relating functions and dispositions using nonmonotonic reasoning
TRANSCRIPT
Introduction Functions and dispositions Conclusions
Relating functions and dispositions usingnonmonotonic reasoning
Robert Hoehndorf1,2, Janet Kelso2, Heinrich Herre1
1Institute for Informaticsand
Research Group Ontologies in Medicine, Institute for Medical Informatics,Statistics and Epidemiology, University of Leipzig
2Department of Evolutionary Genetics, Max-Planck-Institute for EvolutionaryAnthropology
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologies
Gene Ontology (molecule function)
Celltype Ontology (cell function)
FMA, Anatomie (organ function)
Disease Ontology, (Human/Mammalian) Phenotype Ontology(malfunctioning)
OBI (device function)
Protein Ontology
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesA solved problem?
A function f is
1 a realizable dependent continuant, which
2 has a bearer which is an independent continuant, and3 is of a type instances of which typically have realizations; each
realization is1 a process in which the bearer is a participant,2 that occurs in virtue of the bearer’s physical makeup,3 this physical make-up is something which that bearer possesses
because of how it came into being.
Arp and Smith, 2008
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
A function f is
a realizable dependent continuant, which
“To make thumping noises” is realizable.
has a bearer which is an independent continuant, and
The heart is an independent continuant.
is of a type instances of which typically have realizations;
“To make thumping noises” is typically realized.
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
A function f is
a realizable dependent continuant, which
“To make thumping noises” is realizable.
has a bearer which is an independent continuant, and
The heart is an independent continuant.
is of a type instances of which typically have realizations;
“To make thumping noises” is typically realized.
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
A function f is
a realizable dependent continuant, which
“To make thumping noises” is realizable.
has a bearer which is an independent continuant, and
The heart is an independent continuant.
is of a type instances of which typically have realizations;
“To make thumping noises” is typically realized.
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
Each realization is
a process in which the bearer is a participant,
Hearts participate in thumping-noise-making processes.
that occurs in virtue of the bearer’s physical makeup,
Thumping-noise-making occurs due to the physical makeup ofthe heart.
this physical make-up is something which that bearerpossesses because of how it came into being.
Heart possess their makeup due to how they came into being.
Therefore: The function of the heart is to make thumping noises.(BFO)
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
Each realization is
a process in which the bearer is a participant,
Hearts participate in thumping-noise-making processes.
that occurs in virtue of the bearer’s physical makeup,
Thumping-noise-making occurs due to the physical makeup ofthe heart.
this physical make-up is something which that bearerpossesses because of how it came into being.
Heart possess their makeup due to how they came into being.
Therefore: The function of the heart is to make thumping noises.(BFO)
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
Each realization is
a process in which the bearer is a participant,
Hearts participate in thumping-noise-making processes.
that occurs in virtue of the bearer’s physical makeup,
Thumping-noise-making occurs due to the physical makeup ofthe heart.
this physical make-up is something which that bearerpossesses because of how it came into being.
Heart possess their makeup due to how they came into being.
Therefore: The function of the heart is to make thumping noises.(BFO)
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesBFO: The function of the heart is to make thumping noises
Each realization is
a process in which the bearer is a participant,
Hearts participate in thumping-noise-making processes.
that occurs in virtue of the bearer’s physical makeup,
Thumping-noise-making occurs due to the physical makeup ofthe heart.
this physical make-up is something which that bearerpossesses because of how it came into being.
Heart possess their makeup due to how they came into being.
Therefore: The function of the heart is to make thumping noises.(BFO)
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesFunction in BFO
functions may “typically” not be realized: sperm cells
functions may be acquired after through transformation (notat time of creation): angiotensin I to angiotensin II
what is a realization?
Introduction Functions and dispositions Conclusions
Functions in biomedical ontologiesRealizations
What makes a process a realization of a function?
Participation of the function bearer is not sufficient.
A protein’s function “to transport” is
realized by transport processes,in which the protein participatesas a transporter.
Mode of participation in a process necessary to understandrealizations.
Use of processual or relational roles/qua entities
Introduction Functions and dispositions Conclusions
Ontology of Functions (OF)
Conceptual framework tomodel functions
Implemented in OWL
Introduction Functions and dispositions Conclusions
Ontology of Functions (OF)Open questions
What is the relation between function and disposition?
What is the relation between function and causality?
How do functions come into being?
What is a function?
Introduction Functions and dispositions Conclusions
Larry WrightReducing function to causality
The function of X is Z means
1 X is there because it does Z ,
2 Z is a consequence (or result) of X ’s being there.
Introduction Functions and dispositions Conclusions
John SearleFunctions as social concepts
All functions are socially ascribed by an agent to an object.
Functions are always observer-relative.
Function ascription is based on brute facts.
Introduction Functions and dispositions Conclusions
Nicolai HartmannFunction ascription and causality
1 Setting a goal (in the future)
2 Planning the goal’s realization
3 Realizing the goal (causally)
(1) and (2) create functionality
Must realization be possible?
Introduction Functions and dispositions Conclusions
MalfunctioningsOverview
Setting a goal
Planning
No realization possible: missing disposition
Malfunctioning is function without disposition.
Functionality does not imply causality.
But: normally, function-bearers have the disposition to realizetheir function.
Normally, entities do not malfunction.
Introduction Functions and dispositions Conclusions
MalfunctioningsFormal characterization
If e has the function f (with goal Tgoal), and e is notmalfunctioning, then e has a disposition with goal Tgoal .
A(mf ) = hasFunction(e, f ) ∧ f :: F ∧ ¬mf (e)→∃d(d :: D ∧ isa(D,Disposition) ∧ inheresIn(d , e)∧Treq(F ) = Treq(D) ∧ Tgoal(F ) = Tgoal(D))
Normally, e is not malfunctioning.
A(mf )∧∀P((A(P) ∧ ∀x(P(x)→ mf (x)))→(∀x(P(x)↔ mf (x))))
Introduction Functions and dispositions Conclusions
MalfunctioningsFormal characterization
If e has the function f (with goal Tgoal), and e is notmalfunctioning, then e has a disposition with goal Tgoal .
A(mf ) = hasFunction(e, f ) ∧ f :: F ∧ ¬mf (e)→∃d(d :: D ∧ isa(D,Disposition) ∧ inheresIn(d , e)∧Treq(F ) = Treq(D) ∧ Tgoal(F ) = Tgoal(D))
Normally, e is not malfunctioning.
A(mf )∧∀P((A(P) ∧ ∀x(P(x)→ mf (x)))→(∀x(P(x)↔ mf (x))))
Introduction Functions and dispositions Conclusions
MalfunctioningsNon-monotonicity
Classical (monotonic) inference:
S ⊆ T → S |= ⊆ T |=
non-monotonic inference permits default reasoning
e is not malfunctioning as long as not proven otherwise
use of default logics, circumscription or auto-epistemic logics
implementation using answer-set programming
Introduction Functions and dispositions Conclusions
ApplicationFunctions and malfunctionings
Human (functional) anatomy: Ear CC-hasFunction Hearing
∀x(x :: Ear → ∃y(y :: Hearing ∧ II-hasFunction(x , y)))
Disposition D to participate in hearing processes (realization)as receiver (role)
If an instance e of Ear is not malfunctioning, it has adisposition d (which is an instance of D).
Normally, instances of Ear are not malfunctioning (withrespect to Hearing).
Deafness (HP:0000404) implies malfunctioning of its bearerw.r.t. Hearing
Introduction Functions and dispositions Conclusions
Summary
BFO’s definition of function needs refinement.
Philosophical explanations of biological functions can bedivided in:
reductions to causalitysocial ascription
each relates functionality to causality
most use normality or typicality
non-monotonic reasoning is necessary to formalize normality
focus on necessary conditions and inferences instead ofdefinitions for function
Introduction Functions and dispositions Conclusions
Acknowledgements
Heinrich Herre
Janet Kelso
Patryk Burek
Frank Loebe
Hannes Michalek
Introduction Functions and dispositions Conclusions
Thank you!
Introduction Functions and dispositions Conclusions
Dispositions
An individual e has the disposition d to cause an instance of Tgoal
iff e causes a situation s :: Tgoal whenever e is placed in the rightcircumstances.
Describe “in the right circumstances” using asituational/relational role.
Dispositions are possibilities to cause certain states of affairsto become factual.
What is the relation between function and disposition?