Koichiro wrote:
" . . Prigogine’s requires some exogenous conditions making it dissipative
in the first place." (8578-1)
Isn't this also true with your reaction cycle ? All dissipative structures
are thermodynamically
(e.g., negativity of the Gibbs free energy changes accompanying dissipative
processes) and quantum
mechanically (e.g., conservation of chemical valencies, or the number of
chemical bonds; hydrogen = 1,
oxygen = 2, nitrogen = 3, carbon = 4, etc.) selected to be dissipative
under the environmental conditions
involved.
" In contrast, the network-catalytic reaction cycle can have some
endogenous capacity for making it (8578-2)
dissipative, though of course to a limited extent, thanks to the chemical
affinity extending from the inside
of the cycle toward its outside."
I think the Brusselator (see Figure 1 in the APPENDIX) also has the
'endogenous capacity for making it dissipative".
The intermediates, X and Y, produced in the first (i.e., A ---> X) and
third (i.e., B + X ---> Y + D) steps in the Brusslator,
may be what you call the "endogenous capacity for making it dissipative",
and hence the Brussleator may be
"network-catalytic" in your sense (if I understood you right).
"It functions only when the metallic catalysts such as cerium ions are
provided externally. Those metallic (8578-3)
catalysts are inorganic in the sense that their presence is independent of
the operation of BZ reaction."
This is true, but isn't it also true that all living systems depend on
externally provided metallic catalysts
like the BZ reaction ?
In formulating this email, I noticed that the Brusselator actually can be
viewed as a system of three chemical
reaction networks coupled to one another in an irreducible manner:
(1) A ------> X
(2) B + X ------> Y and D
(3) 2X + Y ------> 3X
What is interesting is the regularity exhibited by these reactions:
Reaction (1) is "unimolecular",
Reaction (2) is "bimolecular", and
Reaction (3) is "termolecular"
so that they should obey the First-order, Second-order and Third-order
kinetic laws, respectively. Can it be that these three
different orders of kinetic laws are essential for all self-organizing
reaction-diffusion systems (SORDS) ? Also can it be that
SORDS constitutes a mathematical category as shown in Figure A with the
three "structure-preserving mappings" f, g and h,
as tentatively identified in the legend?
f
g
First-order kinetics -----------> Second-order kinetics
-----------> Third-order kinetics
|
^
|
|
|____________________________________________________|
h
Figure A. The Brusselator (and by extension all self-organizing chemical
reactions) as a token/instance/instantiation of the ur-category.
f = uncatalyzed reaction (?); g = catalyzed reaction (?); h = heritable
reaction (?) implementing "information flow" from one generation
to the next mediated by the 'endogenous' catalyst (?).
For the convenience of future discussions (if there be any), Figure A may
be referred to as the "irreducibly triadic mechanism (ITM)
of self-organizing reactions", including "self-replication".
If these considerations turn out to be true, in principle, it may be
justified to conclude that
"The Brusselator [1] is the test-tube version of ITM, the Princetonator [2]
(i.e., the origin of biological infomration based on (8578-4)
the concept of "frustrations" which is equivalent to that of "conformons",
conformational strains of biopolymers storing energy
and information thought to be necessary and sufficient for driving all
goal-directed molecular motions in the living cell [3]) is a
the natural versions of ITM, and the hypercycle [4] and the Bhopalator [5,
6] are the cellular versions of ITM."
and that
"All these theoretical models constitute an irreducible system of
explanations essential to account for
(8578-5)
the origin of LIFE, SIGNS and INFORMATION."
With all the best.
Sung
-
Sungchul Ji, Ph.D.
Associate Professor of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
Piscataway, N.J. 08855
732-445-4701
www.conformon.net
References:
[1] Prigogine, I. and Lefever, R. (1968). Symmetry-breaking
instabilities in dissipative systems. II. *J. Chem. Phys*. *48: *
1695-1700.
[2] Anderson, P. W. (1983). Suggested Model of Prebiotic Evolution:
The Use of Chaos. *Proc. Nat. Acad. Sci. USA* *80: *386-3390.
[3] Ji, S. (2000). Free energy and Information Contents of C*onformons*
in proteins and DNA. *BioSystems* *54: 1*07-130.
[4] Eigen & Schuster (1977). The Hypercycle. A Principle of Natural
Self-Organisation. Part A: Emergence of the Hypercycle
<http://jaguar.biologie.hu-berlin.de/~wolfram/pages/seminar_theoretische_biologie_2007/literatur/schaber/Eigen1977Naturwissenschaften64.pdf>
.
Naturwissenschaften *64:* 541–565.
[5] Ji, S. (1985). The Bhopalator – A Molecular Model of the Living
Cell Based on the Concepts of Conformons and
dissipative Structures, *J. theoret. Biol.* *116: *399-426.
[6] Ji, S. (2015). Molecular Theory of the Living Cell: Concepts,
Molecular Mechanisms, and Biomedical Applications.
Springer, New York.
On Sun, May 3, 2015 at 8:21 PM, Koichiro Matsuno <cxq02...@nifty.com> wrote:
> At 4:10 AM 05/04/2015, Sung wrote:
>
>
>
> Is your "reaction cycle" described above different from what Prigogine
> called "dissipative structure" ? If so, in what way ?
>
>
>
> [KM] Although I do appreciate the physical significance of Prigogine’s
> dissipative structure, it differs from a reaction cycle that is
> network-catalytic. Prigogine’s requires some exogenous conditions making it
> dissipative in the first place. In contrast, the network-catalytic reaction
> cycle can have some endogenous capacity for making it dissipative, though
> of course to a limited extent, thanks to the chemical affinity extending
> from the inside of the cycle toward its outside. In this regard, the
> Belusov-Zhabotinsky reaction is not network-catalytic. It functions only
> when the metallic catalysts such as cerium ions are provided externally.
> Those metallic catalysts are inorganic in the sense that their presence is
> independent of the operation of BZ reaction.
>
>
>
> Koichiro
>
>
>
>
>
>
>
---------------------------------------------------- APPENDIX
-----------------------------------------------------
Sungchul Ji <s...@rci.rutgers.edu>
[image: Attachments]Apr 14
to PEIRCE-L, biosemiotics, bcc: Auletta
May 3 (4 days ago)
Ben, Edwina, lists,
(1) Peirce's beautiful quote is reproduced for convenience:
"Thought is not necessarily connected with a brain. It appears in the work
of bees,of crystals, and throughout the purely physical world; and one can
no more deny that it is really there, than that the colors, the shapes,
etc., of objects are really there.... Not only is thought in the inorganic
*³* world, but it develops there."
(CP 4.551)
(2) I wonder if the meanings of the word "thought" that Peirce is using
here can be interpreted in two ways -- (i) as a type and (ii) as a token.
There are many different kinds of thoughts at the concrete 'token' levels
-- human thought, the thought of bees that enabled the construction of
their nests, both being measurable in EEG, and 'thought' of crystals that
do not show any EEG signals. But both these seemingly different kinds of
thoughts can be considered as members of the same, more abstract kind (or
type) of thought, defined in terms of "semiosis" or an "irreducible
triad". In other words, since human thought is a form of semiosis (which
is synonymous with an irreducible triad), all semiosic processes, whether
inorganic or organic systems, can be said to exhibit "thought" in the
category-theoretical sense.
(3) In this category-theoretical sense, all self-organizing chemical
reactions (exemplified by the Belousov-Zhabotinsky reaction which can be
modeled by the Brusselator) can be said to exhibit "thought" and has "mind"
if they are "irreducibly triadic", which seems to be the case (see below).
(4) The Brusselator is probably the simplest theoretical model of chemical
reactions that can self-organize. See the video at
http://en.wikipedia.org/wiki/Brusselator. (Prigogine once told me that the
key step in the Brusselator is the 'termolecular' step, 2X ---> 3 X.) It
has the following 4 chemical steps involving reactants, (A + B), products,
(D + E), and the transient intermediates, (X + Y) that interact obeying the
following rules or mechanisms:
A --------> X
2X + Y --------> 3X
B + X --------> Y + D
X --------> E
______________________________
A + B ----------> D + E
*Figure 1.* The Brussleator -- a theoretical model of self-organizing
chemical reactions, both organic and inorganic.
http://en.wikipedia.org/wiki/Brusselator.
I suggest that the Brusselator, Figture 1, can be mapped onto the
ur-category, Figure 2, as shown in Figure 3. Mathematically speaking,
Figure 1 and Figure 3 are isomorphic (i.e., embody similar regualarites or
principles).
f g
A ----------> B ----------> C
| ^
| |
|_____________________|
h
Figure 2. The ur-category, a high-level category to which all lower-level
categories belong (see the emails attached).
f g
( A+B) -----------> (X+Y) -----------> (D+E)
| ^
| |
|_____________________________|
h
Figure 3. The Brusselator as a semiosic process and hence a member of the
ur-category. f = production step, g = destruction step, h = information
flow (i.e., the structures of E and E are determined by those of A and B
mediated by X and Y).
(5) Since the Brusselator and all its token self-organizing chemical
reactions are capable of semiosis (i.e., "undergoing irreducibly triadic
process") as shown above, it would be logical to conclude that all
self-organizing chemical reactions are associated with "thoughts" or
"minds" of their own. This does not mean that all chemical reactions can be
considered to have thoughts, since not all chemical reactions undergo
irreducibly triadic processes, just as not all utterances from human mouth
can carry information.
All the best.
Sung
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