Biomorphic Computing

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Biomorphic Computing

• Professor Bill Tomlinson
• Tuesday 200-450pm
• Winter 2004
• CS 189

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Week 1

• Introductions
• Syllabus
• Biology
• Biomorphic Computing
• Game of Life
• Lab Time

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Introductions

• Name
• Program
• How much biology and computer science experience
  / relevant classes taken.
• (note cards)

4
Syllabus

• Hand out
• Go over
• Questions?

5
Breaks

• Ill try to remember to take breaks each class
  (every 1-1.5 hours), but if I forget, please
  remind me!

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Reading/work for the whole week

• Spread it out over the whole week.
• Leave time to ask questions.

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Assignments

• I am interested that you understand why code
  works, rather than simply that it works.
  Therefore, please comment your code thoroughly on
  the assignments.
• Many code samples similar to the assignments can
  be found online. You are welcome to use these as
  reference, but please dont cut-and-paste them.

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Final Projects

• Innovative computational implementation based on
  some aspect of a biological phenomenon that has
  never before been explored.
• Readings - Well go over search tools. You find
  the readings.
• Three presentations - proposal, prototype, final.
• Keep your eye out (both in our class work and in
  the rest of your life) for biological phenomena
  that interest you.

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Assignment for next week

• Game of Life programming assignment (handed out
  later in class)
• Read Sims, K. 1991. Artificial Evolution for
  Computer Graphics. Computer Graphics, 25(4), pp.
  319-328. (See syllabus for link.)

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Questions

• Any questions now?
• Throughout the quarter, please come to my office
  hours (Thurs 3-5) or email wmt_at_uci.edu if you
  have any questions or just feel like chatting.

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Introduction to biology

• Merriam Webster
• 1 a branch of knowledge that deals with living
  organisms and vital processes

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Definitions of life

• Break up into pairs
• Each group come up with
• three distinct definitions of life.
• Take 10 minutes.

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Compare definitions

• Come up with ways to break each -
• counter-examples, false positives.

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Merriam-Websters

• 1 a the quality that distinguishes a vital and
  functional being from a dead body b a principle
  or force that is considered to underlie the
  distinctive quality of animate beings -- compare
  VITALISM 1 c an organismic state characterized
  by capacity for metabolism, growth, reaction to
  stimuli, and reproduction

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NASA

• There is no broadly accepted definition of
  'life.' Suggested definitions face problems,
  often in the form of robust counter-examples.
  Here we use insights from philosophical
  investigations into language to argue that
  defining 'life' currently poses a dilemma
  analogous to that faced by those hoping to define
  'water' before the existence of molecular theory.
  In the absence of an analogous theory of the
  nature of living systems, interminable
  controversy over the definition of life is
  inescapable.
• --Cleland, Carol E. Chyba, Christopher F.,
  Origins of Life and Evolution of the Biosphere,
  v. 32, Issue 4, p. 387-393 (2002).

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NASA (http//afc.gsfc.nasa.gov/tco/biology101_01.
htm)

• All life carry on a common set of processes
• Reproduction - the production of new individuals
  of each kind of organism
• Growth - life grows in size
• Nutrition - activities involved in taking in food
  from the environment, digesting the food and
  removal of wastes of digestion.
• Transport - the movement of material into the
  life form (cell) and the distribution of material
  within the cell.
• Respiration - chemical activities that release
  energy from organic molecules for the use of the
  organism.
• Excretion - the elimination of waste products
  from the organism.
• Synthesis - chemical reactions in which molecules
  combine.
• Regulation - the control and coordination of all
  functions (no wonder we are such natural
  bureaucrats it is built into the meaning of life)

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Biology topics(from Campbell Reece, 2001)

• Computational /
• engineering
• implementations
• for each of these
• topics?

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The Chemistry of Life

• The Chemical Context of Life
• Water and the Fitness of the Environment
• Carbon and the Molecular Diversity of Life
• The Structure and Function of Macromolecules
• An Introduction to Metabolism

19
The Cell

• A Tour of the Cell
• Membrane Structure and Function
• Cellular Respiration Harvesting Chemical Energy
• Photosynthesis
• Cell Communication
• The Cell Cycle

20
Genetics

• Meiosis and Sexual Life Cycles
• Mendel and the Gene Idea
• The Chromosomal Basis of Inheritance
• The Molecular Basis of Inheritance
• From Gene to Protein
• The Genetics of Viruses and Bacteria
• Organization and Control of Eukaryotic Genomes
• DNA Technology and Genomics
• Genetic Basis of Development

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Mechanisms of Evolution

• Descent with Modification A Darwinian View of
  Life
• The Evolution of Populations
• The Origin of Species
• Phylogeny and Systematics

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The Evolutionary History of Biological Diversity

• Early Earth and the Origin of Life
• Prokaryotes the Origins of Metabolic Diversity
• The Origins of Eukaryotic Diversity
• Plant Diversity I How Plants Colonized Land
• Plant Diversity II The Evolution of Seed Plants
• Fungi
• Introduction to Animal Evolution
• Invertebrates
• Vertebrate Evolution and Diversity

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Plant Form and Function

• Plant Structure and Growth
• Transport in Plants
• Plant Nutrition
• Plant Reproduction and Biotechnology
• Plant Responses to Internal and External Signals

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Animal Form and Function

• Introduction to Animal Structure and Function
• Animal Nutrition
• Circulation and Gas Exchange
• The Bodys Defenses
• Regulating the Internal Environment
• Chemical Signals in Animals
• Animal Reproduction
• Animal Development
• Nervous Systems
• Sensory and Motor Mechanisms

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Ecology

• An Introduction to Ecology and the Biosphere
• Behavioral Biology
• Population Ecology
• Community Ecology
• Ecosystems
• Conservation Biology

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Summary of Biology

• Living things are successful at exploiting their
  environments.
• They do so in a variety of ways, and on a wide
  range of scales.

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Biomorphic Computing

• Using biology to inform computational systems.

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Possible Dimensions of Biomorphic Computing

• Small (nanotechnology) to large (modeling global
  ecosystems)
• Short (packet-switching based on ant foraging) to
  long (evolving virtual creatures)
• Similar to humans (social HCI) to different from
  humans (simulating the running motion of the
  Deaths Head cockroach)

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Things that move like living things

• Robots (MIT Leg Lab, Stanford PolyPEDAL Lab,
  etc.)
• Simulations (video games, movies)

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Things that think like living things

• Learning (speech recognition, pattern matching)
• Coordinated/cooperative behavior (robot soccer,
  flocking simulations)

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Things that adapt to changing circumstances like
living things

• evolution
• distributed systems

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Things that develop like living things

• Some research, but underexplored

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Things that help us understand how living things
work

• Flocking Simulation
• Simulated evolution
• Computational biology

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Whats the use?

• Living things are very successful. Harness that
  success for computational systems.
• People are used to interacting with living
  things. Make computational systems easy to use.

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Drawing the right lessons

• Its the shape of the wing, rather than the
  flapping, that enables controlled flight.

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Break
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Artificial Life

• MIT CogNet
• Artificial life (A-Life) uses informational
  concepts and computer modeling to study life in
  general, and terrestrial life in particular. It
  aims to explain particular vital phenomena,
  ranging from the origin of biochemical
  metabolisms to the coevolution of behavioral
  strategies, and also the abstract properties of
  life as such ("life as it could be").
• Focus on self-organization
• Ninth International Conference on the Simulation
  and Synthesis of Living Systems
• Artificial Life is the study of life as an
  organizational principle, rather than as it
  exists on Earth as carbon-based.

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Strong ALife vs. Weak ALife

• Is it possible to make machines or computer
  systems that are really alive?
• Or does ALife just help us make functional things
  and understand living things.
• Take a vote.

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References

• Chris Langton(1986)
• Steven Levy (popular press, 1992)
• SAB conference (1990 - present)
• (From Animals to
• Animats 1 through 8)

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Cellular Automata

• Cellular automata are discrete dynamical systems
  whose behaviour is completely specified in terms
  of a local relation. A cellular automaton can be
  thought of as a stylised universe. Space is
  represented by a uniform grid, with each cell
  containing a few bits of data time advances in
  discrete steps and the laws of the "universe" are
  expressed in, say, a small look-up table, through
  which at each step each cell computes its new
  state from that of its close neighbours. Thus,
  the system's laws are local and uniform.
• (http//www.brunel.ac.uk/depts/AI/alife/al-ca.htm
  )

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References

• John Von Neumann(1951, 1966)
• Stanislaw Ulam (1950)
• John Conway (via Gardner, 1970)
• Stephen Wolfram (1982, 1983, 2002)

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One-Dimensional

• One-D - time is the vertical axis.
• http//math.hws.edu/xJava/CA/CA.html
• (Wolfram, 83)

Time
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One-D

• Cellular automata in nature?
• (Wolfram, 83)

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Two-D

• Entire 2D image is replaced each time step.

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John Conways Game of Life

• 2D cellular automata system.
• Each cell has 8 neighbors - 4 adjacent
  orthogonally, 4 adjacent diagonally. This is
  called the Moore Neighborhood.

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Simple rules, executed at each time step

• A live cell with 2 or 3 live neighbors survives
  to the next round.
• A live cell with 4 or more neighbors dies of
  overpopulation.
• A live cell with 1 or 0 neighbors dies of
  isolation.
• An empty cell with exactly 3 neighbors becomes a
  live cell in the next round.

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Is it alive?

• http//www.bitstorm.org/gameoflife/
• Compare it to the definitions

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Game of Life Assignment

• Implement the central genetic laws of the Game of
  Life.

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Hand out assignment and source code

• http//www.ics.uci.edu/wmt/courses/BiomoW04/Biomo
  W04Assignment1.html
• http//www.ics.uci.edu/wmt/courses/BiomoW04/GameO
  fLife.java

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Eclipse

• How many people have used it?

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Lab Time

• Please begin working on your assignments. Ill
  come around and make sure everything is going
  smoothly. Please let me know if you have any
  questions.

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