The Cell Language Theory

Connecting Mind and Matter

Sungchul Ji

• Publisher: WSPC (EUROPE)
• Year: 2017
• ISBN:
  9781911299776
• Topic: Biological Sciences
• Subtopic: Molecular Biology
• Index: Biological Sciences

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This book represents the results of 45 years of research on a wide range of topics, including atomic physics, single-molecule enzymology, whole-cell metabolism, physiology, pharmacology, linguistics, semiotics, and cosmology. It describes the first comprehensive molecular theory of the genotype-phenotype coupling based on two key theoretical concepts: (i) the conformon, the conformational wave packet in biopolymers carrying both the free energy and genetic information; and (ii) the intracellular dissipative structures, the chemical concentration waves inside the cell that serve as the immediate drivers of all cell functions. Conformons provide the driving forces for all molecular machines in the cell, and intracellular dissipative structures coordinate intra- and intercellular processes such as gene expression and cell-cell communications.

One of the predictions made by the cell language theory (CLT) is that there are two forms of genetic information — the Watson–Crick genes transmitting information in time (identified with DNA), and the Prigoginian genes transmitting information in space (identified with RNA expression profiles). The former is analogous to sheet music or written language and the latter is akin to audio music or spoken language, both being coupled by conformons acting as the analog of the pianist. The new theory of DNA structure and function constructed on the basis of CLT can rationally account for most of the puzzling findings recently unearthed by the ENCODE (Encyclopedia of DNA Elements) project.

The Cell Language Theory has important applications in biomedical sciences including drug discovery research and personalized medicine on the one hand and in the mind-body research and consciousness studies on the other.

--> Contents:

• Preface
• About the Author
• Acknowledgements
• Introduction
• Key Terms and Concepts
• The Bhopalator
• Cell Language
• Matrix Mathematics of Genetics
• Biosemiotics
• Applications of the Cell Language Theory to Biomedical Sciences
• The Universality of the Planckian Distribution Equation
• The Universality of the Irreducible Triadic Relation
• The Philosophical Implications of the Cell Language Theory
• Conclusions
• References
• Appendices
• Index

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--> Readership: Students, researchers and practitioners of the biomedical sciences and mind-body research and consciousness studies -->
Keywords:Conformons;Cell Language Theory;Intracellular Dissipative Structures;Watson–Crick Gene;Prigoginian GeneReview:0

Chapter 1

Introduction

1.1 A Chronological List of the Theoretical Concepts Discussed in this Book

As a postdoctoral fellow under David E. Green (1910–1983) at the Institute for Enzyme Research at the University of Wisconsin in Madison from 1970 to 1974, I formulated the concept of the conformon in 1972, defined as conformational strains of biopolymers driving goal-directed molecular motions in living cells. The conformon was postulated to provide the ultimate molecular mechanisms underlying the phenomenon of oxidative phosphorylation (oxphos) in mitochondria. During the past four and a half decades, I have been fortunate to have had the opportunity to continue my theoretical research on the conformon, leading to the formulation of the numerous theoretical concepts related directly or indirectly to the conformon. The results of these research activities are summarized in Table 1.1, and most of these items and their possible applications in biomedical research and philosophy are discussed in the following chapters.

It is interesting to note that G. N. Ling, beginning a decade earlier, formulated a general theory of cell physiology based on his association–induction hypothesis (AIH) (reviewed in [1, 2]; see Section 2.12), which, in essence, posits that asymmetric distributions of ions and other diffusible molecules across the cell membrane are attributable to selective ligand-binding properties of proteins and associated structured water layers in the cytosol and not to any pump (or ion channel) activities present in the plasma membrane [3–5]. The concept of structured water layers formed in the interface between proteins and bulk-phase liquid water, first invoked as a logical consequence of AIH, seems to have been largely substantiated during the past two decades through the pioneering work of Pollack and his associates [5], but the idea that membrane pumps play no role in generating the asymmetric distributions of ions and other molecular species across cell membrane seems to go against the enormous amount of experimental evidence now available. One solution to this long-debated dilemma may be to recognize that there are two kinds of asymmetric ion distributions — the equilibrium distribution advanced by AIH and the dissipative distribution supported by the membrane pump hypothesis, the former being an example of Prigogine’s equilibrium structures and the latter his dissipative structures (see Section 2.6).

Table 1.1 The chronological listing of the key theoretical concepts developed by Ji in 1972–2016.

The diversity of the theoretical concepts originating in connection with the conformon postulate in bioenergetics and bioinformatics evident in Table 1.1 contrasts with the unity of AIH claiming to underlie all cell functions [2].

1.2 Three Stages of Development of Human Knowledge

There appears to be three stages of development in human knowledge: (i) gathering and describing of raw data, (ii) organizing data, and (iii) constructing theories to account for the regularities embedded in organized data. Some examples supporting this view are provided in Table 1.2, where the box located at D3 contains biological theories which are predominantly those that the author has developed over the past four and a half decades and do not include many other theories in the literature for the sake of brevity.

1.3 Gaylord’s Distinction Between Physics and Biology

The American paleontologist Gaylord Simpson [716] stated something to the effect that

Table 1.2 Three stages of the development of scientific knowledge.

Note: The columns are labeled with Arabic numerals and the rows with English letters. Thus, A3 indicates quantum mechanics, B2 indicates the periodic table, etc.

Table 1.3 The laws, principles and concepts from science and engineering that were incorporated into biocybernetics, a general molecular theory of life.

Discipline	Laws, Principles and Concepts
Physics
Newtonian mechanics	1. Mechanical energy
Thermodynamics	2. Free energy
	3. Entropy
	4. Dissipative structures
Statistical mechanics	5. Thermal fluctuations
Quantum mechanics	6. Quantum of action
	7. Franck–Condon principle
	8. Strong f...