Ebook The cell language theory - Connecting mind and matter: Part 1

Part 1 book “The cell language theory – Connecting mind and matter” has contents: Introduction, key terms and concepts, the bhopalator, cell language, matrix mathematics of genetics, biosemiotics.

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b2530 International Strategic Relations and China’s National Security: World at the Crossroads

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Published by

World Scientific Publishing Europe Ltd.

57 Shelton Street, Covent Garden, London WC2H 9HE

Head office: 5 Toh Tuck Link, Singapore 596224

USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601

Library of Congress Cataloging-in-Publication Data

Names: Ji, Sungchul, author.

Title: The cell language theory : connecting mind and matter / by Sungchul Ji

(Rutgers University, USA).

Description: Hackensack, New Jersey : World Scientific, 2017.

Identifiers: LCCN 2017002353 | ISBN 9781848166608 (hc : alk paper)

Subjects: LCSH: Gene expression | Cell interaction | Genetics | Cytology.

Classification: LCC QH450 J5 2017 | DDC 572.8/65 dc23

LC record available at https://lccn.loc.gov/2017002353

British Library Cataloguing-in-Publication Data

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Printed in Singapore

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David E Green (1910–1983) Ilya R Prigogine (1917–2003) Rajendra K Mishra (1924–2009) Jaehyun Lee (on her 63rd birthday)

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Preface

There may be a useful analogy that can be drawn between biology and

cosmology Just as we can recognize five distinct stages of development

in the history of cosmology as indicated in Table P1, so perhaps the

his-tory of biology, i.e., the hishis-tory of the development of our knowledge of

life, may also be divided into at least five major stages One such

possibil-ity is suggested in the right-hand column of Table P1, mainly based on my

own limited research results obtained over the last four-and-a-half

decades

Anyone attempting to write (or read) a book on the living cell, the

basic unit of life, may do well to remember that there are about hundred

thousand million (1011) stars in the Milky Way Galaxy and an equally

numerous number of galaxies in the Universe, whereas we can only see

a few thousand individual stars with our naked eyes on a clear night

[472] If we can compare the discovery in 1953 of the DNA double helix

by Watson and Crick to the earth-centered view of Aristotle’s Universe

of the 4th century BC, the cell-centered biology ushered in by the

theo-retical models of the living cell such as the Bhopalator [15–17]

formu-lated in 1985 may be akin to the sun-centered Universe of Copernicus of

the mid-16th century By the early 20th century, astronomy underwent

three more “revolutions”: (i) our sun is only one of about 1012 stars in the

Milky Way Galaxy, (ii) the Milky Way Galaxy is only one of about 1012

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viii Preface

b2861 The Cell Language Theory: Connecting Mind and Matter “6x9”

galaxies in the Universe, and (iii) the discovery in 1929 by Hubble

(1889–1953) that our Universe is not static as assumed by Newton and

Einstein but rapidly expanding Although there is no theoretical reason

why these three breakthroughs in astronomy should have any

counter-parts in biology, they motivated me to look for three comparable

break-throughs in biology beyond the living cell which I tentatively identify

with (i) the human-centered biology (embodied in the Piscatawaytor

proposed in 1991; see Section 3.2.20), (ii) the earth-centered biology

(embodied in the Princetonator model of the origin of life proposed in

1991; see Section 4.9), and (iii) the cosmos or mind-centered biology

Table P1 A comparison between cosmology and biology [471–473].

Cosmology (External Universe) Biology (Internal Universe)

1 Earth-centered Universe with ~103 stars

(Aristotle, 4th century BC; Ptolemy, c 100 AD)

DNA-centered biology (Watson and Crick, 1953)

2 Sun-centered Universe with ~103 stars

(Copernicus, 1543)

Cell-centered biology (the Bhopalator, 1985)

3 Sun at the center of the Milky Way Galaxy

with ~10 11 –10 12 stars (Jacobus Kapteyn,

early 20th century)

Human-centered biology (the Piscatawaytor, 1991)

4 Sun at the periphery of the Milky Way Galaxy

with ~1011 –10 12 stars (Curtis Shapely, 1917)

Biosphere-centered biology (?) (the Princetonator, 1991)

5 The Universe contains 10 11 –10 12 galaxies with

~10 22 –10 24 stars (Hubble, 1929)

Mind/consciousness-centered biology (?) (the Shillongator, 1991)

6

Retrieved from pedia.org/wiki/Cytoskeleton

https://en.wiki-Galaxies and galaxy clusters (left panel) and

5 galaxy clusters (right panel) Retrieved from

https://en.wikipedia.org/wiki/Galaxy_cluster

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Preface ix

(embodied in the Shillongator proposed in 1991 and further elaborated

on in Section 10.18)

It is interesting to point out that, when I started to construct Table P1,

I had only the first two rows clearly in mind Then when I extended the

left-hand column by three more stages based on the history of cosmology,

I was forced to come up with a comparable extension in biology as shown

in the right-hand column, with the unexpected result of the three more

ators emerging therein The term “X-ator” refers to the theoretical model

of the system of physicochemical processes that organizes itself driven by

its own internal free energy and controls information in such a way as to

perform some function (see Section 2.6), where X is the name of the city

where the major research on the mechanism of the self-organizing

pro-cesses under consideration is carried out

Another unexpected feature of Table P1 is that its right-hand column

lists the main topics discussed in this book in varying degrees of detail,

although the cell-centered biology is the focus of this book as indicated by

its main title, the Cell Language Theory It is hoped that this book will

contribute to advancing our knowledge on the phenomenon of life as

manifested in living cells, our internal Universe, just as the astronomical

research over the last centuries and millennia has been advancing our

knowledge about the external Universe (see row 6 in Table P1).

We are made out of matter Our body contains 25 elements out of

about 100 elements found in the Universe (https://en.wikipedia.org/wiki/

Composition_of_the_human_body) We now know that when these

ele-ments are organized properly in space and time to constitute our body

(which is a system of living cells), they exhibit the property called mind

We also know that, at the moment when our body dies, our mind

disap-pears even though little or no matter is lost immediately after death from

our body This simple thought experience reveals that matter is

sary but not sufficient for mind, leading to the conclusion that the

neces-sary and sufficient condition for the phenomenon of mind must include

not only the material, but also non-material factors (NMFs) I

tenta-tively identify NMFs with “relations” or “edges” in a network diagram

whose “nodes” are material objects There are at least three theoretically

possible relations among matter, body, and mind, as briefly explained in

the legend to Table P2

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x Preface

My bio-theoretical research began in 1970 at the University of Wisconsin,

Madison, as a postdoctoral fellow under David E Green (1910–1983),

lead-ing me to extend in 1970–1990 the wave–particle complementarity of Niels

Bohr (1889–1953) to include the information–energy complementarity as a

major postulate of molecular biology (see Section 2.9) Beginning in the

early 1990s, I came under the influence of the triadic model of the sign (see

Section 6.3) pioneered by the American chemist–logician–philosopher,

Charles Sanders Peirce (1839–1914)

As argued in Section 10.21, it is my opinion that both Bohr’s

comple-mentarity and Peircean semiotics (the science of signs) may be viewed as

belonging to the category which I came to refer to as “triadic monism” to

which the relation among matter, body, and mind may also belong (see the

third row of Table P2)

Table P2 Three possible relations among matter, body, and mind.

(Object) (Sign) (Interpretant)

h Note: (1) The linear model suggests that matter determines the human body which in turn determines

the mind (2) The complementary model suggests that both body and mind are two irreconcilably

opposite aspects of matter such that matter appears as body or as mind, depending on how it is

expe-rienced (3) The triadic monism (see Section 10.21) states that matter, body, and mind are

ontologi-cally one and inseparably fused but appears to human mind as a series of tree entities connected

either diachronically as in the linear model or as synchronically as in the complementary model (see

Section 10.21 for more details).

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About the Author

After 2 years of pre-engineering training at the College of Engineering,

Seoul National University and 1.5 years of mandatory military service in

the Korean Army, Sungchul Ji obtained in 1962 a full scholarship to

con-tinue his education at the University of Minnesota, Duluth, graduating in

1965 with a double major in chemistry and mathematics From 1965 to

1968, he carried out a PhD research at the State University of New York

at Albany, in physical organic chemistry under William D Closson,

completing his thesis in 1970 while teaching at the Department of

Chemistry at the Makato State College, Minnesota, between 1968 and

1970 Between 1970 and 1982, Sungchul Ji performed a series of

inter-disciplinary researches in the following institutions: The Enzyme Institute,

University of Wisconsin, Madison (mitochondriology, theoretical

enzymology), Johnson Foundation, University of Pennsylvania (tissue

biophysics), the Max Planck Institute of Systems Physiology, Dortmund,

Germany (microcirculation, organ physiology), Department of

Pharmacology, School of Medicine, University of North Carolina, Chapel

Hill (pharmacology and toxicology) Since 1982, he has been teaching

pharmacology, toxicology, and theoretical/computational cell biology to

PharmD students at the Ernest Mario School of Pharmacy and

interdisci-plinary seminars on complementarism to first-year and honors students,

both at Rutgers University

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xii About the Author

One of his main research interests is exploring Niels Bohr’s principle

of complementarity as applied to living systems ranging from enzymes to

organelles to cells to the human brain and beyond In the process,

Sungchul Ji has been led to generalize the principle of wave–particle

ity in quantum mechanics to the principle of the energy–information

dual-ity This so-called gnergy complementarity is postulated to underlie all

organizations in the Universe including living systems This postulate (to

be called the gnergy principle of organization, GPO) appears to have

gained some empirical support in the recent (2008– present) findings that

the Planckian distribution equation (PDE), which was derived in 2008

from the blackbody radiation equation (discovered by M Planck in 1900)

by replacing its universal constants and temperature with free parameters,

A, B and C, resulting in y = (A/(x + B)5)/(Exp (C/(x + B) – 1), where x is

the categories or bins and y their frequencies The PDE has been found

to fit almost all long-tailed histograms generated in atomic physics,

pro-tein folding, single-molecule enzymology, cellular mRNA metabolism,

brain neurophysiology, quantitative linguistics, psychology,

econophys-ics, and cosmology (http://www.conformon.net/wp-content/uploads/

2016/09/PDE_Vienna_2015.pdf) Since the first term in Planck’s

black-body radiation equation is related to the number of the standing waves in

the system under consideration and the second term to the average energy

of the standing waves, the first and second terms in PDE probably can be

interpreted similarly, leading to the conclusion that all the

physicochemi-cal processes generating data that fit PDE obeys the wave–particle duality

principle

In 1997, Sungchul Ji found the evidence that living cells use

molec-ular language (called cellese) that shares 10 out of the 13 design features

of human language (humanese) (http://www.conformon.net/wp-content/

uploads/2012/05/Isomorphism1.pdf) Applying the complementarity

principle of Bohr, he inferred in 2012 that cellese and humanese may be

the complementary aspects of a third language called cosmic language

or cosmese Most recently (January/February, 2017) in an unpublished

observation, John Stuart Reid, Ryan Stables, and Sungchul Ji have

shown the histograms generated from water wave patterns induced by

the audio file produced from cancer cells photographed with a digital

CymaScope fitted PDE Therefore, if water wave patterns measured

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About the Author xiii

with CymaScope can be viewed as an example of cosmese (since they

can be shown to carry meaningful information), and since cellese and

humanses have already been shown to obey PDE, it would seem logical

to conclude that all these three languages are different manifestations of

waves and the wave–particle duality in agreement with GPO

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Acknowledgments

I have learned three things from writing this book (i) The book wrote

itself as much as I wrote it, since it took about 3 years instead of 1 as

I originally planned (ii) The content of the book expanded to include

all of the key results of my research dating back to the early 1970s,

whereas my original intention was to cover only those new

develop-ments since my first book The Molecular Theory of the Living Cell,

published by Springer, New York, in 2012 (iii) The social and

environ-mental effects on book writing cannot be ignored I feel extremely

fortunate to have had the physical and mental health and the

opportu-nity to devote the last 45 years of my career continuously in various

universities in the USA and a research institution in Germany to

bio-medical researches focusing almost exclusively on one central concept,

the conformon defined as the mechanical/conformational strains of

biopolymers storing the energy, and information necessary and

suffi-cient to generate goal-directed forces to drive all molecular processes

underlying life on the cellular level

Many individuals have contributed either directly or indirectly to the

birth of the present book My parents, Eung E Ji (1914–1993) and Bok

Nyo Keh (1919–2005), of course, who raised a family of 10 (five sons and

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xvi Acknowledgments

three daughters, of which I, as the eldest son, was the only one to go to

college, since my father’s income as an elementary school principal was

not enough to educate more than one siblings) through politically and

economically challenging periods of modern times which witnessed the

World War II (1939–1945), the division of the Korean peninsula into the

North and South Korea (1945), the Korean War (1950–1953), the 5.16

Military coup in 1961 led by General Chung Hee Park, and the

immigra-tion to and resettling in Trenton, New Jersey, of the Ji family which now

grew in size to 32 members (1974–1982)

I am greatly indebted to the late Professor Chester W Wood of the

University of Minnesota-Duluth (UMD), who secured a full scholarship

(1962–1965) for my study at UMD as an exchange student from the

School of Engineering, Seoul National University; to the Mr and Mrs

Willard Matter and Rev William Halfaker families (1962–1965) in the

Duluth community who generously provided me with full living

accom-modations as their house guest; to the late Professor Shi Won Choi of

Yonsei University, Seoul, whom I had had met in 1961–1962 when we,

still as undergraduates, were serving our mandatory military duties in the

Korean Army as KATUSAs (Korean Augmentation to US Army) and who,

by selling in 1962 his only voice recorder that he had received as the

first-place winner in a national concours voice competition in Seoul, provided

me with the critically needed fare for my transportation from Inchon,

Korea, to San Francisco on a US Naval vessel carrying US soldiers

return-ing home after their military services in South Korea; to the late Professor

William D Closson (1965–1970) who advised me in my Ph.D research at

the Department of Chemistry, State University of New York, Albany; to

the late Professor David E Green (1970–1974) who, as my postdoctoral

mentor at the Enzyme Institute, University of Wisconsin, Madison,

trans-formed me from a physical organic chemist to a theoretical

mitochondri-ologist; to the late Britton Chance (1974–1976) under whom I, as a

postdoctoral fellow, was instrumental in developing the micro-light guide

with which we were able to measure redox metabolic heterogeneity in

living tissues; to Professor Manfred Kessler (1976–1979) who invited

me to the Max Planck Institute for Systems Physiology as a B1 researcher

to apply the micro-light guide method to monitor the regional redox

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Acknowledgments xvii

metabolic activities in perfused rat livers; to the late Professor Ronald

Thurman (1979–1982) who provided me with a research associate

profes-sor position in his group at the Department of Pharmacology, School of

Medicine, University of North Carolina, Chapel Hill, where I developed

the mini-oxygen electrode method to complement the micro-light guide

method, using both of which we were able to demonstrate experimentally

for the first time the long-predicted metabolic gradients across the liver

lobules; to Professor Robert Snyder (1982–1990) who offered me in 1982

the first tenure-track academic position at the Department of Pharmacology

and Toxicology, Ernest Mario School of Pharmacy, Rutgers University,

Piscataway, where I initially (1982–1987) performed teaching in

pharma-cology and experimental toxipharma-cology research using the micro-light guide

and mini-oxygen electrode methods to elucidate the mechanisms

underly-ing acetaminophen (Tylenol®) toxicity in perfused rat liver and later

(after ~1987) turned almost exclusively to theoretical and computational

cell biology research which I am currently continuing with my Pharm D

students at Rutgers; to the late Professor Rajendra K Mishra (1983–1990)

who invited me to the International Colloquia on Living State held in

Bhopal, India, in 1983 and again in Shillong, India, in 1985, attending both

of which was instrumental in my formulating the Bhopalator in 1985 and

the Shillongator in 1991, the models of the living cell and the Universe,

respectively, based on the principle of self-organization advanced by the

late Professor Prigogine (1917–2003) and his colleagues; to my wife

Jaehyun Lee (1991–present) without whose love, IT assistance, and

far-sighted encouragement the writing of the book probably would have been

impossible; to my son, Douglas Sayer Ji (2016–present), the founder of

GreenMedInfo.com, whose deep understanding of my life-long research

results and encouragement of my on-going bio-theoretical research are the

constant source of my joy and inspiration

I also would like to thank many of my colleagues at Rutgers for their

direct and indirect support for my research activities, including Professors

Debra Laskin, Kenneth Reuhl, Robert Snyder and Frederick Kauffman, and

Deans John L Colaizzi and Joseph A Barone, and my Pharm D and

non-Pharm D students, especially Mr Kenneth So, whose computational work

performed as a pre-med student in pharmacology elective course was

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xviii Acknowledgments

essential in developing the Planckian distribution equation (PDE)-based

analysis of mRNA and fMRI (functional magnetic resonance imaging) data

and many other long-tailed histograms discussed in the book

Last but not least, I thank Ms Mary Simpson and Mr Ram Mohan of

Imperial College Press/World Scientific for their patience and

profes-sional assistance in editing my book

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1.1 A Chronological List of the Theoretical Concepts

1.2 Three Stages of Development of Human Knowledge 71.3 Gaylord’s Distinction Between Physics and Biology 7

2.2.4 Peircean Information (IPe) in Relation to

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xx Contents

2.3 Burgin’s Parametric Definition of Information 202.4 Complementarity vs Supplementarity 202.4.1 The Principle of Generalized

2.6 Self-Organization, Dissipative Structures

(Dissipations), and Self-Organizing Whenever

and Wherever Needed (SOWAWN) Machines 272.7 The Generalized Franck–Condon Principle 29

2.9 The Gnergy Principle of Organization (GPO) 332.10 The Principle of Irreducible Triadicity 34

2.12 The Association–Induction Hypothesis 35

2.13.1 The Ling–Pollack Water Structures 392.13.2 Coherence Domains and the Benveniste–

2.13.3 Systome Medicine: The Complementary Union of System Medicine and

2.14 Cell Water as a Four-Dimensional Proton Transfer Network: Water is to Cell Language

2.15 The Equilibrium and Dissipative Structures

3.1 Three Stages of Development in Cell Biology 513.2 The Principles and Major Concepts Embedded

in the Bhopalator Model of the Living Cell 54 3.2.1 The IDS-Cell Function Identity (ICFI)

Hypothesis 56 3.2.2 The Information–Energy Complementarity

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Contents xxi

3.2.3 Electromechanochemical Energy Transduction 58 3.2.4 The Wave–Particle Duality in the Living Cell 67 3.2.5 Three Categories of Enzyme Catalyzes 68 3.2.6 The GFCP, Pre-fit Mechanisms, and Scalar

3.2.7 The GFCP and Translational Enzyme Catalysis 71 3.2.8 The GFCP and Rotary Enzyme Catalysis 75

3.2.10 Allosterism, Bohr Effect, and Wyman’s Pseudolinkage 833.2.11 The Brownian Distance of Biopolymers 923.2.12 The Principle of Microscopic Reversibility 923.2.13 The Information–Energy Complementary Landscape Theory of Protein Folding 943.2.14 Three Classes of Molecular Structures

3.2.15 Five Classes of Factors Affecting the

3.2.16 An Atom–Cell Comparison Based on Aristotle’s Four Causes Doctrine 1013.2.17 The Cell Force: A Comparison with the

3.2.18 The Cell as the Atom of Semiosis 1033.2.19 The Triadic Structures of the Living Cell 1043.2.20 The Piscatawaytor: A Model of the Human Body Viewed as a Self-Organizing System

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xxii Contents

3.3.2 Conformon Production, Transfer, and Utilization 119 3.3.3 Deconstructing the Chemiosmotic Model 122 3.3.4 A Comparison Between the Chemiosmotic and Conformon Models of Oxidative Phosphorylation 126 3.3.5 The Rochester–Noji–Helsinki (RoNoH) Model of Oxidative Phosphorylation 131 3.3.6 Mitchel vs Williams Protons 136 3.3.7 Active vs Passive Conformational

3.3.8 Active vs Passive ATP Syntheses 140 3.3.9 Cytochrome c Oxidase an Electron-

3.3.10 Proton-Transfer Chains/Complexes as the Fourth-Phase Water Structures of Ling

3.4.1 Direct Experimental Evidence for Conformons or Conformational Waves 1513.4.2 DNA Supercoils, the White Formula,

3.4.3 Stress-Induced Duplex Destabilizations as Conformons 1573.4.4 Virtual and Real Conformons:

Mechanisms of Conformon Generation

Force Generation from Chemical Reactions 1623.4.8 The Conformon Model of Muscle

Contraction 164

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Contents xxiii

4.1.1 Macro-, Micro-, and Holo- Communications 1744.1.2 The Universality of Double Articulations 1774.1.3 Cell Language (Cellese) Defined 1794.2 Some Linguistic Terms for Non-linguists 1804.2.1 Double Articulation Extended to Triple

4.3 Application of the Information Theory to Signal

4.4 Isomorphism Between Cell and Human Languages 1854.5 Isomorphism Between the Immune System

4.6 Triple Articulation in Cell Language 1894.7 Decoding DNA Based on the Semiotic Lessons Learned from Decoding the Rosetta Stone 190

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xxiv Contents

4.15 Water Standing Waves (Aquaresonances) as the

Possible Cause of the Origin of Life 2214.16 Decoding CymaGlyphs May Be Akin to

4.17 The Water Thesis: Water Can Represent,

4.18 Cosmic Language (Cosmese) as the Irreducible Triad of Wave Language (CymaGlyphs), Cell Language (e.g., RNA glyphs), and Human Language (e.g., Hieroglyphs) 225

4.19 CymaScope as an Experimental Tool

4.21 The Dissipative-to-Equilibrium Reversibility

4.22 Exosomes as Extracellular Text Messages That May Be Deciphered by Digital CymaScopy 234

5.2 The Mathematical Similarity between the Genetic Code and the I-Ching Hexagrammatology 244

5.3 The Molecular Language (Moleculese) 248

6.1.6 Biocybernetic Models of Living Systems

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Contents xxv

6.2 A Comparison between Physics, Biology,

6.3.1 Peircean Definition of Signs 2616.3.2 Peircean Categories: Firstness,

6.4 Macrosemiotics vs Microsemiotics 264

6.6 The Quark Model of the Peircean Sign [279] 269

6.6.3 Derivation of the 10 Classes of Signs from Nine Types of Signs Based on the Analogy between e-Signs and Quarks in Elementary

6.6.4 Derivation of “Nilsign” and Its Associated Category Called “Zeroness” Based on the Quark Model of the Peircean Sign 2766.6.5 The Neo-Semiotics and the Possible

6.7 Application of the Concept of Signs to

Molecular Biology: Microsemiotics 282

6.9 Division of Sign Processes Based on the

6.10 Peirce’s Metaphysics as the Basis for Unifying Sciences 286

Chapter 7 Applications of the Cell Language Theory to

7.1 The Need for a New Paradigm in Biomedical Sciences 2907.1.1 The Inefficiency of the Current Methods

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Spectroscopy is to Atomic Physics 3017.3 Analysis of Human Breast Cancer Microarray Data 3057.3.1 The Mechanism Circle-Based Analysis 3067.3.2 PDE-Based Method for Identifying

Patient-Specific Breast Cancer Genes 3157.3.3 Can PDE Be to Cell Biology What PRE is

8.2 Single-Molecule Enzyme Catalysis 336

8.2.2 Explanation: Quantization of Energy

8.2.3 RASER Model of Enzyme Catalysis 3398.3 Examples of Long-Tailed Histograms Fitting

PDE 3418.3.1 Atomic Physics (Figure 8.6(a)) 3478.3.2 Protein Folding (Figure 8.6(b)) 3478.3.3 Single-Molecule Enzyme Kinetics of

Cholesterol Oxidase (Figure 8.6(c)) 349

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8.3.6 Human T-cell Receptor Variable Region

Sequence Diversity (Figure 8.6(f)) 350

8.3.7 7-Mer Frequency Distribution in P abyssi

8.3.8 Codon Usage Profile in the Human

8.3.9 Protein-Length Frequency Distribution in

8.3.10 Stress-Induced Alterations in the Neuroarchitecture

of the Mouse Brain (Figure 8.6(j)) 3538.3.11 Impulse-Induced Electrocorticogram

(ECoG) Response of the Rabbit Olfactory

8.3.12 fMRI Signals from the Human Brain before and after Psilocybin (Figure 8.6(l)) 3548.3.13 Sentence-Length Frequency Distributions

in Private Letters (Figure 8.6(m)) 3548.3.14 Word-Length Frequency Distributions in

8.3.15 Word-Length Frequency Distribution in

8.3.16 The Pitch Histogram of Sylvia Plath’s

Reading of Her Poem (Figure 8.6(p)) 3558.3.17 Decision-Time Histograms

8.3.18 The 1996 and 2013 US Annual Income

Distributions (Figures 8.6(r) and 8.6(s)) 3588.3.19 Polarized Cosmological Microwave

Background (CMB) Radiation

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xxviii Contents

8.4.1 Planckian Processes as Selected Gaussian Processes 3608.4.2 The Wave–Particle Duality in Biology

Informational 3668.6 Possible Relations among Planckian

8.7 PDE-based CymaScopy (PCS) as a Novel Experimental

Chapter 9 The Universality of the Irreducible Triadic

Relation 3779.1 The Peircean Sign as the Origin of the

9.2 Peirce’s Simple Concepts Applicable to Every Subject 3799.3 ITR in Peirce’s Hypostatic Abstraction 383

9.4.7 ITR in Mathematics, Philosophy,

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10.3 Signs, Thoughts, and “Thoughtons” 401

10.4 The “New Jersey Theory of Mind”

(NJTM) 404

10.6 The Triadic Architectonics of Human Knowledge 41010.7 On the Possible Relation Between Quantum

10.8 The Hertz–Rosen–Pattee (HRP) Model

10.9 The Signless and the Dao as the Source

10.12 A Theory of the Origin of Information

10.14 A “Philosophical Table” for Classifying

10.15 The Information–Energy–Entropy Relation:

10.16 The First Law of Informatics: Information

10.18.1 The Shillongator Model of

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xxx Contents

10.18.4 The Self-Knowing Universe and the

Anthropic Cosmological Principle 45710.19 The Universe as a Self-Organizing Musical

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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

pro-vide 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

indi-rectly to the conformon The results of these research activities are

sum-marized 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,

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

1 Conformon 1972–1974 The bioenergetic and bioinformatic principle rooted

in conformational energy stored in specific sites in biopolymers

1974 GFCP-based model of enzyme catalysis; opposite to

the induced-fit hypothesis

Section 3.2.9 [7, pp 50–56; 13]

4 Conformon model of oxidative phosphorylation (oxphos)

1976 Model of oxphos based on the conformon principle

of bioenergetics; subsumes the chemiosmotic model of Mitchell

Section 3.3.1 [8–11, 14]

5 Bhopalator model of the cell

1985 First molecular model of the living cell based on

conformons and intracellular dissipative structures

Chapter 3 [15–17]

6 Cell force 1991 The force responsible for maintaining the orderly

molecular motions of living cells despite the randomizing influence of Brownian motions, postulated to be the fifth force of nature

Section 3.2.17 [7, pp 90–118]

7 Gnergy tetrahedron 1991 The body-centered tetrahedron as a geometric

representation of the ultimate reality having four

irreducible elements — energy, matter,

information , and life

Sections 10.10 and 10.18

[7, pp 234–237]

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9 Cell as smallest based molecular computer

DNA-1999 Cells can measure, compute, and communicate Section 3.2.18 [18, 192]

10 Complementarism 2004 The claim that the ultimate reality is the

complementary union of irreconcilable opposites,

synonymous with the Yin-Yang Doctrine of the

Daoist philosophy

[24]

11 PDE (Planckian distribution equation, also called BRE, blackbody radiation-like equation)

2008 A mathematical equation that quantifies the

organized complexities of Weaver

Chapter 8 [25, pp 433–444;

26, 27]

12 Universality of the wave–

particle duality

2012 The wave–particle duality principle is not only

confined to quantum mechanics, but also applies

to biomedical and human sciences

Chapter 8 [25–27]

13 Intracellular dissipative structure–cell function identity (ICFI) hypothesis

2012 The postulate that the immediate cause of cell

functions is the intracellular dissipative structures including ion gradients

Section 3.2.1 [25, pp 273–274,

398–400]

14 Category theory of everything (cTOE)

2012 A gnergy tetrahedron-based theory that attempts to

integrate energy, matter, information, knowledge,

life, body, mind, natural system, and formal system on the basis of (i) two symmetry

principles, complementarity and supplementarity , (ii) the irreducible triadic relation (ITR) of

Peirce, and (iii) category theory

Section 10.20 [25, pp 639–642;

751]

(Continued)

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15 Theory of targeting drugs

dissipaton-2012 Traditional drug targets are equilibrium structures

(or equilibrons); in contrast, it is predicted that

there exists a new class of drugs that target

dissipative structures (or dissipatons)

2015 “Signal-induced deactivation of thermally excited

metastable state leading to function” is postulated

to underlie all Planckian processes defined as those physicochemical processes generating data that fit PDE

Section 8.23 [27]

18 Cell water as a dimensional proton transfer network

four-2016 Cytoplasmic water is postulated to be organized as a

space- and time-dependent network of four-phase water molecules of Ling and Pollack in order to facilitate proton transfer by the Grotthuss mechanism

Section 2.14 This book

19 Systome medicine 2016 Health and diseases are the properties of systomes,

not systems

Section 2.13.3 This book

20 Triadic monism 2016 A philosophical framework built on Peircean

semiotics and Bohrian complementarism

21 Equilibrium and dissipative structures of water (also called E- and D-aquastructures)

2016 n water molecules forming structures that are stable or

dissipative, where n can be a few to 109 or more,

similar to “coherence domains” of Del Guidice et al.

[364; this book]

Table 1.1 (Continued)

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22 Human body–Internet isomorphism

2016 The human body and the Internet are both complex

systems sharing a set of common properties at six different levels

Section 3.2.21 This book

23 Water as the medium of cell language

2016 Water is to cell language what air is to human

language; without water, no communication in and among organisms

Section 4.11 [601]

24 Cytocymatics (“cyma” =

“wave”)

2016 Study of the cell structure and functions as

manifestations of vibrations and waves at all scales, from atoms to the whole cells

25 Aquaresonance model of the origin of life

2016 Aquaresonances are postulated to be the first

self-replicating material systems that eventually gave rise to organisms

Section 4.15 [601]

26 The water thesis 2016 Water, either in or outside the living cell, can

represent, compute, and communicate

27 Cosmic language as an irreducible triad of Fourier language, cell language, and human language

2016 The cosmic language gave rise to Fourier language

(also called wave language), cell language (or cellese), and human language (humanese)

Section 4.18 [25; this book]

28 Supervenience of life on water structures

2016 Water structures determine the living processes at

the transition states and hence life

(Continued)

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29 Dissipative-to-equilibrium reversibility of

aquastructures (DERA)

2016 There are two kinds of aquastructures —

equilibrium and dissipative — and there exist mechanisms by which these two kinds of aquastructures are interconverted

30 Exosomes as molecular texts for intercellular communication

2016 There are three kinds of intercellular messengers —

biochemicals, biopolymers, and extracellular vesicles including exosomes that contain biochemicals and biopolymers thought to be organized into a functional unit

Section 4 22 This book

31 Irreducibly triadic model

of consciousness

2016 Consciousness is a part of an irreducibly triadic set

of body, subjective experience, and objective experience

32 The Gnergy tetrahedron as the mechanism of consciousness

2016 The body-centered tetrahedron model of the

Universe called the Shillongator proposed in 1991 may provide a possible mechanism, both material and formal, underlying the phenomenon of consciousness

Table 1.1 (Continued)

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Introduction 7

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

sub-stantiated 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

molecu-lar 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

asym-metric ion distributions — the equilibrium distribution advanced by AIH

and the dissipative distribution supported by the membrane pump

hypoth-esis, the former being an example of Prigogine’s equilibrium structures

and the latter his dissipative structures (see Section 2.6).

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

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Table 1.2 Three stages of the development of scientific knowledge.

Physics (A) Atomic spectra (e.g., Lyman,

Balmer, Ritz–Paschen, etc

series of hydrogen atomic spectral lines in the 19th century)

Bohr’s atomic model (1913) Quantum mechanics (1926)

Chemistry (B) Chemical structures

Chemical reactions (since the Middle Ages, 5th–15th century)

Periodic table (1869) Thermodynamics (19th century)

Statistical mechanics (late 19th and early 20th centuries) Kinetic theory (early 20th century)

Theory of self-organization (second half of the 20th century) Linguistics (C) Descriptive linguistics (since

DNA scrunching mechanism of transcription initiation (2006)

Darwin’s theory of evolution (1859) Induced-fit hypothesis of enzyme catalysis (1958) [13, 28]

Pre-fit hypothesis of enzyme catalysis (1974) [12, 25,

pp 209–213]

Biocybernetics (1972–1991) [7]

Conformon theory of molecular machines (1972–1974) [7, pp 31–38]

Cell force postulate (1991–2012) [7, pp 90–118]

Cell language theory (1995–2000) [19–23]

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Introduction 9

Table 1.3 The laws, principles and concepts from science and engineering that were

incorporated into biocybernetics, a general molecular theory of life.

24 Maximum information principle

25 Machine or systems concept

26 Law of requisite variety

Source: Reproduced from [19, Table 5]

Physicists study the principles that apply to all phenomena; biologists

In view of the potential importance of this statement, we may refer to

it as the “Simpson conjecture”, the “Simpson thesis”, or the “Simpson

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