[Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-11-06 Thread Jerry LR Chandler
List, Loet, Joe:

This email responds to several questions raised in response to my long post of 
Oct. 16, 2011.

 Loet asks:
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")
JLRC: 
1. There is no equivalence between a bit of information and the science of 
chemistry. Chemical information must be encoded into a number just as any other 
semantic message. 
If their were such an equivalence, there would be no need for the clear, 
separate and distinct natural symbol system developed from signs from natural 
things and Dalton's rule that material things can be categorized as ratio of 
small whole numbers of weights and volumes.

Chemistry can be thought of as a semiotic science. 
C.S.Peirce stated it well when he insisted (rejecting Kant) that the following 
role of symbols is necessary for formal logic:

"Thing - Representation - Form."
or, more precisely:
"Thing - Representation - Iconic form"

In other words, the formal logic of chemistry depends on the sort of 
representation selected. This formal logic is an encoding of impressions on the 
mind into a coherent symbol system that constructs iconic representations of 
particular things. 
. 
In Shannon information, the concept of encoding any message is used to assert 
that every thing can be encoded (represented in Peircian rhetoric) into a 
number AS a string of bits, a string of 0,1's, a string of true-false 
propositions. (Note the ambiguity of meaning of encoding as a representation!) 
The purpose of Shannon's logic was to communicate any message within a 
generalized inductive argument about communication. The purpose of Dalton's was 
to communicate a particular graph form that was particular to a specific form. 

The following are a list of propositions that underlie the communication of 
chemical information. 

1. The chemical concept of an atomic number is a rhetoric phrase.
2. The adjective "atomic" modifies the noun "number".  
3. Consequently, the concept of a chemical number is not the same as the 
concept of a artificial number.
4. The adjective "atomic" has a particular meaning that modifies the the LOGIC 
of operations on the noun. 
5. The concepts of an atomic number and of an artificial number both are exact 
representations of concepts. 

6. The representations of number in both cases are positions in a list. 
7. The adjective "atomic" as used to represent chemical things, corresponds 
exactly with the count of the positive charge on the nucleus and the count of 
the negative charges of the electrons.
8.  These two counts are identical.  ((Schelling's "polar opposites" 
neutralizing one another.) 
9. These two counts correspond with a specific thing with specific physical 
properties.
10. These two counts correspond to the rhetorical name of each chemical element.

11. These two counts form TWO SORTS of nodes in a mathematical graph.
12.One sort of node represents each electron as a unit.
13. The other sort of node represents the integer count of the nucleus.
14. These two sorts of nodes can be represented as a graph.
15. This graph is terms a labeled bipartite graph because it has two sorts of 
nodes that can not be substituted for one another.

16. All logical operations in the chemical sciences are based on the atomic 
numbers.
17. The simple logical operations are logical conjunctions of two or more atoms 
to form a particular molecule.
18. The conjunctive operation of creating a molecule from two atoms is a 
copulative verb, not a predicative verb.
19. The logic of this conjunctive operation creates a new identity, a new 
graphic object (a new icon in the sense of Peirce)
20. The conjunctive operation of two atomic numbers is an additive relation 
with respect to the properties of both number and weight (or mass), giving rise 
to the logical terms, molecular formula and the molecular weight.

21, The conjunctive operations on atomic numbers are formal operations that are 
extensive to all the sciences that study things with specific identities and 
properties.  
22. The atomic numbers are the source of all molecular biological descriptions 
of life - genetic, development, anatomy, much of physiology, toxicology, 
pharmacology, clinical medicine.
23,.The atomic numbers are not applicable to artificial numbers such as 
irrational numbers, imaginary numbers, transcendental numbers, surrealistic 
numbers, the various efforts that attempts to represent infinity or the 
continuum. 
24. A series of relationships can be used to transliterate the atomic numbers 
into artificial numbers - these are the Rosetta relationships. Such 
transliterations change the formal logical relations between the symbols from 
the copulative logic of the chemical sciences to the predicative logic of 
physical sciences.
25. The communication of chemical 

Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-18 Thread Loet Leydesdorff
> without excluding either.

And without confounding one another! 
We are able to specify the differences and then to translate meaningfully
between different discourses. 

Best, 
Loet


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Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-18 Thread Joseph Brenner
Dear Michel, Jerry and Loet,

Welcome back to the fray, Jerry, but I recall a kind of "gentlemen's 
agreement" we made at our meeting in Liège, namely, that I can find a place 
for your theory, but you should reciprocally find a place for mine! In the 
following, I will try to disentangle two major issues in the recent 
exchanges.

1. Jerry's theory of Perplex Numbers, underlying his comments, is not a 
physical theory. It is a model derived from some of the numerical 
characteristics of the atomic structure of elements due in reality to 
underlying physical constraints (e.g., the Pauli Exclusion Principle).

2. Mathematics captures some of the "essential features of the information 
content of chemical structures" but by no means all of them. Are the 
dynamics of atomic and chemical structures, and their potential for reaction 
not also information?

3. There is no problem in talking about "parity of iconic representations" 
as irregular, but if you say electrical, you bring in physics, the iconic 
representations are no longer applicable, and "modern chemical logic and 
category theory" are no longer adequate.

4. No "practice of mathematics" or proof theory could have applied to the 
results of my own research nor could apply to recent major advances in, say, 
organometallic catalytic chemistry (see any recent issue of SCIENCE). 
Combinatorial chemistry and its efficacy for screening, in which I see Jerry 
was personally successful, is only one, limited domain of chemistry.

5. Jerry's critique of Loet is perhaps justified, and I will pass on the 
debate as whether chemoinformatics is a part of information theory or not. 
My view is that talking about the "identity of matter" and three-tailed 
Peircean graphs is diversionary. Jerry understates Rosen's contribution, 
even if he is correct about the chemoinformatics aspects. Rosen's work is 
valuable because his vision went beyond thermodynamic considerations to 
concepts like anticipation which underlie some current systems approaches.

6. To conclude, the "physical basis of chemical logic" may be well 
understood, but this "chemical logic" is an abstract, partial model of what 
is going on. It cannot be an adequate basis for the informational processes 
that occur in real chemical systems.

7. Loet and I can get back to a "debate" about morphology and information 
theory on other grounds. As a reminder, on Oct. 14 Loet wrote: "It seems to 
me that the issue of morphology and its evolution is a red herring in a 
discussion about information theory. A shape (e.g., a network) can be 
described as a graph or also numerically. This numerical description can 
easily be evaluated in terms of information theory. Information theory, also 
offers options to develop measures for the evolution over time (such as, 
Kullback-Leibler divergence, cf. Theil (1972).)" This statement implies that 
morphology or shapes cannot be dynamic processes and, again, if not fully 
describable mathematically are "lost" to information theory. This takes us 
back to the question of the primacy of quantitative over qualitative 
properties, or, better, over qualitative + quantitative properties. This for 
me is the real area for discussion, and points to the need for both lines 
being pursued, without excluding either.

Thank you and best wishes,

Joseph

----- Original Message - 
From: "Michel Petitjean" 
To: 
Sent: Monday, October 17, 2011 1:39 PM
Subject: Re: [Fis] Chemo-informatics as the source of morphogenesis - both 
practical and logical.


Dear Loet and dear Jerry,

2011/10/17 Loet Leydesdorff :
> Dear Jerry,
>> ...
> 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")
> ...

If (1) can be answered, thus chemoinformation enters in the field of
information theory. That would be a very strong result.
Alas, I am afraid that it can't. Sets of flexible 3D realized graphs
seem hard to give raise ti bits of information.
But I didn't proved that. Who knows, if a good mathematician can
answer to (1), it would be a great advance in the field.
And I did not speak about (2) ...

Best,
Michel.
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Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-18 Thread Gavin Ritz
 

 

Karl

Dear Loet and Jerry,

let me comment on your interesting exchange:

you write:
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.

 



contribution:
In the Addition Table one sees specific arrangements and configurations.
There is no red herring in natural numbers.

you write:
 the strength of Shannon's information theory is its grounding in
probability theory. This is more abstract and not field specific.

contribution:
The Order Theory (not, as was suggested, Category Theory) 

The entire study needs a category theory construct.

 

that one can read off a Table of a+b=c has its grounding in axiomatic logic.


This is only one part of the map in category theory (arrow) you need the
object (set of variables maybe in this case) to complete the map.

 

And the bookkeeping laws of associations and identity take care of the
arrangements and configurations. The probability part is then taken care of
by the subobject classifier (truth value object) of a Topos.

 

That is even more basic - fundamental - than probability theory. Natural
numbers are even more abstract and less field specific than probability
theory.

This can be taken care of by the "limit" axiom of a Topos (quantity).



you write:
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.

That's why one can use category theory.

 

Regards

Gavin



contribution:
The specifics of morphology and spatial arrangements have not first to be
rewritten numerically. They are alrady there as implications of a+b=c. One
only needs to do a few steps, namely:
1. create 136 additions (between 1+1=2 and 16+16=32)
2. create 9 aspects of the additions
(a,b,a+b,2b-a,b-a,3b-2a,2a-b.17-(a+b),3a-2b)
3. order /sort/ the 136 additions on two of the aspects
4. reorder /resort/ the additions into a distinct sorting order
5. use 2x3 and 2x2 sorting orders as spatial grids (Euclid coordinates)
6. observe the interdependence between morphology and spatial arrangements.

So, what you have asked for is already there for the doing of the exercise
of building the Addition Table.
Karl

2011/10/17 Loet Leydesdorff 

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 Dal

Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-18 Thread karl javorszky
Dear Loet and Jerry,

let me comment on your interesting exchange:

you write:
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.

contribution:
In the Addition Table one sees specific arrangements and configurations.
There is no red herring in natural numbers.

you write:
 the strength of Shannon's information theory is its grounding in
probability theory. This is more abstract and not field specific.

contribution:
The Order Theory (not, as was suggested, Category Theory) that one can read
off a Table of a+b=c has its grounding in axiomatic logic. That is even more
basic - fundamental - than probability theory. Natural numbers are even more
abstract and less field specific than probability theory.

you write:
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.

contribution:
The specifics of morphology and spatial arrangements have not first to be
rewritten numerically. They are alrady there as implications of a+b=c. One
only needs to do a few steps, namely:
1. create 136 additions (between 1+1=2 and 16+16=32)
2. create 9 aspects of the additions
(a,b,a+b,2b-a,b-a,3b-2a,2a-b.17-(a+b),3a-2b)
3. order /sort/ the 136 additions on two of the aspects
4. reorder /resort/ the additions into a distinct sorting order
5. use 2x3 and 2x2 sorting orders as spatial grids (Euclid coordinates)
6. observe the interdependence between morphology and spatial arrangements.

So, what you have asked for is already there for the doing of the exercise
of building the Addition Table.
Karl

2011/10/17 Loet Leydesdorff 

> 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 sy

Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-17 Thread Michel Petitjean
Dear Loet and dear Jerry,

2011/10/17 Loet Leydesdorff :
> Dear Jerry,
>> ...
> 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")
> ...

If (1) can be answered, thus chemoinformation enters in the field of
information theory. That would be a very strong result.
Alas, I am afraid that it can't. Sets of flexible 3D realized graphs
seem hard to give raise ti bits of information.
But I didn't proved that. Who knows, if a good mathematician can
answer to (1), it would be a great advance in the field.
And I did not speak about (2) ...

Best,
Michel.
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Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-17 Thread Loet Leydesdorff
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 possib

[Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-16 Thread Jerry LR Chandler
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 "engineering" 
extension of the potential for simple combinatorics (graphs) of atomic numbers 
to generate sequences of subgraphs. Again, the "combinatorial explosion" rears 
it head. Each potential sequence has its own unique form.  The morphogenesis of 
spatial forms of matter is studied by the several methodologies, such as x-ray 
diffraction patterns.  

One example with which I have had several years of experience with is the 
development of a drug for epilepsy.  On average, between 1,000 and 10,000 
different unique structures were examined for each drug that eventually made it 
to market.  Chemo-informatics and biological assays and clinical trials were 
all critical components of the process. All three sorts of empirical studies 
were necessary to identify a useful medicine. The morphological form of the 
isomers are critical components of matching of 'drug' to  a 'receptor'. 

I bring this example to the discussion to illustrate the application of 
chemo-informatics as a practical way of sending messages to the human body. 
Such messages, contained within a mathematically-defined iconic form, are 
intimately interrelated to bio-informatics, the expression of forms of genetic 
information. 

Thus, Loet, I can not concur with your following assertions.
> 
> It seems to me that the issue of "morphology" and its evolution is a red 
> herring in a discussion about information theory. A shape (e.g., a network) 
> can be describe