1. VT

2. Bodies and Bodily Systems Barry Smith and Igor Papakin

4. INTEGUMENTARY (SKIN) SYSTEM

5. MUSCULO- SKELETAL SYSTEM

6. CONNECTIVE SYSTEM

7. The Connective System The connective system contains all the bona fide boundaries in the interior of the body: the membranes and layers of fat which create an internal framework of support for the organs This system performs active work by maintaining the internal sub-environments in the necessary conditions

9. DIGESTIVE SYSTEM

10. RESPIRATORY SYSTEM

11. URINARY SYSTEM

12. IMMUNE SYSTEM

13. CIRCULATORY SYSTEM

14. (Principal Organs)

15. NERVOUS SYSTEM

16. The autonomous part of the nervous system This is the oldest part of the nervous system from the standpoint of evolution. It regulates the vegetative functions of the body. ‘Vegetative’ means: automatic, not dependent on one’s mind.

17. Example I decide to run. I can decide to start or stop running because running is controlled by the somatic part of the nervous system. BUT: when I’m running my heart is beating more quickly because my muscles need more oxygen for their work The autonomous part of the nervous system is responsible for these changes. You cannot decide to start or stop digesting the food that is already in your stomach Digestion and heart-beat are vegetative processes

18. The autonomous part of the nervous system (regulatory links to other systems)

19. ENDOCRINE SYSTEM

20. The endocrine system is like a system of the radio transmitters which are broadcasting to the every cell of the body. Their ‘waves’ are hormones. The medium of transmission is the blood. The cell have ‘receivers’ –specific receptors for particular hormones

21. ENDOCRINE SYSTEM

22. IMMUNE SYSTEM

23. Bodily Systems are Component Parts of Bodies respiratorydigestive skeletal circulatory musculatory immune

25. A system for keeping your tools safe

26. A system for keeping your jewels safe

27. Bodily Systems interconnect

28. plus NERVOUS SYSTEM (Regulatory Links)

29. Thus bodily systems are separated from each other by fiat boundaries

30. MUSCULO- SKELETAL SYSTEM

31. Why one system?

32. Rather than two:

33. MUSCLE SYSTEMSKELETAL SYSTEM

34. because without muscle the skeletal system would fall apart and without bone the muscles would have nothing to attach themselves

35. Why talk of one nervous system rather than two? Is the boundary between the autonomous and vegetative system porous (can you train yourself to control vegetative processes?)

36. Bodily systems are like arms and legs

37. but the fiat boundaries separating them from their surroundings are much more complicated

38. plus NERVOUS SYSTEM (Regulatory Links)

39. Where to fit bodily systems into an ontology?

40. Problems of Medical Ontology Knowledge Mining Tacit Knowledge Doctors don’t know ontology Aristotle is no help either

41. System (OED) I. An organized or connected group of objects. II. A set of principles, etc.; a scheme, method.

42. System (OED) I.An organized or connected group of objects. 1.A set or assemblage of things connected, associated, or interdependent, so as to form a complex unity; a whole composed of parts in orderly arrangement according to some scheme or plan 2.Physics. A group of bodies moving about one another in space under some particular dynamical law, as the law of gravitation; 3.Biol. A set of organs or parts in an animal body of the same or similar structure, or subserving the same function, as the nervous, muscular, osseous, etc. systems, the digestive, respiratory, reproductive, etc. systems; also, each of the primary groups of tissues in the higher plants. 4.In various scientific and technical uses: A group, set, or aggregate of things, natural or artificial, forming a connected or complex whole.

43. System (OED) 4. In various scientific and technical uses: A group, set, or aggregate of things, natural or artificial, forming a connected or complex whole. a. of natural objects or phenomena, as geological formations, mountains, rivers, winds, forces, etc.; also of lines, points, etc. in geometry. b. of artificial objects or appliances arranged or organized for some special purpose, as pulleys or other pieces of mechanism, columns or other details of architecture, canals, railway lines, telegraphs, etc. c. Geol. A major stratigraphic division, composed of a number of series and corresponding to a period in time; the rocks deposited during any specific period. d. The set of the various phases that two or more given metals are capable of forming at different temperatures and pressures, as alloy system. e. Linguistics. A group of terms, units, or categories, in a paradigmatic relationship to one another. f. Computers. A group of related programs; spec. = operating system

44. System (OED) II. A set of principles, etc.; a scheme, method. 8. The set of correlated principles, ideas, or statements belonging to some department of knowledge or belief 9. An organized scheme or plan of action, esp. one of a complex or comprehensive kind; an orderly or regular method of procedure. Now usually with defining word or phrase. … d. Any method devised by a gambler for determining the placing of his bets. 10. In the abstract (without a or pl.): Orderly arrangement or method; systematic form or order.

45. Bodily systems are SNAP entities

46. Substances and processes exist in time in different ways substance t i m e process

47. SNAP and SPAN 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

48. Need for different perspectives Not one ontology, but a multiplicity of complementary ontologies Cf. Quantum mechanics: particle vs. wave ontologies

49. SNAPshot Video (SPAN) ontology ontology substance t i m e process

50. SNAP and SPAN stocks and flows commodities and services product and process anatomy and physiology synchrony and diachrony

51. SNAP and SPAN SNAP entities - have continuous existence in time - preserve their identity through change - exist in toto if they exist at all SPAN entities - have temporal parts - unfold themselves phase by phase - exist only in their phases/stages

52. SPQR… entities States, powers, qualities, roles … functions, dispositions, plans, shapes SPQR… entities are all dependent on substances

53. SOME SYSTEMS ARE SPQR ENTITIES legal systems languages (as systems of competences) religions (as systems of beliefs)

54. The SPAN Ontology t i m e

55. SNAP ontology many sharp boundaries SPAN ontology many smeered boundaries Fiat boundaries can be drawn in each (Cf. Ingvar‘s theory of 4-D shapes)

56. Mesoscopic reality isdivided at its joints into substances: animals, bones, rocks, potatoes and into parts of substances: ARMS LEGS and BODILY SYSTEMS

57. Processes Processes merge into one another Process kinds merge into one another … few clean joints either between instances or between types

58. boundaries are mostly fiat t i m e everything is flux

59. SNAP: Entities existing in toto at a time

60. Three kinds of SNAP entities 1.Substances 2.SPQR… entities 3.Spatial regions, Contexts, Niches

61. Functions The function of the heart is to pump blood

63. SNAP Fiat part of substance Extremity (hand, arm) Bodily System

64. SPAN: Entities extended in time

66. Functioning The heart’s pumping of blood

67. Granularity spatial regionsubstance parts of substances are always substances

68. Granularity spatial regionsubstance parts of spatial regions are always spatial regions

69. Granularity process parts of processes are always processes

70. MORAL Relations crossing the SNAP/SPAN border are never part-relations

71. John’s life substance John physiological processes sustaining in existence

72. How do you know whether an entity is SNAP or SPAN?

73. problem cases traffic jam forest fire anthrax epidemic hurricane Maria waves shadows

74. forest fire: an object (complex substance) Compare: a pack of monkeys jumping from tree to tree the Olympic flame: a process or a thing? anthrax spores are little monkeys

75. System (OED) I.An organized or connected group of objects. 1.A set or assemblage of things connected, associated, or interdependent, so as to form a complex unity; a whole composed of parts in orderly arrangement according to some scheme or plan

76. Roman Ingarden Material Ontology Theory of Causality Theory of Relatively Isolated Systems Modularity

77. Roman Ingarden: organisms, in order to be able to sustain themselves effectively as identical through time, must be at least in some respects “bounded off from the surrounding world and partially isolated or, better, shielded from it.”

78. Each complex multi-cellular organism is a relatively isolated causal system which is organized in modular fashion in such a way as to contain within itself numerous further relatively isolated causal systems on successively lower levels. The latter are hierarchically ordered and at the same time both partially interconnected (they collaborate in their functioning) and also partially segregated from each other via coverings or membranes which protect their interiors from certain external influences and also allow other kinds of influences and substances to pass through them.

79. MODULARITY: Bodily Systems can be viewed at different levels of granularity

80. NERVOUS SYSTEM

81. Relative Isolation The container formed by the skin or hide around a bodily system may be topologically highly complicated

82. The whole body “is surrounded by a well-defined enclosure—for man this is the skin, for the majority of animals— the hide.” The skin or hide is itself a complex organ which is composed of many layers and has many functions in the life-process, precisely because it forms the boundary between the body and the external world. Thus it is a permeable membrane, which participates in the expulsion of water and waste-products.

83. Organisms order to be able to sustain themselves effectively as identical through time, must be at least in some respects “bounded off from the surrounding world and partially isolated or shielded from it.”

84. Each multi-cellular organism is a system of relatively isolated causal systems organized in modular fashion in such a way as to contain within itself further relatively isolated causal systems on successively lower levels. The systems within this modular hierarchy are both partially interconnected (they collaborate in their functioning) and also partially segregated via coverings or membranes which protect their interiors from certain external influences and also allow other kinds of influences and substances to pass through them

85. Bodily systems are not absolutely closed off from each other: they are partially open and partially shielded. There are paths between them along which a certain restricted spectrum of causal influences and substances may flow. Each sense organ is a partially open system which is “attuned to a special selection of outside processes and at the same time also shielded in other respects.”

86. Two kinds of fiat boundaries

87. Recall: Bodily systems have fiat boundaries Endocrine system unified as a system of scattered radio transmitters is unified: through transmitted waves

88. How are these fiat boundaries determined? Mario Bunge, Treatise of Basic Philosophy, vol. 4: Ontology II: A World of Systems, "Every science studies systems of some kind, whether natural (physical, chemical, biological, or social) or artificial (technical). Moreover most sciences study nothing but systems“ (p.1). Ingvar: I agree whole-heartedly. [But in my view:] systems make up some special species of the genus pattern … and patterns have fiat boundaries

89. Better systems make up some special species of the genus pattern But: systems are patterns = tokens Token patterns have fiat boundaries Thus systems have fiat boundaries

90. Causal Systems 1.A causal system contains things with properties and corresponding spatial and spatiotemporal patterns. 2.A causal system contains a lot of property- grounded relations, but it is not identical with a set or an aggregate of such relations. 3. A causal system contains a lot of both spatial, temporal, and causal relations, but it is not identical with a set or an aggregate of such relations.

91. Causal Systems 1.A causal system contains things with properties and corresponding spatial and spatiotemporal patterns. 2.A causal system contains a lot of property-grounded relations, but it is not identical with a set or an aggregate of such relations. 3. A causal system contains a lot of both spatial, temporal, and causal relations, but it is not identical with a set or an aggregate of such relations.

92. Spatial patterns

93. Spatial properties

94. Functions: Spatio-temporal patterns = 4-dimensional shapes Property-grounded relations: e.g. is taller than, grounded in the respective heights

95. Causal Systems 1.A causal system contains things with properties and corresponding spatial and spatiotemporal patterns. 2.A causal system is held together by a lot of property-grounded relations, but it is not identical with a set or an aggregate of such relations. 3. A causal system is held together by a lot of both spatial, temporal, and causal relations, but it is not identical with a set or an aggregate of such relations.

96. Causal Systems 4. A causal system contains a specific kind of causal unity. STILL NEEDS TO BE DETERMINED 5. The type-identity of a causal system is independent of its spatiotemporal size. 6. Causal systems can be represented by mind-dependent patterns. 7. Causal systems are fiat objects.

97. Ingvar The kinds of possible causal interactions which constitute a causal system have to be chosen from all the possible ones. This means that every causal system is a fiat system. By fiat we decide to focus attention only on some kinds of interactions. But conventionality can fuse with mind- independence. The "fiatness" of causal systems, just like the "fiatness" of spatial patterns, does not cancel mind-independence.

98. What gives a bodily system its unity? Why do we divide up the bodily systems in this way rather than in that? Because each performs some CRITICAL FUNCTION = if functioning ceases the organism will die

99. Sustaining in Existence John’s life John sustaining in existence John’s nervous system functioning of John’s nervous system

100. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism

101. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-sceletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism SkinSeparates the internal environment from the external medium

102. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-sceletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism Musculo- skeletal Maintains the shape of the body and its movement in confrontation with gravity

103. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism ConnectiveSeparates sub-environments inside the body, maintains the internal organs mechanically

104. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism DigestiveExchanges substances (solid substances in-out, liquids in)

105. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies the all systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism RespiratoryExchanges substances (gas in-out)

106. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies the all systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part) Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism UrinaryExchanges substances (liquid out)

107. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies the all systems of the organism with blood Nervous Directed, fast, ‘question-answer’ like regulation of the movement of the body and of the vegetative functions of the internal organs Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism CirculatorySupplies all the systems of the organism with blood

108. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies the all systems of the organism with blood Nervous Directed, fast, ‘question-answer’ like regulation of the movement of the body and of the vegetative functions of the internal organs Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism NervousDirected, fast, ‘question- answer’-like regulation of the movement of the body (somatic part) and of the vegetative functions of the internal organs (autonomous part)

109. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’ like regulation of the movement of the body and of the vegetative functions of the internal organs Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism EndocrineBroadcasting-type regulation of the metabolism, the growth and development and sexual differentiation of the organism

110. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body and of the vegetative functions of the internal organs Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism ImmuneRegulation of the substantial identity of the organism

111. SNAPSPAN Skin Separates the internal environment from the external medium Musculo-skeletal Maintains the shape of the body and its movement in confrontation with gravity Connective Separates sub-environments inside the body, maintains the internal organs mechanically DigestiveExchanges substances (solid substances in-out, liquids in) RespiratoryExchanges substances (gas in-out) UrinaryExchanges substances (liquid out) CirculatorySupplies all the systems of the organism with blood Nervous Directed, fast, ‘question-answer’-like regulation of the movement of the body and of the vegetative functions of the internal organs Endocrine Broadcasting-type regulation of the metabolism, the growth and the development and the sexual differentiation of the organism ImmuneRegulation of the substantial identity of the organism ReproductiveReproduction of the organism Reproductiv e Reproduction of the organism

112. Millikan’s “proper function” “The proper function of some mechanism, trait, or process is what it is supposed to do, what it has been designed to do, what it ought to do.”

113. Millikan “An item X has proper function F only if: (i) X is a reproduction of some prior item that, because of the possession of certain reproduced properties, actually performed F in the past, and X exists because of this performance; or (ii) X is the product of a device that had the performance of F as a proper function and normally performs F by way of producing an item like X.”

114. Critical Function An item X performs the critical function F for organism Y if and only if: (i) F is the proper function of X and (ii) the continuing to exist of Y is dependent on the continued functioning of F

115. Definition of Bodily System X is a bodily system for organism Y if and only if (i) X is part of Y and (ii) there is a critical function of Y and X performs this critical function Or: has the disposition/capacity to perform this critical function

116. Evidence The visual system is not classified in medical science as a bodily system in its own right (It is a module of the nervous system) because it is non-critical part of the body’s redundancy

117. Problems: Prostheses (Heart pacemakers …) Are they parts of the body or analogous to foreign bodies in the interior of the body Solve this problem by adding condition of reciprocal dependence (Pacemaker does not change in light of its functioning and of the functioning of associated systems)

118. Problems: Kidney dialysis (is the operation of the kidney a critical function?) Cryptobiosis – the condition that some creatures (e.g. shrimp) surivive in after drying out and shutting down: this means that they can survive even though their bodily systems are not functioning

119. Problems: Reproductive system: Not critical to the life of the individual critical to the life of the species of the population? Mother and baby share an endocrine system?

120. Problems Maximality Is the endocrine system one system or seven?

121. Questions: If these systems are critical, how could they evolve? By splitting from prior systems?

122. Questions: Does every system contain at least one organ? How is ‘organ’ to be defined? Are muscles organs? Are bones organs?

123. Questions How many of these systems are present in all organisms? In all multi-cellular organisms? In all vertebrates? How many of these systems have analogues in other sorts of systems (antivirus software in computer systems)

124. Functions are SNAP entities Their functionings (realizations, expressions,...) are SPAN entities. A function f is dependent on its bearer b b is a SNAP entity b's continuing to exist (b's life) is a SPAN entity A function F is critical to its bearer B =df. the continuing to exist of B is dependent on the functioning of F