I once had cause to refer, somewhat mischievously, to “a kind of pasta from Tuscany, which is almost identical to spaghetti, but slightly different”; this was on a mailing list that was used by many Italians. It provoked the expected response; an offended Tuscan responded “I don’t know what you are talking about; but if you mean pici”, which I did, “it’s nothing like spaghetti”.
Recently, on the OBI mailing list, there has been much discussion about labels, markers or tracers. What ever you wish to call it, the basic idea is the same; a molecule which is easily detectable, is used to trace something else. This can involve adding a small amount of a radioactive isotope (P32). This makes it possible to follow the molecule (which is otherwise hard) by tracing the radiation (which is generally easy).
So, how do we model this? As with many parts of ontology building, it turns out to be not straight-forward; during this discussion, an email from Philipee Rocca-Serra which left me asking the question, are we being too specific? I will work through an example to show what I mean. Feel free to skip to the punchline if you choose.
Consider, for example, the following models; these are not directly taken from OBI, as I want to reduce the complexity for this article; rather they are in the general spirit of the models which raised these questions.
A label, or something that has been labelled is clearly part of an experimental design. It is not intrinsic to this entity, rather it appears to be a role that the entity is playing in the experiment. So:
Class: Label SubClassOf: Role
There are, of course, labels of many sorts. The main types that I can think of are radioactive, fluorescent and what I call adherent. So, we might add the following, with a few subclasses of adherent as explanation.
Class: RadioactiveLabel SubClassOf: Label Class: FluorescentLabel SubClassOf: Label Class: AdherentLabel SubClassOf: Label Class: BiotinilaytedLabel SubClassOf: AdherentLabel Class: AntigenicLabel SubClassOf: AdherentLabel
So far so good. However, for a label to be useful, it needs to be manufactured (often in a bespoke fashion, depending on the experiment being performed) and it needs to be detectable. So, we might add classes like so:
Class: LabellingProcess SubClassOf: Process has_output some Label Class: LabellingDetectionProcess SubClassOf: Process has_input some Sample contains some Label
Now we have three classes for every label type. We can deal with this by
generating a cross-product, either at development time, or at the time
of use if we are using OWL. However, we need something to tie together
these classes. We need a concept to know that we need a
RadioLabellingProcess to produce a
RadioLabel which we detect in a
RadioLabellingDetectionProcess. In short, we need a concept of
Class: RadioactiveEntity SubClassOf: IndependentContinuant, bears some Radioactivity Class: RadioactiveLabel SubClassOf: Role, RadioactiveEntity Class: RadiationDetector SubClassOf: detects some Radioactivity Class: RadioactiveLabelProductionProcess SubClassOf: has_input some RadioactiveEntity
This is where the situation gets difficult. What kind of thing is
Radioactivity? Taking the realist approach, we need to consider this
carefully, determining what this universal is. So, starting from the
top, it is fairly obvious that we have a
Continuant. Next question, do
we have a
IndependentContinuant. Again, this is fairly
clear: radioactivity cannot exist without something to be radioactive,
Radioactivity is a
We have a set of
Radioactivity could be.
Role does not fill well; this is usually ascribed by
socially or, in this case, experimentally determined behaviour. Perhaps,
Disposition would be better. However, this does not really fit either,
Disposition is realised “under specific circumstances”. Now this
is not true of radioactivity. Either something is radioactive or it is
not, and if it is, then it is, to the best of our knowledge, radioactive
under all circumstances. It appears, then, that
Radioactivity is a
Quality, because “it is exhibited if it inheres in an entity at all”.
If we follow the same logic with our other label types, initially, we
come to the same conclusions. However,
Fluorescence is not exhibited
under all circumstances. It only happens when the label is illuminated
with the right kind of light. So,
Fluorescence appears to be a
Disposition. Following a similar logic, this is also true of
Adherent. So the best we can say about the property of the substance
that makes it usable in labelling is that it is a
Radioactivity stand out in this way is a little unsatisfying.
Let’s consider the logic again. One classic experimental form is the
pulse-decay experiment. I can, for example, feed a rat with, say,
radioactive phosphorus briefly. After this, you can trace the course of
phosphorus. Now during the course of this experiment, the rat becomes
radioactive and then ceases to be radioactive again. But, it is notably,
the same rat. So, perhaps, the statement that things are either
radioactive or not is wrong. Perhaps, it is not a
Quality at all. The
flaw in the logic is the assumption that because an atom is either
radioactive or is not, therefore anything made up from atoms must be so.
But an entity can have its atoms totally replaced and still be the same
entity. In this case, what is true of a rat, is also true of its DNA. We
can replace the atoms in a sample of DNA with other ones and still, have
the same DNA. So, maybe,
Radioactivity is a
Quality at an atomic
level of granularity, but is, after all, a
Disposition at others.
Thinking further, however, maybe it is not a
Quality at all. A mass of
P32 is always radioactive, but a single atom? Perhaps not,
since it only displays this when it decays. So, perhaps, it is a
Disposition after all. However, this makes no sense, because
dispositions are displayed under “specific circumstances”. Now, to the
best of our knowledge, radioactive decay is stochastic — it is so
random, that radioactivity is often used to generate randomness. We
cannot specify the circumstances under which it happens, it just does.
More over, after it displays the radioactivity, what has happened to the
atom? Using the same argument as before, we could say that, like the
rat, the atom still exists, it’s just that (some of) the elementary
particles that make it up have changed. But this way, surely, madness
lies, as “being phosophorus” would become some sort of dependent
continuant, which the atom displays during its decay, while it happens
to have the right number of protons. So, probably it makes more sense to
say that, the decay process represents the end of the existence of the
phosophorus atom and the beginning of a new atom (and a radioactive
particle). In which case, even our original decision that
DependentContinuant is wrong. It’s not a
DependentContinuant at all, it’s only a process which over as soon as
So, what have we achieved? Well, I would argue, not a great deal, except for a lot of discussion. More over, we have ended discussing very detailed issues about the physical properties of matter, when we started discussing an ontology of biomedical investigations. This might be entertaining, or it might be very dull, depending on your point-of-view. But, what we have failed to produce is a specific conclusion.
The problem here is realism. A realist ontology represents portions
of reality, that is classes of things that really have instances. We
have to ask these questions to try and determine whether
exists and what kind of thing that it is. We can set realism against
pragmatism. Previously, Robert Stevens has described the problems
that this causes by preventing the ontologist from modelling
such as Newtonian mechanics, or canonical anatomies. The unicorn
principle says, if it is useful to model a concept in an ontology, then
often we should. Here, I introduce what I call the “Pici principle” — if
it is not useful to model a concept then we should not. As a British
native, pasta is pasta; it all tastes much the same to me. Generally, I
do not need the ability to be able to distinguish pici and spaghetti,
unless I want to provoke a response from an over-excitable Tuscan. The
sensible course is not to get involved in the discussion in the first
The same applies in this instance. There is a clear use case for the
Radioactivity; without it, we cannot say that a radio-label
is radioactive, or that a fluorescence detector is not going to work
detecting it. But to achieve this use case, we do not need to understand
very deeply what
Radioactivity is. Describing it as a
DependentContinuant is enough, and it will fulfil the use cases. It
will not enable us to ask questions about which kind of labels detect
qualities and which detect dispositions. But in the absence of a use
case, this is not an issue.
A chemist may care, and may want to classify radioactivity further. This
is fine; as with pasta, we can safely leave these issues to someone
else, in the knowledge that they are probably better qualified to give
an answer anyway. So long as they decide that
Radioactivity is a
DependentContinuant, it does not matter to us what kind of
DependentContinuant; we have said nothing incorrect. So, our ontology
will integrate with theirs, without change to either. By being as vague
as our use cases allow us, we have actually increased the ability of our
ontology to integrate with others.
In short, the pici principle encapsulates the idea that deciding what we should not model in an ontology is as important as what we should model. And this decision comes from use cases, not reality.