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Re: [ontolog-forum] Ontological Assumptions of FOL

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
Cc: md63@xxxxxxxxxxx
From: Ingvar Johansson <ingvar.johansson@xxxxxxxxxxxxxxxxxxxxxx>
Date: Tue, 20 Mar 2007 14:32:47 +0100
Message-id: <45FFE27F.8020103@xxxxxxxxxxxxxxxxxxxxxx>
Erick Antezana schrieb:
> Ingvar,
> We are building an application ontology for the cell cycle process 
> (http://www.cellcycleontology.org) in which some of the key aspects are 
> indeed time and space due to the dynamic essence of this biological 
> process. Actually, we are planning on "connecting" these three 
> components: physical entities (= 'what') playing a role in the cell 
> cycle process such as genes, proteins, etc; space (='where') entities 
> such as cytoplasm, mitochondria, etc; and time (='when') entities such 
> as S-phase of the cell cycle, mitosis, etc. So in that sense we are 
> coming up with ways to represent it in the ontology (still under 
> development). However, I was wondering whether we could get some hints 
> (for dealing with spatio-temporal entities) from some articles so that 
> our ontology would try to "comply with" with the philosophical (as well 
> as biological) ways of looking at that picture.
> regards,
> erick
>       (01)

Erick,    (02)

Now I think I understand you, and even why you used the  expression  
'time/space is physical'.  In what is traditionally called the  
philosopphy of space and time (which I first thought of), you will 
probaly not find anything of interest for you. Here one is concerned 
with the nature of the utmost space and time in which everything 
spatiotemporal is assumed to exist. But you are (I take it now) looking 
for a 'space' or spatial structure that is to cell theory what the 
skeleton is to anatomy. In my opinion, such a 'space' is not like the 
utmost space a *particular*; it is like properties/qualities and natural 
kinds a *universal*. That is, such a 'space' can exist at many 
places/regions simultaneously, and it might well be called a 
'qualitative space'. Similar remarks can be worked out for 'qualitative 
time'.    (03)

Perhaps you can benefit from things done under the title 'spatial 
reasoning', but I am not in general familiar with these things. Here, 
though, you get links to two papers that discuss formal features of the 
kind of 'spaces' you seem to be interested in: < 
http://ontology.buffalo.edu/geo/Layers.pdf > and
< http://www.acsu.buffalo.edu/~md63/RelPlApOnFin.pdf >    (04)

Ingvar    (05)

> Ingvar Johansson wrote:
>> Erick Antezana schrieb:
>>> Ingvar,
>>>     are there any articles or books that could be pointed out regarding 
>>> those issues (time/space is physical)?
>>> thanks,
>>> erick
>> Tell me a little more about what you are looking for, and then I will 
>> come back. By the way, I didn't make the point that "time/space is 
>> physical", which I happen to believe is false, even though General 
>> Relativity may be taken to imply such a view (i.e., space-time is a 
>> mass-energy field, and physical things are nothing else than lumps of 
>> mass-energy). My point is rather that if you think a little more in tune 
>> with common sense, classical physics, and molecular biology (which I 
>> think is much more relevant for today's information sciences than GR) 
>> then it seems natural to regard property instances as being 
>> spatiotemporally located without regarding them as in themselves being 
>> physical entities.
>> best wishes,
>> Ingvar
>>> Ingvar Johansson wrote:
>>>> Pat Hayes schrieb:
>>>>> Well, I can see a lot of problems with this. If 
>>>>> you believe, for example, that all spatiotemporal 
>>>>> entities are in some sense physical, you will get 
>>>>> into trouble. 
>>>> Let me from my philosophical corner just add one long sentence: No 
>>>> famous philosophical ontologist who posits physical (material) things in 
>>>> space and time has argued that everything that exists in space and time 
>>>> is physical (material); for instance, many claim that property instances 
>>>> *inhere in* physical things, but this does not mean that these 
>>>> spatiotemporal instances *are* physical entities.
>>>> /Ingvar J
>       (06)

Ingvar Johansson
IFOMIS, Saarland University
     home site: http://ifomis.org/
     personal home site:
     http://hem.passagen.se/ijohansson/index.html      (07)

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