[Fis] Informational Bookkeeping

Wed Sep 17 12:39:04 CEST 2014

Dear Colleaugues,

The "bookkeeping" or "accounting" approach to theoretical genetics is the
application of the simple principle that one deals with a finite amount of
logical entities, which are numerically equivalent according to some
arithmetic rules.

In business accounting, the equivalence appears between the sums on both
sides of the ledger, in physics, one maintains that no matter or energy can
be created, and so forth.

In genetics, the equivalence means that there can be no more translatable
DNA sequences than livable organisms and no more livable organisms than
translatable DNA sequences. This means that the Grand Total of
possibilities must in all cases agree, like in business accounting the
Grand Total necessarily agrees, regardless of what has taken place in the
actual commerce.

Like the step-by-step realisation of the business idea in a day-by-day
commerce restricts the alternatives for a gain or loss in the accounting
period, the realisation of the perscription by the DNA by its translation
into a part of the more-dimensional entity that is the organism restricts
step-by-steps the reamining possibilities for the organism to have
properties. At the end, one arrives at the telomeres, which mean: no more
alternatives, this way of putting the equivalence has run out of
alternatives.

The funny thing with genetics is that Nature uses an accounting trick that
makes use of the interdependence between linear and non-linear assemblies
(that is: reading the symbols off an assembly one-after-the-other vs.
group-wise). The relevant interdependence is truly innovative accounting.
Nature needs this to produce that accounting paradox that variations and
mutations can both appear in the copying of information from the DNA to the
organism and from the organism to the DNA.

It is highly counter-intuitive to imagine copying from a data set into a
different data set and back in ways that are both injective and surjective,
and still not bijective, only more or less bijective.

The visualisation of the accounting trick can be seen at www.
http://oeis.org/A242615/a242615.pdf.

Karl

2014-09-15 14:07 GMT+02:00 Pedro C. Marijuan <pcmarijuan.iacs at aragon.es>:

> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> -------------------------------------------------
> 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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