Re: [Fis] ON MOLECULAR BIONETWORKS (IV) On Number

Re: [Fis] ON MOLECULAR BIONETWORKS (IV) On Number

From: Jerry LR Chandler <[email protected]>
Date: Mon 23 Jan 2006 - 03:04:14 CET

Dear Igor:

Your reponse includes many threads of science and philosophy that are
co-mingled with mathematical concepts.
The usage of language co-mingles many concepts that must be kept
separate if one is to conceptualize a theory of biological
information that includes calculations of the genetic structures and
reproductive metabolism.

  A few comments which may provide you some concrete examples that
separate our world views, particularly about mathematics. Your
philosophy of mathematics is a rather traditional one in the physical
world. I have sought to explain why this view of continuous
mathematics is not adequate for discrete relations among electro-
chemical particles, electrochemical individuals we call the chemical
elements.

If you are serious about understanding the mathematical distinction,
I suggest you attempt to use the atomic number in basic arithmetic,
such as the distributive law and the commutative law.

I suggest you demonstrate how your view of mathematics applies to
these numbers and report back to the list your conclusions.

On Dec 25, 2005, at 11:32 AM, Igor Rojdestvenski wrote:

> Dear Jerry,
>
> I will answer "my part" in green:
>
> Igor writes (vol. 488, 6)
>
> A cell mechanism A adapts (measures) to the cell environment, which
> it is part of. During this adaptation it increases its complexity
> and changes (by its very presence) the cell environment, which thus
> also increases its complexity. Given that there are many such
> mechanisms (enzyme catalyzed chemical reactions, organelles,
> membranes, etc), each mechanism increases its complexity by
> reflecting on the presence of the totality of the other mechanisms.
>
> JLRC:
> Reading your words from a 'big picture' frame of mind, I concur.
>
> I would prefer to express the concepts in terms of the flow of
> electrical particles...
>
> It may be flow of electric particles, e.g. "measurement" as
> exchange of electrons or radicals in chemical reactions, which
> leads to saturations of concentrations of products and thus changes
> the environment;
The concept of "measurement" is hardly a natural concept of
information. Measurement is a concept introduced with the French
revolution and the international units of the decimal system.
Unfortunately, chemical measures are based firstly on the natural
units of elements and only secondarily on the concept of mass.
Electrical flows are intrinsic to chemical structures and do not
depend on saturation, etc. Flow is merely motion, is it not?

> It may be flow of photons, e.g. photosyntetic apparatus of
> green plants "measures" the incident light by producing flow of
> protons further used in ATP production and flow of electrons for
> NADPH production. These flows change, for example, the pH in
> certain parts of chloroplast, which, in turn, changes the flows
> themselves, including the available photon flow by, for example,
> epoxydation/deepoxydation of xantofills, "screening" photosystems
> from light;
> It may be flow of ions (changes in the state of the neuron
> through activity of calcium and potassium channels
> It may be flow of genetic information, e.g. transcription of
> RNA as a reaction to change in the cell environment, which leads to
> production of enzymes, which, in turn, modify this cell environment
> (e.g. reaction to heat shock or to strong light)
>
> Many more examples possible...
>
> In all these cases change, occuring as a reaction to a certain
> flow, is a measurement of this flow, and it, in turn, forces the
> changes to this flow.
>
> Yes, one may say that most of these phenomena deal with either
> flows of charged particles or photons. This is, however, trivial.
Trivial? If these electrical flows are trivial, perhaps you may wish
to write the equations for reproduction of a cell in terms of these
flows.
Are you conflating the possibility of a philosophical narrative with
doing science? In the FIS case, we would like to calculate
information content in a cell? If this is a trivial matter, please
demonstrate how you would address the problem.

> Indeed, there exist only 4 force fields -- electromagnetic,
> gravity, strong and weak. In case of living matter, at the level of
> description of biomolecular networks, we deal only with the first
> one, with electromagnetic field.
As far as I am aware, no conclusive evidence can be provided that
ONLY four force fields exist. Perhaps you mean to say that thus far,
physicists have not found a way to view the term "force field" in a
unified way and thus create a narrative that justifies a statement
that at least four distinctions are necessary.

I have no idea why you reject a gravitational field in bio networks.
For example, our blood pressure adapt when we move from a reclining
to an upright position.

> Hence, the only material objects that really matter are those which
> interact with the electromagnetic field or are produced by it, i.e.
> photons and charges (ions and electrons)
This is an intersting philosophy of science. I disagree.

>
> The term "mechanism" can be used in either a mathematical sense, a
> chemical sense, or a general sense. In what sense is it being used
> in this paragraph?
>
> When I say "mechanism" I mean:
> a chemical system of interactions between the biomolecules,
> ions and quanta, NECESSARILY in the structural context, i.e. in the
> organelles and compartments, where such interaction happen.
(This is not a Newtonian description but rather a jargon or usage
defined within chemistry; this usage obscures the relations between
matter, electrical flow, time and space and genetics. It is a nice
narrative.)

> a mathematical abstraction in the form of system of equations
> for the biochemical networks, that represents our understanding of
> the above.
A foundation question for FIS is precisely the relation between these
two sentences. Can you calculate it?

>
> Nature as such does not know equations and networks,
Are you placing man outside of nature? Man (scientists) are emergent
from chemical systems and as part of nature we know how simple
equations and simple networks work.

> these are means of our interpretation of what happens out there. I
> think that this is more or less in line with Robert Rosen's views.
>
My reading of Robert Rosens texts is radically different than yours.
I am referring to two texts, "Life Itself" and "Anticipatory
Systems". Which texts are you referring to?
>
> More specifically, in the narrative you provide, how does one
> create relations between electrical particles and the dynamics of
> bionetworks? Although only a small number of different electrical
> particles exist, how does one create the range of organisms in an
> ecosystem?
>
> As it is known from the theory of systems (examples being Lorentz
> attractor and other strange attractors, swarm theory, fractal
> structures, and many many more), it is quite possible to develop
> very complex systems from very small number of simple elements. The
> source of this complexity is the nonlinearity and instability of
> the system, or, in a more mathematical sense, the positive Lyapunov
> exponential in a finite and bounded phase space. It is, for
> example, known, that all possible patterns on the sea shells may be
> reproduced in modeling by means of a system of two simple nonlinear
> equations (this was in Journal of Theoretical Biology some time in
> 1987). Please also refer to the works of Karl Simms ("virtual
> creatures") and works in experimental mathematics of evolution by
> Chris Langton and other guys from Santa Fe institute.
A clear example of what you mean would be a calculation.
For example, calculate the number of isomers of (alpha) NAD to show
how the methods work.

>
> Another argument: One needs only 0 and 1 values for the bit to
> convey in a string of bits as much information as one needs to.
If this were true, how much information is in an NAD molecule?
Please show how you would start with Shannon information and
calculate a value.

> How can we make such concepts EXACT such that they become a
> meaningful method of scientific prediction? This is the challenge
> for bionetworks at all levels of perplexity. How does
> individuality arise from such a narrative?
>
> The problem is that we are oftentimes dealing here with the
> unstable non-equilibrium systems which are deterministic but
> unpredictable.
Are you aware that chemical structures can not be entered into
Thermodynamics? Only the ratio of concentrations of a specified
reaction can be transferred from chemical theory into continuous
mathematical equations. .

> This means that we cannot predict their behavior but can explain it
> afterwards.
A very interesting remark. The remark reminds me of my children
when they were teenagers.

> A good example is the game of pool. It is absolutely impossible to
> predict (before the stroke is made) exactly where each ball lands
> after the first stroke made into the "triangle" of balls. However,
> all the interactions, of course, obey Newtonian laws, and backward
> reconstruction of the process is possible.
> Same with evolution of biological systems and, in a way, with
> bionetworks.
I fail to see any meaningful comparison between a game of pool and
emergence of life and biological reproduction. For example, what is
the correspondence between a genetic system and the forces of a fixed
set of inelastic collisions? No generative operations are needed to
describe a pool game.
> Only general features of it may be probabilistically predicted. And
> this is exactly how the individuality comes into picture. Had it
> not been for these instabilities and extreme sensitivity to small
> variations in initial and boundary conditions, we would have been
> all alike and all the same.
>
>
Igor: Your belief in mathematical appears to me to be full, complete
and totally classical physics.

The challenge to you is to tackle some real chemical and biological
problems to test your theories, EXACTLY. Narratives are easy to
generate but the real test is in calculations. If Poincare was
correct, you have some real challenges.

I would add that chemical theory provides an exact method of
calculation of electrical flows as well as the representation of
electrical particles in chemical structures. The consequences of
chemical calculations is a collection of relations that become the
starting point for physical calculations attempting to describe the
motion of the electrical particles in time and space. The chemical
calculations are antecedent to physical calculations.

Two other comments:

1. I use the word 'exactly' to mean EXACTLY, not approximately.

2. One of the philosophical differences between your world view and
mine is that revealed by the ancient distinction between species and
genera. It appears that you view mathematical generalities as
universally applicable. I view the world as composed from species.
Classical mathematical generalities are seldom applicable exactly to
chemical or biological species. (or, was Poincare wrong?)

Of course, I could be wrong... if you can calculate the number of
isomers of NAD using classical mathematical combinatorics, I would be
forced to reconsider the entire structure of my logic. (And
chemical sciences would have to reconsider the nature of valence.)

Cheers

Jerry

>
>
> Igor
>

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Received on Mon Jan 23 03:10:27 2006


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