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Silveira Et Al. - Modeling & Simulating Morphology
Silveira Et Al. - Modeling & Simulating Morphology
INTRODUCTION
Morphogenesis is certainly one of the most complex problems in biology (6,
7), but evolutionary rules that generate patterns of development may be simpler
than we may think. Computer simulations of the evolutionary aspects are based
on very rudimentary rules that, sometimes surprisingly, mimics real life. If we
consider the fact that the whole biosphere evolved through a process of very
tiny errors in the transcription of a 4-letter alphabet, together with selection of
the favorable new words, we may be led to the somewhat simplified conclusion
that life started based on a simple set of rules. Development can be viewed as
involving only a small set of rules of cellular and mechanochemical interactions
that can generate complex morphologies (1, 2, 8). This does not imply that, if it
is possible to use computer algorithms to simulate complex behaviors using a
set of simple rules, so Nature evolved in a similar fashion. Otherwise, we must
think about how simple are the rules for DNA duplication in relation to the
effects we can observe, namely, life or ecosystems. Natural life on earth is
organized into molecular level, cellular level, organism level, and population-
1
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2 SILVEIRA AND MASSAD
ecosystem level. A living thing at any of these levels is a complex adaptive system
that emerges from the interaction of a large number of elements from the level
below (13).
Another matter of contention is that computational rules may not be the same
set of natural rules, or, in other words, if a model correlates well with a process,
it does not necessarily mean that the process was generated by the same set of
rules in the simulation. We believe that the answer would be, most often, a ‘‘no.’’
It is almost certain that we are not building a natural set of rules, since they are
a computational, artificial, and ad hoc set of rules. According to Prusinkiewicz
(10), ‘‘the relationship between the rules expressing the behavior of individual
components and the resulting developmental processes, patterns, and forms is
often nonintuitive and difficult to grasp, and computer simulations play an essen-
tial role in the study of morphogenesis.’’
Taylor and Jefferson (13), assume that there is a major intellectual divide
between the modeling tools designed to accomplish some complex tasks (even
if only distantly related to the way natural systems accomplish it) and systems
meant to accurately model biological systems and intended for testing biological
hypotheses. We think it is a didactic way to classify the computational models,
but there is not a clear limit between them.
The model discussed in this paper was inspired in cellular automata (CA)
and evolutionary algorithm principles. It intends to study biological evolution
considering morphological aspects by offering a computer-based environment.
The individual morphology evolves on the conditions of the environment,
applying artificial rules. We believe that, if this model is able to follow its rules
consistently, it is useful to be applied to solve some complex tasks as predator/
prey emergence, populational strategies, parasitism evolution, evolution, and
differentiation of a species in another two species, and so on, testing biological
hypotheses, even if it is distantly related to the way natural systems accomplish it.
The environment presented here is a matrix represented on a computer, seen
as a chessboard. Each position can contain an individual, a portion of food, an
obstacle or another kind of element in study. All algorithms have local scope,
i.e., as is in biological systems, all decisions are not taken by demographic parame-
ters, but they depend only on individual state and the state of its nearby neighbor-
hood. In the model presented here, most of decisions are influenced by the
individual shape like its movement, its probability of mating, and its energy
consumption; i.e., individual shape is used as a decisional parameter by the
algorithms. This is an aspect of the model inspired in CA methodology.
The model is also inspired by techniques from artificial life (Alife) and evolu-
tionary algorithms. This field of study emerged in the last few years and has
been developed by some independent groups (4). It consists of five great divisions:
genetic algorithms (GA), evolutionary programming (EP), evolution strategies
(ES), classifier systems (CFS), and genetic programming (GP). As a common
aspect, all of them are related with Darwinian evolutionary theories and the
survival of the fittest. The inspired algorithms are thus termed evolutionary
algorithms (see [4] for a detailed discussion about GA, EP, ES, CFS, and GP
SIMULATING MORPHOLOGICAL EVOLUTION 3
METHODS
The program was developed in a computer environment based on a CISC
architecture in C computer language. Details of the initial conception of our
computer program can be found in Silveria et al. (12). An example of its applica-
tion in studies related to infectious diseases can be found in Silveira et al. (11).
The computational environment is represented by a square matrix and individ-
uals are placed in it. The square matrix is 200 3 200 positions.
Each individual is represented by its variables of life and genetic components
(genotype) used as parameters by the algorithms. Simple rules are used to deter-
mine the genotype and phenotype of individuals, and their relationships with
behavioral aspects and individual decisions, like the reproductive age, movement,
and the rules to reproduce and form gametes with variation (mutation), the two
basic requisites to selection in a Darwinian sense (see below).
Simple algorithms are applied to each individual in repeated life cycles. The
scopes of these algorithms are local, mimicking a biological system, where individ-
ual decisions use inputs provided by the neighborhood and the current state of
the individual.
The main variables of life are: age, amount of ingested food and its spatial
position (x, y) in the environment. The genotype is described by two genes:
recursion gene (R) and morphology gene (M ).
R determines the size of the individual, whose body is generated by R iterations
from (x, y) initial position of the individual. Recursion may assume values from
0 to 31 (5 bits). M is an array, where each element of the array may assume values
from 0 to 3, representing the orientation of growing, namely: 0 5 downwards;
1 5 rightwards; 2 5 upwards; 3 5 leftwards. For instance, an individual with
genotype as in Table 1 is six cells large. Its adult shape (phenotype) is shown in
Fig. 1.
4 SILVEIRA AND MASSAD
TABLE 1
Example of Genotype of an Individual
R M0 M1 M2 M3 M4 M5 M6 M7 ... M31
5 2 2 3 3 2 ? ? ? ... ?
TABLE 2
Parameters of the Model
Final cycle Total duration of the simulation in life cycles (number of itera-
tions)
Initial number of individuals Initial number of individuals in cycle 0.
Area of influence Distance that each cell of each individual can reach to mate or
feed.
Metabolic parameter Used to determine how many points of food are consumed for an
individual to maintain its ‘‘body’’.
Agitation The position (x, y) of each individual is disturbed by (x 6 agita-
tion, y 6 agitation) in each cycle, determined randomly.
Floor depth The basement of the environment cannot be occupied by (x, y)
cell. An individual may be able to grow in this direction (by
predominance of alleles 0 in M ) in order to acquire accumu-
lated food.
Food by cycle Amount of food randomly distributed over the environment in
each cycle.
Area of food distribution Determines the depth (from top downwards to the bottom) that
food is distributed in the environment.
Initial food Amount of food that each individual has in cycle 0.
Food donation Proportion of food that each parental individual donates to the
offspring when reproducing (see main text).
Food by descendant Each newborn receives a determined amount of food from the
parents. Depending on parental reserve of food, more or less
offspring are generated in each reproduction.
Mutation Mutation rate is determined by one of two ways: (1) acting on
each ‘‘bit’’ that represents the genotype of each individual in
each cycle or (2) on the whole gene (see main text).
Probability of fatal accident All individuals are submitted to a constant probability of death
by accident in each cycle.
Maximum age Maximum age that an individual may achieve.
FIG. 2. Examples of different phenotypes: (a) a one-celled individual is unable to move itself by
its own resources and it tends to fall downwards. (b) a two-celled individual that tends to move
upwards by one position in each cycle; since the ‘‘force of gravity’’ move it downwards the same
amount, this kind of individual is able to ‘‘float’’ in the environment. (c) an example of ‘‘heavy’’
individual; it tends to move downwards two positions each cycle, one by itself and one by force of
gravity. (d) a ‘‘light’’ individual able to move up by one position in each cycle. (e) this individual
displays a composed movement, moving upwards by two positions and moving rightwards by two
positions. (f) a more complex morphology, showing a ‘‘heavy’’ individual that tends to move leftwards.
TABLE 3
Initial Conditions to the Simulation Described in Fig. 3
FIG. 3. (a) Evolution of a population showing initial oscillation. The amount of distributed food
in each cycle is the main parameter to limit the amount of living individuals. (b) When the population
stabilize the average age oscillates around a certain average. (c) The amount of ingested food per
capita did not change during this simulation. (d) Causes of death by accident (constant to all ages
and all individuals during simulations) and by lack of food. (e) Evolution of recursion gene R showing
two phases. Simulation was initiated with R 5 0 (binary 5 00000). Allele R 5 8 (binary 5 01000)
was initially successful. Allele R 5 24 (binary 5 11000) won the competition. (f) Position occupied
by the individuals during the simulation. The food is distributed in the upper fraction of the environ-
ment and ‘‘light’’ individuals evolved.
8 SILVEIRA AND MASSAD
FIG. 4. Snapshots of a simulation from cycle 0 to 2100 showing aspects of evolution of phenotypes
that are able to move upwards. Individuals represented in black and food in gray. Observe that
some favorable individuals were able to move upwards at cycle 100 but they reproduced in significant
number around cycle 200 competing by food. This caused lack of food for the individuals living
close to the floor at cycle 350. In the sequence larger individuals were able to evolve.
FIG. 5. Simulation A: (a) distribution of food over the upper 10 lines of the environment generates
‘‘light’’ individuals, able to move upwards; (b) succession of some prevalent phenotypes during the
simulation. Initial cells are assigned by 3.
SIMULATING MORPHOLOGICAL EVOLUTION 9
10 SILVEIRA AND MASSAD
always the same. As the reserve of parental food is variable, probably depending
on its fitness, this is a supersimplification of real life, although somewhat realis-
tic—in biological species this donation varies in a range from the parents that
donate all their bodies to the descendants (like bacteria) to parents that donate
part of their reserves depending on their nutritional state (as mammals). In this
model the amount of the parents’ food would be an indirect consequence of its
shape, and available food is the major constraint in the environment. Therefore,
individuals with higher fitness would have more reserve and would be able to
generate more offspring.
The initial age is zero and the position of the offspring is an average of the
parental positions:
● Aging. All individuals become one cycle older at each simulation cycle.
● Energy consumption. It corresponds to the basic metabolism of an individual
and determines how many points of ingested food it spends in each cycle. The
calculation of this amount of consumed food depends on the size of its ‘‘body.’’
Considering that a one-celled individual with an ‘‘area of influence’’ equals to
1 has 8 neighboring positions, this means that it has 8 possibilities to find food.
A two-celled individual has 7 neighboring positions around each cell. We can
presume that if this individual consumes two points of food, it is disadvantaged
in comparison to the one-celled individual.
In order to allow the appearance of larger individuals, a metabolic parameter
m (ranged from 0 to 1) is applied to calculate the food consumption, C, in each
cycle as a function of the size s (number of cells) of the ‘‘body,’’ according to
C5 Om.
s
i51
i
RESULTS
Typical simulation parameters and results are shown in Table 3 and Fig. 3.
Observe that the ‘‘bit-mutation’’ model (Fig. 3e) generated gene R equal to 0,
8, and 24 in rapid succession. This is not desirable since it may be difficult ‘‘fine-
FIG. 6. Simulation B: (a) distribution of food over 40 lines of the environment generates individuals
with ‘‘force’’ to move upwards of two cells (one of them opposed by force of gravity); (b) succession
of some prevalent phenotypes during the simulation. Observe the lateral appendices developed to
capture falling food.
SIMULATING MORPHOLOGICAL EVOLUTION 11
12 SILVEIRA AND MASSAD
tuning’’ the system. For instance, if the fittest individual would be, for instance,
R 5 15 (binary 5 01111), the system would take a long time to find this value.
Compare it with the results below (Fig. 9).
Figure 4 shows selected aspects of the computer screen. Observe that the
simulation begins with food randomly distributed over the environment, except
in its upper portion, where food will be distributed at each cycle in the subsequent
snapshots. One-celled individuals (R 5 0) are also randomly distributed over
the environment. At cycle 50 the force of gravity is concentrating the individuals
close to the floor and part of food is concentrated below floor depth as described
in Table 2. At cycle 100 few ‘‘light’’ individuals emerge and begin to move
towards the upper portion of the environment. When they are well established
no more food falls over the ‘‘heavy’’ variety. Part of food escaped from these
individuals during their transition from the bottom portions of the model. At
around cycle 350 all food has been consumed. The result is the extinction of the
‘‘heavy’’ variety. Larger individuals were able to be developed on the upper
portion of the environment presumably as a function of the evolution of a more
‘‘efficient’’ morphology.
In order to show that it is possible to observe evolutionary issues out of these
simulations, the following are results from simulations performed with the same
initial conditions except by the area of food distribution. All the following simula-
tions used the ‘‘gene-mutation’’ model (as defined in the description of the steps
of a simulation under ‘‘Reproduction’’).
Four simulations were performed. On simulation A, food was distributed close
to the upper fraction of the environment. In this case, individuals evolved towards
a shape able to move upwards (Fig. 5a). This movement generated a population
exhibiting high ‘‘demographic’’ concentration. In consequence, a convex shape,
probably by maximizing food capture, evolved (Fig. 5b). It is suggested that the
competition for food was more difficult in this simulation than in the following,
since the deaths caused by lack of food (Fig. 9) was higher in simulation A than
the others, except simulation B.
In simulation B (Fig. 6), the distribution of food was over the quarter upper
fraction of the environment. In this case, ‘‘light’’ individuals evolved, but they
are less efficient than individuals of simulation A (compare Figs. 5b and 6b)
since these individuals have only two cells to move upwards and one of them is
opposed by the force of gravity. The evolved individuals are able to occupy the
upper fraction of the environment, without the disadvantage of high concentra-
tion as in simulation A. On the other hand, they evolved a kind of plate useful
to capture falling food.
In simulations C and D (Figs. 7 to 8) food was spread over the upper three
quarters and over all the environment. In both cases, ‘‘floating’’ individuals
FIG. 7. Simulation C: (a) distributing food over 140 upper lines generates ‘‘floating’’ individuals;
(b) succession of some prevalent phenotypes during the simulation. Note the lateral appendices.
SIMULATING MORPHOLOGICAL EVOLUTION 13
14 SILVEIRA AND MASSAD
FINAL COMMENTS
Instead of describing populational behavior as a function of equations we
describe individual behaviors as computer algorithms. This kind of model is able
to mimic some real life situations and it deals with the problem of the incomplete
information necessary to simulate real systems based on mathematical modeling,
by circumventing some of the steps involved in the process of model construction.
The model can also avoid some of the difficulties of dealing with heterogeneity,
due to the construction of algorithms that act on each individual of the population.
The two main disadvantages of Alife models against equatorial models are that
(1) Alife models are time-consuming to run in the currently available personal
computers and (2) a subjective component provided by the researcher intervenes
with the model building. The first problem could be solved with technology
evolution. The second is also true for equational models, but it is minimized
with progressive mathematical formalization.
If the populational behavior of a simulation correlates well with a biological
observation, the model may be useful as an exploring tool. The set of rules may
be not the same for a biological environment, since it is a more controlled model
than reality. For instance, if we are studying mortality and each individual has
a gene D that determines its probability of death, it is not relevant if a natural
individual has its mortality based on a single gene. Probably not, but the model
would be an initial approach to the question, devoted to clarify some basic
mechanisms and influences in an overall evolution of the mortality of the species
in a poligenic universe.
This discussion gains importance when we consider the processes of mechaniza-
tion of real systems in the form of a computer simulation. Through this technique,
we state certain rules, for instance, mathematical functions or maps or procedural
algorithms, which generate outputs that can be compared to real systems after
a set of iteration–correction processes. Simpler tools, such as CA, are proving to
be extremely useful to simulate complex patterns, like the evolution of biological
shapes and sizes, based on comparatively simple rules (10).
FIG. 8. Simulation D: (a) distributing food over all environment generates ‘‘floating’’ individuals.
On the other hand, there are ‘‘heavy’’ phenotypes living close to the floor of the environment;
(b) succession of some prevalent phenotypes during the simulation. The usual lateral appendices
were developed.
SIMULATING MORPHOLOGICAL EVOLUTION 15
16 SILVEIRA AND MASSAD
ACKNOWLEDGMENT
We thank CNPq for financial support.
SIMULATING MORPHOLOGICAL EVOLUTION 17
REFERENCES
1. Alberch, P. Ontogenesis and morphological diversification. Amer. Zool. 20, 653–667 (1980).
2. Alberch, P. Developmental constraints in evolutionary processes. In ‘‘Evolution and Develop-
ment.’’ Dahlem Conference Rep, Vol. 20, (J. T. Bonner, Ed.), pp. 313–332. Springer-Verlag,
Berlin/Heidelberg/New York, 1982.
3. Dawkins, R. A. ‘‘The Blind Watchmaker,’’ Oxford Univ. Press, London, 1986.
4. Heitkötter, J., and Beasley, D. (Eds.) The hitch-hiker’s guide to evolutionary computation: A
list of frequently asked questions (FAQ). USENET: comp.ai.genetic (1995). Available by Internet
(FTP anonymous) from ftp://rtfm.mit.edu:/pub/usenet/news.answers/ai-faq/genetic/, 103 pages.
5. Kot, M., Sayler, C. S., and Schultz, T. W. Complex dynamics in a model microbial system. Bul.
Math. Biol. 54(4), 619–648 (1992).
6. Maynard-Smith, J. ‘‘Problems of Biology,’’ Oxford Univ. Press, London, 1987.
7. Murray, J. D. Mathematical biology, 2nd Ed., Springer-Verlag, USA (1993).
8. Oster, G. F., Alberch, P. Evolution and bifurcation of developmental programs. Evolution: 36,
444–459 (1982).
9. Pianka, E. R. Evolutionary Ecology, 3rd Ed., Harper & Row Publishers, Inc., USA (1983).
10. Prusinkiewicz, P. Visual models of morphogenesis. Artificial Life: 61–74. C. L. Langton (Ed.),
MIT Press, Cambridge, Massachusetts, USA. (1995).
11. Silveira, P. S. P., Yang, H. M., Azevedo Neto, R. S., Massad, E. Mathematical and computer
models for infective contact rates. Math. Modelling Sci. Comput. 6, 793–798, 1996.
12. Silveira, P. S. P., Yang, H. M., and Massad, E. Computer-based environment for the study of
ecological systems. Environ. Manag. Health 6(4), 19–28. (1995).
13. Taylor, C., and Jefferson, D. Artificial life as a tool for biological inquiry, In ‘‘Artificial Life
MIT Press, Cambridge, MA, pp. 1–13. (C. L. Langton, Ed.), 1995.