From L'Homme Machine to metabolic closure: Steps towards understanding life

Journal of Theoretical Biology

Volumn 286, Issue 1, 2011, Pages 100-113

  Letelier, Juan Carlos ^a   Cárdenas, María Luz ^b   Cornish Bowden, Athel ^b  

^a UNIVERSITY OF CHILE   (Chile)

^b CNRS   (France)

Author keywords

(M,R) systems; Autopoiesis; Chemoton; Origin of life; Self organization

Indexed keywords

DNA;

METABOLISM; MOLECULAR ANALYSIS; ORIGIN OF LIFE; SELF ORGANIZATION; THEORETICAL STUDY;

AUTOCATALYSIS; AUTOPOIESIS; CATALYSIS; CHEMICAL REACTION; CYBERNETICS; DNA REPLICATION; HUMAN; LIFE; METABOLIC REGULATION; METABOLISM; MOLECULAR BIOLOGY; NONHUMAN; PHILOSOPHY; PRIORITY JOURNAL; PROTEIN DEGRADATION; REVIEW; SENSORIMOTOR FUNCTION; SYSTEMS BIOLOGY; THEORY; THEORY OF LIFE;

BIOGENESIS; CYBERNETICS; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR BIOLOGY; SYSTEMS BIOLOGY;

EID: 80052155234     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.06.033     Document Type: Review

References (113)

1. Avery O.T., MacLeod C.M., McCarty M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III. J. Exp. Med. 1944, 79:137-158.
2. Barbieri M. The Organic Codes: An Introduction to Semantic Biology 2003, Cambridge University Press, Cambridge.
3. von Bertalanffy L. General System Theory 1969, George Braziller, New York.
4. Brenner K., You L., Arnold F.H. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol. 2008, 26:483-489.
5. Buchner E. Alkoholische Gährung ohne Hefezellen (Alcoholic fermentation without yeast cells). Ber. Dt. Chem. Ges. 1897, 30:117-124. (English translation by H.C. Friedmann (1997). In: Cornish-Bowden, A. (Ed.), New Beer in an Old Bottle. Universitat de València, Valencia, pp. 25-31.).
6. Cárdenas M.L., Letelier J.-C., Gutierrez C., Cornish-Bowden A., Soto-Andrade J. Closure to efficient causation, computability and artificial life. J. Theor. Biol. 2010, 263:79-92.
7. Carnot S. Réflexions sur la Puissance Motrice du Feu et sur les Machines propres à Développer cette Puissance (Reflections on the Motive Power of Fire and on the Machines able to Develop that Power) 1824, Bachelier, Paris.
8. Chemero A., Turvey M.T. Complexity and "closure to efficient cause". ALIFE X: Workshop on Artificial Autonomy 2006, 13-18. MIT Press, Cambridge, MA. K. Ruiz-Moreno, R. Barandiaran (Eds.).
9. Chu D., Ho W.K. The localization hypothesis and machines. Artif. Life 2007, 13:299-302.
10. Chu D., Ho W.K. Computational realizations of living systems. Artif. Life 2007, 13:369-381.
11. Ciechanover A., Hod Y., Hershko A. A heat-stable polypeptide component of an ATP-dependent proteolytic system from reticulocytes. Biochem. Biophys. Res. Commun. 1979, 81:1100-1105. 2020The name was spelt incorrectly as Ciehanover in the original publication.
12. Cornish-Bowden A. Putting the systems back into systems biology. Perspect. Biol. Med. 2006, 49:475-489.
13. Cornish-Bowden A., Cárdenas M.L. Systems biology may work when we learn to understand the parts in terms of the whole. Biochem. Soc. Trans. 2005, 33:516-519.
14. Cornish-Bowden A., Cárdenas M.L. Organizational invariance in (M,R) systems. Chem. Biodivers. 2007, 4:2396-2406.
15. Cornish-Bowden A., Cárdenas M.L. Self-organization at the origin of life. J. Theor. Biol. 2008, 252:411-418.
16. Cornish-Bowden A., Cárdenas M.L. Specificity of non-Michaelis-Menten enzymes: necessary information for analyzing metabolic pathways. J. Phys. Chem. B 2010, 114:16209-16213.
17. Cornish-Bowden A., Cárdenas M.L., Letelier J.-C., Soto-Andrade J., Guíñez Abarzúa F. Understanding the parts in terms of the whole. Biol. Cell. 2004, 96:713-717.
18. Cornish-Bowden A., Cárdenas M.L., Letelier J.-C., Soto-Andrade J. Beyond reductionism: metabolic circularity as a guiding vision for a real biology of systems. Proteomics 2007, 7:839-845.
19. Cull P. The mathematical biophysics of Nicolas Rashevsky. BioSystems 2007, 88:178-184.
20. de la Mettrie J.J.O. L'Homme Machine (Man a machine) 1748, Elie Luzac, Leyden.
21. Dyson F.J. A model for the origin of life. J. Mol. Evol. 1982, 18:344-350.
22. Eastes, R.-E., Darrigan, C., Querbes, S., 2006. Jardins chimiques. La Recherche no. 400 (September 2006), pp. 90-97.
23. Eigen M., Schuster P. The hypercycle: a principle of natural self-organization. Part A: emergence of the hypercycle. Naturwissenschaften 1977, 11:541-565.
24. Elsasser W.M. Synopsis of organismic theory. J. Theor. Biol. 1964, 7:53-67.
25. Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
26. Entwistle T. Towards sustainable waste management: central steering, local enabling or autopoiesis?. Policy Politics 1999, 27:375-388.
27. Feistel R. On the evolution of biological macromolecules. III. Precellular organization. Stud. Biophys. 1983, 93:113-120.
28. Fernando C. The good symbiont. Lecture Notes in Computer Science 2005, 695-704. Springer, Berlin.
29. Fruton J.S. Proteins, Enzymes, Genes 1999, Yale University Press, New Haven, pp. 392-398.
30. Gánti T. Az Élet Princípuma (The Principle of Life) 1971, Gondolat, Budapest.
31. Gánti T. Organization of chemical reactions into dividing and metabolizing units: the chemotons. BioSystems 1975, 7:15-21.
32. Gánti T. The Principles of Life 2003, Oxford University Press, Oxford.
33. Griesemer, J., 2003. The philosophical significance of Gánti's work. Chapter 5 (pp. 169-186) of Gánti (2003).
34. Gromov M. Crystals, proteins, stability and isoperimetry. Bull. Am. Math. Soc. 2011, 48:229-257.
35. Heinrich R., Rapoport T.A. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 1974, 42:89-95.
36. Hershey A.D., Chase M. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 1952, 36:39-56.
37. Hodgkin A.L., Huxley A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. (Lond.) 1952, 117:500-544.
38. Hofmeyr J.-H.S. The biochemical factory that autonomously fabricates itself: a systems biological view of the living cell. Systems Biology: Philosophical Foundations 2007, 217-242. Elsevier, Amsterdam. F.C. Boogerd, F.J. Bruggeman, J.H.-S. Hofmeyr, H.V. Westerhoff (Eds.).
39. Hordijk W., Steel M. Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol. 2004, 227:451-461.
40. Horowitz N.H., Miller S.L. Current theories on the origin of life. Fortschr. Chem. Org. Naturst. 1962, 20:423-459.
41. Jagers op Akkerhuis G.A.J.M. Analysing hierarchy in the organization of biological and physical systems. Biol. Rev. 2008, 83:1-12.
42. Jagers op Akkerhuis G.A.J.M. Towards a hierarchical definition of life, the organism, and death. Found. Sci. 2010, 15:245-262.
43. Jaramillo, S., Honorato-Zimmer, R., Pereira, U., Contreras, D., Reynaert, B., Hernández, V., Soto-Andrade, J., Cárdenas, M.L., Cornish-Bowden, A., Letelier, J.C., 2010. (M,R) systems and RAF sets: common ideas, tools and projections. In: Proceedings of the ALIFE XII Conference, Odense Denmark, August 2010, pp. 94-100.
44. Joyce G.F. Foreword. Origins of Life 1994, xi-xii. Jones and Bartlett, Boston. D.W. Deamer, G.R. Fleischacker (Eds.).
45. Kacser H., Burns J.A. The control of flux. Symp. Soc. Exp. Biol. 1973, 27:65-104.
46. Kauffman S.A. Autocatalytic sets of proteins. J. Theor. Biol. 1986, 119:1-24.
47. Kauffman S.A. The Origins of Order 1993, Oxford University Press, New York, p. 299.
48. King G.A.M. Symbiosis and the origin of life. Origins Life 1977, 8:39-53.
49. King G.A.M. Symbiosis and the evolution of prokaryotes. BioSystems 1977, 9:35-42.
50. King G.A.M. Recycling, reproduction, and life's origins. BioSystems 1982, 15:89-97.
51. Langton C.G. Artificial Life. Artificial Life 1987, 1-47. Addison-Wesley, Redwood City, CA. C.G. Langton (Ed.).
52. Leduc S. La Biologie Synthétique (Synthetic Biology) 1912, Poinat, Paris.
53. Letelier J.-C., Marín J., Mpodozis J. Autopoietic and (M,R) systems. J. Theor. Biol. 2003, 222:261-272.
54. Letelier J.-C., Kuboyama T., Yasuda T.H., Cárdenas M.L., Cornish-Bowden A. A self-referential equation, f(f)=f, obtained using the theory of (M,R) systems: overview and applications. Algebraic Biology 2005, 115-126. Universal Academy Press, Tokyo. H. Anai, K. Horimoto (Eds.).
55. Letelier J.-C., Soto-Andrade J., Guíñez Abarzúa F., Cornish-Bowden A., Cárdenas M.L. Organizational invariance and metabolic closure: analysis in terms of (M,R) systems. J. Theor. Biol. 2006, 238:949-961.
56. Lettvin J.Y., Maturana H.R., McCulloch W.S., Pitts W.H. What the frog's eye tells the frog's brain. Proc. Inst. Radio Eng. 1959, 47:1940-1951.
57. Lindenmayer A. Mathematical models for cellular interactions in development. I. Filaments with one-sided inputs. J. Theor. Biol. 1968, 18:280-299.
58. Lindenmayer A. Mathematical models for cellular interactions in development. II. Simple and branching filaments with two-sided inputs. J. Theor. Biol. 1968, 18:300-315.
59. Louie A.H. A living system must have noncomputable models. Artif. Life 2007, 13:293-297.
60. Luisi P.L. Autopoiesis: a review and a reappraisal. Naturwissenschaften 2003, 90:49-59.
61. Luisi P.L. The Emergence of Life: from Chemical Origins to Synthetic Biology 2006, Cambridge University Press.
62. McMullin B. Thirty years of computational autopoiesis: a review. Artif. Life 2004, 10:277-295.
63. Manapat M.L., Chen I.A., Nowak M.A. The basic reproductive ratio of life. J. Theor. Biol. 2010, 263:317-327.
64. Maturana, H., 1970. BCL Report 9. Biological Computing Laboratory, Urbana-Champaign, IL.
65. Maturana, H.R., Varela, F., 1973. De Máquinas y Seres Vivos (Of Machines and Living Beings). Editorial Universitaria, Santiago, Chile.
66. Maturana H.R., Varela F. Autopoiesis and Cognition: the Realisation of the Living 1980, D. Reidel Publishing Company, Dordrecht.
67. Maynard Smith J., Szathmáry E. The Major Transitions in Evolution 1995, Freeman, Oxford.
68. Medina E. Designing freedom, regulating a nation: socialist cybernetics in Allende's Chile. J. Lat. Am. Studies 2006, 38:571-606.
69. Meléndez-Hevia E., Montero-Gómez N., Montero F. From prebiotic chemistry to cellular metabolism-the chemical evolution of metabolism before Darwinian natural selection. J. Theor. Biol. 2008, 252:505-519.
70. Mesarović M.D. Systems theory and biology-view of a theoretician. Systems Theory and Biology 1968, 59-87. Springer-Verlag, New York. M.D. Mesarović (Ed.).
71. Michailakis D. Law as an autopoietic system. Acta Sociol. 1995, 38:323-337.
72. Miescher F. Uber die chemische Zusammensetzung der Eiterzellen (On the chemical composition of pus cells). Med.-chem. Untersuch. 1871, 4:441-460.
73. Monod J. Chance and Necessity 1971, Knopf, New York.
74. Montero F., Nuño J.C., Meléndez-Hevia E., Olasagasti F., Vázquez S., Morán F. Stoichiometric analysis of self-maintaining metabolisms. J. Theor. Biol. 2008, 252:427-432.
75. Mossio M., Longo G., Stewart J. A computable expression of closure to efficient causation. J. Theor. Biol. 2009, 257:489-498.
76. Negrón-Mendoza A. Alfonso L. Herrera: a Mexican pioneer in the study of chemical evolution. J. Biol. Phys. 1995, 20:11-15.
77. Pauling L. Schrödinger's contribution to chemistry and biology. Schrödinger: Centenary Celebration of a Polymath 1987, 225-233. Cambridge University Press, Cambridge. C.W. Kilminster (Ed.).
78. Perutz M. Physics and the riddle of life. Nature 1987, 326:555-558.
79. Piedrafita G., Montero F., Morán F., Cárdenas M.L., Cornish-Bowden A. A simple self-maintaining metabolic system: robustness, autocatalysis, bistability. PLoS Comput. Biol. 2010, 6:e1000872.
80. Prunetti L., Infossi P., Brugna M., Ebel C., Giudici-Orticoni M.T., Guiral M. New functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium Aquifex aeolicus. J. Biol. Chem. 2010, 285:41815-41826.
81. Rashevsky N. On the theory of nervous conduction. J. Gen. Physiol. 1931, 14:517-528.
82. Rashevsky N. Topology and life: in search of general mathematical principles in biology and sociology. Bull. Math. Biol. 1954, 16:317-348.
83. Ratner V.A., Shamin V.V. Mathematical Models of Evolutionary Genetics 1980, ICG, Novosibirsk.
84. Red'ko V.G. The behaviour of sysers in coacervates. Biofizika 1986, 31:701-707. (in Russian).
85. Red'ko V.G. Adaptive syser. Biofizika 1990, 35:1007-1011. (in Russian).
86. Rosen R. A relational theory of biological systems. Bull. Math. Biophys. 1958, 20:245-260.
87. Rosen R. The representation of biological systems from the standpoint of the theory of categories. Bull. Math. Biophys. 1958, 20:317-341.
88. Rosen R. A relational theory of biological systems. II. Bull. Math. Biophys. 1959, 21:109-128.
89. Rosen R. A note on replication in (M,R) systems. Bull. Math. Biophys. 1966, 28:149-151.
90. Rosen R. Some realizations of (M,R) systems and their interpretation. Bull. Math. Biophys. 1971, 33:303-319.
91. Rosen R. On the dynamical realization of (M,R) systems. Bull. Math. Biol. 1973, 35:1-9.
92. Rosen R. On the dynamical realization of automata. J. Theor. Biol. 1975, 54:109-120.
93. Rosen R. Life Itself 1991, Columbia University Press, New York.
94. Rössler O.E. Ein systemtheoretische Modell zur Biogenese (A system theoretic model for biogenesis). Z. Naturforsch. B 1971, 26:741-746.
95. Savageau M.A. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology 1976, Addison-Wesley, Reading, MA.
96. What we don't know: 125 questions. Science 2005, 309:75-102. Science.
97. Schrödinger E. What is Life? 1944, Cambridge University Press, Cambridge.
98. Segrè D., Pilpel Y., Lancet D. Mutual catalysis in sets of prebiotic organic molecules: evolution through computer simulated kinetics. Physica A 1998, 24:558-564.
99. Szathmáry, E., 2003. The biological significance of Gánti's work in 1971 and today. Chapter 4 (pp. 157-168) of Gánti (2003).
100. Tsokolov S. A theory of circular organization and negative feedback: defining life in a cybernetic context. Astrobiology 2010, 10:1031-1042.
101. Varela F.G., Maturana H.R., Uribe R. Autopoiesis: the organization of living systems, its characterization and a model. Curr. Mod. Biol. 1974, 5:187-196.
102. Vasas V., Szathmáry E., Santos M. Lack of evolvability in self-sustaining autocatalytic networks constrains metabolism-first scenarios for the origin of life. Proc. Natl. Acad. Sci. USA 2010, 107:1470-1475.
103. Vieira de Carvalho M. "New music" between search for identity and autopoiesis-or, the "tragedy of listening". Theory Cult. Soc. 1999, 16(4):127-135.
104. Watson J.D., Crick F.H.C. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
105. Wells A.J. In defense of mechanism. Ecol. Psychol. 2006, 18:39-65.
106. Westerhoff H.V., Koster J.G., van Workum M., Rudd K.E. On the control of gene expression. Control of Metabolic Processes 1990, 399-412. Plenum Press, London. A. Cornish-Bowden, M.L. Cárdenas (Eds.).
107. White D.H. A theory for the origin of a self-replicating chemical system. I: natural selection of the autogen from short, random oligomers. J. Mol. Evol. 1980, 16:121-147.
108. Wiener N. Cybernetics: or Control and Communication in the Animal and the Machine 1948, Hermann, Paris.
109. Woese C.R. A new biology for a new century. Microb. Molec. Biol. Rev. 2004, 68:173-186.
110. Wolkenhauer O. Interpreting Rosen. Artif. Life 2007, 13:291-292.
111. Wolkenhauer O., Hofmeyr J.-H.S. An abstract cell model that describes the self-organization of cell function in living systems. J. Theor. Biol. 2007, 246:461-476.
112. Zeleny M., Klir G.J., Hufford K.D. Precipitation membranes, osmotic growth and synthetic biology. Artificial Life 1987, 125-139. Addison-Wesley, Redwood City CA. C.G. Langton (Ed.).
113. Zepik H.H., Blöchliger E., Luisi P.L. A chemical model of homeostasis. Angew. Chem. Int. Ed. Engl. 2001, 40:199-202.