Introduction to Biosemiotics (eBook)

MARCELLO BARBIERI is University professor of Embryology at the University of Ferrara, Italy. He has conducted research on embryonic development and ribosome crystallization at the Medical Research Council in Cambridge, UK, the National Institutes of Health in Bethesda, USA, and the Max-Planck-Institut für Molekulare Genetik in Berlin. He has published books on embryology and evolution, and has taught biophysics, molecular embryology and theoretical biology respectively at the Universities of Bologna, Sassari and Turin. His research interests include embryology, evolution and biosemiotics. He is president of the Italian Association for Theoretical Biology and Editor-in-Chief of the Journal of Biosemiotics. His major books include The Semantic Theory of Evolution (1985), Harwood Academic Publishers, New York, and The Organic Codes. An Introduction to Semantic Biology (2003), Cambridge University Press, Cambridge UK. Web page: www.cambridge.org/uk/catalogue/catalogue.asp?isbn=0521531004 Web site: http://www.biologiateorica.it

TABLE OF CONTENTS 6
EDITORIAL 8
ACKNOWLEDGEMENTS 10
REFERENCES 11
CHAPTER 1 THE EVOLUTIONARY HISTORY OF BIOSEMIOTICS 12
A PERSONAL PRELUDE: MY STROLL THROUGH THE WORLDS OF SCIENCES AND SIGNS 12
A BRIEF HISTORY OF THE TYING OF A GORDIAN KNOT 15
PHASE ONE: SEMIOTICS WITHOUT SCIENCE 16
AUGUSTINE: THE “NATURAL” AND “GIVEN” SIGNS 17
ARISTOTLE: ON LIFE AND ON INTERPRETATION 18
SIGN DIVERGENCE AND CONVERGENCE IN THE LATE MIDDLE AGES 21
PHASE TWO: SCIENCE WITHOUT SEMIOTICS 24
DESCARTES: BIFURCATING THE NATURAL WORLD INTO BODY AND SPIRIT 25
“NOTHING LOST”: MODERNITY PROCEEDS APACE 28
FROM DYADIC TO TRIADIC RELATIONS: “INFORMATION” INVADES THE SCENE 32
PHASE THREE: SCIENCE WITH SEMIOTICS 36
JOINING SIGN SCIENCE WITH LIFE SCIENCE: THOMAS A. SEBEOK 37
SEBEOK’S SYNTHESIS OF SCHOLARSHIP EAST AND WEST 38
SEBEOK’S SYNTHESIS OF CHARLES S. PEIRCE 40
SEBEOK’S SYNTHESIS OF JAKOB VON UEXKÜLL 42
A PROJECT OF MASS CROSS-POLLINATION: SEBEOK’S SYNTHESIS OF RESEARCHERS 44
SEBEOK’S LEGACY AND THE CONTINUATION OF THE BIOSEMIOTIC PROJECT 46
JOINING LIFE SCIENCE WITH SIGN SCIENCE: JESPER HOFFMEYER 48
A DIVERSE ECOSYSTEM OF RESEARCHERS: THE GATHERINGS IN BIOSEMIOTICS 52
CONTRIBUTIONS FROM OUTSIDE THE COPENHAGEN-TARTU NEXUS 53
DEVELOPMENTS AND CHALLENGES 2001–2005 54
MARCELLO BARBIERI: NOT INTERPRETATION, BUT ORGANIC CODES 57
A PARTING PROLOGUE: THE FUTURE HISTORY OF BIOSEMIOTICS 61
NOTES 65
WORKS CITED 68
CHAPTER 2 SEMIOSIS IN EVOLUTION 79
BIOSEMIOTICS FROM A PERSONAL POINT OF VIEW 79
CONCEPTUAL DEMARCATION 81
LIFE IN THE FRAMEWORK OF COSMOLOGY 83
EVOLUTIONARY SEMIOSIS 87
FUNDAMENTALS IN THE INTERPRETANT 91
THE CODES MAPPING SEMIOSIS 96
DOUBLE CODING 100
ASYMMETRIES IN BIOSEMIOSIS 102
REFERENCES 107
CHAPTER 3 HAS BIOSEMIOTICS COME OF AGE?*+ AND POSTSCRIPT+ 111
INTRODUCTION 112
THE MAKING OF BIOSEMIOTICS 113
THE REDEPLOYMENT OF JAKOB VON UEXKÜLL 114
THE ENDORSEMENT OF A NON-MECHANISTIC BIOLOGY 116
THE BIOSEMIOTIC APPROACH TO MEANING 118
A MECHANISTIC APPROACH TO MEANING 119
CONCLUSION 121
POSTSCRIPT (AUGUST 2005) 121
REFERENCES 122
CHAPTER 4 THE NECESSITY OF BIOSEMIOTICS: MATTER-SYMBOL COMPLEMENTARITY 124
LIFE DEPENDS ON SEMIOTIC CONTROLS 124
THE RELATION BETWEEN PHYSICAL LAWS AND CONTROL CONSTRAINTS 125
RATE-INDEPENDENT CONSTRAINTS SYMBOL SYSTEMS
PHYSICAL LAWS CANNOT ADDRESS THIS QUESTION 127
THE EPISTEMIC PROCESS IN BIOLOGY 128
SYMBOLIC CONTROL IS NECESSARY FOR EVOLVABILITY 129
VON NEUMANN’S DESCRIPTION AND CONSTRUCTION 129
VON NEUMANN’S LOGIC OF SELF-REPLICATION 131
VON NEUMANN’S “MORE IMPORTANT” QUESTION 132
PHYSICAL REQUIREMENTS FOR EFFICIENT MEMORY 133
PHYSICAL REQUIREMENTS FOR CODING AND CONSTRUCTION 134
THE PHYSICAL REQUIREMENTS FOR FOLDING AND FUNCTION 134
THE SEMIOTIC CLOSURE REQUIREMENT FOR “SELF” 135
EVOLUTION REQUIRES POPULATION DISTRIBUTIONS 136
REQUIREMENTS FOR EFFICIENT SEARCH AND SELECTION 137
ANALOGIES AND DISANALOGIES OF GENETICS WITH NATURAL LANGUAGE 138
NOTES 139
REFERENCES 139
CHAPTER 5 WHAT IS THE SCOPE OF BIOSEMIOTICS? INFORMATION IN LIVING SYSTEMS 142
INTRODUCTION 142
INFORMATION AND SEMIOSIS 143
INFORMATION AND HISTORY 144
REPRESENTATION IN DNA 145
THE ORIGIN OF LIFE 147
SUPRAGENETIC INFORMATION 148
CONCLUSION 154
ACKNOWLEDGEMENTS 154
NOTES 155
BIBLIOGRAPHY 155
APPENDIX 156
CHAPTER 6 SEMIOTIC SCAFFOLDING OF LIVING SYSTEMS. 158
LIFE AND MEASURING: BASICS OF A SEMIOTIC ONTOLOGY 158
THE SCAFFOLDING OF LIFE PROCESSES 161
THE CONCEPT OF SCAFFOLDING 163
SCAFFOLDING AND EMERGENCE 165
SPAM 167
ANTICIPATION AND BRAINS 169
SEMIOTICS AND RELATIVE BEING 171
NOTES 174
LITERATURE 175
CHAPTER 7 BIOSEMIOTICS AND BIOPHYSICS — THE FUNDAMENTAL APPROACHES TO THE STUDY OF LIFE 176
THE DEVELOPMENT (OR SPECIATION) THAT HAS RESULTED IN BIOSEMIOTICS 176
SEMIOTICS AND PHYSICS 178
THE PRINCIPLE OF CODE PLURALITY 182
BIOSEMIOTICS AND BIOPHYSICS: INSTEAD OF CONCLUSION 183
ACKNOWLEDGEMENTS 184
NOTES 184
REFERENCES 185
CHAPTER 8 IS THE CELL A SEMIOTIC SYSTEM? 187
INTRODUCTION 188
PART 1 – SEMIOSIS AND THE ORIGIN OF LIFE 189
PART 2 – THE ORGANIC CODES 196
PART 3 – INFORMATION AND MEANING 203
PART 4 – THE MODELS OF BIOSEMIOTICS 208
REFERENCES 213
CHAPTER 9 COMPUTING CODES VERSUS INTERPRETING LIFE 216
1. INTERPRETING LIFE: LANGUAGE AS THE UNIVERSAL MEDIUM OF ORGANIC EXISTENCE 219
2. COMPUTING CODES: LANGUAGE AS AN ORGANIZATIONAL PRINCIPLE OF LIVING SYSTEMS 223
3. A MODEL-THEORETICAL DEFINITION OF ORGANIC CODES 227
ACKNOWLEDGEMENT 234
NOTES 234
REFERENCES 238
CHAPTER 10 TOWARDS A DARWINIAN BIOSEMIOTICS. LIFE AS MUTUAL UNDERSTANDING 241
INTRODUCTION 241
A HISTORICAL EXCURSION 243
BEING IN THE WORLD 246
SEMIOSPHERE 250
CORPOREALITY, LIFE, LANGUAGE 255
CONCLUSION 259
ACKNOWLEDGEMENTS 260
NOTES 260
REFERENCES 260
CHAPTER 11 FROM THE LOGIC OF SCIENCE TO THE LOGIC OF THE LIVING 262
1. BIOSEMIOTICS AND PEIRCE 262
2. HOW PEIRCE’S SEMEIOTIC CAN BE APPLIED IN METAPHYSICS AND BIOSEMIOTICS 268
3. HOW TO MAKE OUR IDEAS CLEAR — PRAGMATICISM 272
4. CONSEQUENCES OF PRAGMATICISM IN UNDERSTANDING PEIRCE 275
ACKNOWLEDGEMENTS 281
NOTES 282
BIBLIOGRAPHY 286
CHAPTER 12 TOWARDS A STANDARD TERMINOLOGY FOR (BIO)SEMIOTICS 288
INTRODUCTION 288
FORM AND REFERENT 289
MODELING SYSTEMS THEORY 296
CONCLUDING REMARKS 301
REFERENCES 301
CHAPTER 13 INFORMATION THEORY AND ERROR-CORRECTING CODES IN GENETICS AND BIOLOGICAL EVOLUTION 304
1. INTRODUCTION 305
2. AN INTUITIVE OUTLINE OF INFORMATION THEORY AND ERROR-CORRECTING CODES 308
3. CONSERVING THE GENOME NEEDS ERROR CORRECTION 326
4. HOW GENOMIC ERROR-CORRECTING MEANS FIT IN WITH THE LIVING WORLD AND ITS EVOLUTION 335
5. GENOMIC ERROR-CORRECTING CODES AS ‘SOFT CODES’ 339
6. IDENTIFICATION OF GENOMIC ERROR CORRECTION MEANS 342
7. ON THE EPISTEMOLOGICAL STATUS OF INFORMATION AND ITS RELATION TO SEMANTICS 345
8. CONCLUSION 348
NOTES 349
REFERENCES 349
CHAPTER 14 RNA AS CODE MAKERS: A BIOSEMIOTIC VIEW OF RNAi AND CELL IMMUNITY 351
INTRODUCTION 352
UNITY OF LIFE – CELL MAKING 357
UNITY OF LIFE – SELF-MAKING 359
UNITY OF LIFE – SENSE MAKING 361
CELL, SELF, SENSE – CONCLUSION AND RESEARCH PERSPECTIVES 365
REFERENCES 367
CHAPTER 15 CELLULAR SEMIOTICS AND SIGNAL TRANSDUCTION 369
1. INTRODUCTION 370
2. BIOLOGICAL INFORMATION BETWEEN LEVELS OF COMPLEXITY AND THE “INTEGRATIVE AGENDA” 373
3. THE SIGNALOME 375
4. TOWARDS AN INTEGRATIVE CONCEPT OF “BIOLOGICAL INFORMATION” 376
5. CELLULAR SEMIOTIC NETWORKS 378
6. SIGNALS THAT BUILD SIGNS: ZOOMING THE SYSTEM 381
7. MODULARITY 384
8. CROSS-TALK AND CATEGORIAL SENSING 386
9. DIGITAL-ANALOGICAL CONSENSUS 388
10. THE CA2+ CODE 391
11. WHY CATEGORIAL SENSING? 397
12. THE CA2+ CODE AS AN EXAMPLE OF CATEGORIAL SENSING 399
13. FURTHER SEMIOTIC CONSIDERATIONS IN METABOLIC CODES 403
14. FROM SYSTEMS BIOLOGY TO SYSTEMS OF CORRESPONDENCES 406
15. CONCLUSIONS AND FINAL REMARKS 407
NOTES 408
REFERENCES 410
CHAPTER 16 INNER REPRESENTATIONS AND SIGNS IN ANIMALS 412
INTRODUCTION 413
PART ONE: VERTEBRATES AND REPRESENTATION 416
PART TWO: INVERTEBRATES AND REPRESENTATION 423
CASE STUDY III: Representation of Prey in the Moon Jellyfish/Herring 425
FROM SIGNAL TO SIGN. THE EMOTIONAL WORM 437
PART THREE: THEORETICAL FRAMEWORK 443
CONCLUSION 448
REFERENCES 452
CHAPTER 17 A BIOSEMIOTIC APPROACH TO EPIGENETICS: CONSTRUCTIVIST ASPECTS OF OOCYTE-TO-EMBRYO TRANSITION 459
INTRODUCTION 460
A GENERAL MODEL OF SEMIOSIS: THE SEMIOSIC MATRIX 461
APPLYING THE SEMIOSIC MATRIX TO THE OOCYTE-TO-EMBRYO TRANSITION 463
EPIGENETIC MECHANISMS FOLLOWING MAMMALIAN FERTILIZATION REVEAL BASIC PRINCIPLES OF CONSTRUCTIVIST EPISTEMOLOGY 466
DISCUSSION 470
ACKNOWLEDGMENTS 471
REFERENCES 471
CHAPTER 18 LANGUAGE AND INTERSPECIFIC COMMUNICATION EXPERIMENTS: A CASE TO RE-OPEN? 474
PROBLEMS AND THESES 474
A BRIEF HISTORY OF INTERSPECIFIC COMMUNICATION EXPERIMENTS 477
SEMIOTIC SCEPTICISM 484
THE CASE FOR ANTHROPOMORPHISM 487
FURTHER CRITICAL REMARKS ON THE ICE 490
THE ROLE OF THE SUBJECT IN ICE AND OTHER UNDERRATED ISSUES 500
CONCLUSION: A MARTINELLI’S CANON? 507
NOTES 515
REFERENCES 518
AUTHOR INDEX 520
SUBJECT INDEX 525