[Fis] "How Molecules Became Signs": Models, Signs and Reality

[joe.brenner at bluewin.ch]

Dear Terry,
 I would like to join others in thanking you for this new statement
of your approach. As Karl wrote in his first comments of Feb. 21, “You give us insight into your epistemological system of
concepts”. But my first comment is a question: do you agree with this characterization
of your system as ‘epistemological’? Whether your answer is yes or no, it begs
the question of the ontology to which this epistemology might be related.
 As I read your article, I see it as constructed from three major
pieces, not totally commensurable with one another: 1) a discourse on models;
2) a discourse on signs; and 3) a most intriguing suggestion of the scientific relation
between structure and dynamics in proteins and the nucleic acids of which they
are constituted.
 I will start with 2): despite the presence of ‘signs’ in the title,
I consider that the paper amounts to a demonstration of the inability of semiosis
and semiotics to tell us anything novel about the world. Molecules may be signs
– of themselves – to the semiotician, but this concept has no purport to a
chemist like myself. A sign always refers to a reality of which it is a sign, and whose properties cannot be fully captured by the latter.
 Regarding 1), as you know, I have been familiar (and critical) of
the concept of autogenesis since it appeared in 2012. In particular, I have
argued that it is ipso facto inapplicable to real systems since no such
system starts without prior systems having had the potential for its
emergence and exists without having some potential for the emergence of
new systems. However, I was glad to see that you have now dealt with this
aspect by describing two additional forms of autogenesis, context-sensitive and
template-mediated in which “interaction constraints become offloaded onto a
molecular structure”. However, I find the last sentences on p. 18, although
correct, to be literally convoluted. Recursion inheres in physical, not only
semiotic processes due to their movement between potential and actual, and vice
versa.
 I conclude that interpretative processes, for all their
complex structure, are purely epistemological and do not bring additional support
to your conclusion on p. 21. For me, no further proof of principle of relationships
emerging from the ontological co-dependent dynamics of the real processes
involved is required. My approach thus fully supports the inversion of the
Crick central dogma as well as much else.
 As far as information is concerned, the Section starting on p. 14 –
>From Storage to Template to Information corresponds to my view except for the
phrase on p. 15 “polynucleotide molecules could evolve to serve semiotic as
well as energetic functions”. This reduces information to semiosis, whereas
the emphasis must in my view be on the energetic properties of information.
These for me include interaction constraints in their co-instantiation of
actuality and potentiality.
 If you will allow my view at least for discussion, you will see
that it has the dynamics necessary to handle more complex cognitive phenomena in
human and social systems. These would include not only recursion but stasis and
regression. Identification from an informational standpoint of the “molecules”
undergoing change in the corresponding processes could follow a model very
similar to yours.
 Thank you again and best wishes,
 Joseph
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