The ancestor

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Thomas S. Ray An approach to the synthesys of
life
presenting Ady Ecker
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Contents

• Introduction
• Tierra system description
• Mac-tierra
• Results
• Discussion

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Introduction
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Introduction

• Exploration of life in general is limited
• Tierra is an artificial life model to explore the
  origin of diversity

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What Is Life?

• 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 preconceived by the creator.

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Tierra sytem description
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The Tierra Simulator

• Virtual parallel computer
• Cellularity each program gets its own memory and
  CPU time. Each cell can read and execute every
  instruction but has write permission to its own
  or its daughter cell
• The operating system executes the code of each
  cell in the computers memory

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operating system fetch - decode - execute
main memory
daughter cell
instruction codes
cells
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The Language

• Special machine language to be portable and
  secure
• Small instruction set (32 instructions, operands
  included), that is less fragile when the code is
  mutated
• Jumps addressing by templates

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The Operating System

• The slicer processor time sharing mechanism
• Control time for large/small creatures
• The reaper kills cells when the memory is full
  from the top of a queue
• The creature starts at the bottom of the queue
• It moves up the queue when it fails to execute
  instructions (because its algorithm is flawed),
  and stays where it is, or moves down when it
  succeeds
• The genebank saves information about each genome

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Mutation

• Cosmic mutations cause the flipping of random
  bits in the soup at a low frequency
• Copy errors result in replication errors
• Flaws can occur during execution. The result is
  off by ?1 at some low frequency
• Creatures activity scramble the soup

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The Digital Environment Self-replicating
computer programs (colored geometric objects)
occupy the RAM memory of the computer (orange
background). Mutations (lightning) cause random
changes in the code. Death (the skull)
eliminates old or defective programs.
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The ancestor

• The simulation start with one simple self
  replicating ancestor - 80 instructions.
• This ancestor evolve communities of interacting
  living creatures, due to mutations.

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Ancestors Genome
01 (nop_1) 01 (nop_1) 01 (nop_1) 01 (nop_1) 04
(zero) 02 (or1) 03 (shl) 03 (shl) 18 (mov_cd) 1c
(adrb) 00 (nop_0) 00 (nop_0) 00 (nop_0) 00
(nop_0) 07 (sub_ac) 19 (mov_ab) 1d (adrf) 00
(nop_0) 00 (nop_0) 00 (nop_0)
01 (nop_1) 08 (inc_a) 06 (sub_ab) 01 (nop_1) 01
(nop_1) 00 (nop_0) 01 (nop_1) 1e (mal) 16
(call) 00 (nop_0) 00 (nop_0) 01 (nop_1) 01
(nop_1) 1f (divide) 14 (jmp) 00 (nop_0) 00
(nop_0) 01 (nop_1) 00 (nop_0) 05 (if_cz)
01 (nop_1) 01 (nop_1) 00 (nop_0) 00 (nop_0) 0c
(push_ax) 0d (push_bx) 0e (push_cx) 01 (nop_1) 00
(nop_0) 01 (nop_1) 00 (nop_0) 1a (mov_iab) 0a
(dec_c) 05 (if_cz) 14 (jmp) 00 (nop_0) 01
(nop_1) 00 (nop_0) 00 (nop_0) 08 (inc_a)
09 (inc_b) 14 (jmp) 00 (nop_0) 01 (nop_1) 00
(nop_0) 01 (nop_1) 05 (if_cz) 01 (nop_1) 00
(nop_0) 01 (nop_1) 01 (nop_1) 12 (pop_cx) 11
(pop_bx) 10 (pop_ax) 17 (ret) 01 (nop_1) 01
(nop_1) 01 (nop_1) 00 (nop_0) 05 (if_cz)
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Ancestor
1111
1100
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx
copy procedure Save registers to stack
1010
move bx ? ax decrement cx
if cx0 jump 0100
increment ax bx
1101
jump 0101
reproduction loop Allocate daughter ? ax
1011
call 0011 (copy procedure)
restore registers
cell division
return
1110
jump 0010
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The Ancestral Program - consists of three
genes (green solid objects). The CPU (green
sphere) is executing code in the first gene,
which causes the program to measure itself.
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Mac Tierra
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Results
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The Parasite

• Uses the ancestors copy procedure to copy
  himself
• The host is not affected by the parasite
• Superior competitor
• 45 instructions
• Population cycles

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1111
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx
Ancestor parasite
1111
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx
1101
reproduction loop Allocate daughter ? ax
call 0011 (copy procedure)
cell division
jump 0010
1100
copy procedure Save registers to stack
1101
reproduction loop Allocate daughter ? ax
1010
move bx ? ax decrement cx
call 0011 (copy procedure)
if cx0 jump 0100
increment ax bx
cell division
jump 0101
jump 0010
1011
restore registers
return
1110
1110
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A Parasite (blue, two piece object) uses its CPU
(blue sphere) to execute the code in the third
gene of a neighboring host organism (green) to
replicate itself, producing daughter
parasite (two-piece wire frame object).
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The Hyper-Parasite

• Robust self-replicate program by itself
• When a parasite tries to use the hyper-parasite,
  the hyper-parasite cause the parasite to
  replicate the hyper-parasite
• Drive the parasites to extinction

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1100
Hyper-parasite
1111
copy procedure
1101
self exam find 0000 start? bx find 0001 end
? ax calculate size ? cx
1010
reproduction loop Allocate daughter ? ax
move bx ? ax decrement cx
if cx0 jump 1100
call 0011
increment ax bx
cell division
jump 0101
jump 0000
1110
parasite
1101
reproduction loop Allocate daughter ? ax
1111
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx
call 0011 (copy procedure)
cell division
jump 0010
1110
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A Hyper-parasite (red, three piece object) steals
the CPU from a parasite (blue sphere). Using the
stolen CPU, and its own CPU (red sphere) it is
able to produce two daughters (wire frame
objects on left and right) simultaneously.
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Symbionts

• Manually created
• One contains the self-exam and copy procedure
• The other contains the self-exam and reproduction
  loop
• 46 and 64 instructions

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symbionts
1111
1111
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx jump 0010
self exam find 0000 start? bx find 0001 end ?
ax calculate size ? cx jump 0010
1100
copy procedure Save registers to stack
1010
1101
reproduction loop Allocate daughter ? ax
move bx ? ax decrement cx
call 0011 (copy procedure)
if cx0 jump 0100
cell division
increment ax bx
jump 0010
jump 0101
1110
1011
restore registers
return
1110
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Social Hyper-Parasites

• Appear when there is genetic uniformity
• Cooperate with the previous social hyper-parasite
  cell
• 61 instructions
• Jumping templates of size 3

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Cheaters Hyper Hyper Parasites

• Invade the social system
• Position themselves between aggregating hyper
  parasites to capture the instruction pointer
• 27 instructions

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Experiments (Simulations)
Hosts, red, are very common. Parasites, yellow,
have appeared but are still rare.
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Hosts, are now rare because parasites have become
very common. Immune hosts, blue, have appeared
but are rare.
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Immune hosts are increasing in frequency,
separating the parasites into the top of memory.
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Immune hosts now dominate memory, while
parasites and susceptible hosts decline in
frequency. The parasites will soon be driven to
extinction.
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Experiments (Simulations)

• Changing parameters
• Mutation rate
• Selection for small/large cells
• Exploring the ecology in controlled environment
• Run two competing cells without mutation
• Run a fixed population of cells
• Micro/macro scales

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Discussion
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Emergence

• Cariani defined emergence relative to the
  expected model as the state when the model no
  longer describes the system
• Emergence types
• Syntactic
• Semantic
• Pragmatic

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AL and Biology Theory
AL
experimental study test biological theories
suggest the model suggest the factors
Biology
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Biological Factors of Diversity

• Adaptation to biologic evolving environment vs.
  To physical environment
• Emergent fitness function
• Size, shape, distribution, fragmentation,
  heterogeneity

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Possible Extensions

• Predators
• Multi-cellular organs
• Introducing energy costs
• Separating genotype from phenotype

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Summary

• A framework for synthesis of life was presented
• Natural-like behavior was detected in the system
• This system opens the way for inter-disciplinary
  future research

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Resources

• The Tierra homepage - Thomas Ray
• www.hip.atr.co.jp/ray/tierra/tierra.html
• Mac Tierra - Simon Fraser
• www.santfe.edu/smfr/mactierra.html
• Core life - Erik de Neve
• www.xs4all.nl/alife/corelife.htm

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The END