Towards Robust Bio-Inspired Circuits: The Embryonics Approach

ÉCOLE POLYTECHNIQUEFÉDÉRALE DE LAUSANNE

Daniel MangeDaniel Mange

Towards Robust Bio-Inspired Circuits:Towards Robust Bio-Inspired Circuits: The Embryonics Approach The Embryonics Approach

ECAL’99, LausanneECAL’99, Lausanne

September 15, 1999September 15, 1999

Towards Robust Bio-Inspired Circuits: The Embryonics ApproachTowards Robust Bio-Inspired Circuits: The Embryonics ApproachDaniel MangeDaniel Mange ECAL’99: Sept. 15ECAL’99: Sept. 15


Caenorhabditis ElegansCaenorhabditis Elegans

11 December 1998



Caenorhabditis ElegansCaenorhabditis Elegans

From S.F. Gilbert, Developmental Biology, Sinauer, 1991



Multicellular OrganizationMulticellular Organization

959 somatic cells



Cellular DivisionCellular Division

mother celldaughter celldaughter cell



Cellular DifferentiationCellular Differentiation

Pharynx

Intestine



Embryonics: Why?Embryonics: Why?

Design of robust integrated circuits Design of robust integrated circuits able to:able to:

• • self-repair (healing)self-repair (healing)

• • self-replicate (cloning)self-replicate (cloning)



Embryonics: How?Embryonics: How?

Iterative electronic circuit based on Iterative electronic circuit based on 3 features:3 features:

• • multicellular organizationmulticellular organization

• • cellular divisioncellular division

• cellular differentiation



Electronic ImplementationElectronic Implementation

X,YRBDMRAMOGSBCELLX,YRBDMRAMOGSBCELLX,YRBDMRAMOGSBCELLX,YRBDMRAMOGSBCELLX,YRBDMRAMOGSBCELLX,YRBDMRAMOGSBCELL



Multicellular OrganizationMulticellular Organization

O R GCELLgeneACEBDF21123YX



Embryonics LandscapeEmbryonics LandscapeMUXCOMPMUXdMOLCODEMOLECULEORGORGORGORG Population level

(population = Σ )organisms Organismic level

( = organism Σ )cells Cellular level

( = cell Σ )molecules Molecular level

( )basic FPGA's elementcbadefACEBDF : RG ribosomic genome: PG polymerase genome: OG operative genomeORGCELL



StopWatchStopWatch

MINSECRESETSTARTSTOP



StopWatchStopWatch

MINSECMINSEC



StopWatchStopWatch

StopWatchORGCELLgene1123YXCountmod 6Countmod10Countmod 6Countmod104



StopWatchStopWatch

6106101234OG: operative genomegene



StopWatchStopWatch

X = (WX+1) mod 4case of X: X = 1: Countmod 6 (10 minutes) X = 2: Countmod 10 (minutes) X = 3: Countmod 6 (10 seconds) X = 4: Countmod 10 (seconds)

OG: operative genome



StopWatchStopWatch

X=(WX+1)mod4case of X:X = ...operativegenome (OG)HOXgenesswitchgenesfunctionalgenes



Cellular DifferentiationCellular Differentiation

6106101234X = 1610610123461061012346106101234210t136t2104t3



Self-ReplicationSelf-Replication1YX61061061061061061061061016106106106106106106106101YX610610610610610610610610t112610610610610610610610610t111YX610610610610610610610610t1t2123610610610610610610610610t2t111YX610610610610610610610610t1t2t3MOTHER ORG1234610610610610610610610610t2t3t11



Self-ReplicationSelf-Replication1YXt1t2t3MOTHER ORGt412341t2t3t4t1DAUGHTER ORG # 116106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106101YXt1t2t3MOTHER ORGt5t4123412t2t3t4t5t1DAUGHTER ORG # 116106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106101YXt1t2t3MOTHER ORGt5t6t41234123t2t3t4t6t5t1DAUGHTER ORG # 116106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106101YXt1t2t3MOTHER ORGt5t6t7t4DAUGHTER ORG # 212341234t2t3t4t6t7t5t1DAUGHTER ORG # 116106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106106101YXt1t2t3MOTHER ORGt5t6t7t4DAUGHTER ORG # 212341234t2t3t4t6t7t8t5t1DAUGHTER ORG # 1DAUGHTER ORG # 31Directions of self-replication610610610610610610610610610610610610610610610610610610610610610610610610610610610610610610610610



Self-RepairSelf-Repair

1YX610610610610610610610610ORIGINAL ORG610610610610123412SPARE CELLSDirection of self-repair1YX61061061061061061061061012412KILL=1SCAR106106101YX610610610610610610610610123KILL=1SCAR106106101YX6106106106106106106106101234KILL=1NEW ORGNEW ORGSCAR106106101YX61061061061061061061061012341KILL=1NEW ORGNEW ORGSCARSPARE CELL10610610



BioWatchBioWatch

1123YXmod3mod10/4mod6mod104mod6mod1056Modulo-24 counterStopWatch



BioWatchBioWatch



Embryonics LandscapeEmbryonics Landscape

ORG = StopWatchCELLMOLECULEPopulation level(population = Σ )organisms

Organismic level( = organism Σ )cells

???Cellular level( = cell Σ )molecules

???Molecular level( )basic FPGA's element

106106ORGORGORGORG



MUXTREE MoleculeMUXTREE Molecule



Space DividerSpace Divider

PGX=1



Space DividerSpace Divider

PGPG2X=134SPARE CELL



Cellular Self-ReplicationCellular Self-Replication

RG+OG234X=1SPARECELL



Cellular Self-RepairCellular Self-Repair

RG+OG234X=1SPARECELL

faulty molecule



Cellular Self-RepairCellular Self-Repair

RG+OG234X=1SPARECELL3 4KILL=1



The MUXTREE MoleculeThe MUXTREE Molecule



Molecular ImplementationMolecular ImplementationSMEMREGQDCNTGATESMUXDMUXREGXspare column



Embryonics LandscapeEmbryonics Landscape

MUXCOMPMUXMOLCODEORG = StopWatchCELLMOLECULEPopulation level(population = Σ )organisms

Organismic level( = organism Σ )cells

Cellular level( = cell Σ )molecules

Molecular level( )basic FPGA's element

106106ORGORGORGORGSBDMSMEMPG+RG OG



Artificial GenomeArtificial Genome

X=(WX+1)mod4case of X:X = ...operativegenome (OG)HOXgenesswitchgenesfunctionalgenesmolecular codesspace divider programming datapolymerasegenome (PG)ribosomicgenome (RG)



The Future of EmbryonicsThe Future of Embryonics

Towards Robust Bio-Inspired Circuits: The Embryonics Approach

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