Praise of Chromosome Folly: Confessions of an Untamed Molecular Structure (Leverhulme Lectures)

When examined carefully at the molecular level, the chromosome turns out to have created its own private world full of tricks, back door exits and novel solutions. This folly makes it an untamed innovator. Geneticists have been bewildered for decades. What kind of creature was actually the chromosome? Was it plastic, changing by innumerous rearrangements and mutations all the time; or was it a rigid structure which has preserved its basic organisation and functions since the dawn of the cell? It is this conflicting state that seems to be at the base of its folly . Perplexed by this behavior, cell biologists have called it a junkyard and even the ultimate parasite. Moreover, the chromosome has been regarded as a passive cell organelle prone to random mutations and subjected to the mercy of selection. The latest molecular information discloses a radically different picture in which the chromosome appears as an independent molecular structure that follows its own path. It does not obey gravity, randomness, selection or magnetism. By anchoring the chromosome s contradictory behavior on molecular processes directed by atomic self-assembly, Lima-de-Faria expands a novel view of the chromosome with unexpected implications for genetics, evolution and physics. This timely book contains the latest information on the molecular organization of the chromosome. The information is original and is presented in an unorthodox way, while carefully chosen elucidating and attractive figures serve to add clarity to the subject treated. Thus, the book will add greatly to the general debate on the evolution of living organisms, and will be of particular interest to those in the biotechnological field. Contents: To the Reader; Introductory Note; Part I The Source of "Folly" and the Reason for Confessions; Part II Who Cares for Gravity; Part III Who Cares for Randomness; Part IV Who Cares for Selection; Part V Who Cares for Magnetism; Part VI Biological Order Is the Product of Self-Assembly and Self-Assembly Is the Product of Atomic Recognition; Part VII Where Did the Chromosome Come From and Where Is It Going; References; Sources of Illustrations; Simplified Glossary; Acknowledgements; Index. Contents......Page 8 To the Reader......Page 6 References......Page 7 Introductory Note......Page 18 Part I The Source of “Folly” and the Reason for Confessions......Page 20 1. I am an Inconspicuous and Unattractive Creature Painted with Lipstick......Page 22 2. They Say That I Resemble a Sausage......Page 26 3. The Cell Is My Castle and Prison But I May Swim and Dance like an Odalisque in a Harem......Page 27 4. The Striptease Show — How I Dress and Undress at Every Cell Division......Page 30 5. I Have Created My Own Private World Full of Tricks, Back Door Exits and Novel Solutions — I am an Untamed Innovator......Page 35 6. My Origins Were Humble — The Antithetical Nature of Matter Left a Mark on My Construction......Page 38 7. My Split Personality — The Source of “Folly”......Page 41 8. The Reason for Confessions......Page 45 9. I Have Been Abused and Covered With Insults......Page 47 10. The Wisdom of the Foolish......Page 50 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......Page 55 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......Page 58 13. In the Last 20 Years the Number of Human Genes was Reduced from 200,000 to 32,000, and This Figure Remains Uncertain......Page 60 14. The Models of Chromosomes Have Varied Drastically with Time......Page 62 References......Page 67 Sources of Illustrations......Page 70 Part II Who Cares for Gravity......Page 72 15. The Chromosome in Its Organization and Activity Follows Its Own Path — It Does Not Obey Gravity, Randomness, Selection or Magnetism......Page 74 16. Definition of Gravity — Newton’s Laws Are Good for Planets and Apples......Page 76 17. What Is a Force — The Four Fundamental Forces......Page 78 18. Newton’s Laws Do Not Apply in Quantum Mechanics......Page 80 19. Not All Bodies Fall When Unsupported......Page 82 20. The Ascent of Sap in Trees-Another Unexplained Phenomenon......Page 83 21. An Unknown Process Decides Which Cells Are Going to Grow in the Direction of Gravity and Which Are Going to Counteract It......Page 86 22. Physicists Construct Antigravity Devices that Oblige Frogs and Plants to Float......Page 90 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......Page 92 24. Levitation in Metals — What Was Impossible Became Possible......Page 94 25. Animals, like Plants, Have Created Devices that Counteract Gravity......Page 96 26. In Giraffes the Distance between the Heart and the Head Is Over Two Meters......Page 98 27. No Chromosome Obeys Newton’s Laws — In Their Movements Chromosomes Bypass Gravity......Page 101 28. Chromosomes Move in All Directions of the Mariner’s Compass......Page 103 29. It Is the Programmed Pattern of the Organism that Decides the Direction of Movement......Page 105 30. The Devices Used by the Chromosome Which Result in Particular Movements......Page 106 31. Chromosomes Move Inside the Nucleus, like Goldfish in an Aquarium, without the Use of Spindle Fibers......Page 107 32. The Chromosome’s Autonomy Takes Many Forms — The Chromosome Ends May Take Over the Function of Active Mobility on the Spindle......Page 110 33. Chromosomes Inherited from the Father May Be Sent to a Different Compartment than Those Inherited from the Mother......Page 112 34. How to Move Equally Well without Guiding Asters and Centrosomes......Page 113 35. DNA Replication Already Disregarded Gravity......Page 114 36. Mineral Crystallization Disposes Also of Gravity and Imposes Massive Copying......Page 116 37. The Egg Contents Rotate and the Cells Move within the Embryo Independently of Gravity......Page 118 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......Page 120 39. It Comes as a Revelation that the Chromosome Does Not Need Strong Magnets and Extreme Low Temperatures to Evade Gravity......Page 123 40. Goddesses Do Not Obey Earthly Laws......Page 124 References......Page 126 Sources of Illustrations......Page 129 Part III Who Cares for Randomness......Page 132 41. Randomness Was Originally Foreign to Science......Page 134 42. Randomness Is an Economic Concept Introduced into 17th Century Science......Page 136 43. Randomness Is Synonymous with Ignorance — “The Folly of Probability”......Page 141 44. It Took the Last 20 Years to Demonstrate that What Were Considered Chromosome Accidents Were Ordered Events......Page 143 45. The Transmission of Hereditary Traits — From Confusion to the Ability to Predict......Page 144 46. Mutation Has Been the Main Example of a Random Event......Page 146 47. How the Prevailing Fashion Led to Fashionable Results, or How Random Mutations Turned Out to be Non-Random......Page 147 48. Rearrangements that Were Random Events Turned Out to be Directed by Mobile Elements......Page 150 49. The Repeat Sequences of the Human Genome Are, Instead of Being “Junk,” a Treasure Trove of Information......Page 152 50. Genes with Similar Functions Could Not be Located Nearby — Random Mutations and Rearrangements Would Disrupt Any Possible Order......Page 153 51. The Gene Turns Out to Consist of a Highly Ordered Procession of DNA Stations Locked by Well Defined Starting and Finishing Sites......Page 156 52. The Gene Is Never Alone......Page 160 53. The Periodic Packaging of DNA Along Chromosomes Has Turned Out to be Predictable......Page 161 54. In Cell Division the Proper Movement of Chromosomes Is Maintained by Correction of Improper Attachment to the Moving Apparatus......Page 162 55. Cells Sense and Stop Uncontrolled Divisions Released by Cancer Stimuli. Moreover, RNAs Are Able to Silence Genes......Page 164 56. Prevention of Failing of Chromosome Pairing and of Recombination......Page 167 57. Brownian Motion — The Trap of the Physicist and Biologist......Page 169 58. The Cell Was Seen as a Pea Soup, But Now Most of Its Molecules Are Known to Have an Address......Page 171 59. “The Genetic Code Is Certainly Not Random”......Page 174 60. Noise Is Disorder — Music Is Order and Unity......Page 175 61. The Distinction between Genetic Noise and Genetic Music......Page 176 62. “Errors” Are Not of All Possible Kinds......Page 178 References......Page 179 Sources of Illustrations......Page 183 Part IV Who Cares for Selection......Page 186 63. Selection Is a Political, Not a Scientfic Concept......Page 188 64. Three Myths in Science: Phlogiston in Chemistry, Ether in Physics and Selection in Biology......Page 191 65. Definitions of Selection......Page 194 66. Selection Is Not a Material Component that Can be Measured......Page 196 67. The Distinction between Evolution and Darwinism......Page 197 68. The Merits and Limitations of Darwinism......Page 199 69. An Interpretation of Evolution Based on Physico-Chemical Processes......Page 200 70. How the Chromosome Evades Selection......Page 202 71. A Chaotic Chromosome Could Not Evade Selection But an Organized One Cannot Do Anything Else But Circumvent It......Page 203 72. The Chromosome Does Not Need Selection to Conserve, Innovate and Explore......Page 205 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......Page 206 74. Without DNA Repair No Human Would Exist......Page 207 75. RNA Integrity Which is an Obligatory Condition for Normal Cell Function Is Maintained by Another Type of Repair......Page 210 76. RNA Surveillance — An Additional Mechanism that Improves Safety by Creating Quality Control......Page 212 77. “Molecular Chaperones” Are Proteins that Ensure that a Correct Molecular Assembly Will Predominate......Page 216 78. How to Confuse Evolutionists — The Correction Can Function Backwards, Ancestral RNAs Can Restore the Original DNA Sequence......Page 218 79. Innovation by Creation of New Gene Sequences......Page 220 80. Exploration Is Achieved by Change of Genetic Pathways into New Functional Alleys......Page 222 81. How Plasmids and Accessory Chromosomes Evade Selection......Page 224 82. There Are Genes Which Are Able to “Cheat” Natural Selection......Page 226 83. Sensing Mechanisms Are Used by the Chromosome to Adjust Gene Number and Switch on Genes That Improve Survival......Page 227 84. The Multitude of Protective Mechanisms Devised by the Chromosome “Prohibit Natural Selection”......Page 229 85. The Aggregation and Cell Adhesion of Dictyostelium Cells Follow the Same Chemical Solutions Employed by Embryos of Higher Organisms......Page 231 86. The Egg Is a Storehouse of Information, Prepared by the Mother’s Chromosomes — This Guarantees the Formation of an Identical Body Pattern......Page 232 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......Page 234 88. Minute Cell RNAs, that Previously were Despised, Turn Out to Coordinate Messenger RNAs......Page 235 89. The Mechanisms Responsible for Coherence and Order Have Been Experimentally Demonstrated......Page 237 90. The Drastic Reshapings that Occur in the Embryo Are Directed by Specific Proteins......Page 239 91. Cells of One Group Change the Shape, Mitotic Rate and Pattern of Their Neighbors......Page 244 92. The Chromosome Has Made Sure that the Organism Not Only Protects Itself from Inner Errors But Also from Outer Enemies......Page 246 93. Cell Death Is as Programmed as Cell Life......Page 248 94. Cells Can Commit Suicide but Amoebae Are Potentially Immortal......Page 250 95. Both the Cell and the Chromosome Have an Unfailing Memory......Page 251 96. When King Louis XV of France Was Going to be Married, the Princess in Question Could Give Birth to Rabbits......Page 256 97. Why Should a Woman Not Produce a Mouse......Page 258 References......Page 261 Sources of Illustrations......Page 268 Part V Who Cares for Magnetism......Page 270 98. Magnetism and Electricity Are Two Manifestations of the Same Phenomenon......Page 272 99. Bacteria, Bees, and Pigeons Orient According to the Magnetic Field......Page 276 100. Cells Generate Electricity and Magnetism......Page 279 101. 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......Page 281 102. When Fertilized Eggs Are Divided into Separate Cells, Each Cell Acquires the Properties of the Initial Egg Giving Rise to Separate Embryos......Page 283 103. Separate Embryos Which Are Fused Result in a Single Normal Organism......Page 286 104. 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......Page 289 105. The Same Chromosomes May Disassemble and Reassemble Maintaining Their Genetic Properties — A Deer Species May be Formed with 35 or Only 3 Chromosomes......Page 291 106. Ants May be Produced Using a Single Chromosome But Also 94......Page 296 107. Plants of the Same Genus Have Been Formed with 4 or 36 Chromosomes......Page 298 108. A Protozoan Can be Produced with 2 Chromosomes But Also with 500......Page 299 109. In Birds and Plants a Series of Minute Chromosomes Are an Obligatory Component of Their Chromosome Set......Page 300 110. The Separation of Chromosomes into Minor Units, as well as Their Reunion, Follows Well-Defined Solutions......Page 302 111. The Properties Shared by Magnets and Chromosomes May Have Their Origin in the Polarization Already Present at the DNA Level......Page 305 References......Page 308 Sources of Illustrations......Page 311 Part VI Biological Order Is the Product of Self-Assembly and Self-Assembly Is the Product of Atomic Recognition......Page 314 112. How Clocks and Other Machines Differ from Cells......Page 316 113. Definition of Self-Assembly and Its Basic Properties......Page 318 114. The Mechanism Responsible for Self-Assembly Is Independent of External Information......Page 321 115. The Self-Assembly of an Enzyme Is So Rapid that It Takes Less Time than the Synthesis of Its Component Polypeptides......Page 324 116. No One Believed in the Self-Assembling Capacity of Viruses......Page 325 117. The Bacterial Virus T4 Has a Programmed Pathway of Assembly that Has Been Described in the Utmost Detail......Page 327 118. The Self-Assembly of Ribosomes Has Been Obtained in the Test Tube......Page 330 119. Self-Assembly of the Chromosome Fiber and of Other Chromosome Structures Involved in Its Movement......Page 332 120. Single Sponge Cells Have the Information to Produce a Whole Organism......Page 334 121. A Hydra with Its Highly Complex Tissues can Self-Assemble from Dispersed Cells......Page 335 122. Dictyostelium Is an Impressive Example of the Cell’s Organizing Capacity......Page 337 123. The Self-Assembly of Cells Leading to Tissue Formation Is Like the Precipitation of Crystals Out of a Solution......Page 340 124. The Unfailing Power and Accuracy Inherent to Self-Assembly — The Nuclear Envelope Has Reassembled with Precision during an Untold Number of Cell Divisions......Page 342 References......Page 345 Sources of Illustrations......Page 349 Part VII Where Did the Chromosome Come From and Where Is It Going......Page 352 125. “Where Do We Come From? What Are We? Where Are We Going?” Paintings Which Represent the Origin of Life and of the Chromosome......Page 354 126. The Origin of the Cell and of the Chromosome Are not Known......Page 358 127. The Origins of the Chromosome Can Be Traced Back to the Periodicity of the Chemical Elements......Page 361 128. Anomalies Exist at the Level of Chemical Periodicity, but the Alternatives Are Already Limited......Page 365 129. 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......Page 367 130. Evolutionary Decisions Which Were Made Before DNA Arrived on the Scene......Page 370 131. The Role of DNA in Heredity Is Not as Powerful as We Tend to Believe......Page 375 132. The Whole Human Genome May Be Packed into a Single Chromosome......Page 378 133. Where Is the Chromosome Going?......Page 379 134. Physics Is Still an Underdeveloped Science, but It May Hold the Key to the Understanding of Chromosome Behavior......Page 381 References......Page 386 Sources of Illustrations......Page 389 Simplified Glossary......Page 392 Acknowledgements......Page 397 Name Index......Page 398 Subject Index......Page 408 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 Enquiring Minds To Have Harbored Doubts About The Correctness Of Prevailing Monolithic Ideas And Have Been Looking For Alternative Explanations. By Anchoring The Chromosome's Contradictory Behavior On Molecular Processes Directed By Atomic Self-assembly, Antonio Lima-de-faria Expands A Novel View Of The Chromosome With Unexpected Implications For Genetics, Evolution And Physics.--jacket. To The Reader -- Introductory Note -- Part I The Source Of Folly And The Reason For Confessions -- Part Ii Who Cares For Gravity -- Part Iii Who Cares For Randomness -- Part Iv Who Cares For Selection -- Part V Who Cares For Magnetism -- Part Vi Biological Order Is The Product Of Self-assembly And Self-assembly Is The Product Of Atomic Recognition -- Part Vii Where Did The Chromosome Come From And Where Is It Going -- References -- Sources Of Illustrations -- Simplified Glossary -- Acknowledgements -- Index. Antonio Lima-de-faria. Includes Bibliographical References (p. 367-369) And Index.