Path: utzoo!utgpu!watmath!uunet!umbc3!chiafari
From: chiafari@umbc3.UMBC.EDU (Mr. Frank Chiafari )
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: Response to the recent discussion.
Message-ID: <2089@umbc3.UMBC.EDU>
Date: 31 May 89 21:31:17 GMT
References: <1482:Wallace@fmi.ch>
Reply-To: chiafari@umbc3.umbc.edu.UMBC.EDU (Mr. Frank Chiafari (BIOL-GRAD))
Organization: University of Maryland, Baltimore County
Lines: 37


Gentleman,
	I have been reading bio-matrix news for a long time and feel a 
responsibilty to answer dave's request for input from the biological community
	The idea of a bio-matrix being built to inter-relate data between 
organizational levels in biology may be premature. It concerns me that biology
as a field has not developed sufficently to enable rational relationships to
be derived from between disiplines. I also do not believe that the historically
accepted divisions of biology represent hierarchical levels of information 
which should be integrated to effect data interpretation. An example of
where such an integration would have been disastrous is in the application of
homeotic sequences from their original finding in drosophila to higher verts. 
I remember a number of embryologists and ecologists claiming that any
homology found couldn't possibly have developmental implications!! Any organ-
ization of ideas, by definition, limits the choices available. 
	There exists, however, a need to apply computers to the problems of 
database managment and to build up from data gained at the molecular level to 
applications in system organization.. I have attempted such a project, but
within the same level, taking sequences recognized by promoters and trying to
determine a consensus sequence and recognition model. I ran into a number of
problems:
   1) The question I was asking required many computer hours and a working 
understanding of computers so that I could program the machine myself when
building new models. Few programers were willing to spend the time necessary 
to learn enough biology to understand the problem.
   2) The results I obtained were not readily accepted by the community, and
they may never have been published if experimental results had not "caught-up"
with my predictions.
   3) Specific to sequence analysis, the literature is relatively inconsise as
to how to decide the signifigance of a result. This may reflect my own failing
rather than a shortcomming of the field.
	In summary, I offer concern, NOT condemnation

Please excuse the need to repost

With Regards
	Francis A. Chiafari