Wholes and parts

claude aflalo aflaloc at bgumail.bgu.ac.il
Thu Dec 6 21:10:58 EST 2001


Hello Athel and everybody,

I first apologize for the possible cross postings.

On 3 Dec 2001, (Athel Cornish-Bowden) wrote:

> [pudic and somewhat embarrassed snip...]
> 
> "We are then left, once again, with the question: 'In today's biology
> dominated by the _ethos_ of mechanism, who will pay for the long-term need
> to know?' A researcher interested in questioning the role of wholes over
> parts stands a very  poor chance of obtaining support for that kind of
> question..."
> [re-snip...]
> "But one thing is certain. If you want to understand the whole you need to
> study the whole". (Is that right Douglas? more or less what he said,
> anyway).
> 
> athel

There might be another way yet: study the interfaces between the parts,
which represent the glue that makes the whole what it is. 
This has yielded some valuable insights in the shift from enzymes to
metabolic pathways, but there still are many lacunes in many more
dimensions in the intricate way to the whole.
Some would say these sections are still 'dominated by the _ethos_ of
mechanism', but isn't that the critical oh-so-missing link?

It seems also these topics are naturally related to the new "centers of
gravity" of modern biology: control and regulation. These became so
important that some bad tongues expressed the whish, it shoudn't be left
to biologists (culturally intoxicated by that '_ethos_ of mechanism') to
study...

I think otherwise. and if 'Mohamed doesn't come to the mountain, then the
mountain will come to Mohamed'. This place represents not only the cradle
of the above-mentionned conceptual change, but it should be assertively
instrumental in its consolidation and the recruitment of new participants,
resources and, yes, fields and even disciplines.

There are many efforts invested by many good people out there who are
barely aware of each other. Some of these even have initiated a long
awaited organization step.

Following is a list of URL's to different groups/software packages which
are/should work in coordination. I realize that most of us are aware of
most groups, and that the list is far from complete, but that's a start...

http://gepasi.dbs.aber.ac.uk/btk/home.htm
http://www.cellml.org/public/about/what_is_cellml.html
http://www.cds.caltech.edu/erato/
http://www.nrcam.uchc.edu/
http://www.zoo.cam.ac.uk/comp-cell/StochSim.html
http://mitpress.mit.edu/ICSB2000/stelling.html
http://www.e-cell.org/
http://websites.ntl.com/~igor.goryanin
http://www-aig.jpl.nasa.gov/public/mls/
http://www.lbl.gov/~aparkin/

Many of the groups have their own distribution list, which should somehow
unite. Again, two representative newsgroups are:

btk-mca at hgmp.mrc.ac.uk
sysbio at caltech.edu

How all this can be done is a real problem...

Season Greetings,
Claude

Claude Aflalo ########################## Phones: Office 972-8-6472118 ####
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