On Mar 19, 2015, at 5:52 PM, Chris Mungall <cjmungall@xxxxxxx> wrote: (01)
>
>
> On 19 Mar 2015, at 7:34, Pat Hayes wrote:
>
>> On Mar 19, 2015, at 2:40 AM, Matthew West <dr.matthew.west@xxxxxxxxx>
>> wrote:
>>
>>> Dear Chris,
>>>
>>> <snip>
>>>
>>> ...
>>> [MW>] This argument is not really about a distinction, no one (well
>>> at least
>>> not me) is arguing that you cannot have both physical objects and
>>> activities
>>> in your ontology, the question is whether they are mutually exclusive
>>> or
>>> not. That is a constraint. Endurantism has the belief/insistence that
>>> this
>>> constraint is always true. If you find that it is not always true,
>>> then it
>>> is unhelpful to insist on it, because when it is untrue you will have
>>> extra
>>> work to do to work round on it.
>>
>> Exactly. But let me suggest that the real constraint here is that when
>> something is considered to be an object or a process, then each way of
>> thinking of it has to come with a particular way of formalizing it.
>> This is completely unnecessary, and if this purely syntactic
>> constraint is lifted, then the philosophical disagreements become just
>> that, purely philosophical matters, irrelevant to the actual practice
>> of ontology building. Ontological frameworks like OBO require writing
>> things like (Relation x T) when x is a continuant and (Relation (stage
>> x T)) when x is an occurrent, so they must keep a rigid separation
>> between the two categories.
>
> Can we translate this to a concrete example? I feel you keep pointing
> out imaginary problems in what your conception of the OBO framework is. (02)
My conception is based on working, some years ago, with Barry Smith on
formalizing the basic high-level ontologies of the OBO foundry. I found that
virtually every axiom had to be written out twice, in appropriately modified
forms, once for continuants and once for occurrents. Exactly the same facts
were obliged to be re-stated with different quantifier patterns because of the
'rules' about where the time parameter had to be located. (03)
> Let's say we have a relation 'has substrate', and it has a domain
> constraint of process, and a range constraint of molecule (continuant),
> and it connects the process to a molecule that is changed somehow by the
> process. You're saying the framework here is a problem because you're
> unable to say
>
> molecule1 has-substrate molecule2
> process1 has-substrate process2
>
> I suppose I'm so indoctrinated that I see this as a feature, not a bug. (04)
I guess I am wondering why this distinction, between process of a change in
something, and the thing undergoing the change, was ever made in the first
place, necessitating the introduction of this 'substrate' relation. Every day I
grow olderr. Is a process of my aging using me a substrate? Or am I simply
getting older? I strongly suspect that this relation has-substrate is what I
have elsewhere called an axiomatic dongle: a piece of sytnax whose only purpose
is to connect things that should never have been separated in the first place.
(Other examples of dongles, by the way, include rdf:type and the ancient "is-a"
construct, both of which are a relation used to express a predication.) (05)
>> Until one knows which category a new concept is in, one is quite
>> literally unable to write even the simplest axioms about it, so the
>> ontology engineering process cannot even begin.
>
> I can see how this might be a problem if you were sitting down to make
> an ontology of chemical structures and just couldn't decide if chemical
> structures were processes or structures. Or if you were making an
> ontology of biological processes and couldn't decide if the biological
> processes were processes or physical entities. (06)
I know that such debates do in fact take place, and are often found puzzling by
subject-matter experts. And to my ears, this entire discussion has something of
a surreal flavor, since I see no strong or principled difference between things
undergoing change and processes of change in things. (07)
> Meanwhile, in the real world of OBO ontologies developed by domain
> scientists outside of philosophy land, this hasn't turned out to be a
> problem.
>
>> But suppose that these two ways of saying that R is true of x at a
>> time T are interchangeable, interderivable, and have exactly the same
>> meaning, both intuitivel
>> y and in the Tarskian model theory, so that the choice between them is
>> purely one of axiom-writers taste or convenience, a matter of ontology
>> engineering aesthetics, no more. Then work can continue without
>> resolving what might be a difficult and lengthy (or even meaningless)
>> debate, and indeed can continue and be completed, without ever needing
>> to resolve such a dispute. It no longer matters whether x is a
>> continuant or an occurrent; and in time, I suspect, this distinction
>> would simply wither and die from under-use, as having no bearing on
>> the actual practice of ontology construction. Or perhaps Chris M is
>> right and the distinction is critically embedded in intuitive human
>> thinking
>
> I'm not sure I would go so far. But in the OBO world at least the
> distinction between objecty things and processy things arose naturally
> independent of philosophical involvement. (commitment to finer grained
> or more exotic upper level categories is a different matter entirely, I
> will grant you) (08)
Fine, as a general heuristic distinction I agree it can be intuitively useful,
and sometimes close to essential, to maintain such a distinction, for example
when processes involve interactions between multiple objects and one does not
want to invent a super-object for this to be a change of state of. But when a
distinction is welded into the highest ontology of an entire system of
ontologies, as the cont/occur is in OBO, it has much more force than a
heuristic intuitive guide: it is a rigid distinction that *must* be obeyed at
all times and in all instances, and to blur which is to create an immediate
inconsistency. (09)
>> : fine, by all means keep it around, if it suits you. But it need no
>> longer have this arbitrary connection to syntactic axiomatic style.
>
> Sorry, I don't know what you mean by syntactic axiomatic style. All OBO
> ontologies used an OWL concrete form as syntax. (010)
I did not mean the choice of surface syntax, which is essentailly irrelevant
(though when you use something a limiting as OWL, it does cramp your style
somewhat :-). I meant decisions such as whether to treat a concept as a
relation or a function or an individual, where to locate the temporal
parameters, whether or not one uses a discipline to keep differently typed
parameters distinct, and if so what it is, and so on. There are many
alternative ways to express a given set of facts in a given formal language,
even one as inexpressive as OWL. (011)
> I wasn't aware of any
> syntactic styles imposed by choosing to differentiate between physical
> entities and processes. (012)
The cited passage from my email, just below, gives you one.
>
>> You can write (R x T) when x is a process (or an object) and you can
>> also write (R (Stage xT)) when x is an object (or a process). Work can
>> proceed while the philosophical dogs are barking at each other.
>
> I'm not sure what these philosophical dogs are (013)
Sorry, this was my barbed witticism, an extended analogy comparing ontological
philosophers to dogs. I enjoy this partly because it offends philosophers who
take their discipline too seriously. (014)
> , and what exactly the
> perceived problem is with OBO ontologies distinguishing processes from
> physical entities. (015)
The problem is forcing the distinction in all cases, and enforcing distinct
ways of describing the two categories of entity, and the axiom-bloat that this
creates. (016)
> If I'm understanding correctly, you'd like domain/range restrictions and
> other upper level constraints to be lifted for relations like R? You
> object to not being able to say a 'fruit ripening' is part of a 'fruit',
> and having to use a different relation? (017)
Yes to the second sentence. It seems simply obvious to me that a fruit's
ripening is a temporal part of the fruit. I genuinely do not understand how
anyone can disagree with this. (What else would it be? *Where* else would it
be?) But in any case, for sure, I want to be able to apply the language of
ripening to the name denoting the fruit, without receiving error messages
telling me I have violated someone's peculiar ideas about things not being
processes. (A judgement, I would add, which has no scientific basis.) (018)
> If there is a problem with OBO ontologies, help me fix things. Give me
> concrete examples. Otherwise I guess the problems are philosophical. (019)
I do not claim that OBO is broken in the sense that it does not work, or cannot
express reality adequately. But I will claim that I, myself, would not wish to
use it. I don't think about the world in the way that it presumes I must. In
fact, I have on several occassions recused myself from collaborations that
would have required me to work with OBO, for this very reason. I suspect that
others may share my pain, if not my stubbornness. (020)
Pat Hayes (021)
>
>> Pat Hayes
>> ------------------------------------------------------------
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>>
>>
>>
>>
>>
>>
>>
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