The Many Facets of

Natural Computing
Lila Kari
Dept. of Computer Science
University of Western Ontario
London, ON, Canada
http://www.csd.uwo.ca/~lila/
lila@csd.uwo.ca
 Natural Computing

Investigates models and computational

techniques inspired by nature
Attempts to understand the world around us
in terms of information processing
Interdisciplinary field that connects
computer sciences with natural sciences

Lila Kari, University of Western Ontario

 Natural Computing
(i) Nature as Inspiration
(ii) Nature as Implementation Substrate
(iii) Nature as Computation

Lila Kari, University of Western Ontario

 (i) Nature as Inspiration
Cellular Automata self-reproduction
Neural Computation the brain
Evolutionary Computation evolution
Swarm Intelligence group behaviour
Immunocomputing immune system
Artificial Life properties of life
Membrane Computing cells and membranes
Amorphous Computing - morphogenesis
Lila Kari, University of Western Ontario
 1.Cellular Automata
Cellular automaton = dynamical system consisting
of a regular grid of cells
Space and time and discrete
Each cell can be in a finite number of states
Each cell changes its state according to a list of
transition rules, based on its current state and the
states of its neighbours
The grid updates its configuration synchronously
Lila Kari, University of Western Ontario
 CA Example: Rule 30
111 110 101 100 011 010 001 000
0 0 0 1 1 1 1 0

Lila Kari, University of Western Ontario

Conus Textile pattern

Lila Kari, University of Western Ontario

 2.Neural Computation
Artificial Neural Network: a network of
interconnected artificial neurons
Neuron A : * n real- valued inputs x1,, xn
* weights w1,,wn
* computes
fA(w1x1 + w2x2 + + wnxn)

Network Function = vectorial function that,

for n input values, associates the outputs of the m
pre-selected output neurons
Lila Kari, University of Western Ontario
Applications to Human Cognition
[T.Schultz, www.psych.mcgill.ca/labs/lnsc]

Lila Kari, University of Western Ontario

 3.Evolutionary Computation
Constant or variable-sized population
A fitness criterion according to which
individuals are evaluated
Genetically inspired operators (mutation or
recombination of parents) that produce the
next generation from the current one

Lila Kari, University of Western Ontario

 Genetic Algorithms
Individuals = fixed-length bit strings
Mutation = cut-and-paste of a prefix of a parent
with a suffix of another
Fitness function is problem-dependent
If initial population encodes possible solutions to a
given problem, then the system evolves to produce
a near-optimal solution to the problem
Applications: real-valued parameter optimization
Lila Kari, University of Western Ontario
 Using Genetic Algorithms to
Create Evolutionary Art [M.Gold]

Lila Kari, University of Western Ontario

 4.Swarm Intelligence
Swarm: group of mobile biological
organisms (bacteria, ants, bees, fish, birds)
Each individual communicates with others
either directly or indirectly by acting on its
environment
These interactions contribute to collective
problem solving = collective intelligence

Lila Kari, University of Western Ontario

 Particle Swarm Optimization
Inspired by flocking behaviour of birds
Start with a swarm of particles (each
representing a potential solution)
Particles move through a multidimensional
space and positions are updated based on
* previous own velocity
* tendency towards personal best
* tendency toward neighbourhood best
Lila Kari, University of Western Ontario
 Ant Algorithms
Model the foraging behaviour of ants
In finding the best path between nest and a
source of food, ants rely on indirect
communication by laying a pheromone trail
on the way back (if food is found) and by
following concentration of pheromones (if
food is sought)

Lila Kari, University of Western Ontario

Lila Kari, University of Western Ontario
 5.Immunocomputing
Immune systems function = protect our
bodies against external pathogens
Role of immune system: recognize cells
and categorize them as self or non-self
Innate (non-specific) immune system
Adaptive (acquired) immune system

Lila Kari, University of Western Ontario

 Artificial Immune Systems
Computational aspects of the immune
system: distinguishing self from non-self,
feature extraction, learning, immunological
memory, self-regulation, fault-tolerance
Applications: computer virus detection,
anomaly detection in a time-series of data,
fault diagnosis, pattern recognition

Lila Kari, University of Western Ontario

 6.Artificial Life
ALife attempts to understand the very
essence of what it means to be alive
Builds ab initio, within in silico computers,
artificial systems that exhibit properties
normally associated only with living
organisms

Lila Kari, University of Western Ontario

 Lindenmayer Systems
Parallel rewriting systems
Start with an initial word
Apply the rewriting rules in parallel to all
letters of the word
Used, e.g., for modelling of plant growth
and morphogenesis

Lila Kari, University of Western Ontario

 L-Systems Applications
Plant growth [Fuhrer, Wann Jensen, Prusinkiewicz 2004-05]
Architecture and design [J.Bailey, Archimorph]

Lila Kari, University of Western Ontario

 Mechanical Artificial Life
Evolving populations of artificial creatures
in simulated environments
Combining the computational and
experimental approaches and using rapid
manufacturing technology to fabricate
physical evolved robots that were selected
for certain abilities (to walk or get a cube)

Lila Kari, University of Western Ontario

 How to insert pdf file

Lila Kari, University of Western Ontario

 7.Membrane Computing
Inspired by the compartmentalized internal
structure of cells
Membrane System = a nested hierarchical
structure of regions delimited by
membranes
Each region contains objects and
transformation rules + transfer rules

Lila Kari, University of Western Ontario

 8.Amorphous Computing
Inspired by developmental biology
Consist of a multitude of irregularly placed,
asynchronous, locally interacting computing
elements
The identically programmed computational
particles communicate only with others situated
within a small radius
Goal: engineer specified coherent computational
behaviour from the interaction of large quantities
of such unreliable computational particles.

Lila Kari, University of Western Ontario

 Amorphous Computing
[Generating patterns: Abelson, Sussman, Knight, Ragpal]

Lila Kari, University of Western Ontario

 (ii) Nature as Implementation
Substrate
Molecular Computing (DNA Computing)
Uses biomolecules, e.g., DNA, RNA
Quantum Computing
Uses, e.g., ion traps, superconductors,
nuclear magnetic resonance

Lila Kari, University of Western Ontario

 (ii-1) Molecular Computing
Data can be encoded as biomolecules
(DNA, RNA)
Arithmetic/logic operations are performed
by molecular biology tools
The proof-of-principle experiment was
Adlemans bio-algorithm solving a
Hamiltonian Path Problem (1994)

Lila Kari, University of Western Ontario

 Molecular (DNA) Computing
Single-stranded DNA is a string over the
four-letter alphabet, {A, C, G, T}

Lila Kari, University of Western Ontario

 Power of DNA Computing
Data: DNA single and double strands
WatsonCrick Complementarity:
W(C) = G, W(A) = T
Bio-operations: cut-and-paste by enzymes,
extraction by pattern, copy, read-out

R.Freund, L.Kari, G.Paun. DNA computing based on

splicing: the existence of universal computers. Theory
of Computing Systems, 32 (1999).

Lila Kari, University of Western Ontario

 DNA-Encoded Information
DNA strands interact with each other in
programmed but also undesirable ways
The information has no fixed location
The results of a biocomputation are not
deterministic, as they depend e.g. on
concentration of populations of DNA
strands, diffusion reactions, statistical laws

Lila Kari, University of Western Ontario

 DNA-Motivated Concepts
-periodicity
w = u1u2un where ui is in {u, (u)}
and is an antimorphic involution
Generalize Lyndon-Schutzenberger
u^n v^m = w^m
-prefix, -infix, -compliant codes

Lila Kari, University of Western Ontario

 Our DNA Information Research
L. Kari, S. Seki, On pseudoknot-bordered words and their
properties, Journal of Computer and System Sciences,
(2008)
L.Kari, K.Mahalingam, Watson-Crick Conjugate and
Commutative Words, Proc. DNA Computing 13, LNCS
4848 (2008)
L. Kari, K. Mahalingam, S. Seki, Twin-roots of words and
their properties, Theoretical Computer Science (2008)
E.Czeizler, L.Kari, S.Seki. On a Special Class of Primitive
Words. MFCS (2008)
M. Ito, L. Kari, Z. Kincaid, S. Seki, Duplication in DNA
sequences. Proc. of Developments in Language Theory
(2008)

Lila Kari, University of Western Ontario

 Computing by Self-Assembly

Self-Assembly = The process by which objects

autonomously come together to form complex
structures
Examples
Atoms bind by chemical bonds
to form molecules
Molecules may form crystals or
macromolecules
Cells interact to form organisms
Lila Kari, University of Western Ontario
 Motivation for Self-Assembly
Nanotechnology: miniaturization in medicine,
electronics, engineering, material science,
manufacturing
Top-Down techniques: lithography
(inefficient in creating structures with size
of molecules or atoms)
Bottom-Up techniques: self-assembly

Lila Kari, University of Western Ontario

 Computing by Self-Assembly
of Tiles
Tile = square with the edges labelled from a
finite alphabet of glues

Tiles cannot be rotated

Two adjacent tiles on the plane stick if they
have the same glue at the touching edges

Lila Kari, University of Western Ontario

Computation by DNA Self-Assembly
[Mao, LaBean, Reif, , Seeman, Nature, 2000]

Lila Kari, University of Western Ontario

 Our Self-Assembly Research
L.Adleman, J.Kari, L.Kari, D.Reishus, P.Sosik.
The Undecidability of the Infinite Ribbon Problem:
Implications for Computing by Self-Assembly
(SIAM Journal of Computing, to appear, 2009)
This solves an open problem formerly known as the
unlimited infinite snake problem
Undecidability of existence of arbitrarily large
supertiles that can self-assemble from a given tile set
(starting from an arbitrary seed)
E.Czeizler, L.Kari, Geometrical tile design for complex
neighbourhoods (2008, submitted)
L.Kari, B.Masson, Simulating arbitrary
neighbourhoods by polyominoes (2008, in preparation)

Lila Kari, University of Western Ontario

DNA Clonable Octahedron
[Shih, Joyce, Nature, 2004]

Lila Kari, University of Western Ontario

Nanoscale DNA Tetrahedra
[Goodman, Turberfield, Science, 2005]

Lila Kari, University of Western Ontario

 DNA Origami
[Rothemund, Nature, 2006]

Lila Kari, University of Western Ontario

 (ii-2) Quantum Computing
A qubit can hold a 0, a 1 or a quantum
superposition of these
Quantum mechanical phenomena such as
superposition and entanglement are used to
perform operations on qubits
Shors quantum algorithm for factoring
integers (1994)

Lila Kari, University of Western Ontario

 Quantum Crytography
Unbreakable encryption unveiled (BBC News,
Oct 2008)
Perfect secrecy has come a step closer with the
launch of the world's first computer network
protected by unbreakable quantum encryption.
The network connects six locations across Vienna
and in the nearby town of St Poelten, using 200
km of standard commercial fibre optic cables.

Lila Kari, University of Western Ontario

 (iii) Nature as Computation
Understand nature by viewing
natural processes as information processing
Systems Biology
Synthetic Biology
Cellular Computing

Lila Kari, University of Western Ontario

 (iii-1) Systems Biology
Attempt to understand complex interactions
in biological systems by taking a systemic
approach and focusing on the interaction
networks themselves and on the properties
that arise because of these interactions
* gene regulatory networks
* protein-protein interaction networks
* transport networks
Lila Kari, University of Western Ontario
 The Genomic Computer
[Istrail, De Leon, Davidson, 2007]

Molecular transport replaces wires

Causal coordination replaces imposed temporal
synchrony
Changeable architecture replaces rigid structure
Communication channels are formed on an
as-needed basis
Very large scale
Robustness is achieved by rigorous selection
Lila Kari, University of Western Ontario
 (iii-2) Synthetic Biology
TIMES best inventions 2008 : #21
The Synthetic Organism [C.Venter et al.]
Generate a synthetic genome (5,386bp) of a virus by self-assembly
of chemically synthesized short DNA strands

Lila Kari, University of Western Ontario

 (iii-3) Cellular Computing
Computation in living cells: ciliated protozoa

Lila Kari, University of Western Ontario

 Ciliates: Gene Rearrangement

Photo courtesy of L.F. Landweber Lila Kari, University of Western Ontario

Our Cellular Computing Research
L.Landweber, L.Kari. The evolution of cellular
computing: nature's solution to a computational
problem. Biosystems 52(1999)
L.Kari, L.F.Landweber. Computational power of
gene rearrangement. Proc. DNA Computing 5,
DIMACS Series, 54(2000)
L.Kari, J.Kari, L.Landweber. Reversible molecular
computation in ciliates. In Jewels are Forever,
Springer-Verlag (1999)

Lila Kari, University of Western Ontario

 Natural Computing
Nature as inspiration: cellular automata, neural
networks, evolutionary computation, swarm
intelligence, immunocomputing, ALife,
membrane computing, amorphous computing
Nature as implementation substrate: molecular
(DNA) computing*, quantum computing
Nature as computation: systems biology,
synthetic biology, cellular computing*
* Research interests of the UWO Biocomputing Lab

Lila Kari, University of Western Ontario

 Biocomputing at Western
* UWO Biocomputing Lab
http://www.csd.uwo.ca/~lila/biocomplab.html
DNA COMPUTING, CS 9562B/4462B
http://www.csd.uwo.ca/~lila/cs662.html
UWO Biocomputing Student Award
http://www.csd.uwo.ca/~lila/award.html

Lila Kari, University of Western Ontario

Natural Sciences, Ours to Discover

Biology and computer science

life and computation are related.
I am confident that at their interface great
discoveries await those who seek them
[Leonard Adleman, Scientific American, August 1998]

Lila Kari, University of Western Ontario