Bodily Systems and the Spatial-Functional Structure of the Human Body

hystericalcoolΚινητά – Ασύρματες Τεχνολογίες

10 Δεκ 2013 (πριν από 4 χρόνια και 5 μήνες)

106 εμφανίσεις

Bodily Systems and the Spatial
Structure of the Human Body

Barry Smith, PhD
, Igor Papakin
, Katherine Munn

Institute for Formal Ontology and Medical Information Science

Faculty of Medicine, University of Leipzig, Leipzig, Germany

ment of

, University at Buffalo, Buffalo, NY, USA


The human body as conceived by medical science is a system made of
systems. The body is divided into bodily systems proper, such as the endocrine and
circulatory systems. These are sub
divded into many subsystems at a variety of levels
whereby all systems and subsystems engage in massive causal interaction with other
systems and subsystems. In this
we offer an explicit definition of bodily system,
and explicit means for understandi
ng these causal interactions. Whereas informality is
acceptable in documentation created for human beings, it falls short of what is needed
for computer representations. In our analysis we will define bodily system, and will take
some first steps toward un
derstanding the causal relationships bodily systems have with
their subsystems.

1. Introduction

Ontology plays an increasingly significant role in work on terminology and knowledge
management systems in the domain of biomedical informatics, and we hold
that it will play an
essential role in biomedical research of the future. The term ‘ontology’ must, however, be
understood in the right way [1]. The domin
ant paradigm might be referred to as ‘appli
ontology.’ This holds that the ontologist should

focus primarily on the construction of
ontologies as working software applications, a view which often goes hand in hand with the
thesis that the expressive power of an ontology is limited effectively to that of one or another
version of Description Logic

[2]. This means that an ontology, when applied to complex
domains such as those of biomedicine, is forced to deal with simplified models. There is,
however, a second ‘reference ontology’ school of thought, which focuses primarily on the
development of ont

of the entities in given domains. Such theories are
marked by a high degree of representa
tional adequacy and are designed to be used as controls
on the results achieved by working applica
tions rather than as substitutes for these workin
applications themselves [3].

Three levels of reference ontology can be dis
guished in the biomedical domain:

1. formal ontology: a top
level domain
independent theory involving the use of
concepts such as: object, process, identity, part, location;

2. domain ontology: a top
level theory applying the structure of a formal ontology to
the medical domain, involving concepts such as: body, disease, therapy, organ, tissue,

3. terminology
based ontology: a very large lower
level system, based on med
logies such as UMLS, and involving specific concepts such as: inflammatory
change in the gastric mucosa.

The Institute for Formal Ontology and Medical Information Science in Leipzig is
constructing a reference ontology for the domain of biomed
icine [4]. This ontology is
designed not as a computer application in its own right but as a framework of axioms and
definitions relating to such general concepts as: organism, tissue, disease, therapy. Here we
focus on the concept
bodily system
, which we
believe will serve as a central factor in a robust
ontology of the human organism.

Rosse and Mejino [5] have recognized the need in bioinformatics for domain ontologies
of the human body, and they and their co
workers are creating such a domain ontology o
human anatomy, the Foundational Model of Anatomy (FMA). The FMA symbolically
represents the structural organization of the human body from the macromolecular to the
macroscopic levels, with the goal of providing a robust and consistent scheme for classif
anatomical entities on the basis of explicit definitions. This scheme also provides a template
for modeling pathology, physiological function and genotype
phenotype correlations, and it
can thus serve as a reference ontology in biomedical informatics.

Our aim, like that of Rosse and Mejino, is not applications ontology, but rather a
reference ontology. That is, we seek to provide a theoretical framework that, when fully
developed, can serve as the theoretical basis for applications ontologies. Whereas
Rosse and
Mejino’s ontology represents the anatomy of the human body in the purely structural context,
our ontology of bodily systems will encompass anatomical structures
in a context which takes
account of functions and their realizations.
We aim, in oth
er words, to link anatomy with

One way in which our work supplements that of Rosse is in providing a definition of the
notion of ‘system.’ The definitions of the FMA use this term, but leave it unanalyzed.
believe that the concept of

can serve as a unifying top
level element in a robust
ontology of the human organism designed for the purpose of medical informatics.

Concepts like


are used throughout contemporary medical science,
and medical references and text
books overflow with reasoning about systems of different
kinds which are constituents of the body.
Much implicit medical knowledge factors into such
Our goal here is to apply philosophical rigor to a definition of ‘bodily system’
in a way
that makes this knowledge explicit.

2. Bodily Systems in Medicine

Contemporary medical science represents the living human body, or the human organism, as a
system made of systems. The body’s systems serve as major provinces in our maps of human
y; they thus play a central role also in a variety of domains, from medical pedagogy
and dynamic modeling to com
puter visualization. An understanding of the con

moreover a necessary part of any understanding of cognate concepts such as
, and it is a prerequisite for understanding systemic diseases, both those which are
localized in single systems and those, such as diabetes, which affect a plurality of systems

We are interested primarily in the top
most node
s in the hierarchy of bodily systems; i.e.,
in those major bodily systems towards whose functioning other, smaller systems contribute.
In Table 1 we provide examples of divisions of the human body in terms of such highest level
systems derived from standar
d sources.

Clearly, the division of the body into its major systems is by no means unproblematic.
Medical textbooks rest on informal explications of the systems that concern us here, and
rarely if ever do they offer anything more than a passing descriptio
n of the concepts that these
explications presuppose

including the concepts of ‘function’ and ‘system’ themselves.
While such informality is acceptable in documentation created for human beings, who can use
their tacit knowledge of the entities involved

to achieve sufficient understanding, biomedical
information systems will require precise and explicit definitions of the relevant terms. The
analysis presented here is intended as a first step towards providing a framework for such



National Library of

Heidegger’s Atlas of
Human Anatomy


Foundational Model of


Skeletal system;


Articular system;


Muscular system;

Alimentary system;

Respiratory system;

Thoracic cavity,


Urinary system;

Genital system;



Endocrine glands;



Lymphoid system;

Nervous system;

Sense organs;

the integument

Musculoskeletal system

Respiratory system


Hemic and lymphatic


Gastrointestinal system

Urogenital system

Endocrine system

Nervous system

Motor system



Synovial joint, muscle, tendon


Skin and fingernails

Circulatory system

Cardiovascular system

Adult circulatory

Fetal circulatory system

Blood vessels of trunk

Lymphatic and organ systems

Lymphatic system and
endocrine organs

Digestive and respiratory


Urogenital system

Central and peripheral nervous


Central and peripheral nervous


Spinal cord and spinal nerves

Automatic nervous system

Vegetative nervous system


Integumentary system

Musculoskeletal system

Nervous system


Peripheral nervous


Autonomic nervous



nervous system

Enteric nervous system

Sympathetic nervous



nervous system

Hematopoietic system

Cardiovascular system

Alimentary system

Urinary system

Male genital system

Female genital system



Hemolymphoid system

Endocrine system

Table 1:
Brief overview of bodily systems distilled from four standard sources

2.1 Analyzing Traditional Views of Bodily Systems

Partitioning the body into systems in the way that we do is a cognitive proces
s. But it is a
cognitive process which involves representing aspects of reality: the body is not a continuum,
but rather is already partitioned on various levels into constituents of various sorts. This is
why, in constructing a domain ontology of medicine
, we need to start with the results of
medical science as set forth in standard textbooks.
Unfortunately the medi
cal literature
provides at best informal definitions of terms such as ‘bodily system,’ ‘organ,’ and so forth,
which helps to explain why there

is a less than perfect agreement on the rosters of bodily
systems provided by different sources. Medical textbooks rest on tacit knowledge concerning
such highly general concepts. That is, while their authors understand perfectly well how the
living human

body is organized and what the functions of bodily systems are

they deal with
such systems and their workings every day of their lives

they do not formulate this know
ledge in an explicit way.

We do not wish to impose spurious precision in an area th
at is marked intrinsically by a
certain vagueness and informality. But again: where for human beings a high degree of
informality is acceptable, it becomes problematic where human reason
ing must be simulated
inside a computer. The analyses presented below

are intended as a first step towards filling
this gap. Distilling an overview of the adult human body’s repertoire of systems from the
sources listed on Table 1 gives us the following [8]:

Supportive Systems:
These provide the framework, or structure, w
ithin which the other
systems are located. They include:


skin system
separates and isolates the organ
ism from its surroundings and participates
actively in maintaining the organism’s internal environment. Its functions include
thermoregulation, tactil
e sensitivity, participation in the maintenance of water balance, and
defense (it has an innate and acquired immune response against bacteria and viruses).


musculoskeletal system
is an ordered assemb
ly of bones, muscles, and ligaments that
maintains t
he body’s shape and allows movement in counteraction with external forces such
as gravity. It also creates an internal framework of support for the organs of the body.

Systems for Substance
These support the normal ways in which the organism
changes substances both within itself and with the surrounding world. They include:

The digestive system
, which itself includes
inter alia
the oral cavity, the esophagus,
stomach, duodenum, small and large int
ines (the digestive tract), and additional

parenchimatous organs like the salivary glands, liver, and pancreas. This system ensures that
solid and liquid substances are absorbed into the body in such a way that they can serve as a
source of energy and as building blocks for other bodily systems.

The respiratory system
includes the nasal cavity, lar
ynx, lungs, trachea, and bronchus. It
performs respiration, i.e. it enables the absorption of oxygen and the excretion of carbon
dioxide to take place within the body.

The circulatory system
includes th
e heart, blood vessels, and microcirculatory vessels, as
well as the blood it
self. It serves as a universal transporter of sub
stances to the body’s cells via
two circuits: the pulmonary and the systemic.
The pulmonary circuit ex
changes gases with the
xternal medium in the lungs
. The systemic circuit supplies all the organs of the body with
genated blood and provides for gas exchange be
tween the blood and the cells of other

The urogenital system
includes the kidneys, the ureters, the urinar
y bladder, and the
urethra, as well as the external and internal genitals (reflecting the close anatomical and
functional relation of the latter with the urinary organs). It is responsible for the excretion of
surplus water, and of the waste products that
appear in the cells as a result of physiological
processes, and for regulating the body’s ion balance.

Systems for Regulation:
These act as supervisors and coordinators in the work of the other
bodily systems:

The immune system

includes the thymus, bone
marrow, spleen, lymphatic nodules and
lymphatic vessels, as well as the lymphatic tissue in the pharynx, the intestine, and the
population of immunocompetent cells working through the body. Its first task is to recognize
and break down or eliminate substan
ces that might damage the body’s integrity.

The nervous system
includes the brain and spinal cord (the central nervous system),
together with the peripheral nerves, ganglia, plexi and sensory organs. It regulates all the
body’s systems and provides the se
nsitive (sensory) functions of the body.

The endocrine system

consists of the endocrine glands and of the active endocrine tissue
in other glands. Together these serve as a battery of transmitters that broadcast instructions to
all the cells of the body. O
nly those cells that have a ‘receiver’

i.e. a specific receptor in
their membranes

can recognize and use this regulatory sign.

The above is provided merely as a preliminary orientation for the discussions which follow,
for the division of the body in
to its major systems is by no means clear
cut. There are
elements of exchange systems (for example parts of the liver and pancreas) which play a role
also in regulatory systems, and the three regulatory systems themselves realize their functions
of regulat
ion via a certain sort of substance
exchange. The rationale for our proposed division
will, however, become clear in the course of what follows.

3. Toward an Ontology

The task of reference ontology is not to replace medical sci
ence. Rather, its job is
to provide a
framework within which medical knowledge can be formalized in a way that supports
causally predictive theories, and at the same time counteracts the effects of terminological and
other inconsistency and impre
cision. Such a framework must star
t out from the ways
knowledge is formulated in the medical literature, and one criterion of a good definition of
‘system’ is that it yields a roster of systems that is very like the standard rosters. As we have
seen, however, it needs to go beyond textbook

formulations if it is to achieve the sort of
formal clarity we need for the purposes of reference ontology.

How, then, are we to define the notion of a bodily system? The discipline of systems
theory is of little help to us here, since its definition of
a system as a
complex of interacting

[9] is far too general for our purposes and is made more specific only by the use of
mathematical tools which leave unanswered pre
cisely those questions pertaining to the nature

systems which we are cal
led upon to answer.

We can make some progress, on the other hand, if we examine how the word ‘system’ is
most commonly used in both technical and non
technical contexts by speakers of English.
Oxford English Dictionary
defines ‘system’ under the princ
ipal head
ing of ‘an organized
or connected group of objects,’ or more precisely: ‘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 sch
eme or plan.’ Under the heading ‘Biology’ it
gives: ‘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, et
c. systems.’

One might be critical of such definitions on the grounds that a system is not a mere set or
aggregate but rather something

(think of the solar system). We can do justice to such
criticisms, however, by distinguishing systems themselves

from the

in which they
are involved, or in other words from the
of systems [10]. As we shall see, systems
are able to carry out processes, or to realize their functions, only via a physical structure, or
aggregate of parts. Systems o
n this view are no more dynamic in nature than organisms.
Indeed organisms

systems on the analysis we shall defend.

Examining our list of systems above, we see that each of them consists of a certain
organized or some
how connected group of objects

such as organs, associated tissues, and
populations of cells

to which some complex function is attributed. Unfortunately there are
many organized collections of bodily parts with which functions can be associated, including
each and every individual cell
. So in order to make an analysis of ‘system’ along these lines
work, and yield the sorts of answers we need for our questions about bodily systems, we will
first need to provide a specification of the particular notion of ‘function’ that is at issue here.

And before we do this we must discuss the organized parts of the body that have functions.

3.1 The Body’s Modular Hierarchy

There is a collection of bits of biological matter in the human body that medical science
designates as the circulatory system.
What is it about this collection of vessels, organs, and
blood in virtue of which it is referred to as a system? Could we designate as a system our
heart, plus our salivary glands, plus our big toenail, plus our right ear? The reason that the
former are co
nsidered a system and the latter a mere conglomeration is because the heart,
vessels, and blood are related to each other in special ways. There are anatomical connections,
which can be described in terms of mereological relations: the left ventricle is pa
rt of the
heart, a capillary is attached to a venule. And there are physiological connections, which can
be described in terms of causal relations: the myocardium causes the heart to pump by electro
chemical stimulation. In other words, a system is charact
erized simultaneously by a certain
, and by a set of
in which that structure participates.

It is this complex structure that allows the processes to participate as they do. Without a
tendon connecting a muscle to a bone and a gro
up of motoneurons connecting the muscle to
the central nervous system, the process of movement could not take place. Because there is
such a multiplicity of complicated processes that takes place in the body, the structure that
accommodates them is also co
mplicated. This structure is a modular one: the body as a whole
can be divided into units, each unit can be divided into sub
units, and so on. Every complex
organism has modular units at many levels. Your brain contains neurons, the neur
ons contain
lles, the organelles con
tain mole
cules, which are composed of atoms, which are
composed in turn of subatomic particles. Modular units at lower levels have mereological
relationships vertically with modular units of which they are the parts. The alveoli a
re lower
level parts of the respiratory system, and are parts of the lungs, which are higher
level parts of
this system.

Modular units also have causal relations horizontally with modular units in other systems,
and vertically with modular units of which t
hey form a part. The alveoli are parts of the lungs
and have a function in the context of the respiratory system. The alveoli have a horizontal
relationship with the capillaries, which have a function in the context of the circulatory
system. It is the alv
eoli and the capillary wall where the exchange of oxygen and carbon
dioxide takes place between the blood and the air.

Modular units also have diagonal causal relationships with units from other systems. The
liver is for example an element in the alimenta
ry system, but it has functions in the contexts of
several other bodily systems at various levels. In the context of the circulatory system, it
produces proteins for the coagulation of blood. In the context of the digestive system, it
produces bile for bre
aking down chyme. Bile also has a function in the context of the
excretory system: the body mixes waste with bile and excretes this mixture as feces. The liver
also produces proteins that have a receptor function in the context of the immune system.

It is

this specific and complex structure that allows physiological processes to be carried
out within the body. This structure enables certain items in the body to causally relatively
isolated from other items. This causal relative isolation is what enables pr
ocesses to take place
without getting in the way of other processes. It is also what allows certain processes to have
causal relationships with certain other processes. As the philosopher Roman Ingarden
expressed the matter, each multi
cellular organism is

a relatively isolated system of a very high order, and as such contains in itself very
numerous, like
wise relatively isolated, systems of lower and lower levels, which
are hierarchically ordered and variously situated within the organism, and are at the

same time both partially interconnected and al
so partially segregated, as a
consequence of which they can exercise the specific functions which are
characteristic to them relatively undisturbed [11].

Our task here is to provide the beginnings of an acco
unt of this modular hierarchy and of the
layers from which it is built, from macromolecules via cells and organs through to the whole
organism, but in a context in which we pay attention to the functionings of the various
modular units.
To anticipate some
what, we can say that the highest level of this modular
organization is the whole organism itself

and that t
he level immediately beneath is
bodily systems

3.2 SNAP and SPAN in Bodily Systems

Ontology offers tools for formalizing the aspects o
f anatomy and physiology we have just
discussed. The first tool we will need provides us a way of distinguishing between the body’s
complex structure and the processes in which that structure participates. The structure can be
understood as occupying three

dimensions of space; the processes require in addition the four
dimensions of time. Ontology also provides a way of talking about the relationship between
the structures and processes. What is called for is an ontology that distinguishes between
ensional objects that endure through time (
, for short), and the four
dimensional processes (
for short) in which these objects participate.

Grenon and Smith provide such an ontology [12]. The body’s structure is three
dimensional: it
can be apprehended as it were in one glance as in a snapshot; hence Grenon
and Smith call it a SNAP ontology. A SNAP ontology of the circulatory system includes
endurants such as the heart and the blood. The processes that take place in the body are four
imensional: they cannot be captured in a snapshot, but require instead something like a
videotape, which allows them to be captured in their temporal extendedness as they unfold
over a certain timespan

hence Grenon and Smith call it a SPAN ontology. A SP
ontology of the circulatory system includes perdurants such as the beating of the heart and the
flowing of the blood. In a SNAP ontology, endurants are visible but perdurants are not; in a
SPAN ontology, perdurants are visible but endurants are not. SNA
P and SPAN thus represent
two complementary perspectives on the same reality.

In order to talk about bodily systems, we need both of these perspectives. We need a
SNAP ontology of the endurant parts of the body that make up the modular hierarchy, and we
ed a SPAN ontology of the perdurant processes that this structure allows for. This
ontological distinction between endurants and perdurants helps us explain why the heart,
blood, and blood vessels comprise the circulatory system, whereas our heart taken to
with our salivary glands and our right ear comprise no system. Endurants in the body must
have certain causal relationships with each other in order to constitute a system in the sense
that is relevant to us here.

The heart, blood, and blood vessels

are parts of the human body. They are also parts of
the circulatory system. A SNAP ontology suffices to show us how these parts relate to each
other spatially. But in order to see how these relations play out in the form of processes in
which the correspo
nding objects participate, we need a SPAN view. We must distinguish,
then, between two kinds of parts: parts of the body, which can be seen in SNAP alone; and
what we will call
of the body, which are the results of demarcating the body into
s in a way which involves taking account of not only the SNAP but also of the SPAN

The concept of element can be understood, roughly, as a generalization of concepts such

, or even bodily system. Whereas parts are the building bloc
ks from which the
body is constructed, elements are the building blocks from which bodily

constructed. At the highest level of the modular hierarchy, the bodily systems proper are
elements of the system that is the whole human body. If it turns

out that there are nine top
level bodily systems, then the human body will be a system composed of nine elements.

It almost goes without saying that all elements of the body are also parts of the body. Not
all mereological parts, however, are also element
s. The heart is an element of the circulatory
system, and it is a part of the circulatory system’s complex physical structure, which is in turn
a part of the body. The foot is a part of the body, but is an element of no system. Certain parts
of the foot, h
owever, such as its bones, capillaries, or nerve endings, are elements in various
systems. The bones are elements in the skeletal system, the nerve endings in the nervous
system, and the capillaries in the circulatory system.

Elements are distinguished by

the fact that they have special kinds of causal relations
with larger wholes, called systems. If an element becomes causally disconnected from its
system, as when a heart is refrigerated in the course of a heart
transplant operation, then it
ceases to be
an element for a certain period of time. As Aristotle expressed it: ‘A dead body
has exactly the same configuration as a living one; but for all that is not a man…. no part of a
dead body, such I mean as its eye or its hand, is really an eye or a hand’ [13

While the elements in a given system are distinguished from parts in general within the
system by their causal connection with other elements, they are distinguished from
systems by their
causal relative isolation
from their surroundings. This ca
usal relative
isolation at many different levels is part and parcel of the body’s complex structure, and it is
what allows for elements to have
within the workings of the body as a whole.

Some examples of elements and their corresponding functio
ns: The elements of the
digestive system include the esophagus and the stomach, the serous membrane, the layers of
smooth muscular tissue, and so forth. Some corresponding functions are: to provide the way
for a bolus to pass from the mouth cavity into the

stomach, to advance the process of
digestion by mixing the bolus with hydrochloric acid and pepsin (stomach juice), to allow for
the external coverage of the stomach and its constriction respectively.

The heart is a system consisting of the myocardium, en
docardium, and so forth. These
elements have their own specific functions and comprehend their own elements in still
another layer (for example different types of cells). The liver consists of several types of
tissue, including the hepatic parenchyma, conn
ective tissue, and capillary vessels. The blood
consists of cellular elements (red blood cells, leucocytes, lymphocytes, monocytes, platelets)
and plasma, which contains albumins, globulins and hormones. Each cell is a system that
consists of elements such

as nucleus, mitochondria, endoplasmic reticulum, ribosomes, which
are in turn systems in their own right with their own specific functions.

As we shall see, elements are often shared by different systems, and they then manifest
distinct functions

one o
r more in the context of each system to which they belong.
instance, the pharynx has the function of enabling both the passage of the bolus into the
digestive tract and the passage of air into the lungs; as such it is an element of the digestive
and re
spiratory systems simultaneously.

3.3 Granular Partitions and System Elements

The second ontological tool we will need is a theory of
granular partitions


provides a way of formalizing our description the structure of the body’s modular hiera
A theory of granular partitions represents reality in terms of partitions each of which
highlights entities of a different grain. An organism is a bona fide object: it exists
independently of our partitions. An organism is also a totality of atoms. A
t the same time, it is
a totality of cells, and a totality of molecules. It is also a single unitary substance. All of these
express distinct granular partitions of the organism.

A theory of granularity preserves realism, even as it accounts for the possib
ility of having
different perspectives on reality. Each granular partition highlights certain aspects of the
unified whole. Think of a tourist map as a granular partition: it represents a given city, but it
highlights only certain selected tourist location
s. A map of bus routes is another granular
partition of the same city. Each grain in the partition is an item on the map. Grains themselves
are divisible into ever smaller grains.

All of the items appearing on the tourist map have one attribute in common:
they are of
interest to tourists. All of the items on the bus map have something else in common: their
relevance to the purpose of navigating through the city by bus. Similarly, a granular partition
of bodily systems highlights those items in the body that

have some feature or features in
common, and leaves out items that do not have these features. What is the feature in virtue of
which a granular partition includes bodily systems?

Recall that a system is characterized simultaneously by a complex modular
which is a SNAP entity, and by a family of associated
which are SPAN entities.
The processes occur as they do because the body is structured in the way that it is. Thus the
processes that this structure allows for are highly specific.
These structures and processes,
then, are the features that granular partitions of bodily systems and the associated bodily
processes must highlight. Your right leg from the knee down would not appear as a modular
unit in a granular partition of bodily sys
tems: there is no physiological process in your body
that is dependent on its being structured in this way.

The most, then, that we can say about your right leg from the knee down is that it is a part
of your leg, which is a part of your body. A granular
partition of human anatomy might
include your right leg from the knee down (it is an interesting question which connected parts
of the body ae properly included in a strictly structurally
based ontology of human anatomy
); but in a granular partition o
f bodily systems it would be invisible.

Your heart, on the other hand, is a structure on which the carrying out of certain
physiological processes depends. It is one link in a causal chain that results in blood being
pumped through the veins. Your heart, t
hen, is visible in a granular partition of bodily
systems, and so also are your veins. This is because heart and veins are modules in the
hierarchy that enables certain associated physiological processes: they are elements of the
circulatory system. Furthe
r, your aorta and ventricles appear in the same granular partition,
because they are crucial to your heart’s structure, and to the processes the structure enables;
they are also elements of your circulatory system.

3.4 Functions in Bodily Systems

A gran
ular partition that is subdivided into many different grains is needed to highlight the
human body’s systems and their elements on successive levels. Each element is distinguished
by a specific structure that allows for specific physiological processes. In

the everyday
language of life science, this element is said to have a
. A function, like an element, is
a SNAP entity or endurant. Unlike an element, however, a function is an endurant that is
ontologically dependent

on another endurant. For examp
le, the heart has the function: ‘to
pump blood’

this function could not exist if the heart did not exist. Similarly, color is a
dependent SNAP entity: your eyes have a token color (brown) which would not exist if your
eyes did not exist. A function is de
pendent for its existence on a SNAP entity; but it is
in a process, a SPAN entity. The heart’s function: to pump blood is realized in the
process of blood being pumped.

It may now look as though recognizing both functions and processes in an onto
represents a case of ontological double
counting. Certainly it is true that every function is
correlated with some class of processes (of functioning) at some given level. But many
processes are not realizations of functions, including for example all

those processes in the
human body which are malfunctionings.

Also, many elements have functions which are
overwhelmingly never realized in processes. It is not only true of, but essential to the nature
of, fish eggs that, other things being equal, they de
velop into fish. The statistical situation is
even worse than usual: in many species, the vast majority of eggs never develop into fish,
most being eaten or destroyed. And yet each fish egg has the function to develop into a fish,
not, say, the function to

be eaten by predators in order to protect the other eggs. It is a
contingent fact that most fish eggs do not develop into fish. Thus the concept of function
cannot be reduced to explanation in terms of processes.

A quick word about the concept of function

in philosophy. Some philosophers have
criticized the function
talk that life scientists use unreflectively (for example in the
designation of disciplines like
functional genomics
), and have tried to reduce the notion of
function to the notions of causalit
y or natural selection.

We hold, however, that biological
functions are real, irreducible features of the world.
With Johansson
et al
[19], we support the
view that the functions of bodily systems and their elements are

functions: that is,
ctions of parts within the context of a larger whole. This follows from our understanding
of elements as components of a bodily system distinguishable by their structure and by the
specific processes which that structure enables. An element is only an elem
some larger
system. Thus the function that the element has can also only exist within the context of this
larger system. Further, it is only in the context of a larger system that the function can be
realized in a process of functioning.

The resul
ting picture is a complex hierarchy, or taxonomy, that is at once spatial and
functional. The heart, for example, is at once a part of the circulatory system and an element
in that system. As a part, it is a mereological component of a physical structure v
isible in a
SNAP ontology. As an element, it has a function that is realized in processes, and therefore
requires reference also to a SPAN ontology.

On the spatial
functional hierarchy proposed by Johansson
et al
., the circulatory system is
at the top leve
l, the heart is located at the next level down, and its elements: ventricles, atria,
valves, and so on, at the next level thereafter. Each of the latter bears a function in relation to
the higher
level functioning of the heart. On the account we will defen
d, the circulatory
system itself is an element of the human body proper.

Now, of course, we run into a problem: what is the function of the human body, in
relation to which the circulatory system and other bodily systems have part
whole functions?
et al.

address this problem by distinguishing between several possible types of
functions the human body may have: (a) a part
whole function of some larger whole, say a
species; (b) an objectively existing function, which is intrinsic to the human body,

or (c) a

merely ascribed or imputed to the human body in the conventions of
using human beings along the lines proposed by John Searle [16].

Picking (c) is inconsistent with our presupposition that the functions of the bodily
stems exist in objective reality. It would also, as Johansson
et al
. note, ‘seem to license
cultural relativity or even pure subjectivity to enter into science’ [19, p. 3]. Science itself, on
the other hand, often talks about functions intuitively as if th
ey exist in objective reality.
et al
. point out that neither (a) nor (b) contradicts the proposition that part
functions exist objectively, and it is possible to hold either (a) or (b) consistently with an
account of part
whole functions at

every level below the human body itself.

Even so, both (a) and (b) are problematic for their own reasons: (a) is problematic
because it calls for an account of what the larger whole is within which the human body
functions, and further seems to be therea
fter a vicious regress: where does the spatial
functional hierarchy stop? (b) is problematic because there is as yet no successful scientific
definition of ‘intrinsic function.’

Here, therefore, following Johansson
et al
., we bracket the question of what
kind of
function the human body has, and concern ourselves only with the functioning of its elements.

3.5 Spatial
functional Hierarchy

We are now prepared to go into further detail about the body’s modular hierarchy. What we
have said so far is enough
to show that the concept of modularity is too narrow to describe
bodily systems. While modularity does describe the structure of the human body, this is all it
describes. A hierarchy of systems must encompass physiology as well.


See [16], [17]


Philosophers of science who support etiological theories of biological functionality have claimed to have successfully define
d (intrinsic)
biological function (see, e.g., [21]). There are enough who disagree with this cl
aim, ourselves included, to take it as by no means given that
intrinsic functions have been successfully defined.

To this end Johansson

propose a

hierarchy, which yields a
taxonomy of the body’s anatomical structures in addition to the functions these structures
As we will see, the body’s anatomy and physiology lend themselves readily to such a
taxonomy. The sp
atial half of the hierarchy taxonomizes the body’s anatomy according to a
modular structure (i.e. in terms of what is a part of what): a nephron is a part of a kidney. The
functional half of the hierarchy taxonomizes the body according to which functions c
ause, or
enable, which other functions to occur. One nephron has the function of removing waste from
the blood, which is the function that the kidney as a whole performs on a large scale. Fusing a
spatial taxonomy with a functional taxonomy yields a spatia
functional hierarchy.

As we might suspect, the two halves match up.
Why would we suspect this? Because, as
we mentioned earlier, functions are dependent SNAP entities which depend for their existence
on independent SNAP entities. The body’s complex anat
omical structure allows for processes
to occur, which means that the body is structured in such a way that the functions realized by
the body can be ordered in a hierarchy which parallels the structure.
Thus a cellular
mitochondria in a myocyte provides th
e chemical energy without which the myocyte cannot
contract, and therefore contributes to the pumping of the heart.




With an ontology that can account for endurants and processes, with a theory of granular
partitions, and with a spa
functional hierarchy of part
whole functions, we are now
prepared to define ‘element:’

X is an

of Y if and only if:


X is lower on the spatial
functional hierarchy than the organism as a whole;


X has one or more specific functions


X is causally relatively isolated from the parts of the organism that surrounds it;


X is maximal, in the sense that an element is not a proper part of any item

on the same level of the spatial
functional hierarchy satisfying conditions


to (iii).

Ad (i): An element is an element only in the context of a given system, within which it
has a part
whole function.
The body as a whole is not an element of any larger organic
system. Thus only items that are proper parts of the body can be elem

Ad (ii): Causal relations are made possible by the complex structures of the system and
its component elements. In virtue of this complex structure, and the processes which that
structure enables within the context of its overarching system, an elem
ent has a function.
Functions in bodily systems are in every case part
whole functions relative to some larger
whole. It should be noted that there is no reason to exclude an element’s having more than
one function in the context either of the same system
or of different systems. The liver has
relative to the digestive system the function: to produce bile. Relative to the circulatory
system it has the function: to produce plasma enzymes that contribute to the clotting function
of the blood. A function is a
dependent endurant entity; it is the function of some element
(like the heart). It realizes itself in perdurant entities, also called processes or activities.

However, it must be noted that in order to exist a function need not be realized at all
times, or

even once in the course of an organism’s lifetime. For example, whether or not a
woman becomes pregnant, a function of her uterus is to make it possible to house an embryo.
This is the function of her uterus even if for some reason she cannot have childre

Further, according to our definition of element, only those entities which have part
functions in the body are elements of the body. Thus a virus may take on a functional role in
your body, directing the cell to construct certain proteins that the

virus needs for reproduction.
The virus is however not an element of your body

indeed it is not even a part of your body

because the directions given by the virus interfere with your body’s functioning [21].

Ad (iii): The complex structure of bodily
systems and elements enables processes to take
place by providing elements which enjoy a relative causal isolation from other elements in the
same and other systems. The causal processes mentioned in (ii) can only occur if other causal
processes do not int
erfere. In other words, at least in the sorts of cases that concern us here,
tight causal connections within and between elements require some degree of causal isolation
from the processes of other elements. Each element is partially isolated from certain
causal influences (for example by the presence of a porous membrane which at the same time
allows certain kinds of influences and substances to encroach into its interior). This relative
causal isolation is what allows systems or elements to be sel
contained yet responsive to
stimuli from the outside. It is the complex structure of the body, which allows for the body’s
tight causal organization, that enables body systems and their elements to engage in causal
relationships with their environments (
which include other bodily systems and elements), yet
not have their integrity threatened, or break down, as a result of these relationships.

Ad (iv): The spatial
functional hierarchy of the human body works on the supposition
that every element is compose
d of elements that enable it to realize its function, and that this
is the case all the way down to an as yet unspecified bottom level. Elements are maximal: this
means that on any given level of the hierarchy an element is not a proper part of any element

on the same level. A cell is an element; a half
cell is not. The fibula is an element; the upper
fibula is not, because it is not maximal. The principle of maximality is linked to the spatial
functional hierarchy via the connection between function and re
lative causal isolation. An
element’s relative causal isolation is what enables it to engage in substance exchange; this
substance exchange is in turn what produces the function. Thus physical maximality as we
understand it here entails causal relative iso

The bottom half of a lung, for example, does not have a separate function from the whole
lung, for the lung is physically maximal. As such it is causally relatively isolated from the the
rest of the organs and fluids in the thorax. The lung’s rela
tive causal isolation is what enables
it to exchange oxygen and carbon dioxide without disrupting or being disrupted by other
processes in the body. If this causal relative isolation were disturbed, it would no longer be
able to realize this function


other elements in the body would be prevented from
realizing theirs. Rupturing a lung would cause air to flow from it to the thorax. Not only
would the lung be prevented from realizing its function effectively, many of the elements in
the thorax would bec
ome too compressed to be able to realize theirs.

Just as systems can be divided into elements, so functions, too, can be divided into sub
functions (corresponding to the elements which perform them). Functions located at lower
levels of the spatial
nal hierarchy interact in complex ways to enable functions at
higher levels. For example, the function of a particular neuron, e.g. to provide a path for
electric impulses, is realized in a composite process that consists of smaller interrelated

such as the exchange of potassium and sodium ions through the cellular membrane.
The function of the kidney is to excrete urine. This function is executed via a composite
process that consists of smaller interrelated processes that occur on lower levels o
granularity: the excretion of urea and creatinine, absorption of necessary ions and excretion of
redundant ions and water.

5. Demarcating Bodily Systems

The relation between elements and functions is complicated by the fact that there is no perfect
one correspondence between them. This is because many elements in the human body
have a multiplicity of functions.

Recall that
the body’s elements are unified together within a single whole

namely the
corresponding bodily system

which is able to r
egulate its own state and structure, and that it
is in the context of this whole that elements have the functions they have. On this account, the
blood has several different functions in several different systems. In the context of the
digestive system, th
e blood’s function is to transport nutrients and allow for nutrient and
waste exchange at the cellular level; in the context of the respiratory system, its function is to
transport gases and allow for gas exchange at the cellular level. Blood, therefore, l
ike most
elements, can be located simultaneously at different horizontal levels of the spatial
hierarchy, for it has different functions within the context of each system.

We must now discuss the interconnections among the bodily systems in mor
e detail. We
have thus far pointed out merely that bodily systems and their elements are distinguished first
by a complex structure that enables causal connection and causal isolation of elements. We
have also pointed out that elements have functions relat
ive to the larger system to which the
elements belong, and that the largest system that is a whole in a part
whole function is the
human body itself.

5.1 Evaluating Functionings

Medical science can demarcate one bodily system from another in terms of
the way each
contributes to the task of keeping the human body alive. It now becomes possible to evaluate
a particular functioning of a particular type of system based on the success or failure of its
contribution to this functioning of the whole.

The spa
functional hierarchy gives us objective criteria in terms of which we can
effect an evaluation of functionings. In a spatial
functional hierarchy built from a taxonomy
of part
whole functions, an element succeeds at performing its function when that
erformance contributes to the whole in such a way that the whole can contribute to the
functioning of the larger whole of which it is an element. And so on, until we reach the
maximal whole, the human body. The body’s survival becomes the benchmark of eval
of functionings.

For example, all else being equal, a circulatory system with clogged arteries is less
efficient, and therefore less successful, than a circulatory system with clear arteries. This is
because the former contributes poorly to the sur
vival of the body as a whole relative to the

There are in the real world degrees of functioning in each case relative to one or more
prototypical functionings. Johansson [22] points out that an element’s functioning can be
measured by a prototype i
n a similar way to that in which an object’s weight can be measured
by a scale. In order for a functioning to be successful, it need not match the prototype. Thus a
screwdriver can still realize its function even though its head is somewhat loose. There ar
many dimensions along which a functioning can be plotted in relation to its prototype. One
dimension we are concerned with here is that of the success or failure of a given functioning
to enable functionings at higher levels. Presumably there is an ideal
, or prototypical, pumping
of the heart that contributes optimally to the survival of the body as a whole. If the pumping
of the heart is disabled by a myocardial infarction, then its functioning can move far enough
away from the prototypical functioning t
hat it no longer succeeds in supplying the brain with
oxygen. As we move away from the prototype, we can order actual pumpings, and actual
transport of blood by the arteries, according to the degree to which they contribute to the
systems that their functi
ons are parts of.

Once a functioning crosses a particular threshold at a particular distance from the
prototype, it is no longer successful enough to play its part in the functioning of the whole
system that it contributes to, in ways which must lead eithe
r to death or substitution.

The threshold for success of a given type of functioning

for example, the taking in of
oxygen by the lungs

is relative both to the individual organism and to its specific
environment at some given time. A bioinformatician s
itting at a computer all day has a
threshold for successful oxygen intake that is much farther from the prototype than a manual
laborer on a high
altitude farm in the Andes.

The survival of the body as a whole can be used as an objective standard for evalu
functionings in the body according to their proximity to the prototype functioning that is most
conducive to the functioning of the system one level up. As we will see, having this objective
standard of evaluation brings us one step closer to showing

the reasoning behind medical
science’s demarcation of bodily systems.

5.2 Critical Functions

We have just pointed out that functionings

can be ordered according to their success or failure
in contributing to the functioning of the overarching system to

which they belong. A
functioning is successful if it matches or comes close to the prototype, and it fails the instant it
crosses a threshold beyond which it no longer contributes sufficiently to the functioning of the
level system.

It is also poss
ible to order functions

themselves. There are many ways in which functions
can be ordered. The way that concerns us here is to order functions on the basis of the degree
of importance they have for their functional whole. The heart’s function to pump blood

is for
example more important for the survival of the body than is the function of one skin cell to
guard the body against the invasion of foreign substances. Or, as we will say, the heart’s
function is more
to the survival of the body than is th
e function of one skin cell. After
we subject the notion of criticality to further analysis, we will see that it is this dimension of
evaluation of functions that yields the principle for the division of the body into its major

But first a note ab
out the difference between a
successful functioning
, which is a SPAN
entity, and a
critical function
, which is a SNAP entity. We have suggested a means of
evaluating functionings qualitatively, based on their proximity to a prototype functioning. The
r exemplifies the ideal functioning of an element in relation to the ideal functioning of the
system it belongs to. Evaluating functionings means comparing one type of functioning, say
the heart’s beating, with the prototypical functioning of the ideal hea

Ordering functions according to how critical they are to the body’s survival, on the other
hand, means comparing one type of function with another type of function, say the heart’s
function to beat with a skin cell’s function to protect the body from f
oreign invasion.
terms of comparison are: how critical is a given type of function to the function of the body as
a whole?

It should be noted that we use the notion of criticality in a somewhat non
standard sense;
or rather, that we are expanding on o
ne standard sense of the term. In everyday speech,
criticality refers to some highest degree of importance: a drought can approach criticality by
becoming more and more severe. In physics a point of criticality is the point at which a
nuclear reaction beco
mes self
sustaining. In medical science, criticality refers to the point at
which the body can no longer survive: a disease is critical if it threatens the patient’s life.
Along similar lines, we understand a function to be critical if the body as a whole
survive without it.

F is a
critical function

for organism Y if and only if [23]:


some element of Y has F as its function;

the continuing to function of organism Y is causally dependent on the continued
performing of F by X.

The func
tion of the digestive system is critical to the survival of the body, as is that of the
immune system. As we will see, then, criticality can also admit of degree. The function of the
vocal cords is not critical to the survival of the body, and neither is t
he function of the thigh
muscle. But the function of the thigh muscle is probably
more critical,
or in other words has a
higher degree of criticality
, than the function of the vocal cords. This is because, at least in
the case of most organisms and most en
vironments, it is harder for an organism to survive if it
cannot run or walk than if it cannot utter sound.

An element’s function can also be critical for the continued functioning of a system at
levels below that of the whole organism.
Our definition of
critical function can be restated
with the overarching system as the context:

F is a
critical function

for system Y if and only if [23]:


some element of Y has F as its function;

(ii) the continuing to function of organism Y is causally dependent o
n the continued
performing of F by X.

Thus if a chloride channel in a mucous
producing gland has some kind of genetically
inherited defect, it can cause the gland to malfunction and produce an excessively thick fluid.
If the gland is in the respiratory ep
ithelium, where its function is to produce a thin slime to
moisten the surface of the epithelium, this can cause problems in respiration. Or if the gland is
in the pancreas, it can cause the pancreatic fluid to be too viscous to leave the pancreas. In this

case, the pancreas malfunctions and causes problems related to nutrition
intake. Thus it is
possible for one low
level element to be critical not only for one system but for many.

5.2.1 Degrees of Criticality

A system element has a low degree of critic
ality if the system can still achieve its function if
the element is set out of action. For example, the circulatory system still functions if some
particular arterial branch is occluded by a thrombus in such a way that it no longer functions
to supply cer
tain regions with blood. For in practice the needed blood flow will be provided
via collateral arteries. That means that this particular arterial vessel has a low degree of
criticality to the circulatory system.

The arterial branches of the aorta, on the
other hand, have a high degree of criticality to
this system.
If they are set out of action this does not mean that the circulatory system will
stop functioning, but it will be impaired to a much higher degree than in the case of the
absence of a smaller b
ranch. And in some cases branches of an aorta being set out of action
can issue in the death of the organism.

The criticality of a given function to the survival of a given individual is sometimes
relative to the individual and to his environment.
The fu
nction of the thigh muscle is more
critical than that of the vocal chords in a society where people must hunt for food. In this
respect, an evaluation of functions according to their criticality is similar to an evaluation of
functionings according to thei
r success or failure. Note however that criticality of functions
can only be relativized in certain limited cases. The function of the heart is always more
critical than the function of the thigh muscle.

There are other respects in which an evaluation of f
unctions according to criticality
overlaps with an evaluation of functionings according to success or failure. There is not
enough room here for a comprehensive account of this overlap. Suffice it to mention a few
brief points. One is that an element with
a critical function probably has a thinner margin
within which its functioning can deteriorate from its prototype without ill effects for the
organism as a whole, as compared to an element without a critical function. The liver, for
example, must realize i
ts function to remove waste much more successfully than the tonsils
must realize their function to guard the oropharynx.

Another point at which evaluation of the success of a functioning overlaps with
evaluation of the criticality of a function is in certa
in abnormal circumstances. For example,
the lungs and kidneys are both elements of systems responsible for the mainten
ance of the
body’s homeostasis. One function of the kidneys is to main
tain ion and water balance, which
they realize in part by excretin
g redundant ions in order to avoid acidosis (the pH level
becoming more acidic). If the kidneys are unsuccessful in this performance then the lungs
take over: they can maintain the blood pH level, making it more alkaline by means of a more
intensive gas ex
change. But the lungs can substitute for the kidneys’ function in this way only
temporarily. The lungs, then, have one function that becomes critical in the unusual
circumstance of kidney failure, but the lungs cannot perform this function successfully
ugh to contribute to the survival
function of the body.

5.3 Critical Functions and the Spatial
functional Hierarchy

Recall that the spatial
functional hierarchy is organized on the basis of two features of the
human body: its complex anatomical struct
ure, and the functions that occur because of the
processes that this structure allows for. Elements on lower levels are parts of elements on
higher levels, and, correspondingly, their functionings contribute to the functionings of the
elements on these hig
her levels.

The circulatory system exists one level down from the body as a whole. As such, its
functioning (transporting nutrients, waste material, oxygen, and cells among bodily systems)
contributes to the survival of the whole body. The heart is an ele
ment of the circulatory
system one level down: it is both a part of the circulatory system, and it has a function that
contributes to its function.

We can now see that a correlation emerges between criticality and spatial
Elements with f
unctions at higher spatial
functional levels are also more critical. In
other words, the fewer systems you have to count upward from a function before you reach
the function of the body as a whole, the more critical the function is to the whole organism.
or example, the brain exists on a high spatial
functional level: there is only one brain in the
whole body, and it has a critical function. Each single neuron, on the other hand, exists on a
low spatial
functional level and does not have a critical functio
n because it stands in a relation
of redundancy to other neurons.

This correlation between criticality and spatial
functional level casts light on the way in
which redundancy factors into the spatial
functional hierarchy.
Briefly, we can say that the

the spatio
functional level, the fewer examples we find of criticality and the greater the
redundancy of functionings. Thus the mutation of one single cell does not cause cancer in
normal conditions (which means: where the immune system is functioning suc
cessfully). For
this we need the presence of the same mutant gene in a multiplicity cells within a single

It should further be noted that it is functions, not elements, that are critical.
It might sound
strange to say that it is your aorta’s functi
on that is critical to the functioning of your heart
rather than your aorta itself. But consider what happens when your aorta is replaced by a
prosthesis: it is then the prosthesis that acquires the function of the aorta in the context of your

y, elements may acquire critical functions in special circumstances.
One of your
two kidneys has a non
critical function in the body’s normal state, but it becomes critical if
the contralateral kidney is damaged or removed and nothing else performs its fun
ction. Your
kidneys taken together, however, do have a critical function.

There are clearly many types of criticality. Is the heart more critical than the stomach
because the body will die sooner in virtue of a malfunctioning of the heart? An expansion of
this account can break down criticality among its different types. For now, however, since we
have explored how the criticality of a function goes hand in hand with its placement on the
functional hierarchy, we have what we need to explain the reas
oning behind a division
of the body into its major systems.

6. How the Body is Demarcated into Bodily Systems

Note that the demarcation lines among bodily systems are to some degree a matter of fiat;
they are boundaries inserted by human beings for the

purposes of constructing good
(predictively powerful) causal theories [24]. There are physical discontinuities, such as
membranes, between many of the elements in bodily systems, but as we have noted these
discontinuities only provide partial causal isola
tion. And many elements have functions for
more than one system.

We suggest that it is some implicit notion of criticality that has provided the basis for the
reasoning underlying current classifications of bodily systems.
Medical scientists, in
g such systems, had to take into account the whole body, since it is in the context of
the latter that part
whole functions realize their functionings. Accordingly, all of the top
elements of the body, its bodily systems, are critical to the body’s c
ontinued survival.

We can see that the bodily systems are interconnected in such a way that if one system
ceases to function then so also, by virtue of the ensuing death of the whole organism, do all
the other systems.
The death of one is the death of all.

there is a certain
sequentiality to this interdependence, so that the pathologist is in the overwhelming majority
of cases able to establish
system was responsible for causing the organism’s life
processes to cease.

Consider how this appli
es to the regulatory systems. The autonomous nervous system,
which is a regulatory system of the vegetative functions of the body, has as a critical element
the brain stem (hypothalamus). A mild stroke in the area of the hypothalamus, where the
centres of regulation are localized, is life
threatening. Another regulatory system is
the endocrine system, of which the pancreas is a critical element. If the pancreas does not
realize its function to excrete insulin, the organism will not be able to use

glucose, and it will
die. The immune system has as critical elements T
lymphocytes, whose function is to kill
alien cells. If this function is not performed, the organism can die of something as simple as
sepsis caused by the saprophytic microflora that n
ormally inhabit the lungs and the intestines
(as in the case of AIDS, for example).

Our approach suggests also how we might formulate an explanation of the reason why
the standard roster of bodily systems, while including certain commonalities, still diffe
among themselves in certain specific ways. Some textbooks of anatomy, for example, include
both bones and joints in the skeletal system, whereas both the


and the


[6] represent bones and muscles as two separate systems.
As we
there is a certain sequentiality to the interdependence of bodily systems. If one system
ceases to function, then others will follow in its train and in a certain order. If two putatively
distinct systems always cease to function simultaneously

as in the case of the
and the systemic components of the circulatory system

then they may for this reason be
counted as
parts of the same system

rather than as systems in their own right. Do the bones
and muscles constitute two separate syste
ms or only one? To answer this question is to answer
the question whether one can fail without the other thereby

failing also.

We now wish to assert the hypothesis that
all critical functions performed by elements of
the body’s hierarchical organization at

lower spatial
functional levels are contributions to
the performance of critical functions by larger systems on higher levels.

Eventually we reach
some maximal level, where we are dealing with critical functions belonging to elements that
contribute to th
e functioning of no larger system of the body than the body as a whole. The
elements on this maximal level are precisely the body’s major systems.

We can then define:

X is a bodily system for organism Y if and only if:


X has a critical function fo
r Y;


X is not a part of any other system that has a critical function for Y.

Bodily systems are in other words the
largest elements

of the human body that have
critical functions.
Note that (ii) does not exclude isolated elements of X having critica
functions in other systems. This is important in accounting for how the failure of one system
can cause the failure of other systems. For example, liver failure causes the osmotic pressure
in the blood to fail, which causes wide disturbances in the body’
s homeostasis. In addition,
the liver cannot produce components of the coagulation system, and generalized hemorrhage
will occur.

Just as some elements belong to a spatial
functional level that is immediately below that
of the system of which they form a

the heart is an example of such an element, since it
is not a proper part of any other element of the circulatory system

so bodily systems belong
to the spatial
functional level that is immediately below that of the whole organism.
functions p
erformed by the body’s systems are then given in Table 2.




To separate the internal environment from the external medium


To move (including: to main the shape of the body and its movement in
confrontation with gravity
; to separate sub
environments inside the
body; to maintain the internal organs mechanically)


To digest (to exchange substances: solid substances in
out, liquids in)


To breathe (to exchange substances: gas in


To su
pply all the systems of the organism with blood


To regulate the movement of the body (somatic part) and the vegetative
functions of the internal organs (autonomous part)


To regulate metabolism, growth and development and the sexual
erentiation of the organism


To preserve the substantial integrity of the organism


To urinate (to exchange substances: liquid out)

Table 2.

Bodily systems and their functions

Of course it is possible that, if an element several levels bel
ow the body as a whole ceases to
function, then the life of the the body itself could be brought to an end. Does this undercut a
functional hierarchy? No; rather it forces us to take into account causal processes that
relate one spatial
level to another and to some environments. The heart is a critical
element of the circulatory system; the circulatory system is a critical element of the whole
body. If the heart stops, the body dies. But it is not the heart’s stopping that directly

body to die; rather, the heart’s stopping causes the circulatory system to stop functioning,
which in turn is what causes the body to die. So an element on a lower spatial
level, separated from the body as a whole by several other levels, d
oes not directly cause the
body to stop working. It does so only by means of intermediate causal links. A spatial
functional hierarchy accounts for these links.

7. Conclusion: Evidence for this Account

The first piece of evidence for the correctness of
our account is that it yields a roster of bodily
systems that corresponds very well to those given in the standard reference sources. Such
sources do not, for example, classify the visual and other perceptual systems as bodily
systems alongside those given

in our list above. Our analysis enables us to understand also
why there is no shared opinion on how to classify the reproductive system within such
standard rosters. Some accounts tack the reproductive system onto the urinary system and
refer to one compo
site ‘urogenital system’; some accounts refer to a ‘genital system;’ and
some accounts do not mention reproduction at all. We see this as additional evidence for the
correctness of our analysis, which should cast light not only on what is broadly shared by

standard rosters of the body’s systems but also on the ways in which these rosters differ
among themselves.

Clearly the reproductive system does not have a critical function in maintaining the
body’s life processes (though it might be said that it does h
ave a function critical for the
survival of the species, if our account of system turned out to be applicable to systems outside
the locus of the body itself). The reproductive system differs further from the other systems in
that it comes in two, mutually

complementary forms.
For its functioning we need individuals
of two sexes, each of which contains only part (a half) of the system as a whole.

Our approach suggests how we might formulate an explanation of the reason why some
textbooks of anatomy include

both bones and joints in the skeletal system, while others,
including both the

[25] and the
Terminologia Anatomica

[6], represent bones and
joints as two separate systems.

We have sought to set out some ontological tools for providing an anal

of ‘bodily
system,’ in a way that will do justice to the way the term is used in existing standard sources,
while at the same time providing the nec
essary degree of formal pre
cision to form the basis
for a future domain ontology of functional anatomy.

This work was supported by the Alexander von Humboldt Foundation
under the auspices of its Wolfgang Paul Program. Our thanks go also to Anand Kumar for
helpful comments.


[1] Smith B. Ontology. In: L. Floridi (ed.), Blackw
ell guide to philosophy, information and
computers, Oxford: Blackwell, 2003.

[2] Baader F. et al.
The description logic handbook. Cambridge: Cambridge University Press,

[3] Borgo S, Gangemi A, Guarino N, Masolo C, Oltra
mari A. Ontology roadMap: On
structure for the Semantic Web,

[4] Grenon P, Goldberg L, Smith B. Biodynamic Ontology: A
pplying BFO in the biomedical
domain. In: D. Pisanelli, Ontologies in Medicine: Proceedings of the Workshop on Medical
Ontologies, Rome, October 2003. Amsterdam: IOS Press, forthcoming.

[5] Structural Informatics Group at the University of Washington Dep
artment of Biological
Structure; and Division of Biomedical and Health Informatics, Department of Medical
Education and Biomedical Informatics. Digital Anatomist Foundational Model,

[6] Terminologia anatomica: international anatom
ical terminology, Federative Committee on
ical Terminology (FCAT), Stuttgart: Thieme, 1998.

[7] World Health Organization training course on N
ational Library of Medicine classification,

[8] Köpf
Maier P, ed., Wolf
Heidegger’s atlas of human anatomy, Vol. 1, 5th Edition, Berlin,

[9] Bertallanfy L. General system theory, New York: George Braziller, 1968. p. 17.

[10] Smith B. Basic formal ontology, http://onto
f, 2003.

[11] Ingarden R. Man and value, Munich: Philosophia, 1983, p. 87.

[12] Grenon P, Smith B
. SNAP and SPAN: Towards dynamic spatial ontology. In: Spatial
cognition and computation, 4:1, forthcoming.

[13] Aristotle. On the parts of the animals. Translated by: Ogle, W. In:

[14] Bittner T, Sm
ith B. A theory of granular parti
tions. In: Foundations of geographic
information science, London: Taylor & Francis, 2003.

[15] Rosse C, Mejino JL.
A reference ontology for bioinformatics: the Foundational Model of
Anatomy. Journal of biomedical Informat
ics, 2003. In press.

[16] Searle J. The construction of social reality, New York: Free Press, 1995.

[17] Millikan RG.
Language, thought, and other biological categories.
Cambridge, MA: MIT
Press, 1984.

[18] Bigelow J, Pargetter R. Functions. In: The Jou
rnal of philosophy 84, 1987, pages 181

[19] Johansson I, Tsikolia N, Ernst D, Elsner K, Siebert D, Munn K, Smith B. Bi
functional anatomy: a new proposal for medical data integration. Under review for the
International Workshop on Data I
ntegration in the Life Sciences, 2004, Leipzig, Germany.

[20] Buller J. Etiological theories of function: a geographical survey. In: Biology and
philosophy 13, 1998, pages 505

[21] Donnelly M. On holes and parts: The spatial structures of the human
body. IFOMIS
Reports 03/03, Leipzig, Germany, 2003.

[22] Johansson I. Functions, function concepts, and scales. Forthcoming in: The Monist 1,

[23] Smith B, Papakin I, Munn K. Bodily systems and the modular structure of the human
body. In: Proceedin
gs of AIME 2002: 9

Conference on Artificial Intelligence in Medicine

[24] Smith B, and Varzi A C. Fiat and bona fide boundaries. In: Philosophy and
phenomenological research, 2000, page 60.

[25] Nomina anatomica, 4

Amsterdam: Excerpta Med
ica, 1977.