Quantum biology at the cellular level - Elements of the research program

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed.

[1]  Peter Hänggi,et al.  Control of molecular chirality , 1997 .

[2]  A. D. Hershey,et al.  The Bacteriophage Lambda. , 1971 .

[3]  J. Cirac,et al.  Effective size of certain macroscopic quantum superpositions. , 2002, Physical review letters.

[4]  W. Bean Physics and Philosophy, the Revolution in Modern Science. , 1959 .

[5]  S. Jinks-Robertson,et al.  An examination of adaptive reversion in Saccharomyces cerevisiae. , 1992, Genetics.

[6]  J. Bell On the Problem of Hidden Variables in Quantum Mechanics , 1966 .

[7]  Philip Ball,et al.  Physics of life: The dawn of quantum biology , 2011, Nature.

[8]  Alexis Mari Pietak,et al.  Structural evidence for electromagnetic resonance in plant morphogenesis , 2012, Biosyst..

[9]  Lloyd Demetrius,et al.  Quantum statistics and allometric scaling of organisms , 2003 .

[10]  P. Davies,et al.  Does quantum mechanics play a non-trivial role in life? , 2004, Bio Systems.

[11]  C. Maley,et al.  Cancer is a disease of clonal evolution within the body1–3. This has profound clinical implications for neoplastic progression, cancer prevention and cancer therapy. Although the idea of cancer as an evolutionary problem , 2006 .

[12]  V. Vedral,et al.  Classical, quantum and total correlations , 2001, quant-ph/0105028.

[13]  D. A. Edwards The mathematical foundations of quantum mechanics , 1979, Synthese.

[14]  J. Roth,et al.  Rebuttal: Adaptive Mutation in Escherichia coli (Foster) , 2004, Journal of bacteriology.

[15]  B. Hall Selection-induced mutations. , 1992, Current opinion in genetics & development.

[16]  Measurement-based measure of the size of macroscopic quantum superpositions , 2006, quant-ph/0611121.

[17]  J. Roth,et al.  Rebuttal: Adaptive Point Mutation (Rosenberg and Hastings) , 2004, Journal of bacteriology.

[18]  D. Court,et al.  A new look at bacteriophage lambda genetic networks. , 2007, Journal of bacteriology.

[19]  Martin A. Nowak,et al.  The role of chromosomal instability in tumor initiation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[20]  E. Giudice,et al.  Spontaneous symmetry breakdown and boson condensation in biology , 1983 .

[21]  K Matsuno,et al.  How can quantum mechanics of material evolution be possible? Symmetry and symmetry-breaking in protobiological evolution. , 1985, Bio Systems.

[22]  G. Edelman Neural Darwinism: The Theory Of Neuronal Group Selection , 1989 .

[23]  Nicolaas P. Landsman,et al.  Essay Review of: Maximilian Schlosshauer, Decoherence and the Quantum-To-Classical Transition (Springer, Berlin, 2007) , 2009 .

[24]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[25]  Abir U. Igamberdiev,et al.  Biomechanical and coherent phenomena in morphogenetic relaxation processes , 2012, Biosyst..

[26]  Andrei Khrennikov,et al.  Quantum-like model of cognitive decision making and information processing , 2009, Biosyst..

[27]  P. Nowell The clonal evolution of tumor cell populations. , 1976, Science.

[28]  Thierry Paul,et al.  Quantum computation and quantum information , 2007, Mathematical Structures in Computer Science.

[29]  V. Ogryzko,et al.  A quantum-theoretical approach to the phenomenon of directed mutations in bacteria (hypothesis). , 1997, Bio Systems.

[30]  Paul Adrien Maurice Dirac,et al.  A new notation for quantum mechanics , 1939, Mathematical Proceedings of the Cambridge Philosophical Society.

[31]  R. Gatenby Commentary: carcinogenesis as Darwinian evolution? Do the math! , 2006, International journal of epidemiology.

[32]  C. McClare A Quantum Mechanical Muscle Model , 1972, Nature.

[33]  W F Bodmer,et al.  The mutation rate and cancer. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Leo P. Kadanoff,et al.  Teaching the Renormalization Group. , 1978 .

[35]  M Conrad Quantum mechanics and cellular information processing: the self-assembly paradigm. , 1990, Biomedica biochimica acta.

[36]  Christopher Voigt Methods for part/device characterization and chassis engineering , 2011 .

[37]  G. Roger,et al.  Experimental Test of Bell's Inequalities Using Time- Varying Analyzers , 1982 .

[38]  E. Schrödinger,et al.  What is life? : the physical aspect of the living cell , 1946 .

[39]  L. Loeb,et al.  Reply: Is There Any Genetic Instability in Human Cancer? , 2010, DNA repair.

[40]  S. Rosenberg,et al.  Rebuttal: Growth under Selection Stimulates Lac+ Reversion (Roth and Andersson) , 2004, Journal of bacteriology.

[41]  S. Rosenberg Evolving responsively: adaptive mutation , 2001, Nature Reviews Genetics.

[42]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[43]  T. Cech,et al.  Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena , 1982, Cell.

[44]  J. Ignacio Cirac,et al.  Toward quantum superposition of living organisms , 2009, 0909.1469.

[45]  R. Alicki,et al.  Decoherence and the Appearance of a Classical World in Quantum Theory , 2004 .

[46]  A size criterion for macroscopic superposition states , 2003, quant-ph/0310193.

[47]  J. Roth,et al.  Origin of mutations under selection: the adaptive mutation controversy. , 2006, Annual review of microbiology.

[48]  M. Redhead Quantum theory and measurement , 1984 .

[49]  A. Davydov,et al.  The theory of contraction of proteins under their excitation. , 1973, Journal of theoretical biology.

[50]  W. Zurek,et al.  Quantum discord: a measure of the quantumness of correlations. , 2001, Physical review letters.

[51]  R. A. Harris,et al.  Superpositions of Handed Wave Functions , 1995, Science.

[52]  M. Kimura,et al.  Evolution in Sexual and Asexual Populations , 1965, The American Naturalist.

[53]  W. Heisenberg,et al.  Physics and Philosophy , 1943, Nature.

[54]  Maximilian Schlosshauer-Selbach Decoherence and the quantum-to-classical transition , 2008 .

[55]  J. Roth,et al.  Multiple pathways of selected gene amplification during adaptive mutation , 2006, Proceedings of the National Academy of Sciences.

[56]  P. Grangier,et al.  Experimental Realization of Einstein-Podolsky-Rosen-Bohm Gedankenexperiment : A New Violation of Bell's Inequalities , 1982 .

[57]  Priscilla E. M. Purnick,et al.  The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.

[58]  Vasily Ogryzko,et al.  On Two Quantum Approaches to Adaptive Mutations in Bacteria , 2008, 0805.4316.

[59]  Andrei Khrennikov,et al.  A model of quantum-like decision-making with applications to psychology and cognitive science , 2007, 0711.1366.

[60]  S. Lloyd,et al.  Environment-assisted quantum walks in photosynthetic energy transfer. , 2008, The Journal of chemical physics.

[61]  W. Stein,et al.  Analysis of cancer incidence data on the basis of multistage and clonal growth models. , 1991, Advances in cancer research.

[62]  T. Vincent,et al.  An evolutionary model of carcinogenesis. , 2003, Cancer research.

[63]  J. Cairns,et al.  Adaptive reversion of a frameshift mutation in Escherichia coli. , 1991, Genetics.

[64]  Nicolas Gisin,et al.  Reply to the "Comment on: Testing the speed of 'spooky action at a distance' " , 2008, 0810.4607.

[65]  Jeffrey D. Stumpf,et al.  Amplification of lac Cannot Account for Adaptive Mutation to Lac+ in Escherichia coli , 2007, Journal of bacteriology.

[66]  S. Gilbert,et al.  Life of Alexander G. Gurwitsch and his relevant contribution to the theory of morphogenetic fields. , 1997, The International journal of developmental biology.

[67]  H. Stapp The importance of quantum decoherence in brain processes , 2000, quant-ph/0010029.

[68]  E. Schrödinger Die gegenwärtige Situation in der Quantenmechanik , 1935, Naturwissenschaften.

[69]  B. Hall,et al.  Adaptive mutations in Escherichia coli as a model for the multiple mutational origins of tumors. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[70]  D. Court,et al.  A New Look at Bacteriophage λ Genetic Networks , 2006 .

[71]  Gary James Jason,et al.  The Logic of Scientific Discovery , 1988 .

[72]  A. Knudson Mutation and cancer: statistical study of retinoblastoma. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Lilach Hadany,et al.  Mutability and Importance of a Hypermutable Cell Subpopulation that Produces Stress-Induced Mutants in Escherichia coli , 2008, PLoS genetics.

[74]  Abir U Igamberdiev,et al.  Quantum computation, non-demolition measurements, and reflective control in living systems. , 2004, Bio Systems.

[75]  D. Parkhomchuk,et al.  Use of high throughput sequencing to observe genome dynamics at a single cell level , 2009, Proceedings of the National Academy of Sciences.

[76]  Michal Cifra,et al.  Electrodynamic eigenmodes in cellular morphology , 2012, Biosyst..

[77]  Javier Prior,et al.  The role of non-equilibrium vibrational structures in electronic coherence and recoherence in pigment–protein complexes , 2013, Nature Physics.

[78]  H. Fröhlich Long-range coherence and energy storage in biological systems , 1968 .

[79]  K. B. Whaley,et al.  Quantum entanglement in photosynthetic light-harvesting complexes , 2009, 0905.3787.

[80]  T. Mančal,et al.  Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems , 2007, Nature.

[81]  L. Hardy Quantum Theory From Five Reasonable Axioms , 2001, quant-ph/0101012.

[82]  Diederik Aerts,et al.  Applications of Quantum Statistics in Psychological Studies of Decision Processes , 1995 .

[83]  E. Liberman,et al.  Quantum molecular computer model of the neuron and a pathway to the union of the sciences. , 1989, Bio Systems.

[84]  P. Vineis,et al.  The population dynamics of cancer: a Darwinian perspective. , 2006, International journal of epidemiology.

[85]  Wojciech H. Zurek,et al.  Probabilities from entanglement, Born's rule p{sub k}= vertical bar {psi}{sub k} vertical bar{sup 2} from envariance , 2005 .

[86]  I. Stamatescu,et al.  Decoherence and the Appearance of a Classical World in Quantum Theory , 1996 .

[87]  B. Hall Selection-induced mutations occur in yeast. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[88]  S. Takeno,et al.  Davydov model: The quantum, mixed quantum-classical, and full classical systems , 1997 .

[89]  A. Louisa,et al.  コロイド混合体における有効力 空乏引力から集積斥力へ | 文献情報 | J-GLOBAL 科学技術総合リンクセンター , 2002 .

[90]  Lloyd Demetrius,et al.  Quantum metabolism explains the allometric scaling of metabolic rates , 2010, Journal of The Royal Society Interface.

[91]  P. Grangier,et al.  Experimental Tests of Realistic Local Theories via Bell's Theorem , 1981 .

[92]  T J Newman Life and death in biophysics. , 2011, Physical biology.

[93]  I. Lakatos Falsification and the Methodology of Scientific Research Programmes , 1976 .

[94]  P. Goymer Natural selection: The evolution of cancer , 2008, Nature.

[95]  Anton Zeilinger,et al.  Wave–particle duality of C60 molecules , 1999, Nature.

[96]  Stuart R. Hameroff,et al.  Ultimate computing - biomolecular consciousness and nanotechnology , 1987 .

[97]  A. Murray,et al.  Seeing Mutations in Living Cells , 2010, Current Biology.

[98]  Niels Bohr,et al.  Discussion with Einstein on Epistemological Problems in Atomic Physics , 1996 .

[99]  M. Lieber,et al.  Is there any genetic instability in human cancer? , 2010, DNA repair.

[100]  G. Scholes Quantum-Coherent Electronic Energy Transfer: Did Nature Think of It First? , 2010 .

[101]  L. Loeb,et al.  Mutator phenotype may be required for multistage carcinogenesis. , 1991, Cancer research.

[102]  J. Klinman,et al.  Structural bases of hydrogen tunneling in enzymes: progress and puzzles. , 2004, Current opinion in structural biology.

[103]  A. Jackson,et al.  The mutation rate and cancer. , 1998, Genetics.

[104]  J. Delft,et al.  Measuring the size of a quantum superposition of many-body states , 2008 .

[105]  W. McClure,et al.  Mechanism and control of transcription initiation in prokaryotes. , 1985, Annual review of biochemistry.

[106]  M. Lipinski,et al.  PUB-MS: a mass spectrometry-based method to monitor protein-protein proximity in vivo. , 2011, Journal of proteome research.

[107]  D. Green,et al.  Means to an end : apoptosis and other cell death mechanisms , 2011 .

[108]  B. Hall Adaptive Mutagenesis at ebgR Is Regulated by PhoPQ , 1998, Journal of bacteriology.

[109]  H. Muller Some Genetic Aspects of Sex , 1932, The American Naturalist.

[110]  Lurias,et al.  MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE’-’ , 2003 .

[111]  M. Kimmel Evolution and cancer: a mathematical biology approach , 2010, Biology Direct.

[112]  Imre Lakatos,et al.  The Methodology of Scientific Research Programmes , 1978 .

[113]  V. Ogryzko,et al.  Erwin Schroedinger, Francis Crick and epigenetic stability , 2007, Biology Direct.

[114]  S. Rosenberg,et al.  Mutation as a Stress Response and the Regulation of Evolvability , 2007, Critical reviews in biochemistry and molecular biology.

[115]  Vlatko Vedral,et al.  Quantum physics meets biology , 2009, HFSP journal.

[116]  N. Mermin Quantum theory: Concepts and methods , 1997 .

[117]  F. J. Ryan,et al.  Spontaneous Mutation in Non-Dividing Bacteria. , 1955, Genetics.

[118]  E. Koonin,et al.  Is evolution Darwinian or/and Lamarckian? , 2009, Biology Direct.

[119]  David J. Earl,et al.  Evolvability is a selectable trait. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[120]  S. Hameroff,et al.  Quantum computation in brain microtubules: decoherence and biological feasibility. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[121]  B. Vogelstein,et al.  p53 mutations in human cancers. , 1991, Science.

[122]  Derek Abbott,et al.  PLENARY DEBATE: QUANTUM EFFECTS IN BIOLOGY: TRIVIAL OR NOT? , 2008 .

[123]  J. Overbaugh,et al.  The origin of mutants , 1988, Nature.

[124]  Valeria Souza,et al.  Stress-Induced Mutagenesis in Bacteria , 2003, Science.

[125]  W. Zurek Decoherence, einselection, and the quantum origins of the classical , 2001, quant-ph/0105127.