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Re: [ontolog-forum] confounded models

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Gary Berg-Cross" <gary.berg-cross@xxxxxxxx>
Date: Wed, 18 Jul 2007 10:09:46 -0400
Message-id: <330E3C69AFABAE45BD91B28F80BE32C90104D600@xxxxxxxxxxxxxx>
Kathy, Pat, Barry    (01)

The discussion has meandered into several examples and I'm learning more
about "light" all the time.      (02)

But I wanted to step over Barry's "cat on the mat" to return from the
white snows of quantum and mechanicist Physics to collect a few more
flower cell "examples"  from the biological realm.    (03)

What I'm still seeking is a common understanding of what we mean, as an
example, when we build an ontology for some aspect of the biological
realm.      (04)

I've suggested that there are alternative biological models that serve
as the basis for biological "reality".  I think that this has
implications for what the ontology represents (independent of the
model-theoretic underlying the ontology). Here is an example of what
troubles me.    (05)

Recent  Linneus' hierarchical classification system, have (generally)
adopting five kingdoms of living organisms - as discussed in Purves et
al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com). In this view Viruses, are not considered living. Ok
leave that aside for this discussion it's an explicit assumption.    (06)

But recent studies suggest that there might be a sixth Kingdom, the
Archaea.     (07)

As discussed in the Wikipedia:     (08)

"currently in textbooks from the United States, a system of six kingdoms
(Animalia, Plantae, Fungi, Protoctista, Archaea and Prokaryota), while
in British and Australian textbooks, five kingdoms (Animalia, Plantae,
Fungi, Protist, Bacteria) are used."    (09)

 Above these in the  (also in Wikipedia ) there is a simple phylogenetic
representation of three Domains of life: Archaea, Bacteria (Eubacteria),
and Eukaryota -    (010)

 But in the hierarchical classification system (also in Wikipedia) there
are 2 "superkingdoms" and 4 kingdoms.
r_kingdomsAssociates     (011)

Now, if I had relied on earlier biological understanding I would have a
different taxonomy of life, kingdoms etc.  No superkingdoms at all.     (012)

Did this earlier view reflect biological reality?  Which of the
alternatives discussed above reflects reality now?      (013)

To me this is a different question (and closer to what Barry was asking)
than saying "no problem I can represent any of these as a logical
collection of axioms in which  Tarksi is satisfied and someone now
believes that these formalism are anchored below by a model theoretic
and in another way by reality (and perhaps the Biologist "heart".  It
seems that we are expressing hypotheses about reality here, as earlier
message have discussed.  These classifications arise as part of a
complex scientific process that John and Pat have debated.  To me the
reason we might believe that our axioms will cohere is that the science
uses all of its tools to induce generalizations from hypotheses tested
empirically.  But there are limits to the scope of this understanding (a
simple version of which  Pat argued persuasively against earlier, but we
haven't yet responded to appropriately - more on this later perhaps) at
this stage of Biology (and maybe even more so of Medicine, to get Barry
attention here).     (014)

But perhaps Barry, Pat, Kathy (and John, Ingvar, Waclaw, Rick etc. )
would disagree or express this differently. 
 If so how?    (015)

Gary Berg-Cross, Ph.D.
Spatial Ontology Community of Practice (SOCoP)
Executive Secretariat
Semantic Technology
Suite 350  455 Spring park Place
Herndon VA  20170
703-742-0585    (016)

-----Original Message-----
From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx
[mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Kathryn
Blackmond Laskey
Sent: Tuesday, July 17, 2007 1:24 PM
To: [ontolog-forum] 
Subject: Re: [ontolog-forum] confounded models    (017)

>However, at any give time science may have alternative explanations
>about phenomena so we'd have to formalize these also and they are
>competing theories of truth. 
>Something like "snow is white" "snow is grey" (when it's in the road
>a while),  etc.    (018)

A better example:  "Light is a particle" versus "Light is a wave."    (019)

Each of those competing theories could be formalized consistently, 
but they were mutually inconsistent.    (020)

Quantum theory resolved the inconsistency, and the original theories 
emerge as special cases of the new theory under appropriate 
assumptions.  That is, they aren't inconsistent -- each is an 
approximation that works well in its respective domain of 
applicability.    (021)

Today we have "Matter is a quantum wave function evolving in time 
according to Schrodinger's equation" versus "Matter warps spacetime". 
These theories are mutually inconsistent -- when you try to create a 
wavefunction for macroscopic systems that warp spacetime, you get 
divide-by-zero errors.    (022)

Most physicists think there will some day be a new theory that 
resolves the inconsistency and out of which the other theories emerge 
as special cases.    (023)

>But given Kathy's idea of logical consistency, doesn't it become
>important that someone who knows about Botony is likely to be thinking
>more consistently than some non-Botanist thinking about plants?  Could
>be anyone.  Are they all Tarskian at heart?    (024)

I didn't say botanists were Tarskian at heart.  At heart they are 
botanists!!!  But if they are logically consistent botanists, I could 
develop an axiom system and Tarskian model that was a pretty good 
approximation to the phenomenonogy of their assertions. That does NOT 
mean it is a good model of their actual throught processes!    (025)

K    (026)

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