A review of morphogenetic engineering

Natural Computing

Volumn 12, Issue 4, 2013, Pages 517-535

  Doursat, René ^a   Sayama, Hiroki ^b   Michel, Olivier ^c  

^a DREXEL UNIVERSITY   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

^c UNIVERSITÉ PARIS EST CRÉTEIL   (France)

Author keywords

Agent based modeling; Artificial life; Collective construction; Complex systems; Evolutionary development; Generative grammars; Morphogenesis; Self organization; Swarm robotics; Systems engineering

Indexed keywords

AGENT-BASED MODEL; ARTIFICIAL LIFE; COLLECTIVE CONSTRUCTIONS; EVOLUTIONARY DEVELOPMENT; GENERATIVE GRAMMARS; MORPHOGENESIS; SELF ORGANIZATIONS; SWARM ROBOTICS;

CELLULAR AUTOMATA; LARGE SCALE SYSTEMS; PRODUCT DESIGN; SYSTEMS ENGINEERING;

EMBEDDED SYSTEMS;

ANALYTIC METHOD; ARTICLE; COMPUTER LANGUAGE; COMPUTER PROGRAM; COMPUTER SYSTEM; ENGINEERING; GRAMMAR; INFORMATION SYSTEM; MATHEMATICAL COMPUTING; METHODOLOGY; MORPHOGENESIS; MORPHOGENETIC ENGINEERING; ORGANIZATION; ROBOTICS;

EID: 84890510984     PISSN: 15677818     EISSN: 15729796     Source Type: Journal    
DOI: 10.1007/s11047-013-9398-1     Document Type: Article

References (110)

1. Abelson H, Allen D, Coore D, Hanson C, Homsy G, Knight TF Jr, Nagpal R, Rauch E, Sussman GJ, Weiss R (2000) Amorphous computing. Commun ACM 43(5):74-82
2. Alonso-Mora J, Breitenmoser A, Rufli M, Siegwart R, Beardsley P (2011) Multi-robot system for artistic pattern formation. In: IEEE international conference on robotics and automation (ICRA), pp 4512-4517
3. Arbuckle DJ, Requicha AAG (2012) Issues in self-repairing robotic self-assembly. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 141-155
4. Bai L, Breen D (2012) Chemotaxis-inspired cellular primitives for self-organizing shape formation. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 209-237
5. Baldassarre G, Parisi D, Nolfi S (2006) Distributed coordination of simulated robots based on self-organization. Artif Life 12(3):289-311
6. Ball P (1999) The self-made tapestry. Oxford University Press, Oxford
7. Barabási AL, Albert R (1999) Emergence of scaling in random networks. Sci Agric 286(5439):509-512
8. Barrat A, Barthélemy M, Vespignani A (2008) Dynamical processes on complex networks. Cambridge University Press, New York
9. Beal J (2005) Programming an amorphous computational medium. In: Unconventional programming paradigms, pp 97-97
10. Beal J (2012) Functional blueprints: an approach to modularity in grown systems. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 313-329
11. Beal J, Bachrach J (2006) Infrastructure for engineered emergence on sensor/actuator networks. IEEE Intell Syst 21(2):10-19
12. Beal J, Dulman S, Usbeck K, Viroli M, Correll N (2012) Organizing the aggregate: languages for spatial computing. Comput Res Repos:abs/1202.5509
13. Bentley P, Kumar S (1999) Three ways to grow designs: a comparison of embryogenies for an evolutionary design problem. In: Proceedings of the genetic and evolutionary computation conference, vol 1. Morgan Kaufmann, San Francisco, pp 35-43
14. Bhalla N, Bentley PJ (2012) Programming self-assembling systems via physically encoded information. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 157-188
15. Bhalla N, Bentley PJ, Jacob C (2007) Mapping virtual self-assembly rules to physical systems. In: Unconventional Computing, p 167
16. Bonabeau E, Dorigo M, Theraulaz G (1999) Swarm intelligence: from natural to artificial systems. Oxford University Press, Oxford
17. Brooks R (1986) A robust layered control system for a mobile robot. IEEE J Robot Autom 2(1):14-23
18. Bullock S, Ladley D, Kerby M (2012) Wasps, termites, and waspmites: Distinguishing competence from performance in collective construction. Artif Life 18(3):267-290
19. Carroll SB (2005) Endless forms most beautiful: the new science of Evo Devo and the making of the animal kingdom. W. W. Norton, New York
20. Christensen AL, O'Grady R, Dorigo M (2007) Morphology control in a multirobot system. IEEE Robot Autom Mag 14(4):18-25
21. Coen E (2000) The art of genes. Oxford University Press, Oxford
22. Coen E, Rolland-Lagan AG, Matthews M, Bangham JA, Prusinkiewicz P (2004) The genetics of geometry. Proc Natl Acad Sci USA 101(14):4728-4735
23. Coore DN (1999) Botanical computing: a developmental approach to generating interconnect topologies on an amorphous computer. PhD Thesis, MIT
24. Cussat-Blanc S, Pascalie J, Mazac S, Luga H, Duthen Y (2012) A synthesis of the cell2organ developmental model. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 353-381
25. Detweiler C, Vona M, Yoon Y, Yun S, Rus D (2007) Self-assembling mobile linkages. IEEE Robot Autom Mag 14(4):45-55
26. Dorigo M, Stützle T (2004) Ant colony optimization. MIT, Cambridge
27. Doursat R (2006) The growing canavas of biological development: multiscale pattern generation on an expanding lattice of gene regulatory networks. InterJournal 1809
28. Doursat R (2008) Organically grown architectures: creating decentralized, autonomous systems by embryomorphic engineering. In: Würtz RP (eds) Organic computing, understanding complex systems. Springer, Berlin, pp 167-199
29. Doursat R (2009) Facilitating evolutionary innovation by developmental modularity and variability. In: Proceedings of the 11th annual conference on genetic and evolutionary computation (GECCO). ACM, New York, pp 683-690
30. Doursat R, Sayama H, Michel O (eds) (2012a) Morphogenetic engineering: toward programmable complex systems. understanding complex systems. Springer, New York
31. Doursat R, Sayama H, Michel O (2012b) Morphogenetic engineering: Reconciling self-organization and architecture. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems. Understanding complex systems. Springer, New York, pp 1-25
32. Doursat R, Sánchez C, Dordea R, Fourquet D, Kowaliw T (2012c) Embryomorphic engineering: emergent innovation through evolutionary development. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 275-311
33. Eggenberger P (1997) Evolving morphologies of simulated 3D organisms based on differential gene expression. In: Proceedings of the fourth European conference on artificial life, pp 205-213
34. Endy D (2005) Foundations for engineering biology. Nat Biotechnol 438(7067):449-453
35. Giavitto JL, Michel O (2002) The topological structures of membrane computing. Fundam Inf 49(1-3):123-145
36. Giavitto J-L, Godin C, Michel O, Prusinkiewicz P (2002) Modelling and Simulation of biological processes in the context of genomics. In: Computational models for integrative and developmental biology. Hermes
37. Gierer A, Meinhardt H (1972) A theory of biological pattern formation. Biol Cybern 12(1):30-39
38. Goldstein S, Campbell J, Mowry T (2005) Programmable matter. IEEE Comput Archit Lett 38(6):99-101
39. Goodwin BC (1994) How the leopard changed its spots: the evolution of complexity. Scribner, New York
40. Grouchy P, Lipson H (2012) Evolution of self-replicating cube conglomerations in a simulated 3D environment. Artif Life 13:59-66
41. Hammarlund P, Lisper B (1993) On the relation between functional and data parallel programming languages. In: Proceedings of the conference on functional programming languages and computer architecture. ACM, New York, pp 210-219
42. Hebb DO (1949) The organization of behavior. Wiley, New York
43. Holland JH (1992) Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence. MIT, Cambridge
44. Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci USA 79(8):2554-2558
45. Hornby GS, Pollack JB (2001) The advantages of generative grammatical encodings for physical design. In: Proceedings of the 2001 congress on evolutionary computation, vol 1, pp 600-607
46. Jin Y, Meng Y (2011) Morphogenetic robotics: an emerging new field in developmental robotics. IEEE Trans Syst Man Cybern C 41(2):145-160
47. Jin Y, Meng Y (2012) Morphogenetic robotics: a new paradigm for designing self-organizing, self-reconfigurable and self-adaptive robots. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 61-87
48. Joachimczak M, Wróbel B (2008) Evo-devo in silico: a model of a gene network regulating multicellular development in 3d space with artificial physics. In: Artificial life XI: proceedings of the eleventh international conference on the simulation and synthesis of living systems, pp 297-304
49. Joachimczak M, Kowaliw T, Doursat R, Wróbel B (2012) Brainless bodies: Controlling the development and behavior of multicellular animats by gene regulation and diffusive signals. In: Artificial life 13: proceedings of the thirteenth international conference on the simulation and synthesis of living systems, pp 349-356
50. Kauffman SA (1993) The origins of order: self organization and selection in evolution. Oxford University Press, New York
51. Kauffman SA (2008) Reinventing the sacred: a new view of science, reason, and religion. Basic Books, New York
52. Kennedy J, Eberhart R (1995) Particle swarm optimization. In: Proceedings of IEEE international conference on neural networks, vol 4. University of Western Australia, Perth, pp 1942-1948
53. Kephart JO, Chess DM (2003) The vision of autonomic computing. Comput Aided Des 36(1):41-50
54. Kernbach S, Meister E, Schlachter F, Jebens K, Szymanski M, Liedke J, Laneri D, Winkler L, Schmickl T, Thenius R et al (2008) Symbiotic robot organisms: replicator and symbrion projects. In: Proceedings of the 8th workshop on performance metrics for intelligent systems. ACM, Gaithersburg, pp 62-69
55. Knight T (2003) Idempotent vector design for standard assembly of biobricks. Tech. Rep., DTIC Document
56. Kowaliw T, Banzhaf W (2012) Mechanisms for complex systems engineering through artificial development. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 331-351
57. Kowaliw T, Grogono P, Kharma N (2004) Bluenome: A novel developmental model of artificial morphogenesis. In: Genetic and evolutionary computation GECCO '04. Springer, Seattle, pp 93-104
58. Lipson H, Pollack JB (2000) Automatic design and manufacture of robotic lifeforms. Nat Biotechnol 406(6799):974-978
59. Liu W, Winfield AFT (2012) Distributed autonomous morphogenesis in a self-assembling robotic system. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 89-113
60. Lobo D, Vico FJ (2010) Evolutionary development of tensegrity structures. Biosyst Eng 101(3):167-176
61. Lobo D, Fernández JD, Vico FJ (2012) Behavior-finding: morphogenetic designs shaped by function. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 441-472
62. Malsburg C (2008) Organic computing. In: Würtz RP (ed) Organic computing, understanding complex systems. In: The organic future of information technology. Springer, New York, pp 7-24
63. Mamei M, Vasirani M, Zambonelli F (2004) Experiments of morphogenesis in swarms of simple mobile robots. Appl Artif Intell 18(9-10):903-919
64. Marzano S, Aarts E (2003) The new everyday view on ambient intelligence. Uitgeverij 010 Publishers, Rotterdam
65. Miller JF, Banzhaf W (2003) Evolving the program for a cell: from french flags to Boolean circuits. In: Kumar S, Bentley P (eds) On growth, form and computers. Academic Press, London, pp 278-301
66. Minai AA, Braha D, Bar-Yam Y (2006) Complex engineered systems: Science meets technology. In: Braha D, Bar-Yam Y, Minai AA (eds) Complex engineered systems: a new paradigm. Springer, Cambridge, pp 1-21
67. Montagna S, Viroli M (2012) A computational framework for multilevel morphologies. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 383-405
68. Murata S, Yoshida E, Kamimura A, Kurokawa H, Tomita K, Kokaji S (2002) M-tran: self-reconfigurable modular robotic system. IEEE/ASME Trans Mechatron 7(4):431-441
69. Nagpal R (2001) Programmable self-assembly: constructing global shape using biologically-inspired local interactions and origami mathematics. PhD Thesis, MIT
70. Nagpal R (2002) Programmable self-assembly using biologically-inspired multiagent control. In: Proceedings of the first international joint conference on autonomous agents and multiagent systems: part 1, ACM, New York, pp 418-425
71. Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci USA 103(23):8577-8582
72. Nunes de Castro LN (2006) Fundamentals of natural computing: basic concepts, algorithms, and applications. CRC Press, Boca Raton
73. O'Grady R, Christensen AL, Dorigo M (2012) Swarmorph: morphogenesis with self-assembling robots. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 27-60
74. Pearson JE (1993) Complex patterns in a simple system. Sci Agric 261(5118):189-192
75. Pfeifer R, Bongard J, Grand S (2006) How the body shapes the way we think: a new view of intelligence. MIT, Cambridge
76. Prusinkiewicz P, Lindenmayer A (1991) The algorithmic beauty of plants. Springer, New York
77. Rieffel J, Valero-Cuevas F, Lipson H (2009) Automated discovery and optimization of large irregular tensegrity structures. Comput Struct 87(5):368-379
78. Rothemund PWK (2006) Folding dna to create nanoscale shapes and patterns. Nat Biotechnol 440(7082):297-302
79. Rubenstein M, Ahler C, Nagpal R (2012) Kilobot: a low cost scalable robot system for collective behaviors. In: IEEE international Conference on robotics and automation (ICRA), pp 3293-3298
80. Rus D, Vona M (2000) A physical implementation of the self-reconfiguring crystalline robot. In: Proceedings, ICRA'00, IEEE international conference on robotics and automation, vol 2, pp 1726-1733
81. Sano K, Sayama H (2006) Wriggraph: a kinetic graph model that uniformly describes ontogeny and motility of artificial creatures. In: Artificial life X: proceedings of the tenth international conference on the simulation and synthesis of living systems, vol 10. MIT, Cambridge, p 77
82. Sayama H (2007) Generative network automata: a generalized framework for modeling complex dynamical systems with autonomously varying topologies. In: IEEE symposium on artificial life, 2007. ALIFE'07, pp 214-221
83. Sayama H (2009) Swarm chemistry. Artif Life 15(1):105-114
84. Sayama H (2011) Seeking open-ended evolution in swarm chemistry. In: IEEE symposium on artificial life (ALIFE), pp 186-193
85. Sayama H (2012a) Morphologies of self-organizing swarms in 3D swarm chemistry. In: Proceedings of the fourteenth international conference on genetic and evolutionary computation conference. ACM, New York
86. Sayama H (2012b) Swarm-based morphogenetic artificial life. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 191-208
87. Schramm L, Jin Y, Sendhoff B (2011) Emerged coupling of motor control and morphological development in evolution of multi-cellular animats. In: Advances in artificial life. Darwin meets von Neumann, Budapest, pp 27-34
88. Sims K (1994) Evolving 3D morphology and behavior by competition. Artif Life 1(4):353-372
89. Spicher A, Michel O, Giavitto J-L (2010) Declarative mesh subdivision using topological rewriting in MGS. In: International conference on graph transformation, vol 6372. LNCS, The Netherlands, pp 298-313
90. Spicher A, Michel O, Giavitto J-L (2011) Interaction-based simulations for integrative spatial systems biology. In: Understanding the dynamics of biological systems. Springer, pp 195-231
91. Spicher A, Michel O, Giavitto J-L (2012) Interaction-based modeling of morphogenesis in MGS. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 409-440
92. Stanley KO, Miikkulainen R (2003) A taxonomy for artificial embryogeny. Artif Life 9(2):93-130
93. Stepney S, Braunstein SL, Clark JA, Tyrrell A, Adamatzky A, Smith RE, Addis T, Johnson C, Timmis J, Welch P, Milner R, Partridge D (2005) Journeys in non-classical computation I: a grand challenge for computing research. Int J Parallel Emergent Distrib Syst 20(1):5-19
94. Tanenbaum AS, van Steen M (2002) Distributed systems: principles and paradigms. Prentice Hall, Upper Saddle River
95. Tomita K, Kurokawa H, Murata S (2002) Graph automata: natural expression of self-reproduction. Physica D 171(4):197-210
96. Ulieru M, Doursat R (2011) Emergent engineering: a radical paradigm shift. Int J Auton Adapt Commun Syst 4(1):39-60
97. Verdenal A, Combes D, Escobar-Gutiérrez A (2012) Programmable and self-organised processes in plant morphogenesis: the architectural development of ryegrass. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 501-517
98. Vicsek T, Czirók A, Ben-Jacob E, Cohen I, Shochet O (1995) Novel type of phase transition in a system of self-driven particles. Phys Rev Lett 75(6):1226-1229
99. Virgo N, Fernando C, Bigge B, Husbands P (2012) Evolvable physical self-replicators. Artif Life 18(2):129-142
100. von Mammen S, Jacob C (2007) Genetic swarm grammar programming: ecological breeding like a gardener. In: IEEE congress on evolutionary computation, 2007, CEC 2007, pp 851-858
101. von Mammen S, Phillips D, Davison T, Jamniczky H, Hallgrímsson B, Jacob C (2012) Swarm-based computational development. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 473-499
102. Webster G, Goodwin BC (1996) Form and transformation: generative and relational principles in biology. Cambridge University Press, Cambridge
103. Weiser M (1993) Some computer science issues in ubiquitous computing. Commun ACM 36(7):75-84
104. Werfel J (2012) Collective construction with robot swarms. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 115-140
105. Werfel J, Nagpal R (2006) Extended stigmergy in collective construction. IEEE Intell Syst 21(2):20-28
106. Winfield AFT, Nembrini J (2012) Emergent swarm morphology control of wireless networked mobile robots. In: Doursat R, Sayama H, Michel O (eds) Morphogenetic engineering: toward programmable complex systems, understanding complex systems. Springer, New York, pp 239-271
107. Winfield A, Harper C, Nembrini J (2005) Towards dependable swarms and a new discipline of swarm engineering. In: Swarm robotics, pp 126-142
108. Wolpert L (1969) Positional information and the spatial pattern of cellular differentiation. J Theor Biol 25(1):1-47
109. Würtz RP (2008) Organic computing. Springer, Berlin
110. Zykov V, Mytilinaios E, Adams B, Lipson H (2005) Self-reproducing machines. Nat Biotechnol 435(7039):163-164