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Definitions; March 27, 2005
Cell and some of its parts; round 2
The comments revolve around distinctions between prokaryotic and eukaryotic cells and
the accommodation of non-nucleated cells in the definition. I first address some general
issues you brought up and then revisit the definitions of those cell parts that are critical
for defining cell before dealing with cell.
Exceptions in definitions
Do we allow exceptions to definitions? No, we should not. That would be bad practice.
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?
I would have serious reservations with setting out on such a course.
IMHO the definition should specify necessary and sufficient conditions true of all
instances of that class, not just typical instances.
This is the only legitimate way. We provide selected examples in the text definition but
the definition should support comprehensive instantiation of the class. If it does not, the
definition has to be revised. Indeed, all definitions should be evaluated through such
instantiation. In building the FMA we had to revise definitions many times as a result of
such a process.
For the latter how about we generate a list of things that
we would consider cells and things that we would not consider cells
(our example use cases) and use these to insure that the definition
works appropriately. Keeping these lists is the only change I'd
suggests. Here is a simple start:
Cells:
mycoplasma, RBC, more examples?
Not cells:
mitochondria
chloroplasts
vacuoles
viruses
This process was employed in the FMA and I am sure also in Cell ontology, but this is
not our task. We are not generating a cell ontology from ground up; we are working topdown.
Prokaryote/Eukaryote Decision
I think there are 2 things we need
to do. One is to always bear in mind that these are structural
relationships only (so forget the eukaryote vs. prokaryote distinction)
I thought FMA only utilised a structural axis of classification? Prokaryote-vs-Eukaryote
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,non-nucleated} cell, which
leads to multiple inheritance – anathema to the FMA!
But, I suppose it is fine, because it is all within the context of the FMA human anatomy.
The definitions I proposed do indeed come from the FMA and the FMA currently
pertains to human anatomy. But for the purposes of SOFG, we have to generate
definitions that generalize beyond human anatomy. This mandate is consonant with the
intent of the FMA; we intend FMA definitions of high level classes such as cell and
organ to be valid for all types of cells and all types of organs. But we had in mind
mammals or vertebrates and as far as cells and cell parts are concerned, only Eukaryotes.
I think this cut-off would satisfy the needs of SOFG. But let us see what the definitions
look like after the amendments.
Cell parts that define cell
We agree that at least first we want to write structural definitions and therefore in most
instances we need to deal with parts of the entities we want to define. It is unfortunate
that we do not have collective terms like nuts and bolts for describing the objects of
which cells are made. For want of a better term we call these entities cell parts and
therefore our definition of cell in terms of its parts may appear circular. In fact it is not.
Let us start from the bottom up and define the cell parts that we need for defining cell.
Your comments confirmed that we agree on the following:
cytosol + cytoplasmic organelles = cytoplasm
cytoplasm + nucleus = protoplasm
protoplasm + plasma membrane = nucleated cell
cytoplasm + plasma membrane = non-nucleated cell
The last two assertions lead us up to two classes of cells without using the term cell to
define what these two classes are. So we are clean. To reiterate, for want of a better term,
we call the universal that subsumes all these entities that are part of a cell the class ‘cell
part’. ‘Cell part’ provides the genus for all the individual cell parts we want to define if
they are anatomical structures. Only cytosol is a substance rather than an anatomical
structure.
Therefore we can write
Cytosol
Cell substance which fills the interior compartment of non-nucleated cells and the compartment
between the plasma membrane and the nuclear membrane in nucleated cells. [FMA]
We cannot use GO’s definition because it leads to circularity in defining cytoplasm:
Cytosol: That part of the cytoplasm that does not contain membranous or particulate
subcellular components.
Cytoplasm
Cell part which has as its direct parts cytosol and cytoplasmic organelles. Examples: cytoplasm of
hepatocyte, cytoplasm of erythrocyte, cytoplasm of thrombocyte, cytoplasm of axon.
We cannot use GO’s definition because it defines cytoplasm by what it is NOT rather than by
what it is:
Cytoplasm: All of the contents of a cell excluding the plasma membrane and nucleus,
but including other subcellular structures. ( from AmiGO)
We need to specify “as its direct parts“ because the parts of parts, like atoms, are also parts.
In addition, an inconsistency exists between the definition itself and the examples, which
is overlooked essentially by everyone. The examples illustrate that by cytoplasm we
mean not just any odd droplet of cytoplasm but an amount or portion of it that is maximal
for a particular cell; not the portion of the hepatocyte’s cytoplasm around its nucleus or
subjacent to its cell membrane, but the whole of it. Therefore we have to amend the
definition:
Maximally connected portion of cytoplasm
Cell part which has as its direct parts a maximally connected portion of cytosol and cytoplasmic
organelles. Examples: cytoplasm of hepatocyte, cytoplasm of erythroblast, cytoplasm of
erythrocyte, cytoplasm of megakaryocyte, cytoplasm of thrombocyte.
We need to apply this rationale in the other definitions also.
Maximally connected portion of protoplasm
Cell part which has as its direct parts a maximally connected portion of cytoplasm and at least
one cell nucleus. Examples: protoplasm of hepatocyte, sarcoplasm, protoplasm of
megakaryocyte.
Maximally connected portion of plasma membrane
Cell part that surrounds a maximally connected portion of cytoplasm and has as its direct parts a
phospholipid bilayer and associated proteins. Examples: plasma membrane of hepatocyte,
sarcolemma, plasma membrane of erythrocyte.
That is, an arbitrary piece of plasma membrane or a portion that covers a cilium, for
example, is distinguished from the plasma membrane as a whole.
Definition of cell
The following definitions are sensibly derived from the above:
Nucleated cell
Cell which has as its direct parts maximally connected portions of protoplasm and plasma
membrane. Examples: hepatocyte, erythroblast, skeletal muscle fiber, megakaryocyte.
Non-nucleated cell
Cell which has as its direct parts maximally connected portions of cytoplasm and plasma
membrane. Examples: erythrocyte, corneocyte, lens fiber thrombocyte.
Although the surround relation between membrane and the cell’s interior is omitted, the
direct part relation demands that the whole cell occupy the same spatial region as the
mereological sum of the parts referenced in the definition. But we can add the surround
relation if you think it serves a useful purpose.
Because protoplasm always has cytoplasm as one of its direct parts, it follows that the
latter definition also suffices for Cell if the genus is changed.
Cell
Anatomical structure which has as its direct parts maximally connected portions of cytoplasm and
plasma membrane. Examples: hepatocyte, erythroblast, skeletal muscle fiber, megakaryocyte,
erythrocyte, corneocyte, lens fiber thrombocyte.
You provided the GO definition for cell, which, of course is not a structural definition.
“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”.
Are viruses organisms? I think so; in which case, according to GO, they must have a
plasma membrane, etc. Also the definition conflicts with GO’s definition of
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
Are external encapsulating structures such as the cell wall and cell envelope part of the
cell or not? They are outside the plasma membrane and therefore in the external
environment.
Am I making the problems clear?
Accommodate prokaryotic cells
You point out that they have nucleoids without a nuclear membrane rather than nuclei,
they lack “cytoplasmic” organelles and they are said to have protoplasm rather than
cytoplasm. Although we are not proposing a definition as yet for organism, we take it for
granted that Prokaryotes are organisms and hence they are anatomical structures.
Thus the genus ‘anatomical structure’ in the cell definition is fine; so is plasma
membrane as one of the differentiae, only cytoplasm is inappropriate.
From the above definitions it would follow that prokaryotic cells
1. do not have cytoplasm only cytosol
2. rather than one or more nuclei, one or more nucleoids are suspended in cytosol
Can your suggestion help?
Perhaps redefine subclasses with nuclear material and without nuclear
material, or add a third child for cells with nucleoids in which the
nuclear
material is in a visible nuclear region, but not bounded by a membrane?
Cell
Anatomical structure which has as its direct parts maximally connected portions of cytosol and
plasma membrane [with or without the presence of nuclear material]
I have a feeling that this version would not please anybody even though it may be
factually correct.
Another option is to change the definition of protoplasm to
Protoplasm
Cell part which has as its direct parts a maximally connected portion of cytosol and at least one
cell nucleus or nucleoid.
This abrogates the connection between cytoplasm and protoplasm in eukaryotic cells but
otherwise makes sense. The change would accommodate the fact that prokaryotic cells do
not have cytoplasm whereas eukaryotic ones do.
Yet another option would be to consider another one of your suggestions:
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?
This is true. The definition would then read
Cell
Anatomical structure which has as its direct parts maximally connected portions of cytosol and
plasma membrane and at least in the early stages of its existence one or more nuclei or
nucleoids.
I think this actually reads better than the previous versions. The definitions of nucleated
and non-nucleated cells as well as of prokaryotic cells could logically follow from this
definition. The FMA would not include the latter but other abstractions might.
There is, however, at least one reason why this definition is flawed: thrombocytes are
bona fide cells, yet they never had a nucleus of nucleoid; they bud off from the cytoplasm
of a megakaryocyte, with which they are clearly not identical.
Please voice your preferences. Also state whether you’d prefer to disregard prokaryotic
cells.
Some of you raised objections to the last suggestion questioning the veracity of identity.
It is an important point and therefore I will deal with it.
Identity
My concern is about the cell definition and his suggestion to insert
the following in this definition: "....has a nucleus at some point
during its existence". I am not sure about that. There are specific
cells which represent paradigms of non-nucleated cells. He brings up
the subject of the erythrocyte and he claims that "...at some
point in time even the mammalian erythrocyte must contain a nucleus and
sometime after the erythrocyte has fully differentiated the nucleus is
pushed out". I disagree with that. A nucleated erythroid cell is an
erythroblast, regardless of the differentiation stage. A non-nucleated
erythroid cell can be a young or immature one (reticulocyte) or a
mature one (erythrocyte). I would not include this statement in the
cell definition.
I don’t know about paradigms of non-nucleated cells, but if I understand the comment
correctly, it asserts that a reticulocyte or an erythrocyte is not identical with erythroblasts
because the latter are nucleated and the former are not. The assertion misses the meaning
of identity.
There are several generations of cells in the erythroid lineage which are called
erythroblasts [proerythroblasts, basophilic erythroblasts, polychromatic erythroblasts and
orthochromatic erythroblasts]. There are several cell divisions along this lineage; some
estimates are as high as 7. When a cell divides it gives rise to two new individuals which
are not identical with the parent or with one another [identical twins of congenic animals
are not identical either; they have distinct and complete boundaries]. The last division in
the lineage occurs in the polychromatic stage and the last polychromatic twins transform
without a cell division into two orthochromatic cells which extrude their nuclei and are
then renamed reticulocytes; when the latter lose their complement of RNA the cells are
renamed erythrocytes. It should be evident that identity is maintained after the last
division even though there is a change in phenotype. I with my grey beard, bold head,
missing teeth and wrinkled skin am the same individual as I was 40 years ago brimming
with machoness. The same is the case with each of the twin polychromatic erythroblasts
produced by the last cell division. They change their colour and may lose a tooth, but
each remains the same individuals circulating around in the blood stream as it was in its
colourful youth within the bone marrow. This story provides a good example for
illustrating identity, which is a very important concept particularly when we consider
lineages and development.