Skip to main content

Behavior-Finding: Morphogenetic Designs Shaped by Function

  • Chapter
  • First Online:
Morphogenetic Engineering

Part of the book series: Understanding Complex Systems ((UCS))

Abstract

Evolution has shaped an incredible diversity of multicellular living organisms, whose complex forms are self-made through a robust developmental process. This fundamental combination of biological evolution and development has served as an inspiration for novel engineering design methodologies, with the goal to overcome the scalability problems suffered by classical top-down approaches. Top-down methodologies are based on the manual decomposition of the design into modular, independent subunits. In contrast, recent computational morphogenetic techniques have shown that they were able to automatically generate truly complex innovative designs. Algorithms based on evolutionary computation and artificial development have been proposed to automatically design both the structures, within certain constraints, and the controllers that optimize their function. However, the driving force of biological evolution does not resemble an enumeration of design requirements, but much rather relies on the interaction of organisms within the environment. Similarly, controllers do not evolve nor develop separately, but are woven into the organism’s morphology. In this chapter, we discuss evolutionary morphogenetic algorithms inspired by these important aspects of biological evolution. The proposed methodologies could contribute to the automation of processes that design “organic” structures, whose morphologies and controllers are intended to solve a functional problem. The performance of the algorithms is tested on a class of optimization problems that we call behavior-finding. These challenges are not explicitly based on morphology or controller constraints, but only on the solving abilities and efficacy of the design. Our results show that morphogenetic algorithms are well suited to behavior-finding.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 139.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Andersen, T., Newman, R., Otter, T.: Shape homeostasis in virtual embryos. Artif. Life 15(2), 161–183 (2009)

    Article  Google Scholar 

  2. Basanta, D., Miodownik, M., Baum, B.: The evolution of robust development and homeostasis in artificial organisms. PLoS Comput. Biol. 4(3), e1000,030 (2008)

    Google Scholar 

  3. Bentley, P., Kumar, S.: Three ways to grow designs: a comparison of embryogenies for an evolutionary design problem. In: Proceedings Genetic Evolutionary Computation Conference (GECCO), vol. 1, pp. 35–43. Morgan Kaufmann (1999)

    Google Scholar 

  4. Bongard, J.C., Pfeifer, R.: Repeated structure and dissociation of genotypic and phenotypic complexity in artificial ontogeny. In: Proceedings Genetic Evolutionary Computation Conference (GECCO), pp. 829–836. Morgan Kaufmann (2001)

    Google Scholar 

  5. Bongard, J.C., Pfeifer, R.: Evolving complete agents using artificial ontogeny. In: Hara, F., Pfeifer, R. (eds.) Morpho-functional Machines: The New Species, pp. 237–258. Springer (2003)

    Google Scholar 

  6. Chavoya, A., Duthen, Y.: A cell pattern generation model based on an extended artificial regulatory network. Biosystems 94(1–2), 95–101 (2008)

    Article  Google Scholar 

  7. Coates, P., Broughton, T., Jackson, H.: Exploring three-dimensional design worlds using lindenmayer systems and genetic programming. In: Bentley, P.J. (ed.) Evolutionary Design by Computers, pp. 323–341. Morgan Kaufmann (1999)

    Google Scholar 

  8. Davidich, M., Bornholdt, S.: The transition from differential equations to boolean networks: a case study in simplifying a regulatory network model. J. Theor. Biol. 255(3), 269–277 (2008)

    Article  Google Scholar 

  9. Davidson, E.H.: The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, 1 edn. Academic Press, London (2006)

    Google Scholar 

  10. Davidson, E.H., Erwin, D.H.: Gene regulatory networks and the evolution of animal body plans. Science 311(5762), 796–800 (2006)

    Article  Google Scholar 

  11. Dellaert, F., Beer, R.D.: A developmental model for the evolution of complete autonomous agents. In: Proceedings from Animals to Animats: International Conference on Simulation of Adaptive Behavior (ISAB), pp. 393–401. MIT Press (1996)

    Google Scholar 

  12. Devert, A., Bredeche, N., Schoenauer, M.: Robust multi-cellular developmental design. In: Proceedings Genetic Evolutionary Computation Conference (GECCO), pp. 982–989. ACM (2007)

    Google Scholar 

  13. Devert, A., Bredeche, N., Schoenauer, M.: Unsupervised learning of echo state networks: a case study in artificial embryogeny. In: Proceedings of International Conference on Artificial Evolution (EA). Springer (2008)

    Google Scholar 

  14. de Garis, H.: Genetic programming: artificial nervous systems, artificial embryos and embryological electronics. In: Proceedings of Parallel Problem Solving Nature (PPSN). Springer (1991)

    Google Scholar 

  15. de Garis, H.: Artificial embryology: the genetic programming of cellular differentiation. In: Proceedings of the III Workshop in Artificial Life, Santa Fe, New Mexico. Addison-Wesley (1992)

    Google Scholar 

  16. de Jong, H.: Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9(1), 67–103 (2002)

    Article  Google Scholar 

  17. Eggenberger, P.: Cell interactions as a control tool of developmental processes for evolutionary robotics. In: Proceedings from Animals to Animats: International Conference Simulation Adaptive Behavior (ISAB), pp. 440–448. MIT Press (1996)

    Google Scholar 

  18. Eggenberger, P.: Evolving morphologies of simulated 3D organisms based on differential gene expression. In: Proceedings of European Conference on Artificial Life (ECAL), pp. 205–213. MIT Press (1997)

    Google Scholar 

  19. Eggenberger, P.: Genome-physics interaction as a new concept to reduce the number of genetic parameters in artificial evolution. In: Proceedings of IEEE Congress on Evolutionary Computation (CEC), pp. 191–198. IEEE-Press (2003)

    Google Scholar 

  20. Federici, D., Downing, K.: Evolution and development of a multicellular organism: scalability, resilience, and neutral complexification. Artif. Life 12(3), 381–409 (2006)

    Article  Google Scholar 

  21. Fernández, J.D., Vico, F.J.: Automating the search of molecular motor templates by evolutionary methods. Biosystems 106, 82–93 (2011)

    Article  Google Scholar 

  22. Fernández-Blanco, E., Dorado, J., Rabuñal, J.R., Gestal, M., Pedreira, N.: A new evolutionary computation technique for 2D morphogenesis and information processing. WSEAS Trans. Inf. Sci. Appl. 4(3), 600–607 (2007)

    Google Scholar 

  23. Floreano, D., Keller, L.: Evolution of adaptive behaviour in robots by means of Darwinian selection. PLoS Biol. 8(1), e1000,292 (2010)

    Google Scholar 

  24. Gruau, F.: Genetic micro programming of neural networks. In: Kinnear, K.E. (ed.) Advances in Genetic Programming, pp. 495–518. MIT Press (1994)

    Google Scholar 

  25. Haddow, P.C., Hoye, J.: Achieving a simple development model for 3D shapes: are chemicals necessary? In: Proceedings of Genetic Evolutionary Computation Conference (GECCO), pp. 1013–1020. ACM (2007)

    Google Scholar 

  26. Hemberg, M., O’Reilly, U.M.: Integrating generative growth and evolutionary computation for form exploration. Genet. Program. Evol. Mach. 8(2), 163–186 (2007)

    Article  Google Scholar 

  27. Hogeweg, P.: Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. J. Theor. Biol. 203(4), 317–333 (2000)

    Article  Google Scholar 

  28. Hornby, G.S.: Functional scalability through generative representations: the evolution of table designs. Environ. Plan. B 31(4), 569–587 (2004)

    Article  Google Scholar 

  29. Hornby, G.S., Lipson, H., Pollack, J.B.: Evolution of generative design systems for modular physical robots. In: Proceedings of IEEE International Conference on Robotics and Automation (ICRA), vol. 4, pp. 4146–4151. IEEE-Press (2001)

    Google Scholar 

  30. Hornby, G.S., Lipson, H., Pollack, J.B.: Generative representations for the automated design of modular physical robots. IEEE Trans. Robot. Autom. 19(4), 703–719 (2003)

    Article  Google Scholar 

  31. Hornby, G.S., Pollack, J.B.: Creating high-level components with a generative representation for body-brain evolution. Artif. Life 8(3), 223–246 (2002)

    Article  Google Scholar 

  32. Joachimczak, M., Wróbel, B.: Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics. In: Proc. International Conference on the Simulation and Synthesis of Living Systems (Artificial Life XI), pp. 297–304. MIT Press (2008)

    Google Scholar 

  33. Kauffman, S.: Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22(3), 437–467 (1969)

    Article  Google Scholar 

  34. Kniemeyer, O., Buck-Sorlin, G.H., Kurth, W.: A graph grammar approach to artificial life. Artif. Life 10(4), 413–431 (2004)

    Google Scholar 

  35. Komosinski, M., Rotaru-Varga, A.: Comparison of different genotype encodings for simulated 3D agents. Artif. Life 7(4), 395–418 (2002)

    Article  Google Scholar 

  36. Kowaliw, T., Grogono, P., Kharma, N.: The evolution of structural design through artificial embryogeny. In: IEEE Symposium on Artificial Life (IEEE-ALIFE), pp. 425–432 (2007)

    Google Scholar 

  37. Koza, J.R.: Gene duplication to enable genetic programming to concurrently evolve both the architecture and work-performing steps of a computer program. In: Proceedings of International Joint Conference on Artificial Intelligence (IJCAI), vol. 1, pp. 734–740. Morgan Kaufmann (1995)

    Google Scholar 

  38. Kumar, S., Bentley, P.J.: Implicit evolvability: an investigation into the evolvability of an embryogeny. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO). Morgan Kaufmann (2000)

    Google Scholar 

  39. Kumar, S., Bentley, P.J.: Biologically inspired evolutionary development. In: Proceedings of International Conference Evolvable Systems (ICES), pp. 99–106. Springer (2003)

    Google Scholar 

  40. Kundu, S., Sorensen, D.C., Phillips Jr, G.N.: Automatic domain decomposition of proteins by a gaussian network model. Proteins Struct. Funct. Bioinf. 57(4), 725–733 (2004)

    Article  Google Scholar 

  41. Levine, M., Tjian, R.: Transcription regulation and animal diversity. Nature 424(6945), 147–151 (2003)

    Article  Google Scholar 

  42. Lister, I., Schmitz, S., Walker, M., Trinick, J., Buss, F., Veigel, C., Kendrick-Jones, J.: A monomeric myosin VI with a large working stroke. EMBO J. 23(8), 1729–1738 (2004)

    Article  Google Scholar 

  43. Lobo, D., Hjelle, D.A., Lipson, H.: Reconfiguration algorithms for robotically manipulatable structures. In: Proceedings of ASME/IFToMM International Conference on Reconfigurable Mechanisms Robots (ReMAR), pp. 13–22. IEEE-Press (2009)

    Google Scholar 

  44. Lobo, D., Vico, F.J.: Evolution of form and function in a model of differentiated multicellular organisms with gene regulatory networks. Biosystems 102(2–3), 112–123 (2010)

    Article  Google Scholar 

  45. Lobo, D., Vico, F.J.: Evolutionary development of tensegrity structures. Biosystems 101(3), 167–176 (2010)

    Article  Google Scholar 

  46. Lobo, D., Vico, F.J., Dassow, J.: Graph grammars with string-regulated rewriting. Theor. Comput. Sci. 412(43), 6101–6111 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  47. Lu, M.: The role of shape in determining molecular motions. Biophys. J. 89(4), 2395–2401 (2005)

    Article  Google Scholar 

  48. Matsushita, K., Lungarella, M., Paul, C., Yokoi, H.: Locomoting with less computation but more morphology. In: Proceedings of IEEE International Conference on Robotics and Automation (ICRA), pp. 2008–2013. IEEE-Press (2005)

    Google Scholar 

  49. Miller, J.F.: Evolving a self-repairing, self-regulating, french flag organism. In: Proceedings Genetic and Evolutionary Computation Conference (GECCO), pp. 129–139. Springer (2004)

    Google Scholar 

  50. Motro, R.: Tensegrity: Structural Systems for the Future. Butterworth-Heinemann, Oxford (2006)

    Google Scholar 

  51. O’Neill, M., Ryan, C.: Grammatical evolution. IEEE Trans. Evolut. Comput. 5(4), 349–358 (2001)

    Google Scholar 

  52. O’Neill, M., Swafford, J.M., McDermott, J., Byrne, J., Brabazon, A., Shotton, E., McNally, C., Hemberg, M.: Shape grammars and grammatical evolution for evolutionary design. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO), pp. 1035–1042. ACM (2009)

    Google Scholar 

  53. Paul, C.: Morphological computation: a basis for the analysis of morphology and control requirements. Robot. Auton. Syst. 54(8), 619–630 (2006)

    Article  Google Scholar 

  54. Paul, C., Lipson, H., Valero-Cuevas, F.: Evolutionary form-finding of tensegrity structures. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO), pp. 3–10. ACM (2005)

    Google Scholar 

  55. Pfeifer, R., Iida, F., Gomez, G.: Morphological computation for adaptive behavior and cognition. Int. Congr. Ser. 1291, 22–29 (2006)

    Article  Google Scholar 

  56. Pollack, J., Lipson, H., Hornby, G., Funes, P.: Three generations of automatically designed robots. Artif. Life 7, 215–223 (2001)

    Article  Google Scholar 

  57. Prusinkiewicz, P., Lindenmayer, A.: The Algorithmic Beauty of Plants. Springer, New York (1990)

    Google Scholar 

  58. Reil, T.: Dynamics of gene expression in an artificial genome—implications for biological and artificial ontogeny. In: Proceedings of the European Conference on Artificial Life (ECAL), pp. 457–466. Springer (1999)

    Google Scholar 

  59. Rieffel, J., Pollack, J.: The emergence of ontogenic scaffolding in a stochastic development environment. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO), pp. 804–815. Springer (2004)

    Google Scholar 

  60. Rieffel, J., Pollack, J.: Crossing the fabrication gap: evolving assembly plans to build 3D objects. In: Proceedings of IEEE Congress on Evolutionary Computation (CEC). IEEE-Press (2006)

    Google Scholar 

  61. Roggen, D., Federici, D.: Multi-cellular development: is there scalability and robustness to gain? In: Proceedings of the Parallel Problem Solving Nature (PPSN), pp. 391–400. Springer (2004)

    Google Scholar 

  62. Roggen, D., Federici, D., Floreano, D.: Evolutionary morphogenesis for multi-cellular systems. Genet. Program. Evol. Mach. 8(1), 61–96 (2007)

    Article  Google Scholar 

  63. Roggen, D., Floreano, D., Mattiussi, C.: A morphogenetic evolutionary system: phylogenesis of the poetic circuit. In: Proceedings of International Conference on Evolvable Systems (ICES), pp. 153–164. Springer (2003)

    Google Scholar 

  64. Rosenman, M.A.: The generation of form using an evolutionary approach. In: Dasgupta, D., Michalewicz, Z. (eds.) Evolutionary Algorithms in Engineering Applications, pp. 69–86. Springer (1997)

    Google Scholar 

  65. Rudolph, S., Alber, R.: An evolutionary approach to the inverse problem in rule-based design representations. In: Proceedings of International Conference on Artificial Intelligence in Design (AID). Kluwer Publishers (2002)

    Google Scholar 

  66. Schliwa, M., Woehlke, G.: Molecular motors. Nature 422(6933), 759–765 (2003)

    Article  Google Scholar 

  67. Schnier, T., Gero, J.: Learning genetic representations as alternative to hand-coded shape grammars. In: Proceedings of International Conference on Artificial Intelligence in Design (AID). Kluwer Publishers (1996)

    Google Scholar 

  68. Schot, S.H.: Jerk: the time rate of change of acceleration. Am. J. Phys. 46(11), 1090–1094 (1978)

    Article  Google Scholar 

  69. Shea, K., Cagan, J.: Innovative dome design: applying geodesic patterns with shape annealing. Artif. Int. Eng. Des. Anal. Manuf. 11(5), 379–394 (1997)

    Article  Google Scholar 

  70. Shea, K., Cagan, J., Fenves, S.J.: A shape annealing approach to optimal truss design with dynamic grouping of members. J. Mech. Des. 119(3), 388–394 (1997)

    Article  Google Scholar 

  71. Shim, Y.S., Kim, C.H.: Generating flying creatures using body-brain co-evolution. In: Proceedings of Symposium on Computer Animation (SCA), pp. 276–285. Eurographics Association (2003)

    Google Scholar 

  72. Sims, K.: Evolving 3D morphology and behavior by competition. Artif. Life 1(4), 353–372 (1994)

    Article  Google Scholar 

  73. Spector, L., Klein, J., Feinstein, M.: Division blocks and the open-ended evolution of development, form, and behavior. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO), pp. 316–323. ACM (2007)

    Google Scholar 

  74. Stanley, K., Miikkulainen, R.: A taxonomy for artificial embryogeny. Artif. Life 9(2), 93–130 (2003)

    Article  Google Scholar 

  75. Stanley, K.O.: Compositional pattern producing networks: a novel abstraction of development. Genet. Program. Evol. Mach. 8(2), 131–162 (2007)

    Article  MathSciNet  Google Scholar 

  76. Stiny, G.: Introduction to shape and shape grammars. Environ. Plan. B 7(3), 343–351 (1980)

    Article  Google Scholar 

  77. Su, J.: Protein unfolding behavior studied by elastic network model. Biophys. J. 94(12), 4586–4596 (2008)

    Article  Google Scholar 

  78. Taura, T., Nagasaka, I.: Adaptive-growth-type 3D representation for configuration design. Artif. Int. Eng. Des. Anal. Manuf. 13(3), 171–184 (1999)

    Article  Google Scholar 

  79. Tibert, A., Pellegrino, S.: Review of form-finding methods for tensegrity structures. Int. J. Space Struct. 18, 209–223 (2003)

    Article  Google Scholar 

  80. Togashi, Y., Mikhailov, A.S.: Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines. Proc. Natl. Acad. Sci. U S A 104(21), 8697–8702 (2007)

    Article  Google Scholar 

  81. Trefzer, M.A., Kuyucu, T., Miller, J.F., Tyrrell, A.M.: A model for intrinsic artificial development featuring structural feedback and emergent growth. In: Proceedings of IEEE Congress on Evolutionary Computation (CEC), pp. 301–308. IEEE-Press (2009)

    Google Scholar 

  82. Vale, R.D., Milligan, R.A.: The way things move: looking under the hood of molecular motor proteins. Science 288(5463), 88–95 (2000)

    Article  Google Scholar 

  83. Watson, J., Geard, N., Wiles, J.: Towards more biological mutation operators in gene regulation studies. Biosystems 76(1–3), 239–248 (2004)

    Article  Google Scholar 

  84. Willadsen, K., Wiles, J.: Dynamics of gene expression in an artificial genome. In: Proceedings of IEEE Congress on Evolutionary Computation (CEC), pp. 185–190. IEEE-Press (2003)

    Google Scholar 

  85. Yang, L.W.W., Bahar, I.: Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 13(6), 893–904 (2005)

    Article  Google Scholar 

  86. Zhan, S., Miller, J.F., Tyrrell, A.M.: An evolutionary system using development and artificial genetic regulatory networks for electronic circuit design. Biosystems 98(3), 176–192 (2009)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Daniel Lobo .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Lobo, D., Fernández, J.D., Vico, F.J. (2012). Behavior-Finding: Morphogenetic Designs Shaped by Function. In: Doursat, R., Sayama, H., Michel, O. (eds) Morphogenetic Engineering. Understanding Complex Systems. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33902-8_17

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-33902-8_17

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33901-1

  • Online ISBN: 978-3-642-33902-8

  • eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)

Publish with us

Policies and ethics