Conclusion

Therefore, we can conclude that the duopoly of code and context recreate themselves at each level we have considered in this paper. To ignore context is to risk wasting further billions on doomed extensions of the HGP, of simplistic nlp projects, and of programmes for curing autism that fail to reflect the subtlety of the disorder in many cases. It is also to risk the generation of a new type of cognitive science, as remote from the reality of the grace and grit of real human existence as its...

Why the Genetic Code Originated Implications for the Origin of Protein Synthesis

Abstract A theory is developed on the origin of the first codified protein, that is to say the appearance of the first messenger RNA (mRNA). This theory hypothesises a central role in enzyme catalysis played by peptidyl-RNAs, i.e. complexes of peptides and RNAs, in a very early evolutionary stage of genetic code origin. The evolution of peptidyl-RNA would then lead to the origin of peptidyl-tRNA, a key intermediary in the origin of protein synthesis. The appearance of the first mRNA might be...

The tRNA Dimers Orient the Entire Process

In the next sections, data are presented to demonstrate that the description of the entire genetic code through the dimer-oriented rationale is physiologic. The consistency of the results with biochemical data and evolutionary prescriptions is surprising in the light of the constraints imposed by the necessity of attributions having to be inserted into the system obeying the tRNA pairs, which is considered an argument in favor of the model. Our main novelty concerning the role of tRNA dimers is...

The Proteic Synthetases

The tRNAs are considered better guides for developing a model for the structure of the code on the basis of their forming an evolutionarily more conserved class of molecules when compared to proteins in general, that demonstrate enormous plasticity and high openness to regulatory modulation. On another side, the overall plasticity inherent to all kinds of molecular interactions, including those involving nucleic acids, only rarely approaching 100 specificity, leads to spreads that inevitably...

Strings and Folding

The basic constituents of the living system are nucleic acids and proteins so that cells are called nucleoprotein systems. These noblest components are strings, polymers where the monomers are, respectively, nucleotides and amino acids. The nobility in these strings comes from the specificity in the order of the monomers in the sequences, which bring about the main functions of the system. Amino acids are fundamentally 20, at the lower range of the number of letters in the symbolic alphabets of...

References

Abercrombie D (1967) Elements of general phonetics. Edinburgh University Press, Edinburgh Alac M (2005) From trash to treasure Learning about brain images through multimodality Semiotica 156(1 4) 177-202 Barbieri M (2003) The Organic Codes An Introduction to Semantic Biology. Cambridge University Press, Cambridge Barbieri M (2007) Is the cell a semiotic system In Barbieri M (ed.) Introduction to Biosemiotics. Springer Verlag, Berlin, pp. 179-207 Bateson MC (1979) The epigenesis of...

Amino Acid Biosynthesis and Possible Precodes at the Core of the Matrix

The criterion of obedience to the routes of biosynthesis of amino acids has been advocated by various authors as a guide for defining the succession of their entry into the code (see Davis, 1999 Wong, 2005). Nonetheless, the precise precursor-derived relationships are not entirely consensual. We simplified this rationale, saying that the restrictions should refer only to the most basic of the rules of derivation amino acids which are consensually recognized as derived from others belonging in...

Brain Epigenesis and Genelanguage Coevolution

It has to be admitted that on the whole we do not understand how the brain works. Nevertheless, some crucial elements seem to emerge. One is that development of the normal brain is enormously plastic, even though the power of genetic factors is obvious. One classic example is that in the same brain areas of identical twins the two hemispheres of the same individual resemble each other more closely than the same hemispheres in the two people (Changeux, 1983). Another insight is that a tremendous...

Protein Modularity and the Syntactic Units of a Protein Linguistic Grammar

For protein linguistic considerations SYNTAX shall be seen as the branch of linguistics that defines how words (syntactic units) are combined to make phrases and sentences. The PHRASE is a vehicle for defining syntactic units that appear next to each other or stay together in the arrangement of a sentence, and that form a syntactic unit of equal or higher complexity 29 . Definition of the syntax is a necessary prerequisite for any further efforts, as one must have detailed knowledge of the...

The Sequence Codes

In the 1980s and 1990s, Edward Trifonov started a lifelong campaign in favor of the idea that the nucleotide sequences of the genomes carry several messages simultaneously, and not just the message revealed by the classic triplet code. According to Trifonov, in other words, the genetic code is not alone, and there are many other codes in the nucleotide sequences of living organisms. This conclusion rests upon Trifonov's definition that a code is any sequence pattern that can have a biological...

The Formula of the Genetic Code

It does not require sophisticated analytical methods to show to what extent the code is governed by arithmetic. Simple algebra could confirm this fact with scientific accuracy. For example, the symbol of the Egyptian triangle in Fig. 9 could be written down in the form of two Diophantine equations. One of these equations is Gly + Ala + Ser + Pro + Val + Thr + Leu + Arg 333. There are enough phenomena relevant to the case in the genetic code. Their records complete the algebraic system of...

Multiple Role of Inositides in Signal Transduction

In recent years, PI(4,5)P2 has been shown to be not only the source of second messengers at the plasma membrane, but also to be directly involved in regulating a daunting number of cellular processes, including assembly and regulation of the actin cytoskeleton, and of the intracellular trafficking of exo and endocytotic vesicles (Czech, 2002). PI(4,5)P2 is localized in distinct subdomains of the plasma membrane, as well as at the Golgi stacks and endoplasmic reticulum. Its bisphos-phorylated...

Lectins Translators of the Sugar Code

The concept of a recognitive interplay between a sugar ligand and a lectin readily receives support, when the assumed ligand properties can be ascertained. As compiled in Table 1, various experimental approaches exploit the lectin's binding specificity in assays for their detection and characterization. The success in establishing these techniques and the power of affinity chromatography together with expression cloning and homology searches have spurred the transition from the early phase to...

Prediction of the Model

The model here discussed for the origin of protein synthesis and the first mRNA (Fig. 1) does not necessarily seem to be worthless because it makes predictions that can be falsified. The main prediction the model makes is that some molecules characterising above all its final stages (Fig. 1) could still be present in the form of molecular fossils in contemporary cells. In other words, we cannot exclude the possibility that some of the molecules predicted by the model still exist, such as a...

Hypotheses of Early Translation

Attempts at developing a plausible explanation for the formation of the translation system have not been satisfactory so far (Trevors and Abel, 2004). A problem with the direct early translation models stems from their assumption that preexisting RNAs served as templates (early mRNAs) for the alignment of aminoacyl-tRNAs (ac-tRNA or with some early form of the tRNAs) and that this system gradually acquired efficiency and functionality. Following this premise, based on the traditional...

Mathematical Description of the Standard Genetic Code

Table 2 summarizes the degeneracy distribution inside quartets of the standard genetic code, which we aim to describe. For doing so we will use a particular kind of whole number positional representation called a non-power representation. Table 4 Euplotid nuclear version of the genetic code it differs of the standard genetic code only in the assignation of the codon UGA, which in this case is assigned to Cysteine instead of to the Stop signal Table 4 Euplotid nuclear version of the genetic code...

The Anticodon Hairpin as the Ancient Adaptor

The simplest form of evolutionary continuity is provided by conservation of the anticodon hairpin (stem and loop) of tRNAs as the most ancient adaptor, which was charged at position 37 of the modern tRNA molecule, adjacent to the 3'-end of the anticodon (Woese, 1972). The CCH hypothesis has adopted this view (Szathmary, 1996, 1999). As discussed in those papers, such a hairpin offers an ideal transient binding by ribozymes through complementary structures (e.g. in the form of 'kissing'...

Spatio Temporal Patterns of Neural Activity

The nervous system includes several subsystems with peculiar features that add up to the complexity. In addition to the input (sensory channels) and output (motor and humoral channels) subsystems, there is an extensive network of interconnected ganglia and nuclei that are mainly located in the brain, the most prominent of which is the cerebral cortex (for review on the quantitative analysis, see Braitenberg and Schuz, 1991). The cerebral cortex (the cortex) is formed by two hemispheres and...

Where is the Self

I think there is now a need for a novel and fundamental idea that may give a new look to immunological theory. (Jerne, 1974, p. 380) An interesting alternative to Burnet's concept of the self was suggested by Jerne in his network theory of the immune system (Jerne, 1974). This theory clearly corresponds to the Saussurian theory and pushes it to its limits within immunological theory. Jerne suggests that the progress of ideas in immunology follows a path from application (i.e. vaccine) to...

The New Frontier of Biology

Codes and conventions are the basis of all cultural phenomena and from time immemorial have divided the world of culture from the world of nature. The rules of grammar, the laws of government, the precepts of religion, the value of money, the cooking recipes, the fairy tales, and the rules of chess are all human conventions that are profoundly different from the laws of physics and chemistry, and this has led to the conclusion that there is an unbridgeable gap between nature and culture. Nature...

Benchmars Tasks Game Theory

We have used simple 2 x 2 matrix games with one-way pre-play communication as test tasks a coordination and a task-allocation game. There are two reasons we have chosen these games. First, because of their simplicity these scenarios are easy to implement. Second, these games are well studied in the economics literature, and it is shown both theoretically and empirically that (one-way) cost-free, pre-play communication (so called 'cheap talk') can resolve coordination problems in both...

The Reductionist Perspective

How do we know to differentiate between self and nonself The genetic reductionist approach suggests that there is a single genetic criterion for identification of the self a simple code, which is a genetic fingerprint that allows the immune system to differentiate between the self and the other (nonself). In other words, the reductionist perspective offers a simple correspondence between the immune self and a molecular component of the cell. The MHC is the set of gene loci specifying major...

Catalytic Propensity of Amino Acids and the Origins of the Genetic Code and Proteins

d m Kun1,2, S ndor Pongor3,4, Ferenc Jord n2,5, and Eors Szathm ry1,2,6 Abstract The origin of the genetic code is still not fully understood, despite considerable progress in the last decade. Far from being a frozen complete accident, the canonical genetic code is full of patterns that seem to open a window on its evolutionary history. In this chapter we rethink the hypothesis that the primary selective force in favour of the emergence of genetic coding was the added value by amino acids to...

The Cytoskeleton

Protein interaction network diagrams demonstrate the impressive wiring of pathways in cells. The potential interactions of components that are being revealed in the diverse '-omes' (like the proteome, genome, metabolome, interactome, tran-scriptome, etc.) is bewildering. Proteome-wide analysis of a single interaction module that is present, on average, in 100-200 individual molecules can result in over 10,000 potential interactions 5,52,84,88 . Protein-protein interactions consequently lead to...

The Sugar Code Basic Principles

In order to succeed as hardware for information transfer any substance class must offer the potential for specific coding. The message will have to be deciphered with sufficient biochemical affinity and low probability for ambiguities and misinterpretation. A high-density coding capacity is beneficial to keep the size of the active sections of biomolecules small, thereby reducing the energetic expenses during synthesis. Moreover, spatially easy accessibility and the potential for rapid...

Protein Linguistics

The need for protein linguistic analysis arose in the course of the annotation of genomic and proteomic data 12,20 . The prediction of function from a given nucleic acid or amino acid sequence requires precise and unambiguous knowledge of the functions that are attributed to similar sequences 27,72,74 or three-dimensional folds 21,41 . Currently, the ambiguity of annotations in databases is hindering progress in this direction. Protein linguistics deals with the potential categorization of the...

Prime Number

The Universal Genetic Code Table

As regards the genetic code, one should juxtapose the abstract syntax of the arithmetical language with some well-defined sets of units in the genetic code. In other words, these units should be added and their sums within each set should be written temporarily as we are accustomed in decimals. Theoretically, some original number notations should replace these decimals as soon as we uncover the genetic code's primordial number system, if there is one. The art of number notation since the...

The First Messengers RNAs Codified Successions of Interactions Between Different PeptideRNAs

If, as seems to be the case, a stage was reached in which all protocell catalysis was performed by covalent complexes of peptides and RNAs (peptide-RNA) (Wong, 1991 Di Giulio, 1997 Wong and Xue, 2002 Di Giulio, 2003), then any improvement in peptide-RNA synthesis must have had a highly positive effect on protocell activity. More specifically, the improvement of peptide-RNA synthesis must have passed through certain stages. The most elementary must have been a direct interaction between two...

Brain and Language

Analyses of neural activity during the performance of cognitive tasks have become a growth industry. Their sensitivity has increased over the years. These methods are increasingly applied to the recording of brain activity during linguistic performance. The recognition that neural localisation of language can be plastic is now widely known (Nobre and Plunkett, 1997 Neville and Bavelier, 1998 Musso et al., 1999). Studies of brain injury revealed that damage to the left hemisphere before a...

Parity Based Error Detection Correction Methods

A simple method for detecting errors consists in encoding the information (two-letter words in our previous example) by a subset of the redundant binary strings. Doing this, the words can be encoded in such a way that the Hamming distance between different words is maximized. If the least distance between strings pertaining to different words is 2, the arrival at the receiver of a string at a Hamming distance of 1 from one of the strings of the coding table (the allowable strings) is a sure...

Rumers Transformation

Yuri Rumer (1966) was the first who saw an element of information hidden in the genetic code. Rumer gathered the triplets of the solid series into one set and the broken series into the other as shown in Fig. 4a. Both sets have the same number of triplets - 32 each. This halving provides an opportunity to map triplets in a one-to-one manner. A mapping was realized with the help of Rumer's unique transformation T o G, C o A or, in otherwise notation, TCAG GACT. The transformation maps each...

Palindromic Symmetry and the Genetic Code Model

As shown before, we have up to now uncovered a part of the palindromic degeneracy preserving symmetry. Observing Tables 15 and 18, is easily to understand its meaning as a transformation inside the genetic code connecting quartets with the same degeneracy distribution. On the mathematical-model side Table 19 Palindromic symmetry a degeneracy preserving transformation connecting different quartets of the genetic code Table 19 Palindromic symmetry a degeneracy preserving transformation connecting...

Rumers Class

It is very surprising that Rumer's classification can also be presented in a completely analogous way. In Table 20 we show Rumer's classes, that is, the quartets of degeneracy 4 (given in grey) and the quartets of degeneracy-3, 2, and 1. It is easy Fig. 2 Non-linear algorithmic representation of the parity class. Observe the induced chemical dichotomies Y-R in the last letter, and K-Am, in the middle one Fig. 2 Non-linear algorithmic representation of the parity class. Observe the induced...

Reallife Global Balance

An exact equilibration of the nucleon sums within the well-defined sets is one of the two standard representations of the artifactural differences of the genetic code. The unique global balance in Fig. 5 makes use of molecular residues of the amino acid standard blocks from an internal part of a protein and charged ions of side chains from the real-life environment of cytoplasm. The closed circle of the block Fig. 5 The real-life global balance of the genetic code. The nucleon sum of the...

The Musical Code between Nature and Nurture

Ecosemiotic and Neurobiological Claims Abstract This contribution is about sense-making in music. In an attempt to bring together such diverging fields as semiotics and neurobiology, it argues for a processual approach to music, which conceives of 'music users' as organisms that 'cope' with their environment. It is a position which calls forth ecological and epistemological assumptions and which stresses the importance of a conception of music as dealt with rather than a static conception of...

The Neuroheuristic Paradigm

The biological laws of neuroscience developed in the nineteenth and twentieth century, as well as the construction of mathematical axioms, were derived from observations and pertaining to a priori knowledge. If, however, the observation is Fig. 1 Redrawing that partially reproduces a diagram of the brain fourteenth century illustrated on parchment illumination University Library, Cambridge Fig. 1 Redrawing that partially reproduces a diagram of the brain fourteenth century illustrated on...

Virtual Global Balance

In our considerations below we deal with the free neutrally charged amino acid molecules. The second standard representation of the artifactural differences is an accurate superimposition of the decimal syntax onto equilibrated nucleon sums. The virtual global balance is illustrated in Fig. 6 we use the attribute virtual because of the imaginary borrowing . Both global equilibria have the same block-to-chain type, but the ways of balancing are different. The previous balance means that all the...

Introduction

Signal transduction is required to allow the genome to selectively express a gene set in response to environmental changes. Specific chemical interactions between the environmental signals, first messengers, and the genome are not required in signal transduction, since a limited series of adaptors are capable of modifying genome expression. At the present stage of evolution, gene availability can be modulated by proteins belonging to the class of transcription factors. The interaction between...

The Ribonucleoprotein RNP World and Prebiotic Chemistry

Studies on cellular origins became more complicated when it was realized that DNA probably was not an early molecule. Deoxyribonucleotides are derived from ribonucleotides and DNA is vastly less reactive than RNA, not able to participate efficiently in metabolic reactions Orgel, 2002 . To the contrary, cellular RNAs are known to catalyze metabolic transformations - ribozymes, the most remarkable being the ribosomal peptidyl transferase activity Yusupov et al., 2001 . There is in vitro evidence...

Selective Scenarios for the Origin of Language

The issue of the origin of human language has provided fertile ground for speculation and alternative theories have been proposed Box 1 . Most of the theories that suggest a given context for the evolution of human language attempt to account for its functional role. Given that, functionally, all of these theories are more or less plausible, it is almost impossible to decide on their usefulness based only on this criterion. However, recent game theoretical research can help us evaluate various...

The Systematization Principle

The Universal Genetic Code

The systematization principle of the genetic code is a rule that arranges a code calligramme. A calligramme was invented in 1914 by the French poet Guillaume Apollinaire 1980 . He arranged letters and words of his written texts in the two-dimensional space of a book sheet instead of a traditional line. Thereby he created the so-called calligrammes in which texts, semantics, visual images, and symmetries are joined together. A calligramme surpasses a common text in an information capacity and...

Evolutionary Neurogenetic Algorithm

We have developed a software framework called Evolutionary Neurogenetic Algorithm ENGA , which offers researchers a fine control over biological detail in their simulations. Our original intent was to create software with much potential for variability. That is, we wanted a piece of software which is general enough to allow for a wide range of experimentation but appears as a coherent system and does not fall apart into a loosest of unrelated pieces of code. This required careful specification...