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Re: [ontolog-forum] Two ontologies that are inconsistent but bothneeded

To: clynch@xxxxxxxxxxxxxx, "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Sat, 09 Jun 2007 15:01:14 -0400
Message-id: <20070609190250.XHRA28813.mta9.adelphia.net@xxxxxxxxxxxxxxxxxxxxxxxxxxx>
A prion is a protein molecule, is it not? Thus it is a continuant.
BS    (01)

At 03:58 PM 6/9/2007, clynch wrote:
>Barry, In light of the current thinking on 
>prions, I wonder if you might want to rethink 
>the statement of <BS> Having worked long and 
>hard with biologists it has become clear to me 
>that the continuant/occurrent distinction is the 
>most well entrenched of all the joints in nature 
>(the distinction between anatomy and physiology, 
>for example, is very old, and has not been 
>threatened one iota by recent developments in, 
>e.g. cellular anatomy>/BS> I think this does in 
>fact break the long held distinction between 
>anatomy (structure) and physiology, in that the 
>only difference in the infectivity (physiology) 
>of the protein is in its morphology (anatomy). 
>Cecil -----Original Message----- From: 
>On Behalf Of Smith, Barry Sent: Saturday, June 
>09, 2007 5:54 AM To: [ontolog-forum] ; 
>'[ontolog-forum] ' Subject: Re: [ontolog-forum] 
>Two ontologies that are inconsistent but 
>bothneeded Responding to Chris's comments on Pat 
>/ Bill composite: At 05:32 AM 6/9/2007, Chris 
>Partridge wrote: >Pat: 4) Again, following 
>Quine's doctrine, what >are these things for 
>which the >continuant/occurrent distinction 
>is >incoherent?  Presumably, you'd want to 
>be >quantifying over some class of objects for 
>which >you'd like to state some axioms 
>governing, e.g., >property change over time, 
>however that comes >out in your favorite 
>formalism.  Then, by >Quine's doctrine you're 
>committing to the >existence of those 
>things.  Let's call 
>them >Continuoccurrents.  Now you have to 
>elaborate >your theory of Continuoccurrents and 
>distinguish >them from temperatures, numbers, 
>properties, >propositions and all the kinds of 
>other things >you have in your 
>ontology.  Doesn't sound to me >like that 
>project is any less problematic than >the 
>defense of either bicategorialism, 4D, or >any 
>other metaphysical framework.  By this I >mean 
>on a practical, engineering level. > >Chris: It 
>seems, to me at least, there is a >difference 
>between the continuant/occurrent >distinction 
>and some of the other choices. These >other 
>choices (e.g. 4D) seem to be metaphysical, >in 
>that it is difficult to devise an 
>empirical >check on whether they are correct. 
>With the >continuant/occurrent distinction there 
>seem to >be cases that question whether it 
>partitions >objects. You know the standard 
>philosophical >cases ­ avalanches and waves ­ as 
>these have been discussed before. The problem 
>here, I think, is that people assume that 
>fast-moving and fast-changing continuants 
>Consider a pack of monkeys moving through a 
>forest, losing the odd monkey at the rear and 
>gaining the odd monkey towards the front. The 
>pack is a continuant. The processes of losing 
>and gaining are occurrents. Waves are like that 
>(monkeys = water molecules); organisms are like 
>that (monkeys = cells). Avalanche theory is 
>based on the distinction between granular layers 
>(continuants) and flows (which when summed 
>together make the avalanches themselves). >  In 
>ontologies that deal with engineering > 
>artefact, the same phenomena seems to arise > 
>when (when we have a similar structure where) > 
>objects are the components for other objects > 
>built out. A simple example would be a network > 
>of systems, sometimes people see it as the > 
>systems networking, sometime people see it as 
>a > network that things happen to ­ e.g. it 
>goes > down for a while. To go back to Barry’s > 
>example, some biologists see human bodies, 
>e.g. > Fritz’s, as a process, with temporal 
>parts can you give me one or two examples of 
>biologists who think that? >­ and would find it 
>odd to have to distinguish >between Fritz’s body 
>and Fritz’s body’s life. It >seems more as if 
>the distinction is about >different ways of 
>looking at things, that >sometimes can usefully 
>be applied to the same thing. No one is denying 
>that there are different ways of looking at 
>things. Perhaps someone can even look at Fritz's 
>body and see it as a life, though I find it hard 
>to do so. > >My personal experience is that when 
>dealing with >the large bodies of data that 
>exist in >operational systems, when constructing 
>simple >taxonomies of the artefacts this data 
>refers to, >I am (reasonably) often faced with a 
>problem >about which category I want to put them 
>in ­ and >what category to put there more 
>general >supertypes that seem to include both 
>occurrents >and continuants. Of course, I can 
>devise a >practical workaround (for each of 
>these >problematic classes of objects, introduce 
>two >objects ­ the object and its life ­ and 
>ignore >feelings that these seem reminiscent 
>of >Ptolemy’s major epicycles) but this adds 
>noise. So how do you deal with John's lung was 
>healthy 5 years ago and cancerous today? > >It 
>also seems to me pragmatic to, when 
>dealing >with large systems, try to ‘cut nature 
>at its >joints’ and not have too many 
>workarounds making >the systems more complicated 
>than they need to >be. Hence my suspicions (and 
>maybe Pat’s) of this distinction. Having worked 
>long and hard with biologists it has become 
>clear to me that the continuant/occurrent 
>distinction is the most well entrenched of all 
>the joints in nature (the distinction between 
>anatomy and physiology, for example, is very 
>old, and has not been threatened one iota by 
>recent developments in, e.g. cellular anatomy.) 
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