1. Complex Systems Engineering SwE 488 Complexity in Nature Prof. Dr. Mohamed Batouche Department of Software Engineering CCIS – King Saud University Riyadh, Kingdom of Saudi Arabia batouche@ccis.edu.sa

2. Outline Introduction Natural Complex Systems Natural Ants Termites Bees Neurons Immune System Better defense against predators Complexity in Life Conclusion 2

3. Introduction 3

4. "An individual ant is not very bright, but ants in a colony, operating as a collective, do remarkable things. A single neuron in the human brain can respond only to what the neurons connected to it are doing, but all of them together can be Albert Einstein." By Deborah M. Gordon (Stanford University) 4

5. Complex Systems Complex systems are systems that exhibit emergent behavior: Anthills Human societies Financial Markets Climate Nervous systems Immune systems Human societies Cities Galaxies Modern telecommunication infrastructures 5

6. Natural Complex Systems 6 A termite "cathedral" mound produced by a termite colony: a classic example of emergence in nature. Bottom-up behavior: Simple agents following simple rules generate complex structures/behaviors. Fish School Birds Flocking

7. Natural Complex Systems 7

8. NATURAL COMPLEX SYSTEMS 8

9. Natural Ants Individual ants are simple insects with limited memory and capable of performing simple actions. However, an ant colony expresses a complex collective behavior providing intelligent solutions to problems such as: carrying large items forming bridges finding the shortest routes from the nest to a food source, prioritizing food sources based on their distance and ease of access.

10. Natural Ants Moreover, in a colony each ant has its prescribed task, but the ants can switch tasks if the collective needs it. Outside the nest, ants can have 4 different tasks: Foraging: searching for and retrieving food Patrolling: looking for food supply Midden work: Sorting the colony refuse pile Nest maintenance work: construction and clearing of chambers An ant’s decision whether to perform a task depends on: The Physical State of the environment: − If part of the nest is damaged, more ants do nest maintenance work to repair it Social Interactions with other ants

11. How Do Social Insects Achieve Self-organization? Communication is necessary Two types of communication: Direct: antennation, trophallaxis (food or liquid exchange), mandibular contact, visual contact, chemical contact, etc. Indirect: two individuals interact indirectly when one of them modifies the environment and the other responds to the new environment at a later time. This is called stigmergy.

12. Natural ants: How do they do it? How do they know which task to perform? When ants meet, they touch with their antennae, that are organs of chemical perception. An ant can perceive the colony-specific odor that all nest mates share. In addition to this odor, ants have an odor specific to their task, because of the temperature and humidity conditions in which it works. So that an ant can evaluate its rate of encounter with ants of a certain task. The pattern of interaction each ant experiences influences the probability it will perform a task.

13. Natural ants: How do they do it? How can they manage to find the shortest path? "The best possible way for ants to find anything is to have an ant everywhere all the time, because if it doesn't happen close to an ant, they are not going to know about it. Of course there are not enough ants in the colony, so the ants have to move around in a pattern that allows them to cover space efficiently"

14. Natural ants: How do they do it? They establish indirect communication system based on the deposition of pheromone over the path they follow. An isolated ant moves at random, but when it finds a pheromone trail, there is a high probability that this ant will decide to follow the trail. An ant foraging for food deposits pheromone over its route. When it finds a food source, it returns to the nest reinforcing its trail. So, other ants have greater probability to start following this trail and thereby laying more pheromone on it. This process works as a positive feedback loop system because the higher the intensity of the pheromone over a trail, the higher the probability of an ant start traveling through it.

15. Natural ants: How do they do it? Since the route B is shorter, the ants on this path will complete the travel more times and thereby lay more pheromone over it. The pheromone concentration on trail B will increase at a higher rate than on A, and soon the ants on route A will choose to follow route B Since most ants will no longer travel on route A, and since the pheromone is volatile, trail A will start evaporating Only the shortest route will remain!

16. Natural ants: Experiments (1) Ants finished all using the same path (each one of the 2 paths, 50% of times) (2) Ants use the short path (3) Ants get to find the shortest path (1) (2) (3) (1)(2)

17. 17 Shortest path discovery Ants get to find the shortest path after few minutes …

18. 6/18/201518 slides from EVALife

19. 6/18/201519 slides from EVALife

20. 6/18/201520 slides from EVALife

21. 6/18/201521 slides from EVALife

22. 6/18/201522 slides from EVALife

23. 6/18/201523 slides from EVALife

24. 6/18/201524 Adaptive Path Optimization slides from iridia.ulb.ac.be/~mdorigo

25. 6/18/201525 Adaptive Path Optimization slides from iridia.ulb.ac.be/~mdorigo

26. 6/18/201526 Adaptive Path Optimization slides from iridia.ulb.ac.be/~mdorigo

27. 6/18/201527 Adaptive Path Optimization slides from iridia.ulb.ac.be/~mdorigo

28. TERMITES CONSTRUCTION 28

29. Termite Constructions Termite mounds are often built on a huge scale:  millions of builders  thermoregulation, defence, agriculture, climate control, créches, graveyards, even optimal acoustic properties !!!!

30. Termites Cone-shaped outer walls and ventilation ducts Brood chambers in central hive Spiral cooling vents Support pillars What is more astonishing is that the termites which construct these nests are blind !!!

31. 6/18/201531 Basic Mechanism of Construction (Stigmergy) Worker picks up soil granule Mixes saliva to make cement Cement contains pheromone Other workers attracted by pheromone to bring more granules There are also trail and queen pheromones Fig. from Solé & Goodwin

32. Termite Mounds Giant African fungus-growing termites build a high-rise termitarium from dried mud-pellets, which can be up to 26 feet high and about 10ft across. These ‘skyscrapers’ are well ventilated inside by a network of tunnels with fresh air being drawn in through nest walls and warm air rising from below escapes outside through tall ‘chimneys,’ minute holes in the hard surface. 32

33. BEES 33

34. Bees Colony cooperation Regulate hive temperature Efficiency via Specialization: division of labour in the colony Communication : Food sources are exploited according to quality and distance from the hive

35. Bees Colony 35 Three members of the colony Worker QueenDrone

36. Social behavior in Honey Bees is highly organized The Caste system is when a society has distinct groups in the population that are designed for a particular role. Termites, ants and honey bees have a caste system which results in great efficiency in food collection, reproduction and child rearing. Queen lays egg in a brood cell Worker feeds hatched larva 1 2 Larva grows 3 Worker caps cell Larva spins cocoon and becomes pupa Adult bee leaves cell 4 5 6

37. Communication is important in a social group!! Worker honey bees communicate by performing dances. The dance performed indicates the direction and distance of a good food source. Round Dance Waggle Dance

38. The Round Dance Indicates a food source less than 90m away The Figure Eight or Waggle dance Indicates a food source more than 90m away with direction

39. Waggle dance Two components of the waggle dance 1.Straight run which indicates the direction of the food according to the angle of the waggle run on the vertical surface. If the bee waggles directly up the surface, then the food source is directly toward the sun. If the bee waggles directly down the surface, then the food source is directly away from the sun. If the food source was located 90 degrees to the right of the sun, the bee would waggle 90 degrees to the right. 2.the speed at which the dance is repeated indicates how far away the food is

40. OUR BRAINS 40

41. Our Brains ~100Bn neurons, each with 10K neighbours 1000 trillion synapses for a 3-year-old child Developmentally plastic into adulthood + Chemical processes  Language, logic, emotion, cognition, memory, learning, motor control, memory, learning, motor control, consciousness, etc.

42. The Human Brain Made up of billions of neurons, each of which exhibits very simple behavior, and single-bit memory. Some stochastic characteristics. Assessment: the top-level system (the brain, three pounds) displays an infinitely sophisticated and complicated behavior: language, visual, aural, and tactile I/O, the arts, culture, emotions, as well as logical thought and processing. Robust, adaptive, innovative. A thorough scientific examination of the individual neurons would not predict the behavior of billions of them working together. 42

43. Typical Neuron 43

44. IMMUNE SYSTEM (COMPLEX ADAPTIVE SYSTEM) 44

45. IMMUNE SYSTEM (COMPLEX ADAPTIVE SYSTEM) 45

46. Virus vs. Bacteria Colds are caused by a virus, which is a non- living particle that contains genetic material, and hijacks your cells to reproduce. Bacteria are living organisms that can reproduce on their own.

47. How does the body fight infection/foreign invaders? The Body has three lines of Defense: The Skin (Provides Physical and Chemical barriers) Nonspecific Immune Response Specific Immune Response 47

48. Nonspecific Immune Response These are defenses the body uses no matter what the invader may be. These defenses include: Phagocytosis – done by Macrophages Natural Cell Killers Inflammation - caused by release of Histamine from leukocytes Fever – caused by histamines. The fever (high temp) kills invaders by denaturing their proteins. Macrophage: A phagocytic cell found in the liver, spleen, brain and lungs. Travels to all areas of the body to find and eat pathogens.

49. Inflammatory Response

51. Specific Immune Response This is a specific response to a specific pathogen/antigen. The response involves the creation of Antibodies 51

52. Major players The major players in the immune system include: Macrophage (Phagocyte) T cells (helper, cytotoxic, memory) B cells (plasma, memory) Antibodies

53. Some vocabulary: Antibody: a protein produced by the human immune system to tag and destroy invasive microbes. Antigen: any protein that our immune system recognizes as “not self.” (Infected cell, tagged microbes, Cancer cell)

54. Antigen recognition Cells of the immune system are “trained” to recognize “self” proteins vs. “not self” proteins. If an antigen (“not self”) protein is encountered by a macrophage, it will bring the protein to a helper T- cell for identification. If the helper T-cell recognizes the protein as “not self,” it will launch an immune response.

55. The Pathway of Specific Immune Response Pathogens Pathogens eaten by Macrophage Displays portion of Pathogen on surface Helper-T cell recognizes Pathogen Step 1 Step 2 Step 3

56. Helper T cells Helper T-cells have receptors for recognizing antigens. If they are presented with an antigen, they release cytokines to stimulate B-cell division. The helper T-cell is the key cell to signal an immune response. If helper T-cells are disabled, as they are in people with AIDS, the immune system will not respond.

57. Activates B- Cell Activates Cytotoxic T- Cell Memory B-Cell Memory T-Cell Kills Infected Cells Antibodies 

58. B cells B-cells in general produce antibodies. Those with antibodies that bind with the invader’s antigen are stimulated to reproduce rapidly. B-cells differentiate into either plasma cells or memory B-cells. Plasma cells rapidly produce antibodies. Memory cells retain the “memory” of the invader and remain ready to divide rapidly if an invasion occurs again.

59. Clonal Selection

60. Role of antibodies Antibodies released into the blood stream will bind to and deactivate the antigens that they are specific for. Antibodies may disable some microbes, or cause them to stick together (agglutinate). They “tag” microbes so that the microbes are quickly recognized by various white blood cells.

61. “Killer” T cells While B-cells divide and differentiate, so do T-cells. Some T-cells become cytotoxic, or “killer” T- cells. These T-cells seek out and destroy any antigens in the system, and destroy microbes “tagged” by antibodies. Some cytotoxic T-cells can recognize and destroy cancer cells.

62. Lunch an immune response Bring invader to helper T Cell Plasma cells rapidly produce antibodies. Killer T Cell

63. Calling a halt When the invader is destroyed, the helper T-cell calls a halt to the immune response. Memory T-cells are formed, which can quickly divide and produce cytotoxic T- cells to quickly fight off the invader if it is encountered again in the future.

64. Immune Response Summary Antigen Macrophage Helper T - Cell Active Cytotoxic T-Cell Kills Infected Cells Memory T- Cell Active B - Cell Plasma Cell Antibodies Deactivates Antigens Memory B-Cell Displays copy of antigen on surface of cell Cellular Immunity Antibody Immunity

65. Better defense against predators (Cooperation & Co-Evolution) 65

66. 6/18/201566 Avoiding Predation More compact aggregation predator risks injury by attacking Confusing predator by: united erratic maneuvers (e.g. zigzagging) separation into subgroups (e.g., flash expansion & fountain effect)

67. 6/18/201567 Flash Expansion Fig. from Camazine & al., Self-Org. Biol. Sys.

68. 6/18/201568 Flash Expansion Fig. from Camazine & al., Self-Org. Biol. Sys.

69. 6/18/201569 Fountain Effect Fig. from Camazine & al., Self-Org. Biol. Sys.

70. 6/18/201570 Fountain Effect Fig. from Camazine & al., Self-Org. Biol. Sys.

71. 6/18/201571 Fountain Effect Fig. from Camazine & al., Self-Org. Biol. Sys.

72. 6/18/201572 Fountain Effect Fig. from Camazine & al., Self-Org. Biol. Sys.

73. COMPLEXITY OF LIFE 73

74. The Hydrologic Cycle

75. The Carbon Cycle

76. The Nitrogen Cycle

77. 77 Conclusions

78. 78 Conclusions We can learn from nature and take advantage of the problems that she has already solved. Many simple individuals interacting with each other can make a global behavior emerge. Techniques based on natural collective behavior are interesting as they are cheap, robust, and simple. They have lots of different applications.  Think Biology, Emergence, Complex Systems …

79. References 79

80. References Jay Xiong, New Software Engineering Paradigm Based on Complexity Science, Springer 2011. Claudios Gros : Complex and Adaptive Dynamical Systems. Second Edition, Springer, 2011. Blanchard, B. S., Fabrycky, W. J., Systems Engineering and Analysis, Fourth Edition, Pearson Education, Inc., 2006. Braha D., Minai A. A., Bar-Yam, Y. (Editors), Complex Engineered Systems, Springer, 2006 Gibson, J. E., Scherer, W. T., How to Do Systems Analysis, John Wiley & Sons, Inc., 2007. International Council on Systems Engineering (INCOSE) website (www.incose.org).www.incose.org New England Complex Systems Institute (NECSI) website (www.necsi.org).www.necsi.org Rouse, W. B., Complex Engineered, Organizational and Natural Systems, Issues Underlying the Complexity of Systems and Fundamental Research Needed To Address These Issues, Systems Engineering, Vol. 10, No. 3, 2007.

81. References Wilner, M., Bio-inspired and nanoscale integrated computing, Wiley, 2009. Yoshida, Z., Nonlinear Science: the Challenge of Complex Systems, Springer 2010. Gardner M., The Fantastic Combinations of John Conway’s New Solitaire Game “Life”, Scientific American 223 120–123 (1970). Nielsen, M. A. & Chuang, I. L.,Quantum Computation and Quantum Information, 3rd ed., Cambridge Press, UK, 2000. 81