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...

Conclusion

There are two great facts about life that shed a new light on the mechanisms of evolution. The first is that genes and proteins are produced by copying and coding, by transcription and translation, i.e. by two fundamentally different mechanisms. The second is that natural selection is the long-term result of copying, i.e. of only one of those two basic mechanisms. This implies that coding is a distinct mechanism of molecular change and, in the long run, a distinct mechanism of evolutionary...

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...

References

Altenm ller E (2003) How many music centres are in the brain In Peretz I, Zatorre R (eds) The Cognitive Neuroscience of Music. Oxford University Press, Oxford New York, pp. 346-353 Amunts K, Schlaug G, J ncke L, Steinmetz H, Schleicher A, Dabringhaus A, Zilles K (1997) Motor cortex and hand motor skills structural compliance in the human brain. Human Brain Map 5 206-215 Arom S (2000) Prolegomena to a biomusicology. In Wallin N, Merker B, Brown S (eds) The Origins of Music. The MIT Press,...

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...