The Protein Ontology: A structured representation of protein forms and complexes
1 An Introductory Course in Ontology and the Forms of Social Organization.
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Transcript of 1 An Introductory Course in Ontology and the Forms of Social Organization.
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1
An Introductory Course in Ontology
and the Forms of Social Organization
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1. The Meaning of Life
2. The Tools of Ontology
3. A Unified Theory of Granularity and Vagueness (UMCS)
4. Partitions of Reality: How Can We Live in Several Worlds at Once
5. John Searle's Ontology of Social Reality and Its Problems
6. The Ontology of the Environment: Objects and Their Settings
7. The Ontology of Geography
8. The Ontology of Social Reality: What Sorts of Objects are Social Wholes
9. The Metaphysics of Real Estate: Economics, Politics and History
10.Concluding Lecture: Social Reality and the Meaning of Life
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The Meaning of Life
The Tools of Ontology
A Unified Theory of Granularity and Vagueness (UMCS)
Partitions of Reality: How Can We Live in Several Worlds at Once
John Searle's Ontology of Social Reality and Its Problems
The Ontology of the Environment: Objects and Their Settings
The Ontology of Geography
The Ontology of Social Reality: What Sorts of Objects are Social Wholes
The Metaphysics of Real Estate: Economics, Politics and History
Concluding Lecture: Social Reality and the Meaning of Life
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Why
happiness happiness
does not make a life worth living
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The Meaning of Life
The Tools of Ontology
A Unified Theory of Granularity and Vagueness (UMCS)
Partitions of Reality: How Can We Live in Several Worlds at Once
John Searle's Ontology of Social Reality and Its Problems
The Ontology of the Environment: Objects and Their Settings
The Ontology of Geography
The Ontology of Social Reality: What Sorts of Objects are Social Wholes
The Metaphysics of Real Estate: Economics, Politics and History
Concluding Lecture: Social Reality and the Meaning of Life
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The Meaning of Life
The Tools of Ontology
A Unified Theory of Granularity and Vagueness (UMCS)
Partitions of Reality: How Can We Live in Several Worlds at Once
John Searle's Ontology of Social Reality and Its Problems
The Ontology of the Environment: Objects and Their Settings
The Ontology of Geography
The Ontology of Social Reality: What Sorts of Objects are Social Wholes
The Metaphysics of Real Estate: Economics, Politics and History
Concluding Lecture: Social Reality and the Meaning of Life
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The Meaning of Life
The Tools of Ontology
A Unified Theory of Granularity and Vagueness (UMCS)
Partitions of Reality: How Can We Live in Several Worlds at Once
John Searle's Ontology of Social Reality and Its Problems
The Ontology of the Environment: Objects and Their Settings
The Ontology of Geography
The Ontology of Social Reality: What Sorts of Objects are Social Wholes
The Metaphysics of Real Estate: Economics, Politics and History
Concluding Lecture: Social Reality and the Meaning of Life
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WhyHappiness,Happiness,
Love,Love,
Knowledge,Knowledge,
Money,Money,
FriendshipFriendship
and Religion,and Religion,
do not make a life worth living
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This Lecture:An Introduction to Ontology
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Institute for Formal Ontology and Medical Information Science
(IFOMIS)
University of Leipzig
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Formal Ontology
term coined by Husserl
= the theory of those ontological structures
such as part-whole, universal-particular
which apply to all domains whatsoever
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Edmund Husserl
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Logical Investigations¸1900/01
– Aristotelian theory of universals
– the theory of part and whole
– the theory of dependence
– the theory of boundary, continuity and contact
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Formal Ontology vs. Formal Logic
Formal ontology deals with the interconnections of things
with objects and properties, parts and wholes, relations and collectives
Formal logic deals with the interconnections of truths
with consistency and validity, or and not
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Formal Ontology vs. Formal Logic
Formal ontology deals with formal ontological structures
Formal logic deals with formal logical structures
‘formal’ = obtain in all material spheres of reality
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for Frege, Russell, Lesniewski,
Wittgenstein, Quine, Woodger:
Logic is a ‘Zoology of Facts’
Formal theories are theories of reality
with one intended interpretation
= the world
Better: formal ontology is a zoology of facts (or of entities in general)
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a directly depicting language
‘John’ ‘( ) is red’
Object Property
Frege
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Wittgenstein’s Tractatus
Propositions
States of affairs
are pictures of
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a language to map
formal-ontological structures in reality
how deal with dynamic entities?
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a new methodof constituent ontology
to study a domain ontologically
is to establish the parts and moments of the domain
and the interrelations between them
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A Network of Domain Ontologies
Material (Regional) Ontologies
Basic Formal Ontology
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A Network of Domain Ontologies
BFO
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A Network of Domain Ontologies
B(Chem)O
BFO
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A Network of Domain Ontologies
B(Med)O
B(Chem)O
BFO
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A Network of Domain Ontologies
B(Cell)O
B(Med)O
B(Chem)O
BFO
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A Network of Domain Ontologies
B(Gen)O B(Cell)O
B(Med)O
B(Chem)O
BFO
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Reality
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Reality
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Reality
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Reality
is complicated
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What is the best language to describe this complexity?
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Anglocentric Realism
We have a huge amount of knowledge of reality,
at many different levels of granularity,
from microphysics to cosmology
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Sources of Ontological Knowledge
the study of ancient texts
the construction and testing of formal theories
the consideration of difficult counterexamples
the results of the natural sciences
technically extended English
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Anglocentric Realism
TEE = Technically Extended English
= English extended by the technical vocabularies of
chemistry, genetics, medicine, astronomy, etc.
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Anglocentric Realism
Our knowledge of reality as expressed in Technically Extended English
is increasing by the hour
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Unfortunately
… there are problems with TEE as a formal representation language
(cf. Tarski)
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Nouns and verbs
Substances and processes
Continuants and occurrents
In preparing an inventory of reality
we keep track of these two different categories of entities in two different ways
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Natural language
glues them together indiscriminately
substance
t i m
e
process
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Snapshot vs. Video
substance
t i m
e
process
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Mesoscopic reality
is divided at its natural joints
into substances:
animals, bones, rocks, potatoes
(This applies also at other levels of granularity – atoms, molecules, cells, planets, galaxies)
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The Ontology of Substances
Substances form natural kinds
(universals, species + genera)
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Processes
t i m e
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Processes
merge into one another
Process kinds merge into one another
… few clean joints either between tokens or between types
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Processes
t i m e
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Some clean joints
derive from the fact that processes are dependent on substances
(my headache is cleanly demarcated from your headache)
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Some clean joints
in realms of artefactual processes:
weddings
chess games
dog shows
ontology tutorials
some sharp divisions imputed via clocks, calendars
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Clean joints
also through language
= fiat demarcations
Quinean gerrymandering ontologies are attractive for processes
not for substances
Quine: there are no substances
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Two sorts of dependent entities
processes: unfold in time
individual qualities, roles, functions, powers: like substances: they exist in toto at any instant of time when they exist at all)
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Processes and qualities, like substances, are concrete denizens
of reality
My headache, like this lump of cheese, exists here and now,
and both will cease to exist at some time in the future.
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Substances and processes
t i m
e
process
demand different sorts of inventories
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Substances demand 3-D partonomies
space
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Processes demand 4D-partonomies
t i m e
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Processes and qualities
tropes, individual properties
Examples of processes
a whistling, a blushing, a speech, a run,
Examples of qualities:
my knowledge of French
the whiteness of this cheese
the warmth of this stone
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Processes may have temporal parts
The first 5 minutes of my headache is a temporal part of my headache
The first game of the match is a temporal part of the whole match
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Substances and qualities do not have temporal parts
The first 5-minute phase of my existence is not a temporal part of me
It is a temporal part of that complex Process which is my life
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Substances have spatial parts
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How do we glue these two different sorts of entities together mereologically?
How do we include them both in a single inventory of reality?
How do we fit these two entities together within a single system of representations?
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You are a substance
Your life is a process
You are 3-dimensional
Your life is 4-dimensional
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Substances and processes form two distinct orders of being Substances exist as a whole at every point in time at which they exist at all
Processes unfold through time, and are never present in full at any given instant during which they exist.
When do both exist to be inventoried together?
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John spent the first 25 years of his life in Kansas
when does a truthmaker for this sentence exist?
what do ‘John’ and ‘Kansas’ refer to?
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Main problem
English swings back and forth between two distinct depictions of reality
… imposing both 3-D partitions (yielding substances) and 4-D partitions (yielding processes) at the same time
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Main problem
There is a polymorphous ontological promiscuity of the English sentence,
which is inherited also by the form ‘F(a)’
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Solution: two complementary basic ontologies
Four-dimensionalism
Presentism
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1. Four-dimensionalism
All entities are spatio-temporally extended portions of an atemporal four-dimensional whole called reality
(God’s eye perspective)
Problem:
change does not exist
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2. Presentism
Both substances and processes exist, but only what exists now exists at all.\
(Perspective of mortal man)
Problem:
‘Napoleon ruled before Clinton’
‘John lived in Kansas for 25 years’
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Neither of these solutions is completely adequate
Hence
a good formal ontology must somehow contain them both
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A good formal ontology
must divide into two sub-ontologies:
1. a four-dimensionalist ontology (of processes)
cf. Quine
2. a modified presentist ontology
cf. Brentano, Aristotle, Chisholm
(takes tense seriously)
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These represent two views
of the same rich and messy reality, the reality captured promiscuously by TEE
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The Four-Dimensionalist Ontology
t i m e
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boundaries are mostly fiat
t i m e
everything is flux
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mereology works without restriction everywhere here
t i m e
clinical trial
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here time exists as part of the domain of the ontology
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The Time-Stamped Ontology
t1
t3t2
here time exists outside the ontology, as an index or time-stamp
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mereology works without restriction in every instantaneous 3-D section through
reality
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Three views/partitions of the same reality
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all contain huge amounts of knowledge of this reality
against Kant
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The Time-Stamped (3-D) Ontology
t1
t3t2
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ontology as a sequence of filmed images
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each section through reality is to be conceived in presentist terms
each section includes everything which exists, including everything which is happening,
at the corresponding now
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the two ontologies can be glued together as a video is
glued together out of snapshots
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each section through realitycontains both substances
and qualities
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each section through realitycontains both substances
and qualities
standing to each other in a relation of one-sidedontological dependence
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Basic Formal OntologyConcrete Entity
[Exists in Space and Time]Concrete Entity
[Exists in Space and Time]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology
[Perdure. Unfold in Time]
Processual EntityProcessual EntitySpatio-Temporal Region
Dim = T, T+0, T+1, T+2, T+3Spatio-Temporal Region
Dim = T, T+0, T+1, T+2, T+3
Spatial Regionof Dimension 0,1,2,3
Spatial Regionof Dimension 0,1,2,3 Dependent EntityDependent Entity
Independent EntityIndependent Entity
Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]
Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]
Role, Function, PowerHave realizations (called: Processes)
Role, Function, PowerHave realizations (called: Processes)
Substance[maximally connected causal unity]
Substance[maximally connected causal unity]
Boundary of Substance *Fiat or Bona Fide or MixedBoundary of Substance *
Fiat or Bona Fide or Mixed
Aggregate of Substances * (includes masses of stuff? liquids?)
Aggregate of Substances * (includes masses of stuff? liquids?)
Fiat Part of Substance * Nose, Ear, Mountain
Fiat Part of Substance * Nose, Ear, Mountain
Process [Has Unity]Clinical trial; exercise of role
Process [Has Unity]Clinical trial; exercise of role
Fiat Part of Process*Fiat Part of Process*
Aggregate of Processes*Aggregate of Processes*
Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*
Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*
Quasi-ProcessJohn’s Youth. John’s Life
Quasi-ProcessJohn’s Youth. John’s Life
Quasi-Quality Prices, Values, Obligations
Quasi-Quality Prices, Values, Obligations
Quasi-SubstanceChurch, College, Corporation
Quasi-SubstanceChurch, College, Corporation
Quasi-Role/Function/PowerThe Functions of the PresidentQuasi-Role/Function/Power
The Functions of the President
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Basic Formal Ontology
Concrete EntityConcrete Entity
Entity in 3-D OntologyEntity in 3-D OntologyEntity in 4-D OntologyEntity in 4-D Ontology
ProcessProcessSpatio-Temporal
Region Spatio-Temporal
Region Spatial RegionSpatial Region Dependent EntityDependent Entity Independent EntityIndependent Entity
Quality (Your Redness,
My Tallness)
Quality (Your Redness,
My Tallness)
Substance(John, his ox)Substance
(John, his ox)
3D 4Dsnapshot video
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Basic Formal OntologyConcrete Entity
[Exists in Space and Time]Concrete Entity
[Exists in Space and Time]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology
[Perdure. Unfold in Time]
Processual EntityProcessual EntitySpatio-Temporal Region
Dim = T, T+0, T+1, T+2, T+3Spatio-Temporal Region
Dim = T, T+0, T+1, T+2, T+3
Spatial Regionof Dimension 0,1,2,3
Spatial Regionof Dimension 0,1,2,3 Dependent EntityDependent Entity
Independent EntityIndependent Entity
Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]
Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]
Role, Function, PowerHave realizations (called: Processes)
Role, Function, PowerHave realizations (called: Processes)
Substance[maximally connected causal unity]
Substance[maximally connected causal unity]
Boundary of Substance *Fiat or Bona Fide or MixedBoundary of Substance *
Fiat or Bona Fide or Mixed
Aggregate of Substances * (includes masses of stuff? liquids?)
Aggregate of Substances * (includes masses of stuff? liquids?)
Fiat Part of Substance * Nose, Ear, Mountain
Fiat Part of Substance * Nose, Ear, Mountain
Process [Has Unity]Clinical trial; exercise of role
Process [Has Unity]Clinical trial; exercise of role
Fiat Part of Process*Fiat Part of Process*
Aggregate of Processes*Aggregate of Processes*
Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*
Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*
Quasi-ProcessJohn’s Youth. John’s Life
Quasi-ProcessJohn’s Youth. John’s Life
Quasi-Quality Prices, Values, Obligations
Quasi-Quality Prices, Values, Obligations
Quasi-SubstanceChurch, College, Corporation
Quasi-SubstanceChurch, College, Corporation
Quasi-Role/Function/PowerThe Functions of the PresidentQuasi-Role/Function/Power
The Functions of the President
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Basic Formal OntologyConcrete Entity
[Exists in Space and Time]Concrete Entity
[Exists in Space and Time]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 3-D Ontology[Endure. No Temporal Parts]
Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology
[Perdure. Unfold in Time]
ProcessProcessDependent EntityDependent Entity Independent Entity
Independent Entity
Quasi-ProcessMoney earning
interest
Quasi-ProcessMoney earning
interest
Quasi-Quality Prices, Values,
Obligations
Quasi-Quality Prices, Values,
Obligations Quasi-SubstanceChurch, College,
Corporation
Quasi-SubstanceChurch, College,
Corporation
Quasi-RoleFunction/PowerThe Functions
of the President
Quasi-RoleFunction/PowerThe Functions
of the President