Unsolved or Poorly Solved Computational Problems

Richard Scott rtscott at forgetspamPacbell.net
Thu Mar 6 05:09:21 EST 2003

Greetings again Bob,

I have a basic question which I think you are best able to answer.  Namely,
what could be the motivations for developing accurate simulation
capabilities in biotechnology?  I say, "simulation" because clearly there
are many reasons for other IT development in biotechnology such as data base
design and so on.  I surmised in my last post that "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.".  Is that true?  What are the other

Thank you,
"Bob" <xyzbbruner at uclink4.berkeley.edu> wrote in message
news:3e60203a.28367625 at agate.berkeley.edu...
> 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
> >both starting points and an historical context into which I can put what
> >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
> >are trying to solve)." Later, in the last paragraph, you defined
> >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
> >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
> >real progress in this "new" field.
> >
> >This leads to two other issues which I have encountered in both the
> >and commercial aspects of computer science, and which I suspect are big
> >problems in biotechnology. First, the lack of the right sort of
> >data in key areas (e.g., actual disk accessing patterns on request by
> >request basis). Second, an unwillingness to design and construct
> >accurate and complete simulation models (e.g., timing accurate disk
> >simulations).
> >
> >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
> >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
> >modeling the "MC", a simulation of the electrostatics of chained
> >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
> >to be little or nothing available in terms of dynamically simulating
> >interactions. Also, the sequencing algorithms seem to be all statistical
> >nature rather than trying to find exact or near exact matches. Is that
> >result of the huge size of the problem, or performance considerations.
> >happens if you might find more than one exact match? Some of these
> >are a result of sheer ignorance on my part for which I apologize but I
> >suspect there also issues of modeling inaccuracy and computational
> >intractability.
> >
> >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
> >sequential chains of entities such as atoms, molecules or representations
> >bases.
> >
> >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.
> bob

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