Re: Is FIS in semiotics?

Dear FISers,

I am introducing a few 'introns' (gulp, should I use 'exons' instead?)
within the James-John C exchange. They are also related to some aspects of
the Edwina-Jerry's mess.

>At 03:02 PM 01/07/02, James wrote:
>>
>>The main reason I introduced the point about enzymes being "fooled" by
>>pharmaceutical molecules (and, of course, by many natural ones, as
>>well), though, was to emphasize a point that is stressed in the
>>philosophical literature on biological functions. That is, that
>>normativity is of the essence. That is, for something to count as a
>>function in the proper (biological) sense of the word, there is
>>something that it is supposed to do, something that it can get either
>>right or wrong. In short, the concept of function entails that of
>>malfunction (as well as success, or correct function, of course).
>>

The right or wrong normativity for biomolecular function is more or less OK
in many cases, but it is far from being a general rule (and not at all THE
rule). For instance, what happens evolutionarily with the legion of
PARALOGOUS genes --those coming from e.g. duplications-- that are initially
'vacant' or idle, so 'unfunctional', and little by little acheive a new
specific function? Think on the mammals four batteries of homeogenes
against the ancestral background of just a single battery with less than
half dozen genes. In the vertebrate lineage there are strong evidences of
around 2 duplications of the ENTIRE GENOME; also in plants. IThis means
continents of supernumerary agents gradually (and saltatorily) evolving new
functionalities our from their initial unfunctioning. Besides, the
evolution of DNA regulatory cis-sequences, really crucial in eukaryots, is
based on the fact that the transcription factor will recognize the mutated
target sequence with slight changes in affinity / specificity. But slightly
different kinetics in the transcription of e.g. a selector gene in the
developmental process of a crucial tissue will bring amazing final
differences (eg, development of brain in homo / anthropoids). And needless
to argue about the really obscure ranges of functionality hidden in our
apparently noncoding DNA (95 % genome).

I
>>I wanted to make this point about function entailing malfunction because
>>I believe this is where the roots of "purpose" lie in biology (which you
>>were questioning). And insofar as information, properly speaking, must
>>be recognized as having a semantic component, and insofar as meaning is
>>likewise a normative and teleological concept, then I believe that the
>>roots of information lie in this same knot of problems, as well. In
>>sum, as I see it, all of our aporiae in theoretical biology revolve
>>around the ontological status of purpose and value.
>

I was discussing the above aspect not to run against your discussion of
biological purpose (I share your interest in naturalizing that concept,
which I also see very closely related with info conceptualization) but to
call the attention upon premature generalizations that actually leave on
the rack (proper idiom?) very strategic empirical items. In this case, it
is the really frequent 'fuzziness' of biological function. Its inherently
many-to-many mapping nature. So, robustness and resilience are emerging
properties that quite many, many signaling and metabolic, and
gene-expression circuits share. We can make an individual agent
'malfunction' (either totally, or, as mentioned, more or less, within a
very large variation domain). It does not matter. Quite frequently the
FUNCTIONAL CLUSTER which includes the agent will globally compensate (in
cancer, eg, a mutated Ras may be perfectly counteracted by a correct p53;
and if I am not wrong, p16 would compensate for both Ras and p53
simultaneous malfunction).

The point I want to make is the need for new interpretation schemes, mostly
BOTTOM UP inspired, and without excessive preconceptions or urges to proof
the validity of our a priori chosen theoretical views. The best example I
can think of (tomorrow I will try to continue with it) is the historical
invention of ZERO. It is not only a metaphor. Indeed, absences have not
been properly taken as ways of controlling biofunctionality (in your
constructive-degradative system do not care about idle presences, worry
about the important absences). Let me add that the idea of 'functional
voids' seems to me a necessary complement to the accompanying mechanistic
side of functional clusters control... together with many other
formal-non-formal exploratory attempts...

We are in a prediscovery phase, not in a post discovery one. So, the
discussion following largely TOP DOWN doctrines that reproduce endless
formal discussions on THE correct way to interpret info phenomena is for me
not much relevant (some spicy is always fine)...

Sorry, I have to leave--the bus is getting out right now!

Pedro
Received on Wed Jul 10 14:29:35 2002