Preface – About Reading this Book xv
Introduction 1
Part I. Evolution 15
Chapter 1. The Evolution of Evolution 17
Darwinian Evolution 17
Self-Criticism 20
Genetics and Neo-Darwinism 22
Molecular Genetics 24
Evolutionary Developmental Genetics 28
Chapter 2. The Tree of Life 31
Extinctions 32
Tree of Life 36
Horizontal Gene Transfer 38
Preparation for the Cambrian Explosion 39
Chapter 3. The Cambrian Explosion 41
Evolution is Not Directed 48

Part II. Intelligent Answers to Intelligent Design 49
Darwinian Evolution ‘Just a Theory’ 50
Chapter 4. Does The Cambrian Explosion Disprove
Darwin’s Theory? 53
Gene Duplication and Unequal Crossing Over 57
Homeotic Genes 60
HOX Genes 61
How Do the HOX Genes Work? 62
Switches and Evolution 63
Other Homeotic Genes 63
Top-Down versus Bottom –up 64
Lysyloxidase 64
Hemoglobin 65
A Universal Cambrian Genome 65
The Environment 65
Evidence there was Plenty of Time for the Cambrian
Explosion 65
Chapter 5. No Intermediate Fossils Anywhere? 69
Speciation by Geographic Isolation 71
Acceleration of Speciation by Diversity 72
Horse Evolution 73
The Burgess Shale 76
Diatoms 76
Mollusks and Species Extinctions 77
Trilobites 78
Sea to Land 80
From Meat Eater to Leaf Eater 80
Chapter 6. Not Enough Time? 83
SNPs and SNMs 84
STRPs and STRMs 85
Microsatellite DNA 85
Implications for Evolution 88
Proof of the Role of STRPs in Evolution 90
The Face of a Dog and Homopeptides of the
RUNX2 Gene 91
Darwin’s Finches and Rapid Evolution 92
The Role of Gene Splicing and Evolution 92
Other Mechanisms of Rapid Genetic Change 94
Endosymbiosis 95
Whole Genome Duplication 95
Gene Duplication 95
Hybridization 95
Gene Displacement/Gene Opportunism/Cooption 95
Chromosome Rearrangement 96
Horizontal Gene Transfer 96
Jumping Genes 96
Sexual Recombination 96
Alu Sequences 96
Exon Shuffling and Domain Exchange 96
Repetitious Peptides 97
Chapter 7. Complexity – Introduction 99
Complexity and Cellular Automata 100
Computer Models of Evolution – Avida 103
Computer Models of Evolution – EV 105
The Real Thing 106
Monkeys and Typewriters 107
Basic Argument from Improbability 109
Modularity 119
Chapter 8. Complexity – Eyes 115
A Computer Model of the Evolution of the
Refractory Index 116
Chapter 9. Complexity – Ears 121
Evolution of the Mammalian Jaw 121
Chapter 10. Complexity – Citric Acid Cycle 125
Chapter 11. Complexity – Blood Clotting 129
Chapter 12. Complexity – Cilia 137
Chapter 13. Complexity – Flagella 137
Chapter 14. Evolution Now: Introduction 151
Definition of a darwin 151
Chapter 15. Evolution Now: The Peppered Moth and
Industrial Melanism 153
Attacks on the Peppered Moth Story 156
Defense Against the Attacks 158
Chapter 16. Evolution Now: Darwin’s Finches 163
Studies of the Grant’s 165
The Drought 166
The Flood 168
Principle of Divergence 169
Speciation by Hybridization 170
Death Knell to Anti-evolutionist 170
The Creationist Anti-evolutionary Spin 170
Chapter 17. The Evolution of Man 173
Lemurs – Our Earliest Ancestors 174
The Human tree 175 African Mitochondrial Eve 176
Increase in Brain Size in Human Evolution 177
The Evolution of Brain Complexity 179
Role of specific genes 179
Role of Nutrition 180
Origin of Speech 181
Larynx 181
Brain 181
The FOXP2 Gene 183
General Screen for Genes Involved in the
Evolution of Man 183
Examination of proteins 183
Examination of mRNA expression 184
Examination of DNA sequences 186
Changes in Promoter Regions 187
Changes in Copy Number 187
Changes in Non-coding RNA 188
Changes in HARs 188
Sex for All Seasons 189
Other Distinguishing Features of Homo sapiens 189
Chapter 18. The Origin of Life 195
The Narrow Origin of Life Window 195
The Miller-Urey Experiment 195
Creationists Objections to the Miller-Urey Experiment 196
There was Virtually No Oxygen in the Early Earth’s
Atmosphere 196
There was a Hydrogen-rich Early Earth Atmosphere 196
Comets and Meteorites Provide Prebiotic Organic
Compounds 197
Hydrothermal Systems 197
Theories of the Origin of Life 198
Protometabolism – A Chemical World 198
The Co-evolution of RNA and Proteins 202
Are We Alone? 206 Chapter 19. Evolution: Conclusions 209
Is Darwinism Poison to Religion? 213

Part III. Cosmology 217
Chapter 20. The Weird World of Quantum Physics 219
Interference 219
The Uncertainty Principle 223
Entanglement 226
Is Quantum Weirdness Relevant to
Human Spirituality? 229
Chapter 21. The Big Bang 233
The Forces of the Universe 233
Particles of the Universe 235
History of the Big Bang 237
Background Micro-radiation 238
Current Version of the Big Bang 239
Inflation and the Speed of Light 242
The Rate of Expansion of the Universe is Accelerating 243
Dark Matter and Dark Energy 243
Black Holes 245
Origin of the Solar System and the Earth 245
Is the Big Bang Relevant to Theology and
Human Spirituality? 246
Chapter 22. String Theory: A Cosmic Symphony 247
Strings 247
String Theory 248
M-theory 249
Multiple Universes – Darwinian Selection of Universe 250
Branes, Parallel Universes and Cyclic Cosmology 250
A Universe from Nothing 253
Implications of String Theory for Theology
and Spirituality 253
Chapter 23. The Anthropic Principle 253
1. Weak Anthropic Principle (WAP) 253
2. Strong Anthropic Principle (SAP) 254
3. Participatory Anthropic Principle (PAP 254
4. Final Anthropic Principle 255
What are the Constants that Must be Exactly
as they are for Life To Exist? 255
N, ε Q, D 255
A More Complete List of Anthropic Constants 257
Comments by Various Scientists 258
Strong Selective Effect 259
Is Life in the Universe Rare? 259
Religious and Spiritual Implications of the
Anthropic Principle 260
Chapter 24. Cosmology and Spirituality 261
1. Quantum Physics 261
Does the Uncertainty Principle Mean
We Have Free Will? 253
Does Quantum Physics and Entanglement
Support the Eastern Religious View of a Cosmic
Consciousness Where All Parts of the
Universe are Interconnected? 265
Quantum Physics and Metaphysics 267
2. The Big Bang 268
Is God Required to Stabilize the Universe? 270
3. String Theory
Does String Theory Eliminate the
Theological Advantage of the Big Bang? 270
4. Does the Anthropic Principle Prove that God Exists? 271
The Participatory Anthropic Principle, Human
Consciousness and the Universe 272
Science and Mysticism 274

Part IV. The Neurology of Reason and Spirituality 279
Chapter 25. Consciousness, the Spirit and the Soul 283
Damasio and Consciousness 282
Edelman and Consciousness 287
Crick and Consciousness 289
Imaging Studies of Subjects in a Persistent
Vegetative State 291
Information Integration and Consciousness 292
The Spirit and the Soul 293
Chapter 26. The Frontal Lobes 297
Luria and the Frontal Lobes 301
Animal Studies and the Frontal Lobes 302
The Prefrontal Lobes, Consciousness and Civilization 303
The Frontal Lobes and ADHD 304
The Dorsolateral versus Orbitofrontal Areas 305
The Dorsolateral Syndrome 306
Chapter 27. The Pleasure Brain 309
The Reward Pathways 309
Chapter 28. The Social Brain 315
The Limbic System 316
The Amygdala 328
The Prosocial Hormones Oxytocin and Vasopressin 329
The Orbitofrontal Prefrontal Cortex and the Man Who
Who Borrowed Cars 322
The “Theory of Mind” 326
The Mirror System 328
Chapter 29. The Rational Brain 333
The Right Brain – Left Brain 333
Novelty versus Routine 335
Working Memory 336
What is Rational Thought? 337
Where is Rational Thought Localized? 338
Brain Imaging Studies 340
Chapter 30. The Spiritual Brain 345
Anatomy of the Temporal Lobe 345
Temporal Lobe Epilepsy (TLE) – History 347
Wilder Penfield and Mapping of the Spiritual
Human Brain 348
Stimulation of the Amygdala and Hippocampus 354
More Out of Body Experiences 355
Spiritual and Religious Experiences and Temporal
Lobe Epilepsy (TLE) 355
Feeling of a Presence 362
The Role of TLE in History and Religion 352
Near Death Experience 366
REM Dreams and the Right Temporal Lobe 375
Magnetic Brain Stimulation of the Temporal Lobes
and Spirituality 376
LSD, the Temporal Lobes and Spirituality 378
DMT and Spirituality 380
Psilocybin and Spirituality 386
Right Temporal Lobe or Both Temporal Lobes? 387
Persinger, Temporal Lobe Transients, and
he God Experience 390
Speaking in Tongues (Glossolalia) 394
Julian Jaynes, God and the Bicameral Mind 395
The Temporolimbic Marker Model of Saver and Rabin 396
Chapter 31. The Meditating Brain 405
The Types of Meditation 406
Effects of Meditation 410
The Dalai Lama, Compassionate Meditation
and Gamma Waves 411
The Effect of Meditation on Brain Function as
Determined by Imaging Studies 403
Brain Imaging during Religious and Mystical
Experiences 419
Chapter 32. The Hopeful Brain 423
How the Placebo Effects Complicate Drug Studies 424
Pain Pathways 426
Placebo Effect, Pain and Endorphins 428
Placebo Effect and the Prefrontal Cortex 429
Placebo Effect and Acupuncture 431
Placebo, PET and Parkinson’s Disease 432
Endorphins, PET and the COMT Gene 433
Nocebo Effect 434 Chapter 33. The Happiness Brain 437
Social Relationships 439
Being in Control 439
Helping Others 440
Chapter 34. The Biology of Faith versus Reason 443
Complex Decisions are made in the Unconscious, Simple
Decisions in the Conscious Brain 445
Man’s Craving for Information and the Pleasure
it Produces 446
Man’s Resistance to Changes in His Belief System 448
Chapter 35. Neurology: Summary 453
Part V. The Genetics of Reason and Spirituality 457
Chapter 36. Polygenic Inheritance 461
A Threshold Model 462
How Many Genes? 462
Polygenes 462
Epistasis 463
Chapter 37. The Genetics of Bad Behavior 467
Conduct Disorder (CD) is a Life-long Condition 467
Family Studies of CD 470
Twin Studies of CD 470
Twin Studies of Juvenile Delinquency and Adult Crime 471
Adoption Studies of Antisocial Behavior 472
Adolescence Limited and Life-Course
Persistent Antisocial Behavior 473
Some Specific Genes – MAO 475
Chapter 38. The Genetics of Good Behavior 479
Altruism 467
Indirect Reciprocal Altruism and Reputation 480
Strong Reciprocal Altruism, Altruistic Rewarding
and Punishing 480
The Genetics of Altruism 482
Unfairness, Emotion and Reason 482
Altruistic Behavior and Dopamine Reward Pathways 483
Altruistic Behavior and Dopamine Genes 484
Chapter 39. The Genetics of Reason 487
Intelligence Tests 487
What is Intelligence? 489
The Genetics of Intelligence 489
Importance of IQ to Success in Society 492
Chapter 40. The Genetics of Spirituality 495
Twin Studies of Religious Belief 496
Twin Studies of Spirituality 500
Twin Studies of Spiritual but not Religious 502
Church Attendance 504
The Role of Specific Genes 505

Part VI. Natural Selection 509
Chapter 41. The Evolution of Intelligence 511
What Parts of the Human Brain have Shown the
Greatest Evolutionary Increase in Size? 511
What Cognitive Skills are Unique to Humans? 513
The Role of the Ice Ages in the Evolution
of Human Intelligence 513
The Time Frame for the Evolution of Human I
ntelligence 514
The Role of Social Skills in the Evolution of
Human Intelligence 516
Chapter 42. The Evolution of Spirituality 519
Is Spirituality a Spandrel 519
Is Spirituality a Meme? 521
Spirituality Alleviates Man’s Fear of his Own Death,
of his Mortality 522
Spirituality Gives Man Control over a Threatening
World 524
Spirituality and Near-death Experiences 524
Spirituality and Opitmism 525
Spirituality, Religion and Societal Cohesiveness 525
Religion and Natural Selection 526
Spirituality as a Defense Mechanism 527
Inborn Spirituality as a Moral Watchdog 527
A Spiritual Mate 529

Part VII. Other Aspects of Spirituality and Reason 531
Chapter 43. The Origins of Religion 533
Animism and the “Primitive Religions” 533
Polytheism 535
Plato, Aristotle and the Ancient Greeks 535
Zoroastrianism 535
The Eastern Religions 536
Hinduism 536
Buddhism 538
Jainism 539
Sikhism 539
Taoism 539
The Origins of Monotheism and Judaism 540
The Origins of Christianity 542
Islam 544
Chapter 44. Mysticism 549
Plotinus 550
Kabbalah 550
St. Teresa of Avila 552
Sufi 553
Al-Ghazali 553
Mysticism for the Common Man 555
Chapter 45. Myth and Ritual 557
Myth 557
Ritual 559
Chapter 46. Psychedelics and Religion 563
Psilocybin Mushrooms and Mesoamerica 564
Ayahuasca and the Amazon Basin 568
Mescaline, Peyote and the Native American Church 570
Amanita muscaria, Soma and Hinduism 571
The Soma of Hinduism 574
The Amrita of Buddhism 575
The Soma of Siberia 575
Mushrooms and Western Religion 576
Chapter 47. Does God Play Favorites? 583
The Chosen People 583
The Rapture 584
Chapter 48. The Evils of Religion 589
The Old Testament 590
The New Testament 591
The Inquisitions 592
The Crusades 593
Cromwell’s Slaughter of Catholics 593
The Qur’an and Islam 594
The Assassins 594
Wahhabinism 594
Suicide Bombings and Islam 596
Islam and the Selling of Nuclear Secrets 596
Belief in the Apocalypse 597
Eastern Religions 598
Recent Religious Wars 598
Negative Health Consequences of Religion 598
The Literal Interpretation of Sacred Texts 599
Fundamentalism and Politics 600
Chapter 49. The Benefits of Religion 603
Religion and Health 604
Does Prayer Work? 611
Petitionary Prayer 611
Intercessory Prayer 612
Chapter 50. The Problem of Evil 617
The Gnostics 617
The Deists 618
Theodicy 618
The “Man Created God” Solution 620
Chapter 51. Are the Sacred Books Literally True? 623
Who Wrote the Bible? 623
Inconsistencies in the Bible 624
Man Made Changes in Sacred Texts 626
Chapter 52. Is God Dead? Ask the Pentecostals 631
Pentecostalism 632
Origins of Pentecostalism 632

Part VIII. Summary: Did Man Create God? 639
Definition of God 640
The Creation Theory 641
The Theory of the Soul 642
The Prayer Theory 642
The Spiritual Brain 643
An Inborn Moral Law 644
Spirituality: An Evolved Trait 644
Other Aspects of Religion and Spirituality 644
Multiple Religions 645
Psychedelics and Religion 645
The Problem of Evil 645
The Inerrancy of the Sacred Books 645
Is God Dead? 645
The Problem of Postponement 646
Is Religion Necessary for a Moral Life? 646
Is Religion Necessary for a Happy, Meaningful or
Purposeful Life? 647
How do We Answer the Three Questions of
Pope John Paul II? 647
Is Man Inherently Sinful and Evil? 648
Is Science Incompatible with Religion? 649
Is the Rational Brain Incompatible with Spirituality? 650
Is the Rational Brain Incompatible with
Religion and Faith? 650
1. Maximally Compatible 650
2. Compatible with Minor Qualifications 652
3. Compatible with Major Qualifications 654
Spiritual but not Religious 654
4. Incompatible 654
Is Religion Doomed or is Science Doomed 655
Glossary 657
Index 659

Did Man Create God?

A Scientific Examination of Religious Beliefs