[Fis] Informational Bookkeeping

[Pedro C. Marijuan]

Dear colleagues,

Continuing with bookkeeping and cycles, some further speculations could 
be made. Keeping in mind some of Terry Deacon's ideas -in order to make 
easy the initial considerations- we could say that the basic bookkeeping 
of an individual (enzymic) work cycle is an instance of "homeodynamics", 
where a orthograde process and a countergrade process are tied (eg, the 
favorable ATP hydrolysis propels most enzyme counter-current works). In 
the case of a whole cycle of reactions that involves numerous compounds 
(& their specific enzymes), this more complex instance probably 
represents a  "morphodynamic" exemplar. In both cases the thermodynamic 
and physico-chemical bookkeepings provide good sense on the system's 
evolution. Arguably, there are "proto-signals" such as enzyme effectors 
(activators & inhibitors) that impinge in the dynamics without 
apportioning any substantial energy; and in the reactions cycles there 
emerge complex systemic relationships with the overall system that may 
remarkably amplify or dampen the individual changes occurring within the 
cycle (via alterations in effectors, substrates or products). At the 
time being, not much informational saying; with considerable likelihood 
the max. entropy production is a good principle making sense of the 
overall bookkeeping results.

Then we go to the "autogenic" stage, where something else dominates the 
bookkeeping. We assume that the bacterial life cycle (and even more in 
the multicellular organism) implicitly takes along its selection process 
a new reference--the "fitness" referent as the gauging instrument to 
ascertain what is the impact of the individual change (or received 
communication) along the self-production process. Signals from the 
environment (communication) encounter a life cycle in progress.  And 
each signal "means" molecularly what it produces in metabolic and gene 
expression changes. We hide from view (and the cell itself, at least 
behaviorally) the enormous complexity inside. Glucose "means" good for 
the cycle, while strong pH "means" bad;  there is evolutionary blueprint 
& connectivity imprinted that applies instantly throughout the signaling 
system that controls the movement of E. coli: it automatically 
orientates towards high fitness places. This fitness bookkeeping is 
verosimil and quite useful, even more in the case of complex 
multicellular organisms. See a recent comment in Nature (pp. 138-9, 512, 
August 2014) "What females really want" referred to fruit flies' complex 
courtship, on how male signals become indicators of "fitness" but they 
are meant within each particular life-cycle state and past history of 
the female.

To summarize this new autogenic stage, both the organismic 
self-production process and the communication (signaling system) that we 
find in action appear as bona fide "informational". And this term looks 
more congenial and simplifying than the rather cumbersome nomenclature 
that Deacon continues to develop. So we may depart from his terms as we 
are finally in the province of information science, and subsequently a 
perspective similar to the previous one might have currency in more and 
more informational self-constructions around. Thus, in the human life 
cycle we find quite many new bookkeeping terms, such as "profit", 
"utility", "value", etc. which may be interpreted as new instances to 
hide inner complexity and facilitate behavior in progress by the 
individual within highly sophisticate cultural constraints...

The bookkeeping and the cycle, as Koichiro emphasized, become quite 
fertile a place to reflect. But please take all the above speculations 
"cum grano salis", with the customary grain of salt --or spoonful!

best --Pedro


Pedro C. Marijuan wrote:
> Dear Koichiro,
>
> Nice that you have left your hibernation for a while!
> I quite agree with your excellent comment. On the one side the 
> bookkeeping of molecules has plenty of tools to ascertain what is 
> happening with each other in an uncorrelated way (state variables, 
> force/mass/ energy, entropy, enthalpy, Helmholtz free energy, Gibbs 
> free energy, etc.). But trying to synchronize their happenstances 
> becomes daunting: tough external constraints have to be entered in 
> order to keep a decent bookkeeping and make useful workings. And this 
> is where the bookkeeping of life starts: building upon cycles as basic 
> functional constraints: the work cycle of the individual enzyme, the 
> multiple reaction cycles, the life cycle of the whole bacterium or the 
> unicellular. In aggregate, the life cycle is the great referent of 
> biological information, and the source of its "meaning". It is this 
> different inner reference what makes invalid the maximum entropy 
> principle for life--sometimes it is followed, sometimes it is just the 
> opposite. It depends on the intertwining of external "signals" and on 
> the advancement of the self-production process.
> And with this I have already spent my "two cents" for the week...
>
> best
>
> --Pedro
>
> PS. After the crash the list has more complex management (that I 
> cannot handle very well) and message processing. People willing to 
> check whether their messages have passed or not may directly check 
> at:  http://listas.unizar.es/pipermail/fis/
>
> Koichiro Matsuno wrote:
>> At 9:14 PM 09/05/2014, Pedro wrote:
>>
>> Who knows, focusing on varieties of bookkeeping might be quite 
>> productive!
>>
>> [KM] Pedro, your kick was loud enough to waken me up from my long
>> hibernation. Suppose there are many things popping up here and there
>> concurrently with no synchronization among them on the spot. Then, we 
>> would
>> be totally at a loss what to do when asked to tell what is going on 
>> there.
>> One plan as a last resort would be to make an appeal to a scheme of
>> synchronization even if conceivable out of the blue. One candidate 
>> would be
>> Bob U's energy, in reference to which we can safely say which are
>> synchronized and which are sequential. One more candidate of this 
>> sort might
>> be a reaction cycle of a natural origin, since any component reaction 
>> going
>> round the cycle is ipso facto made synchronous with the occurrence of 
>> the
>> cycle itself.   
>>    Koichiro
>>
>>
>>
>>
>>
>>   
>
>


-- 
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Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta X
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.iacs at aragon.es
http://sites.google.com/site/pedrocmarijuan/
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