To:
Members of the SOFG-Definitions Group
From:
Cornelius
Subject:
Definition of Cell
Date:
January 24, 2005
Comments: February 7, 2005 [cjm]
Comments: Feb 15, 2005 [mah]
First I cite and analyze Stedman’s definition of cell and then present the FMA
definition. For comparison I also include definitions from OBO and GO.
1. Stedman’s: Cell
“The smallest unit of living structure capable of independent existence, composed of a
membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid.
Cells are highly variable and specialized in both structure and function, though all must
at some stage replicate proteins and nucleic acids, utilize energy, and reproduce
themselves.”
Targeted users: trainees, researchers and practitioners in health care and biology
Comment:
A good definition, because it starts with a genus [The smallest unit of living
structure], followed by structural and functional differentiae.
Do we also need to define “independent existence”?
1.1. Structural component of definition [i.e., structural differentiae]:
“composed of a membrane-enclosed mass of protoplasm and containing a nucleus or
nucleoid.
Comment:
1. This is true of living and dead cells.
2. What kind of a membrane has to enclose the protoplasm?
A plasma membrane or plasmalemma is the lipid bilayer enclosing a cell by
definition, though this requires the definition of cell…
3. There are cells that are devoid of a nucleus or nucleoid. Examples from FMA:
[mammalian] erythrocyte, corneocyte, non-nucleated lens fibre. Stedman’s
definition excludes such cells.
Do we allow exceptions to definitions? do we have to specify exceptions in the
definition (eg all mammalian non-erythrocytes have a nucleus), or can exceptions
be defined in specific subclasses which ‘break’ with default behaviour?
IMHO the definition should specify necessary and sufficient conditions true of all
instances of that class, not just typical instances.
Here is one potential solution to the “erythrocyte problem”. I believe that even
mammalian erythrocytes must contain a nucleus at some point in time. Some
time after the erythrocyte has fully differentiated, the nucleus is pushed out. The
erythrocyte (with nucleus) at time t0 is the same erythrocyte as the one (sans
nucleus) at time t(n+1), they share the same identity, the value of the has_nucleus
attribute varies over time. Thus the def could be reworded to say “has a nucleus at
some point during its existence”. See the Smith et al OBO relations paper for a
discussion of identity at relations pertaining to time.
Of course, the problem may rear its head again eg with reticulocytes?
4. Please assure me that the Stedman’s definition is valid for prokaryotic cells. Do
you call the inside of a prokaryotic cell protoplasm or cytoplasm or something
else?
5. Is the nucleus or nucleoid part of the protoplasm or not? Stedman gives
contradictory information on this point.
“Protoplasm: The total cell material, including cell organelles.” Since nucleus is an
organelle, the definitions of cell and protoplasm are inconsistent, confirmed by Stedman’s
definition of Nucleus: “In cytology, typically a rounded or oval mass of protoplasm within
the cytoplasm of a plant or animal cell.” I.e., nucleus is part of or is the same as
protoplasm.
Historically, protoplasm has referred to the aqueous translucent colloid within all
parts of the cell; the cytoplasm would be the protoplasm outside the nucleus and
the nucleoplasm the protoplasm inside the nucleus. Since prokaryotes do not
have a nuclear membrane, one would not differentiate between nuclear and nonnuclear parts of the cell. Therefore, prokaryotes have only protoplasm. However,
cytoplasm seems to be a term that is used rather loosely to refer to the contents of
ANY cell. In addition, many definitions for protoplasm are as Stedman’s: they
include all parts of the cell, the plasma membrane, organelles, the nucleus, etc. I
am not sure one could differentiate this definition of “protoplasm” from that of
“cell.”
The following definitions of the cell parts are non-contradictory, generally
consistent with the structural FMA definitions below, and include prokaryotes as
having non-differentiated protoplasm:
protoplasm = all contents within the plasma membrane, including all organelles
cytoplasm = all contents within the plasma membrane including cytoplasmic
organelles and outside the nucleus; cytoplasm= cytosol + cytoplasmic organelles
where cytosol is basically the historical definition of cytoplasm described above.
Please comment on this.
Although for the moment we are not concerned with defining cell parts, since the
differentiae for the definition of Cell are in terms of protoplasm and nucleus, we
must be explicit and non-ambiguous about what those defining parts are.
1.2. Functional component of definition [i.e., functional differentiae]:
“capable of independent existence” ….
“… at some stage replicate proteins and nucleic acids, utilize energy, and reproduce
themselves”
Comment:
1. There are many cells that are incapable of independent existence; these do not
qualify as cells.
2. I like the second set of differentiae, but I would reword them: “at some stage of
their existence replicate proteins and nucleic acids and utilize energy”.
The definition could stop there, because only cells have the inherent potential at
some stage of their existence to replicate proteins and nucleic acids. There is no
need for “and reproduce themselves”, because it is arguable whether the cell that
lost the ability for selfreplication is the same cell as its precursor capable of
realizing this function. And we do not need to get into those arguments.
2. FMA: Cell
Anatomical structure which has as its parts cytoplasm and plasma membrane. Examples:
lymphocyte, fibroblast, erythrocyte, neuron.
Targeted users: machines and humans, primarily those concerned with the
development of biomedical ontologies and applications relating to biomedical
research and education, and health care, as well as biology in general.
Comment:
1. The FMA deals only with biological structure (not function or processes) and
all its definitions are structural. They should be valid for living and dead
structures [i.e., applicable to fixed and stained specimens prepared for gene
expression analysis].
2. Since the FMA relates only to human anatomy, cell is understood to be a
eukaryotic cell.
3. Validating the definition calls for defining also the differentiae [plasma
membrane and cytoplasm] and the genus [Anatomical Structure]. I put the
discussion of Anatomical structure in a separate document, because it will pertain
to the definition of all the entities we will have to deal with.
I like the clear separation of the genus-differentiae definition from the examples.
Cytoplasm
Cell part which has as its parts cytosol and cytoplasmic organelles.
Plasma membrane
Cell part that surrounds the cytoplasm and has as its parts a phospholipid bilayer with associated
proteins. Examples: plasma membrane of hepatocyte, sarcolemma, axolemma
Protoplasm
Cell part which has as its parts cytoplasm and cell nucleus. Examples: protoplasm of hepatocyte,
sarcoplasm.
Comment
1. Note that the FMA distinguishes between Cell nucleus and Cytoplasmic
organelle. These are the two subclasses of Organelle. Therefore: cytoplasm +
nucleus = protoplasm; cytosol + cytoplasmic organelles = cytoplasm.
2. Note also that it is redundant to state in the definition of cell that the plasma
membrane surrounds the cytoplasm, because the definition of plasma membrane
includes this statement.
3. I don’t know what the parts are of the membrane that surrounds a eukaryotic
cell. Plasma membrane may be too specific for eukaryotic cells, yet just
“membrane’ as used in the Stedman definition is not specific enough. Any
suggestions from those of you who know about prokaryotic cells? Do prokaryotic
cells have organelles? [I think you can sense that microbiology was not a
favourite subject of mine.] Prokaryotic cells do not have organelles, and their cell
membrane is also called a plasma membrane.
4. Note that there are six synonyms of Plasma membrane in the FMA, all of
which will take the user to the same place in the ontology.
5. A pertinent additional point to note is that the FMA distinguishes two major
classes of cells as the immediate subclasses of Cell: Non-nucleated cell and
Nucleated cell. The definitions are:
Non-nucleated cell
Cell which has as its parts cytoplasm and plasma membrane. Examples: erythrocyte, corneocyte,
lens fiber.
Nucleated cell
Cell which has as its parts protoplasm and plasma membrane.
Comment:
1. To make the definition include prokaryotic protoplasm one could add “or
nucleoid”. Would that do it?
2. As I warned you, FMA definitions were not intended to include prokaryotic
cells. If our objective is to include prokaryotic cells in the class Cell, we have to
discuss how to do that. I would suggest we create Prokaryotic cell and Eukaryotic
cell as two immediate subclasses of Cell. The FMA definitions will apply to
eukaryotic cells and if need be, we will have to generate additional definitions for
prokaryotic cells.
I thought FMA only utilised a structural axis of classification? Prokaryote-vsEukaryote does not seem like a structural differentium. If we allow this then we
presumably also allow subclasses with differentia such as avian, mammalian etc.
This will give us multifaceted classes such as {mammalian,avian}{nucleated,nonnucleated} cell, which leads to multiple inheritance – anathema to the FMA!
3. Other definitions
I put definitions from additional sources in this separate section in order not to clutter the
previous sections. GO does not define Cell, since it deals with subcellular entities. Here is
a definition of Cell from OBO [there may be others; someone please find them for us]:
GO does indeed define cell, in the cellular_component ontology:
“The basic structural and functional unit of all organisms. Includes the plasma membrane
and any external encapsulating structures such as the cell wall and cell envelope”. I think
the cell ontology def and GO def should be unified.
Cell
Minute protoplasmic masses that make up organized tissue\, usually consisting of a nucleus
which is surrounded by protoplasm which contains the various organelles and is enclosed in
the cell or plasma membrane. Cells are the fundamental\, structural\, and functional units of
living organisms." [MESH:A.11]
For comparison with the FMA definitions, I include definitions of cell parts from GO, but
shall not comment on them since we will discuss these when we get to ‘cell part’.
Cell membrane
The membrane surrounding a cell that separates the cell from its external environment. It
consists of a phospholipid bilayer and associated proteins. ( from AmiGO)
Cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other
subcellular structures. ( from AmiGO)
[Intracellular] Protoplasm
The living contents of a cell; the matter contained within (but not including) the
plasma membrane, usually taken to exclude large vacuoles and masses of secretory or
ingested material. In eukaryotes it includes the nucleus and cytoplasm. (from AmiGO)
Targeted users: same as Stedman’s
If you are aware of, or find, other definitions of cell, please share it with the group. You
can also distribute definitions of the cell parts discussed above if you think they would be
useful when we deal with them. But I think we will deal with ‘cell part’ as a class and not
with all the individual cell parts.
4. “Homework”
1. Please comment on the definitions and comments I presented.
2. Propose functional and developmental definitions for Cell.
3. Also tell me whether you find the approach to our task useful based on this first
example and be liberal with suggestions for alternate ways of proceeding.