Wallace@fmi.ch (Andrew Wallace) (05/28/89)
Regarding Dave Kristofferson's request for a response from other biologists
about the current bio-matrix discussions, I would like to give my views about
this topic rather than be one of the passive readers.
Since I don't know anything about informatics theory, qualitative modelling or
any of that stuff I cannot give a technical response but I must say that I am
completely blown out by the size of the tasks being contemplated. It seems to
me that a project to collect and represent all biological knowledge would make
the Human Genome Mapping Project appear small by comparison. Indeed, the
complete human genome would be just a subset of the overall matrix.
This is not to say that such a goal should not be aimed for, it is just that
I and probably many others are concerned with more immediate tasks. For
example, I would really like to see a model or system (call it whatever you
like) which could _accurately_ predict the function of a gene product from
its primary sequence. Maybe this is theoretically impossible, if the required
information is not encoded in the protein or nucleic acid sequence but is
somehow a combination of events from interaction with "chaperone" proteins
or whatever else you can think of to bring about the final functional state.
I don't know how to address this issue, but certainly its a problem which is
relevant to my own research.
Another area which relates to the development of the matrix (which I know
many others have talked about already) is the overall usage of computer-
based information tools by the biological community. I think there are
two, closely related, problems here. One is that the general proficiency
of biologists with computers is not very high compared to other fields.
Most of my (particularly more senior) colleagues barely know how to use
the computer as a word-processor, never mind do a database search, sequence
alignment, access Medline or much else. Secondly the "management" (again
mainly senior colleagues) tend to be indifferent to, suspicious of, or
even openly hostile to using a computer other than to type a letter.
As Dave Kristofferson pointed out however, these problems will tend to
disappear once today's students, who form the major body of computing
biologists, become the assistant professors and staff scientists of
tomorrow. Still, this will take time.
To sum up, the matrix project is a great goal to aim for in the long-term,
but if tomorrows computing biologists are to be attracted to it, they must
be convinced that computers can help them to solve more immediate problems,
relevant to their own research needs.
Andrew Wallace, Friedrich Miescher Institute, Basel, Switzerland.
Disclaimer: The opinions expressed above are my own, not those of the FMI
or its other staff.chiafari@umbc3.UMBC.EDU (Mr. Frank Chiafari ) (06/01/89)
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