Conflicting Models for the Origin of Life

Stoyan Smoukov, PhD, is a Professor at Queen Mary University of London, leading the Active & Intelligent Materials (AIM) Lab (previously from 2012-2017 at the University of Cambridge). He has led pioneering research in multi-functional materials with the support of the prestigious European Research Council individual ERC grant. His focus on bottom-up design for inanimate materials has yielded novel artificial muscles, supercapacitors, multifunctional materials which can replace whole devices, the discovery of artificial morphogenesis, and combinatorial approaches to multi-functionality. Prof. Smoukov has published more than 95 journal papers, cited over 4000 times, with an H-index of 35. Joseph Seckbach, PhD, is a retired senior academician at The Hebrew University of Jerusalem, Israel. He earned his PhD from the University of Chicago and did a post-doctorate in the Division of Biology at Caltech, in Pasadena, CA. He served at Louisiana State University (LSU), Baton Rouge, LA, USA, as the first selected Chair for the Louisiana Sea Grant and Technology transfer. Professor Joseph Seckbach has edited over 40 scientific books and authored about 140 scientific articles. Richard Gordon, PhD, is a theoretical biologist who retired from the Department of Radiology, University of Manitoba in 2011. Presently he is at Gulf Specimen Marine Lab & Aquarium, Panacea, Florida. His interest in exobiology (now astrobiology) dates from 1960s undergraduate work on organic matter in the Orgueil meteorite with Edward Anders. He has published critical reviews of panspermia and the history of discoveries of life in meteorites, and with Stoyan Smoukov, worked on shaped droplets supporting the Archaea First Hypothesis.

Foreword, “Are There Men on the Moon?” by Winston S. Churchill xiii

Preface xix

Appendix to Preface by Richard Gordon and George Mikhailovsky xxv

Part I: Introduction to the Origin of Life Puzzle 1

1 Origin of Life: Conflicting Models for the Origin of Life 3
Sohan Jheeta and Elias Chatzitheodoridis

1.1 Introduction 3

1.2 Top-Down Approach—The Phylogenetic Tree of Life 6

1.3 Bottom-Up Approach—The Hypotheses 11

1.4 The Emergence of Chemolithoautotrophs and Photolithoautotrophs? 19

1.5 Viruses: The Fourth Domain of Life? 22

1.6 Where are We with the Origin of Life on Earth? 25

References 25

2 Characterizing Life: Four Dimensions and their Relevance to Origin of Life Research 33
Emily C. Parke

2.1 Introduction 33

2.2 The Debate About (Defining) Life 35

2.2.1 The Debate and the Meta-Debate 35

2.2.2 Defining Life is Only One Way to Address the Question “What is Life?” 37

2.3 Does Origin of Life Research Need a Characterization of Life? 39

2.4 Dimensions of Characterizing Life 41

2.4.1 Dimension 1: Dichotomy or Matter of Degree? 41

2.4.2 Dimension 2: Material or Functional? 43

2.4.3 Dimension 3: Individual or Collective? 44

2.4.4 Dimension 4: Minimal or Inclusive 46

2.4.5 Summary Discussion of the Dimensions 47

2.5 Conclusion 48

Acknowledgments 48

References 48

3 Emergence, Construction, or Unlikely? Navigating the Space of Questions Regarding Life’s Origins 53
Stuart Bartlett and Michael L. Wong

3.1 How Can We Approach the Origins Quest(ion)? 53

3.2 Avian Circularities 54

3.3 Assuming That 56

3.4 Unlikely 56

3.5 Construction 58

3.6 Emergence 60

References 63

Part II: Chemistry Approaches 65

4 The Origin of Metabolism and GADV Hypothesis on the Origin of Life 67
Kenji Ikehara

4.1 Introduction 68

4.2 [GADV]-Amino Acids and Protein 0th-Order Structure 70

4.3 Exploration of the Initial Metabolism: The Origin of Metabolism 71

4.3.1 From What Kind of Enzymatic Reactions Did the Metabolic System Originate? 71

4.3.2 What Kind of Organic Compounds Accumulated on the Primitive Earth 72

4.3.3 What Organic Compounds were Required for the First Life to Emerge? 74

4.4 From Reactions Using What Kind of Organic Compounds Did the Metabolism Originate? 75

4.4.1 Catalytic Reactions with What Kind of Organic Compounds Were Incorporated Into the Initial Metabolism? 76

4.4.2 Search for Metabolic Reactions Incorporated Into the Initial Metabolism 76

4.4.3 Syntheses of [GADV]-Amino Acids Leading to Produce [GADV]-Proteins/Peptides Were One of the Most Important Matters for the First Life 76

4.4.4 Nucleotide Synthetic Pathways were Integrated at the Second Phase in the Initial Metabolism 78

4.5 Discussion 80

4.5.1 Protein 0 th -Order Structure Was the Key for Solving the Origin of Metabolism 80

4.5.2 Validity of GPG-Three Compounds Hypothesis on the Origin of Metabolism 82

4.5.3 Establishment of the Metabolic System and the Emergence of Life 83

4.5.4 The Emergence of Life Viewed from the Origin of Metabolism 84

Acknowledgments 85

References 86

5 Chemical Automata at the Origins of Life 89
André Brack

5.1 Introduction 89

5.2 Theoretical Models 90

5.2.1 The Chemoton Model 90

5.2.2 Autopoiesis 90

5.2.3 Biotic Abstract Dual Automata 91

5.2.4 Automata and Diffusion-Controlled Reactions 91

5.2.5 Quasi-Species and Hypercycle 91

5.2.6 Computer Modeling 91

5.2.7 Two-Dimensional Automata 92

5.3 Experimental Approach 92

5.3.1 The Ingredients for Life 92

5.3.2 Capabilities Required for the Chemical Automata 93

5.3.2.1 Autonomy 93

5.3.2.2 Self-Ordering and Self-Organization 93

5.3.2.3 About Discriminating Aggregation 94

5.3.2.4 Autocatalysis and Competition 95

5.4 Conclusion 95

References 96

6 A Universal Chemical Constructor to Explore the Nature and Origin of Life 101
Geoffrey J. T. Cooper, Sara I. Walker and Leroy Cronin

6.1 Introduction 102

6.2 Digitization of Chemistry 109

6.3 Environmental Programming, Recursive Cycles, and Protocells 117

6.4 Measuring Complexity and Chemical Selection Engines 122

6.5 Constructing a Chemical Selection Engine 125

Acknowledgements 126

References 126

7 How to Make a Transmembrane Domain at the Origin of Life: A Possible Origin of Proteins 131
Richard Gordon and Natalie K. Gordon

7.1 Introduction 131

7.2 The Initial “Core” Amino Acids 132

7.3 The Thickness of Membranes of the First Vesicles 142

7.4 Carbon–Carbon Distances Perpendicular to a Membrane 144

7.5 The Thickness of Modern Membranes 144

7.6 A Prebiotic Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides 145

7.7 A Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides 148

7.8 RNA World with the Protein World 150

7.9 Conclusion 153

Acknowledgements 154

References 155

Part III: Physics Approaches 175

8 Patterns that Persist: Heritable Information in Stochastic Dynamics 177
Peter M. Tzelios and Kyle J. M. Bishop

8.1 Introduction 178

8.2 Markov Processes 181

8.2.1 Simple Examples of Markov Processes 181

8.2.2 Stochastic Dynamics 183

8.2.3 Master Equation 185

8.2.4 Dynamic Persistence 186

8.2.5 Coarse Graining 187

8.2.6 Entropy Production 188

8.3 Results 189

8.3.1 The Persistence Filter 189

8.4 Mechanisms of Persistence 190

8.5 Effects of Size N and Disequilibrium γ 192

8.6 Probability of Persistence 194

8.6.1 Continuity Constraint 195

8.6.2 Locality Constraint 196

8.6.3 New Strategies for Persistence 197

8.7 Measuring Persistence in Practice 198

8.7.1 Computable Information Density (CID) 198

8.7.2 Quantifying Persistence in Dynamic Assemblies of Colloidal Rollers 200

8.8 Conclusions 203

8.9 Methods 205

8.9.1 Coarse-Graining 205

8.10 Monte Carlo Optimization 206

8.11 Experiments on Ferromagnetic Rollers 206

8.12 A Persistence in Equilibrium Systems 207

Acknowledgements 209

References 209

9 When We Were Triangles: Shape in the Origin of Life via Abiotic, Shaped Droplets to Living, Polygonal Archaea During the Abiocene 213
Richard Gordon

9.1 Introduction 213

9.1.1 What Correlates with Archaea Shape? Nothing! 214

9.1.2 Archaea’s Place in the Tree of Life 219

9.1.3 The Discovery and Exploration of Shaped Droplets 222

9.1.4 Shaped Droplets as Protocells 223

9.1.5 Comparison of Shaped Droplets with Archaea 223

9.1.6 The S-Layer 224

9.1.7 The S-Layer as a Two-Dimensional Liquid with Fault Lines 224

9.1.8 The Analogy of the S-Layer to Bubble Rafts 229

9.1.9 Energy Minimization Model for the S-Layer in Polygonal Archaea 229

9.2 Discussion 236

9.3 Conclusion 240

Acknowledgements 240

References 240

10 Challenges and Perspectives of Robot Inventors that Autonomously Design, Build, and Test Physical Robots 263
Fumiya Iida, Toby Howison, Simon Hauser and Josie Hughes

10.1 Introduction 263

10.2 Physical Evolutionary-Developmental Robotics 264

10.2.1 Robotic Invention 265

10.2.2 Physical Morphology Adaptation 266

10.3 Falling Paper Design Experiments 269

10.3.1 Design–Behavior Mapping 270

10.3.2 More Variations of Paper Falling Patterns 272

10.3.3 Characterizing Falling Paper Behaviors 274

10.4 Evolutionary Dynamics of Collective Bernoulli Balloons 274

10.5 Discussions and Conclusions 276

Acknowledgments 277

References 277

Part IV: The Approach of Creating Life 279

11 Synthetic Cells: A Route Toward Assembling Life 281
Antoni Llopis-Lorente, N. Amy Yewdall, Alexander F. Mason, Loai K. E. A. Abdelmohsen and Jan C. M. van Hest

11.1 Compartmentalization: Putting Life in a Box 282

11.2 The Making of Cell-Sized Giant Liposomes 283

11.3 Coacervate-Based Synthetic Cells 285

11.4 Adaptivity and Functionality in Synthetic Cells 288

11.5 Synthetic Cell Information Processing and Communication 291

11.6 Intracellular Information Processing: Making Decisions with All the Noise 292

11.7 Extracellular Communication: the Art of Talking and Selective Listening 294

11.8 Conclusions 296

Acknowledgments 296

References 297

12 Origin of Life from a Maker’s Perspective–Focus on Protocellular Compartments in Bottom-Up Synthetic Biology 303
Ivan Ivanov, Stoyan K. Smoukov, Ehsan Nourafkan, Katharina Landfester and Petra Schwille

12.1 Introduction 303

12.2 Unifying the Plausible Protocells in Line with the Crowded Cell 309

12.3 Self-Sustained Cycles of Growth and Division 311

12.4 Transport and Energy Generation at the Interface 314

12.4.1 Energy and Complexity 315

12.4.2 Energy Compartmentation 316

12.5 Synergistic Effects Towards the Origin of Life 319

References 320

Part V: When and Where Did Life Start? 327

13 A Nuclear Geyser Origin of Life: Life Assembly Plant – Three-Step Model for the Emergence of the First Life on Earth and Cell Dynamics for the Coevolution of Life’s Functions 329
Shigenori Maruyama and Toshikazu Ebisuzaki

13.1 Introduction 330

13.2 Natural Nuclear Reactor 331

13.2.1 Principle of a Natural Nuclear Reactor 331

13.2.2 Natural Nuclear Reactor in Gabon 332

13.2.3 Radiation Chemistry to Produce Organics 333

13.2.4 Hadean Natural Nuclear Reactor 334

13.3 Nuclear Geyser Model as a Birthplace of Life on the Hadean Earth 336

13.4 Nine Requirements for the Birthplace of Life 338

13.5 Three-Step Model for the Emergence of the First Life on Hadean Earth 340

13.5.1 The Emergence of the First Proto-Life 341

13.5.1.1 Domain I: Inorganics 342

13.5.1.2 Domain II: From Inorganic to Organic 342

13.5.1.3 Domain III: Production of More Advanced BBL 343

13.5.1.4 Domain IV: Passage Connecting Geyser Main Room with the Surface and Fountain Flow 343

13.5.1.5 Domain V: Production of BBL in an Oxidizing Wet–Dry Surface Environment 345

13.5.1.6 Domain VI: Birthplace of the First Proto-Life 346

13.5.1.7 Utilization of Metallic Proteins 347

13.5.2 The Emergence of the Second Proto-Life 348

13.5.2.1 Drastic Environmental Change from Step 1 to Step 2 348

13.5.2.2 Biological Response from Step 1 to Step 2 349

13.5.3 The Emergence of the Third Proto-Life, Prokaryote 350

13.5.3.1 Drastic Environmental Changes from Step 2 to Step 3 350

13.5.3.2 Biological Response from Step 2 to Step 3 351

13.6 Concept of the Cell Dynamics: Life Assembly Plant 353

Acknowledgments 356

References 356

14 Comments on the Nuclear Geyser Origin of Life Proposal of the Authors S. Maruyama and T. Ebisuzaki and Interstellar Medium as a Possible Birthplace of Life 361
Jaroslav Jiřík

References 366

15 Nucleotide Photochemistry on the Early Earth 369
Whitaker, D. E., Colville, B.W.F. and Powner, M. W.

15.1 Introduction 369

15.2 Pyrimidine Photochemistry 372

15.2.1 Photohydrates 372

15.2.2 Photodimers 374

15.2.3 Glycosidic Bond Cleavage 376

15.2.4 Addition of Nucleophiles to C 2 378

15.3 Purine Photochemistry 380

15.4 Photochemistry of Noncanonical Nucleosides 382

15.4.1 Photochemical Anomerization of Cytidine Nucleosides 383

15.4.2 Thiobase Irradiation Products 387

15.4.3 Photochemical Decarboxylation of Orotidine 390

15.4.4 Photochemical Synthesis of AICN, a Possible Synthetic Precursor to the Purines 391

15.5 Considering More Complex Photochemical Systems 392

15.6 Concluding Remarks 395

References 395

16 Origins of Life on Exoplanets 407
Paul B. Rimmer

16.1 Introduction 407

16.2 How to Test Origins Hypotheses 408

16.3 Exoplanets as Laboratories 410

16.4 The Scenario 412

16.5 Initial Conditions 414

16.5.1 Chemical Initial Conditions 414

16.5.1.1 Hydrogen Cyanide 414

16.5.1.2 Sulfite and Sulfide 415

16.5.2 Physical Initial Conditions 415

16.6 Chances of Success 417

16.7 Relevance of the Outcome 420

16.8 Conclusions 420

Acknowledgements 421

References 421

17 The Fish Ladder Toy Model for a Thermodynamically at Equilibrium Origin of Life in a Lipid World in an Endoreic Lake 425
Richard Gordon, Shruti Raj Vansh Singh, Krishna Katyal and Natalie K. Gordon

17.1 The Fish Ladder Model for the Origin of Life 426

17.2 Could the Late Heavy Bombardment have Supplied Enough Amphiphiles? 435

17.3 How Many Uphill Steps to LUCA? 438

17.4 How Long Would the Origin of Life Take After the CVC is Achieved? 440

17.5 Conclusion 440

Acknowledgements 443

Appendix (Discussion with David Deamer) 443

References 447

Index 459