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

To: "'Smith, Barry'" <phismith@xxxxxxxxxxx>, "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>, "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "clynch" <clynch@xxxxxxxxxxxxxx>
Date: Sat, 9 Jun 2007 12:44:36 -0700
Message-id: <005c01c7aace$9cac4930$1500a8c0@ontoreason>
Yes indeed it is a protein, a normal protein, unless it folds in a different
way in which it is then an infective protein. So I guess my question is then
that you would define the process of the folding of the protein the
occurrent? And in the case of the lung with the cancer, I presume the cancer
cell is the continuant and the process of loss of suppressor receptors is
the occurrent? Or is it the DNA damage process as the occurrent? Or the
failure of the repair of the DNA the occurrent? How do you ever get to the
clear definition of the occurrent in these biological systems?    (01)

Cecil    (02)

-----Original Message-----
From: Smith, Barry [mailto:phismith@xxxxxxxxxxx] 
Sent: Saturday, June 09, 2007 12:01 PM
To: clynch@xxxxxxxxxxxxxx; [ontolog-forum] ; '[ontolog-forum] '
Subject: Re: [ontolog-forum] Two ontologies that are inconsistent but
bothneeded    (03)

A prion is a protein molecule, is it not? Thus it is a continuant.
BS    (04)

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: 
>ontolog-forum-bounces@xxxxxxxxxxxxxxxx 
>[mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] 
>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.) 
>BS 
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