I.N. Sarkar (01)
Of course, you are right (see your note below) that there are biological
phenomenon that are unaffected by the environment (during a specific part of
that phenomenon's expression). This is a curious truth, but one that one
has to admit... For example, my image of self may be (almost completely)
unaffected by my experience - in many instances. Selective memory helps me
maintain an "autopoiesis" (Maturana and Valera's term "Tree of Knowledge"
1987). (02)
Your comments are to the heart of the current discussion. (03)
I have some questions for you. The purpose of the question is to find out
how you feel about something - and therefore to gain a better understanding
about what you have written. (04)
Biochemistry and Immunobiology are both about living systems, right? (05)
So in this sense there should be, and is, common ontological commitments
shared by some who are familar with both disciplines. Right? If so let us
call this group, group A. (06)
But are there also other knowledgable groups who would disagree with group
A. I believe I am making a observation that everyone will agree with, ie
that there are schools of ontological commitments that cross the bourdaries
of what are regarded as narrowly defined academic disciplines. (07)
The ontological commitments are reflected in the set of relationships that
one group would be comfortable with. However, other groups will wish to
focus on the "science" using a quite different commitment. (08)
I feel that the notion that John Sowa is talking about; some common ontology
core where there is no disagreement has to address the fact that various
groups have quite different and often contridictory ontological commitments. (09)
His and my discussion regarding the nature of "logic" identifies that I am
in one school of thought and he is in another school of thought. What we
must avoid, in my opinion, is setting up a system where a school of thought
takes the position that it is privilaged. (010)
To the question of privilaged ontological commitment (011)
John said to me in a off line discussion: (012)
The short answer is very simple: (013)
> I have to ask why classical logic
> has a privileged status? (014)
It's a subset of English and every other natural
language. All you need to support full classical
first-order logic are the words "and", "not", and
"some" plus the ability to use them with ordinary
English syntax. You can throw in "or", "if", and
"every" as well, but they can be defined in terms
of the above three. (015)
To this I have many things to say, but will withhold. This is not a
discusison about philosophy but about how to move the semantic web and other
future things forward. (016)
-----Original Message-----
From: ontac-forum-bounces@xxxxxxxxxxxxxx
[mailto:ontac-forum-bounces@xxxxxxxxxxxxxx]On Behalf Of I.N. Sarkar
Sent: Saturday, November 26, 2005 12:15 PM
To: ONTAC-WG General Discussion
Subject: Re: [ontac-forum] taxonomy of relationships (017)
Well, maybe in some instances, yes- However, in many other instances
this is not the case. Some molecular structures may indeed act
independently, and there are numerous examples of genetic disorders
that can be associated with single genes, for example Mendelian
disease are often associated with just single genes. Environment
*may* play a factor in some diseases, but it is not the rule.
Biochemistry and immunobiology are very distinct fields, so in your
example, one would probably have separate ontological representations
depending on whether one is focused on immunobiological or
biochemical aspects of the molecule. What is important, and this
might be what you are getting at, is that relationships may be needed
between biochemical and immunobiological ontologies. But, if the
point is to make an upper level representation of all this, maybe the
best way is to not obfuscate the known relationships -- and the known
homologies -- with uncertainty. Or at minimum provide a means to
extract just the simple ontological representations that are at the
higher level-- and leave the nuances of biology or whatever specific
field to the domain expert ontologies being full aware that they will
always be in flux -- which is the whole point of this endeavor, I
believe. (018)
Best. (019)
-Neil. (020)
On 2005 Nov 26, at 13:53 EST, Paul S Prueitt wrote: (021)
> One MUST say that the environment co-caused the state s(3) of the
> macromolecule. How does this happen? An answer might be that
> there is a
> templating of environment to local protein reactions by the "needs"
> of the
> environment. So in each case, s(i) (where i is a ordering index) is a
> representation of the state of the macromolecule in a reaction
> chain which
> is produced (on a regular basis !) by cellular mechanisms. (022)
--
Indra Neil Sarkar, PhD
Bioinformatics Associate
Divisions of Invertebrate Zoology
& Library Services
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024 USA
+1 212 769 5571
--
sarkar@xxxxxxxx
www.genomeCurator.org/people/sarkar
-- (023)
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