eyeling 1.22.6 → 1.22.8

package/examples/act-barley-seed-lineage.n3

@@ -0,0 +1,565 @@
+# ========================================================================
+# ACT barley seed lineage — "can and can't"
+#
+# This is a constructor-theory-of-life example with both:
+#   - CAN  : tasks that are possible for a viable lineage
+#   - CAN'T: tasks that are impossible for contrast lineages
+#
+# The positive lineage:
+#   mainLine
+#
+# The contrast lineages:
+#   analogLine   - hereditary information is not digitally instantiated
+#   fragileLine  - there is no repair support
+#   coatlessLine - there is no protected dormant stage
+#   staticLine   - there is no heritable variation
+#
+# The point is to show not only what a successful lineage can do, but also
+# what other lineages cannot do under explicitly stated conditions.
+# ========================================================================
+
+@prefix : <http://example.org/act/barley/cancant/> .
+@prefix arc: <https://example.org/arc#> .
+@prefix log: <http://www.w3.org/2000/10/swap/log#> .
+
+:case a arc:Case ;
+  arc:question "Can a barley seed lineage achieve accurate self-reproduction, dormancy, development, and adaptive persistence under no-design laws — and what exactly can't happen when key ingredients are missing?" .
+
+# ------------------------
+# Shared world assumptions
+# -------------------------
+
+# The background law-like assumption used in constructor theory of life.
+:world :obeys :NoDesignLaws .
+
+# Digital hereditary medium for viable lineages.
+:dnaRegister a :DigitalInformationMedium .
+
+# A contrasting non-digital hereditary medium.
+:analogRegister a :NonDigitalInformationMedium .
+
+# Shared developmental and environmental resources.
+:zygote a :DevelopmentalBottleneck .
+
+:greenhouse a :GrowthEnvironment ;
+  :condition :WarmthAvailable ;
+  :condition :MoistureAvailable ;
+  :condition :LightAvailable .
+
+:nutrientBed a :RawMaterialSupply .
+:pollinationLoop a :ReproductionSupport .
+:mutationSource a :VariationSource .
+
+:salineBench a :SelectionEnvironment ;
+  :favours :SaltTolerant .
+
+# ---------------------
+# 1. The viable lineage
+# ---------------------
+
+# The hereditary information is digitally instantiated.
+:mainGenome a :Replicator ;
+  :accuracy :High ;
+  :storedIn :dnaRegister ;
+  :variant :SaltTolerant .
+
+# Repair support is present.
+:mainRepair a :RepairVehicle .
+
+# Embryo-side vehicle functions.
+:mainEmbryoVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :CopyingSupport ;
+  :function :CompartmentControl ;
+  :usesRepair :mainRepair .
+
+# Adult-side vehicle functions.
+:mainAdultVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :GameteProduction ;
+  :function :SeedConstruction .
+
+# Protected dormant stage.
+:mainSeedCoat a :Compartment ;
+  :function :DormancyProtection .
+
+:mainSeed a :Organism ;
+  :lifeStage :DormantSeed ;
+  :hasReplicator :mainGenome ;
+  :hasVehicle :mainEmbryoVehicle ;
+  :hasCompartment :mainSeedCoat .
+
+# Adult stage.
+:mainAdult a :Organism ;
+  :lifeStage :AdultPlant ;
+  :hasReplicator :mainGenome ;
+  :hasVehicle :mainAdultVehicle .
+
+# The lineage object ties stages together.
+:mainLine a :Lineage ;
+  :seedStage :mainSeed ;
+  :adultStage :mainAdult ;
+  :replicator :mainGenome ;
+  :variant :SaltTolerant ;
+  :variationStatus :Present .
+
+# ----------------------------------------------
+# 2. Contrast lineages used for the "can't" side
+# ----------------------------------------------
+
+# ----------------------------------------------------------------
+# 2a. analogLine
+#     Same broad biological pattern, but heredity is not digital.
+#     This is the line that cannot achieve accurate genome copying
+#     under no-design laws.
+# ----------------------------------------------------------------
+
+:analogGenome a :Replicator ;
+  :accuracy :High ;
+  :storedIn :analogRegister ;
+  :variant :SaltTolerant .
+
+:analogRepair a :RepairVehicle .
+
+:analogEmbryoVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :CopyingSupport ;
+  :usesRepair :analogRepair .
+
+:analogAdultVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :GameteProduction ;
+  :function :SeedConstruction .
+
+:analogSeedCoat a :Compartment ;
+  :function :DormancyProtection .
+
+:analogSeed a :Organism ;
+  :lifeStage :DormantSeed ;
+  :hasReplicator :analogGenome ;
+  :hasVehicle :analogEmbryoVehicle ;
+  :hasCompartment :analogSeedCoat .
+
+:analogAdult a :Organism ;
+  :lifeStage :AdultPlant ;
+  :hasReplicator :analogGenome ;
+  :hasVehicle :analogAdultVehicle .
+
+:analogLine a :Lineage ;
+  :seedStage :analogSeed ;
+  :adultStage :analogAdult ;
+  :replicator :analogGenome ;
+  :variant :SaltTolerant ;
+  :variationStatus :Present .
+
+# ----------------------------------------------------------------
+# 2b. fragileLine
+#     Heredity is digital, but there is no repair support.
+#     This line cannot achieve reliable damage correction and thus
+#     cannot achieve accurate self-reproduction.
+# ----------------------------------------------------------------
+
+:fragileGenome a :Replicator ;
+  :accuracy :High ;
+  :storedIn :dnaRegister ;
+  :variant :SaltTolerant .
+
+:fragileEmbryoVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :CopyingSupport .
+
+:fragileAdultVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :GameteProduction ;
+  :function :SeedConstruction .
+
+:fragileSeedCoat a :Compartment ;
+  :function :DormancyProtection .
+
+:fragileSeed a :Organism ;
+  :lifeStage :DormantSeed ;
+  :hasReplicator :fragileGenome ;
+  :hasVehicle :fragileEmbryoVehicle ;
+  :hasCompartment :fragileSeedCoat .
+
+:fragileAdult a :Organism ;
+  :lifeStage :AdultPlant ;
+  :hasReplicator :fragileGenome ;
+  :hasVehicle :fragileAdultVehicle .
+
+:fragileLine a :Lineage ;
+  :seedStage :fragileSeed ;
+  :adultStage :fragileAdult ;
+  :replicator :fragileGenome ;
+  :variant :SaltTolerant ;
+  :variationStatus :Present ;
+  :lacksRepair true .
+
+# -------------------------------------------------------------------
+# 2c. coatlessLine
+#     Heredity is digital and repair exists, but the dormant seed
+#     lacks a protective compartment. This line cannot achieve
+#     protected dormancy and therefore cannot achieve lineage closure
+#     through a protected seed phase.
+# -------------------------------------------------------------------
+
+:coatlessGenome a :Replicator ;
+  :accuracy :High ;
+  :storedIn :dnaRegister ;
+  :variant :SaltTolerant .
+
+:coatlessRepair a :RepairVehicle .
+
+:coatlessEmbryoVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :CopyingSupport ;
+  :usesRepair :coatlessRepair .
+
+:coatlessAdultVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :GameteProduction ;
+  :function :SeedConstruction .
+
+:coatlessSeed a :Organism ;
+  :lifeStage :DormantSeed ;
+  :hasReplicator :coatlessGenome ;
+  :hasVehicle :coatlessEmbryoVehicle .
+
+:coatlessAdult a :Organism ;
+  :lifeStage :AdultPlant ;
+  :hasReplicator :coatlessGenome ;
+  :hasVehicle :coatlessAdultVehicle .
+
+:coatlessLine a :Lineage ;
+  :seedStage :coatlessSeed ;
+  :adultStage :coatlessAdult ;
+  :replicator :coatlessGenome ;
+  :variant :SaltTolerant ;
+  :variationStatus :Present ;
+  :lacksDormancyProtection true .
+
+# ------------------------------------------------------------------
+# 2d. staticLine
+#     Heredity is digital, repair exists, and dormancy is protected,
+#     but there is no heritable variation. This line cannot be an
+#     adaptively evolving lineage.
+# ------------------------------------------------------------------
+
+:staticGenome a :Replicator ;
+  :accuracy :High ;
+  :storedIn :dnaRegister ;
+  :variant :SaltTolerant .
+
+:staticRepair a :RepairVehicle .
+
+:staticEmbryoVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :CopyingSupport ;
+  :usesRepair :staticRepair .
+
+:staticAdultVehicle a :Vehicle ;
+  :function :Metabolism ;
+  :function :Development ;
+  :function :GameteProduction ;
+  :function :SeedConstruction .
+
+:staticSeedCoat a :Compartment ;
+  :function :DormancyProtection .
+
+:staticSeed a :Organism ;
+  :lifeStage :DormantSeed ;
+  :hasReplicator :staticGenome ;
+  :hasVehicle :staticEmbryoVehicle ;
+  :hasCompartment :staticSeedCoat .
+
+:staticAdult a :Organism ;
+  :lifeStage :AdultPlant ;
+  :hasReplicator :staticGenome ;
+  :hasVehicle :staticAdultVehicle .
+
+:staticLine a :Lineage ;
+  :seedStage :staticSeed ;
+  :adultStage :staticAdult ;
+  :replicator :staticGenome ;
+  :variant :SaltTolerant ;
+  :variationStatus :None .
+
+# ------------------------------------
+# 3. CAN rules — what a lineage can do
+# ------------------------------------
+
+# If hereditary information is digital and no-design laws
+# hold, accurate genome copying is possible in principle.
+{ :world :obeys :NoDesignLaws .
+  ?Genome a :Replicator ;
+          :storedIn ?Medium .
+  ?Medium a :DigitalInformationMedium . }
+=>
+{ ?Genome :can :GenomeCopyUnderNoDesignLaws . } .
+
+# A protected seed compartment makes protected dormancy
+# possible for that seed stage.
+{ ?Seed a :Organism ;
+        :lifeStage :DormantSeed ;
+        :hasCompartment ?Compartment .
+  ?Compartment :function :DormancyProtection . }
+=>
+{ ?Seed :can :ProtectedDormancy . } .
+
+# Germination needs a dormant seed plus warmth, moisture,
+# and raw materials.
+{ ?Seed a :Organism ;
+        :lifeStage :DormantSeed .
+  :greenhouse :condition :WarmthAvailable .
+  :greenhouse :condition :MoistureAvailable .
+  :nutrientBed a :RawMaterialSupply . }
+=>
+{ ?Seed :can :Germinate . } .
+
+# Adult propagule production needs adult-stage vehicle
+# functions plus pollination support and light.
+{ ?Adult a :Organism ;
+         :lifeStage :AdultPlant ;
+         :hasVehicle ?Vehicle .
+  ?Vehicle :function :GameteProduction .
+  ?Vehicle :function :SeedConstruction .
+  :pollinationLoop a :ReproductionSupport .
+  :greenhouse :condition :LightAvailable . }
+=>
+{ ?Adult :can :PropaguleProduction . } .
+
+# Accurate self-reproduction needs:
+# - genome copying under no-design laws
+# - repair support
+# - a developmental bottleneck
+{ ?Line a :Lineage ;
+        :seedStage ?Seed ;
+        :replicator ?Genome .
+  ?Genome :can :GenomeCopyUnderNoDesignLaws .
+  ?Seed :hasVehicle ?Vehicle .
+  ?Vehicle :usesRepair ?Repair .
+  ?Repair a :RepairVehicle .
+  :zygote a :DevelopmentalBottleneck . }
+=>
+{ ?Line :can :AccurateSelfReproduction . } .
+
+# Lineage closure needs:
+# - protected dormancy at the seed stage
+# - germination from the seed stage
+# - propagule production at the adult stage
+{ ?Line a :Lineage ;
+        :seedStage ?Seed ;
+        :adultStage ?Adult .
+  ?Seed :can :ProtectedDormancy .
+  ?Seed :can :Germinate .
+  ?Adult :can :PropaguleProduction . }
+=>
+{ ?Line :can :LineageClosure . } .
+
+# Heritable variation is possible when the lineage is not
+# static with respect to variants.
+{ ?Line a :Lineage ;
+        :variationStatus :Present . }
+=>
+{ ?Line :can :HeritableVariation . } .
+
+# Adaptive persistence needs:
+# - accurate self-reproduction
+# - heritable variation
+# - a matching selection environment
+{ ?Line a :Lineage ;
+        :variant ?Variant .
+  ?Line :can :AccurateSelfReproduction .
+  ?Line :can :HeritableVariation .
+  :salineBench :favours ?Variant . }
+=>
+{ ?Line :can :AdaptivePersistence . } .
+
+# A lineage is evolvable when it closes its life cycle and
+# can adaptively persist.
+{ ?Line :can :LineageClosure .
+  ?Line :can :AdaptivePersistence . }
+=>
+{ ?Line a :EvolvableLineage . } .
+
+# --------------------------------------------------------------------
+# 4. CAN'T rules — what cannot happen when key ingredients are missing
+# --------------------------------------------------------------------
+
+# No digital hereditary medium under no-design laws:
+# accurate genome copying cannot be achieved.
+{ :world :obeys :NoDesignLaws .
+  ?Genome a :Replicator ;
+          :storedIn ?Medium .
+  ?Medium a :NonDigitalInformationMedium . }
+=>
+{ ?Genome :cannot :AccurateGenomeCopyUnderNoDesignLaws . } .
+
+# If the genome cannot be accurately copied, the lineage
+# cannot achieve accurate self-reproduction.
+{ ?Line :replicator ?Genome .
+  ?Genome :cannot :AccurateGenomeCopyUnderNoDesignLaws . }
+=>
+{ ?Line :cannot :AccurateSelfReproduction . } .
+
+# No repair support:
+# reliable damage correction cannot be achieved.
+{ ?Line a :Lineage ;
+        :lacksRepair true . }
+=>
+{ ?Line :cannot :ReliableDamageCorrection . } .
+
+# If reliable damage correction cannot be achieved, then
+# accurate self-reproduction cannot be achieved.
+{ ?Line :cannot :ReliableDamageCorrection . }
+=>
+{ ?Line :cannot :AccurateSelfReproduction . } .
+
+# No protected dormant compartment:
+# protected dormancy cannot be achieved.
+{ ?Line a :Lineage ;
+        :lacksDormancyProtection true . }
+=>
+{ ?Line :cannot :ProtectedDormancy . } .
+
+# If protected dormancy cannot be achieved, lineage closure
+# through a protected seed phase cannot be achieved.
+{ ?Line :cannot :ProtectedDormancy . }
+=>
+{ ?Line :cannot :LineageClosure . } .
+
+# No heritable variation:
+# adaptive evolution cannot be achieved.
+{ ?Line a :Lineage ;
+        :variationStatus :None . }
+=>
+{ ?Line :cannot :AdaptiveEvolution . } .
+
+# If adaptive evolution cannot be achieved, adaptive
+# persistence cannot be achieved either.
+{ ?Line :cannot :AdaptiveEvolution . }
+=>
+{ ?Line :cannot :AdaptivePersistence . } .
+
+# If either accurate self-reproduction or adaptive
+# persistence is impossible, the lineage is not evolvable.
+{ ?Line :cannot :AccurateSelfReproduction . }
+=>
+{ ?Line :cannot :EvolvableLineage . } .
+
+{ ?Line :cannot :AdaptivePersistence . }
+=>
+{ ?Line :cannot :EvolvableLineage . } .
+
+{ ?Line :cannot :LineageClosure . }
+=>
+{ ?Line :cannot :EvolvableLineage . } .
+
+# ---------
+# 5. Checks
+# ---------
+
+# Positive checks for the viable lineage.
+{ :world :obeys :NoDesignLaws . }
+=> { :case :checkC1 :Passed . } .
+
+{ :mainGenome :can :GenomeCopyUnderNoDesignLaws . }
+=> { :case :checkC2 :Passed . } .
+
+{ :mainSeed :can :ProtectedDormancy . }
+=> { :case :checkC3 :Passed . } .
+
+{ :mainSeed :can :Germinate . }
+=> { :case :checkC4 :Passed . } .
+
+{ :mainAdult :can :PropaguleProduction . }
+=> { :case :checkC5 :Passed . } .
+
+{ :mainLine :can :AccurateSelfReproduction . }
+=> { :case :checkC6 :Passed . } .
+
+{ :mainLine :can :LineageClosure . }
+=> { :case :checkC7 :Passed . } .
+
+{ :mainLine :can :HeritableVariation . }
+=> { :case :checkC8 :Passed . } .
+
+{ :mainLine :can :AdaptivePersistence . }
+=> { :case :checkC9 :Passed . } .
+
+{ :mainLine a :EvolvableLineage . }
+=> { :case :checkC10 :Passed . } .
+
+# Negative checks for the contrast lineages.
+{ :analogLine :cannot :AccurateSelfReproduction . }
+=> { :case :checkC11 :Passed . } .
+
+{ :fragileLine :cannot :AccurateSelfReproduction . }
+=> { :case :checkC12 :Passed . } .
+
+{ :coatlessLine :cannot :LineageClosure . }
+=> { :case :checkC13 :Passed . } .
+
+{ :staticLine :cannot :AdaptiveEvolution . }
+=> { :case :checkC14 :Passed . } .
+
+{ :staticLine :cannot :EvolvableLineage . }
+=> { :case :checkC15 :Passed . } .
+
+# -------------------
+# 6. ARC-style output
+# -------------------
+
+{ :case :checkC1 :Passed .
+  :case :checkC2 :Passed .
+  :case :checkC3 :Passed .
+  :case :checkC4 :Passed .
+  :case :checkC5 :Passed .
+  :case :checkC6 :Passed .
+  :case :checkC7 :Passed .
+  :case :checkC8 :Passed .
+  :case :checkC9 :Passed .
+  :case :checkC10 :Passed .
+  :case :checkC11 :Passed .
+  :case :checkC12 :Passed .
+  :case :checkC13 :Passed .
+  :case :checkC14 :Passed .
+  :case :checkC15 :Passed . }
+=>
+{
+  :out log:outputString """ACT barley seed lineage — can and can't
+
+Answer
+YES for the viable barley lineage.
+NO for the contrast lineages when digital heredity, repair, protected dormancy, or heritable variation are missing.
+
+Reason Why
+The main lineage can achieve genome copying under no-design laws because its hereditary information is digitally instantiated. It can also pass through protected dormancy, germinate, produce propagules, reproduce accurately, close its life cycle, and adaptively persist under saline selection. But the contrast lineages show the "can't" side: non-digital heredity blocks accurate genome copying under no-design laws, lack of repair blocks accurate self-reproduction, lack of dormancy protection blocks lineage closure through a protected seed phase, and lack of heritable variation blocks adaptive evolution and thus blocks evolvability.
+
+Check
+C1  OK - no-design laws are assumed
+C2  OK - the viable genome can be copied under no-design laws
+C3  OK - the viable seed can achieve protected dormancy
+C4  OK - the viable seed can germinate
+C5  OK - the viable adult can produce propagules
+C6  OK - the viable lineage can achieve accurate self-reproduction
+C7  OK - the viable lineage can achieve lineage closure
+C8  OK - the viable lineage can exhibit heritable variation
+C9  OK - the viable lineage can adaptively persist
+C10 OK - the viable lineage is evolvable
+C11 OK - the non-digital lineage cannot achieve accurate self-reproduction
+C12 OK - the repair-deficient lineage cannot achieve accurate self-reproduction
+C13 OK - the coatless lineage cannot achieve lineage closure through protected dormancy
+C14 OK - the static lineage cannot achieve adaptive evolution
+C15 OK - the static lineage cannot be an evolvable lineage
+""" .
+} .