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Unsolved or Poorly Solved Computational Problems

Bob xyzbbruner at uclink4.berkeley.edu
Mon Mar 3 11:47:42 EST 2003

On 28 Feb 2003 09:57:45 -0000, "Richard Scott"
<rtscott at forgetspamPacbell.net> wrote:

>Greetings Kevin,
>Thank you for your thoughtful response. When I read it, I came to the
>conclusion that my question was far too broad to be answered easily by
>someone familiar with the actual details in the field. That might be
>expected when I know so little. However, your response has provided me with
>both starting points and an historical context into which I can put what I
>already have investigated.
>You brought up two points which are especially interesting because they
>occur in many different fields. You stated that, "There are 'religious'
>debates...(which of course depend mainly on how you define the problem you
>are trying to solve)." Later, in the last paragraph, you defined "important"
>problems as "..those that help answer biologically or medically important
>questions". This focuses the issue on defining the term "biologically or
>medically important". You also pointed out the dangers of incorrectly
>abstracting the problem which would render the solutions "useless" in
>answering the "underlying biological question".
>Very insightful and potentially very fruitful observation. There is a short
>book which you might find useful in this regard. It is The Art of Problem
>Solving by Russell L. Ackoff, ISBN 0 471 04289-7. There is a paper backed
>version available from Amazon and others with a different ISBN number.
>Although someone might believe that your points are philosophical rather
>than practical, my experience leads me to believe they could be the key to
>real progress in this "new" field.
>This leads to two other issues which I have encountered in both the academic
>and commercial aspects of computer science, and which I suspect are big
>problems in biotechnology. First, the lack of the right sort of experimental
>data in key areas (e.g., actual disk accessing patterns on request by
>request basis). Second, an unwillingness to design and construct tediously
>accurate and complete simulation models (e.g., timing accurate disk
>The computer industry has no excuses for not properly instrumenting key
>behavioral components in hardware but I imagine that a similar effort in
>molecular chemistry or biology is virtually impossible with today's
>technology. If that assumption is correct, there must be a crucial need for
>accurate simulation capabilities to test various theories. In that regard, I
>have looked at UCSD Professors Nathan Baker's and Michael J. Holst's work on
>modeling the "MC", a simulation of the electrostatics of chained biological
>molecular ( http://www.sciencenews.org/20010901/fob8ref.asp and
>http://www.scicomp.ucsd.edu/~mholst/ ) and several of the gene sequencing
>programs that are publically available (BLAST and so on). Still there seems
>to be little or nothing available in terms of dynamically simulating actual
>interactions. Also, the sequencing algorithms seem to be all statistical in
>nature rather than trying to find exact or near exact matches. Is that the
>result of the huge size of the problem, or performance considerations. What
>happens if you might find more than one exact match? Some of these questions
>are a result of sheer ignorance on my part for which I apologize but I
>suspect there also issues of modeling inaccuracy and computational
>I have started to follow your suggestions regarding CASP experiments and
>would appreciate any specifics you might have regarding the "thousands of
>other problems in bioinformatics" particularly where the issues involve long
>sequential chains of entities such as atoms, molecules or representations of
>Richard Scott

I agree that Kevin's reply was good. Your posts suggest that you are a
serious programmer who wants to make some useful contribution.
Collaborate with people in the field. The odds of you writing anything
useful while on the outside are nil. You need the type of
understanding that comes form being there, and seeing what people are
doing. To some extent, they don't know what they want, so asking them
does not really yield good info. Ongoing, give and take communication
between user and programmer is critical.


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