The Cell Language Theory

The following sections are included:

• Preface
• About the Author
• Acknowledgments
• Contents

The following sections are included:

• A Chronological List of the Theoretical Concepts Discussed in this Book
• Three Stages of Development of Human Knowledge
• Gaylord’s Distinction Between Physics and Biology

The following sections are included:

• What Is a Category?
  • What Is a Functor?
  • The Ur-Category
• What Is Information?
  • The General Characteristics of Information
  • Shannon Information (I_Sh)
  • Planckian Information (I_Pl)
  • Peircean Information (I_Pe) in Relation to the Shannon Information (I_Sh)
• Burgin’s Parametric Definition of Information
• Complementarity vs. Supplementarity
  • The Principle of Generalized Complementarity (PGC)
  • The Complementarian Logic
• System vs. Systome
• Self-Organization, Dissipative Structures (Dissipations), and Self-Organizing Whenever and Wherever Needed (SOWAWN) Machines
• The Generalized Franck–Condon Principle
• The Atom–Cell Isomorphism
• The Gnergy Principle of Organization (GPO)
• The Principle of Irreducible Triadicity
• Symmetries and Symmetry Breakings
• The Association–Induction Hypothesis
• The Fourth-Phase Water
  • The Ling–Pollack Water Structures
  • Coherence Domains and the Benveniste–Montagnier Experiments BMEs
  • Systome Medicine: The Complementary Union of System Medicine and Environmental Medicine
• Cell Water as a Four-Dimensional Proton Transfer Network: Water is to Cell Language What Air is to Human Language
• The Equilibrium and Dissipative Structures of Water

The following sections are included:

• Three Stages of Development in Cell Biology
• The Principles and Major Concepts Embedded in the Bhopalator Model of the Living Cell
  • The IDS-Cell Function Identity (ICFI) Hypothesis
  • The Information–Energy Complementarity in the Living Cell
  • Electromechanochemical Energy Transduction
  • The Wave–Particle Duality in the Living Cell
  • Three Categories of Enzyme Catalyzes
  • The GFCP, Pre-fit Mechanisms, and Scalar Enzyme Catalysis
  • The GFCP and Translational Enzyme Catalysis
  • The GFCP and Rotary Enzyme Catalysis
  • The Pre-fit Hypothesis
  • Allosterism, Bohr Effect, and Wyman’s Pseudolinkage
  • The Brownian Distance of Biopolymers
  • The Principle of Microscopic Reversibility
  • The Information–Energy Complementary Landscape Theory of Protein Folding
  • Three Classes of Molecular Structures in the Living Cell
  • Five Classes of Factors Affecting the Behavior of the Living Cell
  • An Atom–Cell Comparison Based on Aristotle’s Four Causes Doctrine
  • The Cell Force: A Comparison with the Gravitational Force
  • The Cell as the Atom of Semiosis
  • The Triadic Structures of the Living Cell
  • The Piscatawaytor: A Model of the Human Body Viewed as a Self-Organizing System of Bhopalators
  • The Human Body–Internet Metaphor (HIM)
• The Mitochondrion — The Energy Source of the Living Cell
  • The Conformon Model of Oxidative Phosphorylation: Kinematic vs. Dynamic Aspects
  • Conformon Production, Transfer, and Utilization
  • Deconstructing the Chemiosmotic Model
  • A Comparison Between the Chemiosmotic and Conformon Models of Oxidative Phosphorylation
  • The Rochester–Noji–Helsinki (RoNoH) Model of Oxidative Phosphorylation
  • Mitchel vs. Williams Protons
  • Active vs. Passive Conformational Changes of Biopolymers
  • Active vs. Passive ATP Syntheses
  • Cytochrome c Oxidase an Electron-Driven Proton Sink and Pump
  • Proton-Transfer Chains/Complexes as the Fourth-Phase Water Structures of Ling and Pollack
• The Conformon
  • Direct Experimental Evidence for Conformons or Conformational Waves
  • DNA Supercoils, the White Formula, and Conformons
  • Stress-Induced Duplex Destabilizations as Conformons
  • Virtual and Real Conformons: Mechanisms of Conformon Generation Based on the GFCP
  • The Quantization of Conformational Energies of Biopolymers
  • The Conformon Hypothesis of Energy-Coupled Processes in the Living Cell
  • The Conformon Model of Mechanical Force Generation from Chemical Reactions
  • The Conformon Model of Muscle Contraction

The following sections are included:

• Communication and Languages
  • Macro-, Micro-, and Holo-Communications
  • The Universality of Double Articulations
  • Cell Language (Cellese) Defined
• Some Linguistic Terms for Non-linguists
  • Double Articulation Extended to Triple Articulation
  • Rule-Governed Creativity
  • Syntagmatic Relation
  • Paradigmatic Relation
  • Arbitrariness of Signs
• Application of the Information Theory to Signal Transduction in Living Cells
• Isomorphism Between Cell and Human Languages
• Isomorphism Between the Immune System and Human Language
• Triple Articulation in Cell Language
• Decoding DNA Based on the Semiotic Lessons Learned from Decoding the Rosetta Stone
  • Rule-Governed Creativity
  • Double Articulation also called Duality
  • Maximum Information Principle
  • Discreteness
  • Semanticity
• The Biology–Linguistics Connection
• The Origin of Biological Information
• The von Neumann Questions and the Conformon Theory
• Water as the Medium of the Cell (Cellese) and Cosmic Languages (Cosmese)
• Cymatics and Chladni Patterns (or Figures)
• Water as the Molecular Sensor of Sound Waves
• Sonocytology or “Cytocymatics”
• Water Standing Waves (Aquaresonances) as the Possible Cause of the Origin of Life
• Decoding CymaGlyphs May Be Akin to Decoding Hieroglyphs
• The Water Thesis: Water Can Represent, Compute, and Communicate
• Cosmic Language (Cosmese) as the Irreducible Triad of Wave Language (CymaGlyphs), Cell Language (e.g., RNA glyphs), and Human Language (e.g., Hieroglyphs)
• CymaScope as an Experimental Tool for Connecting Mind and Matter
• Life Supervenes on Water
• The Dissipative-to-Equilibrium Reversibility (DER) Postulate of Aquastructures
• Exosomes as Extracellular Text Messages That May Be Deciphered by Digital CymaScopy

The following sections are included:

• The Petoukhov Coincidence
• The Mathematical Similarity between the Genetic Code and the I-Ching Hexagrammatology
• The Molecular Language (Moleculese)

The following sections are included:

• Concepts, Laws, and Principles
  • Molecular Machine
  • Dissipative Structures
  • Intracellular Dissipative Structures
  • The Law of Requisite Variety
  • Cell Language Theory
  • Biocybernetic Models of Living Systems and Processes: “Atorology”
• A Comparison between Physics, Biology, and Philosophy
• The Peircean Theory of Signs
  • Peircean Definition of Signs
  • Peircean Categories: Firstness, Secondness, and Thirdness
• Macrosemiotics vs. Microsemiotics
• Peircean Signs as Gnergons
• The Quark Model of the Peircean Sign
  • The Nine Types of Signs
  • The 10 Classes of Signs
  • Derivation of the 10 Classes of Signs from Nine Types of Signs Based on the Analogy between e-Signs and Quarks in Elementary Particle Physics
  • Derivation of “Nilsign” and Its Associated Category Called “Zeroness” Based on the Quark Model of the Peircean Sign
  • The Neo-Semiotics and the Possible Meaning of Zeroness
• Application of the Concept of Signs to Molecular Biology: Microsemiotics
• Real vs. Virtual Semiosis
• Division of Sign Processes Based on the Nature and Size of Sign Processors
• Peirce’s Metaphysics as the Basis for Unifying Sciences

Most, if not all, human diseases, both somatic and mental, can be said to arise from miscommunication and disregulation of metabolism within individual cells (i.e., intracellular semiosis) or between cells (i.e., intercellular semiosis) in the human body. Hence, the cell language theory and medical sciences are intimately related…

The following sections are included:

• Blackbody Radiation and the Planckian Distribution Equation
• Single-Molecule Enzyme Catalysis
  • Observation and Data
  • Explanation: Quantization of Energy Levels in Enzymes
  • RASER Model of Enzyme Catalysis
• Examples of Long-Tailed Histograms Fitting PDE
  • Atomic Physics (Figure 8.6(a))
  • Protein Folding (Figure 8.6(b))
  • Single-Molecule Enzyme Kinetics of Cholesterol Oxidase (Figure 8.6(c))
  • mRNA Levels in Budding Yeast (Figure 8.6(d))
  • RNA Levels in Human Breast Tissues (Figure 8.6(e))
  • Human T-cell Receptor Variable Region Sequence Diversity (Figure 8.6(f))
  • 7-Mer Frequency Distribution in P. abyssi (Figure 8.6(g))
  • Codon Usage Profile in the Human Genome (Figure 8.6(h))
  • Protein-Length Frequency Distribution in H. influenza (Figure 8.6(i))
  • Stress-Induced Alterations in the Neuroarchitecture of the Mouse Brain (Figure 8.6(j))
  • Impulse-Induced Electrocorticogram (ECoG) Response of the Rabbit Olfactory System (Figure 8.6(k))
  • fMRI Signals from the Human Brain before and after Psilocybin (Figure 8.6(l))
  • Sentence-Length Frequency Distributions in Private Letters (Figure 8.6(m))
  • Word-Length Frequency Distributions in English Text (Figure 8.6(n))
  • Word-Length Frequency Distribution in Kerry’s Speech (Figure 8.6(o))
  • The Pitch Histogram of Sylvia Plath’s Reading of Her Poem (Figure 8.6(p))
  • Decision-Time Histograms (Figure 8.6(q))
  • The 1996 and 2013 US Annual Income Distributions (Figures 8.6(r) and 8.6(s))
  • Polarized Cosmological Microwave Background (CMB) Radiation (Figure 8.6(t))
• The Universality of the PDE
  • Planckian Processes as Selected Gaussian Processes
  • The Wave–Particle Duality in Biology and Medicine
• The Planckian Information (I_P) as a New Measure of Organization
  • The Definition of Planckian Information, I_P
  • The First Law of Informatics: Information Can but Entropy Cannot Be Negative
  • The Brain Is both Entropic and Informational
• Possible Relations among Planckian Information, Quanta, and Entropy
• PDE-based CymaScopy (PCS) as a Novel Experimental Tool for Infostatistical Mechanics

The following sections are included:

• The Peircean Sign as the Origin of the Irreducible Triadic Relation
• Peirce’s Simple Concepts Applicable to Every Subject
• ITR in Peirce’s Hypostatic Abstraction
• Examples of ITRs
  • The Golden Ratio
  • The Fibonacci Numbers
  • Belousov–Zhabotinsky (BZ) Reaction (or the Brusselator)
  • Enzyme Catalysis
  • Gene Expression
  • Practopoiesis
  • ITR in Mathematics, Philosophy, Semiotics, and Religions

The following sections are included:

• Complementarism
  • Complementarity Between Complementarism and Merleau-Ponty’s Flesh Ontology
  • Naturalized Phenomenology
• Complementarism and Semiotics
• Signs, Thoughts, and “Thoughtons”
• The “New Jersey Theory of Mind” (NJTM)
• A Theory of Consciousness
• The Triadic Architectonics of Human Knowledge
• On the Possible Relation Between Quantum Mechanics and Semiotics
• The Hertz–Rosen–Pattee (HRP) Model of Reality
• The Signless and the Dao as the Source of Everything Including Signs
• Cybersemiotics
• Practopoiesis
• A Theory of the Origin of Information Based on Peircean Metaphysics
• Information–Entropy Relation
• A “Philosophical Table” for Classifying Information, Entropy, and Energy
• The Information–Energy–Entropy Relation: The “New Jerseyator”
• The First Law of Informatics: Information Can but Entropy Cannot Be Negative
• Semiotics and Information Theory
• The Model of the Universe
  • The Shillongator Model of the Universe
  • Semiotics of the Universe
  • Iconic Model of Reality
  • The Self-Knowing Universe and the Anthropic Cosmological Principle
• The Universe as a Self-Organizing Musical Instrument (USOMI)
• Semiotics as the Theory of Everything (TOE)
• Triadic Monism
• A Model of Consciousness

Two kinds of regularities or structures have been found to underlie a large number of phenomena occurring at all scales, from atomic systems to enzymes, cells, organisms, languages, decision-making, economic activities, and cosmological microwave background radiation: (a) irreducible triadic relation (ITR; see Figure 9.1) and (b) the Planckian distribution equation (PDE; see Eq. (8.2) or (8.3)). The former is qualitative involving words, while the latter is quantitative involving numbers. Thus, this book provides the evidence that there exist two kinds of functors (defined in Section 2.1.1) — qualitative and quantitative (see the top and the bottom rows of Table 11.1). Furthermore, it is here suggested that these two kinds of functors are connected via the principle of complementarity (discussed in Section 2.4), since quantity and quality can be viewed as complementary aspects of the ultimate reality…

The following sections are included:

• References
• Appendix I: Two Philosophers of the Flesh
• Appendix II
• Index