[Fis] DISCUSSION SESSION: BIOLOGIC

[Pedro C. Marijuan]

Dear FIS Colleagues,

Due to communication problems with Louis (he is attending a conference) 
I am attaching here his presentation. Well, if you have any trouble with 
it, we have uploaded the file in fis web pages too:

http://fis.sciforum.net/fis-discussion-sessions/

By clicking on Louis H. Kaufman session (highlighted in red) you can 
immediately obtain it.
Nevertheless, herewith below a selection of more general ideas from the 
paper. For those interested in previous FIS discussions related with the 
topic: biological information (19998), molecular recognition (2003), 
biomolecular networks (2005), chemical information (2011), etc. They can 
be found in the same above link.

Best greetings--Pedro

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*Biologic - An Introduction
*Louis H. Kaufman/

We explore the boundary shared by biology and formal systems.

/This essay is an introduction to my research on the mathematics of 
self-reference, self-replication
and its applications to molecular biology. This introduction is based on 
my paper [22] and the
reader is encouraged to examine that paper. Other relevant papers will 
be found in the bibliography
of this paper.

I will concentrate here on relationships of formal systems with biology. 
In particular, this
is a study of different forms and formalisms for replication. See 
previous papers by the author
[25, 24, 23]. We concentrate here on formal systems not only for the 
sake of showing how there is
a fundamental mathematical structure to biology, but also to consider 
and reconsider philosophical
and phenomenological points of view in relation to natural science and 
mathematics. The
relationship with phenomenology [37, 35, 36, 9, 1, 39] 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. Our
original point of departure was cybernetic epistemology [44, 43, 41, 34, 
12, 13, 14, 15, 16, 17,
18, 24, 23, 25] and it turns out that cybernetic epistemology has much 
to say about the relation of
the self to structures that may harbor a self. It has much to say about 
the interlacement of selves
and organisms. This study can be regarded as an initial exploration of 
this theme of mathematics,
formalities, selves and organisms - presented primarily from the point 
of view of cybernetic epistemology,
but with the intent that these points of view should be of interest to 
phenomenologists.
We hope to generate fruitful interdisciplinary discussion in this way.

Our point of view is structural. It is not intended to be 
reductionistic. There is a distinct
difference between building up structures in terms of principles and 
imagining that models of the
world are constructed from some sort of building-bricks. The author 
wishes to make this point
as early as possible because in mathematics one naturally generates 
hierarchies, but that does not
make the mathematician a reductionist. We think of geometry as the 
consequences of certain axioms
for the purpose of organizing our knowledge, not to insist that these 
axioms are in any way
other than logically prior to the theorems of the system. Just so, we 
look for fundamental patterns
from which certain complexes of phenomena and ideas can be organized. 
This does not entail
any assumption about “the world” or how the world may be built from 
parts. Such assumptions
are, for this author, useful only as partial forms of explanation...

...In living systems there is an essential circularity that is the 
living structure. Living systems
produce themselves from themselves and the materials and energy of the 
environment. There is
a strong contrast in how we avoid circularity in mathematics and how 
nature revels in biological
circularity. One meeting point of biology and mathematics is knot theory 
and topology. This is
no accident, since topology is indeed a controlled study of cycles and 
circularities in primarily
geometrical systems. In the end we arrive at a summary formalism, a 
chapter in boundary mathematics
(mathematics using directly the concept and notation of containers and 
delimiters of forms)...
/
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