1 Aristotle 2005

2 beta version

3 Organism DNA Protein Organelle Cell Tissue Organ m m m

4 FUNCTIONAL GENOMICS proteomics, reactomics, metabonomics, phenomics, behaviouromics, toxicopharmacogenomics

5 The incompatibilities between different scientific cultures and terminologies immunology genetics cell biology

6 how can we overcome the incompatibilities which become apparent when data from distinct sources are combined?

7 Metaphysically intriguing answer: “Ontology”

8 Google hits (as of yesterday) ontology + Heidegger 58K ontology + Aristotle 77K ontology + philosophy327K ontology + engineering335K ontology + software 468K ontology + database 594K ontology + information systems 702K

9 Ontology = building software artefacts standardized classification systems so that data from one source can be expressed in a language which makes it compatible with data from every other source

10 IFOMIS Institute for Formal Ontology and Medical Information Science

11 A Linnaean Species Hierarchy

12 (Small) Disease Hierarchy

13 Combining hierarchies Organisms Diseases

14 via Dependence Relations Organisms Diseases

15 A Window on Reality

16 Organisms Diseases A Window on Reality

17 A Window on Reality

18 Gene Ontology databases

19 Cancer MD/Saliva databases Informatics.htm

20 New golden age of classification 30,000 genes in human 200,000 proteins 100s of cell types 100,000s of disease types 1,000,000s of biochemical pathways (including disease pathways) … legacy of Human Genome Project

21

22 Inherence Relations Substances Accidents

23 From Species to Genera canary animal bird

24 From Species to Genera animal bird canary can sing is yellow has wings can fly has feathers has skin moves eats breathes species-genus hierarchy as inference machine

25 From Species to Genera animal bird canary can sing is yellow has wings can fly has feathers has skin moves eats breathes fish has fins can swim has gills

26 siamese mammal cat organism substance species, genera animal instances frog

27 siamese mammal cat organism substance types animal tokens frog

28 animal bird canary From Species to Genera can sing is yellow has skin moves eats breathes has wings can fly has feathers species-genus hierarchy as inference machine X

29 Why are species-genus hierarchies good ways to represent our reasoning? 1. They capture the natural ways we think (Kantianism)... species are concepts 2. They capture the way the world is (Aristotelian realism)

30 genus Species-genus trees can be represented also as map-like partitions

31 From Species to Genera canary animal bird

32 From Species to Genera animal bird canary

33 Species Genera as Tree canary animal bird fish ostrich

34 Species-Genera as Map/Partition animal bird canary ostrich fish canary

35 Tree and Map/Partition

36 If Aristotelian realism is right, then such partitions are transparent to the reality beyond

37 A Window on Reality

38

39 Coarse-grained Partition

40 Fine-Grained Partition

41 Artist’s Grid

42 Partitions often come with a labelling and an address system

43 Periodic Table Die periodische Tabelle der chemischen Elemente

44 From Species to Genera animal bird canary can sing is yellow has wings can fly has feathers has skin moves eats breathes fish has fins can swim has gills

45 From Species to Genera animal bird canary can sing is yellow has wings can fly has feathers has skin moves eats breathes fish has fins can swim has gills ostrich has long thin legs is tall can‘t fly y

46 From Species to Genera animal bird canary can sing is yellow has wings can fly has feathers has skin moves eats breathes fish has fins can swim has gills ostrich has long thin legs is tall can’t fly y

47 Theory of vagueness How can -based conceptualizations be transparent, if the world is shaped like this ?

48 hard vs. soft categories Kantianism: we constitute/shape/create (empirical) reality in such a way as to ensure that it corresponds to our categories Aristotelianism: reality in itself is messy, but our categories fit nonetheless

49 How so? because they are made up, not of crisp (hard), but of open (soft) genera and species

50 that is: when we apply our categories to reality we are aware that we have to deal with an opposition... between standard or focal or prototypical instances... and non-standard or ‘fringe’ instances

51 birds ostrich Natural categories have borderline cases sparrow

they have a kernel/penumbra structure kernel of focal instances penumbra of borderline cases

53 animal bird canary ostrich fish every cell in every common-sense partition is subject to this same kernel-penumbra structure:

54 Prototypicality among species some species of a given genus are more typical, standard, than others canary is more typical than ostrich

55 instances Some instances of a given species are more typical than others albino frog

56 The entities in reality are organized into hierarchies of species and genera... and subject to prototypicality

57 In addition to objects (substances), which pertain to what a thing is at all times at which it exists: cow man rock planet

58 the world contains also accidents which pertain to how a thing is at some time at which it exists: red hot hungry obese diabetic

59 An accident = what holds of a substance per accidens

60 Accidents, too, instantiate genera and species Thus accidents, too, form trees

61 quality color red scarlet R232, G54, B24

62 and they are distinguished as between tokens and types (which is to say: between genera and species on the one hand,... and instances on the other)

63 Accidents: Species and instances this individual accident of redness (this token redness – here, now) quality color red scarlet R232, G54, B24

64 substance one substantial category John, man nine accidental categories hunger, your hunger, being hungry your sun-tan your being taller than Mary accidents

65 substance place (in the Lyceum) time (yesterday) position (is sitting) possession (has shoes on) action (cuts) passion (is cut) quantity (two feet long) quality (white) relation (taller than) John accidents

66 substance Substances are the bearers of accidents accidents Bearers

67 substance Substances are the bearers of accidents accidents John = relations of inherence (one-sided existential dependence) Bearers hunger

68 Aristotle 1.0 an ontology recognizing: substance tokens accident tokens substance types accident types + prototypicality + species-genus trees

69 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

70 Alberti’s Grid c.1450

71 Some philosophers accept only part of this ontology

72 Standard Predicate Logic – F(a), R(a,b)... SubstantialAccidental Attributes F, G, R Individuals a, b, c this, that Universal Particular

73 in fact however we need more than Aristotle 1.0

74 Is everything in reality either a substance or an accident?

75 Armchair ontology

76 Positive and negative parts positive part hole (made of matter) (not made of matter)

77 Shoes

78 Temple at Corinth

79

80

81

82 CIRCULATORY SYSTEM

83 CIRCULATORY SYSTEM (Principal Organs)

84 NERVOUS SYSTEM

85 Bodily Systems respiratorydigestive skeletal circulatory musculatory immune

86 Bodily Systems respiratorydigestive skeletal circulatory musculatory immune

87 What is a hole (conduit, cavity)?

88 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion One + Nine Categories

89 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion Holes are places?

90 Places For Aristotle the place of a substance is the interior boundary of the surrounding body (for example the interior boundary of the surrounding water where it meets a fish’s skin) Place hereby confused with boundary And there can be no empty place

91 Parts

92 What is a part?

93 where does a body part start ?... a limb is not a substance

94 nose...and it’s not an accident, either

95 nose... two kinds of boundaries

96 nose fiat boundaries

97 nose bona fide boundaries

98 Systems respiratorydigestive skeletal circulatory musculatory immune

99 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion What is a System?

100 A hydraulic system

101 Systems interconnect with other systems

102 plus NERVOUS SYSTEM (Regulatory Links)

103 bodily systems are separated from each other by fiat boundaries thus systems are not substances... and they’re not accidents either

104 Systems have functions

105 Systems can malfunction Ontology of disease Ontology of death

106 Aristotle 4.0 an ontology of substances + accidents (1.0) + holes (conduits, cavities) + parts + fiat and bona fide boundaries + systems + functions, malfunctions

107 Aristotle 2005

108 Universe/Periodic Table animal bird canary ostrich fish animal biology partition of DNA space (molecular biology)

109 Universe/Periodic Table animal bird canary ostrich fish both are transparent partitions of one and the same reality

110 DNA Protein Organelle Cell Tissue Organ Organism m m m

111 also systems on the molecular level

112

113 many transparent partitions at different levels of granularity will operate with species-genus hierarchies and with an ontology of substances (objects) and accidents (attributes, processes) and holes and parts and systems along the lines described by Aristotle 4.0

114 relative hylomorphism substances and accidents reappear in the microscopic and macroscopic worlds of e.g. molecular biology and astronomy (Aristotelian ontological zooming)

115 Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other

116 Cerebral Cortex

117 Mouse Chromosome 5

cell molecular biology

119 cell anatomy (coarse grain)

cell anatomy (fine grain)

121 All veridical perspectives are equal Each veridical perspective (= transparent partition) captures some corresponding domain of objects

122 An organism is a totality of molecules An organism is a totality of cells An organism is a single unitary substance... all of these express veridical partitions An organism is a totality of atoms

123 all express partitions which are transparent, at different levels of granularity, to the same reality beyond

124 A partition of a given genus

125 Coarse-grained Partition what happens when a fringe instance arises ?

126 Coarse-grained Partition what happens when a fringe instance arises ? Aristotle 1.0: you shrug your shoulders

127 Aristotle 2005 you go out to find a finer grained partition which will recognize the phenomenon in question as prototypical

128 The advance of science is not an advance away from Aristotle towards something better. It is a rigorous demonstration of the correctness of his ontological approach

129 Aristotle THE END