[Fis] "The fiction of function".

Dear Igor:

The assertions in your post are very, very provocative.

Science and information theory have generated a number of symbol
systems in order to facilitate human communication.

At times, one symbol system expresses certain concepts more
efficiently than others. No one symbol system can be shown to be
superior to all others for all circumstances. The symbol system of
chemistry expresses empirical observations.

One must be aware that the objects of biology - the cellular parts
and pieces, exist. Living systems are composed from chemical
entities, not physical theories.

By exist, I mean an intimate association between the concept of
existence, the concept of properties and the concept of name. For
every chemical entity, the concept of existence is necessary in order
to assign properties. The assignment of a name depends on a logic
proof of the associations as exhibited by the properties. Chemical
proof theory is an exact accounting of positions of electrical
particles and a consistent grammar of composition.

 From the vantage point of these philosophical generalities, I
address particular points in the post.

> From: Igor Rojdestvenski
> To: Kevin Kirby (by way of Pedro Marijuan<marijuan@unizar.es>)
> Sent: Saturday, October 01, 2005 9:15 AM
> Subject: Re: [FIS] Re: What is information?
>
> Dear Kevin and others,
>
> Very interesting post, the more interesting to argue. The ribosome
> does not have a function. We assign its behavior a certain goal
> which we call "function". A very interesting treatise on this can
> be found at
>
> http://www.ncbi.nlm.nih.gov/entrez/utils/lofref.fcgi?
> PrId=3051&uid=14555626&db=PubMed&url=http://
> bioinformatics.oxfordjournals.org/cgi/pmidlookup?
> view=reprint&pmid=14555626
>
> The article is called "The fiction of function".
>
> The existence of a network in physical sense is also highly
> questionable.

Chemical networks are not physical networks. This is well known.
Chemical network terminology describes reaction sequences as directed
graphs, not mathematical functions.

> I may seem boringly formal, but as long as we do definitions here,
> we should be.

In the absence of a formal theory of chemistry, I do not know how we
could hope to do this.

> There are no metabolic networks in the Nature, but pools of
> interacting substances (molecules).

Metabolic networks are integrated over evolutionary time spans. The
concept of a "pool" is remote from the abstract concept of the
intimacy of dependencies within a metabolic network.

> Really physical is a molecule and interactions between the molecules.

I do not know the meaning of this sentence. Physical philosophy is
not a chemical object, is it?
> All the rest, like chains of reactions, metabolic networks and so
> on -- all this is our "model", our "explanation" certain chains of
> events and concomitant interactions.

The unity of life is not merely a local phenomenon, but comparable
dynamic flows distributed over comparable chemical structures.
Chemical structures are not variables nor do they correspond exactly
with the notion of mass. Mathematically, each structure is a
particular graph, not a point - mass. Each chemical structure is a
unique object.

I believe that one can accept the power of physical methods and
mathematics while preserving the empirical validity of chemistry and
biology. Is this hypothesis untenable from a physical view point?

> It is like in the world of Feynman diagrammes some diagrammes are
> called "watermelons" for their shape, but nobody expects them to
> really taste sweet and fruity.
>
>
I fail to see any similarity between the jargon of watermelons and
the logic of physics. perhaps you could explain this?

Cheers

jerry

>
Received on Fri Oct 7 07:07:10 2005