Systemic Metaphors and Integrative Biology

Ray Paton



The purpose of this paper is to provide a conceptual framework for examining and integrating systemic thinking in biology through the analysis of a number of systemic metaphors. After a brief examination of the roles that systemic metaphors can play in model development, a general framework is presented for integrating a range of key constructs such as hierarchy and organisation as well as the scope for use of the ecosystem metaphor. The idea of an ecology of biological information is used to encapsulate general thinking about networks, hierarchies and nestings at various scales and times and this leads on to the role played by the cognitive system metaphor. After a discussion of a number of occurrences of the cognitive metaphor a complementary systemic metaphor - verb-glue-text - is discussed. The paper concludes with a brief look at some of the conceptual constraints related to this metaphor. In order to make the paper integrative a broad range of biological examples are discussed from molecules to ecosystems.


methaphors; systemic methaphors; integrative biology; cognitive system metaphor; conceptual constraints

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Albrecht-Buehler, G. (1990), “In Defense of Nonmolecular Biology”, International Review of Cytology, 120, 191-241.

Albrecht-Beuhler, G. (1998) CELL INTELLIGENCE Website

Arhem, P. (1996), “Vertical Information Flow in the Brain: on Neuronal Micro Events and Consciousness”, BioSystems, 38, 2/3, 191-198.

Conrad M (1990), “Quantum mechanics and cellular information processing: the self- assembly paradigm”, Biomed Biochim Acta, 49, 8-9, 743-55.

Conrad, M. (1992), “The Seed Germination Model of Enzyme Catalysis”, BioSystems, 27, 223-233.

Beloussov, L. V. (1998), The Dynamic Architecture of a Developing Organism, Kluwer. Bennett, M. D., 1987, “Variation in Genomic Form in Plants and its Ecological Implications”, New Phytol. 106 (Suppl.), 177-200.

Bertalanffy, L. von (1973) General System Theory, Harmondsworth: Penguin.

Bray, D. (1995), “Protein Molecules as Computational Elements in Living Cells”, Nature, 376, 307-312.

Emmeche, C. & Hoffmeyer, J. (1991), “From Language to Nature: The Semiotic Metaphor in Biology”, Semiotica, 84(1/2), 1-42.

Erdi, P. (1996), “The Brain as a Hermeneutic Device”, Biosystems. 1996;38(2-3): 179-89.

Fillmore, C. J. (1968), “The Case for Case”, in Bach, E. & Harms, R.T. (eds), Universals in Linguistic Theory, New York: Holt, Rinehart & Winston, 1-88.

Fisher, M., Paton, R. C. & Matsuno, K. (in press), “Intracellular Signalling Proteins as ‘Smart’ Agents in Parallel Distributed Processes”, to appear in BioSystems.

Forbes, S. A. (1887), “The Lake as a Microcosm”, Bull. Peoria Sci. Assoc., Illinois Nat. Hist. Surv. Bull., 15, 537-550.

Getting, P. A. (1989), “Emerging Principles Governing the Behaviour Operation of Neural Networks”, Annu. Rev. Neuroscience, 112, 185-204.

Giles, R. H., Peters, D. J. M. & Breuning, M. H. (1998), “Conjunction dysfunction: CBP/p300 in human disease”, Trends in Genetics, 14, 5, 178-183.

Golley, F. B. (1993), A History of the Ecosystem Concept in Ecology, Yale University Press: New Haven.

Harre, R. (1986), Varieties of Realism: a Rationale for the Natural Sciences, Blackwell, Oxford.

Harre, R., (1988), “Parsing the Amplitudes”, in Brown, H.R. & Harre, R. (eds), Philosophical Foundations of Quantum Field Theory, Oxford: Clarendon Press pp59-71.

Holmquist, G. P. & Filipsk, J. (1994), “Organisation of Mutations along the Genome: a Prime Determinant of Genome Evolution”, Trends in Ecology and Evolution, 9, 2, 65-69.

Hutchinson, G. E. (1948), “Circular Causal Systems in Ecology”, Ann. N.Y. Acad. Sci., 50, 221-246.

Hutchinson, G. E. (1965), The Ecological Theatre and the Evolutionary Play, Yale University Press.

Jabłonka, E. (1994), “Inheritance Systems and the Evolution of New Levels of Individuality”, J. theor. Biol., 170, 301-309.

Kampis, G. (1994), “Biological Evolution as a Process Viewed Internally”, in Atmanspacher, H. & Dalenoort, G. (eds), Inside versus Outside, Synergetics Series 63, Berlin: Springer Verlag, 85-110.

Keller, E. F. (1995), Refiguring Life: Metaphors of Twentieth Century Biology, N.Y.: Columbia University Press.

Konopka, A. K. (1994), “Fundamentals of Biomolecular Cryptology”, in Smith, D.W. (ed), Biocomputing Informatics and Genome Projects, London, San Diego: Academic Press, 119-174.

Mansson, B. A., & McGlade, J. M. (1993), “Ecology, Thermodynamics and Odum’s Conjectures”, Oecologia, 93:582-596

Marijuan, P. C. (1996), ‘Gloom in the Society of Enzymes’: on the Nature of Biological Information, BioSystems, 38, 2/3, 163-171.

Markman, E. M., Elorton, M. S. & McLanahan, A. G. (1980), “Classes and Collections: Principles of Organisation in the Learning of Hierarchical Relations”, Cognition, 8, 227-241.

Markman, E. M. & Hutchinson, J. E. (1984), “Children’s Understanding of Constraints of Word Meaning: Taxonomic Versus Thematic Relations”, Cognitive Psychology, 16, 1-27.

Mirowski, P. (1993), “Ecology in the Mirror of Economics”, History of Economics Society, Monthly Guest Editorial for HES, and available from URL:

Paton, R. C. (1992), “Towards a Metaphorical Biology”, Biology and Philosophy, 7, 279-294.

Paton, R. C. (1993a),“Some Computational Models at the Cellular Level”, BioSystems, 29, 63-75.

Paton, R. C. (1993b),“Understanding Biosystem Organisation I: Verbal Relations”, International Journal of Science Education., 15, 4, 395-410.

Paton, R. C. (1997), “Glue, Verb and Text Metaphors in Biology”, Acta Biotheoretica, 45, 1-15.

Paton, R. C. (1998), “The Ecologies of Hereditary Information”, Cybernetics and Human Knowing, 5, 4, 31-44.

Paton, R., Staniford, G. & Kendall, G. (1996), “Specifying Logical Agents in Cellular Hierarchies”, in Cuthbertson, R., Holcombe, M. & Paton, R. (eds), Computation in Cellular and Molecular Biological Systems, World Scientific: Singapore, 105-119

Paton, R. C. & Matsuno, K. (1998), “Some Common Themes for Enzymes and Verbs”, Acta Biotheoretica, 46, 131-140.

Pattee, H. H. (1977), “Dynamic and Linguistic Modes of Complex Systems”, International Journal of General Systems, 3, 259-266.

Pilkis, S. J., Claus, T. H., Kurland, I. J. & Lange, A. J. 1995, “6-Phosphofructo-2-kinase/ Fructose-2,6-Bisphosphatase: A metabolic signalling enzyme”, Annu. Rev. Biochem., 64: 799-835.

Richmond, M. H. (1979), “ ‘Cells’ and ‘Organisms’ as Habitats for DNA”, Proceedings of the Royal Society of London B. 204, 235-250.

Roche, J. (1990), “New Tasks for the Philosophy of Physics”, in Bhaskar, R. (ed) Harre and His Critics, Oxford: Blackwell, pp. 89-111.

Rosen, R. (1985), Anticipatory Systems, Oxford: Pergamon Press.

Rosen, R. (1991), Life Itself Columbia University Press: New York.

Sattler, R. (1986), Biophilosophy, Springer: Berlin.

Schiller, J. (1968), “Physiology’s Struggle for Independence in the First Half of the 19th Century”, History of Science, 7, 64-89.

Shapiro, J. A. (1991), “Genomes as Smart Systems”, Genetica, 84, 3-4.

Shapiro, J. A. (1992), “Barbara McClintock, 1902-1992”, BioEssays 14, 791-792.

Shapiro, J. A. (1997), “Genome Organization, Natural Genetic Engineering and Adaptive Mutation”, Trends in Genetics, 13, 3, 98-104.

Shepherd, G. M. (1990), “The Significance of Real Neural Architectures for Neural Network Simulations”, in E.L. Schwartz (ed), Computational Neuroscience, Cambridge MA: MIT, 82-96.

Thaler, D. S. (1994), “The Evolution of Genetic Intelligence”, Science, 264, 224—225. Thaler, D. S. & Messmer, B. T. (1996), “Evolution of Genetic Intelligence”, in Meyers,

R. A. (ed), Encyclopedia of Molecular Biology and Molecular Medicine Volume 2, Weinheim: VCH, 407-414.

Tansley, A.G. (1935), “The Use and Abuse of Vegetational Concepts and Terms”, Ecology, 16, 3, 284-307.

Taylor, P. J. (1988), “Technochratic Optimism, H. T. Odum, and the Partial Transformation of Ecological Metaphor after World War II”, Journal of History of Biol., 21, 2, 213-244.

Trifonov, E. N. (1989), “The Multiple Codes of Nucleotide Sequences”, Bull. Math. Biol., 51, 4, 417—432.

Trifonov, E. N. (1996), “Interfering Contexts of Regulatory Sequence Elements”, CABIOS, 12, 5, 423—429.

Uyeda, K. (1992), “Interactions of Glycolytic Enzymes with Cell Membrane”, Curr.Topics in Cell Regulation, 33, 31-46.

Varela, F. J. (1979), Principles of Biological Autonomy, New York: North Holland. Welch, G. R. (1987), “The Living Cell as an Ecosystem: Hierarchical Analogy and Symmetry”, Trends in Ecology and Evolution, 2, 10, 305-309.

Welch, G. R. & Keleti, T. (1987), “Is Cell Metabolism Controlled by a Molecular Democracy or by a Supramolecular Socialism?”, Trends in Biochemical Sciences., 12, 216-217.

Welch, G. R. & Kell, D. B. (1986), Not just Catalysts - Molecular Machines in Bioenergetics, in Welch, G.R. (ed), The Fluctuating Enzyme, New York: John Wiley, 451-492.


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