[Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.
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.
> 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 ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.
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. ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.
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.
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.
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. ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.
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.
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