What is this place for?

Dan Davison ddavison at timelord.bms.com
Fri Jun 18 07:59:03 EST 1999

Larry's message reminded me (the alleged moderator of this 
newsgroup) to dig out the following message. It used to
be posted every three months but I guess it stopped
working a few years ago when I moved from the University
of Houston to Bristol-Myers Squibb.

[This is a posting of a notice about the BIO-MATRIX project, its aims,
and current activities. It appears irregularly.] 

BIO-MATRIX is not a database or a functional tool.   The concept's
underpinnings are best described in the Final Report of the Workshop
on Matrix Biology.  I will summarize here my interpretation of
the Matrix concept.

The Matrix of Biological Knowledge is a response to the way biologists
reason about their systems.  Physicists have recourse to first
principles and in the last 20 years we've seen implications of quantum
mechanics on the cosmological scale.  The complexity of biological
systems is such that it's going to be a *long* time before one can
reason a Tetrahymena from first principles.  As each scientist thinks
about their particular system, they consciously (and frequently
unconsiously) reason about their system by analogy.  A striking
example of this appeared recently on the cover of Science; the
three-dimensional structure of _ras_ is essentially identical to one
proposed a few years before, based on what was known about a property
of _ras_, that it binds GTP.  By examining an already-determined
tertiary structure of a GTP-binding protein, they were able to make an
accurate prediction of what _ras_ would look like. 

	The Matrix concept wants to organize biological knowledge so
that the predictive power of models in different disciplines can be
applied to a different, perhaps new, discipline.  Molecular biologists
have been using such reasoning for years; but what does the hydra
biologist know of the models in toxicology?  Are there any
toxicological model systems that speak to a protoist system?  I don't
know the answer, and I doubt that anyone else does either.  

	The Matrix subsitutes reasoning by analogy for reasoning
from first principles.  The proposal is to combine biological
knowledge in three ways; (1) collect data into databases, and have the
agencies that fund research get serious about the proper disposition
of the knowledge they've been funding (such as requiring, as a
condition of grant funding, any resulting data to be submitted to
GenBank for nucleotide information; PIR for protein information; and
Brookhaven for x-ray crystallographic information).  (2) organize the
databases in such a way that access to them is transparent.  You tell
your Macintosh that you want to know all about X; the program
goes and calls MedLine, ToxLine, BRS, and whatever else...including
databases that you may not know exist... and retrieves the information
for you.  This is the knowledge base component of the Matrix (yes,
highly simpilified).  (3) Tools to help get that information even if
you don't know it's there; this is the Information Retrieval component
of the Matrix.

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