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Lecture 1Ontology as a Branch
of Philosophy
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A brief history of ontology
Aristotle (384 BC – 322 BC)
Realist theory of categories
Intelligible universals extending across all domains
Central role of organisms
Medieval scholastics: Aquinas, Scotus, Ockham, … (1200 – 1600)
Aristotelianism as philosophia perennis
Common panscientific ontology and controlled vocabulary (Latin)
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A brief history of ontology
Descartes (1596 – 1650)
Sceptical doubt initiates subversion of metaphysics, rise of epistemology
Central role of mind
Dualism of mind and matter
Kant (1724 – 1804)
Reality is unknowable
Metaphysics is impossible
We can only know the quasi-fictional domains which we ourselves create
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A brief history of ontology
Brentano (1838 – 1917)
Rediscovery of Aristotle
Methods of philosophy and of science are one and the same
Husserl (1859 – 1938)
Inventor of formal ontology as a discipline distinct from formal logic
Showed how philosophy and science had become detached from the ‘life world’ of ordinary experience
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The Four Phases of Philosophy
rapid practical scepticism mysticism
progress interest
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First Cycle
Thales to Stoicism and Pyrrho, Neo-Pythagoreans,
Aristotle Epicureanism Eclectics Neo-Platonists
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Second Cycle
up to Scotism Ockham, Lull,
Aquinas Nominalists Nicholas of Cusa
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Third Cycle
Bacon, Rationalists Hume, Berkeley, Kant
Locke Reid German Idealism
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A brief history of ontologyWittgenstein 1 (ca. 1910 – 1918)
Author of Tractatus
Bases ontology on formal logic in reductionistic atomism
Vienna Circle (1922 – ca. 1938)
Schlick, Neurath, Gödel, Carnap, Gustav Bergmann …
Centrality of logic to philosophy
Construction of philosophy from either physics or sensations as base
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A brief history of ontologyWittgenstein 2 (ca. 1930 – 1951)
Centrality of language and of language games
Metaphysics = language goes on holiday
British Ordinary Language philosophy
Philosophical problems to be solved by the study of the workings of language
Speech Act Theory (J. L. Austin, 1911-1960)
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A brief history of ontologyQuine (ca. 1930 – 1951)
Ontological commitment (study not: what there is, but: what sciences believe there is when logically formalized)
Analytical metaphysics (from ca. 1980): Chisholm, Lewis, Armstrong, Fine, Lowe, … beginnings of a rediscovery of metaphysics as first philosophy
What next?11
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Fourth Cycle (Continental)
Brentano Husserl Heidegger Derrida and
Polish School the French
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Fourth Cycle (Analytical)
Frege Vienna Circle Wittgenstein 2 Rorty
Wittgenstein 1 Quine
Russell
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Each cycle begins with rediscovery of Aristotle and a new theoretical orientation
From the 3rd cycle marked
by invention of new disciplines
3. Empirical natural science
4. Psychology, logic
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Fifth Cycle
Analytical Metaphysics Ontology
Rediscovery of Aristotle
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An example of a practical problem
Increasingly, publishers are exploring ways to tag scientific literature in ways designed to make their contents more easily accessible to computers
For maximal effect, a single set of terms should be used for tagging all literature published in a given domain
How do we select the set of terms (‘ontology’) for each domain?
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from: http://www.ploscompbiol.org/doi/pcbi.1000361
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http://www.biocurator.org
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Most successful ontology venture thus far
$100 mill. invested in literature and database curation using the Gene Ontology (GO)
over 11 million annotations relating gene products (proteins) described in the UniProt, Ensembl and other databases to terms in the GO
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GO provides a controlled system of representations for use in annotating
data and literature that is
• multi-species
• multi-disciplinary
• multi-granularity, from molecules to population
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are structured representations of the domains of molecules, cells, diseases ... which can be used by researchers in many different disciplines who are focused on one and the same biological reality
The GO and its sister ontologies
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The goal: virtual science
• consistent (non-redundant) annotation
• cumulative (additive) annotation
yielding, by incremental steps, a virtual map of the entirety of reality that is accessible to computational reasoning
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This goal is realizable if we have a common ontology framework
data is retrievable
data is comparable
data is integratable
only to the degree that it is annotated using a common controlled vocabulary
– compare the role of seconds, meters, kilograms … in unifying science
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To achieve this end we have to engage in something like philosophy
is this the right way to organize the top level of this portion of the GO?how does the top level of this ontology relate to the top levels of other, neighboring ontologies? 26
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Aristotle’s Metaphysics
The world is organized via types/universals/categories which are hierarchically organized
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This holds, too, of the biological world28
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Porphyrian Hierarchy
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Linnaean Hierarchy
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From Species to Genera
canary
animal
bird
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From Species to Genera
animal
bird
canary can singis yellow
has wings
can fly
has feathers
has skin
moves
eats
breathes
species-genus hierarchyas inference machine
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From Species to Genera
animal
bird
canary can singis yellow
has wings
can fly
has feathers
has skin
moves
eats
breathes
fishhas finscan swimhas gills
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animal
bird
canary
From Species to Genera
can singis yellow
has skin
moves
eatsbreathes
has wingscan flyhas feathers
species-genus hierarchyas inference machine
XX
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Question: Why are species-genus hierarchies good ways to represent the world for purposes of reasoning?
Answer: They capture the way the world is (Aristotelian realism)
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Transcription is_a biological process
Transcription part_of gene expression36
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Species-genusgenus trees can be represented also as map-like partitions
If Aristotelian realism is right, then such partitions, when correctly built are transparent to the reality beyond
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From Species to Genera
canary
animal
bird
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From Species to Genera
animal
bird
canarycanary
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Alberti’s Grid c.1450
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Ontologies: windows on
the universals in reality 41
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Artist’s Grid
as through a transparent grid42
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Species-Genera as Map/Partition
animal
bird
canary
ostrich
fish
canary
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siamese
mammal
cat
organism
substancespecies, genera
animal
instances
frog
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Aristotle’s Metaphysics is focused on objects (things, substances, organisms)
The most important universals in his ontology are substance universals
cow man rock planet
which pertain to what a thing is at all times at which it exists
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For Aristotle, the world contains also accidents
which pertain to how a thing is at some time at which it exists:
= what holds of a substance per accidens
red hot suntanned spinning
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Accidents, too, instantiate genera and species
Thus accidents, too, form trees of greater and lesser generality
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Accidents: Species and instances
this individual accident of redness (this token redness – here, now)
quality
color
red
scarlet
R232, G54, B24
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Nine Accidental Categoriesquid? substance quantum? quantity quale? qualityad quid? relationubi? placequando? timein quo situ? status/contextin quo habitu? habitusquid agit? actionquid patitur? passion
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= relations of inherence(one-sided existential dependence)
John
hunger
Substances are the bearers of accidents
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Aristotle 1.0
an ontology recognizing:substance tokensaccident tokenssubstance typesaccident types
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Aristotle’s Ontological SquareSubstantial Accidental
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
Uni
vers
alP
artic
ular
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Some philosophers accept only part of this four category
ontology
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Standard Predicate Logic – F(a), R(a,b) ...
Substantial Accidental
Attributes
F, G, R
Individuals
a, b, c
this, that
Uni
vers
alP
artic
ular
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Bicategorial NominalismSubstantial Accidental
First substance
this man
this cat
this ox
First accident
this headache
this sun-tan
this dread
Uni
vers
alP
artic
ular
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Process MetaphysicsSubstantial Accidental
Events
Processes“Everything is flux”
Uni
vers
alP
artic
ular
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In fact however we need more than the ontological square
Not everything in reality is either a substance or an accident
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Positive and negative parts
positivepart
negativepartor hole
(made of matter)
(not made of matter)
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Shoes
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Pipe
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Niches, environments are holes
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Places are holes
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Places are holes
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Nine Accidental Categoriesquid? substance quantum? quantity quale? qualityad quid? relationubi? placequando? timein quo situ? status/contextin quo habitu? habitusquid agit? actionquid patitur? passion
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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)
For holes, we need an extension of Aristotle’s metaphysics
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A hole in the ground
Solid physical boundaries at the floor and walls
but with a lid that is not made of matter:
hole66
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Holes involve two kinds of boundaries
bona fide boundaries which exist independently of our demarcating acts
fiat boundaries which exist only because we put them there
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Examples
of bona fide boundaries:
an animal’s skin, the surface of the planet
of fiat boundaries:
the boundaries of postal districts and census tracts
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Mountain
bona fide upper boundaries with a fiat base:
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where does the mountain start ?
... a mountain is not a substance70
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Cerebral Cortex
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Aristotle 1.5
an ontology ofsubstances + accidents+ holes (and other entities not made of matter)+ fiat and bona fide boundaries+ artefacts and environments
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Question
How do those parts and dimensions of reality which we encounter in our everyday experience relate to those parts and dimensions of reality which are studied by science?
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Aristotle 2010
scientific realism coupled with realism about the everyday world
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Universe/Periodic Tableanimal
bird
canary
ostrich
fishfolk biology
partition of DNA space
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Universe/Periodic Tableanimal
bird
canary
ostrich
fish
both are transparent partitions of one and the same reality
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An organism is a totality of atoms
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
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Multiple transparent partitions
at different levels of granularity
operating with species-genus hierarchies and with an ontology of substances and accidents along the lines described by Aristotle
substances and accidents reappear in the microscopic and macroscopic worlds of e.g. of chemistry and evolutionary biology
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we do not assert
that every level of granularity is structured in substance-accident form -- perhaps there are pure process levels, perhaps there are levels structured as fields
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Perspectivalism
PerspectivalismDifferent partitions may represent cuts through the same reality which are skew to each other
Not all need be structured in substance-accident terms – perhaps there are pure process levels, perhaps there are levels structured as fields
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Periodic Table
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Scientific partitions like the Periodic Table or the Gene Ontology
are transparent to the hierarchical order of an associated domain of objects
they capture reality at different levels of granularity
cellular constituents are visible to the GO, molecular constituents not
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Perspectivalism
PerspectivalismDifferent partitions may represent cuts through the same reality which are skew to each other
Different partitions may capture reality in ways which involve different degrees of vagueness
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From Species to Genera
animal
bird
canary can singis yellow
has wings
can fly
has feathers
has skin
moves
eats
breathes
fishhas finscan swimhas gills
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From Species to Genera
animal
bird
canary can singis yellow
has wings
can fly
has feathers
has skin
moves
eats
breathes
fishhas finscan swimhas gills
ostrichhas long thin legsis tallcan‘t fly
yy
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From Species to Genera
animal
bird
canary can singis yellow
has wings
can fly
has feathers
has skin
moves
eats
breathes
fishhas finscan swimhas gills
ostrichhas long thin legsis tallcan’t fly
yy
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Theory of vagueness
How can -based conceptualizations be transparent,if the world is shaped like this
?
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Observe that no such problems arise for the closed worlds constructed in information systems
hierarchies as reasoning tools work very well for the closed worlds of database engineers
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whether a file is in a given folder on your hard-drive is completely determinate:
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Dewey Decimal Classification
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Dewey Decimal Classification (Detail)
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No borderline cases in the closed world of a databaseEvery book is assigned a determinate Dewey Classification Number at birth
111.560xxx
this yields a classificationthat is completely crisp
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... and always up-to-dateTo be a book = to have a reference number in the Catalogue System
Each of the ontologies produced by ontological engineers deals with objects which are constructed (Kant would say “constituted”) by the database itself
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Kant
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Sharpness of database reality vs. vagueness of flesh and blood realityHow to deal with the problemof vagueness of our representations?
How to create adequate representations beyond the quasi-Kantian realm of database engineers
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Kantian Constructivism
There are no species-genus hierarchies in reality unless we put them there
The world – insofar as it is accessible to us through our concepts at all – is a closed system tailored by us to fit those concepts
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Kantianism seems to work very well for the closed worlds of database environments
There Midas-touch epistemology is appropriate
If our database recognizes only two genders, then the world represented in the database is a world in which there are only two genders
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hard vs. soft categories
Kantianism: we constitute/shape (empirical) reality in such a way that it corresponds to our categories
Aristotelianism: reality in itself is messy, but our categories fit nonetheless
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For Aristotelians
when we apply general terms to reality we are aware that we may have to deal with an opposition
... between standard or focal or prototypical instances of the corresponding universals
... and non-standard or ‘fringe’ instances
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birds
ostrich
Natural categories have borderline cases
sparrow
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... they have a kernel/penumbra structure
kernel of focal
instances
penumbra of borderline cases
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Species Genera as Tree
canary
animal
bird fish
ostrich
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Species-Genera as Map/Partition
animal
bird
canary
ostrich
fish
canary
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animal
bird
canary
ostrich
fish
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Coarse-grained Partition
what happens when a fringe instance arises ?
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Aristotle 2010you seek to find a finer grained partition which will recognize the phenomenon in question and allow an explanation of why it deviates from the prototype
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The advance of science
is not an advance away from Aristotle towards something better.
Provided Aristotle is interpreted aright, it is a rigorous demonstration of the correctness of his ontological approach
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Kantianism
each partition gives only a partial view (no complete map) of any reality beyond
and thus it gives a distorted view
– we can only really know what we ourselves have constructed
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For the Aristotelian, there are two sorts of partitions:
those which relate merely to a created, surrogate world (Library of Congress Catalog)
those which are transparent to some independent reality beyond (Gene Ontology)
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Concepts vs. categories
on the Kantian reading species are concepts, which we bring to reality
on the Aristotelian reading the world itself exhibits a species-genus structure independently of how we conceive it and we do our best to map this structure in our representations
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Basic Formal Ontology (BFO)
ContinuantOccurrent(Process)
IndependentContinuant
DependentContinuant
..... ..... ........112