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Re: [ontolog-forum] ISO merged ontology effort "MCO"

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "John F. Sowa" <sowa@xxxxxxxxxxx>
Date: Sat, 18 Apr 2009 13:11:20 -0400
Message-id: <49EA09B8.5010909@xxxxxxxxxxx>
Bill,    (01)

Thanks for the pointer to the book by Roald Hoffmann.  I went to his
list of publications and found some gems that are relevant to many
of the issues we've been discussing on this forum.    (02)

Following is one about chemistry, but the principles apply equally well
to the ontology of any subject:    (03)

http://www.roaldhoffmann.com/pn/modules/Downloads/docs/Under_the_Surface_of_the_Chemical_Article.pdf    (04)

In a section called "A Personal View of Chemistry", Hoffmann discusses
some general principles that can be adapted to ontology:    (05)

1. Science is the acquisition of knowledge about the world    (06)

2. Science is part discovery, part creation    (07)

3. Science is done by human beings and their tools    (08)

4. Science proceeds in part by the rules    (09)

5. Science depends on argument    (010)

6. As a system, science works    (011)

7. Chemistry is the science of molecules    (012)

8. Chemistry is not reducible to physics    (013)

Point #8 can be applied to any field, including ontology:    (014)

    The concepts of any field cannot be reduced to a fixed set
    of universal primitives that are defined outside that field.    (015)

He then talks about "What really goes on in a chemical paper."
Those observations also apply to any ontology.  Following is
just one example:    (016)

> The irrational seems to be effectively suppressed in the
> written scientific word. But of course scientists are human,
> no matter how much they might pretend in their articles
> that they are not. Their inner illogical forces push out.
> Where? If you donít allow them in the light of day, on the
> printed page, then they will creep out or explode in the
> night, where things are hidden, and no one can see how
> nasty you are. I refer, of course, to the anonymous refereeing
> process, and the incredible irrational responses unleashed
> in it by perfectly good and otherwise rational
> scientists. You have to let go sometime . .    (017)

In another article, he comments on his experience in attending
a conference of biologists talking about molecular biology:    (018)

> The more molecular they were, the less I understood.  The
> reason is that I have been bypassed by several generations
> of biochemistry, molecular biology, and genetic engineering.
> And what jargon!  It was my fault to let it happen, but also
> there were a couple of people there who could not conceive
> that someone could not know what 16S rRNA was.    (019)

http://www.roaldhoffmann.com/pn/modules/Downloads/docs/Thermophiles_in_Kamchatka.pdf    (020)

Note the implications of that comment:  a chemist who won a
Nobel prize in organic chemistry cannot understand the jargon
of biologists who are talking about chemistry.    (021)

If Hoffmann couldn't understand the biologists, just imagine how
difficult it would be for a computer.  Even if it had a detailed
ontology of organic chemistry, it couldn't interpret a paper on
chemistry written by a biologist.    (022)

This phenomenon is true of every field, not just chemistry.
Imagine an expert on operating systems for Windows, Unix,
Mac, or IBM mainframes going to a conference for one of
the other systems.    (023)

Following is Hoffman's web site:    (024)

    http://www.roaldhoffmann.com/pn/    (025)

There are 383 articles in his list of publications.  To find the
more general ones, click on "sort by popularity".    (026)

John Sowa    (027)

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