dbd%life@LANL.GOV (Dan Davison) (11/21/89)
[This is the second posting of a monthly or bi-monthly notice about the BIO-MATRIX project, its aims, and current activities.] BIO-MATRIX is not a database or a functional tool. It is a concept, evangelized by Dr. Harold Morowitz of Yale University. 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 (sp?) 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. ------------------------------------------------------------------- Requests to be added to the direct-distribution mailing list should be sent to BIO-MATRIX-REQUEST@BIONET-20.BIO.NET. (BITNET: BIO-MATRIX-REQUEST%BIONET-20.BIO.NET@CUNYVM) Submissions for the list are always encouraged, and should be sent to BIO-MATRIX@BIONET-20.BIO.NET (BITNET: BIO-MATRIX%BIONET-20.BIO.NET@CUNYVM) The BIO-MATRIX archive-server can be contacted from most networks and can reply to all known networks (no failures yet!). For info, send the line help to archive-server@genome.lanl.gov (internet), archive-server%genome.lanl.gov@CUNYVM (bitnet, EARN, IRLEARN) ..cmcl2!lanl!archive-server@genome.lanl.gov (UUCP) (JANET and JUNET can reach the server also, but I haven't figured out the proper path. Please check with your local mail wizard). ------------------------------------------------------------------- Dan Davison Bio-Matrix Project Communications dd@lanl.gov (internet), dd%lanl.gov@CUNYVM (BITNET), ...cmcl2!lanl!dd (uucp old style), dd@lanl.UUCP (new style) (*) (*) these mail addresses will change as of 1 September 1989 to davison@uh.edu (internet), davison@UHOU (bitnet), and the physical mail address to Department of Biochemical and Biophysical Sciences, University of Houston, 4800 Calhoun, Houston, Tx 77204-5500 USA. The e-mail addresses can be used now.