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Code biology

From EverybodyWiki Bios & Wiki


Code Biology is the study of all codes of life, from the genetic code to the codes of culture, with the standard methods of science. It is, first and foremost, an experimental field of research based on the recent discoveries that many organic codes exist in living systems in addition to the genetic code. At the same time, it is a field of research that has outstanding theoretical consequences. Among them, the idea that the greatest events of macroevolution were associated with the origin of new organic codes.[1] Another major concept comes from the fact that the organic codes have been highly conserved in evolution, which means that they are the great invariants of life, the sole entities that have been perpetuated while everything else has been changed.[2] Code Biology, in short, is the exploration of a vast and still largely unexplored dimension of the living world. The International Society of Code Biology has been formally established in 2012 and has been organizing international conferences since 2014.

The Genetic Code

Codes and conventions are the basis of our social life and from time immemorial have divided the world of culture from the world of nature. In this millennia-old framework, the discovery of the genetic code, in the early 1960s, came as a bolt from the blue, but strangely enough it did not bring down the barrier between nature and culture. On the contrary, a protective belt was quickly built around the old divide with an argument that effectively emptied the discovery of all its revolutionary potential. The argument that the genetic code is not a real code because its rules are the result of chemical affinities between codons and amino acids. This is the ‘Stereochemical theory’, an idea first proposed by George Gamow in 1954,[3] and re-proposed ever since in many different forms.[4][5][6][7][8][9][10]

More than fifty years of research have not produced any evidence in favour of this theory and yet the idea is still circulating, apparently because of the possibility that stereochemical interactions might have been important at some early stages of evolution.[11] The deep reason is probably the persistent belief that the genetic code cannot possibly be made of arbitrary rules.

In all known codes – the Morse code, for example, or the highway code – the coding rules, although completely compatible with the laws of physics and chemistry, are not dictated by these laws. In this sense they are arbitrary, and the number of arbitrary relationships is potentially unlimited. In the Morse code, for example, any letter of the alphabet could be associated with countless combinations of dots and dashes, which means that a specific link between them can be realized only by selecting a small number of rules. And this is precisely what a code is: a small set of arbitrary rules selected from a potentially unlimited number in order to ensure a specific correspondence between two independent worlds.

In protein synthesis, a sequence of nucleotides is translated into a sequence of amino acids, and the bridge between them is realized by a third type of molecules, called transfer-RNAs, that perform two distinct operations: at one site they recognize groups of three nucleotides, called codons, and at another site they receive amino acids from enzymes called aminoacyl-tRNA-synthetases. The key point is that there is no deterministic link between codons and amino acids since it has been shown that any codon can be associated with any amino acid.[12][13] Hou and Schimmel, for example, introduced two extra nucleotides in a tRNA and found that that the resulting tRNA was carrying a different amino acid.[14]

The experiments, in other words, have proved that the number of possible connections between codons and amino acids is potentially unlimited, and only the selection of a small set of adaptors can ensure a specific mapping. This is the genetic code: a fixed set of rules between nucleic acids and amino acids that are implemented by adaptors. In protein synthesis, in short, we find all the essential components of a real code: (1) two independents worlds of objects (nucleotides and amino acids), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed.

But how could a set of arbitrary rules evolve on the primitive Earth? This problem has largely been ignored so far, but a first step in that direction has been made.[15]

A World of Organic Codes

In addition to the genetic code, a wide variety of new organic codes have come to light in recent years. Among them: the sequence codes,[16][17][18] the Hox code,[19][20] the adhesive code,[21][22] the splicing codes,[1][23][24][25][26][27][28] the signal transduction codes,[1] the histone code,[29][30][31][32][33][34] the sugar code,[35][36] the compartment codes,[1] the cytoskeleton codes,[1][37] the transcriptional code,[38][39][40][41] the neural code,[42][43] a neural code for taste,[44][45] an odorant receptor code,[46][47] a space code in the hippocampus,[48][49][50][51][52] the apoptosis code,[53][54] the tubulin code,[55] the nuclear signalling code,[56] the injective organic codes,[57] the molecular codes,[58][59] the ubiquitin code,[60] the bioelectric code,[61][62] the acoustic codes,[63] the glycomic code [64][65] and the Redox code.[66]

The living world, in short, is literally teeming with organic codes, but in almost all cases their discoveries have only circulated in small circles and have not attracted the attention of the scientific community at large. The result is that we still have a theoretical framework that contemplates only two codes in Nature: the genetic code that appeared at the origin of life and the codes of culture that arrived almost four billion years later. Which amounts to saying that there have been no other codes in between, and therefore that codes are extraordinary exceptions, not normal components of life and evolution.

In reality, the organic codes have operated throughout the whole history of life. The genetic code evolved in the common ancestor, the signal transduction codes appeared in the first cells (Archaea, Bacteria and Eukarya) and many organic codes arose at various stages of eukaryotic evolution; the splicing codes were instrumental to the origin of the nucleus, the histone code provided the working rules of chromatin, the Hox codes had a crucial role in embryonic development and the neural code in the evolution of the brain.[1][2] The greatest events of macroevolution, in other words, were associated with the appearance of new organic codes, and this gives us a completely new understanding of the history of life.

Code Biology

Code Biology is a new field of scientific research whose aim is the study of all codes that exist in living systems. The genetic code and the codes of culture have been known for a long time and represent the historical foundation of Code Biology. What is really new in this field is the study of all codes that came after the genetic code and before the codes of culture. The existence of these codes is an experimental fact – let us never forget this – but also more than that. It is one of those facts that have extraordinary theoretical implications.

The rules of the codes are not dictated by physical necessity and for this reason they can establish relationships that have never existed before in the Universe, thus bringing absolute novelties into existence. The organic codes, furthermore, are the most highly conserved entities in evolution, which means that they have been perpetuated while virtually everything else has been changing. Code Biology is thus uncovering not only new experimental facts but also new fundamental principles.

The International Society of Code Biology

The synthesis of biology and semiotics that today is known as biosemiotics was developed by Thomas Sebeok in two distinct stages. In 1963, Sebeok extended semiosis from human culture to animals and founded the new research field of zoosemiotics [67]. More than 20 years later, he made a second extension from animals to all living creatures and called it biosemiotics [68] [69]. In biology, the presence of codes (and therefore of semiosis) at the molecular level is well documented by the existence of the genetic code, and this implies that molecular semiosis is produced by coding. In the humanities, the dominant view today is the Peircean concept that semiosis is always an interpretive process, and this implies that animal semiosis is produced by interpretation. There are therefore two types of semiosis in Nature, one based on coding and one based on interpretation, and each of them represents phenomena that undoubtedly exist. There is ample evidence that animals are capable of interpreting the world, and this clearly means that Peircean (or interpretive) semiosis is a reality. But it is also evident that the rules of the genetic code do not depend on interpretation because they have been the same in all living creatures and in all environments ever since the origin of life. The logical conclusion is that both types of semiosis are present in Nature and represent two distinct evolutionary developments. This, however, is precisely what the Peirce followers do not accept. If there is mind, interpretation and semiosis in animals, they claim, it is because there have been forms of mind, interpretation and semiosis in all previous living systems, including the first cells. In recent years, biosemiotics has become increasingly identified with Peircean biosemiotics, a view based on Peirce’s idea that mind-like properties exist everywhere in the universe. This made it clear that a scientific approach to the codes of life could not prosper within that framework, and for that reason, at the end of 2012, Marcello Barbieri resigned as editor-in-chief of Biosemiotics and together with eleven colleagues (Jan-Hendrik Hofmeyr, Peter Wills, Almo Farina, Stefan Artmann, Joachim De Beule, Peter Dittrich, Dennis Görlich, Stefan Kühn, Chris Ottolenghi, Liz Swan and Morten Tønnessen) founded the “International Society of Code Biology” [70]. They also decided to leave no doubt about the scientific nature of the project, and to this end they explicitly wrote in the constitution of the new society that Code Biology is “the study of all codes of life with the standard methods of science”.


References

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