Path: utzoo!utgpu!watmath!uunet!bionet!lanl.gov!dbd%benden
From: dbd%benden@LANL.GOV (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: the bio-matrix IS model-based reasoning!
Message-ID: <8905232332.AA00269@benden>
Date: 23 May 89 23:32:32 GMT
Sender: daemon@NET.BIO.NET
Lines: 121



David Kristofferson says: 
    I would think that the BIO-MATRIX approach has some merit but it
    strikes me that its case is weakened in the eyes of practicing
    biologists every time one brings up this "reasoning from first
    principles" example.

And Randy Smith replied: 
   Dan Davison clearly states (2nd and 4th
   paragraphs) that since biologists cannot (now) reason from first principles,
   the "Matrix substitutes reasoning by analogy for reasoning from
   first principles".

Which is what I meant all along.  I will look over the posting and see
if I can reword something to make this clearer.  Yes, the bio-matrix
concept is about reasoning, but it's reasoning-by-analogy.  This point
was developed at length in the National Academy of Sciences report
"Models for Biomedical Research: A New Perspective (NAS, ISBN
0-309-03538-4).

The Godel example that David Kristofferson invokes is commonly heard
(at least by me) in the wildest contexts.  In this case, we know that
theoretic physics calculations break down at singularities (such as
before 10e-43 seconds after the big bang; this is discussed in
Hawking's "A Brief History of Time").  That breakdown is only of minor
consequence for the issue I was trying to address.  The point is that
we (biologists) have transfinite calculation problems too (protein
structure, molecular dynamics) in which we can't, in the near term,
know all of the parameters involved in the calculation.  In order to
work on that problem *now* we have to do our reasoning at a higher
level.  



Jon Sticklen says:

   By extension, the suggestion inferred that although "first principles" may 
   apply to disciplines like physics,that a project to gather
   biological knowledge and use it as a basis for arguing from
   "first principles" ...

This is the *exact* opposite of what the bio-matrix is all about.

	...may be ill-founded. 

Right.


    Actually, within the AI community, the notion of "reasoning
    from first principles" seems to be giving way to "model
    based reasoning." Model based reasoning is a new sub-field
    of AI which centers on starting with a model of some physical
    phenomena, then, by applying reasoning methods (that are currently
    the object of intense research) deriving how the model will react 
    given boundary conditions.

YES! Exactly.  That's why this project exists--AIers seem to be coming
up with the relevant tools for the problems biologists facing (whether
they know it or not ;->).

    My purpose is not to give a tutorial on model based reasoning here,
    but to suggest to the members of the bio-matrix community that there
    are other ways of capturing "deep understanding" (to use an AI term)
    than to argue from first principles. Current model based qualitative
    reasoning may well be applicable in your project.

That's the point I was trying (obviously very badly) to make.

And Peter Karp (hi Peter!) says: 
    I actually don't think the message that we're all refering to
    (written by Dan Davison?) was meant to inspire such serious debate --
    but perhaps it should have.

I had kinda hoped it would start such a discussion.  I did write that
intro, with large sections taken from Harold Morowitz's section in the
Bio-Matrix Workshop Report.  The original note (on the archive-server)
has the full citation.

    I for one would not mind seeing a tighter definition of the goals 
    of The Matrix; such a definition should probably not include words
    like "evangelize."

Mea culpa.  Although the note was not intended as a "tighter
definition". Let's build one.  See below.


And Jon Sticklen replies: 

   When we try to reduce one level of understanding
   to another, we lose the descriptive power that the terms at the higher
   level afforded, and are forced to use the vocabulary at the lower level.
   Eg, mating behavior of large mammals may be reduced through a number
   of steps (in principle perhaps) to the bio-molecular level and beyond.
   But if we do that, then we cannot use terms like "drive to find a mate"
   because such terms do not exist at the bio-molecular level. One of the
   most pressing needs when trying to represent a phenomena is to search
   for the appropriate level of description to capture understanding.

   Going further, one of the most pressing needs of the bio-matrix project
   (it seems to me) is to find a representation scheme that is robust 
   enough to support descriptions of different phenomena at many different
   level of abstraction, and that allows each description to utilize 
   terms appropriate to the phenomena being described.


This is an excellent, concise summary of the problem and the way the
bio-matrix project should approach its resolution.  I recall that
Peter Karp, Chris Overton, Kimberle Koile, and Rick Lathrop, among
others, had constant discussions about exactly this point at the Santa
Fe workshop.  It was never clear to me how much of their work was
influenced (perhaps limited) by their knowledge representation tools
(I can't recall the names now, nuts).


My statement of the goals has been examined and found lacking.  OK,
let's try to build something better.  Perhaps some of Chris Overton's
introductions to the bio-matrix (see the 1989 summer meeting
announcement) would be more appropriate?

dan davison