[Fis] Biologic - at the interface between biology, topology, logic and cybernetics (by Lou Kauffman)

[Karl Javorszky]

(DNA in its logical habitat 2025 01 06)



Dear Lou,

Your excellent opening statement about how the strands of the DNA are
arranged and how some physiological relations are relevant while it
duplicates, and more, are an enlightening recapitulation of what applied
science has so far discovered.

Due to limits of space, it is impractical to insert your whole essay here.
To cut it short, all your *assertions* are welcomed as true statements.
Specifically, thank you for the concise formulation:

*Mathematical biology is concerned with … structures leading to recursive
generation of structures from themselves and from their environments.*



Your *questions*:

*What is the form of biology? Is there a biology of form?*

Your  own definition above shows biology as a subject of logic to be a
collection of sentences describing circular procedures (that are themselves
subject to periodic processes) determining positions of a limited number of
diverse elements in several dimensions in such a fashion that both
longitudinal and transversal additions add up to such an extent of an
expression of order which is within limits, thus one kind of reading being
a feedback and restriction set of parameters for the other reading. The
concept ‘Order’ denotes sentences that are statements concurrently true
about the properties of an element and its position among its peers.

*The relationship with phenomenology comes about in the questions that
arise about the nature of the observer in relation to the observed that
arise in philosophy, but also in science in the very act of determining the
context and models upon which it shall be based. *

New in the 21st century is that we have now access to tabulating machines
that show us every possible way of combining and recombining the relatively
few diverse elements that are the logical building blocks of our picture of
biology. If we understand the nature of the structural bias* that separates
a human observer from a mechanical observer, and manage to eliminate the
effects of the artefact, there is no need to complicate the observation of
the self-referencing interdependence by investigating whether the observer
is a human, an alien or a machine. (* Cortex imagines using one, Sumerian *N,
*the underlying neurology uses *Nsimilarities, Ndiversities* which is the
correct way within the habitat.)

*What is a part that a world might be built from it?*

Why don’t we try to use the symbols *a, b *to depict two otherwise unknown
entities that through their interactions create structures that can be read
horizontally, vertically, etc.?

*The comparison made, what questions do you ask? … What are the
physical/biological roots of the DNA replication?*

This here group of learned friends has no access to and no knowledge to
operate the apparats applied science uses. Our task is to understand the
data processing procedures that make a linear pointer fragment into an
array of search criteria.

*One wants to know how far a world-view can be extended before it
disintegrates.*

There is a very prosaic answer to that. Once one starts investigating how
more than 137.03 idealized distinct elements interact, one has left reality
as we refer to it in the context of biology. Nature has caught a very small
little opportunity where the number of elements, how these elements are
similar among each other and how these elements are diverse among each
other shows a slight discongruence-based variability. Nature has delineated
a number theoretical habitat (a Nirvana for logical primitives /© M.
Abundis/). Let us name it the Eddington habitat. Within it, objects can be
referenced both sequentially and categorically.

*Temporality may look like a tragedy for the classical mathematics, but it
is exactly what interests us when studying biology.*

Exactly. There are several clocks running within each living animal, these
are coordinated and synchronized (if all goes well) by the Metronome of
that individual organism. The metronomes of the organisms should better be
aligned, being subject to a pressure of evolution, with the periodicity
that blesses and torments the habitat (like the periodicities of Moon,
Earth, Sun affect our real existing Nirvana).

The temporal aspect is useful in establishing the metronome that is valid
within the habitat. In whichever way we rotate *a + b = c *the longest
cycle we find is 129 long. This is practical, because in the grand context
of things, both that is true for either 32 or 97 (two of the Zaragoza
constants, where *n? ~ n!)*, needs to be true also if both are the case.
The metronome cycle is a half-twin of the folding cycle which is 128
elements long. There are only 122 elements that are included in both. There
exists – in a logical-objective reality – an individuating tick along a
counting of recurrent states of the metronome that refers to both temporal
and spatial coordinates of an occurrence. Iterations are unavoidable. There
exist structural and interlude cycles that maintain the overall tact
locally congruent during iteration.



*To close*, let me add a parable about an old man coming back from fishing
and a young fashion influencer at the imperial court. They both miss
something that has not survived contact with reality: the old man the flesh
of his merlin, and the young girl the clothes of the emperor.

*They both agree* that the learned and respected tailors of the emperor
have problems stitching clothes together out of pieces that are serrated
differently.
*The young girl says*: had the right honorable learned tailors not used the
big scissors first to cut out units that can be stitched together, but had
used the appropriate small scissors to prepare parts that will fit together
into a suit, they would have incurred the opportunity costs of not
producing economically with identical units and pay the running costs of
maintaining a complicated catalogue of which cuts fit together with which
cuts, but would gain the benefits of having a variant of suits that really
adapt to the Emperor’s everchanging body.
*To which the old man says*, yes there are costs to generalizing. As they
use the big scissors to establish *a + b = c *they disregard the snippets
that fall off as both of *a, b *suffers being robbed of their individuality
as *a resp. b*. These are distances that get unaccounted for in the
intuitive, generalized, practical Sumerian way of cutting the cloth of
continuity. The Accadians, may they rest in peace, collected these
different snippets and had built their own ideology based on them. The
present day learned tailors point to various part-entities that they give
different names to and would never want to look under the carpet of
generalization into *c *where they had swept the snippets of the
particularities of *a, b.* The snippets are arrays of distances that
accumulate over the history of the elements involved and in the grand
ledger. You cannot make particularities disappear just by not wanting to
see them, concentrating on the general forms of particularities. It will
blow up in your face if you manipulate the accounting to make  arrays of
distances go away, for reasons of ease and practicability of accounting.
*The young girl says: *One should alert the tailors that they are horsing
around with snippets they themselves have generated.

*The old man says: *Do that and see what happens to your social reputation.
Tales will be written about you.



Thank you again for bringing us up to the present state of knowledge in the
wet sciences and for posing the right questions on the solvable riddle,
what such an assembly would look like, in which coincidences and
occurrences were indexed in several aspects concurrently.



Karl
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