Part 1: Emergence and Complexity 1: Foreword Preface Acknowledgments

June 26, 2008
11:1
World Scientific Book - 9in x 6in
quantum
Contents
Foreword
vii
Preface
xiii
Acknowledgments
xvii
Part 1: Emergence and Complexity
1. A Quantum Origin of Life?
Paul C. W. Davies
1.1. Chemistry and Information . . . . . . . . . . . . . . .
1.2. Q-life . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3. The Problem of Decoherence . . . . . . . . . . . . . .
1.4. Life as the Solution of a Quantum Search Algorithm
1.5. Quantum Choreography . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Quantum Mechanics and Emergence
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19
Seth Lloyd
2.1. Bits . . . . . . . . . . . . . .
2.2. Coin Flips . . . . . . . . . . .
2.3. The Computational Universe
2.4. Generating Complexity . . .
2.5. A Human Perspective . . . .
2.6. A Quantum Perspective . . .
References . . . . . . . . . . . . . .
xix
QUANTUM ASPECTS OF LIFE
Imperial College Press
http://www.worldscibooks.com/physics/p581.html
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quantum
Quantum Aspects of Life
xx
Part 2: Quantum Mechanisms in Biology
31
3. Quantum Coherence and the Search for the First Replicator
33
Jim Al-Khalili and Johnjoe McFadden

3.1.
3.2.
3.3.
3.4.
3.5.
3.6.
When did Life Start? . . . . . . . . . . . . . . . .

Where did Life Start? . . . . . . . . . . . . . . .
Where did the Precursors Come From? . . . . . .
What was the Nature of the First Self-replicator?
The RNA World Hypothesis . . . . . . . . . . . .
A Quantum Mechanical Origin of Life . . . . . .
3.6.1. The dynamic combinatorial library . . .
3.6.2. The two-potential model . . . . . . . . .
3.6.3. Decoherence . . . . . . . . . . . . . . . .
3.6.4. Replication as measurement . . . . . . .
3.6.5. Avoiding decoherence . . . . . . . . . . .
3.7. Summary . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . .
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4. Ultrafast Quantum Dynamics in Photosynthesis
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47
47
51
Alexandra Olaya Castro, Francesca Fassioli Olsen,

Chiu Fan Lee, and Neil F. Johnson
4.1.
4.2.
4.3.
Introduction . . . . . . . . . . . . . . . . . . . . .
A Coherent Photosynthetic Unit (CPSU) . . . .
Toy Model: Interacting Qubits with a Spin-star
Conguration . . . . . . . . . . . . . . . . . . . .
4.4. A More Detailed Model: Photosynthetic Unit of
Purple Bacteria . . . . . . . . . . . . . . . . . . .
4.5. Experimental Considerations . . . . . . . . . . .
4.6. Outlook . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . .
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5. Modelling Quantum Decoherence in Biomolecules
71
Jacques Bothma, Joel Gilmore, and Ross H. McKenzie

5.1.
5.2.
5.3.
Introduction . . . . . . . . . . .
Time and Energy Scales . . . .
Models for Quantum Baths and
5.3.1. The spin-boson model .

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Decoherence
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5.3.2. Caldeira-Leggett Hamiltonian . . . . . . .

5.3.3. The spectral density . . . . . . . . . . . . .
5.4. The Spectral Density for the Dierent Continuum
Models of the Environment . . . . . . . . . . . . .
5.5. Obtaining the Spectral Density from Experimental
Data . . . . . . . . . . . . . . . . . . . . . . . . . .
5.6. Analytical Solution for the Time Evolution of the
Density Matrix . . . . . . . . . . . . . . . . . . . .
5.7. Nuclear Quantum Tunnelling in Enzymes and the
Crossover Temperature . . . . . . . . . . . . . . . .
5.8. Summary . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . .
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87
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Part 3: The Biological Evidence
95
6. Molecular Evolution: A Role for Quantum Mechanics

in the Dynamics of Molecular Machines that Read and
Write DNA
97
Anita Goel
6.1.
6.2.
6.3.
Introduction . . . . . . . . . . . . . . . . . . . .
Background . . . . . . . . . . . . . . . . . . . .
Approach . . . . . . . . . . . . . . . . . . . . .
6.3.1. The information processing power of a
molecular motor . . . . . . . . . . . . .
6.3.2. Estimation of decoherence times of the
motor-DNA complex . . . . . . . . . .
6.3.3. Implications and discussion . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . .
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7. Memory Depends on the Cytoskeleton, but is it Quantum?
109
Andreas Mershin and Dimitri V. Nanopoulos

7.1.
7.2.
7.3.
7.4.
Introduction . . . . . . . . . . . . . . . . . . . . .
Motivation behind Connecting Quantum Physics
to the Brain . . . . . . . . . . . . . . . . . . . . .
Three Scales of Testing for Quantum Phenomena
in Consciousness . . . . . . . . . . . . . . . . . .
Testing the QCI at the 10 nm10 m Scale . . .

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quantum
xxii
7.5.
Testing for Quantum Eects in Biological Matter

Amplied from the 0.1 nm to the 10 nm Scale and
Beyond . . . . . . . . . . . . . . . . . . . . . . . .
7.6. Summary and Conclusions . . . . . . . . . . . . . .
7.7. Outlook . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . .
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8. Quantum Metabolism and Allometric Scaling Relations

in Biology
117
120
121
121
127
Lloyd Demetrius
8.1.
8.2.
Introduction . . . . . . . . . . . . . . . . . . . .
Quantum Metabolism: Historical Development
8.2.1. Quantization of radiation oscillators . .
8.2.2. Quantization of material oscillators . .
8.2.3. Quantization of molecular oscillators .
8.2.4. Material versus molecular oscillators . .
8.3. Metabolic Energy and Cycle Time . . . . . . .
8.3.1. The mean energy . . . . . . . . . . . .
8.3.2. The total metabolic energy . . . . . . .
8.4. The Scaling Relations . . . . . . . . . . . . . .
8.4.1. Metabolic rate and cell size . . . . . . .
8.4.2. Metabolic rate and body mass . . . . .
8.5. Empirical Considerations . . . . . . . . . . . .
8.5.1. Scaling exponents . . . . . . . . . . . .
8.5.2. The proportionality constant . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . .
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9. Spectroscopy of the Genetic Code
127
131
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135
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137
138
140
140
140
141
142
144
144
147
Jim D. Bashford and Peter D. Jarvis

9.1.
9.2.
Background: Systematics of the Genetic Code . . . . .

9.1.1. RNA translation . . . . . . . . . . . . . . . . .
9.1.2. The nature of the code . . . . . . . . . . . . .
9.1.3. Information processing and the code . . . . . .
Symmetries and Supersymmetries in the Genetic Code
9.2.1. sl(6/1) model: UA+S scheme . . . . . . . . .
9.2.2. sl(6/1) model: 3CH scheme . . . . . . . . . .
9.2.3. Dynamical symmetry breaking and third base
wobble . . . . . . . . . . . . . . . . . . . . . .

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quantum
Contents
xxiii
9.3.
9.4.
Visualizing the Genetic Code . . . . . . . . . . . . . .

Quantum Aspects of Codon Recognition . . . . . . . .
9.4.1. N(34) conformational symmetry . . . . . . . .
9.4.2. Dynamical symmetry breaking and third base
wobble . . . . . . . . . . . . . . . . . . . . . .
9.5. Conclusions . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . 168
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. . 181
10. Towards Understanding the Origin of Genetic Languages
187
Apoorva D. Patel
10.1. The Meaning of It All . . .
10.2. Lessons of Evolution . . . .
10.3. Genetic Languages . . . . .
10.4. Understanding Proteins . .
10.5. Understanding DNA . . . .
10.6. What Preceded the Optimal
10.7. Quantum Role? . . . . . . .
10.8. Outlook . . . . . . . . . . .
References . . . . . . . . . . . . .
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Languages?
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Part 4: Articial Quantum Life
187
190
193
195
201
204
211
215
217
221
11. Can Arbitrary Quantum Systems Undergo Self-replication?
223
Arun K. Pati and Samuel L. Braunstein

11.1. Introduction . . . . . . . . . . . . . . . .
11.2. Formalizing the Self-replicating Machine
11.3. Proof of No-self-replication . . . . . . .
11.4. Discussion . . . . . . . . . . . . . . . . .
11.5. Conclusion . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . .
12. A Semi-quantum Version of the Game of Life
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223
225
226
227
228
229
233
Adrian P. Flitney and Derek Abbott

12.1. Background and Motivation . . . . . . . . . . . . . . . . . 233
12.1.1. Classical cellular automata . . . . . . . . . . . . . 233

June 26, 2008
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quantum
xxiv
12.1.2. Conways game of life . . . .

12.1.3. Quantum cellular automata
12.2. Semi-quantum Life . . . . . . . . . .
12.2.1. The idea . . . . . . . . . . .
12.2.2. A rst model . . . . . . . . .
12.2.3. A semi-quantum model . . .
12.2.4. Discussion . . . . . . . . . .
12.3. Summary . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . .
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13. Evolutionary Stability in Quantum Games
234
237
238
238
239
242
244
247
248
251
Azhar Iqbal and Taksu Cheon

13.1. Evolutionary Game Theory and Evolutionary Stability
13.1.1. Population setting of evolutionary game
theory . . . . . . . . . . . . . . . . . . . . . .
13.2. Quantum Games . . . . . . . . . . . . . . . . . . . . .
13.3. Evolutionary Stability in Quantum Games . . . . . .
13.3.1. Evolutionary stability in EWL scheme . . . .
13.3.2. Evolutionary stability in MW quantization
scheme . . . . . . . . . . . . . . . . . . . . . .
13.4. Concluding Remarks . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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256
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14. Quantum Transmemetic Intelligence
291
Edward W. Piotrowski and Jan Sladkowski

14.1.
14.2.
14.3.
14.4.
14.5.
14.6.
Introduction . . . . . . . . . . . . . . . . . . . . . . .
A Quantum Model of Free Will . . . . . . . . . . . .
Quantum Acquisition of Knowledge . . . . . . . . .
Thinking as a Quantum Algorithm . . . . . . . . . .
Counterfactual Measurement as a Model of Intuition
Quantum Modication of Freuds Model of
Consciousness . . . . . . . . . . . . . . . . . . . . . .
14.7. Conclusion . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . .

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291
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298
300
301
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Part 5: The Debate
311
15. Dreams versus Reality: Plenary Debate Session on

Quantum Computing
313
16. Plenary Debate: Quantum Eects in Biology: Trivial or Not?
349
17. Nontrivial Quantum Eects in Biology: A Skeptical

Physicists View
381
Howard Wiseman and Jens Eisert

17.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
17.2. A Quantum Life Principle . . . . . . . . . . . . . . . . . .
17.2.1. A quantum chemistry principle? . . . . . . . . . .
17.2.2. The anthropic principle . . . . . . . . . . . . . . .
17.3. Quantum Computing in the Brain . . . . . . . . . . . . .
17.3.1. Nature did everything rst? . . . . . . . . . . . .
17.3.2. Decoherence as the make or break issue . . . . . .
17.3.3. Quantum error correction . . . . . . . . . . . . . .
17.3.4. Uselessness of quantum algorithms for organisms .
17.4. Quantum Computing in Genetics . . . . . . . . . . . . . .
17.4.1. Quantum search . . . . . . . . . . . . . . . . . . .
17.4.2. Teleological aspects and the fast-track to life . . .
17.5. Quantum Consciousness . . . . . . . . . . . . . . . . . . .
17.5.1. Computability and free will . . . . . . . . . . . . .
17.5.2. Time scales . . . . . . . . . . . . . . . . . . . . . .
17.6. Quantum Free Will . . . . . . . . . . . . . . . . . . . . . .
17.6.1. Predictability and free will . . . . . . . . . . . . .
17.6.2. Determinism and free will . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18. Thats Life!The Geometry of Electron Clouds
381
382
382
384
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385
386
387
389
390
390
392
392
392
394
395
395
396
398
403
Stuart Hamero
18.1.
18.2.
18.3.
18.4.
18.5.
What is Life? . . . . . . . . . . . . . . . . . .
Protoplasm: Water, Gels and Solid Non-polar
Van der Waals Forces . . . . . . . . . . . . .
Kekules Dream and Electron Resonance .
ProteinsThe Engines of Life . . . . . . . . .

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Regions
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18.6. Anesthesia and Consciousness . . . . . . . . . . . . . . .

18.7. Cytoskeletal Geometry: Microtubules, Cilia and Flagella
18.8. Decoherence . . . . . . . . . . . . . . . . . . . . . . . . .
18.9. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Appendix 1. Quantum Computing in DNA Electron Stacks
Appendix 2. Penrose-Hamero Orch OR Model . . . . . . . .
Index

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435

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