eyeling 1.22.14 → 1.22.16

package/examples/control-system-becoming.n3

@@ -0,0 +1,203 @@
+# ===============================================================
+# This small Notation3 program models controller design as a
+# process of engineering becoming. A controller revision does not
+# arise from nothing: it inherits validated performance from an
+# earlier design, responds to a new control objective, selects a
+# compatible strategy, and integrates that strategy into a new
+# concrete controller. Once validated, the controller becomes a
+# new approved baseline for future tuning and extension.
+# ===============================================================
+
+@prefix : <http://example.org/control#>.
+
+# ----------
+# CATEGORIES
+# ----------
+
+:ControllerRevision a :Category.
+:Requirement        a :Category.
+:DesignGoal         a :Category.
+:ControlStrategy    a :Category.
+
+# ------------
+# REQUIREMENTS
+# ------------
+
+:stabilityReq             a :Requirement.
+:trackingReq              a :Requirement.
+:overshootReq             a :Requirement.
+:disturbanceRejectionReq  a :Requirement.
+
+# ------------
+# DESIGN GOALS
+# ------------
+
+:reduceOvershoot  a :DesignGoal.
+:rejectDisturbance a :DesignGoal.
+
+:reduceOvershoot  :suggests :leadCompensator;
+                  :introducesRequirement :overshootReq.
+
+:rejectDisturbance :suggests :integralAction;
+                   :introducesRequirement :disturbanceRejectionReq.
+
+# ------------------
+# CONTROL STRATEGIES
+# ------------------
+
+:leadCompensator a :ControlStrategy.
+:integralAction  a :ControlStrategy.
+
+# Strategy compatibility with inherited requirements
+:leadCompensator :compatibleWith :stabilityReq, :trackingReq;
+                 :enables :overshootReq.
+
+:integralAction  :compatibleWith :stabilityReq, :trackingReq, :overshootReq;
+                 :enables :disturbanceRejectionReq.
+
+# --------------------------
+# INITIAL CONTROLLER HISTORY
+# --------------------------
+
+:c1 a :ControllerRevision;
+    :time 1;
+    :satisfies :stabilityReq, :trackingReq;
+    :realizes :baselinePID;
+    :achieves :approvedController.
+
+:c2 a :ControllerRevision;
+    :time 2;
+    :derivesFrom :c1;
+    :designGoal :reduceOvershoot.
+
+:c3 a :ControllerRevision;
+    :time 3;
+    :derivesFrom :c2;
+    :designGoal :rejectDisturbance.
+
+# ---------------------------------------------------------
+# RULE 1
+# A NEW REVISION INHERITS PREVIOUSLY SATISFIED REQUIREMENTS
+# ---------------------------------------------------------
+
+{
+  ?later :derivesFrom ?earlier.
+  ?earlier :satisfies ?req.
+}
+=>
+{
+  ?later :inheritsRequirement ?req.
+}.
+
+# ------------------------------------------------
+# RULE 2
+# A DESIGN GOAL OPENS A CANDIDATE CONTROL STRATEGY
+# ------------------------------------------------
+
+{
+  ?ctrl :designGoal ?goal.
+  ?goal :suggests ?strategy.
+}
+=>
+{
+  ?ctrl :considers ?strategy.
+}.
+
+# ------------------------------------------------------
+# RULE 3
+# A DESIGN GOAL ALSO INTRODUCES A NEW TARGET REQUIREMENT
+# ------------------------------------------------------
+
+{
+  ?ctrl :designGoal ?goal.
+  ?goal :introducesRequirement ?req.
+}
+=>
+{
+  ?ctrl :targets ?req.
+}.
+
+# ------------------------------------------------------
+# RULE 4
+# A COMPATIBLE STRATEGY PRESERVES INHERITED REQUIREMENTS
+# ------------------------------------------------------
+
+{
+  ?ctrl :inheritsRequirement ?req.
+  ?ctrl :considers ?strategy.
+  ?strategy :compatibleWith ?req.
+}
+=>
+{
+  ?ctrl :preserves ?req;
+        :integrates ?strategy.
+}.
+
+# ---------------------------------------------------------
+# RULE 5
+# A STRATEGY CAN ALSO ENABLE THE NEWLY TARGETED REQUIREMENT
+# ---------------------------------------------------------
+
+{
+  ?ctrl :targets ?req.
+  ?ctrl :considers ?strategy.
+  ?strategy :enables ?req.
+}
+=>
+{
+  ?ctrl :satisfies ?req;
+        :integrates ?strategy.
+}.
+
+# ------------------------------------
+# RULE 6
+# WHAT IS PRESERVED IS SATISFIED AGAIN
+# ------------------------------------
+
+{
+  ?ctrl :preserves ?req.
+}
+=>
+{
+  ?ctrl :satisfies ?req.
+}.
+
+# --------------------------------------------------------------
+# RULE 7
+# AN INTEGRATED STRATEGY BECOMES PART OF THE REALIZED CONTROLLER
+# --------------------------------------------------------------
+
+{
+  ?ctrl :integrates ?strategy.
+}
+=>
+{
+  ?ctrl :realizes ?strategy.
+}.
+
+# ------------------------------------------------------------------
+# RULE 8
+# A CONTROLLER THAT REALIZES A STRATEGY BECOMES AN APPROVED BASELINE
+# ------------------------------------------------------------------
+
+{
+  ?ctrl :realizes ?strategy.
+}
+=>
+{
+  ?ctrl :achieves :approvedController;
+        :availableForFutureTuning :yes.
+}.
+
+# --------------------------------------------------------
+# RULE 9
+# APPROVED CONTROLLERS ARE AVAILABLE FOR FURTHER ITERATION
+# --------------------------------------------------------
+
+{
+  ?ctrl :achieves :approvedController.
+}
+=>
+{
+  ?ctrl :status :approvedController.
+}.

package/examples/developmental-genetics-becoming.n3

@@ -0,0 +1,204 @@
+# ================================================================
+# This small Notation3 program models developmental genetics as a
+# process of becoming. A cell state does not arise from nothing:
+# it inherits an expression pattern from an earlier lineage state,
+# responds to a developmental signal, activates a compatible
+# regulatory program, and stabilizes into a new differentiated
+# form. Once stabilized, that state becomes available for further
+# developmental transition. The logic below is therefore a logic
+# of lineage, inheritance, activation, and differentiation.
+# ================================================================
+
+@prefix : <http://example.org/genetics#>.
+
+# ----------
+# CATEGORIES
+# ----------
+
+:CellState         a :Category.
+:GeneMarker        a :Category.
+:Signal            a :Category.
+:RegulatoryProgram a :Category.
+
+# ------------
+# GENE MARKERS
+# ------------
+
+:Sox2    a :GeneMarker.
+:Pax6    a :GeneMarker.
+:NeuroD1 a :GeneMarker.
+:Tubb3   a :GeneMarker.
+
+# ---------------------
+# DEVELOPMENTAL SIGNALS
+# ---------------------
+
+:neurogenicSignal a :Signal.
+:maturationSignal a :Signal.
+
+:neurogenicSignal :suggests :proneuralProgram;
+                  :introducesMarker :NeuroD1.
+
+:maturationSignal :suggests :neuronalMaturationProgram;
+                  :introducesMarker :Tubb3.
+
+# -------------------
+# REGULATORY PROGRAMS
+# -------------------
+
+:proneuralProgram a :RegulatoryProgram.
+:neuronalMaturationProgram a :RegulatoryProgram.
+
+# A compatible program can preserve inherited markers
+# and enable a new marker of differentiation
+:proneuralProgram :compatibleWith :Sox2, :Pax6;
+                  :enables :NeuroD1.
+
+:neuronalMaturationProgram :compatibleWith :Pax6, :NeuroD1;
+                           :enables :Tubb3.
+
+# -----------------------
+# INITIAL LINEAGE HISTORY
+# -----------------------
+
+:s1 a :CellState;
+    :time 1;
+    :expresses :Sox2, :Pax6;
+    :achieves :stableCellState.
+
+:s2 a :CellState;
+    :time 2;
+    :derivesFrom :s1;
+    :receives :neurogenicSignal.
+
+:s3 a :CellState;
+    :time 3;
+    :derivesFrom :s2;
+    :receives :maturationSignal.
+
+# -------------------------------------------
+# RULE 1
+# A NEW CELL STATE INHERITS EXPRESSED MARKERS
+# -------------------------------------------
+
+{
+  ?later :derivesFrom ?earlier.
+  ?earlier :expresses ?marker.
+}
+=>
+{
+  ?later :inheritsMarker ?marker.
+}.
+
+# ---------------------------------------------
+# RULE 2
+# A SIGNAL OPENS A CANDIDATE REGULATORY PROGRAM
+# ---------------------------------------------
+
+{
+  ?cell :receives ?signal.
+  ?signal :suggests ?program.
+}
+=>
+{
+  ?cell :considers ?program.
+}.
+
+# --------------------------------------------
+# RULE 3
+# A SIGNAL ALSO INTRODUCES A NEW TARGET MARKER
+# --------------------------------------------
+
+{
+  ?cell :receives ?signal.
+  ?signal :introducesMarker ?marker.
+}
+=>
+{
+  ?cell :targetsMarker ?marker.
+}.
+
+# ------------------------------------------------
+# RULE 4
+# A COMPATIBLE PROGRAM PRESERVES INHERITED MARKERS
+# ------------------------------------------------
+
+{
+  ?cell :inheritsMarker ?marker.
+  ?cell :considers ?program.
+  ?program :compatibleWith ?marker.
+}
+=>
+{
+  ?cell :preservesMarker ?marker;
+        :integrates ?program.
+}.
+
+# ----------------------------------------------
+# RULE 5
+# A PROGRAM CAN ENABLE THE NEWLY TARGETED MARKER
+# ----------------------------------------------
+
+{
+  ?cell :targetsMarker ?marker.
+  ?cell :considers ?program.
+  ?program :enables ?marker.
+}
+=>
+{
+  ?cell :expresses ?marker;
+        :integrates ?program.
+}.
+
+# -----------------------------------
+# RULE 6
+# WHAT IS PRESERVED REMAINS EXPRESSED
+# -----------------------------------
+
+{
+  ?cell :preservesMarker ?marker.
+}
+=>
+{
+  ?cell :expresses ?marker.
+}.
+
+# --------------------------------------
+# RULE 7
+# AN INTEGRATED PROGRAM BECOMES REALIZED
+# --------------------------------------
+
+{
+  ?cell :integrates ?program.
+}
+=>
+{
+  ?cell :realizes ?program.
+}.
+
+# ------------------------------------------------
+# RULE 8
+# A REALIZED PROGRAM STABILIZES THE NEW CELL STATE
+# ------------------------------------------------
+
+{
+  ?cell :realizes ?program.
+}
+=>
+{
+  ?cell :achieves :stableCellState;
+        :availableForFurtherDifferentiation :yes.
+}.
+
+# ----------------------------------------------------------
+# RULE 9
+# STABLE STATES ARE AVAILABLE FOR FUTURE LINEAGE TRANSITIONS
+# ----------------------------------------------------------
+
+{
+  ?cell :achieves :stableCellState.
+}
+=>
+{
+  ?cell :status :stableCellState.
+}.

package/examples/engineering-becoming.n3

@@ -0,0 +1,167 @@
+# =================================================================
+# This small Notation3 program models engineering iteration as a
+# process of becoming. A new design revision does not begin from
+# nothing: it inherits validated requirements from an earlier
+# baseline, responds to a new design goal, evaluates a feasible
+# option, and integrates that option into a new concrete design.
+# Once validated, the revision becomes an approved baseline for
+# future work. The logic below is therefore not a logic of static
+# objects, but of inheritance, constraint, adaptation, and renewal.
+# =================================================================
+
+@prefix : <http://example.org/engineering#>.
+
+# ----------
+# CATEGORIES
+# ----------
+
+:DesignRevision a :Category.
+:Requirement    a :Category.
+:DesignGoal     a :Category.
+:DesignOption   a :Category.
+
+# ------------
+# REQUIREMENTS
+# ------------
+
+:stiffnessReq a :Requirement.
+:thermalReq   a :Requirement.
+:assemblyReq  a :Requirement.
+
+# ------------
+# DESIGN GOALS
+# ------------
+
+:reduceWeight   a :DesignGoal.
+:improveCooling a :DesignGoal.
+
+# --------------
+# DESIGN OPTIONS
+# --------------
+
+:carbonFrame  a :DesignOption.
+:ribbedHousing a :DesignOption.
+
+:reduceWeight   :suggests :carbonFrame.
+:improveCooling :suggests :ribbedHousing.
+
+# Compatibility of options with requirements
+:carbonFrame   :compatibleWith :stiffnessReq, :assemblyReq.
+:ribbedHousing :compatibleWith :thermalReq, :assemblyReq.
+
+# ----------------
+# INITIAL BASELINE
+# ----------------
+
+:r1 a :DesignRevision;
+    :time 1;
+    :satisfies :stiffnessReq, :assemblyReq;
+    :realizes :aluminumFrame;
+    :achieves :approvedBaseline.
+
+:r2 a :DesignRevision;
+    :time 2;
+    :derivesFrom :r1;
+    :designGoal :reduceWeight.
+
+:r3 a :DesignRevision;
+    :time 3;
+    :derivesFrom :r2;
+    :designGoal :improveCooling.
+
+# ----------------------------------------------
+# RULE 1
+# A NEW REVISION INHERITS SATISFIED REQUIREMENTS
+# ----------------------------------------------
+
+{
+  ?later :derivesFrom ?earlier.
+  ?earlier :satisfies ?req.
+}
+=>
+{
+  ?later :inheritsRequirement ?req.
+}.
+
+# --------------------------------------
+# RULE 2
+# A DESIGN GOAL OPENS A CANDIDATE OPTION
+# --------------------------------------
+
+{
+  ?rev :designGoal ?goal.
+  ?goal :suggests ?opt.
+}
+=>
+{
+  ?rev :considers ?opt.
+}.
+
+# --------------------------------------------------------
+# RULE 3
+# A CANDIDATE OPTION CAN PRESERVE AN INHERITED REQUIREMENT
+# --------------------------------------------------------
+
+{
+  ?rev :inheritsRequirement ?req.
+  ?rev :considers ?opt.
+  ?opt :compatibleWith ?req.
+}
+=>
+{
+  ?rev :preserves ?req;
+       :integrates ?opt.
+}.
+
+# -----------------------------------------
+# RULE 4
+# WHAT IS PRESERVED BECOMES SATISFIED AGAIN
+# -----------------------------------------
+
+{
+  ?rev :preserves ?req.
+}
+=>
+{
+  ?rev :satisfies ?req.
+}.
+
+# -----------------------------------
+# RULE 5
+# WHAT IS INTEGRATED BECOMES REALIZED
+# -----------------------------------
+
+{
+  ?rev :integrates ?opt.
+}
+=>
+{
+  ?rev :realizes ?opt.
+}.
+
+# ---------------------------------------------------------
+# RULE 6
+# A REVISION THAT REALIZES AN OPTION BECOMES A NEW BASELINE
+# ---------------------------------------------------------
+
+{
+  ?rev :realizes ?opt.
+}
+=>
+{
+  ?rev :achieves :approvedBaseline;
+       :availableForFutureIteration :yes.
+}.
+
+# -------------------------------------------------------
+# RULE 7
+# APPROVED BASELINES ARE AVAILABLE FOR FURTHER DERIVATION
+# -------------------------------------------------------
+
+{
+  ?rev :achieves :approvedBaseline.
+}
+=>
+{
+  ?rev :status :approvedBaseline.
+}.

package/examples/output/barley-seed-becoming.txt

@@ -0,0 +1,25 @@
+Barley seed lineage — becoming
+
+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 be read as a becoming: a protected dormant seed can germinate, an adult plant can become a next seed stage, and the lineage can therefore become a self-renewing cycle. Because its hereditary information is digitally instantiated and repair is available, it can also become an accurately reproduced next generation under no-design laws. And because heritable variation is present under a matching selection environment, it can become an adaptively persistent lineage. The contrast lineages mark blocked becomings: non-digital heredity blocks accurate copying, lack of repair blocks reliable renewal, lack of dormancy protection blocks closure through the seed phase, and lack of heritable variation blocks adaptive becoming.
+
+Check
+B1  OK - no-design laws are assumed
+B2  OK - the viable genome can become accurately copied
+B3  OK - the viable seed can become a protected dormant phase
+B4  OK - the viable seed can become a germinating stage
+B5  OK - the viable adult can become a next dormant seed stage
+B6  OK - the viable lineage can become an accurately reproduced next generation
+B7  OK - the viable lineage can become a closed life cycle
+B8  OK - the viable lineage can become a novel variant lineage
+B9  OK - the viable lineage can become adaptively persistent
+B10 OK - the viable lineage is an evolvable becoming
+B11 OK - the non-digital lineage cannot become an accurately reproduced next generation
+B12 OK - the repair-deficient lineage cannot become an accurately reproduced next generation
+B13 OK - the coatless lineage cannot become a closed life cycle
+B14 OK - the static lineage cannot become an adaptive lineage
+B15 OK - the static lineage cannot become an evolvable becoming

package/examples/output/constructor-theory-becoming.n3

@@ -0,0 +1,18 @@
+@prefix : <http://example.org/constructor#> .
+
+:perfectRestoreTask :status :impossibleTask .
+:writeTask :status :possibleTask .
+:writer :retainsCapacityFor :writeTask .
+:stabilizeTask :status :possibleTask .
+:stabilizer :retainsCapacityFor :stabilizeTask .
+:v1 :availableForFurtherTask :yes .
+:damaged1 :availableForFurtherTask :yes .
+:v2 :canUndergo :writeTask .
+:v2 :becomesFrom :v1 .
+:v2 :hasAttribute :encodedMemory .
+:vBad :status :blockedTransition .
+:v2 :availableForFurtherTask :yes .
+:v3 :canUndergo :stabilizeTask .
+:v3 :becomesFrom :v2 .
+:v3 :hasAttribute :stabilizedMemory .
+:v3 :availableForFurtherTask :yes .

package/examples/output/control-system-becoming.n3

@@ -0,0 +1,35 @@
+@prefix : <http://example.org/control#> .
+
+:c1 :availableForFutureTuning :yes .
+:c1 :status :approvedController .
+:c2 :inheritsRequirement :stabilityReq .
+:c2 :inheritsRequirement :trackingReq .
+:c2 :considers :leadCompensator .
+:c3 :considers :integralAction .
+:c2 :targets :overshootReq .
+:c3 :targets :disturbanceRejectionReq .
+:c2 :preserves :stabilityReq .
+:c2 :integrates :leadCompensator .
+:c2 :preserves :trackingReq .
+:c2 :satisfies :overshootReq .
+:c3 :satisfies :disturbanceRejectionReq .
+:c3 :integrates :integralAction .
+:c2 :satisfies :stabilityReq .
+:c2 :realizes :leadCompensator .
+:c2 :satisfies :trackingReq .
+:c3 :realizes :integralAction .
+:c2 :achieves :approvedController .
+:c2 :availableForFutureTuning :yes .
+:c3 :achieves :approvedController .
+:c3 :availableForFutureTuning :yes .
+:c2 :status :approvedController .
+:c3 :status :approvedController .
+:c3 :inheritsRequirement :overshootReq .
+:c3 :inheritsRequirement :stabilityReq .
+:c3 :inheritsRequirement :trackingReq .
+:c3 :preserves :overshootReq .
+:c3 :preserves :stabilityReq .
+:c3 :preserves :trackingReq .
+:c3 :satisfies :overshootReq .
+:c3 :satisfies :stabilityReq .
+:c3 :satisfies :trackingReq .

package/examples/output/developmental-genetics-becoming.n3

@@ -0,0 +1,32 @@
+@prefix : <http://example.org/genetics#> .
+
+:s1 :status :stableCellState .
+:s2 :inheritsMarker :Sox2 .
+:s2 :inheritsMarker :Pax6 .
+:s2 :considers :proneuralProgram .
+:s3 :considers :neuronalMaturationProgram .
+:s2 :targetsMarker :NeuroD1 .
+:s3 :targetsMarker :Tubb3 .
+:s2 :preservesMarker :Sox2 .
+:s2 :integrates :proneuralProgram .
+:s2 :preservesMarker :Pax6 .
+:s2 :expresses :NeuroD1 .
+:s3 :expresses :Tubb3 .
+:s3 :integrates :neuronalMaturationProgram .
+:s2 :expresses :Sox2 .
+:s2 :realizes :proneuralProgram .
+:s2 :expresses :Pax6 .
+:s3 :realizes :neuronalMaturationProgram .
+:s2 :achieves :stableCellState .
+:s2 :availableForFurtherDifferentiation :yes .
+:s3 :achieves :stableCellState .
+:s3 :availableForFurtherDifferentiation :yes .
+:s2 :status :stableCellState .
+:s3 :status :stableCellState .
+:s3 :inheritsMarker :NeuroD1 .
+:s3 :inheritsMarker :Sox2 .
+:s3 :inheritsMarker :Pax6 .
+:s3 :preservesMarker :NeuroD1 .
+:s3 :preservesMarker :Pax6 .
+:s3 :expresses :NeuroD1 .
+:s3 :expresses :Pax6 .

package/examples/output/engineering-becoming.n3

@@ -0,0 +1,26 @@
+@prefix : <http://example.org/engineering#> .
+
+:r1 :availableForFutureIteration :yes .
+:r1 :status :approvedBaseline .
+:r2 :inheritsRequirement :stiffnessReq .
+:r2 :inheritsRequirement :assemblyReq .
+:r2 :considers :carbonFrame .
+:r3 :considers :ribbedHousing .
+:r2 :preserves :stiffnessReq .
+:r2 :integrates :carbonFrame .
+:r2 :preserves :assemblyReq .
+:r2 :satisfies :stiffnessReq .
+:r2 :realizes :carbonFrame .
+:r2 :satisfies :assemblyReq .
+:r2 :achieves :approvedBaseline .
+:r2 :availableForFutureIteration :yes .
+:r2 :status :approvedBaseline .
+:r3 :inheritsRequirement :stiffnessReq .
+:r3 :inheritsRequirement :assemblyReq .
+:r3 :preserves :assemblyReq .
+:r3 :integrates :ribbedHousing .
+:r3 :satisfies :assemblyReq .
+:r3 :realizes :ribbedHousing .
+:r3 :achieves :approvedBaseline .
+:r3 :availableForFutureIteration :yes .
+:r3 :status :approvedBaseline .