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Re: [ontolog-forum] Event Ontology

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: ravi sharma <drravisharma@xxxxxxxxx>
Date: Fri, 11 Sep 2009 12:30:56 -0400
Message-id: <f872f57b0909110930u7ad470fble3844f4fdb0f4fb@xxxxxxxxxxxxxx>
Wonderful analysis and presentation.
Music or sound is what is so primordial experience that it is more inner satisfaction experience closer to self knowledge rather than an understanding. Yes in the case of western music or raga you are confined to patterns and notes and rules. But as music is experiential so is the understanding of life.
There are two well known approaches, synthesis and differentiation (often confused with word analysis). Western science (only one popular and understood to give us all rewards such as medicines for prolonged life) is based on its ability to differentiate and that has for example resulted in wonderful medicines, etc.
For understanding life you need to add all genetics (i.e. differentiations in to ATGC pairs and Protein factory etc) but as epigenetics seems to alter genetics too often (e.g. jumping genes) the parts are not the whole. The answer lies in introducing parts, combination rules, processes allowed and definitely "Consciousness" that helps us complete life as we understand it today. Not to speak of future findings of life beyond our known species in the universe (need not be Carbon based only?)!
P.S. Buddhists and Jains (Source for both in India as starting point) include Nature only (and time) and are shown to be equivalent in reasoning to Sankhya, one of the six parts of Indian Philosophy, however, others (e.g. Hindus) believe in overall source(s) of consciousness but both explain most of observables about life.
Rich - thanks for the comments.
(Dr. Ravi Sharma)
313 204 1740 Mobile

On Fri, Sep 11, 2009 at 11:16 AM, John F. Sowa <sowa@xxxxxxxxxxx> wrote:

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)

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