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Topological explanations and robustness in biological sciences

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Abstract

This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization.

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References

  • Albert R., Barabasi A.-L. (2002) Statistical mechanics of complex networks. Review Modern Physics 74: 47–97

    Article  Google Scholar 

  • Amundson R. (2005) The changing role of the embryo in evolutionary thought. Cambridge University Press, Cambridge

    Google Scholar 

  • Arcos, H., & Pereira, J. (2007) Spacetime: Arena or reality?. In V. Petkov (Ed.), Relativity and the dimensionality of the world. Fundamental theories of physics (Vol. 153, pp. 217–227). Berlin: Springer.

  • Attolini C. S. O., Stadler P. F. (2005) Neutral Networks of interacting RNA secondary structures. Advances in Complex Systems 8(2–3): 275–283

    Google Scholar 

  • Beatty J. (1995) The evolutionary contingency thesis. In: Wolters G., Lennox J. (eds) Concepts, theories, and rationality in the biological sciences. University of Pittsburgh Press, Pittsburgh, pp 45–81

    Google Scholar 

  • Berlow E. L. (1999) Strong effects of weak interactions in ecological communities. Nature 398: 330–334

    Article  Google Scholar 

  • Bernstein H., Byerly H.C., Hopf F.A., Michod R.E. (1985) Genetic damage, mutation, and the evolution of sex. Science 229(4719): 1277–1281

    Article  Google Scholar 

  • Craver C., Bechtel W. (2007) Top-down causation without top-down causes. Biology and Philosophy 22: 547–563

    Article  Google Scholar 

  • Craver, C. (forth.). Functions and mechanisms in contemporary neuroscience. In P. Huneman, (Ed.), Functions: Selection and mechanisms. Berlin: Synthese Library, Springer.

  • Crick F. H. C. (1968) The origin of the genetic code. Journal Molecular Biology 38: 367–379

    Article  Google Scholar 

  • Crutchfield J. (1994) Is anything ever new? Integrative themes. In: Cowan G., Pines D., Melzner D. (eds) Santa Fe Institute studies in the sciences of complexity XIX. Addison-Wesley, Reading, MA

    Google Scholar 

  • Cupal J., Stadler P., Schuster P. (1999) Topology in phenotype space. In: Giegerich J. (Ed.) Computer science in biology. Springer, Berlin, pp 9–15

    Google Scholar 

  • Dawkins R. (1982) The extended phenotype. Oxford University Press, Oxford

    Google Scholar 

  • de Visser J. A. G. M., Hermisson J., Wagner G. P., Ancel Meyers L., Bagheri-Chaichian H., Blanchard J. L., Chao L. (2003) Evolution and detection of genetic robustness. Evolution 57: 1959–1972

    Article  Google Scholar 

  • Dennett D. (1995) Darwin’s dangerous idea. Simons & Shuster, New York

    Google Scholar 

  • Dokholyan N., Li L., Ding F., Shakhnovich E. I. (2002) Topological determinants of protein folding. PNAS 99(13): 8637–8641

    Article  Google Scholar 

  • Dunne J. (2006) The network structure of food webs. In: Pascual M., Dunne J. (eds) Ecological networks: Linking structure to dynamics in food webs. Oxford University Press, Oxford

    Google Scholar 

  • Dunne J. A., Williams R. J., Martinez N. D. (2002a) Network structure and biodiversity loss in food webs: Robustness increases with connectance. Ecology Letters 5: 558–567

    Article  Google Scholar 

  • Dunne J. E., Williams R. J., Martinez N. D. (2002b) Food web structure and network theory: The role of connectance and size. PNAS 99: 12917–12922

    Article  Google Scholar 

  • Fontana W., Stadler P.F., Bornberg-Bauer E., Griesmacher T., Hofacker I.L., Tacker M. et al (1999) RNA folding and combinatory landscapes. Physics Review E 47: 2083–2099

    Article  Google Scholar 

  • Friedman M. (1974) Explanation and scientific understanding. Journal of Philosophy 71: 5–19

    Article  Google Scholar 

  • Gillett (2007). Understanding the new reductionism: The metaphysics of science and compositional reduction. The Journal of Philosophy, 193–216.

  • Gilllett (2010). Moving beyond the subset model of realization: The problem of qualitative distinctness in the metaphysics of science. Synthese. doi:10.1007/s11229-010-9840-1.

    Google Scholar 

  • Gould S. J. (1989) Wonderful life. The Burgess shale and the nature of history. Norton, New-York

    Google Scholar 

  • Granovetter M. (1973) The strength of weak ties. American Journal of Sociology 78(6): 1360–1380

    Article  Google Scholar 

  • Gross J. L., Tucker T. W. (1987) Topological graph theory. Wiley Interscience, Reading, MA

    Google Scholar 

  • Holling G. (1973) Resilience and stability of ecological systems. Annual Review of Ecology and Systematics 4: 1–23

    Article  Google Scholar 

  • Hubbell S. P. (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton

    Google Scholar 

  • Huneman P. (2010). The conceptual foundations of ecological engineering. Stability, individuation, ethics. In S. Barot (Ed.), Ecological engineering, from concepts to applications. Physics Procedia. Amsterdam: Elsevier.

  • Huynen M., Stadler P. F., Fontana W. (1996) Smoothness within ruggedness: The role of neutrality in adaptation. PNAS 93: 397–401

    Article  Google Scholar 

  • Kettlewell H.B.D. (1955) Selection experiments on industrial melanism in the Lepidoptera. Heredity 9: 323–342

    Article  Google Scholar 

  • Kitano H. (2004) Biological robustness. Nature Review Genetics 5: 826–837

    Article  Google Scholar 

  • Kitcher P. (1989) Explanatory unification and the causal structure of the world. In: Kitcher P., Salmon W. (eds) Scientific explanation. University of Minnesota Press, Minneapolis, pp 410–505

    Google Scholar 

  • Lehmann L., Keller L. (2006) The evolution of cooperation and altruism—A general framework and a classification of models. Journal of Evolutionary Biology 19: 1365–1376

    Article  Google Scholar 

  • Levin R., May R., Sugihara C. (2008) Complex systems: Ecology for bankers. Nature 451: 893–895

    Article  Google Scholar 

  • Lewontin R. C. (1970) Units of selection. Annual Review of Ecology and Systematics 1: 1–18

    Article  Google Scholar 

  • Machamer P., Darden L., Craver C. (2000) Thinking about mechanisms. Philosophy of Science 67(1): 1–25

    Article  Google Scholar 

  • Maser G. L., Guichard F., McCann K. S. (2007) Weak trophic interactions and the balance of enriched metacommunities. Journal of Theoretical Biology 247: 337–345

    Article  Google Scholar 

  • May R. M. (1974) Stability and complexity in model ecosystems. Princeton University Press, Princeton

    Google Scholar 

  • McCann K., Hastings J., Huxel R. (1998) Weak trophic interactions and the balance of nature. Nature 395: 794–798

    Article  Google Scholar 

  • Montoya J., Pimm S., Solé R. (2006) Ecological networks and their fragility. Nature 442: 259–267

    Article  Google Scholar 

  • Montoya J. M., Solé R. V. (2002) Small world patterns in food webs. Journal of Theoretical Biology 214: 405–412

    Article  Google Scholar 

  • Morange M. (2000) A history of molecular biology. Harvard University Press, New Haven

    Google Scholar 

  • Neander K. (1991) Functions as selected effects: The conceptual analysts defense. Philosophy of Science 58: 168–184

    Article  Google Scholar 

  • Nowak M. (2005) Five rules to the evolution of cooperation. Science 314(5805): 1560–1563

    Article  Google Scholar 

  • Park J., Newman M. (2003) The origin of degree correlations in the Internet and other networks. Physical Review E 68(2): 026112

    Article  Google Scholar 

  • Pimm S. L. (1984) The complexity and stability of ecosystems. Nature 307: 321–326

    Article  Google Scholar 

  • Pimm S. L. (2001) The balance of nature? Ecological issues in the conservation of species and communities. University of Chicago Press, Chicago

    Google Scholar 

  • Randrup T., Rogen T. (1997) How to twist a knot. Archiv der Mathematik 68(3): 252–264

    Article  Google Scholar 

  • Revilla I., Domingo R., Davidson E. (2003) Developmental gene network analysis. International Journal of Developmental Biology 47: 695–703

    Google Scholar 

  • Romano L.A., Gray G.A. (2003) Conservation of endo 16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 130(17): 4187–4199

    Article  Google Scholar 

  • Salmon W. (1984) Scientific explanation and the causal structure of the world. Princeton University Press, Princeton

    Google Scholar 

  • Santos F. C., Pacheco J. M. (2005) Scale-free networks provide a unifying framework for the emergence of cooperation. Physical Review Letter 95(098104): 1–5

    Google Scholar 

  • Santos F. C., Pacheco J. M. (2006) A new route to the evolution of cooperation. Journal of Evolutionary Biology 19(3): 726–733

    Article  Google Scholar 

  • Schuster P. (2002) A testable genotype-phenotype map: Modeling evolution of RNA molecules. In: Lässig M., Valleriani A. (eds) Lecture notes in physics, 585. Springer, Berlin, pp 55–81

    Google Scholar 

  • Schuster P., Fontana W., Stadler P. F., Hofacker I. (1994) From sequences to shapes and back: A case study in RNA secondary structures. Proceedings of the Royal Society of London Series B 255: 279–284

    Article  Google Scholar 

  • Shapiro L. (2000) Multiple realizations. Journal of Philosophy 97: 635–654

    Article  Google Scholar 

  • Sober E. (1998) Six sayings about adaptationism. In: Hull D., Ruse M. (eds) Oxford readings in philosophy of biology. Oxford University Press, Oxford, pp 72–86

    Google Scholar 

  • Solé R. V., Montoya J. M. (2001) Complexity and fragility in ecological networks. Proceedings of the Royal Society of London Series B 268: 2039–2045

    Article  Google Scholar 

  • Sole R., Valverde S. (2008) Spontaneous emergence of modularity in cellular networks. Journal of the Royal Society Interface 5: 129–133

    Article  Google Scholar 

  • Solé R. V., Ferrer R., Montoya J. M., Valverde S. (2002) Selection, tinkering and emergence in complex networks. Complexity 8: 20–33

    Article  Google Scholar 

  • Stadler P., Stadler P., Wagner G., Fontana W. (2001) The topology of the possible: formal spaces underlying patterns of evolutionary change. Journal Theoretical Biology 213(2): 241–274

    Article  Google Scholar 

  • Stadler B., Stadler P. (2004) The topology of evolutionary biology. In: Ciobanu C. (Ed.) Modeling in molecular biology. Natural computing series. Springer, Berlin, pp 267–286

    Google Scholar 

  • Strogatz S. (2001) Exploring complex networks. Nature 410: 268–276

    Article  Google Scholar 

  • Tilman D. (1996) Biodiversity: Population versus ecosystem stability. Ecology 77(2): 350–363

    Article  Google Scholar 

  • Tylianakis J. (2008) Understanding the web of life: The birds, the bees, and sex with aliens. PLoS Biology 6(2): 224–228

    Article  Google Scholar 

  • Ulanowicz R. (2002) The balance between adaptability and adaptation. Biosystems 64(1–3): 13–22

    Article  Google Scholar 

  • Van Nimwegen E., Crutchfield J., Huynen M. (1999) Neutral evolution of mutational robustness. Proceedings of the National Academy of Sciences of the United States of America 96(17): 9716–9720

    Article  Google Scholar 

  • Vendruscolo M., Dokholyan N., Paci E., Karplus N. (2002) Small-world view of the amino acids that play a key role in protein folding. Physical Review E 65(061910): 1–5

    Google Scholar 

  • Wagner G., Altenberg L. (1996) Complex adaptations and the evolution of evolvability. Evolution 50(3): 967–976

    Article  Google Scholar 

  • Wagner A. (2005a) Robustness and evolvability in living systems. Princeton University Press, Princeton

    Google Scholar 

  • Wagner A. (2005b) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27: 176–188

    Article  Google Scholar 

  • Watts D. (2003) Six degrees of separation. Norton, New York

    Google Scholar 

  • Watts D. J., Strogatz S. H. (1998) Collective dynamics in “small-world” networks. Nature 393: 440–442

    Article  Google Scholar 

  • West S.A., Griffin A.S., Gardner A. (2007) Social semantics: Altruism, cooperation, mutualism, strong reciprocity and group selection. Journal of Evolutionary Biology 20: 415–432

    Article  Google Scholar 

  • White S., Kiester D. (2008) Topology matters: Network topology affects outcomes from community ecology neutral models. Computers, Environment and Urban Systems 32(2): 165–171

    Article  Google Scholar 

  • Wilke C. O., Wang J., Ofria C., Lenski R. E., Adami C. (2001) Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412: 331–333

    Article  Google Scholar 

  • Yodzis P. (1989) Introduction to theoretical ecology. Harper & Row, New York

    Google Scholar 

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  1. IHPST, CNRS/Université Paris I Sorbonne, Paris, France

    Philippe Huneman

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Correspondence to Philippe Huneman.

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Huneman, P. Topological explanations and robustness in biological sciences. Synthese 177, 213–245 (2010). https://doi.org/10.1007/s11229-010-9842-z

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