Praise of Chromosome folly: Confessions of an Untamed Molecular Structure »

This book is for those who have perceived that the scientific endeavor is an ever changing process in which the explanations available at a given time only lead to a partial understanding of the known phenomena. It is directed to inquiring minds who have harbored doubts about the correctness of prevailing monolithic ideas and have been looking for alternative explanations.

To the Reader v

Introductory Note xvii

Part I The Source of "Folly" and the Reason for Confessions 1

1 I am an Inconspicuous and Unattractive Creature Painted with Lipstick 3

2 They Say That I Resemble a Sausage 7

3 The Cell Is My Castle and Prison But I May Swim and Dance like an Odalisque in a Harem 8

4 The Striptease Show - How I Dress and Undress at Every Cell Division 11

5 I Have Created My Own Private World Full of Tricks, Back Door Exits and Novel Solutions - I am an Untamed Innovator 16

6 My Origins Were Humble - The Antithetical Nature of Matter Left a Mark on My Construction 19

7 My Split Personality - The Source of "Folly" 22

8 The Reason for Confessions 26

9 I Have Been Abused and Covered With Insults 28

10 The Wisdom of the Foolish 31

11 Scientific Concepts Are Prone to Change Throughout Time - The Nature of Science Demands that Previous Ideas be Superseded, as New Technologies Allow a Deeper Insight into Matter 36

12 What Seems Ludicrous at a Given Time Turns Out to be the Correct Explanation Several Years Later. The Gene was Considered to Consist of Protein, But Is Now Known to be a Ribbon of DNA 39

13 In the Last 20 Years the Number of Human Genes was Reduced from 200,000 to 32,000, and This Figure Remains Uncertain 41

14 The Models of Chromosomes Have Varied Drastically with Time 43

References 48

Sources of Illustrations 51

Part II Who Cares for Gravity 53

15 The Chromosome in Its Organization and Activity Follows Its Own Path - It Does Not Obey Gravity, Randomness, Selection or Magnetism 55

16 Definition of Gravity - Newton's Laws Are Good for Planets and Apples 57

17 What Is a Force - The Four Fundamental Forces 59

18Newton's Laws Do Not Apply in Quantum Mechanics 61

19 Not All Bodies Fall When Unsupported 63

20 The Ascent of Sap in Trees-Another Unexplained Phenomenon 64

21 An Unknown Process Decides Which Cells Are Going to Grow in the Direction of Gravity and Which Are Going to Counteract It 67

22 Physicists Construct Antigravity Devices that Oblige Frogs and Plants to Float 71

23 Atoms Hide Many Properties that May Disclose the Mechanisms Behind Living Processes - Liquid Helium Can Build a Fountain Ejecting Itself Out of a Flask 73

24 Levitation in Metals - What Was Impossible Became Possible 75

25 Animals, like Plants, Have Created Devices that Counteract Gravity 77

26 In Giraffes the Distance between the Heart and the Head Is Over Two Meters 79

27 No Chromosome Obeys Newton's Laws - In Their Movements Chromosomes Bypass Gravity 82

28 Chromosomes Move in All Directions of the Mariner's Compass 84

29 It Is the Programmed Pattern of the Organism that Decides the Direction of Movement 86

30 The Devices Used by the Chromosome Which Result in Particular Movements 87

31 Chromosomes Move Inside the Nucleus, like Goldfish in an Aquarium, without the Use of Spindle Fibers 88

32 The Chromosome's Autonomy Takes Many Forms - The Chromosome Ends May Take Over the Function of Active Mobility on the Spindle 91

33 Chromosomes Inherited from the Father May Be Sent to a Different Compartment than Those Inherited from the Mother 93

34 How to Move Equally Well without Guiding Asters and Centrosomes 94

35 DNA Replication Already Disregarded Gravity 95

36 Mineral Crystallization Disposes Also of Gravity and Imposes Massive Copying 97

37 The Egg Contents Rotate and the Cells Move within the Embryo Independently of Gravity 99

38 Snails Have a Shell in the Form of a Spiral Which Is Either Left-Handed or Right-Handed - The Choice Is Determined by Genes Which Orient the Axis of Cell Division Independently of Gravity 101

39 It Comes as a Revelation that the Chromosome Does Not Need Strong Magnets and Extreme Low Temperatures to Evade Gravity 104

40 Goddesses Do Not Obey Earthly Laws 105

References 107

Sources of Illustrations 110

Part III Who Cares for Randomness 113

41 Randomness Was Originally Foreign to Science 115

42 Randomness Is an Economic Concept Introduced into 17th Century Science 117

43 Randomness Is Synonymous with Ignorance - "The Folly of Probability" 122

44 It Took the Last 20 Years to Demonstrate that What Were Considered Chromosome Accidents Were Ordered Events 124

45 The Transmission of Hereditary Traits - From Confusion to the Ability to Predict 125

46 Mutation Has Been the Main Example of a Random Event 127

47 How the Prevailing Fashion Led to Fashionable Results, or How Random Mutations Turned Out to be Non-Random 128

48 Rearrangements that Were Random Events Turned Out to be Directed by Mobile Elements 131

49 The Repeat Sequences of the Human Genome Are, Instead of Being "Junk," a Treasure Trove of Information 133

50 Genes with Similar Functions Could Not be Located Nearby - Random Mutations and Rearrangements Would Disrupt Any Possible Order 134

51 The Gene Turns Out to Consist of a Highly Ordered Procession of DNA Stations Locked by Well Defined Starting and Finishing Sites 137

52 The Gene Is Never Alone 141

53 The Periodic Packaging of DNA Along Chromosomes Has Turned Out to be Predictable 142

54 In Cell Division the Proper Movement of Chromosomes Is Maintained by Correction of Improper Attachment to the Moving Apparatus 143

55 Cells Sense and Stop Uncontrolled Divisions Released by Cancer Stimuli. Moreover, RNAs Are Able to Silence Genes 145

56 Prevention of Failing of Chromosome Pairing and of Recombination 148

57 Brownian Motion - The Trap of the Physicist and Biologist 150

58 The Cell Was Seen as a Pea Soup, But Now Most of Its Molecules Are Known to Have an Address 152

59 "The Genetic Code Is Certainly Not Random" 155

60 Noise Is Disorder - Music Is Order and Unity 156

61 The Distinction between Genetic Noise and Genetic Music 157

62 "Errors" Are Not of All Possible Kinds 159

References 160

Sources of Illustrations 164

Part IV Who Cares for Selection 167

63 Selection Is a Political, Not a Scientific Concept 169

64 Three Myths in Science: Phlogiston in Chemistry, Ether in Physics and Selection in Biology 172

65 Definitions of Selection 175

66 Selection Is Not a Material Component that Can be Measured 177

67 The Distinction between Evolution and Darwinism 178

68 The Merits and Limitations of Darwinism 180

69 An Interpretation of Evolution Based on Physico-Chemical Processes 181

70 How the Chromosome Evades Selection 183

71 A Chaotic Chromosome Could Not Evade Selection But an Organized One Cannot Do Anything Else But Circumvent It 184

72 The Chromosome Does Not Need Selection to Conserve, Innovate and Explore 186

73 Repair Mechanisms Ensure the Maintenance of Order by Occurring at Different Molecular Levels - The Production of DNA, RNA and Protein Are Under Different Types of Control 187

74 Without DNA Repair No Human Would Exist 188

75 RNA Integrity Which is an Obligatory Condition for Normal Cell Function Is Maintained by Another Type of Repair 191

76 RNA Surveillance - An Additional Mechanism that Improves Safety by Creating Quality Control 193

77 "Molecular Chaperones" Are Proteins that Ensure that a Correct Molecular Assembly Will Predominate 197

78 How to Confuse Evolutionists - The Correction Can Function Backwards, Ancestral RNAs Can Restore the Original DNA Sequence 199

79 Innovation by Creation of New Gene Sequences 201

80 Exploration Is Achieved by Change of Genetic Pathways into New Functional Alleys 203

81 How Plasmids and Accessory Chromosomes Evade Selection 205

82 There Are Genes Which Are Able to "Cheat" Natural Selection 207

83 Sensing Mechanisms Are Used by the Chromosome to Adjust Gene Number and Switch on Genes That Improve Survival 208

84 The Multitude of Protective Mechanisms Devised by the Chromosome "Prohibit Natural Selection" 210

85 The Aggregation and Cell Adhesion of Dictyostelium Cells Follow the Same Chemical Solutions Employed by Embryos of Higher Organisms 212

86 The Egg Is a Storehouse of Information, Prepared by the Mother's Chromosomes - This Guarantees the Formation of an Identical Body Pattern 213

87 The Genetic Code Does Not Contain Direct Information to Produce a Coherent Organism - This Lies in the Hands of Other Molecular Processes that Charter Development by Building a Road Map 215

88 Minute Cell RNAs, that Previously were Despised, Turn Out to Coordinate Messenger RNAs 216

89 The Mechanisms Responsible for Coherence and Order Have Been Experimentally Demonstrated 218

90 The Drastic Reshapings that Occur in the Embryo Are Directed by Specific Proteins 220

91 Cells of One Group Change the Shape, Mitotic Rate and Pattern of Their Neighbors 225

92 The Chromosome Has Made Sure that the Organism Not Only Protects Itself from Inner Errors But Also from Outer Enemies 227

93 Cell Death Is as Programmed as Cell Life 229

94 Cells Can Commit Suicide but Amoebae Are Potentially Immortal 231

95 Both the Cell and the Chromosome Have an Unfailing Memory 232

96 When King Louis XV of France Was Going to be Married, the Princess in Question Could Give Birth to Rabbits 237

97 Why Should a Woman Not Produce a Mouse 239

References 242

Sources of Illustrations 249

Part V Who Cares for Magnetism 251

98 Magnetism and Electricity Are Two Manifestations of the Same Phenomenon 253

99 Bacteria, Bees, and Pigeons Orient According to the Magnetic Field 257

100 Cells Generate Electricity and Magnetism 260

101 When Magnets Are Divided into Minor Pieces, Each Separate Unit Continues to Behave as a Magnet, Acquiring New North and South Poles, But Small Magnets Can Also Rebuild Large Ones 262

102 When Fertilized Eggs Are Divided into Separate Cells, Each Cell Acquires the Properties of the Initial Egg Giving Rise to Separate Embryos 264

103 Separate Embryos Which Are Fused Result in a Single Normal Organism 267

104 When Chromosomes Are Divided into Minor Pieces, Each Separate Unit Continues to Behave as an Independent Chromosome by Incorporating or Creating New Telomeres and Centromeres 270

105 The Same Chromosomes May Disassemble and Reassemble Maintaining Their Genetic Properties - A Deer Species May be Formed with 35 or Only 3 Chromosomes 272

106 Ants May be Produced Using a Single Chromosome But Also 94 277

107 Plants of the Same Genus Have Been Formed with 4 or 36 Chromosomes 279

108 A Protozoan Can be Produced with 2 Chromosomes But Also with 500 280

109 In Birds and Plants a Series of Minute Chromosomes Are an Obligatory Component of Their Chromosome Set 281

110 The Separation of Chromosomes into Minor Units, as well as Their Reunion, Follows Well-Defined Solutions 283

111 The Properties Shared by Magnets and Chromosomes May Have Their Origin in the Polarization Already Present at the DNA Level 286

References 289

Sources of Illustrations 292

Part VI Biological Order Is the Product of Self-Assembly and Self-Assembly Is the Product of Atomic Recognition 295

112 How Clocks and Other Machines Differ from Cells 297

113 Definition of Self-Assembly and Its Basic Properties 299

114 The Mechanism Responsible for Self-Assembly Is Independent of External Information 302

115 The Self-Assembly of an Enzyme Is So Rapid that It Takes Less Time than the Synthesis of Its Component Polypeptides 305

116 No One Believed in the Self-Assembling Capacity of Viruses 306

117 The Bacterial Virus T4 Has a Programmed Pathway of Assembly that Has Been Described in the Utmost Detail 308

118 The Self-Assembly of Ribosomes Has Been Obtained in the Test Tube 311

119 Self-Assembly of the Chromosome Fiber and of Other Chromosome Structures Involved in Its Movement 313

120 Single Sponge Cells Have the Information to Produce a Whole Organism 315

121 A Hydra with Its Highly Complex Tissues can Self-Assemble from Dispersed Cells 316

122 Dictyostelium Is an Impressive Example of the Cell's Organizing Capacity 318

123 The Self-Assembly of Cells Leading to Tissue Formation Is Like the Precipitation of Crystals Out of a Solution 321

124 The Unfailing Power and Accuracy Inherent to Self-Assembly - The Nuclear Envelope Has Reassembled with Precision during an Untold Number of Cell Divisions 323

References 326

Sources of Illustrations 330

Part VII Where Did the Chromosome Come From and Where Is It Going 333

125 "Where Do We Come From? What Are We? Where Are We Going?" Paintings Which Represent the Origin of Life and of the Chromosome 335

126 The Origin of the Cell and of the Chromosome Are not Known 339

127 The Origins of the Chromosome Can Be Traced Back to the Periodicity of the Chemical Elements 342

128 Anomalies Exist at the Level of Chemical Periodicity, but the Alternatives Are Already Limited 346

129 The Unique Position in the Periodic Table of the Atoms Used in the Construction of the Cell and the Chromosome - So Far There Is No Evidence that Matter Suddenly Changed Its Laws When the Chromosome Emerged 348

130 Evolutionary Decisions Which Were Made Before DNA Arrived on the Scene 351

131 The Role of DNA in Heredity Is Not as Powerful as We Tend to Believe 356

132 The Whole Human Genome May Be Packed into a Single Chromosome 359

133 Where Is the Chromosome Going? 360

134 Physics Is Still an Underdeveloped Science, but It May Hold the Key to the Understanding of Chromosome Behavior 362

References 367

Sources of Illustrations 370

Simplified Glossary 373

Acknowledgements 378

Name Index 379

Subject Index 389