Re: Quantum Physics, Measurements and Robert's Functional Dynamics Concept

[Ionel <***>]

Dear John M:

Again, I appreciate your thoughtful replies and the frank exposition of
your viewpoints. We may differ in our viewpoints and still remain friends.
As P.W. Anderson put it in a published article in 1972 in "Science" -'More
is Different'--that's the title that he used to respond to elementary
particle physicists that said that only 'they are important', and solid-
state-physics, QM or not, is 'dirt'. The story is told in a recent book on
"Complexity" that you have probably seen and read. Perhaps, I do not have
the 'literal' skills that you have, and that Robert had. So, let's briefly
re-cap the facts as they are. I am not attempting to 'skew' anybody's
views, but facts have to be told, so that people can form informed
opinions. This group's, or forum's, discussions started focusing on
Quantum 'Mechanics' to which I feel I can contribute. My point about
quantum theory, improperly  called'mechanics' was and is that it provides
very useful tools in substantial agreement with a huge number of
experiments. Moreover, Schrodinger raised the issue 60 years ago: what
new 'tricks' does Life use to get around the irreversibility associated
with gene duplication?
As Robert pointed out in "Essays..." and elsewhere,  Schrodinger even came
to the correct conclusion that this requires "new physics".
Robert followed this line of thought in his early papers on Quantum
Genetics published in BMB in the early 50's but he went further by posing
mathematically the problem that Schrodinger was grappling with.
(Incidentally, have you read these papers in detail as I did, several
times?--because that makes a certain amount of difference to the level and
relevance of discussion that we/one can have.) As I explained before,
Robert utilized the mathematical- quantum mechanical- apparatus developed
by von Neumann and arrived at the conclusion in his published papers that
the "central dogma of molecular biology is wrong" and that genetic self-
reproduction cannot occur as stated by the dogma then proposed
by molecular biology. He was never challenged in BMB by anybody about his
conclusions on Quantum Genetics. Judith told us also the very interesting
fact that he also arrived , perhaps later, at the conclusion that "QT and
all other existing theories are unable /unuseable for understanding
biology". As I see it, Robert has then developed the (M,R)-systems, and
especially the replication, beta-component, to address the very problems
which he found that "could not be resolved through von Neumann's approach to
quantum mechanics". However, at this stage, around 1966/1967, when
I 'arrived on the scene' of relational biology Robert has not yet come to
the 'complete picture of self-reproduction' that he developed later in
(M,R)-systems.  How do I know? Well, simply I am very familiar with all his
(M,R) papers,(in detail!) and others' papers on (M,R)-systems, as well as
because  of my substantial correspondence with him on the subject when they
were  being developed, so that I could follow the trail of his developments
quite well.
Thus, when he published a paper on (M,R)-systems in 1967 saying in the
title that they are "Abstract Sequential Machines."--another name for
automata--there was a very prompt response from Michael Arbib who then
classified promptly the category of biological systems modelled as (M,R)-
systems as a subcategory of the Category of Automata, in a paper published
in BMB in 1968 (that I listed with my first posting). He was saying in
effect that biological systems--if correctly represented as (M,R)-systems--
are none else but "automata", and therefore let's study them as we would
study automata in Automata Theory with the tools developed there. As you
might expect, a prompt response article followed from Robert in which he
pointed out the conceptual differences between the (M,R)-systems and
automata. It is reasonable therefore to think that this
controversy 'catalized' his further development of (M,R)-systems as we are
discussing it today. It is at this point in time that I and my cowrokers
began contributing to the development of Relational Biology and (M,R)-
systems, specifically. The new point that we introduced was the
significant, hierarchical/organizational 'structure' that (M,R)-systems
must have in order to be able to function as described, and also showed in
detail how they can be constructed using certain canonical functors
(Yoneda) and natural transformations. That is, we brought up and published
the fact that unlike automata or sequential machines, (M,R)-systems have to
be represented by structures of a 'higher algebraic dimension'--or a
supercategory-- (in current algebraic terminology), and not as simple
1-categories, in order to be able to both self-repair and self-reproduce.
Our "On a  Functorial Construction of (M,R)-systems" was submitted in 1971
and  published without any change in 1973 in RRM; my companion paper using
those results, which was "Some Algebraic Properties of (M,R)-systems" was
published promptly, the same year in BMB.  The story does not end up there:
by 1980 it was possible to develop a unified treatment of Rashevsky's
relational biology theory--the organismic sets theory, Robert's (M,R)-
systems theory, and the wide-sense kinetics Molecular Set Theory produced
by Anthony Bartholomay in 1972 and briefly applied by him to begin develop
an approach to Relational Medicine. I published this unified theory, based
on our previously introduced Functorial Construction of (M,R)-systems in
BMB in 1980, and my paper was favorably received by Robert. Its title
is "Natural Transformations of Organsimic Structures."

These are the facts as I know them, and as they are recorded in the
Bulletin of Mathematical Biology. I would really appreciate any specific
comments that one may bring up to improve and develop upon the contents of
this  24-year old paper that I wrote back in 1977, as well as its 1977
companion  paper on Genetic Network Nonlinear Dynamics in terms of N-Valued
Logics (written in 1973).

With best regards,

Ionel


On Sun, 30 May 2004 09:06:02 -0400, John M <***> wrote:

>Dear Ionel,
>
>I stopped my involvement in conventional science after retirement, I even
>resigned from consulting assignments as well, since I realized my
>"professional solitude" - away from the institutional flow of events and
>literature, not to speak about experimetntal activities. Inevitably I am to
>become obsolete, not worthy of the retainers by clients. My earlier
>'pioneer' experience is not enough.
>
>This was the point when - as I said - "I started to think".
>Bogdanov (Malinovsky), Bohm, Bertalanffy, and many others helped me into
the
>'wholistic interconnectedness' worldview, which I found akin to Rosen's
>systematic philosophy (not the math technique based biological examples he
>provided for scientists).
>
>>I have a feeling that your practival (conventional) science does 'flavor'
>even the RR-reminiscences and your explanations are interwoven with
>classical (quantum?) physics. That is no criticism: it si YOU, your
>lifeline, achievements, yourself. I am not 'against' reductionist science,
>I value its practical results (live with them) and realize that this is the
>only productive way of the present level of the human mind. Without
>reductionistic model-learning we would live in the cave.
>We just want to look ahead and find better ideas for understanding.
>
>I want to keep this in mind and remind other listmembers that your very
>persuasive argumentations may skew the Rosennian thinking which is aimed at
>the world of impredicative, wholistic, totally interconnected and
>Turing-noncomputable qualia, not mixable with formalistic and math-
quantized
>physics-based conventional science theories. I drew the line and abandoned
>the latter: I could afford it, I do not belong to any science-related
>establishment.
>
>I appreciate your experience and wisdom, your achievements, but always do
>keep up the filter to separate the conventional (redux) science-aspects
from
>the Rosennian idea. So, as you said, the two of us may have (earlier)
>matching topical periods, but for now I prefer not to argue with you. Our
>worldviews are at different planes.
>
>Best regards
>
>John M
>
>----- Original Message -----
>From: "Professor I.C. Baianu" <***>
>To: <***>
>Sent: Saturday, May 29, 2004 3:44 PM
>Subject: Re: Quantum Physics, Measurements and Robert's Functional Dynamics
>Concept
>
>
>> Dear John M.:
>>
>> I appreciate very much you interesting thougths and timeline; it would
>seem
>> we started opposite ways, somewhat continued going opposite ways, but now
>> we seem to be partially overlapping our 'wave functions'. In the late
80's
>> I had quite a bit of work done and published on organic, as well as
>> biological-origin polymers.
>>
>> I became involved in the exciting field of Relational Biology in 1965/6
>> when I was 20, although I was studying for my master's
>> in Physics & Medical Biophysics; in parallel, although we had plenty of
>> poorly presented maths and so-called "mathematical physics" classes (that
>> were totally useless being presented by mathematical "non-entities", lots
>> of biology, biochemistry (not enough), molecular biology (not quite
>> enough), classical genetics, cytology,physiology, and of course lots and
>> lots of medicine and biophysics classes and labs. My best, local friends
>> were, however, established mathematicians and physical chemists.
>> I audited their new and exciting courses on mathematical applications
>> of Category Theory, and the p.chem. experiments on Fluorescence of DNA,
>> Proteins, Electron Spin Resonance (ESR) and Nuclear Magnetic Resonance
>> (NMR) studies of biological and organic, inorganic systems ---mostly
>> solutions, but solids also. The latter one couldn't do at all without the
>> big Quantum 'Mechanics' Bibles on NMR (e.g., Abragam, 12 editions since
>> 1962, Oxford Univ. press>> 1000 paqges) and ESR (e.g. Abragam and
Bleaney,
>> 1970; Clarendon press, Oxford:DEDICATED TO VAN VLECK ! 911 pages; both
>> chock-full of nicely worked out examples that give very numerous
>> experimental results EXACTLY as predicted by 'standard', Hamiltonian QM
>> computations, with due approximations whenever necessary). I've never
>> stopped using quantum theory computations in my published papers on
>p.chem.
>> applications to inorganics, organics and biological systems, involving
>> Magnetic Resonance. Even managed to write a second phys.chemistry
master's
>> thesis on the Hyperfine analysis of ESR of inorganic and organic
solutions
>> (both liquid and solid) of divalent copper salts, and the Dynamic Jahn-
>> Teller effect at 277K, and static at ~77 K, analized of course with
>> standard quantum theory Hamiltonians (kindly provided by the
>> Bleaney's 'Bible' on ESR). A famous p.chem. advisor was delighted to
>> approve the thesis, seconded by an equally famous 'nuclear'/
>> /magnetic resonance--ESR physics professor. We also looked at ESR of
>> live photosynthetic systems where it has provided, and continues to
>provide
>> invaluable results.
>>  In fact, the largest QT item I wrote was in 1992-- a chapter or two of
>> quantum theory in my textbook on physical chemistry applications.
>> Notably, Magnetic Resonance Imaging  (MRI) is currently one of the highly
>> valued, noninvasive techniques for FUNCTIONAL and Diagnostic Medical
>> Imaging. Behind the MRI operation , the observation principles and
correct
>> analysis are as laid out by quantum theory. This means saving lots and
>lots
>> of people's lives. It did save mine too, as I was the 'diagnostician' who
>> ASKED FOR the MRI and, also produced the correct diagnostic of a
>suspected,
>> but false cancer, after examining two not-so-hot pictures for two full
>> hours!  Because, if I didn't, I would not be writing to you now!!!
>> Therefore, I have to disagree strongly about the usefulness of Quantum
>> Theory: it is established beyond any doubt in phys. chem./ biophys. chem.
>> etc., and also in Medical application developments; sometimes--quite
>often,
>> in fact--a reductionist approach has its uses, as long as it does not
>claim
>> that it provides the final, complete answers, that no modeling can do
>> anyway! And also , as long as it does not make any claim, <that's the
only
>> way 'to skin the cat'>-- be it Schrodinger's or anybody else's.
>>
>> What I did not say so far is that I did/do continue developing the
>> Relational Biology approach throughout the 80' and late 90's looking for
>> the essential mathematical tools, "new physics" and biological data
needed
>> for refining the non-reductionist 'programmatic' approach that Nicolas
>> Rashevsky, Robert and I have assembled back in the early 70's with
>> substantial contributions from others such as George Karreman (Relational
>> Quantum Biology), Anthony Bartholomay (Relational Medicine and
Diagnosis),
>> Matthew Witten (Measurement and Biological Observation theory), W. Foster
>> (M,R)-systems, to name just a few. It's been slow going but things are
>> obviously speeding up from all sides.
>>
>> With best regards,
>>
>> Ionel
>>
>> On Sat, 29 May 2004 10:34:01 -0400, John M <***> wrote:
>>
>> >Dear Ionel,
>> >not that I want to argue, (I am on divergent lines of thinking), just a
>> >remark about my "other" hero: David Bohm:
>> >
>> >He diverted from his conventional physics interest by the 60s and really
>> >became one of the founders of "modern thinking" - from the side of a
>> >physicist what he never ceased to be. (Once a physicist...)
>> >His ~1952 ideas were far from his later philosophy and in my opinion it
>was
>> >a mistake to make a posthumus edition of the physics he wrote THEN,
>without
>> >pointing out his (later) changed natural philosophy system. He WAS a
>great
>> >physicist but a GREATER philosopher.
>> >The "Wholeness and the Implicate Order"  is a fundamental work
>> >and he spent the rest of his thinking life in this domain, even when he
>was
>> >teaching 'college-physics'.
>> >
>> >I wrote my ~100 publications and books in polymer (chemistry) before I
>> >started to "think". My present ideas should not be mixed with the former
>> >(reductionist-researcher) work, as well, as RR also did have different
>> ideas
>> >before developing his "complexity" system.
>> >
>> >Regards
>> >
>> >John Mikes
>> >
>> >----- Original Message -----
>> >From: "Ionel" <***>
>> >To: <***>
>> >Sent: Friday, May 28, 2004 10:04 PM
>> >Subject: Quantum Physics, Measurements and Robert's Functional Dynamics
>> >Concept
>> >
>> >
>> >> I am adding a new part to my response on "States" and the measurement
>> >> problem in Quantum Theory. Some authors, such as David Bohm (fmrly. at
>> >> Oxford) and MacKay at Harvard, feel strongly that Quantum & Mechanics
>is
>> >> a "misnomer" for quite different reasons, although not totally
>> >unconnected.
>> >> Thus David Bohm says that all systems are connected in the entire
>> Universe
>> >> (s?) at the quantum, microscopic level, and that different properties
>of
>> >an
>> >> electron, for example, are exhibited with different interacting
>systems;
>> >> David Bohm in his Quantum Theory (1951 edn, 2nd edn. 1991) also goes
>> >> further in stating that the measurement system/detectors/apparatus and
>> the
>> >> quantum system that is observed have to be considered as a "whole" in
>the
>> >> quantum theory. Bohmm also states that therefore, even 'simple
systems'
>> >> such as the electron exhibit complex behaviors at the microscopic
>level.
>> >>
>> >> This may, thus suggest that complexity, even in Robert's sense, does
>> >> originate at the quantum, microscopic level in biological organisms,
as
>> he
>> >> was pondering on this question back in 1956, in his Quantum Genetics
>> >> article published in BMB.
>> >>
>> >> David Bohm also has some other interesting and provoking thoughts on
>why
>> >> and how quantum processes and the thought process in humans exhibit
>some
>> >> basic similarities, and he also cites some older views by Niels Bohr
>that
>> >> are labelled as 'highly speculative' on this subject. (See also my
>> >previous
>> >> posting on the preprint "N-Categories in Neuroscience" by Ronnie Brown
>> >> (freely downloadable at his site). On the whole, Robert's ideas about
>> >> measurement in complex systems do seem to be rather similar to David
>> >Bohm's,
>> >> although Robert doesn't cite Bohm in either his "Essays on Life..." or
>in
>> >> his original article on Quantum Genetics in 1956. Because, really, the
>> >root
>> >> of all discussion about Schrodinger's "What is Life?" and Robert's
>"Life
>> >> Itself", or F. Crick's "Life Itself..." is Quantum / Molecular
>Genetics.
>> >>
>> >> MacKay' lecture notes at Harvard on the "Mathematical Foundations of
>> >> Quantum Mechanics" (Theory?) makes the point that one cannot define a
>> >Phase
>> >> Space of single, dynamic state points, in Quantum Statistical
Mechanics
>> >> because--according to Heisenberg's principle-- one cannot observe
>> >> simultaneously velocity and position at any "point in time". (Quantum)
>> >> States are then defined by means of a probability measure for certain
>> >> observables whose eigenvalues determined through measurement.
Moreover,
>> >> just like Von Neumann and Robert, he distinguishes between "pure
>states"
>> >> and "mixtures of states" in quantum theory... but no hidden variables.
>> >> David Bohm agrees in his new edition: hidden variables won't work in
>> >quantum
>> >> theory, and therefore, "causality" in the Newtonian mechanical sense-
>or
>> >> Einstein's-- for that matter, won't work in quantum theory.
>> >> Both David Bohm and Werner Heisenberg agree on one thing : quantum
>theory
>> >> is not in the final, completed stage yet, more new physics is needed.
>In
>> >> this, Robert is in agreement with both of them. They seem to separate
>> when
>> >> it comes to the means by which to achieve/ develop the new physics.
>David
>> >> Bohm doesn't exclude biology from the new , quantum physics
>> >> but "speculatively" suggests possible bridges between quantum theory
>and
>> >the
>> >> thinking processes in the human brain. In my paper published back in
>> 1972,
>> >> "A Category- Theoretical Analysis of Processes involved in
>> >EEG.",(RRM),that
>> >> we're scanning soon, I have obtained estimates of the energy needed to
>> >> sustain 'thinking processes' based in neural circuits/networks
>localized
>> >in
>> >> the brain's cortex, based on a combinatorial approach combined with
>> >> Category theory.