1 Aristotle 2005. 2 beta version.

http://ifomis.org 1 Aristotle 2005

http://ifomis.org 2 beta version

http://ifomis.org 3 Organism DNA Protein Organelle Cell Tissue Organ 10 -5 m 10 -1 m 10 -9 m

http://ifomis.org 4 FUNCTIONAL GENOMICS proteomics, reactomics, metabonomics, phenomics, behaviouromics, toxicopharmacogenomics

http://ifomis.org 5 The incompatibilities between different scientific cultures and terminologies immunology genetics cell biology

http://ifomis.org 6 how can we overcome the incompatibilities which become apparent when data from distinct sources are combined?

http://ifomis.org 7 Metaphysically intriguing answer: “Ontology”

http://ifomis.org 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

http://ifomis.org 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

http://ifomis.org 10 IFOMIS Institute for Formal Ontology and Medical Information Science

http://ifomis.org 11 A Linnaean Species Hierarchy

http://ifomis.org 12 (Small) Disease Hierarchy

http://ifomis.org 13 Combining hierarchies Organisms Diseases

http://ifomis.org 14 via Dependence Relations Organisms Diseases

http://ifomis.org 15 A Window on Reality

http://ifomis.org 16 Organisms Diseases A Window on Reality

http://ifomis.org 18 Gene Ontology databases

http://ifomis.org 19 Cancer MD/Saliva databases www.saliva.bme.ucla.edu/ Informatics.htm

http://ifomis.org 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

http://ifomis.org 21

http://ifomis.org 22 Inherence Relations Substances Accidents

http://ifomis.org 23 From Species to Genera canary animal bird

http://ifomis.org 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

http://ifomis.org 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

http://ifomis.org 26 siamese mammal cat organism substance species, genera animal instances frog

http://ifomis.org 27 siamese mammal cat organism substance types animal tokens frog

http://ifomis.org 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

http://ifomis.org 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)

http://ifomis.org 30 genus Species-genus trees can be represented also as map-like partitions

http://ifomis.org 31 From Species to Genera canary animal bird

http://ifomis.org 32 From Species to Genera animal bird canary

http://ifomis.org 33 Species Genera as Tree canary animal bird fish ostrich

http://ifomis.org 34 Species-Genera as Map/Partition animal bird canary ostrich fish canary

http://ifomis.org 35 Tree and Map/Partition

http://ifomis.org 36 If Aristotelian realism is right, then such partitions are transparent to the reality beyond

http://ifomis.org 39 Coarse-grained Partition

http://ifomis.org 40 Fine-Grained Partition

http://ifomis.org 41 Artist’s Grid

http://ifomis.org 42 Partitions often come with a labelling and an address system

http://ifomis.org 43 Periodic Table Die periodische Tabelle der chemischen Elemente

http://ifomis.org 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

http://ifomis.org 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

http://ifomis.org 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

http://ifomis.org 47 Theory of vagueness How can -based conceptualizations be transparent, if the world is shaped like this ?

http://ifomis.org 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

http://ifomis.org 49 How so? because they are made up, not of crisp (hard), but of open (soft) genera and species

http://ifomis.org 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

http://ifomis.org 51 birds ostrich Natural categories have borderline cases sparrow

http://ifomis.org 52... they have a kernel/penumbra structure kernel of focal instances penumbra of borderline cases

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

http://ifomis.org 54 Prototypicality among species some species of a given genus are more typical, standard, than others canary is more typical than ostrich

http://ifomis.org 55 instances Some instances of a given species are more typical than others albino frog

http://ifomis.org 56 The entities in reality are organized into hierarchies of species and genera... and subject to prototypicality

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

http://ifomis.org 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

http://ifomis.org 59 An accident = what holds of a substance per accidens

http://ifomis.org 60 Accidents, too, instantiate genera and species Thus accidents, too, form trees

http://ifomis.org 61 quality color red scarlet R232, G54, B24

http://ifomis.org 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)

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

http://ifomis.org 64 substance one substantial category John, man nine accidental categories hunger, your hunger, being hungry your sun-tan your being taller than Mary accidents

http://ifomis.org 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

http://ifomis.org 66 substance Substances are the bearers of accidents accidents Bearers

http://ifomis.org 67 substance Substances are the bearers of accidents accidents John = relations of inherence (one-sided existential dependence) Bearers hunger

http://ifomis.org 68 Aristotle 1.0 an ontology recognizing: substance tokens accident tokens substance types accident types + prototypicality + species-genus trees

http://ifomis.org 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

http://ifomis.org 70 Alberti’s Grid c.1450

http://ifomis.org 71 Some philosophers accept only part of this ontology

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

http://ifomis.org 73 in fact however we need more than Aristotle 1.0

http://ifomis.org 74 Is everything in reality either a substance or an accident?

http://ifomis.org 75 Armchair ontology

http://ifomis.org 76 Positive and negative parts positive part hole (made of matter) (not made of matter)

http://ifomis.org 77 Shoes

http://ifomis.org 78 Temple at Corinth

http://ifomis.org 82 CIRCULATORY SYSTEM

http://ifomis.org 83 CIRCULATORY SYSTEM (Principal Organs)

http://ifomis.org 84 NERVOUS SYSTEM

http://ifomis.org 85 Bodily Systems respiratorydigestive skeletal circulatory musculatory immune

http://ifomis.org 86 Bodily Systems respiratorydigestive skeletal circulatory musculatory immune

http://ifomis.org 87 What is a hole (conduit, cavity)?

http://ifomis.org 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

http://ifomis.org 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?

http://ifomis.org 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

http://ifomis.org 91 Parts

http://ifomis.org 92 What is a part?

http://ifomis.org 93 where does a body part start ?... a limb is not a substance

http://ifomis.org 94 nose...and it’s not an accident, either

http://ifomis.org 95 nose... two kinds of boundaries

http://ifomis.org 96 nose fiat boundaries

http://ifomis.org 97 nose bona fide boundaries

http://ifomis.org 98 Systems respiratorydigestive skeletal circulatory musculatory immune

http://ifomis.org 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?

http://ifomis.org 100 A hydraulic system

http://ifomis.org 101 Systems interconnect with other systems

http://ifomis.org 102 plus NERVOUS SYSTEM (Regulatory Links)

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

http://ifomis.org 104 Systems have functions

http://ifomis.org 105 Systems can malfunction Ontology of disease Ontology of death

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

http://ifomis.org 107 Aristotle 2005

http://ifomis.org 108 Universe/Periodic Table animal bird canary ostrich fish animal biology partition of DNA space (molecular biology)

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

http://ifomis.org 110 DNA Protein Organelle Cell Tissue Organ Organism 10 -5 m 10 -1 m 10 -9 m

http://ifomis.org 111 also systems on the molecular level

http://ifomis.org 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

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

http://ifomis.org 115 Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other

http://ifomis.org 116 Cerebral Cortex

http://ifomis.org 117 Mouse Chromosome 5

http://ifomis.org 118 http://medix.marshall.edu/~sergeev/images/apoptosis.jpg cell molecular biology

http://ifomis.org 119 cell anatomy (coarse grain) http://www.enchantedlearning.com/subjects/animals/cell/anatomy.GIF

http://ifomis.org 120 http://library.thinkquest.org/C004535/cell_membranes.html cell anatomy (fine grain)

http://ifomis.org 121 All veridical perspectives are equal Each veridical perspective (= transparent partition) captures some corresponding domain of objects

http://ifomis.org 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

http://ifomis.org 123 all express partitions which are transparent, at different levels of granularity, to the same reality beyond

http://ifomis.org 124 A partition of a given genus

http://ifomis.org 125 Coarse-grained Partition what happens when a fringe instance arises ?

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

http://ifomis.org 127 Aristotle 2005 you go out to find a finer grained partition which will recognize the phenomenon in question as prototypical

http://ifomis.org 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

http://ifomis.org 129 Aristotle THE END

1 Aristotle 2005. 2 beta version.

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1 Aristotle 2005. 2 beta version.

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