Emphasizing Extinction in Evolutionary Programming

Garrison W. Greenwood Gary B. Fogel Manuel Ciobanu

Dept. of Computer Science Natural Selection, Inc. Dept. of Computer Science
Western Michigan University 3333 N. Torrey Pines Ct., Suite 200 Western Michigan University
Kalamazoo, MI 49008 La Jolla, CA 92037 Kalamazoo, MI 49008
garry.greenwood@wmich.edu gfogel@natural-selection.com ciobanum@cs.wmich.edu

Abstract-
Evolutionary programming typically uses tournament
selection to choose parents for reproduction. Tourna-
ments naturally emphasize survival. However, a natural
opposite of survival is extinction, and a study of the fos-
sil record shows extinction plays a key role in the evolu-
tionary process. This paper presents a new evolutionary
algorithm that emphasizes extinction to conduct search
the highest scores are selected as parents for the next
generation and the remainder are discarded [1].
There are several alternative views to the selection
process in general, and tournament selection in particu-
lar. Suppose we assume each individual in the popula-
tion represents a distinct species. The selection process
chooses some individuals in the current population to
be parents while others will be discarded. Under the
operations over a tness landscape. species abstraction, we can say that selected individuals
represent species that survive, while discarded individ-
1 Introduction uals represent species that become extinct. It has been
It is now well known that evolutionary programming
(EP) can be an eective search technique. Although
there are several versions of EP, they are all biologically
inspired and generally follow the format depicted in Fig-
ure 1.
initialize
population
shown that extinction plays a signicant role with re-
spect to evolution in the biological world. It is therefore
natural to ask if extinction can be exploited to increase
the eciency of EP. Here we review the role of extinction
in the fossil record and simulate this process in the con-
text of EP. Our preliminary results suggest that extinc-
tion can enhance the performance of EP on a multimodal
function.

evaluate
2 Mass Extinction and the Fossil Record
fitness
The pace of change of species in ecological systems is
closely correlated to the temporal stability of the envi-
select ronments in which they inhabit. During Earth's long his-
survivors
tory, environmental stresses have been prolonged and/or
severe enough to invoke widespread ecological instability.
randomly vary A direct result of this stress is the simultaneous extinc-
individuals
tion of many species that were not able to adapt in ways
suitable to avoid their demise. These events as recorded
in the fossil record are known as mass extinctions [2].
Figure 1: The canonical EP. The \select survivors" block Extinction has played a major role in shaping the his-
includes the selection of parents and the generation of tory of life on Earth. When examining extinction rates
ospring. for a large portion of the fossil record, Raup and Sep-
koski initially noted two modes of extinction: a low-
This paper focuses on methods used for the selection level, continuous background extinction or a sporadic
of survivors as parents for the following generation. The mass extinction rate [3]. Although mass extinctions ac-
most common form of selection used in EP is tourna- count for only a small percentage of all extinctions, they
ment selection, in which the tness of each individual are singularly important because they remove \resilent"
in the population is compared against the tness of a incumbent groups from niches, creating \windows of op-
randomly chosen set of other individuals in the current portunity" for other species to ourish and establish an
population. A \win" is recorded for an individual each ecological niche [4].
time an individual's tness exceeds that of another in Five mass extinctions have been identied: terminal
the tournament set. All individuals are then ranked ac- Ordovician (440 Myr ago)1; late Devonian (365 Myr
cording to their number of wins. Those individuals with 1 Myr denotes one million years.
ago); late Permian (250 Myr ago); terminal Triassic
(215 Myr ago); and terminal Cretaceous (65 Myr 80 species kill (%)














ago). The severity of these extinction events can be dif-





cult to fully comprehend. For instance, it has been
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estimated that 96% of all marine species on Earth went

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extinct by the end of the Permian period [5], representing 50

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52% of all marine vertebrate and invertebrate families

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[3]. Several causes for these events have been proposed

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including global cooling, changes in sea level, and the

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impact of a meteor or comet. Some have suggested that

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there is a periodicity for mass extinctions with a mean

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period of 26 Myr [6, 7], although not all researchers agree

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with this notion (see [8], pg 404-405). 104 105 106 107 108 109
Patterns and processes of species extinction and sur- mean waiting time in years
vival appear to be dierent between background and
mass extinction events. For instance, Jablonski [9] noted
that during background extinction intervals, Cretaceous Figure 2: A kill curve showing the average spacing
gastropods and bivalves with planktotrophic (plankton-
feeding) larvae had longer species durations than those
with nonplanktotrophic larvae. In contrast, larval type
was not a factor during the Cretaceous mass extinction
event. It is clear that not all species were aected equally
across all extinction events. (This fact is a central prin-
ciple behind our incorporation of extinction into an evo-
lutionary algorithm.)
between marine extinction events of specied intensity
(adopted from [11]).
3 Adding Extinction into Evolutionary Algo-
rithms
Our extinction-based evolutionary algorithm started as
a standard evolutionary programming algorithm: repro-
Wolfe and Upchurch [10] noted that one of the major
factors in the transition from predominantly evergreen
to deciduous biotas around the world was correlated to
the cooling during the Cretaceous mass extinction event.
This event led to much higher rates of extinction for
evergreens relative to deciduous plants. As Newton and
Laporte [2] noted,
One answer to the question, `How did tem-
perate deciduous forests arise?' is, `Through
(t) = fs1 ; s2 ; : : : ; sk g, each of which is char-
enhanced survival in the Cretaceous extinc-
tion.' Mass extinctions may have been re-
sponsible for many such cases of evolutionary
replacement in the fossil record.
duction performed only via mutation, a xed strategy
parameter, and tournament selection to chose survivors.
It became necessary to alter this process when modeling
extinction dynamics. For instance, not all members of
the population necessarily reproduce each generation; a
tournament does not always determine survival; and co-
evolution aects only a small subset of the population.
We consider an ecosystem at time t that contains a
species set
acterized by a vector ~x 2 <n . These numbers repre-
sent phenotypical traits which change whenever species
evolve. All species are subjected to an external environ-
mental stress (t), which may be severe enough to cause
some species to become extinct if their tness level is too
Using the stratigraphical ranges of 17,621 marine gen- low. The tness of each si is measured, in part, by an ob-
era over the last 600 Myr, Raup noted that the average jective function f (~x); minimum values of this function in-
species duration was 4 Myr. Using this same data, Raup crease the likelihood of survival. But tness is a relative
[11] developed a \kill curve", shown in Figure 2, that measure, which means f (~x) alone does not completely
described the average spacing between extinction events dene tness unless the mapping function considers the
of varying intensity. For example, an extinction event in
uence of other species in the same environment. We
capable of killing 30% of marine species occurs every 10 used the following mapping scheme. Let fmin t (f t ) de-
max
Myr; an extinction event capable of killing 65% of marine note the minimum (maximum) objective function value
species occurs every 100 Myr. Although many assump- of any species si 2
(t). Then the tness of si at time t
tions were used in the development of this curve, it ap- is given by
pears that extinctions may be continuously distributed
(s ; t) =  + (1 , )
f (~xi ) , fmax
t
in a logarithmic fashion rather than separated into two i (1)
discrete categories. t , fmax
fmin t
where  2 [0; 1]. Such a mapping forces f (~x) 7! [; 1].
(The purpose of the lower bound  will be discussed
shortly.) Other types of mappings could be used; the
above method was chosen because of its simplicity. low-t individuals intuitively have very small barriers|
The steps in our extinction-based evolutionary algo- even a small mutation could lead to a marked improved
rithm are shown below: phenotype. Roberts and Newman chose the species with
the lowest tness to evolve rst in their model; this is
1. Let t = 0 and randomly initialize population
(0). the same approach we have adopted.
Compute (si ; t) 8 i. There is no absolute scale of tness that can be consis-
2. Increment t and let
(t) =
(t , 1). tently applied over all environments; tnesses can there-
fore lie between zero and one without any loss in gener-
3. Randomly choose a stress (t) 2 [0; 0:96]. Make ality. Our algorithm maps all tness values to the subin-
all si 2
(t)j(si ; t) < (t) go extinct (i.e., discard terval [,1], where  is a user selectable parameter. The
them). Let m equal the number of species that lower bound  > 0 serves a useful purpose. Suppose
went extinct.  = 0 so tness values can reside anywhere on the unit
interval. Furthermore, assume a very simplistic mapping
4. If (m > 0) then function is used|simple normalization of all tness val-
fMutate each species to produce multiple new ues to the maximum tness in the current population.
species. Compute (
; t) for all new species. Con- If the evolutionary algorithm is working properly, the
duct a tournament among the new species and de- individuals should eventually evolve to a high state of
terministically choose the m best as replacements
for those species that went extinct.g
else
f Let j = argmin i ((si ; t)). Mutate sj . Randomly
choose 5 more individuals from the current popu-
lation and mutate them also. Compute (
; t) for
all mutated species. g
5. If computation time not exhausted, go to step 2.
Otherwise, exit.
During each generation t, three steps take place. A
random stress (t) is applied against all species, and all
tness, which means all tness values  1. This makes
it very unlikely that an external stress can force species
to become extinct|a behavior that directly contradicts
evidence found in the fossil record. The parameter  cre-
ates a lower threshold for extinction that prevents mass
extinctions from occurring too frequently, while at the
same time not dispensing with them entirely.
Reproduction is done only via mutation:
x0i = xi + N(0,) ; xi 2 ~x
where N(0,) is a normally distributed random variable
species si with tness (si ; t) < (t) are discarded to with zero mean and standard deviation .
simulate extinction. At this point, one generation of a
standard EP is conducted to nd replacement species.
By restricting the replacements to be selected only from
the new species, we model speciation. However, it is
entirely possible that all of the species may have su-
ciently high tness so that none go extinct. In this case 3
the poorest t si |i.e., the species with the lowest objec-
tive function value|is mutated, which simulates a low- f 2
1
level, background evolution in
(t). Whenever a species 1
evolves to some new state, it also aects the state and 0.5
0.
tness other surrounding species. We simulate this co- 0 0 x1
evolution by also mutating ve other randomly chosen 1
species. 0.5
0
-0.5
The stress value (t) is chosen from a uniform distri- -0.5
bution over the interval [0,0.96]. All species see the exact x2 -11
-1
same stress level. The upper limit of 0.96 sets the maxi-
mum percent of species that can go extinct in any single Figure 3: The tness landscape dened by Eq. (2). The
generation; it is close to extinction levels seen during the global minimum is at (0,0).
Permian mass extinction [5].
There is a rationale for choosing that species with the We used our extinction-based evolutionary algorithm
lowest tness as the rst to evolve. Roberts and Newman to search for the global minimum of the multimodal ob-
[12] attached a \barrier" to all species that must be over- jective function
come in order to evolve to a state of higher tness. With
respect to an evolutionary algorithm, this barrier is a re- f (x1 ; x2 ) = x21 + 2x22 , 0:3 cos(3x1 )
gion of relatively low tness and shows the mutation size ,0:4 cos(4x2 ) + 0:7 (2)
necessary to improve phenotypical behavior. Extremely
with x1 ; x2 2 [,1; 1]. This function is shown in Figure relationship. But there is no obvious|let alone direct|
3. The algorithm was run for 10,000 generations
p with relationship between antelope and hippos nor between
N = 100 species and  = 0:8. We chose  = 0:02 and lions and hippos. Does it therefore make any sense to
no self-adaptation was used. compare their phenotypes (equivalently, tnesses)? Yet,
The performance of our algorithm is compared that is exactly what happens during conventional tour-
against a standard EP that was run with the same pop- nament selection.
ulation size; the same initial population; a tournament Our extinction-based evolutionary algorithm at-
size of 20; and an identical method of reproduction.
Our algorithm executes 10,000 generations about three
times faster than a standard EP executes 5,000 gener-
ations. Nevertheless, our extinction-based evolutionary
algorithm consistently outperformed the standard EP in
searches conducted over the landscape depicted in Figure
3. The results are given in Table 1.
EA (w/extinction) standard EP
minimum f (~x) 9.14010,7 6.70010,5
mean 8.29410 , 6 4.49810,4
std. dev. 7.95310 , 6 3.54610,4
Table 1: Performance comparison between the evolution-
ary algorithm with extinction and a standard EP. Both
algorithms used the same initial population to conduct
searches in the landscape shown in Figure 3. The glob-
ally minimum value is f (0; 0) = 0. Table entries are
based on data recorded from 20 independent runs.
4 Discussion
tempts to evolve a population to higher tness values
by emulating dynamics derived from the fossil record|
extinction must be present and tournaments are con-
ducted among species. Although the exact cause of bi-
otic extinction remains debatable, a number of reasons
have been proposed including excessive inbreeding [13]
or environmental stresses such as climatic change, vol-
canic activity, or disease [14]. Our algorithm assumes
environmental stress is culpable. Replacement species
are created by mutating existing species|emulating
speciation|and a tournament among those new candi-
dates determines the new species that survives. This
follows Gause's Principle of Competitive Exclusion [15]
where new species must compete for the same ecological
niche. Note that this tournament does include existing
species in the tournament set even though replacements
can only come from speciation.
Extinctions (%)
100
80
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The material from the two previous sections raises some

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important philosophical issues regarding tournament se-

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lection. In order to compute the number of wins for a

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target individual, a small tournament set is randomly

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chosen from the current population. Fitness values are

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sumes it is both acceptable and appropriate to compare 7000 7200 7400 7600 7800 8000
the tness values of distinct individuals. Tournament Generations
selection makes sense in light of a simulation at the indi-
vidual level, but dierent approaches are required when
modeling evolution at the species level. More specically, Figure 4: Extinctions per generation over a portion of
it may not make sense to conduct head-to-head tness the evolutionary process.
comparisons when individuals in a population are inter-
preted to be distinct species. Indeed, inter-species tness Over 25 years ago, Eldredge and Gould [16] sparked
comparison are valid only in special circumstances. a controversy that continues even today. They viewed
For clarity, let
represent the set of all species that \phyletic gradualism" as a
awed concept that should be
co-exist in a given environment. The phenotype of each replaced by punctuated equilibrium. This concept says
si 2
ultimately re
ects the ability of that species to that evolutionary activity is characterized by periods of
survive in that environment|it is a measure of its t- stasis, with little speciation, interspersed with episodes
ness. But, comparing the phenotypes of two distinct of very intense speciation. Figure 4 shows that our al-
species may not only be dicult, it may be meaningless. gorithm has periods of stasis interspersed with burst of
For example, in the Caprivi Game Park in northeast- extinctions. However, this behavior is not exactly punc-
ern Namibia, one can nd lions, antelopes, and hippos. tuated equilibrium|we immediately replace any extinct
These species all co-exist but do not necessarily have species whereas punctuated equilibrium does not man-
any direct relationship between each other. Of course date that a xed number of species be constantly main-
lions and antelope will since they have a predator-prey tained.
5 Conclusions & Future Work aect distinct species in dierent ways. One obvi-
Evolutionary change cannot be completely explained by
natural selection alone [17]. At the species level, mass
extinctions wipe out entire species for reasons unrelated
to inter-species struggles for survival. Nevertheless, this
does create windows of opportunity for other species to
ourish. Our algorithm follows a similar vein to conduct
searches: episodic mass extinctions prevent stagnation,
and rapid speciation maintains a constant number of so-
lutions.
Our results indicate that extinction can enhance the
performance of an evolutionary search. Granted, only
one multimodal landscape was explored, but the re-
sults are certainly encouraging particularly in light of
the low execution time with respect to a standard EP.
The improved execution time is not unexpected. In
ous way is to let stress be analogous to a tness
penalty and let culling be done by natural selec-
tion.
2. Self-adaptive extinction
The strategy parameter  sets a lower bound on
the percent of a species that can go extinct. As
 ! 0, a large number of mass extinctions be-
come possible|our algorithm then approximates
a (; ) evolution strategy. Conversely, as  ! 1,
virtually no extinctions occur and our algorithm
degenerates into a random walk with replacement.
It would be interesting to investigate the perfor-
mance when  is allowed to evolve.
3. Self-adaptive mutation
the extinction-based algorithm a tournament is not con-
ducted each generation|only background evolution is
simulated. In fact, a tournament is conducted only after
the onset of a mass extinction. On the other hand, the
standard EP conducts a tournament every generation.
Our algorithm can easily accommodate searches over
dynamic landscapes. This will be the subject of future
The current version of our algorithm used a xed
standard deviation () for the normal distribution.
Self-adaptation should improve the performance,
but no single method is universally applicable [19].
4. Other mutation distributions
A number of recent studies indicate that alter-
studies. We have identied some other areas that can native probability distributions for mutation can
deserve further investigation. Specically,
1. Modeling evolution
It is important to note that our algorithm, in its
present form, is not intended to serve as a model
for biotic macro-evolution. Nevertheless, it does
incorporate a number of intriguing features that
improve the performance over some landscapes
[20, 21]. It would be a trivial matter to incorporate
Cauchy mutations into our algorithm.
Acknowledgement
The authors would like to thank L.J. Fogel and D.B.
suggest it could be easily modied to perform that Fogel for their valuable comments that helped to improve
function. A rst step would be to monitor the
branching and termination of species. Ideally, we
should not maintain a constant population size|
speciation should be allowed to proceed in a nat-
ural way with, perhaps, a maximum number of
species that can be supported within the environ-
ment.
Normally a species can expect to undergo a num-
ber of stresses during its lifetime and all species
co-existing in that same environment will be sub-
jected to the same stress|but not all species are
aected to the same degree by that stress. New-
man [18] put it this way:
: : : we have assumed that every stress on
the system aects every species. This
is clearly not realistic. Some stresses
will for example be localized in space,
or will not reach under the sea, or will
only reach under the sea, and so for.
The current version applies the stress (t) equally
to all species. We could specify|or even evolve|
species relationships that permits a stress factor to
this paper.
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