S. Ji. 1 (This manuscript is based on the four lectures given at the Department of Romance Languages, Rovira i Virgili University in Tarragona, Spain, in 2003) Semiotics of Life: A Unified Theory of Molecular Machines, Cells, the Mind, Peircean Signs, and the Universe based on the Principle of Information-Energy Complementarity Sungchul JI Department of Pharmacology and Toxicology Rutgers University Piscataway, N.J. 08855, USA [email protected] S. Ji. 2 TABLE OF CONTENTS ABSTRACT .................................................................................................................................................. 5 1. INTRODUCTION .................................................................................................................................... 5 2. AN OVERVIEW ....................................................................................................................................... 6 2.1 AN INTEGRATION OF FRAGMENTED SCIENCES...................................................................................... 6 2.2 SEMIOTICS: A PRELUDE ........................................................................................................................ 7 PART I PRINCIPLES 3 AXIOMS, DEFINITIONS, AND LAWS ESSENTIAL FOR UNDERSTANDING THE PHENOMENON OF LIFE .........................................................................................................................11 3.1 THE GNERGY PRINCIPLE ......................................................................................................................11 3.2 THE PRINCIPLE OF GENERALIZED COMPLEMENTARITY .......................................................................12 3.3 COMPLEMENTARIAN LOGIC .................................................................................................................13 3.4 THE PRINCIPLE OF IRREDUCIBLE TRIADICITY .......................................................................................14 3.5 THE PRINCIPLE OF MÖBIUS RELATIONS ................................................................................................14 3.6 THE PRINCIPLE OF CLOSURE ................................................................................................................15 3.6.1. Semantic Closure. ......................................................................................................................16 3.6.2 Principle of Ontological and Epistemic Closure. .......................................................................16 3.6.3 The Yin and Yang Principle. .......................................................................................................16 3.6.4 The Diachronic and Synchronic Closure. ...................................................................................16 3.6.5 The Closure Relation between Boundary Conditions and the Dynamics of Physical Systems. ..16 3.6.6 The Anthropic Principle. .............................................................................................................16 3.7 ISOMORPHISM BETWEEN CELL AND HUMAN LANGUAGES ...................................................................17 3.8 THE ‘TABLE THEORY’ .........................................................................................................................19 3.9 THE GENERALIZED FRANCK-CONDON PRINCIPLE ...............................................................................21 3.10 THE PRAGMATIC MAXIM ...................................................................................................................23 3.11 THE TAOISTIC MAXIM .......................................................................................................................23 3.12 THE PRINCIPLE OF SELF-ORGANIZATION ...........................................................................................24 3.13 THE PRINCIPLE OF DYNAMIC BALANCE BETWEEN PRODUCTION AND DEGRADATION (PDBPD) .......25 3.14 THE PRINCIPLE OF INTRACELLULAR DISSIPATIVE STRUCTURES (PIDS) ............................................25 3.15 THE PRINCIPLE OF BIOACTIVITY COEFFICIENTS ...............................................................................25 3.16 THE PRINCIPLE OF RULE-GOVERNED CREATIVITY ...........................................................................26 3.17 THE PRINCIPLE OF RECURSIVITY .......................................................................................................26 PART II MOLECULES 4 WHAT IS LIFE? ......................................................................................................................................27 4.1 DEFINITION OF LIFE .............................................................................................................................27 4.2 LIFE ACCORDING TO SCHRÖDINGER ....................................................................................................27 4.3 LIFE ACCORDING TO PRIGOGINE ..........................................................................................................28 4.4 LIFE ACCORDING TO PATTEE ...............................................................................................................31 4.5 LIFE BASED ON THE PRINCIPLE OF INFORMATION-ENERGY COMPLEMENTARITY.................................31 5 THE CONFORMON THEORY OF MOLECULAR MACHINES AND MOTORS .........................32 5.1 CONFORMONS: EXPERIMENTAL EVIDENCE .........................................................................................32 5.2 MOLECULAR MECHANISMS OF CONFORMON GENERATION BASED ON THE GENERALIZED FRANCK- CONDON PRINCIPLE ...................................................................................................................................38 S. Ji. 3 5.3 THE CONFORMON HYPOTHESIS OF ENERGY-COUPLED PROCESSES IN THE CELL .................................38 5.4 DECONSTRUCTING THE CHEMIOSMOTIC HYPOTHESIS ..........................................................................39 5.5 THE INFORMATION-ENERGY LANDSCAPE THEORY OF PROTEIN FOLDING ...........................................43 5.6 DECODING DNA BASED ON THE SEMIOTIC LESSONS LEARNED FROM DECODING THE ROSETTA STONE ........................................................................................................................................45 PART III CELLS 6 THE CELL AS THE ATOM OF SEMIOSIS ........................................................................................51 6.1 THE BHOPALATOR ...............................................................................................................................51 6.2 IDSS (INTRACELLULAR DISSIPATIVE STRUCTURES) ............................................................................53 6.3 COMPLEMENTARY DNA ARRAYS AND NEW CELL BIOLOGY ...............................................................54 6.4 AN ANALOGY BETWEEN ATOMIC PHYSICS AND CELL BIOLOGY .........................................................59 6.5 RIBONOMICS ........................................................................................................................................62 6.6 DSSIPATIVE STRUCTURES AS THE THIRD ARTICULATION IN CELL BIOLOGY .......................................63 6.7 THREE CLASSES OF DISSIPATIVE STRUCTURES – WITH FIXED, MOVING, AND INFORMED BOUNDARIES .............................................................................................................................66 6.8 THE TRIADIC STRUCTURES OF THE LIVING CELL .................................................................................68 6.9 A TOPOLOGICAL MODEL OF THE LIVING CELL ....................................................................................69 PART IV THE MIND 7. SEMIOTICS AND LIFE SCIENCES ....................................................................................................73 7.1 THE BIOLOGY-LINGUISTICS CONNECTION ...........................................................................................73 7.2 SEMIOTICS: THE PEIRCEAN THEORY OF SIGNS ....................................................................................76 7.3 PEIRCEAN DEFINITION OF SIGNS ..........................................................................................................76 7.4 PEIRCEAN SIGNS AS GNERGONS ..........................................................................................................78 7.5 THE QUARK MODEL OF PEIRCEAN SIGNS ............................................................................................80 7.5.1 9 Types of Signs ..........................................................................................................................81 7.5.2 Ten Classes of Signs ....................................................................................................................83 7.5.3 The Derivation of the 10 Classes of Signs from 9 Types of Signs Based on the Analogy between e-Signs and Quarks in Elementary Particle Physics. ...........................................................................84 7.5.4 An Application of the Concept of c-Signs to Molecular Biology: Microsemiotics .....................85 7.6 SEMIOSIS: REAL VS. VIRTUAL ................................................................................................................86 7.7 THE ORIGINS OF BIOLOGICAL INFORMATION AND LIFE .......................................................................89 7.8 THE VON NEUMANN QUESTIONS AND THE CONFORMON THEORY .......................................................96 8 PEIRCE’S METAPHYSICS AS THE