Re: ORGLIST: Desperately seeking collaborator.

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From: Jacob Zabicky (zabicky$##$bgumail.bgu.ac.il)
Date: Thu Aug 16 2001 - 10:35:45 EDT


Hello Dmitry,

Just to kindle some fire in the line you've started let me put forward some
comments.

1. I'm all for new approaches to everithing. That's the basis for
scientific and social advancement.

2. I'm even for starting with any conceptual approach far removed from
chemistry.

3. When you start approaching your "customers" (say, the chemists) with
your new product, you may find that it is difficult to sale for several
reasons:

a) A language gap

-- you do not understand each other because the same words (e.g.,
structure, bonds, properties) carry a different meaning.

-- translation and rewording are called for.

b) A wrong conception

-- did you ask yourself why does a chemist need a structural
representation? I assume that most probably yes, at least when you started
working.

-- did you ask chemists why do they need structural representations?
Possibly, but probably not many of them.

-- did you compare your own answer with that of the chemists? What did
you decide about the differences?

c) Inflated package of information (an example)

-- it's possible to give quite "mathematical" names to organic chemicals.
Let's take for example
w-keto-x,y-dimethyl-tetracyclo(j.k.l.m.n)heptadecan-z-ol, where the single
letters represent certain specific numbers that I'm too lazy to sort out
now, and add some litte wiggles to make clear where exactly the bridging of
the structure occurs, and some other to express the chirality of the
asymmetric carbons. A chemist knowledgable of the nomenclature will be
able to draw a structure or translate it to your system. However, I doubt
this strictly correct name will remind him the package of knowledge and
physiological associations that the equivalent name "testosterone" could
evoke.

-- certainly information about synthesis of testosterone need not be
included in the structural package. Access to the information on synthesis
using the structure is fine, but its inclusion in the structure may be
totally misleading.

4. Is that effort really necessary?

-- The answer may be a qualified yes. The trouble is that many structures
are not quite definitely known but certainly are of great interest. Some
examples can be the humic acids, lignins, tars, the polysaccharides of the
cell membranes, alumosilicates, inorganic complexes, etc.. The effort to
develop a mathematical system to include such representations may be
unwieldy.

-- Do you know about the linear representation of cyclic stuctures the
Chemical Society (I think) tried to introduce more than 50 years ago?

All the best,

Jacob

At 1:49 15/8/1, Dmitry Korkin wrote:
>(Our apologies if you received this message more than once.)
>
>Dear colleagues,
>
>We are seeking a chemist (or organic chemist), who would be interested
>to actively collaborate with us in the development of a fundamentally new
>approach to the issue of STRUCTURAL REPRESENTATION in chemistry in
>general, and organic chemistry in particular.
>
>We are a small group of mathematicians and computer scientists that have
>just completed (after 2 decades of work) an outline of, what we believe to
>be, the first formal model for structural object/event representation in
>science, whose main features are radically new:
>
> http://www.cs.unb.ca/profs/goldfarb/struct.pdf (theory)
> http://www.cs.unb.ca/profs/goldfarb/cadd.pdf (chemistry)
>
>
>We strongly feel that it should help to turn a relatively popular among
>chemists slogan "Chemistry: the central science" into reality, by allowing
>the chemistry to lead the science in the revolutionary transition from the
>numeric representations (ubiquitous in all sciences) to structural
>representations.
>
>We have identified (very informally) several initial questions around
>which the collaborative work may start:
>
>(a) the new model emphasizes that the structural representation of a
>chemical object must include (as a part of the representation) its
>generalized "synthetic" history hence one needs to correlate this with the
>current knowledge of chemical synthesis.
>
>and
>
>(b) relying on the new model, we plan to develop inductive (based on a
>small set of examples) learning and classification algorithms for small
>and large molecules, which should be able to predict, for example, the
>structure, chemical reactivity, biological activity, etc.
>
>
>Best regards,
>
>
> Lev Goldfarb Tel: 506-458-7271
> Faculty of Computer Science Tel(secret.): 453-4566
> University of New Brunswick Fax: 506-453-3566
> P.O. Box 4400 E-mail: goldfarb$##$unb.ca
> Fredericton, N.B., E3B 5A3 Home tel: 506-455-4323
> Canada
>
>
> http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm
>
>__________________
>
>ORGLIST - Organic Chemistry Mailing List
>Website / Archive / FAQ: http://www.orglist.net/
>List coordinator: Joao Aires de Sousa (jas$##$mail.fct.unl.pt)

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Prof. Jacob Zabicky
Institutes for Applied Research
Ben-Gurion University of the Negev Private: POB 12366, Beer-Sheva 84863
POB 653, Beer-Sheva 84105, ISRAEL Tel. 972-8-6496792
http://profiler.bgu.ac.il/site/main.cfm
Tel. 972-8-6461271/6461062/6472754
Fax. 972-8-6472969
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__________________

ORGLIST - Organic Chemistry Mailing List
Website / Archive / FAQ: http://www.orglist.net/
List coordinator: Joao Aires de Sousa (jas$##$mail.fct.unl.pt)




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