(define-theory Natural-Kinds (Biologic-Functions))

(in-theory 'Natural-Kinds)


(DEFINE-CLASS ALGA (?SELF)
 "A chiefly aquatic plant that contains chlorophyll, but does not form 
embryos during development and lacks vascular tissue."
 :DEF
 (AND (PLANT ?SELF)
      (EXISTS (?A) (AND (LIVES-IN ?SELF ?A) (WATER ?A)))
      (EXISTS (?B) (AND (COMPONENT ?SELF ?B) (CHLOROPHYLL ?B)))
      (VALUE-TYPE ?SELF DEVELOPMENTAL-FORM INCOHERENT)
      (VALUE-TYPE ?SELF COMPONENT INCOHERENT))
 :AXIOM-DEF
 (PROBLEM ALGA
  "(1) <lives-in> needs a special axiomatization: it involves the localization in a 
region-type, the biological necessity, the notion of life, and an interactional notion. 
(2) <component> with substances should be interpreted as a mass-componency; see theory:meronymy")
)
(DEFINE-CLASS AMPHIBIAN (?SELF)
 "A cold-blooded, smooth-skinned vertebrate which characteristically hatches 
as an aquatic larva, breathing by gills. When mature, the amphibian breathes with lungs."
 :DEF
 (AND (VERTEBRATE ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (COLD-BLOOD ?A)))
      (EXISTS (?B) (AND (COMPONENT ?SELF ?B) (LUNGS ?B)))
      (EXISTS (?C) (AND (DEVELOPMENTAL-FORM ?SELF ?C) (AQUATIC-LARVA ?C))))
 :CONSTRAINTS (EXISTS (?D) (AND (COMPONENT ?SELF ?D) (SMOOTH-SKIN ?D))))
(DEFINE-CLASS ANIMAL (?SELF)
 "An organism with eukaryotic cells, and lacking stiff cell walls, plastids and 
photosynthetic pigments. The children of this type in the network are 'Invertebrate', and 'Vertebrate'."
 :DEF (ORGANISM ?SELF) :CONSTRAINTS
 (AND (EXISTS (?A) (AND (EXHIBITS ?SELF ?A) (BEHAVIOR ?A)))
      (EXISTS (?B)
              (AND (FINER-GRAIN-COMPONENT ?SELF ?B)
                   (EUKARYOTIC-CELL-WITH-NON-RIGID-CELL-WALL ?B)))
      (VALUE-TYPE ?SELF COMPONENT INCOHERENT)
      (VALUE-TYPE ?SELF COMPONENT INCOHERENT))
 :AXIOM-DEF (SUBCLASS-PARTITION ANIMAL (SETOF VERTEBRATE INVERTEBRATE))
)
(DEFINE-CLASS ARACHNID (?SELF)
:DEF (ARTHROPOD ?SELF))
(DEFINE-CLASS ARCHAEON (?SELF)
 "A member of one of the three domains of life, formerly called Archaebacteria 
under the taxon Bacteria, but now considered separate and distinct. Archaea are characterized by: 
1) the presence of characteristic tRNAs and ribosomal RNAs; 2) the absence of peptidoglycan cell walls; 
3) the presence of ether-linked lipids built from branched-chain subunits; and 4) their occurrence in unusual 
habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in 
their method of genomic replication. Thermoproteales; Methanospirillum; Haloferax volcanii."
 :DEF
 (AND (ORGANISM ?SELF)
      (VALUE-TYPE ?SELF COMPONENT INCOHERENT)
      (EXISTS (?A)
              (AND (CONSTITUENT-MATERIAL ?SELF ?A)
                   (AND (ETHER-LINKED-LIPID ?A)
                        (EXISTS (?B)
                                (AND (COMPONENT ?A ?B)
                                     (BRANCHED-CHAIN-SUBUNIT ?B)))))))
)
(DEFINE-CLASS ARTHROPOD (?SELF)
:DEF (INVERTEBRATE ?SELF))
(DEFINE-CLASS BACTERIUM (?SELF)
 "A small, typically one-celled, prokaryotic micro-organism." :DEF
 (AND (ORGANISM ?SELF)
      (VALUE-CARDINALITY ?SELF _CELLULAR 1)
      (VALUE-CARDINALITY ?SELF COMPONENT 1))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF REFERENCE-LOCATION-OF
       BIOLOGICALLY-ACTIVE-SUBSTANCE)
      (VALUE-TYPE ?SELF CAUSE-OF PATHOLOGIC-FUNCTION)))
(DEFINE-CLASS BIRD (?SELF)
 "A vertebrate having a constant body temperature and characterized by 
the presence of feathers."
 :DEF
 (AND (VERTEBRATE ?SELF)
      (VALUE-CARDINALITY ?SELF _CONSTANT-TEMPERATURE 1)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (FEATHERS ?A)))))
(DEFINE-CLASS FISH (?SELF)
 "A cold-blooded aquatic vertebrate characterized by fins and breathing by gills. 
Included here are fishes having either a bony skeleton, such as a perch, or a cartilaginous skeleton, such as a 
shark, or those lacking a jaw, such as a lamprey or hagfish."
 :DEF
 (AND (VERTEBRATE ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (COLD-BLOOD ?A)))
      (EXISTS (?B)
              (AND (EMBODIES ?SELF ?B)
                   (AND (BREATHING ?B)
                        (EXISTS (?C) (AND (EMBODIED-IN ?B ?C) (GILLS ?C))))))
      (EXISTS (?D) (AND (LIVES-IN ?SELF ?D) (WATER ?D)))))
(DEFINE-CLASS FUNGUS (?SELF)
 "A eukaryotic organism characterized by the absence of chlorophyll and the 
presence of a rigid cell wall. Included here are both slime molds and true fungi such as yeasts, molds, 
mildews, and mushrooms."
 :DEF
 (AND (ORGANISM ?SELF)
      (EXISTS (?A) (AND (FINER-GRAIN-COMPONENT ?SELF ?A) (EUKARYOTIC-CELL ?A)))
      (VALUE-TYPE ?SELF CONTAINS INCOHERENT)
      (EXISTS (?B) (AND (COMPONENT ?SELF ?B) (RIGID-CELL-WALL ?B))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF REFERENCE-LOCATION-OF
       BIOLOGICALLY-ACTIVE-SUBSTANCE)
      (VALUE-TYPE ?SELF CAUSE-OF PATHOLOGIC-FUNCTION))
)
(DEFINE-CLASS HUMAN (?SELF)
 "Modern man, the only remaining species of the Homo genus. If a term describes 
a human being from the point of view of occupational, family, social status, etc., then a type from the 
'Group' hierarchy is assigned instead."
 :DEF (MAMMAL ?SELF))
(DEFINE-CLASS INSECT (?SELF)
:DEF (ARTHROPOD ?SELF))
(DEFINE-CLASS INVERTEBRATE (?SELF)
 "An animal which has no spinal column. This type has no children 
in the network and is assigned to all invertebrate animals."
 :DEF (AND (ANIMAL ?SELF) (VALUE-TYPE ?SELF COMPONENT INCOHERENT))
)
(DEFINE-CLASS MAMMAL (?SELF)
 "A vertebrate having a constant body temperature and characterized by the presence 
of hair, mammary glands and sweat glands."
 :DEF
 (AND (VERTEBRATE ?SELF)
      (VALUE-CARDINALITY ?SELF _CONSTANT-TEMPERATURE 1)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (HAIR ?A)))
      (EXISTS (?B) (AND (COMPONENT ?SELF ?B) (MAMMARY-GLAND ?B)))
      (EXISTS (?C) (AND (COMPONENT ?SELF ?C) (SWEAT-GLAND ?C)))))
(DEFINE-CLASS MICROORGANISM (?SELF)
:IFF-DEF
 (AND (THING ?SELF)
      (OR (BACTERIUM ?SELF)
          (RICKETTSIA-OR-CHLAMYDIA ?SELF)
          (VIRUS ?SELF)
          (ARCHAEON ?SELF))))
(DEFINE-CLASS PLANT (?SELF)
 "An organism having cellulose cell walls, growing by synthesis of inorganic 
substances, generally distinguished by the presence of chlorophyll, and lacking the power of locomotion. 
Plant parts are included here as well."
 :DEF
 (AND (ORGANISM ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (PEPTIDOGLYCAN-CELL-WALL ?A)))
      (EXISTS (?B)
              (AND (COMPONENT ?SELF ?B)
                   (AND (PIGMENT ?B)
                        (EXISTS (?C)
                                (AND (PRODUCT-OF ?B ?C)
                                     (PHOTOSYNTHESIS ?C)))))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF REFERENCE-LOCATION-OF
       BIOLOGICALLY-ACTIVE-SUBSTANCE)
      (VALUE-TYPE ?SELF CAUSE-OF PATHOLOGIC-FUNCTION))
 :AXIOM-DEF
 (PROBLEM PLANT
  "Plant parts should not be included here because they are not organims. 
A close analysis of the instances should be made, in order to locate plant parts and to distinguish them."))
(DEFINE-CLASS REPTILE (?SELF)
 "A cold-blooded vertebrate having an external covering of scales or horny plates. 
Reptiles breathe by means of lungs and are generally egg-laying."
 :DEF
 (AND (VERTEBRATE ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (COLD-BLOOD ?A)))
      (EXISTS (?B)
              (AND (EMBODIES ?SELF ?B)
                   (AND (BREATHING ?B)
                        (EXISTS (?C) (AND (EMBODIED-IN ?B ?C) (LUNGS ?C))))))
      (EXISTS (?D)
              (AND (COMPONENT ?SELF ?D)
                   (AND (EXTERNAL-COVERING ?D)
                        (EXISTS (?E)
                                (AND (ELEMENT ?D ?E)
                                     (OR (SCALE ?E) (HORNY-PLATE ?E)))))))))
(DEFINE-CLASS RICKETTSIA-OR-CHLAMYDIA (?SELF)
 "An organism intermediate in size and complexity between a virus and a bacterium, 
and which is parasitic within the cells of insects and ticks. Included here are all the chlamydias, also called 
'PLT' for psittacosis-lymphogranuloma venereum-trachoma."
 :DEF
 (AND (ORGANISM ?SELF)
      (EXISTS (?A)
              (AND (PARASITIC ?SELF ?A)
                   (AND (CELL ?A)
                        (EXISTS (?B)
                                (AND (PRIME-COMPONENT-OF ?A ?B)
                                     (OR (INSECT ?B) (TICK ?B))))))))
 :CONSTRAINTS
 (AND (EXISTS (?C)
              (AND (REFERENCE-LOCATION-OF ?SELF ?C)
                   (BIOLOGICALLY-ACTIVE-SUBSTANCE ?C)))
      (VALUE-TYPE ?SELF CAUSE-OF PATHOLOGIC-FUNCTION))
 :AXIOM-DEF
 (FURTHER-MODELLING RICKETTSIA-OR-CHLAMYDIA
  "'parasitic' should be a kind of 'lives-in'."))
(DEFINE-CLASS TICK (?SELF)
:DEF (ARACHNID ?SELF))
(DEFINE-CLASS VERTEBRATE (?SELF)
 "An animal which has a spinal column." :DEF
 (AND (ANIMAL ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (SPINAL-COLUMN ?A))))
 :AXIOM-DEF
 (SUBCLASS-PARTITION VERTEBRATE (SETOF AMPHIBIAN REPTILE FISH BIRD MAMMAL)))
(DEFINE-CLASS VIRUS (?SELF)
 "An organism consisting of a core of a single nucleic acid enclosed in a 
protective coat of protein. A virus may replicate only inside a host living cell. A virus exhibits some 
but not all of the usual characteristics of living things."
 :DEF
 (AND (ORGANISM ?SELF)
      (VALUE-CARDINALITY ?SELF _MOLECULAR 1)
      (EXISTS (?A)
              (AND (PRIME-COMPONENT ?SELF ?A)
                   (AND (NUCLEIC-ACID ?A)
                        (EXISTS (?B)
                                (AND (WITHIN ?A ?B)
                                     (AND (PROTECTIVE-COAT ?B)
                                          (EXISTS
                                           (?C)
                                           (AND
                                            (CONSTITUENT-MATERIAL ?B ?C)
                                            (PROTEIN ?C))))))))))
 :CONSTRAINTS
 (AND (EXISTS (?D)
              (AND (EMBODIES ?SELF ?D)
                   (AND (REPLICATION ?D)
                        (EXISTS (?E)
                                (AND (REFERENCE-LOCATION ?D ?E) (CELL ?E))))))
      (EXISTS (?F)
              (AND (REFERENCE-LOCATION-OF ?SELF ?F)
                   (BIOLOGICALLY-ACTIVE-SUBSTANCE ?F)))
      (VALUE-TYPE ?SELF CAUSE-OF PATHOLOGIC-FUNCTION)))