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BFO and Disease
Barry Smith8/19.2012
A Chart representing how John’s temperature
changes
2
A Chart representing how John’s temperature
changes
3
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
4
BFO: The Very Top
continuant
independentcontinuant
dependentcontinuant
quality
occurrent
temperature 5
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 6
Blinding Flash of the Obvious
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 7
Blinding Flash of the Obvious
temperature types
instances
organism
John John’s
temperature .
8
inheres_in
temperature types
instances
John’s temperature
9
37ºC37.1º
C37.5º
C37.2º
C37.3º
C37.4º
C
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
human types
instances
John
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embryo
fetus adultneonat
einfant child
instantiates at t1
instantiates at t2
instantiates at t3
instantiates at t4
instantiates at t5
instantiates at t6
Temperature subtypesDevelopment-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)
11
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature
12
independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
course of temperature
changes
John’s temperature history
13
independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
temperature process profile
John’s temperature history
independentcontinuant
dependentcontinuant
quality
temperature
organism
John John’s
temperature
occurrent
process
life of an organism
John’s life
15
BFO: The Very Top
continuant occurrent
independentcontinuant
dependentcontinuant
quality disposition
16
Disposition- of a glass vase, to shatter if dropped- of a human, to eat - of a banana, to ripen- of John, to lose hair
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Dispositionif it ceases to exist, then its bearer and/or its immediate surrounding environment is physically changedits realization occurs when its bearer is in some special physical circumstancesits realization is what it is in virtue of the bearer’s physical make-up
18
:.
Function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATP
functions are dispositions which are designed or selected for
19
independentcontinuant
dependentcontinuant
function
to seeeye
John’s eye function of John’s eye: to see
occurrent
process
process of seeing
John seeing
20
OGMSOntology for General Medical
Science
http://code.google.com/p/ogms
21
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Physical Disorder
:.
Physical Disorder
– independent continuant
fiat object part
A causally linked combination of physical components of the extended organism that is clinically abnormal.
23
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
24
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)
25
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.
26
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
27
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.
28
Four distinct classificatory tasks
1. of people (patients, carriers, …)
2. of diseases (cases, instances, problems, …)
3. of courses of disease (symptoms, treatments…)
4. of representations (records, observations, data, diagnoses…)
ICD confuses 1. & 2.
HL7, most standard terminologies, confuse 2. and 4
29
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
30
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
31
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
32
Disorder
1. person
– independent continuantobjects
fiat object part
object aggregate
33
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)
36
A disease is a disposition rooted in a
physical disorder in the organism and
realized in pathological processes.
etiological process
produces
disorder
bears
disposition
realized_in
pathological process
produces
abnormal bodily features
recognized_as
signs & symptomsinterpretive process
produces
diagnosis
used_in37
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: baldness38
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.
39
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.
40
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
41
Cirrhosis - environmental exposure
Etiological process - phenobarbitol-induced 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
42
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 disorder (transient disease course).
43
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
44
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)
45
Arterial AneurysmDisposition – atherosclerosis
realized inPathological process – fatty material collects within the walls of arteries
producesDisorder – artery with weakened wall
bearsDisposition – of artery to become distended
realized_inPathological process – process of distending
producesDisorder – arterial aneurysm
bearsDisposition – of artery to rupture
realized inPathological process – (catastrophic event) of rupturing
producesDisorder – ruptured artery, arterial system with dangerously low blood pressure
bearsDisposition – circulatory failure
realized inPathological process – exsanguination, failure of homeostasis
producesDeath 46
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.
47
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.
48
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