Biogeosciences www.biogeosciences.net 1726-4170 1726-4189 3 3 2006 10.5194/bg-3-281-2006 http://www.biogeosciences.net/3/281/2006/ http://www.biogeosciences.net/3/281/2006/bg-3-281-2006.html http://www.biogeosciences.net/3/281/2006/bg-3-281-2006.pdf 281 291 2006-07-10 The definition of life in the context of its origin Y. N. Zhuravlev zhuravlev@ibss.dvo.ru V. A. Avetisov Institute of Biology and Soil Science, Russian Academy of Sciences, Far Eastern Branch, 100-letia 159, 690022 Vladivostok, Russia The Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina 4, 119991 Moscow, Russia Current life is a complex, multi-level phenomenon that is so diverse in its manifestations that a short and exhaustive definition of life is hardly possible. The high complexity of life, as well as a poor understanding of what life is in essence, are the obstacles to the elaboration of such a definition. Important characteristics of life, such as whole system-, ecosystem-, and information-defined characteristics, have been included in the definition of life only recently. Ecosystem-defined characteristics have been absent in models of the pre-biotic state for a long time. However, without an ecosystem context, the concept of the emergence of life cannot be complete. Interconnections between living and non-living components of a primordial evolving system are decisive for the period of transition from chemical to biological evolution. Information-defined characteristics of life are often reduced to storage and the expression of genetic information, yet the operation of such perfect processes in prebiotic and transitional systems is unlikely. Genetic information, as defined in terms of the Shannon theory of communication, represents only a certain "informational channel" specified with respect to the expression of the structural genes. However, recent findings concerning the molecular mechanisms of the differential regulation of gene activity, and in the genomics, postgenomics and proteomics control mechanisms, suppose a richer diversity of informational flows in the organism. Moreover, considering life in a more general context, other types of related, informational channels, in particular, regarding the differentiation of higher taxa, hiatus, and expansion processes, should be kept in mind. In many publications devoted to the origin of life, the terms "living", "life", and "living organism" are freely interchanged which proves the vagueness of insights about the different levels of the living system. This report considers some variants of the definition of life that have been recently suggested and are based on present-day knowledge of the structures and functions of life. The contradictory demands of a definition, which needs to be complete and short at the same time, are emphasized. A definition characterizing life as a state, a structure, and a process, is proposed. Arber, W.: Elements for a theory of molecular evolution, Gene, 317, 3–11, 2003. Avise, J. C.: Phylogeography. The History and Formation of Species, Harvard University Press, Cambridge/Massachusetts/London, England, 2000. Bendoricchio, G. and Jørgensen, S. E.: Exergy as goal function of ecosystems dynamic, Ecological Modelling, 102, 5–15, 1997. Bertalanffy, von, L.: Problems of Life: an Evaluation of Modern Biological Thought, J. Wiley, N.Y., 1952[1949]. Bohr, N.: Light and life, Nature, 308, 456–459, 1933. Chernavskii, D. S.: The origin of life and thinking from the modern physics point of view (in Russian), Uspechi Physich, Nauk, 170, 157–183, 2000. Claverie, J.-M.: What if there are only 30 000 human genes?, Science, 291, 1255–1257, 2001. Cleland, C. E. and Chiba C.: Defining "life", Origins Life Evol. Biosph., 32, 387–393, 2002. Corning, P. A.: Thermoeconomics: Beyond the second law, J. Bioeconomics, 4, 57–88, 2002. Darwin, C.: The Origin of Species, VI Ed., Studio Editions Ltd., Princess House, London, 1872. Eigen, M. and Schuster, P.: The Hypercycle: a Principle of Natural Self-organization. Berlin: Springer-Verlag, 1979. Eigen, M., Schuster, P., Gardiner, W., and Winkler-Oswatitsch, R.: The origin of genetic information, Sci. Am., 244, 78–94, 1981. Emmeche, C.: Defining life as a semiotic phenomenon, Cybernet. Human Knowing, 5, 3–17, 1998. Engels, F.: Dialectics of Nature, OGIS, (Russian translation), Moscow, 1948. Fleischaker, G. R.: Origins of life: an operational definition, Origins Life Evol. Biosph. 20, 127–137, 1990. Erwin, D. H.: Macroevolution is more than repeated rounds of microevolution. Evolution and Development, 2, 78–84, 2000. Gesteland, R. F., Cech, T. R., and Atkins, J. F. (Eds.): The RNA World, 2nd ed., Cold Spring Harbor Press, 1999. Gilbert, W.: The RNA world, Nature, 319, 618, 1986. Gould, S. G.: The Structure of Evolutionary Theory, Belknap, Harvard Univ. Press, Cambridge, MA, 2002. Haldane, J. B. S.: The origin of life, Rationalist Annu., 148–169, 1929. Hoyle, F. and Wickramasinghe, N. C.: Life Cloud: The Origin of Life in the Universe. Harper and Row, NewYork, 1978. Hutchinson, C. A., Peterson, S. N., Gill, S. R., Cline, R. T., White, O., Fraser, C. M., Smith, H. O., and Venter, J. C.: Global transposon mutagenesis and a minimal mycoplasma genome, Science, 286, 2165–2169, 1999. Islas, S., Becerra, A., Luisi, P. L., and Lazcano, A.: Comparative genomics and the gene complement of a minimal cell, Origins Life Evol. Biosph., 34, 1–2, 243–256, 2004. Jørgensen, S. E., Patten, B. C., and Straskraba, M.: Ecosystems emerging: 4. growth, Ecological Modelling, 126, 249–284, 2000. Jørgensen, S. E.: State-of-the-art of ecological modelling with emphasis on development of structural dynamic models, Ecological Modelling, 120, 2–3, 75–96, 1999. Joyce, G. F.: in: Origins of Life: the Central Concepts, edited by: Deamer, D. W., Fleischaker, G. R., Jones and Bartlett, Boston, p. xi–xii, 1994. Kauffman, S.: Investigations, Oxford University Press, Oxford, Ch. 3, 2000. Kauffman, S.: The Origins of Order: Self-organization and Selection in Evolution, Oxford, University Press, Oxford, 1993. Kirby, K. G.: Biological adaptabilities and quantum entropies, BioSystems, 64, 33–41, 2002. Kolchanov, N. and Hofestaedt, R. (Eds.): Bioinformatics of Genome Regulation and Structure, Kluwer Academic Publishers, Boston/Dordrecht/London, 2004. Kompanichenko, V.: Systemic approach to the origin of life, Frontier Perspectieves, 13, 22–40, 2004. Koshland Jr., D. E.: The seven pillars of life, Science, 295, 2215–2216, 2002. Lombardi, O.: What is information?, Foundation of Science, 9, 105–134, 2004. Luisi, P. L.: About various definitions of life, Origins Life Evol. Biosph., 28, 4–6, 613–622, 1998. Lynch, M.: Gene duplication and evolution, Science, 297, 945–947, 2002. McShea D. W.: The minor transitions in hierarchical evolution and the question of a directional bias, J. Evol. Biol., 14, 502–518, 2001. Morowitz, H. J.: The Beginnings of Cellular Life, Yale University Press, New Haven, 1992. Morowitz, H. J.: Energy flow in biology. Academic Press, New York, 1968. Nekrasov, A. N.: Entropy of protein sequences: an integral approach, J. Biomol. Struct. Dyn., 20, 87–92, 2002. Nielsen, S. N. and Ulanowicz, R. E.: On the consistency between thermodynamical and network approaches to ecosystems, Ecological Modelling, 132, 23–31, 2000. Olson, M. V.: A time to sequence, Science, 270, 394–396, 1995. Oltavai, Z. N. and Barab\'asi, A.-L.: Life's complexity pyramid, Science, 298, 763–764, 2002. Oparin, A. I.: Proiskhozhdenie zhizny (in Russian), Izd. Mosk. Rabochii, Moscow, 1924. Orgel, L. E.: Some consequences of the RNA world hypothesis, Origins Life Evol. Biosph., 33, 211–218, 2003. Pályi, G., Zucci, C., and Caglioti, L. (Eds.): Fundamentals of Life. Elsevier, Paris, 2002. Patten, B. C., Stra\vskraba, M., and Jørgensen, S. E.: Ecosystems emerging: 1. conservation, Ecological Modelling, 96, 221–284, 1997. Prigogine, I.: Nonlinear science and the laws of nature, Int. J. Bifurcat. Chaos, 7, 1917–1926, 1997. Prigogine, I.: Laws of nature, probability and time symmetry breaking, Physica A, 263, 528–539, 1999. Rebay, I., Silver, S. J., and Tootle, T. L.: New vision from eyes absent: transcription factors as enzymes, Trends in Genetics, 21, 163–171, 2005. Roy, P. K., Miller, J. P., and Majumder, D. D.: A control analysis of neuronal information processing: a study of electrophysiological experimentation and non-equilibrium information theory, Lecture Notes in Computer Science, 2275, 191–203, 2002. Ruiz-Mirazo, K., Peretó, J., and Moreno, A.: A universal definition of life: autonomy and open-ended evolution, Origins Life Evol. Biosph., 34, 323–346, 2004. Sagan, C.: Life, in: The Encyclopaedia Britannica, William Benton, London, 1970. Santos, M., Zintzaras, E., and Szathmáry, E.: Origin of sex revisited, Origins Life Evol. Biosph., 33, 405–432, 2003. Schneider, E. D. and Kay, J. J.: Life as a manifestation of the second law of thermodynamics, Mathematical Computer Modelling, 19, 25–48, 1994. Schrödinger, E.: What Is Life?, Cambridge Univ. Press, 1945. Segre, D., Ben-Eli, D., Deamer, D. W., and Lancet, D.: The lipid world, Origins Life Evol. Biosph., 31, 119–145, 2001. Shannon, C. E.: A mathematical theory of communication, Bell Syst. Tech. J., 27, 379–424, 623–656, 1948. Shapiro, J. A.: A 21st century view of evolution, J. Biol. Phys., 28, 745–764, 2002. Simon, H. The Sciences of the Artificial (Russian translation), Editorial URSS, Moscow, 2004. Sites, J. W. and Marshall, J. C.: Delimiting species: a Reneissance issue in systematic biology, Trends in Ecology and Evolution, 18, 462–470, 2003. Smith, M. J.: The Problems of Biology, Oxford University Press, Oxford, 1986. Szathmáry, E.: Biological information, kin selection, and evolutionary transitions, Theor. Popul. Biol. 59, 11–14, 2001. Szathmáry, E. and Demeter, L.: Group selection of early replicators and the origin of life, J. Theor. Biol., 128, 463–486, 1987. Ulanowicz, R. E.: Some steps toward a central theory of ecosystem dynamics, Comput.Biol Chem., 27, 523–530, 2003. Varela, F. J., Maturana, H. R., and Uribe, R.: Autopoiesis: the organization of living systems, its characterization, and a model, Curr. Mod. Biol., 5, 187–196, 1974. Vernadsky, V. I.: Biosphere and Noosphere (Russian edition), Airis-Press, Moscow, 2003. von Bertalanffy, L.: Problems of Life: an Evaluation of Modern Biological Thought, J. Wiley, N. Y., 1952 (1949). Wächtershauser, G.: Before enzymes and templates: theory of surface metabolism, Microbiol. Rev., 52, 452–484, 1988. Wiener, N.: Cybernetics: or Control and Communications in the Animal and the Machine. MIT Press, Cambridge, MA, 1948. Wilhelm, T. and Bruggemann, R.: Goal functions for the development of natural systems, Ecological Modelling, 132, 231–246, 2000. Woese, C. R.: The primary lines of descent and the universal ancestor, in: Evolution from Molecules to Man, edited by: Bendall, D. S., Cambridge University Press, Cambridge, 209–233, 1983. Woodward, A. W. and Bartel, B.: Auxin: regulation, action, and interaction, Annals of Botany (London), 95, 707–735, 2005. Yockey, H. P.: Origin of life on earth and Shannon's theory of communication, Computers and Chemistry, 24, 105–123, 2000. Zavarzin, G. A.: The future is selected by the past (in Russian), Vestnik RAN, 74, 813–822, 2004.