Re: Next stage: Q4, Q5, Q6

Dear John,

Thanks for the questions --and for the insightful preamble. Maybe that we
maintain a nice and open-minded atmosphere is as much important as the
contents we exchange... Well, here there are my replies to your new Qs:

>R. Lahoz-Beltra and Vieri Di Paola say:
>
>================================================
>2. The 'hardware + software' dualism leads to a misleading conception
>of cell. In cells 'biomolecule + function' are inseparable elements in
>contrast with computers. For instance, it is possible to have a computer
>without operating system and software. Of course, it is not useful but in
>cells it is impossible to have biomolecules without biological function.
>================================================
>
>Q4. How important is this difference, and does it have any bearing on the
>issue of whether a formal system can have a semantics that is not implied
>externally?

Very important, in my opinion. Variants on this question-problem may be at
the very heart of different schools of thought: functionalism, behaviorism,
cognitivism, artificial intelligence --in what extent one can extract the
'essential' programs and run them in quite different hardwares and
'wetwares'? In the cellular context the authors (Rafael and Vieri) address
the theme, I believe that Michael Conrad produced the most elaborate views
--biological processing vs. electronic computing-- implying the interplay
of picturability, programmability, evolvability, and processing
architecture. His tradeoff principle represents a very elegant summary.

Besides, the enormous difference in complexity depth of the elementary
components (just comparing enzymes and transistors) has to be emphasized.
There is very efficient models which capture the temporal behavior of the
electronic agents (down to the quantum level) while the converse happens
with proteinaceous stuff. Its function is non-picturable at the quantum
level, as it implies an immense panoply of Coulombian, electro-weak
(dipole, van der Waals, London...), and entropy related forces (eg,
interaction with water). Actually enzymes themselves force us, as limited
scientific observers, to the heterogenous 'superposition' of a variety of
disciplinary approaches: biochemistry, bioenergetics, classical enzymology,
molecular biology, bioinformatics, molecular dynamics, quantum models. And
let us add degradation phenomena (and protein folding).

So, honestly we should admit that characterizing the bioinfo function
posses us a very tough problem. In comparison with its docile and
formalizable electronic counterpart, the 'structural' info dynamics of the
living cell is not properly solved yet. Its relevant 'formal' (?? --I do
not find a better adjective) properties have not been elaborated yet. And,
yes, I believe this relates to the biological fabrication of meaning (in a
strong sense, implying sentience & 'qualia').

>Jerry LR Chandler says:
>
>================================================
>A central hypothesis is that correspondence relations between algebraic
>species and organic species generate a robust basis for message
>specificity and sensitivity. I presuppose that category theory is a
>suitable mathematical framework for a general theory of communication.
>================================================
>
>Q5. Must this correspondence be such that organic species resemble
>computational "agents" as used in Alife programs, in which communication
>is fully formalized in terms of explicit rules ("methods")?

I am friendly with Jerry's goals: interrelating structure with
communication. Cellularly, the items produced as external 'messengers' (or
internally as 'second messengers') are not independent of the ongoing
structural chemical processes. But adumbrating that interrelationship
becomes, again, a pretty difficult task--it obviously relates to the
previous comments on Q4, although let me remark that I am not implying any
intrinsic mysticality or impossibility of the task. It looks to me that it
implies a very serious interdisciplinary challenge and a necessary change
in mind from reductionist towards integrationist stances in larger segments
of the scientific community (eg, today maybe we are paying the easy
dismissal of classical physiology integrative constructs). At the time
being we must consider Alife agents, category theory, multidimensional
partitions... we have to try with every available tool in order to
conceptually capture the 'vertical order' that supports cellular
organization and multicellular and organismic life, our own nervous system
included.

Having said that, let me remind John H's very recent posting on the
vertical info view 'cells (organisms) / firms / states' --well I have
smuggled-in organisms. Shouldn't we attempt a combined
inter-theoretical-exploration too? I mean, we could learn a little bit
about the way the cellular structure organizes its turnover and renovation
of elements and relates with its environment, also by looking on how our
own nervous system organizes its exploration (and abduction) upon the
environmental info items or affordances in order to build a decent life
(Terry's posting!), or how the accounting system of a company extracts a
few info items upon a terrible complex background of micro-operations, or
the way a country 'representatives' decide that it is this or that piece of
info the relevant item to be included into the agenda of a planetary
conference or to be thrown upon a generous dose of 'ordnance'.

In sum, a family of related theoretical problems at multiple 'vertical'
levels are receiving presently a very clumsy contemplation by our social
system of knowledge. We really miss the cogent info sci perspective, not as
the final TOE (theor. of everything) but just as another little voice
singing its part within the global choir of the sciences (a childish voice,
of course).

>Christophe Menant says:
>
>================================================
>A meaning is an information representing the connection between an
>incident information and the constraint of the system.
>
>More completely:
>"A meaning is a meaningful information that is created by a system
>submitted to a constraint when it receives an external information that
>has a connection with the constraint. The meaning is formed of the
>connection existing between the incident information and the constraint of
>the system. The function of the meaningful information is to participate
>to the determination of an action that will be implemented in order to
>satisfy the constraint of the system".
>================================================
>
>Q6. Is this characterization of meaning formalizable, and in particular is
>the notion of the constraint of the system formalizable?

As I had replied to Cristophe in a previous message I am very intrigued
with 'the constraint' notion as an interlevel ascending tool (by the way,
perhaps using 'constraints' would be better). They appear to me as
computational surrogates to climb, or to descend, the commands from an
adjacent level of complexity description. Usually, our sciences establish
new 'principles' and ad hoc disciplines in order to contemplate the
emerging existentialities at higher or lower levels. If so, the
'principles' or 'constraints' or 'reglaments' or 'constitutions' matter
quite a lot for our understanding of the emerging info entities...

I hope the responses were not too long.

Have a good weekend.

Pedro
Received on Fri Jul 5 14:14:42 2002