Re: Modern Physics, Newtonian Paradigm, and the notion of State

[Ionel <***>]

Tim:

If you did not have a chance to look at the 2003 paper by J-C. Letelier et
al, and our 2004 paper on Natural Transformations in Molecular Biology,
this is the chance to link up those two papers with Robert Rosen's
realization of (M,R)-systems as you were discussing it in the cited
paragraph below; hope I did not confuse you with too many facts.

Regards,
Ionel
>
But the really fundamental problems remained refractory to this whole
approach. In a nutshell, the reason lay in the mathematical dichotomy
between set (object) and mapping in the (M,R)-system. In a network
realization, a "state" of the network is a pattern of activation in the
elements that constitute the network, while the "next-state mapping" is
embodied in the wiring diagram of the network. But intuitively, in the
(M,R)-system, both the metabolic map(s) f and the nuclear or repair maps
Phi should themselves be embodied in (or realized by) physical structures,
and their mapping properties should be consequences of these structures.
When we realize Phi(f(a)), for example, this is abstractly a mapping (f:A -
> B) in the (M,R)-system; it is a pattern of excitation (i.e., a single
state) in a network; but it should be a material structure in the kind of
realization we are actually seeking. Even more, the map Phi itself in the
(M,R)-system is a wiring diagram in a network realization, a pattern of
specificities in an operon network, but, in fact, it should be realized
itself as a material structure, from which all these mapping properties
should follow. These considerations led to a fundamental rethinking of the
whole idea of how to go about realizing any kind of abstract relational
description of a material system.... I began to entertain the possibility
that that our conventional mathematical descriptions of physical reality,
which have essentially gone unquestioned for three centuries, might
themselves be fundamentally deficient, that it was this deficiency that was
responsible for the problems posed by an attempt to realize physically an
abstract functional organization." [p. 177-178] >>