Accounting in Genetics

Evolution at a crossroads: The new biology and the …, 1985

The current situation in philosophy of science generally, and in philosophy of biology in particular, is most unsatisfactory. There are at least three general problems that many philosophers thought themselves near to solving twenty years ago, only to find that the anticipated solutions have come unglued. These are (1) the problem of characterizing and understanding the dynamics of conceptual change in science; (2) he problem of understanding the interrelationships among theories including particularly the reduction of one theory to another); and (3) he problem of scientific realism (i.e., the problem of how seriously to take the claims of theoretical science or, at least, of some theoretical scientists, to be describing the world literally--in terms of such theoretical entities as genes and protons, DNA molecules, and quarks). This general situation has significant effects on the philosophical study of particular sciences. In philosophy of biology, for example, although one finds a large number of elegant studies of particular topics, the sad fact is that there is no generally satisfactory large-scale synthesis n sight. We have no agreed-on foundation, no generally acceptable starting point from which to delimit and resolve the full range of theoretical problems of interest to scientists and philosophers regarding biology.

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 selfcatalyzed binding (charging) of tRNA 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 fixed point 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.

Foundations of Science, 2021

Some real life processes, including molecular ones, are context-sensitive, in the sense that their outcome depends on side conditions that are most of the times difficult, or impossible, to express fully in advance. In this paper, we survey and discuss a logical account of contextsensitiveness in molecular processes, based on a kind of non-classical logic. This account also allows us to revisit the relationship between logic and philosophy of science (and philosophy of biology, in particular).

Information, 2016

The genetic code of amino acid sequences in proteins does not allow understanding and modeling of inherited processes such as inborn coordinated motions of living bodies, innate principles of sensory information processing, quasi-holographic properties, etc. To be able to model these phenomena, the concept of geno-logical coding, which is connected with logical functions and Boolean algebra, is put forward. The article describes basic pieces of evidence in favor of the existence of the geno-logical code, which exists in parallel with the known genetic code of amino acid sequences but which serves for transferring inherited processes along chains of generations. These pieces of evidence have been received due to the analysis of symmetries in structures of molecular-genetic systems. The analysis has revealed a close connection of the genetic system with dyadic groups of binary numbers and with other mathematical objects, which are related with dyadic groups: Walsh functions (which are algebraic characters of dyadic groups), bit-reversal permutations, logical holography, etc. These results provide a new approach for mathematical modeling of genetic structures, which uses known mathematical formalisms from technological fields of noise-immunity coding of information, binary analysis, logical holography, and digital devices of artificial intellect. Some opportunities for a development of algebraic-logical biology are opened.

Axiomathes, 2009

The object of this work is the current debate regarding the concept of the gene. The aim is to understand the ontological status of the gene concept, considering it as a theoretical entity inside the framework of the debate about scientific realism.

Grammatical Models of Multi-Agent Systems, …, 1999

Advances in Bioinformatics and Its Applications, 2005

Systems of elements of genetic code are studied by their cognitive presentation in a form of mathematical matrices of symbolic and numerical kinds. This cognitive form of data presentation permits to discover new phenomenological rules of evolution of genetic codes, to reveal two branches of evolution within genetic code, to present hidden interrelations between the golden section and parameters of genetic polyplets, to disclose matrices of a hyperbolic turn in genetic matrices, etc. Mysterious sets of structures, realized by the nature in a hierarchi al system of genetic codes, can be confronted by a heuristic manner with families of mathematical matrices, which contain elements of these structures. A few rules of degeneracy and segregations of genetic codes are revealed in this direction. A new answer on the fundamental question-"why 20 amino acids?"-is proposed as well. .

Molecular logic is an emerging field in biomathematics that considers molecular substrates as computational devices that process chemical or physical inputs to generate outputs based on logical operators ([2]). In it is discussed how logical circuits can be simulated using colonies of bacteria E. Coli. Those colonies, according to Tamsir et al. in [10], exhibit an area in which the fluorescence of the expressed gene is not completely present or absent, which does not allow this behavior to be interpreted as a binary operator. Actually, recent work has used fuzzy logic-based models (e.g. [1]) because Boolean systems are insufficient to capture intermediate states in the catalytic processes of protein modification experimentally observed. Hence, the excluded middle principle, which means in this context that all variables can be in only two possible discrete states, is not realistic at modeling the metabolism of E. Coli. On the other hand, some proteins appear to express contradictory states despite the stability of the systems to which they belong. This "bioparaconsistent" phenomenon is against the classical non-contradictory logical principle which implies that contradictory observations will trivialize the underlying logic. In this paper we discuss these two classical logical principles, too strong for reasoning about the molecular metabolism, by exploring some experimentally observed data.