Morphogenesis,

Lindenmayer Systems and

Generative Encodings

Gabriela Ochoa
http://www.ldc.usb.ve/~gabro/
Content

 Morphogenesis
 Biology
 Alife
 Lindenmayer Systems
 Self-similarity, Rewriting
 D0L-systems
 Graphic Interpretation
 Generative or rule-based
encodings for Evolutionary
Algorithms
Morphogenesis in Biology

 One of the major outstanding

problems in the biological
sciences
 Fundamental question of
how biological form and
structure are generated
 Biological form at many
levels, from individual cells,
through the formation
tissues, to the assembly of
organs and whole
organisms.
Morphogenesis in Alife

 Central Question in Morphogenesis: How the

information coded in linear DNA molecules
becomes translated into a three-dimensional form?
 Going from Genotype to Phenotype
 General assumption: the DNA does not specify 'as
some kind of description' or ‘blueprint’ the final
form of the body. More like 'a recipe' for baking a
cake
 A typical Alife approach is to look at possible, very
general, ways to generate complex forms from
relatively simple rules -- often very abstract
L-Systems

 A model of morphogenesis, based on

formal grammars (set of rules and
symbols)
 Introduced in 1968 by the Swedish
biologist A. Lindenmayer
 Originally designed as a formal
description of the development of
simple multi-cellular organisms
 Later on, extended to describe higher
plants and complex branching
structures.
Self-Similarity
“When a piece of a shape is
geometrically similar to the whole,
both the shape and the cascade
that generate it are called self-
similar” (Mandelbrot, 1982)

The recursive nature of the L-system rules

leads to self-similarity and thereby fractal-
like forms are easy to describe with an L-
system.
Self-Similarity in
Fractals
• Exact
• Example Koch snowflake
curve
• Starts with a single line
segment
• On each iteration replace
each segment by
• As one successively
zooms in the resulting
shape is exactly the same
Self-similarity in
Nature
• Approximate
• Only occurs over a few
discrete scales (3 in this
Fern)

• Self-similarity in plants is a
result of developmental
processes, since in their
growth process some
structures repeat regularly.
(Mandelbrot, 1982)
Rewriting
 Define complex objects by
successively replacing parts of
a simple object using a set of
rewriting rules or productions.
 Example: Graphical object
defined in terms of rewriting
rules - Snowflake curve
 Construction: recursively
replacing open polygons
First four orders of the
Koch Curve
Rewriting Systems on Character Strings

 The most extensively studied rewriting systems

operate on character strings (Late 50s,
Chomsky`s work on formal grammars)
 Later applications to Computer and formal
Languges (BNF form)
 A. Lindenmayer (1968) new type of string-
rewriting mechanism (L-systems).
 In L-systems productions are applied in parallel
Reflects Biological motivation of L-systems
Types of L-systems

 Context-free: production rules refer only to an

individual symbol
 Context-sensitive: the production rules apply
to a particular symbol only if the symbol has
certain neighbours
 Deterministic: If there is exactly one
production for each symbol,
 Stochastic: If there are several, and each is
chosen with a certain probability during each
iteration
D0L-systems
 Simplest class of L-systems, b
deterministic and context free. |
a
 Example: └
 Alphabet = {a,b} ab
┘│
 Rules = {a → ab, b → a}
ab a
 Axiom: b ┘│└
abaab
_/ / ┘ └ \
Syntax of a production rule: abaababa

Initiator → Generator Example of a derivation in a

DOL-System
Graphic Interpretation

 L-systems were conceived as a formal theory of

development. Geometric aspects were not considered
 Later, geometrical interpretations were proposed. Tool
for fractal and plant modelling
 Graphic Interpretation of strings, based on turtle
geometry (Prusinkiewicz et al, 89). State of the turtle: (x, y, α)
 (x, y): Cartesian coordinates, turtle position
 α: angle (heading) direction in which the turtle is facing
 Given the step size d and the angle increment δ, the
turtle can respond to the commands represented by the
following symbols:
Turtle Interpretation of Strings

F Move forward a step of length d. The state of

the turtle changes to (x',y',α), where x'= x + d cos(α)
and y'= y + d sin(α). A line segment between points
(x,y) and (x',y') is drawn
f Move forward a step of length d without drawing a line.
The state of the turtle changes as above
+ Turn left by angle δ. The next state of the turtle is
(x,y, α + δ)
- Turn left by angle δ. The next state of the turtle is
(x, y, α -b)
Turtle Interpretation of Strings

w: F+F+F+F
p: F →F+F-F-FF+F+F-F
Angle (δ) = 90º

Quadratic
Koch island

n= 0 n=1 n=2
Bracketed L-systems

 To represent branching structures, L-systems

alphabet is extended with two new symbols:
[, ], to delimit a branch. They are interpreted
as follows:
[ Push the current state of the turtle onto a pushdown
stack.
] Pop a state from the stack and make it the current state
of the turtle. No line is drawn, in general the position of
the turtle changes
Turtle Interpretation of Bracketed Strings

w: F
p: F → F[-F]F[+F][F]
Angle (δ) = 60º

n=1-5
Modeling in Three Dimensions

 Turtle interpretation of strings can be extended to 3D

 Represent the current orientation of the turtle in spave by
3 vectors: H, L, U, indicating turtle’s Heading, the
direction to the Left, and, the direction to the Right.
 3 rotation matrices: RU, RL, and RH and a fixed angle δ
 The following symbols control turtle orientation in space:
 +, - : Turn left and right, using matrix RU(δ)
 &, ^ : Pitch down and up, using matrix RL(δ)
 \, / : Roll left and right, using matrix RH(δ)
 | : Turning around, using matrix RU(180º)
3D L-Systems
3D Bracketed L-Systems
Generative Encodings for Evolutionary
Algorithms
 EAs has been applied to design
problems. Past work has typically
used a direct encoding of the
solution
 Alternative: Generative encoding,
i.e. an encoding that specifies
how to construct the genotype
 Greater scalability through self-
similar and hierarchical structure
and reuse of parts
 Closer to Natural DNA encoding
Examples of Generative Encoding for
EAs
 Biomorphs, The Blind Watchmaker (R. Dawkins)
 Graph encoding for animated 3D creatures (K. Sims)
 L-Systems: plant-like structures, architectural floor
design, tables, locomoting robots (C.Jacob, G. Ochoa,
G. Hornby & J. Pollack, and others)
 Cellular automata rules to produce 2D shapes (H. de
Garis)
 Context rules to produce 2D tiles (P. Bentley and S.
Kumar)
 Cellular encoding for artificial neural networks (F. Gruau)
 Graph generating grammar for artificial neural networks
(H. Kitano)
Evolving Plant-like Structures

 Alife system for simulating the evolution of

artificial plants
 Genotype: single ruled bracketed D0L-systems.
 L-system: w: F, p: F → F[-F]F[+F][F]
 Chromosome: F[-F]F[+F][F]
 Phenotype: 2D branching structures, resulting
from derivation and graphic interpretation of L-
systems
 Genetic Operators: Recombination and mutation
operators that preserve the syntactic structure of
rules
Recombination
Parents Offspring

F[-FF]+[FFF]-FF[-F-F] F[+F]+[-F-F]-FF[+F][-F][F] F[-FF]+[FFF]-FF[+F] F[+F]+[-F-F]-FF[-F-F][-F][F]

Mutation

Symbol Block
Mutation Mutation

F[+F]+[+F-F-F]-FF[-F-F] FF[+FF][-F+F][FFF]F

F[+F]+[+F-F-F]-F[-F][-F-F] FF[+FF][-F+F][-F]F
Evolving Plant-like Structures

 Selection
 Automated: fitness Function inspired by evolutionary
hypothesis concerning the factors that have had the
greatest effect on plant evolution.
 Interactive: allowing the user to direct evolution towards
preferred phenotypes
 It is difficult of automatically measuring the
aesthetic visual success of simulated objects or
images. In most previous work the fitness is
provided through visual inspection by a human
 Automated Selection

 Hypotheses about plant evolution (K.Niklas, 1985):

 Plants with branching patterns that gather the most light can be
predicted to be the most successful (photosynthesis).
 Evolution of plants was driven by the need to reconcile the ability to
support vertical branching structures
 Analytic procedure, components:
 (a) phototropism (growth movement of plants in response to
stimulus of light),
 (b) bilateral symmetry,
 (c) proportion of branching points.
Results

Considering
Considering symmetry only branching points
only

Considering
phototropism, and
symmetry

Considering
Considering phototropism only
phototropism,
symmetry and
branching points
Sea Stars and Urchins
Obtained by a fitness function
considering symmetry only.
And interactively mutating and
recombining organisms
Some others unexpected figures!

Stars
Animals

Candlestick
Rockets
Developmental rules for Neural
Networks - 1
Firstly, biological neural networks:
there is simply not enough information in all our DNA to
specify all the architecture, the connections within our
nervous systems.

So DNA (... with other factors ...) must provide a

developmental 'recipe' which in some sense (partially)
determines nervous system structure -- and hence contributes
to our behaviour.
Developmental rules for Neural
Networks - 2
Secondly, artificial neural networks (ANNs):
we build robots or software agents with ANNs which act as their
nervous system or control system

Alternatives: (1) Design, (2) Evolve ANN architecture.

Evolving: (2.1) Direct encoding, (2.2) Generative encoding
Early References: Frederick Gruau, and Hiroaki Kitano.

Gruau invented 'Cellular Encoding', with similarities to L-

Systems, and used this for evolutionary robotics.

Kitano invented a 'Graph Generating Grammar‘.: A Graph L-

System that generates not a 'tree', but a connectivity matrix for a
network
Generative Representations for Design
Automation
Evolved Tables: Fitness function
 Dynamical & Evolutionary rewarded structures for maximizing:
Machine Organization (DEMO). height; surface area; stability/volume;
Brandeis University, Boston, USA and minimizing the number of cubes.
Hierarchically Regular Locomoting Robots

Evolve both the morphology and the controllers for

different robots. Generative encoding based on L-
systems

A constructed
genobot

Scorpion Serpent
Grammar Based Representation of
Transmission Towers
Evolutionary
approach was
applied to the
Inverse Problem

i.e. The identification Real world towers

of a grammar that translated into the
generates a grammar language
predetermined tower
Conclusions (based on Hornby et. al)

 Main criticism for the use of EAs for design: it is doubtful

whether it will reach the high complexities necessary for
real applications
 Since the search space grows exponentially with the size
of the problem, EAs with direct encoding will not scale to
large designs
 Generative encoding (i.e. a grammatical encoding that
specifies how to construct a design) can achieve greater
scalability through self-similar and hierarchical structure
 Trough reuse of parts generative encoding is a more
compact encoding of a solution
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