Homology (eBook)

Front Cover 1
Homology: The Hierarchical Basis of Comparative Biology 4
Copyright Page 5
Table of Contents 8
Dedication 6
CONTRIBUTORS 16
INTRODUCTION 18
I. SOME UNANSWERED QUESTIONS 19
II. RICHARD OWEN AND HOMOLOGY 20
III. HISTORY OF THE TERM AND CONCEPT 21
IV. A PHYLOGENETIC DEFINITION OF HOMOLOGY 24
V. EMBRYONIC DEVELOPMENT AND HOMOLOGY 28
VI. CONTINUITY OF INFORMATION AND HOMOLOGY 30
VII. HOMOLOGY IN MOLECULAR BIOLOGY 31
VIII. HOMOLOGY AND BEHAVIOR 31
IX. HOMOLOGY AND PLANT BIOLOGY 32
ACKNOWLEDGMENTS 33
REFERENCES 34
CHAPTER 1. RICHARD OWEN AND THE CONCEPT OF HOMOLOGY 38
I. INTRODUCTION 39
II. THE ARCHETYPE 45
III. THE DEFINITION OF HOMOLOGY 56
IV. DEFINITIONS, CRITERIA, AND EXPLANATIONS 62
V. CONCLUSIONS: RICHARD OWEN AND HOMOLOGY 71
ACKNOWLEDGMENTS 73
REFERENCES 74
CHAPTER 2. HOMOLOGY, TOPOLOGY, AND TYPOLOGY: THE HISTORY OF MODERN DEBATES 80
I. INTRODUCTION 81
II. DEFINING HOMOLOGY 82
III. RECOGNIZING HOMOLOGY 85
IV. CONNECTIVITY VERSUS TOPOLOGY IN THE SEARCH FOR HOMOLOGY 89
V. CHANGING IDENTITIES AND TAXIC HOMOLOGY 101
VI. TRANSFORMATIONAL AND TAXIC APPROACHES 105
VII. HOMOLOGY, TOPOLOGY, AND INDIVIDUALITY 107
VIII. THE HIERARCHY OF TYPES 110
IX. CONCLUSION 111
ACKNOWLEDGMENTS 112
REFERENCES 112
CHAPTER 3. HOMOLOGY AND SYSTEMATICS 118
I. INTRODUCTION 119
II. CLADISTICS 120
III. CONTENTIONS 127
IV. BIOGEOGRAPHY 152
V. CONCLUSIONS 154
ACKNOWLEDGMENTS 155
REFERENCES 155
CHAPTER 4. HOMOLOGY, FORM, AND FUNCTION 168
I. INTRODUCTION 169
II. HOMOLOGY AND STRUCTURE 170
III. SEARCHING FOR THE LOCUS OF HOMOLOGY 173
IV. HOMOLOGY AND PHYLOGENY 183
V. HOMOLOGY AND FUNCTION 195
VI. CONCLUSIONS 204
ACKNOWLEDGMENTS 205
REFERENCES 206
CHAPTER 5. CAN BIOMETRICAL SHAPE BE A HOMOLOGOUS CHARACTER? 214
I. HISTORICAL INTRODUCTION 215
II. EARLIER VERSIONS OF THE ARGUMENT 221
III. GETTING TO THE ROOT OF THE DILEMMA 228
IV. THE INCOMMENSURABILITY OF BIOMETRICS AND SYSTEMATICS 235
V. CONCLUSIONS 241
ACKNOWLEDGMENTS 242
REFERENCES 242
CHAPTER 6. HOMOLOGY, DEVELOPMENT, AND HEREDITY 246
I. INTRODUCTION 247
II. HOMOLOGY: AN UNSOLVED PROBLEM 248
III. HOMOLOGY AS EQUIVALENCE 250
IV. GENERATIVE INVARIANTS 253
V. GENE ACTION 256
VI. UNITARY MORPHOGENETIC FIELDS 259
VII. CONCLUSIONS 260
REFERENCES 261
CHAPTER 7. HISTORY, ONTOGENY, AND EVOLUTION OF THE ARCHETYPE 266
I. INTRODUCTION 267
II. THREE ISSUES IN THE ANALYSIS OF HOMOLOGY 269
III. DEVELOPMENTAL APPROACHES TO HOMOLOGY 273
IV. CONFLICTS BETWEEN HISTORY AND ONTOGENY 276
V. CONCLUSIONS 283
ACKNOWLEDGMENTS 284
REFERENCES 284
CHAPTER 8. HOMOLOGY AND THE MECHANISMS OF DEVELOPMENT 290
I. INTRODUCTION 291
II. WHY IS STRUCTURAL IDENTITY MORE FUNDAMENTAL FOR THE HOMOLOGY CONCEPT THAN COMMON ANCESTRY? 293
III. DEVELOPMENT AND STRUCTURAL IDENTITY 296
IV. AN ANECDOTAL REVIEW OF MORPHOSTATIC DEVELOPMENTAL MECHANISMS 301
V. CONSTRAINTS AND STRUCTURAL IDENTITY 307
VI. CONCLUSIONS 311
ACKNOWLEDGMENTS 312
REFERENCES 312
CHAPTER 9. WITHIN AND BETWEEN ORGANISMS: REPLICATORS, LINEAGES, AND HOMOLOGUES 318
I. INTRODUCTION 319
II. PATTERN "VERSUS" PROCESS 320
III. DEFINITION 322
IV. TYPES OF HOMOLOGY 326
V. SOURCES OF CONTINUITY 328
VI. CONCLUSION 348
ACKNOWLEDGMENTS 350
REFERENCES 350
CHAPTER 10. HOMOLOGY IN MOLECULAR BIOLOGY 356
I. INTRODUCTION 356
II. CLASSES OF MOLECULAR HOMOLOGY 358
III. CONCERTED EVOLUTION OF PARALOGOUS SEQUENCES 362
IV. PARTIAL HOMOLOGY OF MOLECULES: EXON SHUFFLING 365
V. POSITIONAL HOMOLOGY AND SEQUENCE ALIGNMENT 366
VI. HOMOLOGY IN INDIRECT (NONSEQUENCE) MOLECULAR TECHNIQUES 369
VII. SUMMARY 376
ACKNOWLEDGMENTS 378
REFERENCES 378
CHAPTER 11. HOMOLOGY AND BEHAVIORAL REPERTOIRES 386
I. INTRODUCTION 387
II. TWO SERPENTINE EXAMPLES 388
III. CONCEPTUAL AND METHODOLOGICAL ISSUES 394
IV. PROSPECTS AND PROBLEMS 399
ACKNOWLEDGMENTS 402
REFERENCES 402
CHAPTER 12. COMPLEXITY AND HOMOLOGY IN PLANTS 410
I. INTRODUCTION 411
II. BACKGROUND 411
III. MOLECULES AND MORPHOLOGY 412
IV. SIMPLICITY AND COMPLEXITY 413
V. COMPLEXITY AND HOMOPLASY 415
VI. HOMOLOGY AND HOMOPLASY IN PLANTS 419
VII. A POSSIBLE TEST 421
VIII. GENERAL DISCUSSION 430
ACKNOWLEDGMENTS 433
REFERENCES 433
CHAPTER 13. HOMOLOGY, HOMEOSIS, AND PROCESS MORPHOLOGY IN PLANTS 440
I. INTRODUCTION 441
II. HOMOLOGY AND CORRESPONDENCE 444
III. HOMEOSIS AND HOMOLOGY 455
IV. MULTIVARIATE ANALYSIS AND MORPHOLOGICAL DISTANCE 460
V. PROCESS MORPHOLOGY AND HOMOLOGY 467
VI. PROCESS MORPHOLOGY AND EVOLUTION 473
VII. SUMMARY AND CONCLUSIONS 477
ACKNOWLEDGMENTS 482
REFERENCES 483
INDEX 494