Dessalles, Jean-Louis (1992). "Biomimetic Use of Genetic Algorithms".

In R. Mnner & B. Manderick (eds), Parallel Problem Solving from Nature, 2.

Amsterdam : North-Holland, 127-135.

Biomimetic Use of Genetic Algorithms

Jean Louis Dessalles
TELECOM-Paris - Dpartement Informatique, 46 rue Barrault - 75634 PARIS
Cedex 13 - France - E-: dessalles@enst.fr

Abstract:
Genetic algorithms are considered as an original way to solve problems,
probably because of their generality and of their "blind" nature. But GAs are
also unusual since the features of many implementations (among all that could
be thought of) are principally led by the biological metaphor, while efficiency
measurements intervene only afterwards. We propose here to examine the
relevance of these biomimetic aspects, by pointing out some fundamental
similarities and divergences between GAs and the genome of living beings
shaped by natural selection. One of the main differences comes from the fact
that GAs rely principally on the so-called implicit parallelism, while giving to
the mutation/selection mechanism the second role. Such differences could
suggest new ways of employing GAs on complex problems, using complex
codings and starting from nearly homogeneous populations.

1. GENES AND SCHEMATA AS THE UNITS OF SELECTION

A fundamental common feature between GAs and natural genetic systems
comes from the fact that in both situations individuals are not what is selected.
In GAs, individuals are represented by their genome (most often a binary
vector), and are evaluated so that only the best fitted ones have some chance to
reproduce. The hope is that the GA will create individuals which will reach a
maximum of the evaluation function. But this is not sufficient to make a GA:
each pair of "parents" chosen among the best graded individuals enters a
hybridation (crossover) in which genomes are mixed to give the genome of an
offspring. This crossover is essential, as was shown by J. Holland. Without
crossover we have random search, not GA. This requirement has many
consequences for our purpose, as we will see after having compared it with its
natural counterpart.
Figure 1 shows an example which was especially designed to underline the
added value of crossover. Individuals are "marked" according to the sum of the

bits of their genome. Crossover allows the selected 1s to gather in the same
individuals.

Figure 1. A genetic algorithm is asked to maximize the sum of 100 bits. The
right histogram shows the result of 50 generations of 100 individuals: the whole
population scores between 93 and 96. The left diagram shows the histogram
resulting from 5000 random choices, which spreads between 34 and 66.
Crossover allows selection to operate not on individuals, but, as shown by
J. Holland in 1968, on schemata (cf. [Goldberg 1989]). A schema is theoretically
a partial specification of the genome, on which the observer is keeping an eye
through generations. Practically, only schemata that are specified on a short
length have some chance of survive after crossover. For the observer, only those
schemata can pretend to be selection units . It would be indeed nonsense to say
that the population as a whole is selected. And individuals are destroyed at each
generation (if we except the so-called elitist models)! Only short schemata have
a long enough life span so that, after some generations, some of them can be
considered as selected by the observer.
J. Holland showed that at best n3 different schemata were simultaneously
present in a population of n individuals, and since schemata are selected when
individuals are evaluated, he coined the term "implicit parallelism" ([Goldberg
1989]). But we must keep in mind that this counting of schemata is only valid
for a random population.
This observation has to be compared with the ideas of Richard Dawkins,
who pointed out that rigorously natural selection does not operate by selecting
individuals, nor groups, but that it operates on genes (cf. [Dawkins 1978, 1982]).
When considered from the point of view of natural selection mechanisms,
individuals are mere temporary arrangements of genes. Only genes can survive
through generations. Genomic hybridation is thus an essential phenomenon.
Crossover is well known for sexual beings, but it has been also observed among
unicellulars which reproduce normally through division: it is the so-called
conjugation, during which two individuals mix their genome, and by the way no
longer exist as individuals. There are reasons (from genetics and chemistry) to

think that, contrary to what is usually said, crossover is as old as DNA, and that
it is widespread among all living beings, although it has not been observed in
each case. We could hardly speak of species in the absence of genomic
encounters.
Since selection in GAs operates on schemata, one can define an average
fitness value for each schema. But some schemata have also a meaning given by
the designer, and it is often interesting to relate meaning and fitness, as a way
to "explain" the solutions calculated by the algorithm. As we will see, this may
not be possible in the case of biomimetic GAs.

2. BIOMIMETIC CONSTRAINTS ON THE GENETIC CODE

Using GAs is an art which lies for the major part in the coding of the
problem. The designer has to define the semantics of the genome, so that a
"mark" can be assigned to each individual. But the designer has to face several
problems:
nonseparability
- The "coding" of living beings is definitely complex. Natural selection
operates on the phenotype of individuals, and the relation genome --> phenotype
is very complicated (see for example [Petit 1976]): genes have multiple effects on
the phenotype (pleiotropy) and phenotypic characteristics are the result of the
combined action of numerous genes. Furthermore high order genes have been
discovered (e.g. genes which code for the repressor of the activator of another
repressor, cf. [Beardsley 1991]).
But why should the designer of a genetic algorithm choose a complex
coding? An answer could be that a too simple coding often reveals a too simple
problem, for which GAs may sometimes be superfluous. Since schemata are
selection units, one may be led to consider sections of genome as independant
units on which evaluation will operate. This was actually the case in the
example of figure 1: each bit contributes to the global "mark" apart from the
others. But this means that the problem, as far as it can be solved by such a GA,
can be split into as many independent sub-problems as there are independently
evaluated units.
However, interesting problems are often non-divisible (some problems may
be separable, and GAs are precisely used to separate them, finding out
independant schemata, but we are speaking here about complex problems that
cannot be hoped to be separable). Schemata are indeed selection units, but they
cannot be seen as fitness units if the problem is really complex, since the fitness
of a given schema is necessarily highly dependent on the presence or absence of
other schemata in the genome. In such a situation, the use of simple codings is
unuseful. It may even be restricting, because it allows only a restricted
exploration of the fitness landscape, as we will see. Complex codings, on the
other hand, may be needed if we want the link genome evaluation to be
complex, as is the case for example when one uses second order schemata, i.e.

schemata that modify the way other schemata are evaluated (e.g. a group of bits
coding for the number of relevant bits in an other section of the genome).
continuity
- one may think conversely that if a complex coding was chosen to handle a
complex problem (with no hope that this problem may be separable), then this
coding may not follow the continuity principle. This principle claims that
genomes which are close for the Hamming distance (number of elementary
mutations needed to transform one into the other) should have most of the time
about the same evaluations. This is what makes offspring viable and allows
some tolerance to mutations. Manderick [1991] measures this continuity with
the autocorrelation of fitness when elementary mutations are performed.
Unfortunately, it seems that the complex coding we are claiming from a
biomimetic point of view has little chance to respect this continuity principle. If
for instance a second order schema is even slightly mutated, then several other
parts of genome will change meaning, and the global "mark" will be significantly
changed.
So how can we explain that the natural system, which is so complex, is
quite continuous? Part of the answer comes from the fact that genes are
extended. Most of functional natural genes code for complex molecules, proteins.
An elementary mutation will for instance change one aminoacid into another,
which may eventually slightly change the chemical properties of the protein, e.g.
diminishing its catalytic power or specificity. The effect will most probably go
unnoticed, or will even be cancelled (more protein synthesis) at the level of
individual fitness. The problem with many GA-codings is that they concentrate
too much meaning on each bit. An "extended" coding should allow punctual
mutations to have limited effects, and would thus allow complex codes, as
required in biomimetic GAs, to be continuous.
preservation of semantics
The balance between these two requirements: complexity and continuity,
appears thus to be quite difficult to be hold. But the designer must also grant
the preservation of semantics through genetic macro-operators like inversion,
translocations or duplications. Such transformations do occur in nature (very
seldom for some of them). They allow completely new genes to be created, and
"cooperating" genes to become closer and to constitute longer functional genes
(polygenes). In GAs, a complete "gene from locus" separation creates two orders:
a semantic order, which never changes, and a topological order which may
change through macro-operators and which bears neighbourhood relations that
are used during crossover. But such a de-correlation between meaning and position makes offspring very unlikely to be functional after crossover. In the natural counterpart, major changes may go unnoticed if they occur in non-coding
regions of DNA. And genes or polygenes may sometimes change location with no
consequence on their own functioning or the functioning of their genetic environment. This is made possible by the presence of signals within DNA (e.g.
starting position for transcription) that make groups of genes quite independent.
To sum up, macro-operators are biomimetic, but complete gene/locus separation
is not. Biomimetic GAs should instead make use of signals to make absolute
position in the genome less relevant.

The choice of the genetic coding is crucial when we design a genetic

algorithm to process a given problem, but, if we follow the biological metaphor,
it appears also very difficult, since the coding has to meet the requirements of
contradictory constraints: complexity (to allow better exploration of nonseparable problems), continuity, preservation of semantics. Furthermore, such
constraints upon the structure of codings may have consequences for the way we
use GAs. They indicate that the classical way of using GAs is not very
biomimetic, as we will see now.

3. COMPLEXITY IN THE CODING, NOT IN POPULATIONS

Classical genetic algorithms interbreed individuals that are completely
different. In most applications, initial populations are indeed set up randomly.
The GA is then considered to have completed its job when the population
becomes nearly homogeneous. The end of convergence is sometimes handled
differently because GAs become very slow: in a nearly homogeneous population,
crossover looses its major role which is now played by mutation. New solutions
are generated much more by the mutation/selection mechanism than by implicit
parallelism.
However, nature shows us a quite different situation. Individuals that can
be successfully crossed share at least 99% of their genome, and most differences
are phenotypically neutral! This may contribute to explain why the
tremendously complex coding from genotype to phenotype, with genes of high
degree, remains compatible with the continuity principle even through
crossover: offspring look like their parents because both parents are similar, and
crossover creates few changes (quantitatively and qualitatively) when yielding
new genomes.
This questions the biomimetism of GAs as they are classically defined. If
the coding is complex enough (as is required by biomimetism), then a random
initial population will consist of individuals that are unlikely to give viable
offspring when crossed, because offspring will have very low fitness or no
meaning at all. Of course the genome of individuals processed by classical GAs
could be compared to the 1% of the significantly variable genes of a natural
population (less than 1000 genes for mammals). But even in case of a sudden
environmental change, very few of the alleles on these variable loci may become
evolutionary meaningful, contrary to what is expected with GAs.
Genetic algorithms thus appear to be most biomimetic when they seem
least interesting, i.e. at the end of convergence, when the population tends to
become nearly homogeneous, and when the role of mutation dominates the
rearrangement due to crossover (figure 2). At this stage, implicit parallelism no
longer exists.

Figure 2. This schema shows that the GA of figure 1 converges asymptotically.

The mere redistribution due to crossover does not allow to reach optimum (all
bits 1). Admittedly we have a probability of only [1 - (1 - 1/2100)100] 10-28 that
one locus is 0 for all individuals in the initial population. But after the first
generation, if 10% of the population reproduce, this probability reaches 0.1 . In
the trial plotted above (elitist model), it seems that 4 loci remain 0 after 50
generations. If pm is the mutation probability, we have [1 - (1 - pm)4 ] 4.pm
chances that a given individual gains a 1 on one of these loci during the next
generation. On can estimate by 1/10pm the number of generations necessary to
switch all four bits to 1. But increasing pm may be problematic, especially with a
complex coding.
However what we want to suggest here is that the biomimetic use of genetic
algorithms may be legitimate and could prove efficient in certain situations.
Biomimetic GAs characteristics (as summarized in table 1) are legitimate
because they bring the biological metaphor logically further. After all, GAs were
not selected after a competition with all thinkable alternative algorithms. They
were studied in the first place because of heuristic principles like "what
performs well in nature should perform well in optimization". GAs, used
biomimetically as proposed here, are of course less efficient. They lack the
implicit parallelism put forward in most applications. However, they should
appear as worth studying as well, if we can anticipate situations in which they
could bring an added value, as may be the case with problems that cannot be
formulated in terms accessible to usual methods.

Table 1
Main features of biomimetic genetic algorithms
complex coding, with high order genes, in order to allow better exploration
of non-separable problems
extended genes to allow quasi-continuous mutational changes
use of signals (instead of complete gene-locus separation) to allow macrooperators
nearly homogeneous populations, where the mutation/selection mechanism
takes the major role over implicit parallelism in the search for new
solutions

4. BIOMIMETIC GAs ON COMPLEX PROBLEMS

Good solutions for a complex problem are unlikely to be simple. Biomimetic
GAs may be an interesting way to discover good complex solutions.
To examine this point we can consider the interesting attempt of Lavalou
[1990] who tried to apply genetic algorithms to a complex enough problem. His
genetic algorithm handled genomes coding for short music pieces which were
evaluated by a connectionist network. He decided to design a complex coding
with genetically encoded musical operators. For instance, musical themes were
transformed recursively using short patterns, and not only the patterns, but
also the number of recursive transformations were determined by genes.
The idea we want to suggest here in order to promote biomimetic GAs is
that if the problem to be solved is complex (think of a very "tortured" and multidimensional fitness landscape), classical GAs will not perform better than
random search! Crossover between necessarily very different (because initially
randomly determined) individuals will give intermediary offspring which are
very unlikely to obtain a significantly better fitness: if the fitness landscape is
complex enough, each individual of the initial population is isolated in a local
fitness context in which the fitness value of a given locus depends on the values
of many other loci. Specific mutational changes may bring a higher fitness,
while different (and often contradictory) changes would benefit another
individual placed in a very different fitness context. In such a situation,
crossover does not play its role of gathering independent good solutions together
as expected with implicit parallelism, but it produces individuals, located in
totally new fitness contexts, that can be considered as random in these contexts.
The populations processed by classical GAs through generations correspond in
this case to a few thousands of random trials, and if the problem is really
complex, a satisfactory solution has little chance to be obtained this way.
Biomimetic GAs theoretically escape from this difficulty since they operate
on nearly homogeneous populations. The initial random choice that locates the
entire population near a given location in the fitness landscape will then be
slowly, but constantly, improved by the combined effect of mutations and
crossover. This is the mutation/selection mechanism. Then comes another
feature of biomimetic GAs into play: the complexity of coding.
Since the link labelled A in figure 3 is very simple in classical GAs, the
reachable phenotypes will have a quite limited complexity (e.g. algorithmic

complexity as defined in [Chaitin 1987]) because of a lack of combinatorial

power.

A
genes

B
phenotype

evaluation

selection

Figure 3. This schema illustrates the importance of the genotype/phenotype

distinction for biomimetic GAs. This separation allows codings (in A) to create a
"wide" range of phenotypes by complex combinations.
There are many ways to make the link A complex. For instance Werner &
Dyer [1992] designed a system in which evolving creatures learn to
communicate. In this application, the genome of each creature codes for a small
connectionist system (its phenotype) that controls the creature's behavior. But
we may think that combinatorial codes (i.e. with high order genes), as suggested
for biomimetic GAs, may yield even richer genotype -- phenotype links.
If the coding leading from genes to phenotype is too simple (e.g. in the case
of music, each note could be coded separately), then one can imagine that it is
not an efficient way for the population to explore the landscape during its
continuous walk (for instance a combinatorial coding of music pieces like the one
chosen by Lavalou produces pieces of arbitrary length, what a trivial coding will
never do). Simple codings do not have here the advantage of allowing a capture
of parameters that are relevant to the problem (because the problem is not
separable), and they may prove to be too limited in many complex applications.

5. POWER AND LIMITS OF BIOMIMETIC GAs

We may think of the genome of individuals processed by biomimetic GAs as
a blueprint for a kind of machine (the phenotype of individuals). The
mutation/selection mechanism has been invoked in very different contexts as a
way to create complex systems (Darwin's natural selection theory, Burnet's
clonal selection theory, synaptic selection theory of Edelman and Changeux,
aspects of behavioral learning, and even cognition (see [Changeux & Dehaene
1989]), etc.). Can a system like biomimetic GAs create phenotypes that become
increasingly complex? Can we imagine they could reach the same creative power
as their natural counterparts?
Even if they should prove to be an interesting way to explore very complex
problems, there are fundamental reasons why GAs as we know them are also
limited in their creative power (this is particularly relevant to research on

Artificial Life, see [Jefferson et al. 1992]).

The semantics of GAs lies for the major part, and often totally, outside the
genes. If we consider again Lavalou's program, a 5 bit sequence contributing,
say, to a musical pattern has no chance to have any influence on the recursivity
depth. In other words, one cannot imagine any combination of mutations, anywhere in the genome, that could change the semantics of these five bits this
way.
In living beings, on the other hand, the semantics of genes is controlled by
the genome itself, and it may be changed by the mutation/selection mechanism.
If we discover that 5 codons have an influence on eye color, one could
theoretically imagine a group of mutations somewhere else in the genome that
makes these 5 codons control this time tooth length!
One can say that living beings are endosemantic entities, while GAs are
exosemantic. The genome of living beings is the only known endosemantic
system. If we define the "genetic envelope" of a GA as the set phenotypes that it
can reach, then this enveloppe is predetermined (most of the time implicitly) by
the designer of the genes --> phenotype coding. This may prevent us to expect
too "miraculous" properties from GAs, even if they are biomimetic.
But GAs show quite impressive properties (generality, adaptation, learning
capabilities when associated with classifiers,...). We tried to indicate here that,
when used in a biomimetic way, they may be an interesting tool to explore very
complex problems.
acknowledgments: I am grateful to Alain Grumbach, Irne Fournier and Olivier Hudry for
having read an early version of this paper and for their fruitful remarks.

References
Beardsley Tim (1991). La rgulation des gnes. Pour la Science n168, 54-64
Chaitin G. (1987). Algorithmic Information Theory. Cambridge Univ. Press
Changeux Jean-Pierre, Dehaene Stanislas (1989). Neuronal models of cognitive
functions. Cognition, 33, 63-109
Dawkins Richard (1978). Le gne goste (The Selfish Gene). Editions Menges
Dawkins Richard (1982). The Extended Phenotype - The Gene as the Unit of
Selection. W.H. Freeman & Co, Oxford
Goldberg David E. (1989). Genetic Algorithms in Search Optimization &
Machine Learning. Addison Wesley Publishing Company
Jefferson David, Collins Robert, et al. (1992). Evolution as a Theme in Artificial
Life: The Genesys/Tracker System. In Langton C., Taylor C., Farmer J.D.,
Artificial Life II, Addison-Wesley
Lavalou Gilles (1990). Application des algorithmes gntiques la gnration de
squences musicales. Dossier long de fin d'tudes, ENST, Paris
Manderick B. (1991). State of the art in theoretical approaches to genetic
algorithms. conf. 05 dec. 91 Alg. gntiques, ENS Ulm, Paris
Petit Claudine, Zuckerkandl Emile (1976). Evolution: Gntique des populations,
volution molculaire. Hermann, Paris
Werner Gregory M., Dyer Michael G. (1992). Evolution of Communication in
Artificial Organisms. In Langton Christopher, Taylor Charles, Farmer
J.D., Artificial Life II, Addison-Wesley, 659-687