Re: Triple-J ; OnLine Cell Modelling (JWS)

[James N Rose <***>]

Dear Jannie,

Thank you for the inital description of Triple-J and
the active-modelling you are doing.

The focus of my own work has been to achieve a
redefinition of the general relations in systemic
organization, hoping to encompass all levels of
organization - from sub atomic through biochemical
to sociological.

My rationale has been: that there is already sufficient
information and understandings about -what- relations
exist, but that there is an improved meta-paradigm
possible which would end up making better sense of
al the processes and dynamics ... a way of thinking that
would reneder a natural coordination between 'the modelled'
and 'the natural'.

One of the memes I apply is to de-emphasize steady-states
and plateaus, another is to treat no sets as closed, and
another is to apply relativity to the entire forma.  This last
is a most difficult hurdle, because the premise is that
the boundaries of local relations are always always changing, and
as they change, alternate 'sets' with alternate equilibrium
values are continuously in the process of being de-constructed
and re-formed .. with local nodes (possibly notatable as
'attractor basins') appearing as .. all the various stable-forms
that we typically identify; such as .. different molecular
configurations within soups of metabolic pathways.

I use the term 'gaussian bubbles' to speak about these
niche-configurations.  Many exist and there are many tiers
of them as well.  At any given moment of evaluation
or observation of them, a given configuration can be a
stable end state in and of itself, or, an energy sink relative
to some different molecule or packages of molecules, and,
an energy source relative to some alternative group of
molecular-potential states.

So even while it might seem that a single-modelling could
account for the -taxonomy- of molecules present, a dynamics
evaluation shows at least three in-tier gaussian bubbles
present - and- another gaussian in the next tier (which
is the emerged level, such as, the Kreb Cycle).

.. I must leave the computer this morning to go to
my job, but I will close with one last note, so as
not to forget for later discussion. ... About 10 years
ago it came to my attention that pharmaceutical
companies were using the kind of modelling you seem
to be doing, and using virtual reality real-time
equipment to not just do statistical systemic
studies, but to literally do 'hands-on' manipulations
of the configurations of molecules using EM fields
as their criteia - and real experiences of them for
the equipment wearings - to build new molecule-combinant
structures.  Were you aware of this kind of effort?

Best regards,

James
02/27/04