Biology, Genetics and Ecology:

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Lecture 10

• Biology, Genetics and Ecology
• Echoing the emergence

In the beginning was simplicity. Richard
Dawkins There is only one constant - change
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Simple Evolution Algorithm

• do foreverintroduce new members into Population
• allow mutations
• allow reproduction foreach member of
  Population if ( fitness( member ) lt threshold )
  then kill( member ) end
• end

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Evolution as repetitive game
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Fitness Landscapes
Spices are forever trying to find comfortable
places on the fitness landscape
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First Newtons Law for Species

• There exist inertial systems, where all objects
  will remain at rest or move uniformly, unless
  there is an external force that acts on them.

This is true for living beings as well! The
difference is that there is always pressure to
change coming from the environment, so they are
never at rest!
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Co-evolution via Feedback
Dynamics of Frogs and Flies
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Pressure results in innovation
Species force each other to climb the fitness
landscapes by competing for energy
Possibilities for evolution
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Diversity fuels Natural Selection

• Diversity
• Natural Selection
• Replication
• form everlasting feedback loop

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Punctuated Equilibrium

• How do the changes take place?
• They accumulate over time, just as Darwin
  originally outlined, but
• Then, as in any complex systems, there are phase
  transitions - events which correspond to
  transformations of Quantitative changes into
  Qualitative

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Evolution and Optimality

• Does Evolution have a goal of breeding better
  species? No.
• Evolution is blind, it really has no goal
• Do better species arise in the process of
  evolution? Yes!
• How? Through the iterative exploration of
  possibilities

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Evolution and Information

• How do species capture what they learn in the
  game of Evolution? GENES!

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The Language of Genetics

• Mutation, Clone, Crossover

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Mutation and Peak Exploration
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Crossover
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Selfish Gene - Gene Dynamic
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Symbiotic Cell
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Santa Fe Institute

• Formed in 1985
• Think tank to deal with complexity
• Scientists from all areas including physics,
  chemistry, biology, computer science, economics,
  ecology, sociology, history, etc.
• http//www.santafe.edu

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The Flow

• Dynamical systems
• We find ourselves among ever-changing systems
• There is an intractable number of branches
• Feedback
• Systems change and develop by receiving feedback
• from the environment and responding to
  environment.
• Thus systems are inextricable parts of the
  environment
• Self-reference
• The systems around us are heavily recursive,
• self-bootstrapping
• Co-evolution
• There is no stand alone evolution, everything is
• co-evolving. Everything is dependent and
  influences
• everything else.

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Cybernetics

• Norbert Wiener
• Trying to understand how control
• communication worked
• Greek kybernetes (steersman) (Web of life pp..
  97)
• We are but whirlpools in a river of ever-flowing
  water
• Self-regulation
• We are not stuff that abides, but patterns that
  perpetuate themselves

Situation Assessment
Action
Impact on environment
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Open Systems

• Second law of thermodynamics
• In closed system, the amount of entropy in a
  given system does not decrease
• Entropy means disorder
• Living organisms and equilibrium
• Living beings are in order, away from equilibrium
• Open thermodynamical systems
• Nonlinear equations
• Self-Organization

Equilibrium (ice)
Order (edge of chaos)
Chaos (gas)
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Seven basic elements of CAS

• Aggregation
• Economy and markets
• Body and nervous, immune, endocrine system
• World economy and country economies
• Emergence as a result of interactions
• whole gt sum of the parts
• higher level of organization
• meta agents

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Seven basic elements of CAS

• Tagging (mechanism)
• Identification of alike agents
• Grouping
• Attribute
• contracts between firms
• form of adaptation - delegation
• Divisions in a firm Equities, Fixed Income, etc.
• collaboration, formation of aggregate and
• diversification via tagging

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Seven basic elements of CAS

• Nonlinearity (property)
• aggregation tagging
• threshold of emergence (H gtsum(P))
• predator/prey interaction
• nonlinearity is a result of a product instead
• of a sum

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Seven basic elements of CAS

• Flow (property)
• nonlinearity induces flow
• multiplier effect
• feedback and cycles

Dead
Alive
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Seven basic elements of CAS

• Diversity (property)
• arise from exploration of multitude of
• possibilities (local adaptations)
• firms enter and leave market
• mimicry

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Seven basic elements of CAS

• Internal models (mechanism)
• anticipation
• survival of the fittest
• subconscious mode

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Seven basic elements of CAS

• Building blocks (mechanism)
• decomposition
• quark, nucleon, atom, molecule, organelle, cell
• generation of internal models

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Eworld Parameters
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Eworld Resources

• ltRESOURCE CLASSedu.nyu.sejava.iskold.eworld.Homog
  eneousResourcegt
• ltPROPERTY NAMEQuantity VALUE25gt
• ltPROPERTY NAMEBase VALUEagt
• ltPROPERTY NAMERenewable VALUEtruegt
• lt/RESOURCEgt

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Genome of Entities

• - Reservoir (place where excess resources are
  stored)
• - 3 PhenoGenes (externally visible)
• - OffenseGene
• - Defense Gene
• - Mating Gene
• - 3 Rule Genes (internal only)
• - CombatConditionGene
• - TradeConditionGene
• - MatingConditionGene
• - Resource collection gene
• - Trading resource base

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Entity Generators

• ltGENERATOR CLASSedu.nyu.sejava.iskold.eworld.Bas
  icRandomEntityGeneratorgt
• ltPROPERTY NAMEQuantity VALUE25gt
• lt/RESOURCEgt
• ltGENERATOR CLASSedu.nyu.sejava.iskold.eworld.Basi
  cConstrainedEntityGeneratorgt
• ltPROPERTY NAMEQuantity VALUE25gt
• ltPROPERTY NAMEOffenseGeneLength VALUE5gt
• ltPROPERTY NAMEOffenseGeneBases VALUEATgt
• lt/RESOURCEgt

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Entity near Resource

• - Is this resource empty?
• - Does my Resource Collection Gene allow me to
  pick up next base from this resource?

C
NOPE, NO MATCH
NEXT BASE IN SOME RESOURCE
A T G
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Cloning

• - Does my Reservoir contain
• enough bases to clone myself?
• Cloning threshold is at least 1

Offense ACG Defense AAA Mating CGT Combat
Condition AAGT Trade Condition GGG Mating
Condition CG Resource collection AG Trading
resource A
RESERVOIR CONTAINS TWICE THE GENOME
16 A 4 T 6 C 16 G
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Mortality

• - In the end of every round kill entities at
  random
• - The longer entity lives the higher its chance
  of
• dying

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Statistics
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Some book references

• Complexity,
• by M. Mitchell Waldrop
• At Home in the Universe,
• by Stuart Kauffman
• Web Of Life,
• by Frijof Capra
• The Blind Watchmaker,
• by Richard Dawkins