Evolutionary changes in the information content of polypeptides

Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory

A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.

Deterministic hypotheses on the origin of life and of its reproduction

The current theory of the origin of life by random polymerisation and selection of nucleic acids is challenged by the hypothesis that the primitive enzymatic sites would have been formed by abiotic polymerisation of aminoacids, specifically gathered (by saline, hydrogen, or hydrophobic interactions), around the different substrates. The information contained in these proteinoids would have been transferred to messenger-like RNAs by a mechanism reverse of that of the present protein synthesis, and then to DNA. The interactions between aminoacids and nucleotidic sequences would have been at the origin of the genetic code, as hypothesized by several authors. We propose that the specificity of the bindings would have been enhanced and 'frozen' by ternary associations with specific proteinoids (future aminoacyl tRNA synthetases). The role of chance would have been limited to the supply of the products and to the determination of the conditions of reaction. Thermodynamic considerations (dissipation of the free enthalpy through enzymatic activities) may explain the emergence of the biological systems.

Universal regularities in protein primary structure: preference in bonding and periodicity

Utilizing the whole protein data base as well as parts of it (groups and individual representatives), the universal character of the regularities in protein primary structure - preference in bonding (self-ordering) and periodicity - is shown by means of an improved procedure of checking statistical significance. In the vast majority of the cases there is a preference in bonding with the same or with very similar amino acid. Taken as a whole, both regularities show a universal character. The results obtained provide evidence in favour of the conception about the priority of proteins as information polymers.

How can quantum mechanics of material evolution be possible? Symmetry and symmetry-breaking in protobiological evolution

Material self-assembly as a self-organizing process is always accompanied by symmetry-breaking in the material configuration. Self-sequencing of amino acids during their thermal polymerization has lost a certain property of permutation symmetry that was observed in the mixture of free amino acids. The evolutionary precursor state is more symmetrical about its internal material configuration and more degenerate due to the multitude of the indistinguishable individuals. The evolution proceeds in the direction along which the degeneracy in the internal states dissolves owing to the symmetry-breaking originating in material flow equilibrium of open material aggregates. Protobiological information is latent in the material system which is highly symmetrical and highly degenerate in its internal states. Evolution of matter is an endogenous process in which the earlier symmetric property is lost and less degenerate states are approached. Quantum-mechanically, the generation of protobiological information is due to the symmetry-breaking of the Hamiltonian originating in the interaction with the exterior through material flow, in contrast to the Schrödinger equation which preserves a symmetry and the associated invariants.

Electrical excitability of proteinoid microspheres composed of basic and acidic proteinoids

Material flow equilibration, an endogenous interaction adjustment process underlying fulfillment of material flow continuity during material self-assembly, also underlies electrical excitability observed in the proteinoid microspheres as simulated models of the protocell. The spikings of the membrane potentials are attributed to a singular character of the interaction rate coefficients measuring the strengths of the coupling between basic and acidic proteinoids, in which the rates change singularly with time due to material flow equilibration.