BFO and Disease

1. BFO and Disease Barry Smith 8/19.2012

2. A Chart representing how John’s temperature changes

3. A Chart representing how John’s temperature changes

4. 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

5. BFO: The Very Top continuant occurrent independent continuant dependent continuant quality temperature

6. Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

7. Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

8. Blinding Flash of the Obvious inheres_in . organism temperature types instances John John’s temperature

9. temperature types 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature instances

10. human types embryo fetus neonate infant child adult instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John instances

11. 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)

12. independent continuant dependent continuant quality organism temperature types instances John John’s temperature

13. independent continuant dependent continuant occurrent process quality organism course of temperature changes temperature John John’s temperature John’s temperature history

14. independent continuant dependent continuant occurrent process quality organism temperature process profile temperature John John’s temperature John’s temperature history

15. independent continuant dependent continuant occurrent process quality organism life of an organism temperature John John’s temperature John’s life

16. BFO: The Very Top continuant occurrent independent continuant dependent continuant quality disposition

17. Disposition - of a glass vase, to shatter if dropped - of a human, to eat - of a banana, to ripen - of John, to lose hair

18. 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

19. Function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATPfunctions are dispositions which are designed or selected for

20. independent continuant dependent continuant occurrent process function eye process of seeing to see John’s eye function of John’s eye: to see John seeing

21. OGMS Ontology for General Medical Science http://code.google.com/p/ogms

22. Physical Disorder

23. Physical Disorder – independent continuant fiat object part A causally linked combination of physical components of the extended organism that is clinically abnormal.

24. 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

25. 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)

26. 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.

27. 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

28. 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.

29. Four distinct classificatory tasks 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

30. Four distinct BFO categories person (patient, carrier, …) – independent continuant disease (case, instance, problem, …) – specifically dependent continuant course of disease (symptom, treatment…)– occurrent representation (record, datum, diagnosis…)– generically dependent continuant

31. Four distinct BFO categories people (patients, carriers, …) – independent continuants disease (case, instance, problem, condition …) – disposition course of disease (symptom, episode, outbreak …)– realization of dispositions representations (records, data, diagnoses…)– generically dependent continuants

32. 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

33. Disorder person – independent continuant objects fiat object part object aggregate

34. 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)

35. Where does Mount Everest begin and end? Cf. Barry Smith and David M. Mark, “Do Mountains Exist?”, Environment and Planning B, 30, 2003.

36. Big Picture (with thanks to Richard Scheuermann)

37. A disease is a disposition rooted in a physical disorder in the organism and realized in pathological processes. produces bears realized_in etiological process disorder disposition pathological process produces diagnosis interpretive process signs & symptoms abnormal bodily features produces used_in recognized_as

38. 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

39. 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.

40. 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.

41. 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

42. Cirrhosis - environmental exposure • 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 • 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

43. But the disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course). Influenza - infectious • 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 • 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

44. Huntington’s Disease - genetic • 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 • 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

45. 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)

46. 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

47. 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.

48. 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.

49. 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.