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 described as a graph or also numerically. 1. Please provide a reference for the assertion that the conformation of protein structures can be calculated from the chemical graph of the protein. 2. Are you mixing continuous and discrete concepts? > 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).) > > As formalisms from information theory can be applied to any system of > substantive communication, they can also be applied on system of formal > communication, such as sets of coordinates. 3. Metabolic networks are chemo-informatic message networks, generated from biochemical - genetic information. Are you excluding metabolic networks as systems of substantive communication? 4. ditto for mental networks? > > Best wishes, > Loet Loet, your point of view, from my perspective, is based on a generalized inductive argument on formalisms. If a generalized inductive argument for chemo-informatics existed, there would be no need for the particular inductive logic used to construct chemical forms - for the morphogenesis of chemical conformations from atomic numbers. At the abstract logical root, the difference between chemo-informatics and Shannon informatics lies in the empirical basis of induction. The generalized inductive argument of Shannon encodes all messages as numbers and then encodes the numbers into electrical signals. Message transmission in Shannon theory relies on several generalized inductions related to electrical properties of matter. The decoding of such messages inverts the order of the encoding, regenerating the original message. Chemo-informatics lacks any generalized encoding. (Dalton's law would not be an essential part of chemo-informatics if such a generalized encoding existed.) Chemo-informatics is based on the logic of the identity of matter. This concept of identity of a labeled bipartite graph, the basic object of chemo-informatics is not the concept of identity as used in Shannon information. A simple example of the mathematical distinction between chemo-informatics and Shannon informatics is crystal clear. The arithmetic operation of multiplication is integral to Shannon informatics. The arithmetic operation of multiplication on the atomic numbers generates nonsense - if one multiples 2 (helium) by 3 (lithium), one does not get 6 (carbon). The fundamental logical distinction that Dalton introduced over one hundred years ago was a new form of inductive mathematics. The development of the chemical sciences and molecular biology and personalized medicine follows from this form of inductive logic. C. S. Peirce developed a framework for relational logic from the recognition that a thing can be a source of representation and that the method of representation is the source of the form, the source of the message. Chemo-informatics follows Peirce in the sense that it is necessary to distinguish among the symbol for networks of atomic numbers, the indexes for molecules and the iconic representations of the forms of molecules. The physical basis of chemical logic is now well understood in terms of the international system of units. Each atomic number is a different electrical electrical category. Conjoining two different electrical objects creates a new electrical object, a new category. Conjoining N different atomic numbers (a molecular formula) creates the combinatorial explosions, often loosely referred to as the isomer problems. The same N atomic numbers can be combined into N' (N' >>> N) iconic forms. Each of the N' iconic forms has the same mass and the same electrical particles, but each has different identity as a consequence of the arrangements of the parts of the whole. The alternative ways of connecting numbers into graphs lies at the heart of the chemo-informatics challenge. Robert Rosen recognized that a profound difference existed between "natural systems" and formal systems. He postulated that different forms of representation were needed. Rosen's theory, unfortunately, completely excluded chemo-informatics from consideration, he chose to place his logical analysis of biology on thermodynamic considerations. As a consequence, no path from Rosen's system of thought to chemo-informatics has been, to the best of my knowledge, found. The differences in the notion of artificial addition and natural addition of numbers make such a path from Rosen's conjectures to chemo-informatics appear impossible. In summary: Chemo-informatics differs from Shannon informatics as the natural atomic numbers differ from artificial numbers abstracted from the properties of the integers. (By artificial numbers I am referring to the generalized inductive abstractions of irrational, imaginary, and transcendental objects associated with the continuum of the real number line.) Cheers Jerry (Footnote: Greetings to all my friends on the list. I have moved to Minnesota and been in reclusion for several months, completing the logic of the perplex number system. From my reclusion, I am optimistic about a springtime eclosion. :-) :-) :-) ) _______________________________________________ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
