Dear Jerry,
Perhaps, we exchange at cross-purposes. I don't wish to deny that in
specific fields such as chemo-informatics or social-science informatics, one
studies specific arrangements and configurations. (I mentioned graphs.)
However, the red herring emerges when these configurations are made the
subject of "information theory" (in contrast to "informatics") without
further reflection.
It may be easiest to raise some questions:
1. What is the equivalent in chemo-informatics of a bit of information? Can
this be operationalized as a formula like Shannon's H?
2. Can one compute with this formula in fields other than chemistry? For
example, in economics; without using metaphors? ("As if")
I agree that each field has its own specific theories and nobody can forbid
to call these "informatics". However, the strength of Shannon's information
theory is its grounding in probability theory. This is more abstract and not
field specific. At that level, the specifics of the morphology and spatial
arrangements have first to be rewritten numerically (e.g., in terms of
coordinates) before they can be made a subject of analysis and calculation.
Best wishes,
Loet
-Original Message-
From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On
Behalf Of Jerry LR Chandler
Sent: Sunday, October 16, 2011 5:47 PM
To: fis@listas.unizar.es; fis@listas.unizar.es
Subject: [Fis] Chemo-informatics as the source of morphogenesis - both
practical and logical.
FIS, Loet, Joe:
This message is a response to Loet's notion that morphogenesis is a
red-herring.
Before my specific comments, I would like to acknowledge Michel for his
excellent introduction to the conceptualization of chemo-informatics as a
branch of information theory and engineering of chemical systems. The
motivation for the work of developing chemo-informatics come from various
sources, but, generally speaking, they are tied to the concept of DESIGN -
another term for morphogenesis.
Practical chemistry searches for ways to get a job done by finding ways to
use chemical knowledge to solve a problem. Often, this means testing a
range of different chemicals to see if the desired effects are obtained. In
the early history of chemistry, various natural sources of different sorts
of matter were empirically tested. Following the theoretical developments in
the late 18th and early 19th century, mathematical chemistry slowly
developed from the concepts introduced by John Dalton that all chemical
structures were ratios of small whole numbers composed from different
chemical elements. Given the large number of different sorts of chemical
elements and the unbounded number of combinatorial possibilities, the
chemical community gradually developed a system of mathematics which
captured the essential features of the information content of chemical
structures. The mathematical system is simple enough to be taught in high
school but the combinatorial 'explosion' of structures and properties is so
vast that a sub-discipline of 'chemo-informatics' was developed just to
study the interrelations between subsets of chemical structures and subsets
of chemical properties.
Chemo-informatics developed a separate form of information as Michel has
summarized. The form (ie, the morphology) of chemical information is iconic.
The atomic numbers, as icons, are combined to form chemical structures, the
basic mathematical objects of chemo-informatics. Chemo-informatics developed
a separate form of logic. The logic of chemo-informatics has both regular
components, such as those associated with mass (strictly additive) and
irregular components, such as those associated with electrical parity of
iconic representations of atomic numbers. For the electrical associations, a
separate method of relational addition was developed as a theory of valence
(from empirical observations). The later theory is closely akin to and the
precursor of mathematical category theory. The iconic representation of
atomic numbers is calculated in terms of graphs. Chemo-informatics can be
thought of as the logical precursor of both category theory and graph
theory. Charles S. Peirce, 1839-1914, laid the foundations for modern logic,
based on both chemistry (his term - existential graphs as forms of logic)
and Scholastic logic.
Today, the practice of chemistry is a practice of mathematics, a practice of
relational calculations on numbers. Organic chemical analysis and chemical
synthesis, including all molecular biological structures, are based on proof
theory. The notion of "proof of structure" in an exact notion that
establishes an exact graphical relationship between Dalton's 'ratio of small
whole numbers' and the iconic forms of chemical structures.
Chemo-informatics is closely associated with bio-informatics. A substantial
portion of bioinformatics consists of counting possible chemical forms or
closely related forms that differ in sequences. Bio-informatics can be
thought of as "engin
