The emergence of life : from chemical origins to synthetic biology / Pier Luigi Luisi. -- Second edition -- Cambridge, United Kingdom ; New York : Cambridge University Press, c2016. – (58.111 /L953 /2nd ed.)

Contents

Acknowledgments

Introduction

Contents

Part I Approaches to the origin of life

1 Setting the stage

Introduction

1.1 The secular view on the origin of life

Side Box I.I Books on the origin of life

1.2 A few accepted facts

1.3 0parin's view, and its implications

1.4 Determinism and contingency in the origin of life

Conversation with Albert Eschenmoser

1.5 The question of creationism and intelligent design (ID)

1.6 SETI and the anthropic principle

1.7 Panspermia - and bringing in C. G. Jung

1.8 Only one start - or many?

Concluding remarks

2 The hardware

Introduction

2.1 What did we have 4 billion years ago?

Conversation with Sandra Pizzarello

2.2 Molecules from hydrothermal vents

2.3 The chemistry of life. From Oparin to Miller - and beyond

Conversation with David Deamer

Conversation with Errs Szathmrry

2.4 Prebiotic nitrogen bases

2.5 Sugars

2.6 Redox reactions

2.7 The Fischer-Tropsch reaction

2.8 The N-carboxy-anhydride condensation

Concluding remarks

3 Ascending the ramp of complexity

Introduction

3.1 The creativity of contingency

3.2 The primacy of structure

3.3 Thermodynamic and kinetic control

3.4 Self-replication - and the concentration threshold

3.5 Ordered macromolecular sequences

3.6 The question of homochirality

Concluding remarks

4 Experimental approaches to the origin of life

Introduction

4.1 The prebiotic RNA world

Conversation with Ada Yonath

4.2 The ribocell

Conversation with Gerald Joyce

4.3 The compartmentalistic approach

4.4 Primordial cells without DNA?

4.5 The phenomenon of spontaneous overcrowding

4.6 The "prebiotic metabolism" approach

Conversation with Doron Lancet

Concluding remarks

5 Origin of life from ground zero

Introduction

5.1 Prebiotic amino acids and peptides

5.2 Peptides with catalytic power

5.3 Proteins with a reduced alphabet of amino acids

5.4 How to make proteins by prebiotic means?

5.5 About prebiotic vesicles

5.6 Proposals of research projects from ground zero

Concluding remarks

Questions for the reader

Part II What is life? The bio-logics of cellular life

6 Autopoiesis - the invariant property

Introduction

6.1 The visit of the Green Man

6.2 Introducing autopoiesis

6.3 Short historical background on autopoiesls

6.4 Basic autopoiesis

6.5 Criteria of autopoiesis

Conversation with Amy Cohen Varela

6.6 Zooming into the core of autopoiesis

Side Box 6.1 Autopoiesis: three research directions for future developments, by Luisa Damiano

Conversation with Evan Thompson

6.7 What autopoiesis does not include

6.8 Chemical autopoiesis: the case for self-reproduction of micelles and vesicles

6.9 Chemical autopoiesis: a case for homeostasis

6.10 Second order autopoietic structures

6.11 Social autopoiesis

6.12 Autopoiesis and the chemoton: comparison with the views of Tibor Ganti

Concluding remarks

7 Cognition

Introduction

Conversation with Humberto Maturana

7.1 The notion of cognition

7.2 The co-emergence between the living and the environment

7.3 The link with classic biochemistry

7.4 About epistemology in autopoiesis

7.50ntogeny, evolution, information: the view from within

Conversation with Denis Noble

7.6 What is death?

Concluding remarks

Questions for the reader

Part III Order and organization in biological systems

8  Self-organization

Introduction

8.1 About the term self

8.2 Self-organization of simpler molecular systems

8.3 Self-organization and autocatalysis

8.4 Polymerization

8.5 Self-organization and kinetic control

8.6 Self-organization and breaking of symmetry

8.7 Complex proteic systems

8.8 Self-organization of ribosomes

8.9 Self-organization in viruses

8.10 Swarm intelligence

8.11 Can living cells be reconstituted in vitro?

Side Box 8.1 Phenomena of self-organization in Hydra, by Giorgio Venturini

8.12 Touching on the "divine proportion": Φ and the golden mean

8.13 Out-of-equilibrium self-organization

Concluding remarks

9 The notion of emergence

Introduction

9.1 0ntic and epistemic

9.2 A few simple examples of emergence

9.3 Emergence and reductionism

9.4 Deducibility and predictability

9.5 Downward causation

9.6 Emergence and dynamic systems

Side Box 9.1 - The sciences of complexity, by Stuart A. Kauffman

9.7 Life as an emergent property

9.8 Self-organization and finality

Concluding remarks

10 Self-replication and self-reproduction

Introduction

10.1 Self-replication and nonlinearity

10.2 Self-replicating, enzyme-free chemical systems

10.3 One more step towards complexity

10.4 Self-reproducing micelles

10.5 Self-reproducing vesicles

10.6 Nanobacteria?

Concluding remarks

Questions for the .reader

Part IV The world of vesicles

11 The various types of surfactant aggregates

Introduction

11.1  General properties of surfactant aggregates

11.2  Aqueous micelles

11.3  Reverse micelles

11.4  Entrapment of biopolymers in reverse micelles

11.5  Water-in-oil microemulsions

11.6  Cubic phases

11.7  Size and structural properties of vesicles

11.8  Local versus overall concentration

11.9  Prebiotic vesicle-forming surfactants

11.10 Giant vesicles

Concluding remarks

12 Vesicle reactivity and transformations

Introduction

12.1 Growth and division of vesicles: some geometrical relationships

12.2 Experimental studies on the growth of vesicles

12.3 The matrix effect

12.4 Fusion of vesicles

12.5 Size competition of vesicles - and interaction with RNA

Concluding remarks

13 Biochemistry and molecular biology in vesicles

Introduction

13.1 The entrapment of solutes in vesicles

13.2 On the surface of liposomes

13.3 The road map to the minimal cell: complex biochemical reactions in vesicles

Concluding remarks

Questions - and research proposals - for the reader

Part V Towards the synthetic biology of minimal cells

14 A panoramic view of synthetic biology

Introduction

14.1 Main strategies and perspectives of synthetic biology

Conversation with Paul Freemont

Conversation with Sarah Lau

14.2 The case of engineering SB

14.3 A teaching phenomenon: iGEM

Side Box 14.1 Recent iGEM activities

14.4 More on epistemology

14.5 Chemical SB

14.6 The never born proteins

14.7 The never born RNA

Concluding remarks

15 The minimal cell

Introduction

Conversation with Harold Morowitz

15.1 The notion of the minimal cell

15.2 The minimal genome

15.3 The road map to the minimal cell: protein expression in vesicles

15.4 A confederacy of protocells

15.5 About the statistics of entrapment

15.6 A story of spontaneous overcrowding

15.7 The origin of metabolism?

15.8 And (why not?) the origin of life?

Concluding remarks

Questions - and research proposals - for the reader

As a way of conclusion

Appendix The open questions about the origin of life

Selection of the open questions presented in the OQOL Workshop of Erice - 2006

Selection of the open questions presented in the OQOL Workshop of San Sebastian - 2009

Selection of the open questions presented in the OQOL Workshop of Leicester - 2012

Selection of the open questions presented in the OQOL Workshop of Nara- 2014

References

Names index

Subject index