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Re: [ontolog-forum] Event Ontology

From: John F. Sowa <sowa@bestweb.net>
Date: Fri, 11 Sep 2009 11:16:23 -0400
Message-ID: <4AAA69C7.2000501@bestweb.net>
To: Graham Klyne <GK-lists@ninebynine.org>
CC: "[ontolog-forum]" <ontolog-forum@ontolog.cim3.net>, Dan Brickley <danbri@danbri.org>, semantic-web@w3.org
Graham,

Thanks for the reference.  The issue of reductionism is critical
to formal ontology because it focuses attention on the problems
of complexity and the need for intermediate levels as means for
managing complexity.

At every step in computer science, we face combinatorial explosions
that threaten to swamp any further progress.  Some people argue
that the solution to complexity is to limit the expressive power
of the languages we use so that complex problems cannot be stated.
But that approach does not solve the problems.  It just makes it
impossible to represent them or even think about them.

Note that all the major programming languages in use today are
undecidable:  there is no way to predict, in general, whether
any given program will ever halt.  Programmers don't "solve"
that problem by limiting the expressive power of the languages.
Instead, what they do is to define intermediate levels so that
the mapping from one level to the next is manageable with our
limited ability and resources for reasoning about complexity.

JFS>> Although I agree that the principles of biology are based on
 >> chemistry and the principles of chemistry are based on physics,
 >> I also believe that there are laws at each level that would
 >> be extremely difficult, and probably humanly impossible, to
 >> translate directly to the lowest possible level.

GK> In support: I found Prof. Denis Noble's book, The Music of Life,
 > very illuminating on this topic (http://musicoflife.co.uk/).

I followed that pointer to a list of reviews, which discuss those
issues.  See below for some excerpts from those reviews that are
relevant to issues in ontology and knowledge representation.

In reading the following passages, replace 'gene' with 'RDF triple'
to see the relevance to ontology.  Reducing knowledge to a massive
web of triples is useful for many purposes, but it does not lead
to understanding.  In fact, you could consider it a step backward
from knowledge to data in the popular DIKW metaphor.

In short, the critical issue for ontology is to ask what are the
intermediate knowledge levels and how do we develop languages,
tools, and methodologies in ways that highlight those levels and
enable us to manage them effectively.

John Sowa
_____________________________________________________________________

Excerpts from several reviews of _The Music of Life_ by Denis Noble.

Source: http://musicoflife.co.uk/reviews.html

Among other things, [this book] is a timely rebut of the genome-mania 
that has dominated biological science and popular attention paid to it 
over the past decade.  This is not to say that Noble's book is an 
anti-genome book.  On the contrary, Noble presents the view of the 
genome as not more (or less) than another few molecules that make up the 
complex interacting soup of life.

One of the gems in this book is Noble's description of the combinatorial 
explosion associated with the seemingly straightforward task of 
developing gene ontologies -- the assignment of biological functions to 
genes.  Noble explains in simple terms why it is practically impossible 
to enumerate the necessarily immense set of high-level functions 
associated with a specific gene, and why the quest to map functions to 
genes or genes to functions is a hopeless task unless one adopts a 
systems view.  (Daniel A Beard)

Noble argues that a dominant metaphor in biology is blocking the path to 
further understanding.  This is the notion that genes are the "program" 
of life and that they are its fundamental unit.  Instead, the author 
shows, genes are merely a database and cannot do anything without other 
systems interpreting them, and there is ample evidence for "downward 
causation", in which higher-level systems and the environment affect the 
way genes work.  Further, genes rely for their effect on chemical, 
physical and other properties of the natural world, which we all 
"inherit".  (So much, Noble concludes poetically, for the notion of 
inheritance being solely via genes.)  (Steven Poole)

The book sleeve remarks:  'after the full mapping of the human genome 
has yielded a code of three billion letters, we are still far from a 
satisfactory answer to this question' of 'What is Life?'  The sleeve 
continues:  'The reductionist approach of molecular biology has proved 
itself immensely powerful.  But DNA isn't life.  It doesn't even leave 
the nucleus of the cell...'

Chapter 5 mentions crystallographers specifically...  but also the 
fruits of crystallography with the 3D structures of the ion channels. 
In this chapter, for me, coming from a molecular background, Denis Noble 
beautifully captured the complexity of biology with its descriptions of 
the rhythms of the heart and showed the links with the molecular level 
but also the limitations of reductionism.

The book also offers in its final chapters a description of the brain 
and consciousness and then culture...  The last chapter and its links 
with Zen Buddhism has as its quoted Zen parable:  'Each beat and each 
tune indescribably profound, no words needed for those who understand 
music.'  (John R. Helliwell)
Received on Friday, 11 September 2009 15:17:04 UTC

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