechanisms of evolution have been one of the most controversial issues in Biology and the great debate about them has culminated, in the 1930s and 1940s, in the Modern Synthesis, the theoretical framework where natural selection is regarded as the sole mechanism of evolutionary change. Here it is shown that a new approach to these great problem...

Biosemiotics asserts the idea that semiosis is fundamental to life, and that all living creatures are therefore semiotic systems. The idea itself is strongly supported by the evidence of the genetic code — but thus far it has made little impact in the scientific world, and is largely regarded as the basis for a philosophy of meaning, rather than a...

Building on a range of disciplines – from biology and anthropology to philosophy and linguistics – this book draws on the expertise of leading names in the study of organic, mental and cultural codes brought together by the emerging discipline of biosemiotics. The book’s 18 chapters present a range of experimental evidence which suggests that the...

The 2001 Special Issue of Semioticahas been dedicated to celebrating Jakob von Uexküll as a founding father of biosemiotics. The two main points of the volume – the making of biosemiotics and the recovery of Jakob von Uexküll from oblivion – come out with clarity and force, and are definitely a success. The volume is also an excellent example of in...

Semiotics is the study of signs and initially it was thought to be concerned only with the products of culture. Mental phenomena, however, exist also in animals, and cultural semiotics came to be regarded as a special case of biological semiotics, or biosemiotics, a science that started by studying semiotic phenomena in animals and then it was grad...

Genes and proteins are molecular artifacts because they are manufactured by molecular machines that physically stick their subunits together in the order provided by external templates. This implies that all biological objects are artifacts, and therefore that 'life is artifact-making.' Natural objects can be completely accounted for by physical qu...

Vyd. 1.

The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by...

It is shown that information and meaning can be defined by operative procedures, and that we need to recognize them as new types of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because they are not subjective features. Here it is proposed to call them nominab...

Coding characteristics have been discovered not only in protein synthesis, but also in various other natural processes, thus showing that the genetic code is not an isolated case in the organic world. Other examples are the sequence codes, the adhesion code, the signal transduction codes, the splicing codes, the sugar code, the histone code, and pr...

Recent advances in the evolutionary genetics of sex determination indicate that DMRT1 may be a vertebrate equivalent of the Drosophila melanogaster master sex regulator gene, doublesex. The role of DMRT1 seems to be confined to some aspects of male sex differentiation, whereas in Drosophila, doublesex has wider developmental effects in both sexes....

The etiology of most cases of 46,XY gonadal dysgenesis in the absence of extragenital anomalies is not accounted for by mutations in the genes known to date to be involved in sex determination. We have investigated the possibility that mutations in the gene LHX9, whose murine ortholog causes isolated gonadal agenesis when inactivated, might be resp...

Intense efforts are currently being pursued to identify autosomal genes associated with 46,XY male-to-female sex reversal. The genes DMRT1 and 2 are located on distal 9p, a region deleted in 46,XY sex-reversed patients. They are considered excellent candidates because of their homology to regulators of sex development in invertebrates. We present t...

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformation...

New methods of inducing ribosome crystals in chick embryos are described, and it is shown that a close relationship exists between cell stress and ribosome crystallization. The formation of ribosome crystals in the nucleus and/or in the cytoplasm depends on the type of treatment and on the temperature of incubation, but in all cases the key event t...

A comparison between the time-consuming freeze-substitution Lowicryl HM 20 embedding procedure with the Epon embedding method for the immunocytochemical detection of phosphatidylinositol 4,5-bisphosphate (PIP2) by means of a monoclonal antibody is described. The results indicate that the intracellular localization of the phospholipid and the effici...

The intracellular localizations of phosphatidylinositol 4,5-bisphosphate (PIP2) and of its hydrolyzing enzyme phospholipase C (PLC; in this case the beta 1 isoform) have been evaluated by electron microscope immunocytochemistry in cells exposed to mitogenic or differentiating agents. These cells have been previously demonstrated to present a signal...

The complexity of the RNA world has surprised biologists many times in recent years and has led, among other things, to a new definition of a gene. Its implications, however, may go even further than that. It is possible that the ribonucleoproteins form an information processing system which functions as the "brain" of the cell.

The application of image analysis methods to conventional thin sections for electron microscopy to analyze the chromatin arrangement are quite limited. We developed a method which utilizes freeze-fractured samples; the results indicate that the method is suitable for identifying the changes in the chromatin arrangement which occur in physiological,...

The ribotype is defined as the ribonucleoprotein system of any cell. The theory substitutes the genotype-phenotype duality with the trinity genotype-ribotype-phenotype, and proposes that life on earth originated with the ancestors of today's ribotypes.The first three chapters describe separate models on precellular evolution, the evolution of proto...

Ribosome microcrystals have been obtained for the first time in homogenates and extracts of chick embryos mainly in the form of P422 stacks that have average linear dimensions some 40% greater than those obtained in vivo.

Ribosome crystallization within nuclei has been studied in chick embryos with procedures which increase its frequency by various orders of magnitude as compared to previous findings. The extrusion of ribosome microcrystals from nuclei is reported for the first time, and a model for the transfer of ribosomes from nucleus to cytoplasm is proposed.

The relationship between ribosome crystallization and cell degeneration has been studied in chick embryos at various temperatures, and new methods of inducing ribosome microcrystals are described. A model is discussed that reinterprets the role of low temperatures in these phenomena and provides a unitary explanation of the various cases in which t...

Gallery of microcrystals

A new model is proposed on the origin of crystallizable ribosomes and the kinetics of ribosome crystallization. The model assumes that ribosome crystallizability is a property the ribosomes have only in a well-defined period of their life cycle and implies a close relationship between cellular differentiation and structural rearrangements at the ri...

A criterion is proposed to evaluate visually and quantitatively the three-dimensional reconstructions performed by non-linear algorithms from the projections of unknown structures. Utilizing the informational content of this criterion the structure of an existing algorithm is modified and its performance is improved.

Chick embryo fibroblast cultures have been submitted to a rapid cooling treatment in order to induce ribosome crystallization. This treatment induces the appearance of small and rare ribosome crystals in only a very low percentage of the interphasic cells. In order to investigate the metabolic conditions for the formation of ribosome crystals, the...

By utilizing a slow cooling process the occurrence of ribosome crystallization has been demonstrated in lymphoid infiltrating cells in tumorous organs of chickens affected with Marek's disease but not in the parenchymal cells of the same organs. Moreover the slow cooling treatment can induce ribosome crystallization in proliferating cell population...

A method for laying isolated ribosome crystals on grids for ultrastructural investigation is described. Staining of these microcrystals with uranyl acetate gives images stained positively, negatively and intermediately; the shape and dimensions of ribosomes show differences, whereas the crystalline unit cell dimensions do not change. The ultrastruc...

The possibility has been demonstrated of inducing by hypothermia ribosome crystallization in chick oocytes in the last stages of yolk accumulation and in chick embryos from fertilization up to laying. Large quantities of crystallized ribosomes are present in mature oocytes while only very rare ribosome crystals can be observed during the first clea...

A method of isolating large quantities of crystallized ribosomes from hypothermic chick embryos is described.The isolated ribosome crystals maintain the same average dimensions and the same type of aggregations as those prepared in vivo.

Synaptic-vesicle fraction was isolated from brain gray matter (Bos taurus) using density-gradient centrifugation coupled with morphological control in the electron microscope. Analysis of lipid composition of this fraction shows a high lipid content, particularly phospholipids and gangliosides. Using thin-layer chromatography six phospholipid compo...