Dec 312017
 
A paper writen to describe Evolution and Optimization of Digital Organisms.
File TIERRA.ZIP from The Programmer’s Corner in
Category Various Text files
A paper writen to describe Evolution and Optimization of Digital Organisms.
File Name File Size Zip Size Zip Type
TIERRA.DOC 130253 33722 deflated

Download File TIERRA.ZIP Here

Contents of the TIERRA.DOC file




















Evolution and Optimization of Digital Organisms





Thomas S. Ray

School of Life & Health Sciences,
University of Delaware, Newark, Delaware 19716
[email protected]

Thomas S. Ray



Thomas S. Ray
Evolution and Optimization of Digital Organisms

ABSTRACT



Digital organisms have been synthesized based on a computer
metaphor of organic life in which CPU time is the ``energy''
resource and memory is the ``material'' resource. Memory is
organized into informational ``genetic'' patterns that exploit
CPU time for self-replication. Mutation generates new forms,
and evolution proceeds by natural selection as different
``genotypes'' compete for CPU time and memory space. In
addition, new genotypes appear which exploit other
``creatures'' for informational or energetic resources.

The digital organisms are self-replicating computer programs,
however, they can not escape because they run exclusively on a
virtual computer in its unique machine language. From a
single ancestral ``creature'' there have evolved tens of
thousands of self-replicating genotypes of hundreds of genome
size classes. Parasites evolved, then creatures that were
immune to parasites, and then parasites that could circumvent
the immunity. Hyper-parasites evolved which subvert parasites
to their own reproduction and drive them to extinction. The
resulting genetically uniform communities evolve sociality in
the sense of creatures that can only reproduce in cooperative
aggregations, and these aggregations are then invaded by
cheating hyper-hyper-parasites.

Diverse ecological communities have emerged. These digital
communities have been used to experimentally study ecological
and evolutionary processes: e.g., competitive exclusion and
coexistance, symbiosis, host/parasite density dependent
population regulation, the effect of parasites in enhancing
community diversity, evolutionary arms races, punctuated
equilibrium, and the role of chance and historical factors in
evolution. It is possible to extract information on any
aspect of the system without disturbing it, from phylogeny or
community structure through time to the ``genetic makeup'' and
``metabolic processes'' of individuals. Digital life
demonstrates the power of the computational approach to
science as a complement to the traditional approaches of
experiment, and theory based on analysis through calculus and
differential equations.

Optimization experiments have shown that freely evolving
digital organisms can optimize their algorithms by a factor of
5.75 in a few hours of real time. In addition, evolution
discovered the optimization technique of ``unrolling the
loop''. Evolution may provide a new method for the
optimization or generation of application programs. This
method may prove particularly useful for programming massively
parallel machines.

evolution, ecology, artificial life, synthetic life,
emergence, self-replication, diversity, adaptation,
coevolution, optimization


Abstract ii


Thomas S. Ray
Evolution and Optimization of Digital Organisms

CONTENTS




Abstract ................................................ ii

Introduction ............................................. 2

Methods .................................................. 5
The Metaphor ............................................. 5
The Virtual Computer -- TIERRA Simulator ................. 6
The Tierran Language ..................................... 7
The Tierran Operating System ............................. 9
Memory Allocation -- Cellularity ....................... 9
Time Sharing -- The Slicer ............................ 10
Mortality --- The Reaper .............................. 11
Mutation .............................................. 12
The Tierran Ancestor .................................... 13

Results ................................................. 15
Evolution ............................................... 15
Micro-Evolution ....................................... 15
Macro-Evolution ....................................... 19
DIVERSITY ............................................... 20
ECOLOGY ................................................. 21
EVOLUTIONARY OPTIMIZATION ............................... 22

Summary ................................................. 25
GENERAL BEHAVIOR OF THE SYSTEM .......................... 25
INCREASING COMPLEXITY ................................... 26
EMERGENCE ............................................... 26
SYNTHETIC BIOLOGY ....................................... 27
APPLICATIONS ............................................ 28

ACKNOWLEDGMENT .......................................... 30

REFERENCES .............................................. 31

Appendix A: The Tierra virtual CPU. .................... 42

Appendix B: CPU cycle of the Tierra Simulator ........... 43

Appendix C: Code for the ancestral creature ............. 46

Appendix D: Smallest self-replicating creature .......... 49

Appendix E: Central copy loop of the ancestor ........... 50










Contents iii


Thomas S. Ray
Evolution and Optimization of Digital Organisms



Marcel, a mechanical chessplayer... his exquisite
19th-century brainwork --- the human art it took to
build which has been flat lost, lost as the dodo
bird ... But where inside Marcel is the midget
Grandmaster, the little Johann Allgeier? where's
the pantograph, and the magnets? Nowhere. Marcel
really is a mechanical chessplayer. No fakery
inside to give him any touch of humanity at all

--- Thomas Pynchon, Gravity's Rainbow.














































Page 1


Thomas S. Ray
Evolution and Optimization of Digital Organisms

INTRODUCTION




Ideally, the science of biology should embrace all forms of
life. However in practice, it has been restricted to the
study of a single instance of life, life on earth. Life on
earth is very diverse, but it is presumably all part of a
single phylogeny. Because biology is based on a sample size
of one, we can not know what features of life are peculiar to
earth, and what features are general, characteristic of all
life. A truly comparative natural biology would require
inter-planetary travel, which is light years away. The ideal
experimental evolutionary biology would involve creation of
multiple planetary systems, some essentially identical, others
varying by a parameter of interest, and observing them for
billions of years.

A practical alternative to an inter-planetary or mythical
biology is to create synthetic life in a computer. The
objective is not necessarily to create life forms that would
serve as models for the study of natural life, but rather to
create radically different life forms, based on a completely
different physics and chemistry, and let these life forms
evolve their own phylogeny, leading to whatever forms are
natural to their unique physical basis. These truly
independent instances of life may then serve as a basis for
comparison, to gain some insight into what is general and what
is peculiar in biology. Those aspects of life that prove to
be general enough to occur in both natural and synthetic
systems can then be studied more easily in the synthetic
system. ``Evolution in a bottle'' provides a valuable tool
for the experimental study of evolution and ecology.

The intent of this work is to synthesize rather than simulate
life. This approach starts with hand crafted organisms
already capable of replication and open-ended evolution, and
aims to generate increasing diversity and complexity in a
parallel to the Cambrian explosion. To state such a goal
leads to semantic problems, because life must be defined in a
way that does not restrict it to carbon based forms. It is
unlikely that there could be general agreement on such a
definition, or even on the proposition that life need not be
carbon based. Therefore, I will simply state my conception of
life in its most general sense. I would consider a system to
be living if it is self-replicating, and capable of open-ended
evolution. Synthetic life should self-replicate, and evolve
structures or processes that were not designed-in or
pre-conceived by the creator (Pattee [30]; Cariani [5]).

Core Wars programs, computer viruses, and worms (Cohen [6];
Dewdney [10, 11, 13, 14]; Denning [9]; Rheingold [32];
Spafford et al. [33]) are capable of self-replication, but
fortunately, not evolution. It is unlikely that such programs
will ever become fully living, because they are not likely to


Introduction 2


Thomas S. Ray
Evolution and Optimization of Digital Organisms

be able to evolve.

Most evolutionary simulations are not open-ended. Their
potential is limited by the structure of the model, which
generally endows each individual with a genome consisting of a
set of pre-defined genes, each of which may exist in a
pre-defined set of allelic forms (Holland [20]; Dewdney [12];
Dawkins [7, 8]; Packard [29]; Ackley & Littman [1]). The
object being evolved is generally a data structure
representing the genome, which the simulator program mutates
and/or recombines, selects, and replicates according to
criteria designed into the simulator. The data structures do
not contain the mechanism for replication, they are simply
copied by the simulator if they survive the selection phase.

Self-replication is critical to synthetic life because without
it, the mechanisms of selection must also be pre-determined by
the simulator. Such artificial selection can never be as
creative as natural selection. The organisms are not free to
invent their own fitness functions. Freely evolving creatures
will discover means of mutual exploitation and associated
implicit fitness functions that we would never think of.
Simulations constrained to evolve with pre-defined genes,
alleles and fitness functions are dead ended, not alive.

The approach presented here does not have such constraints.
Although the model is limited to the evolution of creatures
based on sequences of machine instructions, this may have a
potential comparable to evolution based on sequences of
organic molecules. Sets of machine instructions similar to
those used in the Tierra Simulator have been shown to be
capable of ``universal computation'' (Aho et al. [2]; Minsky
[26]; Langton [24]). This suggests that evolving machine
codes should be able to generate any level of complexity.

Other examples of the synthetic approach to life can be seen
in the work of Holland [21], Farmer et al. [16], Langton [22],
Rasmussen et al. [31], and Bagley et al. [3]. A
characteristic these efforts generally have in common is that
they parallel the origin of life event by attempting to create
prebiotic conditions from which life may emerge spontaneously
and evolve in an open ended fashion.

While the origin of life is generally recognized as an event
of the first order, there is another event in the history of
life that is less well known but of comparable significance:
the origin of biological diversity and macroscopic
multicellular life during the Cambrian explosion 600 million
years ago. This event involved a riotous diversification of
life forms. Dozens of phyla appeared suddenly, many existing
only fleetingly, as diverse and sometimes bizarre ways of life
were explored in a relative ecological void (Gould [18];
Morris [27]).

The work presented here aims to parallel the second major
event in the history of life, the origin of diversity. Rather


Introduction 3


Thomas S. Ray
Evolution and Optimization of Digital Organisms

than attempting to create prebiotic conditions from which life
may emerge, this approach involves engineering over the early
history of life to design complex evolvable organisms, and
then attempting to create the conditions that will set off a
spontaneous evolutionary process of increasing diversity and
complexity of organisms. This work represents a first step in
this direction, creating an artificial world which may roughly
parallel the RNA world of self-replicating molecules (still
falling far short of the Cambrian explosion).

The approach has generated rapidly diversifying communities of
self-replicating organisms exhibiting open-ended evolution by
natural selection. From a single rudimentary ancestral
creature containing only the code for self-replication,
interactions such as parasitism, immunity, hyper-parasitism,
sociality and cheating have emerged spontaneously. This paper
presents a methodology and some first results.

Apart from its value as a tool for the study or teaching of
ecology and evolution, synthetic life may have commercial
applications. Evolution of machine code provides a new
approach to the design and optimization of computer programs.
In an analogy to genetic engineering, pieces of application
code may be inserted into the genomes of digital organisms,
and then evolved to new functionality or greater efficiency.


Here was a world of simplicity and certainty... a
world based on the one and zero of life and death.
Minimal, beautiful. The patterns of lives and
deaths.... weightless, invisible chains of
electronic presence or absence. If patterns of ones
and zeros were ``like'' patterns of human lives and
deaths, if everything about an individual could be
represented in a computer record by a long string of
ones and zeros, then what kind of creature would be
represented by a long string of lives and deaths?
It would have to be up one level at least --- an
angel, a minor god, something in a UFO.

--- Thomas Pynchon, Vineland .

















Introduction 4


Thomas S. Ray
Evolution and Optimization of Digital Organisms

METHODS






THE METAPHOR


Organic life is viewed as utilizing energy, mostly derived
from the sun, to organize matter. By analogy, digital life
can be viewed as using CPU (central processing unit) time, to
organize memory. Organic life evolves through natural
selection as individuals compete for resources (light, food,
space, etc.) such that genotypes which leave the most
descendants increase in frequency. Digital life evolves
through the same process, as replicating algorithms compete
for CPU time and memory space, and organisms evolve strategies
to exploit one another. CPU time is thought of as the analog
of the energy resource, and memory as the analog of the
spatial resource.

The memory, the CPU and the computer's operating system are
viewed as elements of the ``abiotic'' (physical) environment.
A ``creature'' is then designed to be specifically adapted to
the features of the computational environment. The creature
consists of a self-replicating assembler language program.
Assembler languages are merely mnemonics for the machine codes
that are directly executed by the CPU. These machine codes
have the characteristic that they directly invoke the
instruction set of the CPU and services provided by the
operating system.

All programs, regardless of the language they are written in,
are converted into machine code before they are executed.
Machine code is the natural language of the machine, and
machine instructions are viewed by this author as the ``atomic
units'' of computing. It is felt that machine instructions
provide the most natural basis for an artificial chemistry of
creatures designed to live in the computer.

In the biological analogy, the machine instructions are
considered to be more like the amino acids than the nucleic
acids, because they are ``chemically active''. They actively
manipulate bits, bytes, CPU registers, and the movements of
the instruction pointer (see below). The digital creatures
discussed here are entirely constructed of machine
instructions. They are considered analogous to creatures of
the RNA world, because the same structures bear the
``genetic'' information and carry out the ``metabolic''
activity.

A block of RAM memory (random access memory, also known as
``main'' or ``core'' memory) in the computer is designated as
a ``soup'' which can be inoculated with creatures. The


Methods 5


Thomas S. Ray
Evolution and Optimization of Digital Organisms

``genome'' of the creatures consists of the sequence of
machine instructions that make up the creature's
self-replicating algorithm. The prototype creature consists
of 80 machine instructions, thus the size of the genome of
this creature is 80 instructions, and its ``genotype'' is the
specific sequence of those 80 instructions (Appendix C).




THE VIRTUAL COMPUTER -- TIERRA SIMULATOR


The computers we use are general purpose computers, which
means, among other things, that they are capable of emulating
through software, the behavior of any other computer that ever
has been built or that could be built (Aho et al. [2]; Minsky
[26]; Langton [24]). We can utilize this flexibility to
design a computer that would be especially hospitable to
synthetic life.

There are several good reasons why it is not wise to attempt
to synthesize digital organisms that exploit the machine codes
and operating systems of real computers. The most urgent is
the potential threat of natural evolution of machine codes
leading to virus or worm type of programs that could be
difficult to eradicate due to their changing ``genotypes''.
This potential argues strongly for creating evolution
exclusively in programs that run only on virtual computers and
their virtual operating systems. Such programs would be
nothing more than data on a real computer, and therefore would
present no more threat than the data in a data base or the
text file of a word processor.

Another reason to avoid developing digital organisms in the
machine code of a real computer is that the artificial system
would be tied to the hardware and would become obsolete as
quickly as the particular machine it was developed on. In
contrast, an artificial system developed on a virtual machine
could be easily ported to new real machines as they become
available.

A third issue, which potentially makes the first two moot, is
that the machine languages of real machines are not designed
to be evolvable, and in fact might not support significant
evolution. Von Neuman type machine languages are considered
to be ``brittle'', meaning that the ratio of viable programs
to possible programs is virtually zero. Any mutation or
recombination event in a real machine code is almost certain
to produce a non-functional program. The problem of
brittleness can be mitigated by designing a virtual computer
whose machine code is designed with evolution in mind. Farmer
& Belin [17] have suggested that overcoming this brittleness
and ``Discovering how to make such self-replicating patterns
more robust so that they evolve to increasingly more complex
states is probably the central problem in the study of


Methods 6


Thomas S. Ray
Evolution and Optimization of Digital Organisms

artificial life.''

The work described here takes place on a virtual computer
known as Tierra (Spanish for Earth). Tierra is a parallel
computer of the MIMD (multiple instruction, multiple data)
type, with a processor (CPU) for each creature. Parallelism
is imperfectly emulated by allowing each CPU to execute a
small time slice in turn. Each CPU of this virtual computer
contains two address registers, two numeric registers, a flags
register to indicate error conditions, a stack pointer, a ten
word stack, and an instruction pointer. Each virtual CPU is
implemented via the C structure listed in Appendix A.
Computations performed by the Tierran CPUs are probabilistic
due to flaws that occur at a low frequency (see Mutation
below).

The instruction set of a CPU typically performs simple
arithmetic operations or bit manipulations, within the small
set of registers contained in the CPU. Some instructions move
data between the registers in the CPU, or between the CPU
registers and the RAM (main) memory. Other instructions
control the location and movement of an ``instruction
pointer'' (IP). The IP indicates an address in RAM, where the
machine code of the executing program (in this case a digital
organism) is located.

The CPU perpetually performs a
fetch-decode-execute-increment_IP cycle: The machine code
instruction currently addressed by the IP is fetched into the
CPU, its bit pattern is decoded to determine which instruction
it corresponds to, and the instruction is executed. Then the
IP is incremented to point sequentially to the next position
in RAM, from which the next instruction will be fetched.
However, some instructions like JMP, CALL and RET directly
manipulate the IP, causing execution to jump to some other
sequence of instructions in the RAM. In the Tierra Simulator
this CPU cycle is implemented through the time_slice routine
listed in Appendix B.



THE TIERRAN LANGUAGE


Before attempting to set up a synthetic life system, careful
thought must be given to how the representation of a
programming language affects its adaptability in the sense of
being robust to genetic operations such as mutation and
recombination. The nature of the virtual computer is defined
in large part by the instruction set of its machine language.
The approach in this study has been to loosen up the machine
code in a ``virtual bio-computer'', in order to create a
computational system based on a hybrid between biological and
classical von Neumann processes.




Methods 7


Thomas S. Ray
Evolution and Optimization of Digital Organisms

In developing this new virtual language, which is called
``Tierran'', close attention has been paid to the structural
and functional properties of the informational system of
biological molecules: DNA, RNA and proteins. Two features
have been borrowed from the biological world which are
considered to be critical to the evolvability of the Tierran
language.

First, the instruction set of the Tierran language has been
defined to be of a size that is the same order of magnitude as
the genetic code. Information is encoded into DNA through 64
codons, which are translated into 20 amino acids. In its
present manifestation, the Tierran language consists of 32
instructions, which can be represented by five bits, operands
included.

Emphasis is placed on this last point because some instruction
sets are deceptively small. Some versions of the redcode
language of Core Wars (Dewdney [10, 13]; Rasmussen et al.
[31]) for example are defined to have ten operation codes. It
might appear on the surface then that the instruction set is
of size ten. However, most of the ten instructions have one
or two operands. Each operand has four addressing modes, and
then an integer. When we consider that these operands are
embedded into the machine code, we realize that they are in
fact a part of the instruction set, and this set works out to
be about $10^{11}$ in size. Similarly, RISC machines may have
only a few opcodes, but they probably all use 32 bit
instructions, so from a mutational point of view, they really
have $2^{32}$ instructions. Inclusion of numeric operands
will make any instruction set extremely large in comparison to
the genetic code.

In order to make a machine code with a truly small instruction
set, we must eliminate numeric operands. This can be
accomplished by allowing the CPU registers and the stack to be
the only operands of the instructions. When we need to encode
an integer for some purpose, we can create it in a numeric
register through bit manipulations: flipping the low order bit
and shifting left. The program can contain the proper
sequence of bit flipping and shifting instructions to
synthesize the desired number, and the instruction set need
not include all possible integers.

A second feature that has been borrowed from molecular biology
in the design of the Tierran language is the addressing mode,
which is called ``address by template''. In most machine
codes, when a piece of data is addressed, or the IP jumps to
another piece of code, the exact numeric address of the data
or target code is specified in the machine code. Consider
that in the biological system by contrast, in order for
protein molecule A in the cytoplasm of a cell to interact with
protein molecule B, it does not specify the exact coordinates
where B is located. Instead, molecule A presents a template
on its surface which is complementary to some surface on B.
Diffusion brings the two together, and the complementary


Methods 8


Thomas S. Ray
Evolution and Optimization of Digital Organisms

conformations allow them to interact.

Addressing by template is illustrated by the Tierran JMP
(jump) instruction. Each JMP instruction is followed by a
sequence of NOP (no-operation) instructions, of which there
are two kinds: NOP_0 and NOP_1. Suppose we have a piece of
code with five instruction in the following order: JMP NOP_0
NOP_0 NOP_0 NOP_1. The system will search outward in both
directions from the JMP instruction looking for the nearest
occurrence of the complementary pattern: NOP_1 NOP_1 NOP_1
NOP_0. If the pattern is found, the instruction pointer will
move to the end of the complementary pattern and resume
execution. If the pattern is not found, an error condition
(flag) will be set and the JMP instruction will be ignored (in
practice, a limit is placed on how far the system may search
for the pattern).

The Tierran language is characterized by two unique features:
a truly small instruction set without numeric operands, and
addressing by template. Otherwise, the language consists of
familiar instructions typical of most machine languages, e.g.,
MOV, CALL, RET, POP, PUSH etc. The complete instruction set
is listed in Appendix B.




THE TIERRAN OPERATING SYSTEM


The Tierran virtual computer needs a virtual operating system
that will be hospitable to digital organisms. The operating
system will determine the mechanisms of interprocess
communication, memory allocation, and the allocation of CPU
time among competing processes. Algorithms will evolve so as
to exploit these features to their advantage. More than being
a mere aspect of the environment, the operating system
together with the instruction set will determine the topology
of possible interactions between individuals, such as the
ability of pairs of individuals to exhibit predator-prey,
parasite-host or mutualistic relationships.




Memory Allocation -- Cellularity


The Tierran computer operates on a block of RAM of the real
computer which is set aside for the purpose. This block of
RAM is referred to as the ``soup''. In most of the work
described here the soup consisted of about 60,000 bytes, which
can hold the same number of Tierran machine instructions.
Each ``creature'' occupies some block of memory in this soup.




Methods 9


Thomas S. Ray
Evolution and Optimization of Digital Organisms

Cellularity is one of the fundamental properties of organic
life, and can be recognized in the fossil record as far back
as 3.6 billion years (Barbieri [4]). The cell is the original
individual, with the cell membrane defining its limits and
preserving its chemical integrity. An analog to the cell
membrane is needed in digital organisms in order to preserve
the integrity of the informational structure from being
disrupted easily by the activity of other organisms. The need
for this can be seen in Artificial Life models such as
cellular automata where virtual state machines pass through
one another (Langton [22, 23]), or in core wars type
simulations where coherent structures demolish one another
when they come into contact (Dewdney [10, 13]; Rasmussen et
al. [31]).

Tierran creatures are considered to be cellular in the sense
that they are protected by a ``semi-permeable membrane'' of
memory allocation. The Tierran operating system provides
memory allocation services. Each creature has exclusive write
privileges within its allocated block of memory. The ``size''
of a creature is just the size of its allocated block (e.g.,
80 instructions). This usually corresponds to the size of the
genome. This ``membrane'' is described as ``semi-permeable''
because while write privileges are protected, read and execute
privileges are not. A creature may examine the code of
another creature, and even execute it, but it can not write
over it. Each creature may have exclusive write privileges in
at most two blocks of memory: the one that it is born with
which is referred to as the ``mother cell'', and a second
block which it may obtain through the execution of the MAL
(memory allocation) instruction. The second block, referred
to as the ``daughter cell'', may be used to grow or reproduce
into.

When Tierran creatures ``divide'', the mother cell loses write
privileges on the space of the daughter cell, but is then free
to allocate another block of memory. At the moment of
division, the daughter cell is given its own instruction
pointer, and is free to allocate its own second block of
memory.

\LP \bf 2.4.2 Time Sharing --- The Slicer\rm \eLP



Time Sharing -- The Slicer


The Tierran operating system must be multi-tasking (or
parallel) in order for a community of individual creatures to
live in the soup simultaneously. The system doles out small
slices of CPU time to each creature in the soup in turn. The
system maintains a circular queue called the ``slicer queue''.
As each creature is born, a virtual CPU is created for it, and
it enters the slicer queue just ahead of its mother, which is
the active creature at that time. Thus the newborn will be


Methods 10


Thomas S. Ray
Evolution and Optimization of Digital Organisms

the last creature in the soup to get another time slice after
the mother, and the mother will get the next slice after its
daughter. As long as the slice size is small relative to the
generation time of the creatures, the time sharing system
causes the world to approximate parallelism. In actuality, we
have a population of virtual CPUs, each of which gets a slice
of the real CPU's time as it comes up in the queue.

The number of instructions to be executed in each time slice
may be set proportional to the size of the genome of the
creature being executed, raised to a power. If the ``slicer
power'' is equal to one, then the slicer is size neutral, the
probability of an instruction being executed does not depend
on the size of the creature in which it occurs. If the power
is greater than one, large creatures get more CPU cycles per
instruction than small creatures. If the power is less than
one, small creatures get more CPU cycles per instruction. The
power determines if selection favors large or small creatures,
or is size neutral. A constant slice size selects for small
creatures.





Mortality --- The Reaper


Self-replicating creatures in a fixed size soup would rapidly
fill the soup and lock up the system. To prevent this from
occurring, it is necessary to include mortality. The Tierran
operating system includes a ``reaper'' which begins
``killing'' creatures from a queue when the memory fills to
some specified level (e.g., 80%). Creatures are killed by
deallocating their memory, and removing them from both the
reaper and slicer queues. Their ``dead'' code is not removed
from the soup.

In the present system, the reaper uses a linear queue. When a
creature is born it enters the bottom of the queue. The
reaper always kills the creature at the top of the queue.
However, individuals may move up or down in the reaper queue
according to their success or failure at executing certain
instructions. When a creature executes an instruction that
generates an error condition, it moves one position up the
queue, as long as the individual ahead of it in the queue has
not accumulated a greater number of errors. Two of the
instructions are somewhat difficult to execute without
generating an error, therefore successful execution of these
instructions moves the creature down the reaper queue one
position, as long as it has not accumulated more errors than
the creature below it.

The effect of the reaper queue is to cause algorithms which
are fundamentally flawed to rise to the top of the queue and
die. Vigorous algorithms have a greater longevity, but in
general, the probability of death increases with age.


Methods 11


Thomas S. Ray
Evolution and Optimization of Digital Organisms





Mutation


In order for evolution to occur, there must be some change in
the genome of the creatures. This may occur within the
lifespan of an individual, or there may be errors in passing
along the genome to offspring. In order to insure that there
is genetic change, the operating system randomly flips bits in
the soup, and the instructions of the Tierran language are
imperfectly executed.

Mutations occur in two circumstances. At some background
rate, bits are randomly selected from the entire soup (e.g.,
60,000 instructions totaling 300,000 bits) and flipped. This
is analogous to mutations caused by cosmic rays, and has the
effect of preventing any creature from being immortal, as it
will eventually mutate to death. The background mutation rate
has generally been set at about one bit flipped for every
10,000 Tierran instructions executed by the system.

In addition, while copying instructions during the replication
of creatures, bits are randomly flipped at some rate in the
copies. The copy mutation rate is the higher of the two, and
results in replication errors. The copy mutation rate has
generally been set at about one bit flipped for every 1,000 to
2,500 instructions moved. In both classes of mutation, the
interval between mutations varies randomly within a certain
range to avoid possible periodic effects.

In addition to mutations, the execution of Tierran
instructions is flawed at a low rate. For most of the 32
instructions, the result is off by plus or minus one at some
low frequency. For example, the increment instruction
normally adds one to its register, but it sometimes adds two
or zero. The bit flipping instruction normally flips the low
order bit, but it sometimes flips the next higher bit or no
bit. The shift left instruction normally shifts all bits one
bit to the left, but it sometimes shifts left by two bits, or
not at all. In this way, the behavior of the Tierran
instructions is probabilistic, not fully deterministic.

It turns out that bit flipping mutations and flaws in
instructions are not necessary to generate genetic change and
evolution, once the community reaches a certain state of
complexity. Genetic parasites evolve which are sloppy
replicators, and have the effect of moving pieces of code
around between creatures, causing rather massive
rearrangements of the genomes. The mechanism of this ad hoc
sexuality has not been worked out, but is likely due to the
parasites' inability to discriminate between live, dead or
embryonic code.



Methods 12


Thomas S. Ray
Evolution and Optimization of Digital Organisms

Mutations result in the appearance of new genotypes, which are
watched by an automated genebank manager. In one
implementation of the manager, when new genotypes replicate
twice, producing a genetically identical offspring at least
once, they are given a unique name and saved to disk. Each
genotype name contains two parts, a number and a three letter
code. The number represents the number of instructions in the
genome. The three letter code is used as a base 26 numbering
system for assigning a unique label to each genotype in a size
class. The first genotype to appear in a size class is
assigned the label aaa, the second is assigned the label aab,
and so on. Thus the ancestor is named 80aaa, and the first
mutant of size 80 is named 80aab. The first creature of size

45 is named 45aaa.

The genebanker saves some additional information with each
genome: the genotype name of its immediate ancestor which
makes possible the reconstruction of the entire phylogeny; the
time and date of origin; ``metabolic'' data including the
number of instructions executed in the first and second
reproduction, the number of errors generated in the first and
second reproduction, and the number of instructions copied
into the daughter cell in the first and second reproductions
(see Appendix C, D); some environmental parameters at the time
of origin including the search limit for addressing, and the
slicer power, both of which affect selection for size.




THE TIERRAN ANCESTOR


I have used the Tierran language to write a single
self-replicating program which is 80 instructions long. This
program is referred to as the ``ancestor'', or alternatively
as genotype 0080aaa (Fig. 1). The ancestor is a minimal
self-replicating algorithm which was originally written for
use during the debugging of the simulator. No functionality
was designed into the ancestor beyond the ability to
self-replicate, nor was any specific evolutionary potential
designed in. The commented Tierran assembler and machine code
for this program is presented in Appendix C.

The ancestor examines itself to determine where in memory it
begins and ends. The ancestor's beginning is marked with the
four no-operation template: 1 1 1 1, and its ending is marked
with 1 1 1 0. The ancestor locates its beginning with the
five instructions: ADRB, NOP_0, NOP_0, NOP_0, NOP_0. This
series of instructions causes the system to search backwards
from the ADRB instruction for a template complementary to the
four NOP_0 instructions, and to place the address of the
complementary template (the beginning) in the ax register of
the CPU (see Appendix A). A similar method is used to locate
the end.



Methods 13


Thomas S. Ray
Evolution and Optimization of Digital Organisms

Having determined the address of its beginning and its end, it
subtracts the two to calculate its size, and allocates a block
of memory of this size for a daughter cell. It then calls the
copy procedure which copies the entire genome into the
daughter cell memory, one instruction at a time. The
beginning of the copy procedure is marked by the four
no-operation template: 1 1 0 0. Therefore the call to the
copy procedure is accomplished with the five instructions:
CALL, NOP_0, NOP_0, NOP_1, NOP_1.

When the genome has been copied, it executes the DIVIDE
instruction, which causes the creature to lose write
privileges on the daughter cell memory, and gives an
instruction pointer to the daughter cell (it also enters the
daughter cell into the slicer and reaper queues). After this
first replication, the mother cell does not examine itself
again; it proceeds directly to the allocation of another
daughter cell, then the copy procedure is followed by cell
division, in an endless loop.

Fourty-eight of the eighty instructions in the ancestor are
no-operations. Groups of four no-operation instructions are
used as complementary templates to mark twelve sites for
internal addressing, so that the creature can locate its
beginning and end, call the copy procedure, and mark addresses
for loops and jumps in the code, etc. The functions of these
templates are commented in the listing in Appendix C.































Methods 14


Thomas S. Ray
Evolution and Optimization of Digital Organisms

RESULTS






EVOLUTION


Evolutionary runs of the simulator are begun by inoculating
the soup of about 60,000 instructions with a single individual
of the 80 instruction ancestral genotype. The passage of time
in a run is measured in terms of how many Tierran instructions
have been executed by the simulator. The original ancestral
cell executes 839 instructions in its first replication, and
813 for each additional replication. The initial cell and its
replicating daughters rapidly fill the soup memory to the
threshold level of 80% which starts the reaper. Typically,
the system executes about 400,000 instructions in filling up
the soup with about 375 individuals of size 80 (and their
gestating daughter cells). Once the reaper begins, the memory
remains roughly 80% filled with creatures for the remainder of
the run.




Micro-Evolution


If there were no mutations at the outset of the run, there
would be no evolution. However, the bits flipped as a result
of copy errors or background mutations result in creatures
whose list of 80 instructions (genotype) differs from the
ancestor, usually by a single bit difference in a single
instruction.

Mutations in and of themselves, can not result in a change in
the size of a creature, they can only alter the instructions
in its genome. However, by altering the genotype, mutations
may affect the process whereby the creature examines itself
and calculates its size, potentially causing it to produce an
offspring that differs in size from itself.

Four out of the five possible mutations in a no-operation
instruction convert it into another kind of instruction, while
one out of five converts it into the complementary
no-operation. Therefore 80% of mutations in templates destroy
or change the size of the template, while one in five alters
the template pattern. An altered template may cause the
creature to make mistakes in self examination, procedure
calls, or looping or jumps of the instruction pointer, all of
which use templates for addressing.




Results 15


Thomas S. Ray
Evolution and Optimization of Digital Organisms

parasites


An example of the kind of error that can result from a
mutation in a template is a mutation of the low order bit of
instruction 42 of the ancestor (Appendix C). Instruction 42
is a NOP_0, the third component of the copy procedure
template. A mutation in the low order bit would convert it
into NOP_1, thus changing the template from 1 1 0 0 to: 1 1 1
0. This would then be recognized as the template used to mark
the end of the creature, rather than the copy procedure.

A creature born with a mutation in the low order bit of
instruction 42 would calculate its size as 45. It would
allocate a daughter cell of size 45 and copy only instructions
0 through 44 into the daughter cell. The daughter cell then,
would not include the copy procedure. This daughter genotype,
consisting of 45 instructions, is named 0045aaa.

Genotype 0045aaa (Fig. 1) is not able to self-replicate in
isolated culture. However, the semi-permeable membrane of
memory allocation only protects write privileges. Creatures
may match templates with code in the allocated memory of other
creatures, and may even execute that code. Therefore, if
creature 0045aaa is grown in mixed culture with 0080aaa, when
it attempts to call the copy procedure, it will not find the
template within its own genome, but if it is within the search
limit (generally set at 200--400 instructions) of the copy
procedure of a creature of genotype 0080aaa, it will match
templates, and send its instruction pointer to the copy code
of 0080aaa. Thus a parasitic relationship is established (see
ECOLOGY below). Typically, parasites begin to emerge within
the first few million instructions of elapsed time in a run.




immunity to parasites


At least some of the size 79 genotypes demonstrate some
measure of resistance to parasites. If genotype 45aaa is
introduced into a soup, flanked on each side with one
individual of genotype 0079aab, 0045aaa will initially
reproduce somewhat, but will be quickly eliminated from the
soup. When the same experiment is conducted with 0045aaa and
the ancestor, they enter a stable cycle in which both
genotypes coexist indefinitely. Freely evolving systems have
been observed to become dominated by size 79 genotypes for
long periods, during which parasitic genotypes repeatedly
appear, but fail to invade.







Results 16


Thomas S. Ray
Evolution and Optimization of Digital Organisms

circumvention of immunity to parasites


Occasionally these evolving systems dominated by size 79 were
successfully invaded by parasites of size 51. When the immune
genotype 0079aab was tested with 0051aao (a direct, one step,
descendant of 0045aaa in which instruction 39 is replaced by
an insertion of seven instructions of unknown origin), they
were found to enter a stable cycle. Evidently 0051aao has
evolved some way to circumvent the immunity to parasites
possessed by 0079aab. The fourteen genotypes 0051aaa through
0051aan were also tested with 0079aab, and none were able to
invade.




hyper-parasites


Hyper-parasite have been discovered, (e.g., 0080gai, which
differs by 19 instructions from the ancestor, Fig. 1). Their
ability to subvert the energy metabolism of parasites is based
on two changes. The copy procedure does not return, but jumps
back directly to the proper address of the reproduction loop.
In this way it effectively seizes the instruction pointer from
the parasite. However it is another change which delivers the
coup de gr\^{a}ce: after each reproduction, the hyper-parasite
re-examines itself, resetting the bx register with its
location and the cx register with its size. After the
instruction pointer of the parasite passes through this code,
the CPU of the parasite contains the location and size of the
hyper-parasite and the parasite thereafter replicates the
hyper-parasite genome.




social hyper-parasites


Hyper-parasites drive the parasites to extinction. This
results in a community with a relatively high level of genetic
uniformity, and therefore high genetic relationship between
individuals in the community. These are the conditions that
support the evolution of sociality, and social hyper-parasites
soon dominate the community. Social hyper-parasites (Fig. 2)
appear in the 61 instruction size class. For example, 0061acg
is social in the sense that it can only self-replicate when it
occurs in aggregations. When it jumps back to the code for
self-examination, it jumps to a template that occurs at the
end rather than the beginning of its genome. If the creature
is flanked by a similar genome, the jump will find the target
template in the tail of the neighbor, and execution will then
pass into the beginning of the active creature's genome. The
algorithm will fail unless a similar genome occurs just before


Results 17


Thomas S. Ray
Evolution and Optimization of Digital Organisms

the active creature in memory. Neighboring creatures
cooperate by catching and passing on jumps of the instruction
pointer.

It appears that the selection pressure for the evolution of
sociality is that it facilitates size reduction. The social
species are 24% smaller than the ancestor. They have achieved
this size reduction in part by shrinking their templates from
four instructions to three instructions. This means that
there are only eight templates available to them, and catching
each others jumps allows them to deal with some of the
consequences of this limitation as well as to make dual use of
some templates.




cheaters: hyper-hyper-parasites


The cooperative social system of hyper-parasites is subject to
cheating, and is eventually invaded by hyper-hyper-parasites
(Fig. 2). These cheaters (e.g., 0027aab) position themselves
between aggregating hyper-parasites so that when the
instruction pointer is passed between them, they capture it.




a novel self-examination


All creatures discussed thus far mark their beginning and end
with templates. They then locate the addresses of the two
templates and determine their genome size by subtracting them.
In one run, creatures evolved without a template marking their
end. These creatures located the address of the template
marking their beginning, and then the address of a template in
the middle of their genome. These two addresses were then
subtracted to calculate half of their size, and this value was
multiplied by two (by shifting left) to calculate their full
size.




an intricate adaptation


The arms race described in the paragraphs above took place
over a period of a billion instructions executed by the
system. Another run was allowed to continue for fifteen
billion instructions, but was not examined in detail. A
creature present at the end of the run was examined and found
to have evolved an intricate adaptation. The adaptation is an
optimization technique known as ``unrolling the loop''.


Results 18


Thomas S. Ray
Evolution and Optimization of Digital Organisms

The central loop of the copy procedure performs the following
operations: 1) copies an instruction from the mother to the
daughter, 2) decrements the cx register which initially
contains the size of the parent genome, 3) tests to see if cx
is equal to zero, if so it exits the loop, if not it remains
in the loop, 4) increment the ax register which contains the
address in the daughter where the next instruction will be
copied to, 5) increment the bx register which contains the
address in the mother where the next instruction will be
copied from, 6) jump back to the top of the loop.

The work of the loop is contained in steps 1, 2, 4 and 5.
Steps 3 and 6 are overhead. The efficiency of the loop can be
increased by duplicating the work steps within the loop,
thereby saving on overhead. The creature from the end of the
long run had repeated the work steps three times within the
loop, as illustrated in Appendix E, which compares the copy
loop of the ancestor with that of its decendant.




Macro-Evolution


When the simulator is run over long periods of time, hundreds
of millions or billions of instructions, various patterns
emerge. Under selection for small sizes there is a
proliferation of small parasites and a rather interesting
ecology (see below). Selection for large creatures has
usually lead to continuous incrementally increasing sizes (but
not to a trivial concatenation of creatures end-to-end) until
a plateau in the upper hundreds is reached. In one run,
selection for large size lead to apparently open ended size
increase, evolving genomes larger than 23,000 instructions in
length. These evolutionary patterns might be described as
phyletic gradualism.

The most thoroughly studied case for long runs is where
selection, as determined by the slicer function, is size
neutral. The longest runs to date (as much as 2.86 billion
Tierran instructions) have been in a size neutral environment,
with a search limit of 10,000, which would allow large
creatures to evolve if there were some algorithmic advantage
to be gained from larger size. These long runs illustrate a
pattern which could be described as periods of stasis
punctuated by periods of rapid evolutionary change, which
appears to parallel the pattern of punctuated equilibrium
described by Eldredge & Gould [15] and Gould & Eldredge [19].

Initially these communities are dominated by creatures with
genome sizes in the eighties. This represents a period of
relative stasis, which has lasted from 178 million to 1.44
billion instructions in the several long runs conducted to
date. The systems then very abruptly (in a span of 1 or 2
million instructions) evolve into communities dominated by


Results 19


Thomas S. Ray
Evolution and Optimization of Digital Organisms

sizes ranging from about 400 to about 800. These communities
have not yet been seen to evolve into communities dominated by
either smaller or substantially larger size ranges.

The communities of creatures in the 400 to 800 size range also
show a long-term pattern of punctuated equilibrium. These
communities regularly come to be dominated by one or two size
classes, and remain in that condition for long periods of
time. However, they inevitably break out of that stasis and
enter a period where no size class dominates. These periods
of rapid evolutionary change may be very chaotic. Close
observations indicate that at least at some of these times, no
genotypes breed true. Many self-replicating genotypes will
coexist in the soup at these times, but at the most chaotic
times, none will produce offspring which are even their same
size. Eventually the system will settle down to another
period of stasis dominated by one or a few size classes which
breed true.




DIVERSITY


Most observations on the diversity of Tierran creatures have
been based on the diversity of size classes. Creatures of
different sizes are clearly genetically different, as their
genomes are of different sizes. Different sized creatures
would have some difficulty engaging in recombination if they
were sexual, thus it is likely that they would be different
species. In a run of 526 million instructions, 366 size
classes were generated, 93 of which achieved abundances of
five or more individuals. In a run of 2.56 billion
instructions, 1180 size classes were generated, 367 of which
achieved abundances of five or more.

Each size class consists of a number of distinct genotypes
which also vary over time. There exists the potential for
great genetic diversity within a size class. There are
32$^{80}$ distinct genotypes of size 80, but how many of those
are viable self-replicating creatures? This question remains
unanswered, however some information has been gathered through
the use of the automated genebank manager.

In several days of running the genebanker, over 29,000
self-replicating genotypes of over 300 size classes
accumulated. The size classes and the number of unique
genotypes banked for each size are listed in Table 1. The
genotypes saved to disk can be used to inoculate new soups
individually, or collections of these banked genotypes may be
used to assemble ``ecological communities''. In
``ecological'' runs, the mutation rates can be set to zero in
order to inhibit evolution.




Results 20


Thomas S. Ray
Evolution and Optimization of Digital Organisms

ECOLOGY


The only communities whose ecology has been explored in detail
are those that operate under selection for small sizes. These
communities generally include a large number of parasites,
which do not have functional copy procedures, and which
execute the copy procedures of other creatures within the
search limit. In exploring ecological interactions, the
mutation rate is set at zero, which effectively throws the
simulation into ecological time by stopping evolution. When
parasites are present, it is also necessary to stipulate that
creatures must breed true, since parasites have a tendency to
scramble genomes, leading to evolution in the absence of
mutation.

0045aaa is a ``metabolic parasite''. Its genome does not
include the copy procedure, however it executes the copy
procedure code of a normal host, such as the ancestor. In an
environment favoring small creatures, 0045aaa has a
competitive advantage over the ancestor, however, the
relationship is density dependent. When the hosts become
scarce, most of the parasites are not within the search limit
of a copy procedure, and are not able to reproduce. Their
calls to the copy procedure fail and generate errors, causing
them to rise to the top of the reaper queue and die. When the
parasites die off, the host population rebounds. Hosts and
parasites cultured together demonstrate Lotka-Volterra
population cycling (Lotka [25]; Volterra [35]; Wilson &
Bossert [36]).

A number of experiments have been conducted to explore the
factors affecting diversity of size classes in these
communities. Competitive exclusion trials were conducted with
a series of self-replicating (non-parasitic) genotypes of
different size classes. The experimental soups were initially
inoculated with one individual of each size. A genotype of
size 79 was tested against a genotype of size 80, and then
against successively larger size classes. The interactions
were observed by plotting the population of the size 79 class
on the $x$ axis, and the population of the other size class on
the $y$ axis. Sizes 79 and 80 were found to be competitively
matched such that neither was eliminated from the soup. They
quickly entered a stable cycle, which exactly repeated a small
orbit. The same general pattern was found in the interaction
between sizes 79 and 81.

When size 79 was tested against size 82, they initially
entered a stable cycle, but after about 4 million instructions
they shook out of stability and the trajectory became chaotic
with an attractor that was symmetric about the diagonal
(neither size showed any advantage). This pattern was
repeated for the next several size classes, until size 90,
where a marked asymmetry of the chaotic attractor was evident,
favoring size 79. The run of size 79 against size 93 showed a
brief stable period of about a million instructions, which


Results 21


Thomas S. Ray
Evolution and Optimization of Digital Organisms

then moved to a chaotic phase without an attractor, which
spiraled slowly down until size 93 became extinct, after an
elapsed time of about 6 million instructions.

An interesting exception to this pattern was the interaction
between size 79 and size 89. Size 89 is considered to be a
``metabolic cripple'', because although it is capable of
self-replicating, it executes about 40% more instructions than
normal to replicate. It was eliminated in competition with
size 79, with no loops in the trajectory, after an elapsed
time of under one million instructions.

In an experiment to determine the effects of the presence of
parasites on community diversity, a community consisting of
twenty size classes of hosts was created and allowed to run
for 30 million instructions, at which time only the eight
smallest size classes remained. The same community was then
regenerated, but a single genotype (0045aaa) of parasite was
also introduced. After 30 million instructions, 16 size
classes remained, including the parasite. This seems to be an
example of a ``keystone'' parasite effect (Paine [28]).

Symbiotic relationships are also possible. The ancestor was
manually dissected into two creatures, one of size 46 which
contained only the code for self-examination and the copy
loop, and one of size 64 which contained only the code for
self-examination and the copy procedure (Figure 3). Neither
could replicate when cultured alone, but when cultured
together, they both replicated, forming a stable mutualistic
relationship. It is not known if such relationships have
evolved spontaneously.




EVOLUTIONARY OPTIMIZATION


In order to compare the process of evolution between runs of
the simulator, a simple objective quantitative measure of
evolution is needed. One such measure is the degree to which
creatures improve their efficiency through evolution. This
provides not only an objective measure of progress in
evolution, but also sheds light on the potential application
of synthetic life systems to the problem of the optimization
of machine code.

The efficiency of the creature can be indexed in two ways: the
size of the genome, and the number of CPU cycles needed to
execute one replication. Clearly, smaller genomes can be
replicated with less CPU time, however, during evolution,
creatures also decrease the ratio of instructions executed in
one replication, to genome size. The number of instructions
executed per instruction copied, drops substantially.




Results 22


Thomas S. Ray
Evolution and Optimization of Digital Organisms

Figure 4 shows the changes in genome size over a time period
of 500 million instructions executed by the system, for eight
sets of mutation rates differing by factors of two. Mutation
rates are measured in terms of 1 in N individuals being
affected by a mutation in each generation. At the highest two
sets of rates tested, one and two, either each (one) or
one-half (two) of the individuals are hit by mutation in each
generation. At these rates the system is unstable. The
genomes melt under the heat of the high mutation rates. The
community often dies out, although some runs survived the 500
million instruction runs used in this study. The next lower
rate, four, yields the highest rate of optimization without
the risk of death of the community. At the five lower
mutation rates, 8, 16, 32, 64 and 128, we see successively
lower rates of optimization.

Additional replicates were made of the runs at the mutation
rate of four (Fig. 5). The replicates differ only in the seed
of the random number generator, all other parameters being
identical. These runs vary in some details such as whether
progress is continuous and gradual, or comes in bursts. Also,
each run decreases to a size limit which it can not proceed
past even if it is allowed to run much longer. However,
different runs reach different plateaus of efficiency. The
smallest limiting genome size seen has been 22 instructions,
while other runs reached limits of 27 and 30 instructions.
Evidently, the system can reach a local optima from which it
can not easily evolve to the global optima.

The increase in efficiency of the replicating algorithms is
even greater than the decrease in the size of the code. The
ancestor is 80 instructions long and requires 839 CPU cycles
to replicate. The creature of size 22 only requires 146 CPU
cycles to replicate, a 5.75--fold difference in efficiency.
The algorithm of one of these creatures is listed in Appendix
D.

Although optimization of the algorithm is maximized at the
highest mutation rate that does not cause instability,
ecological interactions appear to be richer at slightly lower
mutation rates. At the rates of eight or 16, we find the
diversity of coexisting size classes to be the greatest, and
to persist the longest. The smaller size classes tend to be
various forms of parasites, thus a diversity of size classes
indicates a rich ecology.

An example of even greater optimization is illustrated in
Appendix E and discussed above in section 3.1.1.8. Unrolling
of the loop results in a loop which uses 18 CPU cycles to copy
three instructions, or six CPU cycles executed per instruction
copied, compared to 10 for the ancestor. The creature of size
22 also uses six CPU cycles per instruction copied. However,
the creature of Appendix E uses three extra CPU cycles per
loop to compensate for a separate adaptation that allows it to
double its share of CPU time from the global pool. Without
this compensation it would use only five CPU cycles per


Results 23


Thomas S. Ray
Evolution and Optimization of Digital Organisms

instruction copied.

























































Results 24


Thomas S. Ray
Evolution and Optimization of Digital Organisms

SUMMARY






GENERAL BEHAVIOR OF THE SYSTEM


Once the soup is full of replicating creatures, individuals
are initially short lived, generally reproducing only once
before dying, thus individuals turn over very rapidly. More
slowly, there appear new genotypes of size 80, and then new
size classes. There are changes in the genetic composition of
each size class, as new mutants appear, some of which increase
significantly in frequency, eventually replacing the original
genotype. The size classes which dominate the community also
change through time, as new size classes appear, some of which
competitively exclude sizes present earlier. Once the
community becomes diverse, there is a greater variance in the
longevity and fecundity of individuals.

In addition to an increase in the raw diversity of genotypes
and genome sizes, there is an increase in the ecological
diversity. Obligate commensal parasites evolve, which are not
capable of self-replication in isolated culture, but which can
replicate when cultured with normal (self-replicating)
creatures. These parasites execute some parts of the code of
their hosts, but cause them no direct harm, except as
competitors. Some potential hosts have evolved immunity to
the parasites, and some parasites have evolved to circumvent
this immunity.

In addition, facultative hyper-parasites have evolved, which
can self-replicate in isolated culture, but when subjected to
parasitism, subvert the parasites energy metabolism to augment
their own reproduction. Hyper-parasites drive parasites to
extinction, resulting in complete domination of the
communities. The relatively high degrees of genetic
relatedness within the hyper-parasite dominated communities
leads to the evolution of sociality in the sense of creatures
that can only replicate when they occur in aggregations.
These social aggregations are then invaded by
hyper-hyper-parasite cheaters.

Mutations and the ensuing replication errors lead to an
increasing diversity of sizes and genotypes of
self-replicating creatures in the soup. Within the first 100
million instructions of elapsed time, the soup evolves to a
state in which about a dozen more-or-less persistent size
classes coexist. The relative abundances and specific list of
the size classes varies over time. Each size class consists
of a number of distinct genotypes which also vary over time.




Summary 25



Thomas S. Ray
Evolution and Optimization of Digital Organisms

The rate of evolution increases with the mutation rate until
the system becomes unstable, and the community dies at rates
above one mutation per four generations. Ecological
interactions are richer and more sustained at slightly lower
rates, one mutation per eight or 16 generations. At mutation
rates of one per four generations, under selection for small
sizes, creatures will optimize to a genome size in the 22 to
30 instruction size range within as little as 300 million
instructions of elapsed time. Each of these runs will reach a
local optima which it evidently cannot escape from, although
it may not be the global optima.




INCREASING COMPLEXITY


The unrolled loop (section 3.1.1.8) is an example of the
ability of evolution to produce an increase in complexity,
gradually over a long period of time. The interesting thing
about the loop unrolling optimization technique is that it
requires more complex code. The resulting creature has a
genome size of 36, compared to its ancestor of size 80, yet it
has packed a much more complex algorithm into less than half
the space (Appendix E).

This is a classic example of intricate design in evolution.
One wonders how it could have arisen through random bit flips,
as every component of the code must be in place in order for
the algorithm to function. Yet the code includes a classic
mix of apparent intelligent design, and the chaotic hand of
evolution. The optimization technique is a very clever one
invented by humans, yet it is implemented in a mixed up but
functional style that no human would use (unless perhaps very
intoxicated).




EMERGENCE


The ``physical'' environment presented by the simulator is
quite simple, consisting of the energy resource (CPU time)
doled out rather uniformly by the time slicer, and memory
space which is completely uniform and always available. In
light of the nature of the physical environment, the implicit
fitness function would presumably favor the evolution of
creatures which are able to replicate with less CPU time, and
this does in fact occur. However, much of the evolution in
the system consists of the creatures discovering ways to
exploit one-another. The creatures invent their own fitness
functions through adaptation to their biotic (``living'')
environment. These ecological interactions are not programmed
into the system, but emerge spontaneously as the creatures


Summary 26


Thomas S. Ray
Evolution and Optimization of Digital Organisms

discover each other and invent their own games.

In the Tierran world, creatures which initially do not
interact, discover means to exploit one another, and in
response, means to avoid exploitation. The original fitness
landscape of the ancestor consists only of the efficiency
parameters of the replication algorithm, in the context of the
properties of the reaper and slicer queues. When by chance,
genotypes appear that exploit other creatures, selection acts
to perfect the mechanisms of exploitation, and mechanisms of
defense to that exploitation. The original fitness landscape
was based only on adaptations of the organism to its physical
environment. The new fitness landscape retains those
features, but adds to it adaptations to the biotic
environment, the other creatures. Because the fitness
landscape includes an ever increasing realm of adaptations to
other creatures which are themselves evolving, it can
facilitate an auto-catalytic increase in complexity and
diversity of organisms.

Evolutionary theory suggests that adaptation to the biotic
environment (other organisms) rather than to the physical
environment is the primary force driving the auto-catalytic
diversification of organisms (Stanley [34]). It is
encouraging to discover that the process has already begun in
the Tierran world. It is worth noting that the results
presented here are based on evolution of the first creature
that I designed, written in the first instruction set that I
designed. Comparison to the creatures that have evolved shows
that the one I designed is not a particularly clever one.
Also, the instruction set that the creatures are based on is
certainly not very powerful (apart from those special features
incorporated to enhance its evolvability). It would appear
then that it is rather easy to create life. Evidently,
virtual life is out there, waiting for us to provide
environments in which it may evolve.




SYNTHETIC BIOLOGY


One of the most uncanny of evolutionary phenomena is the
ecological convergence of biota living on different continents
or in different epochs. When a lineage of organisms undergoes
an adaptive radiation (diversification), it leads to an array
of relatively stable ecological forms. The specific
ecological forms are often recognizable from lineage to
lineage. For example among dinosaurs, the Pterosaur,
Triceratops, Tyrannosaurus and Ichthyosaur are ecological
parallels respectively, to the bat, rhinoceros, lion and
porpoise of modern mammals. Similarly, among modern placental
mammals, the gray wolf, flying squirrel, great anteater and
common mole are ecological parallels respectively, to the
Tasmanian wolf, honey glider, banded anteater and marsupial


Summary 27


Thomas S. Ray
Evolution and Optimization of Digital Organisms

mole of the marsupial mammals of Australia.

Given these evidently powerful convergent forces, it should
perhaps not be surprising that as adaptive radiations proceed
among digital organisms, we encounter recognizable ecological
forms, in spite of the fundamentally distinct physics and
chemistry on which they are based. Ideally, comparisons
should be made among organisms of comparable complexity. It
may not be appropriate to compare viruses to mammals.
Unfortunately, the organic creatures most comparable to
digital organisms, the RNA creatures, are no longer with us.
Since digital organisms are being compared to modern organic
creatures of much greater complexity, ecological comparisons
must be made in the broadest of terms.

Trained biologists will tend to view synthetic life in the
same terms that they have come to know organic life. Having
been trained as an ecologist and evolutionist, I have seen in
my synthetic communities, many of the ecological and
evolutionary properties that are well known from natural
communities. Biologists trained in other specialties will
likely observe other familiar properties. It seems that what
we see is what we know. It is likely to take longer before we
appreciate the unique properties of these new life forms.




APPLICATIONS


The phenomenon of synthetic life is so new that it is
impossible to know what its practical applications might be.
Perhaps the most immediate application is as a technique for
the optimization of machine codes.

A new version of the Tierran language is currently under
development which will retain those features of the language
that make it evolvable, while at the same time expanding its
functionality to the point that is should be possible to
develop cross-assemblers between it and real assembler
languages. Application code written and compiled to run on
real machines could be cross-assembled into the new Tierran
language. Each procedure could then be inserted into the
genome of a creature. Creatures could be rewarded with CPU
time in proportion to the efficacy and efficiency of the
evolving inserted code. In this way, artificial selection
would lead to the optimization of the inserted code, which
could then be cross-assembled back into the real machine code.

If this proved to be practical, it would be worthwhile to
render the Tierran virtual instruction set in silicon, thereby
greatly accelerating the process. At present, maximum
optimization can be achieved in a few hours of running the
Tierran virtual computer. If a real computer were based on
the architectural principals of the Tierran computer, such


Summary 28


Thomas S. Ray
Evolution and Optimization of Digital Organisms

optimization could be achieved in minutes. If machine code
could evolve that quickly, then there is the possibility of
using it as a generative process in addition to an
optimization procedure. There may also be some potential
application in the areas of machine learning or adaptive
programming.

Another interesting possibility is the study of evolving
communities of digital organisms as a source of new paradigms
for the programming of massively parallel machines. It is
already known that digital organisms have spontaneously
evolved linear programming tricks used by humans (like
unrolling loops). The kinds of ecological interactions
already observed in digital communities could in another
light, be viewed as optimization techniques for parallel
programming (e.g., the sharing of code fragments). However,
these interactions evolve in a ``jungle''-like environment
where most interactions are of an adversarial nature. When
evolving large parallel application programs, the most viable
model would be a multi-cellular one, where many cells would
cooperate on a common problem. A multi-cellular model is
under development. In the end, evolution may prove to be the

best method of programming massively parallel machines.



































Summary 29


Thomas S. Ray
Evolution and Optimization of Digital Organisms

ACKNOWLEDGMENT



I thank Marc Cygnus, Robert Eisenberg, Doyne Farmer, Walter
Fontana, Stephanie Forrest, Chris Langton, Dan Pirone, Stephen
Pope, and Steen Rasmussen, for their discussions or readings
of the manuscripts. Contribution No. 150 from the Ecology
Program, School of Life and Health Sciences, University of
Delaware.
















































ACKNOWLEDGMENT 30


Thomas S. Ray
Evolution and Optimization of Digital Organisms

REFERENCES




[1] Ackley, D. H. & Littman, M. S. ``Learning from natural
selection in an artificial environment.'' In: Proceedings of
the International Joint Conference on Neural Networks, Volume
I, Theory Track, Neural and Cognitive Sciences Track , IJCNN
Winter 1990, Washington, DC. Hillsdale, New Jersey: Lawrence
Erlbaum Associates, 1990.

[2] Aho, A. V., Hopcroft, J. E. & Ullman, J. D. The design
and analysis of computer algorithms . Reading, Mass.:
Addison-Wesley Publ. Co, 1974.

[3] Bagley, R. J., Farmer, J. D., Kauffman, S. A., Packard, N.
H., Perelson, A. S. & Stadnyk, I. M. ``Modeling adaptive
biological systems.'' Unpublished paper, 1989.

[4] Barbieri, M. The semantic theory of evolution . London:
Harwood Academic Publishers, 1985.

[5] Cariani, P. ``Emergence and artificial life.'' In:
Artificial Life II, edited by C. Langton, D. Farmer and S.
Rasmussen. Redwood City, CA: Addison-Wesley, 1991, 000--000.

[6] Cohen, F. Computer viruses: theory and experiments . Ph.
D. dissertation, U. of Southern California, 1984.

[7] Dawkins, R. The blind watchmaker . New York: W. W.
Norton & Co., 1987.

[8] Dawkins, R. ``The evolution of evolvability.'' In:
Artificial life: proceedings of an interdisciplinary workshop
on the synthesis and simulation of living systems , edited by
C. Langton. Redwood City, CA: Addison-Wesley, 1989, 201--220.

[9] Denning, P. J. ``Computer viruses.'' Amer. Sci. 76
(1988): 236--238.

[10] Dewdney, A. K. ``Computer recreations: In the game
called Core War hostile programs engage in a battle of bits.''
Sci. Amer. 250 (1984): 14--22.

[11] Dewdney, A. K. ``Computer recreations: A core war
bestiary of viruses, worms and other threats to computer
memories.'' Sci. Amer. \bf 252 (1985a): 14--23.

[12] Dewdney, A. K. ``Computer recreations: Exploring the
field of genetic algorithms in a primordial computer sea full
of flibs.'' Sci. Amer. 253 (1985b): 21--32.

[13] Dewdney, A. K. ``Computer recreations: A program called
MICE nibbles its way to victory at the first core war
tournament.'' Sci. Amer. 256 (1987): 14--20.


REFERENCES 31


Thomas S. Ray
Evolution and Optimization of Digital Organisms


[14] Dewdney, A. K. ``Of worms, viruses and core war.'' Sci.
Amer. 260 (1989): 110--113.

[15] Eldredge, N. & Gould, S. J. ``Punctuated equilibria: an
alternative to phyletic gradualism.'' In: Models in
Paleobiology , edited by J. M. Schopf. San Francisco:
Greeman, Cooper, 1972, 82--115.

[16] Farmer, J. D., Kauffman, S. A., & Packard, N. H.
``Autocatalytic replication of polymers.'' Physica D 22
(1986): 50--67.

[17] Farmer, J. D. & Belin, A. ``Artificial life: the coming
evolution.'' Proceedings in celebration of Murray Gell-Man's
60th Birthday. Cambridge: University Press. In press.

[18] Gould, S. J. Wonderful life, the Burgess shale and the
nature of history . New York: W. W. Norton & Company, 1989.

[19] Gould, S. J. & Eldredge, N. ``Punctuated equilibria: the
tempo and mode of evolution reconsidered.'' Paleobiology 3
(1977): 115--151.

[20] Holland, J. H. Adaptation in natural and artificial
systems: an introductory analysis with applications to
biology, control, and artificial intelligence . Ann Arbor:
Univ. of Michigan Press, 1975.

[21] Holland, J. H. ``Studies of the spontaneous emergence of
self-replicating systems using cellular automata and formal
grammars.'' In: Automata, Languages, Development , edited by
Lindenmayer, A., & Rozenberg, G. New York: North-Holland,
1976, 385--404.

[22] Langton, C. G. ``Studying artificial life with cellular
automata.'' Physica 22d (1986): 120--149.

[23] Langton, C. G. ``Virtual state machines in cellular
automata.'' Complex Systems 1 (1987): 257--271.

[24] Langton, C. G. ``Artificial life.'' In: Artificial
life: proceedings of an interdisciplinary workshop on the
synthesis and simulation of living systems , edited by
Langton, C. Vol. 6 in the series: Santa Fe Institute studies
in the sciences of complexity. Redwood City, CA:
Addison-Wesley, 1989, 1--47.

[25] Lotka, A. J. Elements of physical biology . Baltimore:
Williams and Wilkins, 1925, reprinted as Elements of
mathematical biology , Dover Press, 1956.

[26] Minsky, M. L. Computation: finite and infinite
machines . Englewood Cliffs, N.J.: Prentice-Hall, 1976.




REFERENCES 32


Thomas S. Ray
Evolution and Optimization of Digital Organisms

[27] Morris, S. C. ``Burgess shale faunas and the cambrian
explosion.'' Science 246 (1989): 339--346.

[28] Paine, R. T. ``Food web complexity and species
diversity.'' Am. Nat. 100 (1966): 65--75.

[29] Packard, N. H. ``Intrinsic adaptation in a simple model
for evolution.'' In: Artificial life: proceedings of an
interdisciplinary workshop on the synthesis and simulation of
living systems , edited by C. Langton. Redwood City, CA:
Addison-Wesley, 1989, 141--155.

[30] Pattee, H. H. ``Simulations, realizations, and theories
of life.'' In: Artificial life: proceedings of an
interdisciplinary workshop on the synthesis and simulation of
living systems , edited by C. Langton. Redwood City, CA:
Addison-Wesley, 1989, 63--77.

[31] Rasmussen, S., Knudsen, C., Feldberg, R. & Hindsholm, M.
``The coreworld: emergence and evolution of cooperative
structures in a computational chemistry'' Physica D 42
(1990): 111--134.

[32] Rheingold, H. (1988). Computer viruses. Whole Earth
Review Fall (1988): 106.

[33] Spafford, E. H., Heaphy, K. A. & Ferbrache, D. J.
Computer viruses, dealing with electronic vandalism and
programmed threats . ADAPSO, 1300 N. 17th Street, Suite 300,
Arlington, VA 22209, 1989.

[34] Stanley, S. M. ``An ecological theory for the sudden
origin of multicellular life in the late precambrian.'' Proc.
Nat. Acad. Sci. 70 (1973): 1486--1489.

[35] Volterra, V. ``Variations and fluctuations of the number
of individuals in animal species living together.'' In:
Animal Ecology , edited by R. N. Chapman. New York:
McGraw-Hill, 1926, 409--448.

[36] Wilson, E. O. & Bossert, W. H. A primer of population
biology . Stamford, Conn: Sinauer Associates, 1971.
















REFERENCES 33


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Figure 1. Metabolic flow chart for the ancestor, parasite,
hyper-parasite, and their interactions: ax, bx and cx refer
to CPU registers where location and size information are
stored. [ax] and [bx] refer to locations in the soup
indicated by the values in the ax and bx registers. Patterns
such as 1101 are complementary templates used for addressing.
Arrows outside of boxes indicate jumps in the flow of
execution of the programs. The dotted-line arrows indicate
flow of execution between creatures. The parasite lacks the
copy procedure, however, if it is within the search limit of
the copy procedure of a host, it can locate, call and execute
that procedure, thereby obtaining the information needed to
complete its replication. The host is not adversely affected
by this informational parasitism, except through competition
with the parasite, which is a superior competitor. Note that
the parasite calls the copy procedure of its host with the
expectation that control will return to the parasite when the
copy procedure returns. However, the hyper-parasite jumps out
of the copy procedure rather than returning, thereby seizing
control from the parasite. It then proceeds to reset the CPU
registers of the parasite with the location and size of the
hyper-parasite, causing the parasite to replicate the
hyper-parasite genome thereafter.


































REFERENCES 34


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Figure 2. Metabolic flow chart for social hyper-parasites,
their associated hyper-hyper-parasite cheaters, and their
interactions. Symbols are as described for Fig. 1.
Horizontal dashed lines indicate the boundaries between
individual creatures. On both the left and right, above the
dashed line at the top of the figure is the lowermost fragment
of a social-hyper-parasite. Note (on the left) that
neighboring social hyper-parasites cooperate in returning the
flow of execution to the beginning of the creature for
self-re-examination. Execution jumps back to the end of the
creature above, but then falls off the end of the creature
without executing any instructions of consequence, and enters
the top of the creature below. On the right, a cheater is
inserted between the two social-hyper-parasites. The cheater
captures control of execution when it passes between the
social individuals. It sets the CPU registers with its own
location and size, and then skips over the self-examination
step when it returns control of execution to the social
creature below.






































REFERENCES 35


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Figure 3. Metabolic flow chart for obligate symbionts and
their interactions. Symbols are as described for Fig. 1.
Neither creature is able to self-replicate in isolation.
However, when cultured together, each is able to replicate by
using information provided by the other.




















































REFERENCES 36


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Figure 4. Evolutionary optimization at eight sets of mutation
rates. In each run, the three mutation rates: move mutations
(copy error), flaws and background mutations (cosmic rays) are
set relative to the generation time. In each case, the
background mutation rate is the lowest, affecting a cell once
in twice as many generations as the move mutation rate. The
flaw rate is intermediate, affecting a cell once in 1.5 times
as many generations as the move mutation rate. For example in
one run, the move mutation will affect a cell line on the
average once every 4 generations, the flaw will occur once
every 6 generations, and the background mutation once every 8
generations. The horizontal axis shows elapsed time in
hundreds of millions of instructions executed by the system.
The vertical axis shows genome size in instructions. Each
point indicates the first appearance of a new genotype which
crossed the abundance thresholds of either 2% of the
population of cells in the soup, or occupation of 2% of the
memory. The number of generations per move mutation is
indicated by a number in the upper right hand corner of each
graph.





































REFERENCES 37


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Figure 5. Variation in evolutionary optimization under
constant conditions. Based on a mutation rate of four
generations per move mutation, all other parameters as in Fig.
4. The plots are otherwise as described for Fig. 4.





















































REFERENCES 38


Thomas S. Ray
Evolution and Optimization of Digital Organisms


Table 1: Genebank. Table of numbers of size classes in the
genebank. Left column is size class, right column is number
of self-replicating genotypes of that size class. 305 sizes,
29,275 genotypes.






















































REFERENCES 39


Thomas S. Ray
Evolution and Optimization of Digital Organisms

0034 1 0092 362 0150 2 0205 5 0418 1 5213 2
0041 2 0093 261 0151 1 0207 3 0442 10 5229 4
0043 12 0094 241 0152 2 0208 2 0443 1 5254 1
0044 7 0095 211 0153 1 0209 1 0444 61 5888 36
0045 191 0096 232 0154 2 0210 9 0445 1 5988 1
0046 7 0097 173 0155 3 0211 4 0456 2 6006 2
0047 5 0098 92 0156 77 0212 4 0465 6 6014 1
0048 4 0099 117 0157 270 0213 5 0472 6 6330 1
0049 8 0100 77 0158 938 0214 47 0483 1 6529 1
0050 13 0101 62 0159 836 0218 1 0484 8 6640 1
0051 2 0102 62 0160 3229 0219 1 0485 3 6901 5
0052 11 0103 27 0161 1417 0220 2 0486 9 6971 1
0053 4 0104 25 0162 174 0223 3 0487 2 7158 2
0054 2 0105 28 0163 187 0226 2 0493 2 7293 3
0055 2 0106 19 0164 46 0227 7 0511 2 7331 1
0056 4 0107 3 0165 183 0231 1 0513 1 7422 70
0057 1 0108 8 0166 81 0232 1 0519 1 7458 1
0058 8 0109 2 0167 71 0236 1 0522 6 7460 7
0059 8 0110 8 0168 9 0238 1 0553 1 7488 1
0060 3 0111 71 0169 15 0240 3 0568 6 7598 1
0061 1 0112 19 0170 99 0241 1 0578 1 7627 63
0062 2 0113 10 0171 40 0242 1 0581 3 7695 1
0063 2 0114 3 0172 44 0250 1 0582 1 7733 1
0064 1 0115 3 0173 34 0251 1 0600 1 7768 2
0065 4 0116 5 0174 15 0260 2 0683 1 7860 25
0066 1 0117 3 0175 22 0261 1 0689 1 7912 1
0067 1 0118 1 0176 137 0265 2 0757 6 8082 3
0068 2 0119 3 0177 13 0268 1 0804 2 8340 1
0069 1 0120 2 0178 3 0269 1 0813 1 8366 1
0070 7 0121 60 0179 1 0284 16 0881 6 8405 5
0071 5 0122 9 0180 16 0306 1 0888 1 8406 2
0072 17 0123 3 0181 5 0312 1 0940 2 8649 2
0073 2 0124 11 0182 27 0314 1 1006 6 8750 1
0074 80 0125 6 0184 3 0316 2 1016 1 8951 1
0075 56 0126 11 0185 21 0318 3 1077 5 8978 3
0076 21 0127 1 0186 9 0319 2 1116 1 9011 3
0077 28 0130 3 0187 3 0320 23 1186 1 9507 3
0078 409 0131 2 0188 11 0321 5 1294 7 9564 3
0079 850 0132 5 0190 20 0322 21 1322 7 9612 1
0080 7399 0133 2 0192 12 0330 1 1335 1 9968 1
0081 590 0134 7 0193 4 0342 5 1365 11 10259 31
0082 384 0135 1 0194 4 0343 1 1631 1 10676 1
0083 886 0136 1 0195 11 0351 1 1645 3 11366 5
0084 1672 0137 1 0196 19 0352 3 2266 1 11900 1
0085 1531 0138 1 0197 2 0386 1 2615 2 12212 2
0086 901 0139 2 0198 3 0388 2 2617 9 15717 3
0087 944 0141 6 0199 35 0401 3 2671 7 16355 1
0088 517 0143 1 0200 1 0407 1 3069 3 17356 3
0089 449 0144 4 0201 84 0411 22 4241 1 18532 1
0090 543 0146 1 0203 1 0412 3 5101 15 23134 14
0091 354 0149 1 0204 1 0416 1 5157 9







REFERENCES 40


Thomas S. Ray
Evolution and Optimization of Digital Organisms



























































REFERENCES 41


Thomas S. Ray
Evolution and Optimization of Digital Organisms

APPENDIX A: THE TIERRA VIRTUAL CPU.



Structure definition to implement the Tierra virtual CPU. The
complete source code for the Tierra Simulator can be obtained
by contacting the author by email.

struct cpu { /* structure for registers of virtual cpu */
int ax; /* address register */
int bx; /* address register */
int cx; /* numerical register */
int dx; /* numerical register */
char fl; /* flag */
char sp; /* stack pointer */
int st[10]; /* stack */
int ip; /* instruction pointer */
} ;








































Appendix A: The Tierra virtual CPU. 42


Thomas S. Ray
Evolution and Optimization of Digital Organisms

APPENDIX B: CPU CYCLE OF THE TIERRA SIMULATOR



Abbreviated code for implementing the CPU cycle of the Tierra
Simulator.





















































Appendix B: CPU cycle of the Tierra Simulator 43


Thomas S. Ray
Evolution and Optimization of Digital Organisms

void main(void)
{ get_soup();
life();
write_soup();
}

void life(void) /* doles out time slices and death */
{ while(inst_exec_c < alive) /* control the length of the run */
{ time_slice(this_slice); /* this_slice is current cell in queue */
incr_slice_queue(); /* increment this_slice to next cell in queue */
while(free_mem_current < free_mem_prop * soup_size)
reaper(); /* if memory is full to threshold, reap some cells */
}
}

void time_slice(int ci)
{ Pcells ce; /* pointer to the array of cell structures */
char i; /* instruction from soup */
int di; /* decoded instruction */
int j, size_slice;
ce = cells + ci;
for(j = 0; j < size_slice; j++)
{ i = fetch(ce->c.ip); /* fetch instruction from soup, at address ip */
di = decode(i); /* decode the fetched instruction */
execute(di, ci); /* execute the decoded instruction */
increment_ip(di,ce); /* move instruction pointer to next instruction */
system_work(); /* opportunity to extract information */
}
}

void execute(int di, int ci)
{ switch(di)
{ case 0x00: nop_0(ci); break; /* no operation */
case 0x01: nop_1(ci); break; /* no operation */
case 0x02: or1(ci); break; /* flip low order bit of cx, cx ^= 1 */
case 0x03: shl(ci); break; /* shift left cx register, cx <<= 1 */
case 0x04: zero(ci); break; /* set cx register to zero, cx = 0 */
case 0x05: if_cz(ci); break; /* if cx==0 execute next instruction */
case 0x06: sub_ab(ci); break; /* subtract bx from ax, cx = ax - bx */
case 0x07: sub_ac(ci); break; /* subtract cx from ax, ax = ax - cx */
case 0x08: inc_a(ci); break; /* increment ax, ax = ax + 1 */
case 0x09: inc_b(ci); break; /* increment bx, bx = bx + 1 */
case 0x0a: dec_c(ci); break; /* decrement cx, cx = cx - 1 */
case 0x0b: inc_c(ci); break; /* increment cx, cx = cx + 1 */
case 0x0c: push_ax(ci); break; /* push ax on stack */
case 0x0d: push_bx(ci); break; /* push bx on stack */
case 0x0e: push_cx(ci); break; /* push cx on stack */
case 0x0f: push_dx(ci); break; /* push dx on stack */
case 0x10: pop_ax(ci); break; /* pop top of stack into ax */
case 0x11: pop_bx(ci); break; /* pop top of stack into bx */
case 0x12: pop_cx(ci); break; /* pop top of stack into cx */
case 0x13: pop_dx(ci); break; /* pop top of stack into dx */
case 0x14: jmp(ci); break; /* move ip to template */
case 0x15: jmpb(ci); break; /* move ip backward to template */
case 0x16: call(ci); break; /* call a procedure */
case 0x17: ret(ci); break; /* return from a procedure */


Appendix B: CPU cycle of the Tierra Simulator 44


Thomas S. Ray
Evolution and Optimization of Digital Organisms

case 0x18: mov_cd(ci); break; /* move cx to dx, dx = cx */
case 0x19: mov_ab(ci); break; /* move ax to bx, bx = ax */
case 0x1a: mov_iab(ci); break; /* move instruction at address in bx
to address in ax */
case 0x1b: adr(ci); break; /* address of nearest template to ax */
case 0x1c: adrb(ci); break; /* search backward for template */
case 0x1d: adrf(ci); break; /* search forward for template */
case 0x1e: mal(ci); break; /* allocate memory for daughter cell */
case 0x1f: divide(ci); break; /* cell division */
}
inst_exec_c++;
}














































Appendix B: CPU cycle of the Tierra Simulator 45


Thomas S. Ray
Evolution and Optimization of Digital Organisms

APPENDIX C: CODE FOR THE ANCESTRAL CREATURE



Assembler source code for the ancestral creature.






















































Appendix C: Code for the ancestral creature 46


Thomas S. Ray
Evolution and Optimization of Digital Organisms

genotype: 80 aaa origin: 1-1-1990 00:00:00:00 ancestor
parent genotype: human
1st_daughter: flags: 0 inst: 839 mov_daught: 80
2nd_daughter: flags: 0 inst: 813 mov_daught: 80

nop_1 ; 01 0 beginning template
nop_1 ; 01 1 beginning template
nop_1 ; 01 2 beginning template
nop_1 ; 01 3 beginning template
zero ; 04 4 put zero in cx
or1 ; 02 5 put 1 in first bit of cx
shl ; 03 6 shift left cx
shl ; 03 7 shift left cx, now cx = 4
; ax = bx =
; cx = template size dx =
mov_cd ; 18 8 move template size to dx
; ax = bx =
; cx = template size dx = template size
adrb ; 1c 9 get (backward) address of beginning template
nop_0 ; 00 10 compliment to beginning template
nop_0 ; 00 11 compliment to beginning template
nop_0 ; 00 12 compliment to beginning template
nop_0 ; 00 13 compliment to beginning template
; ax = start of mother + 4 bx =
; cx = template size dx = template size
sub_ac ; 07 14 subtract cx from ax
; ax = start of mother bx =
; cx = template size dx = template size
mov_ab ; 19 15 move start address to bx
; ax = start of mother bx = start of mother
; cx = template size dx = template size
adrf ; 1d 16 get (forward) address of end template
nop_0 ; 00 17 compliment to end template
nop_0 ; 00 18 compliment to end template
nop_0 ; 00 19 compliment to end template
nop_1 ; 01 20 compliment to end template
; ax = end of mother bx = start of mother
; cx = template size dx = template size
inc_a ; 08 21 to include dummy statement to separate creatures
sub_ab ; 06 22 subtract start address from end address to get size
; ax = end of mother bx = start of mother
; cx = size of mother dx = template size
nop_1 ; 01 23 reproduction loop template
nop_1 ; 01 24 reproduction loop template
nop_0 ; 00 25 reproduction loop template
nop_1 ; 01 26 reproduction loop template
mal ; 1e 27 allocate memory for daughter cell, address to ax
; ax = start of daughter bx = start of mother
; cx = size of mother dx = template size
call ; 16 28 call template below (copy procedure)
nop_0 ; 00 29 copy procedure compliment
nop_0 ; 00 30 copy procedure compliment
nop_1 ; 01 31 copy procedure compliment
nop_1 ; 01 32 copy procedure compliment
divide ; 1f 33 create independent daughter cell
jmp ; 14 34 jump to template below (reproduction loop, above)


Appendix C: Code for the ancestral creature 47


Thomas S. Ray
Evolution and Optimization of Digital Organisms

nop_0 ; 00 35 reproduction loop compliment
nop_0 ; 00 36 reproduction loop compliment
nop_1 ; 01 37 reproduction loop compliment
nop_0 ; 00 38 reproduction loop compliment
if_cz ; 05 39 this is a dummy instruction to separate templates
; begin copy procedure
nop_1 ; 01 40 copy procedure template
nop_1 ; 01 41 copy procedure template
nop_0 ; 00 42 copy procedure template
nop_0 ; 00 43 copy procedure template
push_ax ; 0c 44 push ax onto stack
push_bx ; 0d 45 push bx onto stack
push_cx ; 0e 46 push cx onto stack
nop_1 ; 01 47 copy loop template
nop_0 ; 00 48 copy loop template
nop_1 ; 01 49 copy loop template
nop_0 ; 00 50 copy loop template
mov_iab ; 1a 51 move contents of [bx] to [ax]
dec_c ; 0a 52 decrement cx
if_cz ; 05 53 if cx == 0 perform next instruction, otherwise skip it
jmp ; 14 54 jump to template below (copy procedure exit)
nop_0 ; 00 55 copy procedure exit compliment
nop_1 ; 01 56 copy procedure exit compliment
nop_0 ; 00 57 copy procedure exit compliment
nop_0 ; 00 58 copy procedure exit compliment
inc_a ; 08 59 increment ax
inc_b ; 09 60 increment bx
jmp ; 14 61 jump to template below (copy loop)
nop_0 ; 00 62 copy loop compliment
nop_1 ; 01 63 copy loop compliment
nop_0 ; 00 64 copy loop compliment
nop_1 ; 01 65 copy loop compliment
if_cz ; 05 66 this is a dummy instruction, to separate templates
nop_1 ; 01 67 copy procedure exit template
nop_0 ; 00 68 copy procedure exit template
nop_1 ; 01 69 copy procedure exit template
nop_1 ; 01 70 copy procedure exit template
pop_cx ; 12 71 pop cx off stack
pop_bx ; 11 72 pop bx off stack
pop_ax ; 10 73 pop ax off stack
ret ; 17 74 return from copy procedure
nop_1 ; 01 75 end template
nop_1 ; 01 76 end template
nop_1 ; 01 77 end template
nop_0 ; 00 78 end template
if_cz ; 05 79 dummy statement to separate creatures












Appendix C: Code for the ancestral creature 48


Thomas S. Ray
Evolution and Optimization of Digital Organisms

APPENDIX D: SMALLEST SELF-REPLICATING CREATURE



Assembler source code for the smallest self-replicating
creature.

genotype: 0022abn parent genotype: 0022aak
1st_daughter: flags: 1 inst: 146 mov_daught: 22 breed_true: 1
2nd_daughter: flags: 0 inst: 142 mov_daught: 22 breed_true: 1
InstExecC: 437 InstExec: 625954 origin: 662865379 Wed Jan 2 20:16:19 1991
MaxPropPop: 0.1231 MaxPropInst: 0.0568

nop_0 ; 00 0
adrb ; 1c 1 find beginning
nop_1 ; 01 2
divide ; 1f 3 fails the first time it is executed
sub_ac ; 07 4
mov_ab ; 19 5
adrf ; 1d 6 find end
nop_0 ; 00 7
inc_a ; 08 8 to include final dummy statement
sub_ab ; 06 9 calculate size
mal ; 1e 10
push_bx ; 0d 11 save beginning address on stack in order to `return' there
nop_0 ; 00 12 top of copy loop
mov_iab ; 1a 13
dec_c ; 0a 14
if_cz ; 05 15
ret ; 17 16 jump to beginning, address saved on stack
inc_a ; 08 17
inc_b ; 09 18
jmpb ; 15 19 bottom of copy loop (6 instructions executed per loop)
nop_1 ; 01 20
mov_iab ; 1a 21 dummy statement to terminate template























Appendix D: Smallest self-replicating creature 49


Thomas S. Ray
Evolution and Optimization of Digital Organisms

APPENDIX E: CENTRAL COPY LOOP OF THE ANCESTOR



Assembler code for the central copy loop of the ancestor

(80aaa) and decendant after fifteen billion instructions
(72etq). Within the loop, the ancestor does each of the
following operations once: copy instruction (51), decrement cx
(52), increment ax (59) and increment bx (60). The decendant
performs each of the following operations three times within
the loop: copy instruction (15, 22, 26), increment ax (20, 24,
31) and increment bx (21, 25, 32). The decrement cx operation
occurs five times within the loop (16, 17, 19, 23, 27).
Instruction 28 flips the low order bit of the cx register.
Whenever this latter instruction is reached, the value of the
low order bit is one, so this amounts to a sixth instance of
decrement cx. This means that there are two decrements for
every increment. The reason for this is related to another
adaptation of this creature. When it calculates its size, it
shifts left (12) before allocating space for the daughter
(13). This has the effect of allocating twice as much space
as is actually needed to accomodate the genome. The genome of
the creature is 36 instructions long, but it allocates a space
of 72 instructions. This occurred in an environment where the
slice size was set equal to the size of the cell. In this way
the creatures were able to garner twice as much energy.
However, they had to compliment this change by doubling the
number of decrements in the loop.






























Appendix E: Central copy loop of the ancestor 50


Thomas S. Ray
Evolution and Optimization of Digital Organisms


nop_1 ; 01 47 copy loop template COPY LOOP OF 80AAA
nop_0 ; 00 48 copy loop template
nop_1 ; 01 49 copy loop template
nop_0 ; 00 50 copy loop template
mov_iab ; 1a 51 move contents of [bx] to [ax] (copy instruction)
dec_c ; 0a 52 decrement cx
if_cz ; 05 53 if cx = 0 perform next instruction, otherwise skip it
jmp ; 14 54 jump to template below (copy procedure exit)
nop_0 ; 00 55 copy procedure exit compliment
nop_1 ; 01 56 copy procedure exit compliment
nop_0 ; 00 57 copy procedure exit compliment
nop_0 ; 00 58 copy procedure exit compliment
inc_a ; 08 59 increment ax (point to next instruction of daughter)
inc_b ; 09 60 increment bx (point to next instruction of mother)
jmp ; 14 61 jump to template below (copy loop)
nop_0 ; 00 62 copy loop compliment
nop_1 ; 01 63 copy loop compliment
nop_0 ; 00 64 copy loop compliment
nop_1 ; 01 65 copy loop compliment (10 instructions executed per loop)

shl ; 000 03 12 shift left cx COPY LOOP OF 72ETQ
mal ; 000 1e 13 allocate daughter cell
nop_0 ; 000 00 14 top of loop
mov_iab ; 000 1a 15 copy instruction
dec_c ; 000 0a 16 decrement cx
dec_c ; 000 0a 17 decrement cx
jmpb ; 000 15 18 junk
dec_c ; 000 0a 19 decrement cx
inc_a ; 000 08 20 increment ax
inc_b ; 000 09 21 increment bx
mov_iab ; 000 1a 22 copy instruction
dec_c ; 000 0a 23 decrement cx
inc_a ; 000 08 24 increment ax
inc_b ; 000 09 25 increment bx
mov_iab ; 000 1a 26 copy instruction
dec_c ; 000 0a 27 decrement cx
or1 ; 000 02 28 flip low order bit of cx
if_cz ; 000 05 29 if cx == 0 do next instruction
ret ; 000 17 30 exit loop
inc_a ; 000 08 31 increment ax
inc_b ; 000 09 32 increment bx
jmpb ; 000 15 33 go to top of loop (6 instructions per copy)
nop_1 ; 000 01 34 bottom of loop (18 instructions executed per loop)














Appendix E: Central copy loop of the ancestor 51


 December 31, 2017  Add comments

Leave a Reply