Evolutionary Bioinformatics (eBook)

Contents 8
Note on the Second Edition 10
Abbreviations 11
Prologue 12
To Select is Not To Preserve 12
That Sort of Clearness 13
A Buck or Two 14
The Dawn 15
Homo bioinformaticus 15
Further Veils? 16
Scope 17
Goals 21
Part 1 Information and DNA 24
Chapter 1 25
Memory – A Phenomenon of Arrangement 25
Priorities 25
Textual and Hereditary Information 27
Mental Information 29
Periodical Rhythms 32
Food 35
Informational Macromolecules 36
Translation 40
Variation 43
Latency 46
Summary 47
Chapter 2 49
Chargaff's First Parity Rule 49
Error-Detection 49
In-Parallel Redundancy 50
DNA Structure 50
Turnover 58
Promiscuous DNA 59
Haploidy and Diploidy 60
In-Series Redundancy 61
Bits and Bats 62
Accidents and Non-Accidents 65
Summary 67
Chapter 3 68
Information Levels and Barriers 68
Symbols and Code 68
Primary and Secondary Information 69
Primary Information for Protein 70
Information Barriers 72
Barriers Preserve Discontinuity 73
To Select is Not to Preserve 77
Another Order of Variation 79
Context as Barrier 81
Not a Palimpsest 83
Hybrid Disciplines and Hybrid Sterility 85
Summary 87
Part 2 Parity and Non-Parity 88
Chapter 4 89
Chargaff’s Second Parity Rule 89
Information Conflict 89
Prose, Poetry and Palindromes 90
Intrastand Parity 92
Polarity and Complementarity 93
Duplets and Triplets 97
Species Specificity of Tuple Frequencies 101
Metagenomics 103
Introns Obey Better Than Exons 103
Level of Selection? 105
Inter-chromosomal Accounting 108
Summary 110
Chapter 5 111
Stems and Loops 111
Transfer RNA 111
The Bacteriophage Paradox 114
Genome-Level Selection 115
Calculation from Single Base Pairs 116
Role of Base Composition 120
Calculation from Dinucleotide Pairs 121
RNA Structure and Conflict 123
PR2 Revisited 126
Symmetrical Extrusions 127
DNA as Substrate 128
Summary 129
Chapter 6 130
Chargaff’s Cluster Rule 130
Base Clusters 130
Clusters of Clusters 131
Polarity 134
Origin of Replication 135
Gene Movements 138
Leading and Lagging Strands 139
Purine loading 141
Pyrimidine-Loading in Mitochondria 144
Summary. 146
Part 3 Variation and Speciation 147
Chapter 7 148
Mutation 148
The Genetic Code 150
One Base at a Time 151
RNY Rule 153
Negative and Positive Selection 155
Neutral Mutations 157
Genome Phenotype 158
Compensatory Mutations 161
Were First Mutations Synonymous? 163
Phylogenetic Trees 165
Limits of Natural Selection 166
Summary 168
Chapter 8 169
Species Survival and Arrival 169
Blending or Discrete Inheritance? 170
Mendelism 172
Multigenic Characters 174
Reproductive Isolation 175
Cycling through the Generations 177
Jurrasic Park 178
Branching Evolution 180
Dobzhansky and Muller 182
Pattern Change 183
Summary 185
Chapter 9 186
The Weak Point 186
Cryptic Variability of the Reproductive System 187
Collective Variation of a Population Subset 189
Sporadic and Regular Sterilities 189
Chromosomes and the Residue or Irresoluble Base 193
Two Factors must Complement to Produce Sterility 194
Complementation like Sword and Scabbard 197
Modern Chromosomal Views 199
Darwin’s Difficulties 201
Species Selection 202
Summary 203
Chapter 10 204
Chargaff’s GC rule 204
Uniformity of (G+C)% 205
The Holy Grail 205
Language 206
Crick’s Unpairing Postulate 209
Structure-Mediated Homology Recognition 210
(G+C)% Controls Pairing 213
Mutational Meltdown 215
Coinfecting Viruses 216
Protein Pressure Reinforces 217
Polyploidy 217
Saltum? 218
Summary 219
Chapter 11 220
Homostability 220
Gene Duplication and Isochores 221
Isochores Early 226
The Gene as a Unit of Recombination 228
The Boundary Problem 230
Thermophiles 231
Summary 233
Part 4 Conflict within Genomes 234
Chapter 12 235
Conflict Resolution 235
Two Levels of Information 236
Codon Bias 237
GC-Pressure versus Protein-Pressure 240
Species Barcode in Mitochondria 242
Species versus Genes 244
Species Win at (G+C)% extremes 247
Intermediate (G+C)% Allows Compromise 250
Levels of Selection 251
Dog Wags Tail 252
AG-Pressure versus Protein-Pressure 253
GC-Pressure versus AG-Pressure 255
AG-Pressure and ‘Placeholder’ Amino Acids 257
Thermophiles 259
Summary 261
Chapter 13 262
Exons and Introns 262
Introns Interrupt Information 263
Protein versus DNA 267
Achilles Heels 272
Mirror Repeats 272
RNA versus DNA 273
Overlapping Genes 274
Simple Sequences 274
Multiple Pressures 277
Summary 279
Chapter 14 280
Complexity 280
Scoring Information Potential 280
The New Bioinformatics 281
Protein or Nucleic Acid Level Function? 282
Base Pair Pressures 284
Epstein-Barr Virus 286
Malaria 291
Conflict with Fold Potential 295
Roles of Low Complexity Segments 297
Short Tandem Repeats 298
AC-Pressure and Asymmetric Fold Potential 301
Repetitive Sequences and Speciation 302
Long-Range Periodicities 303
Summary 304
Part 5 Conflict between Genomes 305
Chapter 15 306
Self/Not-Self? 306
Homology Search 307
Antibody Response 309
Antibody Variable Genes 310
Prototypic Immune Systems 311
Polymorphism Creates Host Unpredictability 315
Junk DNA 316
Repetitive Elements 317
All Hands on Deck! 320
The Double-Stranded RNA Alarm 321
Purine-Loading to Self-Discriminate 323
Entropy 324
The Hidden Transcriptome 326
CRISPR 328
Summary 329
Chapter 16 330
The Crowded Cytosol 330
Piles of Coins 331
Homoaggregates 333
Collective Pressure 334
Concentration Fine-Tuning 335
Heteroaggregates 336
Protein ‘Immune Receptors’ 337
Phenotypic Plasticity 338
Polymorphism Makes You Individual 339
Polymorphism Also Makes You Vulnerable 341
Death at Home or in Exile 342
Selfish Genes and the Menopause 343
Molecular Chaperones 343
Positive Repertoire Selection 346
Summary 347
Part 6 Sex and Error-Correction 349
Chapter 17 350
Rebooting the Genome 350
Redundancy 351
Recombination Repair 352
Strand Guidance 354
DNA Damage 356
Piano Tuning 358
Spot Your Reprotype? 358
Haldane’s Rule 359
Sex Chromosomes 360
Sex and Speciation 363
Sex Chromosome Dosage Compensation 366
Summary 369
Chapter 18 371
The Fifth Letter 371
Editing of DNA 371
Restriction Enzymes 372
CpG Islands 375
CpG Suppression 376
Methylation Differences in Twins 378
Imprinting 378
Transgenerational Inheritance 380
Editing of RNA 381
Summary 382
Part 7 Information and Mind 383
Chapter 19 384
Memory – What is Arranged and Where? 384
The Organ Par Excellence 384
The Cupboard is Bare 385
The Conventional Wisdom 386
Tomorrow 387
Savants and Information Measurement 388
Internal Signal Detection and Emission 389
Cloud Computing 390
The Physics of Space 391
Syntax 392
Argument from Incredulity 393
A Hilbertian List 394
Summary 396
Epilogue 397
To Preserve is Not To Select 397
Percepts 397
Torch Passed 398
Voting with Facts 400
False Leads? 402
Marketing 404
Joining the Dots 405
Cogito Ergo …? 407
Appendices 408
Appendix 1 409
What the Graph Says 409
Horizontal Lines 409
Tilted Lines 412
Curved Lines 413
No Lines 414
A Caution 414
Appendix 2 415
Scoring Information Potential 415
Two Units 415
Four Units 416
Twenty Units 416
Meaning 417
Appendix 3 419
No Line? 419
Setting the Stage 419
Rules of Thumb 421
Probabilities 422
No Beginning? 423
Can Intermediate States Exist? 425
Contradiction Shall Reign! 427
Acknowledgements 429
References and Notes 432
Prologue – To Select is Not To Preserve 432
Chapter 1 – Memory: A Phenomenon of Arrangement 433
Chapter 2 – Chargaff’s First Parity Rule 437
Chapter 3 – Information Levels and Barriers 438
Chapter 4 – Chargaff’s Second Parity Rule 439
Chapter 5 – Stems and Loops 441
Chapter 6 – Chargaff’s Cluster Rule 442
Chapter 7 – Mutation 445
Chapter 8 – Species Survival and Arrival 446
Chapter 9 – The Weak Point 448
Chapter 10 – Chargaff’s GC Rule 448
Chapter 11 – Homostability 451
Chapter 12 – Conflict Resolution 453
Chapter 13 – Exons and Introns 454
Chapter 14 – Complexity 457
Chapter 15 – Self/Not-Self? 459
Chapter 16 – The Crowded Cytosol 461
Chapter 17 – Rebooting the Genome 463
Chapter 18 – The Fifth Letter 465
Chapter 19 Memory – What is Arranged and Where? 467
Epilogue – To Preserve in Not To Select 470
Appendix 3 – No Line? 473
Index 475