Life Sciences, Information Sciences

Developed from presentations given at the Cerisy SVSI (Sciences de la vie, sciences de l'information) conference held in 2016, this book presents a broad overview of thought and research at the intersection of life sciences and information sciences. The contributors to this edited volume explore life and information on an equal footing, with each considered as crucial to the other. In the first part of the book, the relation of life and information in the functioning of genes, at both the phylogenetic and ontogenetic levels, is articulated and the common understanding of DNA as code is problematized from a range of perspectives. The second part of the book homes in on the algorithmic nature of information, questioning the fit between life and automaton and the accompanying division between individualization and invariance. Consisting of both philosophical speculation and ethological research, the explorations in this book are a timely intervention into prevailing understandings of the relation between information and life.

Autorentext

Thierry Gaudin is an engineer at MINES ParisTech and holds a doctorate in Information Sciences and Communication from Paris Nanterre University. He is a widely renowned expert in innovation policy and has worked with the OECD, European Commission and the World Bank.

Dominique Lacroix is a web publisher and photographer. After studying Classics at the University of Nice in France, she acquired diverse experience in multimedia. She is a co-founder, with Thierry Gaudin, of the 2100 Foundation.

Marie-Christine Maurel is Professor at Pierre and Marie Curie University (UPMC) and the Muséum National d'Histoire Naturelle in Paris. Her research focuses on the informational and catalytic properties of DNA and RNA and their role in the origin of life.

Jean-Charles Pomerol is a specialist in Decision Support Systems and former project leader for information technology in the Engineering Sciences Department at the CNRS. He was formerly in charge of the Artificial Intelligence laboratory at UPMC, Paris, as well as being the President of UPMC between 2006 and 2011.

Inhalt

Preface xv

Selection of Publications xix

Introduction xxiii

Part 1. From Gene to Species: Variability, Randomness and Stability 1

**Chapter 1. The Emergence of Life: Some Notes on the Origin of Biological Information 3
**Antonio LAZCANO

1.1. Acknowledgments 12

1.2. Bibliography 12

**Chapter 2. Fluctuating RNA 17
**Giuseppe ZACCAI, Marie-Christine MAUREL and Ada YONATH

2.1. The ribosome 17

2.2. Ribosome dynamics 18

2.3. Primitive RNA, ribozymes and viroids 20

2.4. The proto-ribosome 21

2.5. Bibliography 22

**Chapter 3. Artificial Darwinian Evolution of Nucleic Acids 23
**Frédéric DUCONGÉ

3.1. Refresher on Darwin's theory of evolution 23

3.2. The molecular mechanisms of evolution 24

3.3. Molecular evolution external to the being 25

3.4. Imagery of molecular evolution 26

3.5. Conclusion 27

3.6. Acknowledgments 27

3.7. Bibliography 27

**Chapter 4. Information and Epigenetics 29
**András PÁLDI

4.1. Bibliography 34

**Chapter 5. Molecular Forces and Motion in the Transmission of Information in Biology 37
**Giuseppe ZACCAI

5.1. The dynamicsfunction hypothesis 37

5.2. From thermodynamics to molecular forces 38

5.3. Like the devil, biology is in the details 39

5.4. The guitar in the river: theoretical MD 40

5.5. Experimental MD 40

5.6. Measuring average MD in whole cells 41

5.7. Dynamics response to stress 41

5.8. Conclusion: evolution is obliged to select dynamics 42

5.9. Bibliography 42

**Chapter 6. Decline and Contingency, Bases of Biological Evolution 45
**Bernard DUJON

6.1. Introduction 45

6.2. Too many genes in the genomes 46

6.3. Parasitism and symbiosis 48

6.4. Asexual eukaryotes 49

6.5. Yeasts 50

6.6. Conclusion 52

6.7. Bibliography 52

**Chapter 7. Conservation, Co-evolution and Dynamics: From Sequence to Function 55
**Alessandra CARBONE

7.1. Introduction 55

7.2. Reverse engineering: from the protein described in a single dimension to its 3D properties 56

7.3. Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized 57

7.3.1. Proteins are dynamic objects 57

7.3.2. Proteins have a history 57

7.3.3. Some proteins share the same evolutionary history 57

7.4. Chance and selection govern the generation of observed sequences 58

7.5. Conservation and interaction sites of proteins 59

7.6. Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein 60

7.7. Co-evolution used to reconstruct proteinprotein interaction networks in viruses 61

7.8. Molecular modeling of several partners used to reconstruct proteinprotein interaction networks for prokaryotic and eukaryotic organisms 63

7.9. Dynamics and function 64

7.10. Conclusions 64

7.11. Acknowledgments 65

7.12. Bibliography 65

**Chapter 8. Localization of the Morphodynamic Information in Amniote Formation 69
**Vincent FLEURY

8.1. Introduction 69

8.2. Schematic view of an amniote 70

8.3. Mechanism of amniote formation 74

8.4. Additional features 77

8.5. Discussion and conclusion 78

8.6. Bibliography 79

Chapter 9. From the Century of the Gene to that of the Organism: Introduction to New Theoretical **Perspectives 81
**Maël MONTÉVIL, Giuseppe LONGO and Ana SOTO

9.1. Introduction 81

9.2. Philosophical positions 87

9.3. From the inert to the living 87 <p&g...