Cell Simulation

Rich Cooper richcooper1 at mindspring.com
Sun Oct 29 14:06:44 EST 2000

> Your approach to the simulation of molecular processes in the living
> cell seems to be based on ideas from business management ("activity
> planning", "factory shop floor activities").  I think that could be
> interesting, because often scientific innovations do come from the most
> unexpected cross-fertilization between diverse areas of human knowledge.

Actually, the ideas originated in computer science when people were
trying to define an algorithm that could adapt to unforseen circumstances.
It got named "the planning problem" back in the sixties and seventies.  The
original problem definition came about because there was a need for robots
that could cope with real world changes instead of theoretical worlds.  One
obvious area of application is in factory work flow planning against a
of orders and schedules of available resources.  When just-in-time theories
of factory management became popular, the planning algorithm transferred
under the business oriented name of "advanced planning systems".  But
the algorithm wasn't completely worked out until the mid eighties.

> However, in answer to your question: "what I would need" (personally)
> before I'd even look at your software is the following.  I would "need"
> you to publish in a peer-reviewed journal (the peer-reviewed attribute
> is important!) some sort of a theoretical framework convincing the
> research community that the theoretical or mathematical tools of
> business management (e.g., scheduling factory floor activities) *are* in
> some way applicable to understanding the metabolism of the living cell.

Yes, I think you're right about that.  The planning algorithm has already
been proven correct, but not in application to biology.  Also, it has some
limitations related to explosive combinatorics that have to be understood
to use it properly.  So a paper on plan generation in biological
sounds like a very good suggestion.

> Probably the most suitable journal that comes to mind is  the "Journal
> of Theoretical Biology":  I have reviewed a few articles for them, and I
> remember that the scope of the journal specifically encourages
> theoretical studies (experiments are actively discouraged).

Thanks for the pointer.  A web search found them at
where the sample issue does indeed contain articles that seem similar in
scope and purpose, though different in technology and approach.

The journal "Artificial Life" at
is primarily a computer science journal, though articles sometimes deal
with biological first principles.  Would that be a reasonable alternative?
Pankaj Agarwal wrote an article "The Cell Programming Language"
which I found very interesting, though it isn't in the formal logic area.
(In fact, someone on this newsgroup point out the article to me).

I think a journal article is a good idea, but the background required for
understanding the proof is a very mathematical one.  The planning algorithm
be proven correct, but to understand the proof, you have to also understand
temporal logic math and automatic theorem proving math.  Both are now
well documented, so its just a matter of reading the literature.  The point
just that the journal should appeal to people who read formal logic
articles as well as biochemistry articles, and I can't think of a journal
does appeal to both groups, though there probably are such journals.  Any
suggestions would be appreciated.

> Of course
> the Editors might have a great difficulty finding two or three reviewers
> (or even one!) able to read and evaluate your work.  In that kind of
> situation, it is perfectly O.K. if you suggest a list of referees, but
> they do have to be well known in the field.  Kind of tricky, but it can
> be done.

Maybe that would be a good approach.  I want this product to reach
biochemistry researchers, so the Journal of Theoretical Biology would
be a good choice from that perspective.

> Hope this helps,
> -- Petr

Yes it does, and thanks for your continuing interest.

-Rich Cooper

> P e t r   K u z m i c,  Ph.D.               mailto:pkuzmic at biokin.com
> BioKin Ltd. * Software and Consulting           http://www.biokin.com

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