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Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…
Ultraviolet light incident on organic material can initiate its spontaneous dissipative structuring into chromophores which can then catalyze their own replication. This may have been the case for one of the most ancient of all chromophores…
How the very first nervous systems evolved remains a fundamental open question. Molecular and genomic techniques have revolutionized our knowledge of the molecular ingredients behind this transition but not yet provided a clear picture of…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a…