Transcript BFO and Disease

BFO and Disease
Barry Smith
8/19.2012
A Chart representing how
John’s temperature changes
2
A Chart representing how
John’s temperature changes
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John’s temperature,
the temperature he has throughout his
entire life, cycles through different
determinate temperatures from one
time to the next
John’s temperature is a physiology
variable which, in thus changing,
exerts an influence on other physiology
variables through time
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BFO: The Very Top
continuant
independent
continuant
occurrent
dependent
continuant
quality
temperature
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Blinding Flash of the Obvious
independent
continuant
dependent
continuant
quality
organism
John
temperature
John’s
temperature
types
instances
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Blinding Flash of the Obvious
independent
continuant
dependent
continuant
quality
organism
John
temperature
John’s
temperature
types
instances
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Blinding Flash of the Obvious
inheres_in
organism
John
temperature
John’s
temperature
types
instances
8
types
temperature
37ºC
instantiates
at t1
37.1ºC
instantiates
at t2
37.2ºC
instantiates
at t3
37.3ºC
instantiates
at t4
37.4ºC
instantiates
at t5
37.5ºC
instantiates
at t6
John’s temperature
instances
9
types
human
embryo
instantiates
at t1
fetus
instantiates
at t2
neonate
instantiates
at t3
infant
child
instantiates
at t4
instantiates
at t5
adult
instantiates
at t6
John
instances
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Temperature subtypes
Development-stage subtypes
are threshold divisions (hence we do
not have sharp boundaries, and we
have a certain degree of choice, e.g. in
how many subtypes to distinguish,
though not in their ordering)
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independent
continuant
dependent
continuant
quality
organism
John
temperature
types
John’s
temperature
instances
12
independent
continuant
organism
John
dependent
continuant
occurrent
quality
process
temperature
John’s
temperature
course of
temperature
changes
John’s
temperature history
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independent
continuant
organism
John
dependent
continuant
occurrent
quality
process
temperature
temperature
process profile
John’s
temperature
John’s
temperature history
independent
continuant
organism
John
dependent
continuant
occurrent
quality
process
temperature
John’s
temperature
life of an
organism
John’s
life
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BFO: The Very Top
continuant
independent
continuant
occurrent
dependent
continuant
quality
disposition
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Disposition
-
of
of
of
of
a glass vase, to shatter if dropped
a human, to eat
a banana, to ripen
John, to lose hair
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Disposition
if it ceases to exist, then its bearer
and/or its immediate surrounding
environment is physically changed
its realization occurs when its bearer is in
some special physical circumstances
its realization is what it is in virtue of the
bearer’s physical make-up
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Function
-
of
of
of
of
liver: to store glycogen
birth canal: to enable transport
eye: to see
mitochondrion: to produce ATP
functions are dispositions which are
designed or selected for
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:.
independent
continuant
eye
John’s eye
dependent
continuant
occurrent
function
process
to see
process of
seeing
function of John’s
eye: to see
John seeing
20
OGMS
Ontology for General Medical
Science
http://code.google.com/p/ogms
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Physical Disorder
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Physical Disorder
– independent
continuant
fiat object part
A causally linked combination
of physical components of the
extended organism that is
clinically abnormal.
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:.
Clinically abnormal
– (1) not part of the life plan for an organism
of the relevant type (unlike aging or
pregnancy),
– (2) causally linked to an elevated risk
either of pain or other feelings of illness,
or of death or dysfunction, and
– (3) such that the elevated risk exceeds a
certain threshold level.*
*Compare: baldness
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Realizable dependent continuants
Role: nurse role, pathogen role, food role
Disposition: fragility, virulence, susceptibility,
genetic disposition to disease X
Function: to pump (of the heart), to unlock
(of the key)
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Role (Externally-Grounded
Realizable Entity)
role =def. a realizable entity
• which exists because the bearer is in
some special physical, social, or
institutional set of circumstances in which
the bearer does not have to be, and
• is not such that, if it ceases to exist, then
the physical make-up of the bearer is
thereby changed.
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Disposition (Internally-Grounded
Realizable Entity)
disposition =def.
a realizable entity which if it ceases to
exist, then its bearer is physically
changed, and
whose realization occurs when this
bearer is in some special physical
circumstances, in virtue of the bearer’s
physical make-up
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Function (A Disposition Designed or
Selected For)
function =def.
a disposition that
exists in virtue of the bearer’s physical make-up,,
and
this physical make-up is something the bearer
possesses because it came into being, either
through evolution (in the case of natural biological
entities) or through intentional design (in the case
of artifacts), in order to realize processes of a
certain kind.
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Four distinct classificatory tasks
1.
2.
3.
4.
of people (patients, carriers, …)
of diseases (cases, instances, problems, …)
of courses of disease (symptoms, treatments…)
of representations (records, observations, data,
diagnoses…)
ICD confuses 1. & 2.
HL7, most standard terminologies, confuse 2. and 4
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Four distinct BFO categories
1. person (patient, carrier, …)
– independent continuant
2. disease (case, instance, problem, …)
– specifically dependent continuant
3. course of disease (symptom, treatment…)
– occurrent
4. representation (record, datum, diagnosis…)
– generically dependent continuant
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Four distinct BFO categories
1. people (patients, carriers, …)
– independent continuants
2. disease (case, instance, problem, condition …)
– disposition
3. course of disease (symptom, episode, outbreak …)
– realization of dispositions
4. representations (records, data, diagnoses…)
– generically dependent continuants
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Disposition
Internally-Grounded Realizable Entity
A disposition is
a realizable entity which is such that, if it
ceases to exist, then its bearer is
physically changed,
whose realization occurs, in virtue of the
bearer’s physical make-up, when this
bearer is in some special physical
circumstances
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Disorder
1. person
– independent continuant
objects
fiat object part
object aggregate
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Disorder
A fiat object part of an organism which
serves as the bearer of a disposition of a
certain sort
This fiat object may have no determinate
boundaries
(compare: Downtown Santa Barbara)
34
Where does Mount Everest begin and end?
Cf. Barry Smith and David M. Mark, “Do Mountains
Exist?”, Environment and Planning B, 30, 2003.
35
Big Picture (with thanks to Richard Scheuermann)
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A disease is a disposition rooted in a
physical disorder in the organism and
realized in pathological processes.
produces
etiological process
bears
disorder
realized_in
disposition
pathological process
produces
diagnosis
interpretive process
produces
signs & symptoms
used_in
abnormal bodily features
recognized_as
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Elucidation of Primitive Terms



‘bodily feature’ - an abbreviation for a physical
component, a bodily quality, or a bodily process.
disposition - an attribute describing the propensity to
initiate certain specific sorts of processes when
certain conditions are satisfied.
clinically abnormal - some bodily feature that



(1) is not part of the life plan for an organism of the relevant
type (unlike aging or pregnancy),
(2) is causally linked to an elevated risk either of pain or
other feelings of illness, or of death or dysfunction, and
(3) is such that the elevated risk exceeds a certain threshold
level.*
*Compare: baldness
38
Definitions - Foundational Terms

Disorder =def. – A causally linked combination of
physical components that is clinically abnormal.

Pathological Process =def. – A bodily process that is
a manifestation of a disorder and is clinically
abnormal.

Disease =def. – A disposition (i) to undergo
pathological processes that (ii) exists in an organism
because of one or more disorders in that organism.
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Dispositions and Predispositions




All diseases are dispositions; not all dispositions are
diseases.
A predisposition is a disposition.
Predisposition to Disease of Type X =def. – A disposition
in an organism that constitutes an increased risk of the
organism’s subsequently developing the disease X.
HNPCC is caused by a
 disorder (mutation) in a DNA mismatch repair gene that
 disposes to the acquisition of additional mutations from
defective DNA repair processes, and thus is a
 predisposition to the development of colon cancer.
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Definitions - Clinical Evaluation Terms


Sign =def. – A bodily feature of a patient that is
observed in a physical examination and is deemed by
the clinician to be of clinical significance. (Objectively
observable features)
Symptom =def. – A experienced bodily feature of a
patient that is observed by and observable only by the
patient and is of the type that can be hypothesized by a
patient to be a realization of a disease. (A restricted
family of phenomena including pain, nausea, anger,
drowsiness, which are of their nature experienced in the
first person)
Symptoms are subjective. But this does not mean that there is
no objective fact of the matter whether a given symptom exists
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Cirrhosis - environmental exposure







Etiological process - phenobarbitolinduced hepatic cell death
 produces
Disorder - necrotic liver
 bears
Disposition (disease) - cirrhosis
 realized_in
Pathological process - abnormal tissue
repair with cell proliferation and
fibrosis that exceed a certain
threshold; hypoxia-induced cell death
 produces
Abnormal bodily features
 recognized_as
Symptoms - fatigue, anorexia
Signs - jaundice, splenomegaly







Symptoms & Signs
 used_in
Interpretive process
 produces
Hypothesis - rule out cirrhosis
 suggests
Laboratory tests
 produces
Test results - elevated liver enzymes in
serum
 used_in
Interpretive process
 produces
Result - diagnosis that patient X has a
disorder that bears the disease
cirrhosis
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Influenza - infectious







Etiological process - infection of
airway epithelial cells with influenza
virus
 produces
Disorder - viable cells with influenza
virus
 bears
Disposition (disease) - flu
 realized_in
Pathological process - acute
inflammation
 produces
Abnormal bodily features
 recognized_as
Symptoms - weakness, dizziness
Signs - fever







Symptoms & Signs
 used_in
Interpretive process
 produces
Hypothesis - rule out influenza
 suggests
Laboratory tests
 produces
Test results - elevated serum antibody titers
 used_in
Interpretive process
 produces
Result - diagnosis that patient X has a
disorder that bears the disease flu
But the disorder also induces normal
physiological processes (immune response)
that can results in the elimination of the 43
disorder (transient disease course).
Huntington’s Disease - genetic







Etiological process - inheritance of
>39 CAG repeats in the HTT gene
 produces
Disorder - chromosome 4 with
abnormal mHTT
 bears
Disposition (disease) - Huntington’s
disease
 realized_in
Pathological process - accumulation of
mHTT protein fragments, abnormal
transcription regulation, neuronal cell
death in striatum
 produces
Abnormal bodily features
 recognized_as
Symptoms - anxiety, depression
Signs - difficulties in speaking and
swallowing







Symptoms & Signs
 used_in
Interpretive process
 produces
Hypothesis - rule out Huntington’s
 suggests
Laboratory tests
 produces
Test results - molecular detection of
the HTT gene with >39CAG repeats
 used_in
Interpretive process
 produces
Result - diagnosis that patient X has a
disorder that bears the disease
Huntington’s disease
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HNPCC - genetic pre-disposition







Etiological process - inheritance of a mutant mismatch repair gene
 produces
Disorder - chromosome 3 with abnormal hMLH1
 bears
Disposition (disease) - Lynch syndrome
 realized_in
Pathological process - abnormal repair of DNA mismatches
 produces
Disorder - mutations in proto-oncogenes and tumor suppressor genes with
microsatellite repeats (e.g. TGF-beta R2)
 bears
Disposition (disease) - non-polyposis colon cancer
 realized in
Symptoms (including pain)
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Arterial Aneurysm
Disposition – atherosclerosis
realized in
Pathological process – fatty material collects within the walls of arteries
produces
Disorder – artery with weakened wall
bears
Disposition – of artery to become distended
realized_in
Pathological process – process of distending
produces
Disorder – arterial aneurysm
bears
Disposition – of artery to rupture
realized in
Pathological process – (catastrophic event) of rupturing
produces
Disorder – ruptured artery, arterial system with dangerously low blood pressure
bears
Disposition – circulatory failure
realized in
Pathological process – exsanguination, failure of homeostasis
produces
Death
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Definition: Etiology

Etiological Process =def. – A process in an organism that
leads to a subsequent disorder.

Example: toxic chemical exposure resulting in a mutation in
the genomic DNA of a cell; infection of a human with a
pathogenic virus; inheritance of two defective copies of a
metabolic gene

The etiological process creates the physical basis of that
disposition to pathological processes which is the disease.
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Definitions - Diagnosis

Clinical Picture =def. – A representation of a
clinical phenotype that is inferred from the
combination of laboratory, image and clinical
findings about a given patient.

Diagnosis =def. – A conclusion of an interpretive
process that has as input a clinical picture of a given
patient and as output an assertion to the effect that the
patient has a disease of such and such a type.
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Definitions - Qualities

Manifestation of a Disease =def. – A bodily feature of a
patient that is (a) a deviation from clinical normality that exists
in virtue of the realization of a disease and (b) is observable.





Observability includes observable through elicitation of response or
through the use of special instruments.
Preclinical Manifestation of a Disease =def. – A
manifestation of a disease that exists prior to its becoming
detectable in a clinical history taking or physical examination.
Clinical Manifestation of a Disease =def. – A manifestation
of a disease that is detectable in a clinical history taking or
physical examination.
Phenotype =def. – A (combination of) bodily feature(s) of an
organism determined by the interaction of its genetic make-up
and environment.
Clinical Phenotype =def. – A clinically abnormal phenotype.49