Dear colleagues,
Both the extension & "intension" of Jerry's recent posting make quite
challenging the business of penning down a response... but here it is;
well, a few pills at least.
At 22:52 28/11/2005, you wrote:
>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.
In my view, what changed dramatically was not only the relationship with
numbers but, above all, the way to "validate" knowledge: from "disputatio"
to "experimentatio" (rhetorics becoming subsidiary to experimental
procedures--the big point of the scientific revolution). This point is not
trivial concerning our nascent field, as quite many parties disregard any
empirical grounding (abandoning the quest for "facts" to ingrain their
theoretical-doctrinary views). Given that, potentially, fis also implies a
new vision on info and knowledge, and the contemporary role of sciences at
the social realm, this may lead to fine-tune our views on what
thought-collectives actually do... in any case, the "mystification of
numbers" looks a very good point for future discussions.
> 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. )
I have had to drop very interesting paragraphs, rather unjustly, but
perhaps this is the right place to point at a relative absence: that the
whole bionetwork deals basically with self-production activities. The cell,
as Changeux put it, is but "an enormous factory" devoted to the production
of molecular machines. In the 70's it was argumented under the label of
"AUTOPIESIS" by Maturana and Varela, unfortunately they did not continue
the integration of new biomolecular facts and their synthesis was left
suffering the usual "premature closure" ailment, and somehow pretentious
and empty for our times. Thus, to continue with Jerry's taxonomy, the
problem is that the self-production network is a mere label for an enormous
landscape of molecular interactions and processes of quite a heterogeneous
nature. Let me take home the term "molecular landscape".
>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.
Excellent paragraphs! Perhaps I would encapsulate another conclusion too:
the whole transformations in the molecular landscapes within a cell are
demanding a vast collaboration of disciplinary fields which have to be
guided by new integrative abstractions.
>... 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.... 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!
>
>... "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.
Again I have dropped a lot of text --- well, maybe I am misunderstanding
the above, but if we retake the molecular landscape vision, or better, if
we transport ourselves in front of a "real" landscape, a beautiful natural
scenario, could we say about our verbal/scientific reports that "it is a
logical process of some sort of another." Nope. We would be forced to
heterogeneous descriptions, implying terribly different logics (even
"pictorial" ones).
To argue more on scientific matters, the logical schemes that work so well
in the "artificial" are based on a separation from the world of chemical
happenstance. Think on computers. Their design precludes the participation
of chemical processes and relies on solid state transistors that implement
electrically boolean networks. The topology of the implied connections is
awfully complex (the wiring of the LSI circuits, basically devoted to
interconnect masses of transistors through metallic bonding). In the
bionetwork self-production scheme, everything is connected potentially with
everything (around different 5.000 molecular types in a minimalist cell),
and the whole is capable to advance towards culminating a reproduction
cycle due to the "specificity" of compounds, each one being endowed with
"molecular recognition" capabilities. If we drop the specificity of
molecular recognition events, the cell disappears into a blob of gel.
>1. What is the nature of biological computations if atomic numbers are not
>arithmetic numbers?
A vast, general study of molecular recognition (Shu-Kun, Meggs, Carlton...
to name very few authors who have taken similar paths). And Jerry's own
texts these days are a very elegant contribution too.
>2. What are the consequences of atomic numbers for the computerization of
>chemical structures?
Necessary, but not sufficient ---atomic numbers are working in Mars, or the
Moon too... obviously no life there. Thus the conditions of the living
organization are situated far above atomic numbers --and my opinion is that
the origins of life is a monumentally unsolved scientific question
(curiously, some of Steve's points on science in the US may be taken the
other way around for the socio-political conditions in most European and
Asian countries).
>3, What is the appropriate language for describing the exchange of
>"knowledge" (molecular recognition) within a bionetwork?
As said, not done yet.
>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?
A change in view is needed. We are too dominated by ways of thinking that
put together the schemes of the artificial and of the natural ---under the
guidance of the former. The "semantic metabolism", to recreate an idea of
late Tom Stonier (exposed in this very list in the 90's, one of his last
writings!), occurs in our selves too; and it does not hinge on detached
processing but on "ingestion of signals", which alter the ongoing
relationships of cellular production / degradation of enzymes and proteins,
the advancement of cell cycles and checkpoints in a variety of tissues, of
neurotransmitters, modulators and neurohormones... the embodiment of our
perplexification capabilities. We are not "systems", we have not
"components", we do not perform detached "information
processing"... (the usage of "systems biology" in contemporary
bioinformatics is really an oxymoron).
Unfortunately I do not have the alternative wording for what occurs along
the bioinformational paths of adaptability, and am merely using the
"processual" term applied to life cycles (that which occurs when cells and
organisms "ingest" or "abduce" environmental "affordances"). Shouldn't
we
aspire to produce elegant terms and abstractions on how life thrives on
information? Aren't they badly needed?
Thanks, Jerry, for the really inspiring catalog of comments and questions.
A proper response would have needed far more time...
greetings
Pedro
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Received on Wed Dec 7 14:44:15 2005
