Dear FISers:
This email seeks to address topics of discussion during the past
week. In order to seek some sense of coherence to the on-going
exchanges, I will attempt to frame the commentary in terms of the
second question poised in the opening contribution. I start with the
concepts of the Nous and Aristotelian categories.
>> Historically, in the 1840�s, Kirchhoff�s theory of flow in
>> electrical networks grounds the metaphor of the conceptual
>> framework for molecular bionetworks. However, the relatively
>> simplicity of the flow of electrons in comparison to the flow of
>> life restricts the analogy severely. Nevertheless, biomolecules
>> are composed from electrical particles and certain electron flow
>> patterns are intrinsic to metabolic networks in living systems.
>>
>> 2. From the perspective of information, how is it possible that
>> bionetworks construct the informed flows of electrical current
>> flow and how is it related metabolic flows?
>>
Classical philosophy explored the classifications of relations among
logic, ethics and "physics" (as a name for nature / medicine.).
The Aristotelian categories served as the source of classification of
substance (matter). These categories addressed the issues of concern
to modern experimentalist with ONE EXCEPTION. In modern English, the
interrogatories (who, what, when where, how and why) serve as a
useful parallel to the Aristotelian categories. The Aristotelian
categories played a fundamental role in medieval education until the
Newtonian path lead to the mystification of numbers (irrational
numbers, transcendental numbers, surreal numbers) and the Kantian
meltdown of rational philosophy.
The categorization of the concept of Bionetworks was not adequately
addressed in my initial post but is important for the discussion that
follows. The notion of networks is closely related to the concept of
logic trees. The logical distinction between 'trees" and 'networks'
is not simple. For our purposes here we will consider "the tree of
life" as a logic tree, that is, a common root and sequences of
bifrucations that separate the flows into distinct species. Networks
differ from trees by the inclusion of cycles. (One may consider the
cycles to be be either feedback or feed forward cycles that influence
flows. So, bionetworks include cyclic relations, cyclic categories,
cyclic regulatory processes.
When we speak of bionetworks we wish to include the following
classes of networks, starting from simple and growing increasingly
perplex:
1. the networks of chemical communications of simple cells that
generate cellular functions and reproduction
2. the networks of chemical communications among the cells of a
multicellular organism
3. the networks of electrical communication in organisms with central
nervous systems
4. the networks of internal mental communication in higher organisms
such that consciousness is generated.
5. the networks of external communications among members of social
and cultural communities.
6. the networks of eco-system "communications" that sustain the
dynamics of ecosystems as organizations of species and geological
circumstances.
(This categorization of bionetworks is somewhat arbitrary but is
adequate for this general discussion. The important point, with one
exception, is that the concept of bionetworks is given clarity and
distinctiveness by separation of Aristotelian categories. )
The exception to the Aristotelian categories mentioned above emerges
from the discovery of the properties of electricity in the 17, 18 and
19 th Centuries. Aristotelian categories FAIL to address electrical
phenomenon. The description of electrical cycles (networks) by
Kirchhoff in the 1840s was a major event in the history of science.
(The modern concepts of informations are closely associated with
electronic communications technology that are direct applications of
Kirchhoff networks or circuits.) However, Kirchhoff's laws applied
only to the flow of one category of electricity, the electrons. The
second category of electric particles, the nuclei, to not follow
Kirchhoff's laws and circuitry. Thus, the mystery of how to classify
the electrical properties of biological systems can not be addressed
in terms of Kirchhoff's networks.
As noted in FIS post number II, the mathematical of bionetworks
depends on the atomic numbers and the combinations of chemical
elements. This mathematics was developed by chemists in order to
describe empirical observations in laboratory experiments and living
systems. The fact that the description of bionetworks at all levels
of organization depends on the mathematics of atomic numbers and
chemical combinations is deeply inconvenient to theorists, who often
attempt to ignore the importance of the mathematical roots of
bionetworks and their description in terms of molecules. The direct
correspondence between electrical particles, associative rules, and
bionetwork behaviors is the basis for genetic information and
chemical communication in all categories of bionetworks outlined above.
For examples of the meaning of chemical mathematics and chemical
logic in information theory, consider the following:
1. The science of thermodynamics excludes chemical structures from
the equations of energy and entropy. The linkage between
electrochemical particles and thermodynamic equations is only via the
number of particles and the equilibrium constant for re-arrangements
of particles. CHEMICAL STRUCTURAL INFORMATION is excluded from
thermodynamics. Consequently, the formalism that operates during
cellular reproduction of its chemical components is also excluded by
thermodynamics. There is nothing mystical or revolutionary about
this conclusion. The necessity of continuous mathematics is
intrinsic to the differential equations that are the root of the
mathematical theory of thermodynamics. Statistical mechanics, an
approximation of the theory, is a valid approximation for very large
populations of molecules, not for a single molecule of DNA.
2. Quantum mechanics, as a mechanical theory, merely describes the
motion of electrical particles in space and time. The notion of a
species of a network is absent from quantum mechanics. In order to
attempt to apply mathematical formula to a collection of electrical
particles, one must start by describing the particular isomer, the
particular organization of the electrical particles. CHEMICAL
STRUCTURAL INFORMATION becomes the starting point for quantum
mechanical description of bionetworks, not vice-versa.
These two lines of reasoning lead to a deep conclusion.
We need a new theory of information for living systems. A principle
task of the new science will be to describe the flow of electrical
particles in bionetworks.
I now turn to posts of the last week.
Michel message (Digest 482) includes:
"An example here: there are various file formats used to store chemical
structures on computer (mol, mol2, pdb, cas, csd, etc..), and many
users are asking for an universal format. BABEL do conversions, but
developpers would like to programme themselves the input/output modules
reading/writing molecular structures. There are tasks groups working
on this topic, but I am not optimistic: as a consequence of the multiple
definitions of "structure", it is impossible to define a file format
handling all situations for all users: it would be an enormous dataset,
so much complicated that nobody would use it."
JLRC response:
It is important to separate the concepts of chemical structure from
the physical phase issues. Water (hydrogen oxide? dihydro oxygen?) )
as electrical particles is a name constructed from the components.
Properties of populations of molecules must include the interaction
among the individuals.) The distinction can be classified as the
distinction between esoteric and exoteric, the internal and the
external.
Yes, anyone familiar with the efforts to reduce chemical logic to
binary logic understands the challenges of representing matter. I
think the general scientific public lacks appreciation for the
perplexity of matter and its formal properties. The steady stream of
assertions that quantum mechanics and thermodynamics are substitutes
for Aristotelian categories has persuaded nearly everyone, including
almost the entire philosophical community, that science is merely
physics and life is merely a footnote to the differential equations
of continuous variables. The concrete examples of the relations
between atomic numbers and chemical structures (in post II) refute
this argument conclusively. Of course, the challenges of the
discrete mathematics of DNA vastly exceed the simple concrete example
of benzene as well as the millions of examples you cite.
I am puzzled by the silence of the proponents of QM and TD with
respect to information theory.
Should we assume silence is assent?
Ana's message (Digest 483) includes:
"Commonly in chemistry the "general feeling" when talking about
standards is
not really optimistic."
> "Markup languages and particularly XML are often considered to be
the
universal format for structured documents on the web. But today this
meta-language is widely used for representing any structured data, and
> particularly scientific and hence chemistry data."
After discussing current efforts toward standards, she concludes:
"I think it is one
of the ways to consolidate a chemical standard."
JLRC response:
Thank you for the extensive listing of websites. FISers who seek a
deeper knowledge of the practical challenges of representing matter
will find these links to be a rich source of information, tactics and
strategies.
With regard to these efforts to translate chemical structures into
some derivative of binary logic, I share your pessimism. ( I worked
in this area for several years while designing drugs for epilepsey.)
As noted above, I believe the theoretical problem is much deeper and
that the challenge lies at the root of the interfaces between
classification and representation. Aristotelian categories fail
because electrical concepts are not included. These categories are
constructed for the visible world. Chemical logic is based on
individual particles in an INVISIBLE world. How does one apply the
notion of "universals" to the invisible world of electrical particles?
Pedro (Digest 484) writes:
"Arguing or exploring about an overarching "logic of chemistry" (and
around "non arithmetic" atomic numbers) as Jerry suggests, may be
fertile, but one may easily forget that chemistry has to tackle a
"plurality of simultaneous occurrences", in general involving very
complex physical interactions about, for instance, charge, spin,
lattice, orbitals... where, in each one, by large nonlinearities
dominate; and where the "composite" object --eg, a complex
biomolecule-- becomes miles away from being "reduced" bona fide in
its chemical global properties down to a reasonable system of
physical-mathematical laws."
JLRC response:
Certainly, the composition, the putting together, of various theories
leads to vast mathematical challenges. The intractability of such
calculations is well established. The emergence of intractability of
the mathematics of dynamical systems whenever three or more bodies
are present is well known (since Poincare.) That is not the issue at
hand for chemical information.
Pedro, in a portion of your comment, I think you are overlooking the
obvious. Namely, that chemical calculations work for any stable
chemical molecule. The chemical calculations for DNA molecules with
millions of electrical particles yield exact solutions. Poincare's
rule of three objects ("Three implies chaos") is what fails.
From another perspective, your remark is on target. Chemistry is
based on exact relations between number, properties and identities.
However, the relations between number and identity can be created
with a small subset of the properties, not all the properties of the
identity must be known to create the name.
A similar rule is used for the uniqueness of bionetworks and names of
biological species. The classification of a new species only
requires that one identifies the substantial distinctions between the
known and the unknown. The chemical identity of bionetworks is much
stronger than the traditional biological basis of genera and species
(derived from Aristotelian categories). Thus, chemical logic has
lead to a revolution in the classifications of biological taxonomies.
Pedro continues:
"Maybe the points on natural computer science raised by Kevin and
Gordana are related. We may easily take for granted that a coverage
under the umbrella of "mathematical machines" working on sophisticate
topological properties of electronic circuits, by the use of Boolean
networks operating on solid-state devices (and functionally
independent), is the natural theoretical model for any "informational
or computational occurrence." Even the world itself, not only as a
theoretical object, may appear as a gigantic computer, a la Wheeler
(nope... or maybe, yes, but along a dramatic reinterpretation of the
whole three mechanics --classical, statistical, quantum? Excuse me
the wild derivation)"
JLRC response:
I think you are presupposing that somehow or other, a certain
"Aristotelian universality" of quantity ensures that all computations
will work with the same number system. I think the evidence is the
opposite. A range of computational processes exist. In particular,
modern electronic computations are all based on the binary system of
logical trees. Conceptually, these trees are of the same general
nature as the logical trees of Aristotelian categories or biological
classification. The failure of the binary system of computation for
chemical computation with electrical particles was already addressed
in terms of relations to empirical fact. If you would like to play
with these concepts, pick up an introductory chemical textbook and
attempt to classify valences of elements in molecules as logical
trees. You will quickly see that it is a hopeless task, even for
simple ionic matter.
Each bionetwork performs its own particular calculating processes
that transform numerical relationships. The bioprocessing of genetic
information is specific to the species. Note that this view of
individual identity FOLLOWS from the concept of atomic numbers and is
EXCLUDED by the simple arithmetic rules!
Pedro concludes with:
"If I could bring order into these studies, the starting point, or
say one of the basic pillars of the "information bridge" upon the
biomolecular turbulent waters, in my opinion, should be built around
the characterization of molecular recognition events, downwards and
upwards."
JLRC response:
I concur with the sentiment but do not not like the roots of some of
the words chosen to express it.
"recognition" as a form of cognition does not suggest the possibility
of inference. Biomolecules, under the circumstances of living
systems, infer conclusions from the organizations of numbers. The
inferential processes can be described as encodings and decodings.
It is a logical process of some sort or another.
Steven Zenith (Digest 485) states many strong conclusions. I am
uncertain as to how they fit into the discussion of the concept of
bionetworks, so I will respond with questions:
1. What notions of classical philosophy support the views expressed?
2. Why are the scientific problems within the USA different from
scientific problems elsewhere?
3. How would an improved theory of information, in particular,
bionetwork information theory, contribute to transdisciplinary
communication?
4. Which of the foundations of logic do you refer to?
Stan (Digest 486) writes:
"It is clear that while our models of the world are
as fully explicit as possible (thereby modeling the world as
mechanistic),
the world itself is to one degree or other vague."
JLRC response:
I do not concur that are models of the world are "as fully explicit
as possible."
The richness of mathematical explication is simply beyond imagination.
Indeed, science remains in its infancy, particularly the chemical
sciences.
Perhaps you read much to much into physical theories?
And the intractability of continuous dynamics?
The assertion that:
"the world itself is to one degree or other vague"
is gratuitous philosophy and appears to run counter to the history of
science, particularly the chemical sciences.
Stan, if my memory serves me correctly, you were educated as a chemist.
May I ask you a question?
From you philosophical perspective, and from the perspective of
mathematical philosophy that numbers are abstractions,
and from the success of the atomic numbers in providing an
organization framework for chemical calculations,
how do you distinguish among the concepts of number, matter and
identity?
Rafael (Digest 487) introduces a number of salient terms and
perspectives:
Starting with Shannon information, the concepts of encoding,
transmission and decoding create relations among at least three
distinct dynamical systems - three potential Poincare objects. The
mutual pre-understanding of the encoding and decoding mechanisms in
Shannon machines is a prerequisite for message communication. The
mutual pre-understanding of binary message arrangements remove the
potential for chaos and reduce the choices to one or zero, a signal
or no signal at all. Thus it functions as a logic tree.
While similar circumstances prevail in bionetworks, the messages are
not binary, rather they are polynomials in the sense that each
molecule has a name composed from many parts.
Secondly, while the parts of the Shannon machine are easily
distinguished such is not the case for bionetworks. The demands of
biological reproduction require that each part functions in multiple
roles. In addition, the bionetwork as a whole must be able to
construct itself.
The structure of time is a special issue in itself. The bionetwork,
not as a logical tree, but as a system of feedback and feedforward
cycles, constructs, in contingency with its exoteric ecosystem, its
own time domain - its life cycle.
Within Rafael's message, a quote from Loet caught my eye.
"Loets answer was that "we can make an analogy among almost every
system. This may serve us a heuristics."
Does Loet wish to imply that the direct inferences between molecular
genetic events and human health are merely heuristics?
While the difficulties of the multiple contingencies of development
are daunting, I do not think the relations are analogies at all. The
bionetworks generate adults from zygotes, that is established fact.
The challenge is to find a language, or invent a science, that keeps
the many perspectives in collaborative moods. In other words, the
task is in the choice of verbs, not the choice of nouns. The nouns
are given to use by the existence of correspondence relations - the
existential logic of the bionetwork.
Writing this message has already consumed much of my day. I must
close and return to other tasks. In closing, it appears that the
concept of bionetworks generates several deep issues with regard to a
theory of information for living systems:
1. What is the nature of biological computations if atomic numbers
are not arithmetic numbers?
2. What are the consequences of atomic numbers for the
computerization of chemical structures?
3, What is the appropriate language for describing the exchange of
"knowledge" (molecular recognition) within a bionetwork?
4. What is the appropriate language for describing the sentences of
relations in perplexifiction or the layering of semantic structures
on the basis of size?
5. What is Steven seeking to communicate?
6. What are the consequences, beyond the preservation of
calculability, of separating the concept of structure from the
concept of dynamics?
7. What would be a suitable form of Aristotelian categories such that
the concepts of electricity would be inclusive within the logical
tree of categorization?
8. Most puzzling of all, how has it come to be that modern
philosophy has come to exclude the logic of chemistry and biology
from what is known as "analytic" philosophy?
Cheers
Jerry
Jerry LR Chandler
Research Professor
Krasnow Institute for Advanced Study
George Mason University
Received on Mon Nov 28 22:55:25 2005
