[Fis] Resetting of FIS List (Keep this message)

[Pedro C. Marijuan]

Dear FISers,

The message below tells that the List has to follow the recent European 
Law on Data Protection. It means that everyone has to confirm and give 
explicit consent to participate in the list. I understand that today or 
during next days you will receive a confirmation message (probably in 
Spanish?) and you have to respond affirmatively before 15 June. In any 
case, after 15 June you will be able to subscribe by yourself in the 
address below:


https://listas.unizar.es/cgi-bin/mailman/listinfo/fis

This week I am starting a trip and conference ("Code Biology") and will 
correspond rather poorly.

Sorry for the inconveniences.
All the best--Pedro


 Mensaje reenviado 
Asunto: Responsable de lista fis : consentimiento RGPD obligatorio
Fecha:  Fri, 01 Jun 2018 14:50:29 +0200
De: nore...@unizar.es
Para:   pcmarijuan.i...@aragon.es



Nos dirigimos a usted como administrador de la lista fis

Las leyes de protección de datos de la UE están cambiando y esto afectará a la 
forma en que nos comunicamos.

Conforme a lo establecido en el nuevo Reglamento General de Protección de Datos 
necesitamos recabar consentimiento explícito de cada miembro de la lista fis 
para mantener el contacto a través de ella.

El lunes 4 de junio vamos a solicitárselo para que nos lo comuniquen antes del 
próximo 15 de junio. Los usuarios que no lo den serán eliminados de ella.

En caso de que el usuario no confirme su suscripción antes de la fecha indicada 
o cuando retire su consentimiento, eliminaremos de inmediato sus datos 
personales de la lista. No obstante, podrá suscribirse en el futuro a través de 
la lista fis (https://listas.unizar.es/cgi-bin/mailman/listinfo/fis).

Indicamos a los usuarios que sus datos personales no se cederán a terceros, ni 
se harán transferencias de los mismos a terceros países.

A partir del 15 de junio el responsable no podrá suscribir a nuevos miembros en 
su lista, únicamente podrá enviar invitaciones y aceptar las suscripciones que 
reciba de los usuarios.

Les recordamos que tampoco se pueden utilizar los datos personales de las 
personas registradas para fines diferentes a los de la lista en que están 
suscritos.

Puede consultar nuestra política de privacidad accediendo al siguiente enlace: 
http://www.unizar.es/politica-de-privacidad

La Universidad de Zaragoza cuenta con una página de Protección de Datos en la 
que incluye legislación, información y modelos: 
https://protecciondatos.unizar.es/



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Re: [Fis] If always n>0 why we need log

[Pedro C. Marijuan]

Sorry Sung, you know about the rules of engagement in this list... you 
have gone to 5 msgs. And that means one and half weeks of sanction. Even 
more after having warned you privately several times.
Anyhow, tomorrow I will make public an embarrassing bureaucratic 
procedure that the list has to suffer next days.

Best wishes--Pedro

El 03/06/2018 a las 19:42, Sungchul Ji escribió:

Hi Krassimir,

I think the main reason that we express 'information'  as a 
logarithmic function of the number of choices available, n, may 
be because the human brain finds it easier to remember (and 
communicate and reason with)  10 than  100, or 100 than 
10. . . . 0, etc.


All the best.

Sung




*From:* Krassimir Markov 
*Sent:* Sunday, June 3, 2018 12:06 PM
*To:* Foundation of Information Science
*Cc:* Sungchul Ji
*Subject:* If always n>0 why we need log
Dear Sung,

A simple question:

If always n>0 why we need log in

I = -log_2(m/n) = - log_2 (m) + log_2(n)   (1)

Friendly greetings

Krassimir




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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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-



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[Fis] Abiding by the rule

[Pedro C. Marijuan]

Participants are reminded about the limit of two messages per 
week--those not abiding are sanctioned offline.


Best--Pedro

 
-

Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group

pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] TOWARDS A NEW SESSION

[Pedro C. Marijuan]

Dear FIS Colleagues,

A very interesting discussion theme has been proposed by Mark Burgin 
--he will post at his early convenience.
Thanks are due to Alberto for his "dataism" piece. Quite probably we 
will need to revisit that theme, as it is gaining increasing momentum in 
present "information societies", in science as well as in everyday life...

Thanks also to Sung for his interesting viewpoint and references.

Best wishes to all,
--Pedro

 
-

Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-



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Re: [Fis] Is Dataism the end of classical hypothesis-driven research and the beginning of data-correlation-driven research?

[Pedro C. Marijuan]

Thanks Plamen, very interesting references and comments. There are many 
new avenues opening around data, from nasty ones (recent politics) to 
the economic, biomedical and scientific in general. It is a very 
important "information" theme of our time. Perhaps I disagree that deep 
learning could not develop similar processes to what we call intuition 
and analogy. If we situate ourselves within one particular neuron of our 
nervous system, those intuitions and analogies passing by are but more 
of the same: electro-molecular mechanisms and topology. Plus "something" 
else, of course... Let us continue the discussion after Easter vacations.

Best--Pedro

El 27/03/2018 a las 14:25, Dr. Plamen L. Simeonov escribió:


Dear Alberto, Pedro and All,

I could not follow this discussion in the past 3 weeks since I was 
engaged in other activities, but again ß with respect to my other 
question regarding the value of the FIS exchange as a forum and 
virtual currency, please find below two articles (December 2017) that 
could inspire your imagination:



https://www.nature.com/articles/d41586-017-08589-4 



http://www.europarl.europa.eu/RegData/etudes/IDAN/2017/581948/EPRS_IDA(2017)581948_EN.pdf 




I believe that data-driven research is just a fashion and that new 
commercial trends like cryptocurrency technology will be driven by 
regulation to a different direction, namely the one that is the 
discussed in the articles above. Indeed, the whole idea is not new at 
all. I actually found myself as the inventor of a precursor solution 
to blockchain back in 1999. And this idea alone stems from analogies I 
have driven from active networks and attributed graph grammars back in 
the 1980ies..., long before there was an Internet Protocol at all. So, 
honestly, I do not believe that data will be the top of the knowledge 
pyramid, and to have data we create the models and invent theories 
also by analogy and intuition, the methods that folks like Poincare 
and Einstein were working with pen and paper on. Computers and AI/ML 
will remain just tools, but they will never become wise as people or 
even animals. By the way, we are planning another special issue on 
Integral Biomathics in 2019 in the footsteps of the previous ones in 
2013, 2015 and 2017 --


2017 JPBMB Focused Issue on Integral Biomathics: The Necessary 
Conjunction of Western and Eastern Thought Traditions for Exploring 
the Nature of Mind and Life 
 *


* free promotional access to all focused issue articles until June 
20th, 2018


and devoted to animal and natural intelligence. I just wish to inform 
you earlier about this. An official call will be distributed in this 
forum later this year.


I wish you a Happy Easter!

All the best.

Plamen





On Sat, Mar 10, 2018 at 11:46 PM, Alberto J. Schuhmacher 
> wrote:


Dear Plamen, Pedro and Collegues,

I am enjoying a lot this forum.

I absolutely foresee Scientific Blockchain as a continuously
growing list of scientific records and contributions (blocks)
linked and secured using cryptography, somehow a kind of peer
reviewed process. Would you be able to publish it in a journal
based on their scientific value?

Dataist-machines won chess players but still are learning Science,
they are completing their “Bachelor”. Their use for biomedical
applications is growing everyday. For example, their accuracy for
in biomedical imaging diagnosis will be similar to humans soon.
For other applications, such as genetic predisposition and health
prediction/prognosis the conversion to a fanatic dataism may abuse
of “predictivity” and forget the relevance of the
organism-environment. It will take some time for machines to
complete their “Philosophical Doctorate”. Technology could be
ready soon for data driven hypothesis but our knowledge of
fundamental aspects of life are still weak.

All the best,
AJ

El 10-03-2018 21:05, PEDRO CLEMENTE MARIJUAN FERNANDEZ escribió:


Dear Plamen and Colleagues,

If it can be feasible, I would very much welcome what you
propose. Yes, it would be great developing a general articulation
amongst all our exchanges. Roughly, I feel that a fundamental
nucleous of neatly conceptualized information is still evading
us, but outside that nucleous, and somehow emanating from it,
there are different branches and sub-branches in quite different
elaboration degrees and massively crisscrossing and intermingling
their contents. A six-pointed star, for instance, radiating from
its inner fusion the computational, physical, biological,
neuronal, social, and economic. 

Re: [Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear FISers,

Apart from the very interesting critique by Sungchul, there is an 
intriguing comment I would like to make respect the new evolutionary 
views presented. I will risk to discuss on a topic, topology, too far 
from my usual fields. So I trust the benevolence of FIS readers.


As far as we have been told, the germ line cells, the gametes, contain 
each one a DNA algorithmic "hemi-description" of the future 
multicellular ensemble organism. When fertilization occurs, the two 
different hemi-descriptions are put together in a unique, complete DNA 
algorithm. Then, paying attention to the BUT (Borsuk Ulam Theorem) 
insights presented in this list by Tozzi and Peters, we might interpret 
that two 3D projections are fused into a 4D one. The gain in information 
is evident, and it is this gain what makes possible the construction of 
the multicellular ensemble. That 4D structures and dynamics are present 
in the multicellular may be evidenced by the fractality of most of that 
construction (systems such as circulatory, pulmonary, renal, brain, 
etc.). Actually the presence of 4D dynamics in cerebral information 
processing has been repeatedly highlighted by different authors. Now, 
what John Torday argues, is that an essential mission of the 
multicellular construct becomes the gathering of adaptive epigenetic 
marks editing the 3D hemi-descriptions, so that the future ensemble may 
be better adapted to its environment...


In the extent to which the above has any cogency, there emerges a new 
disciplinary front to check the enigmatic continuation of the 
gamete/zigote/organism along the eons of life.


Best--Pedro


El 24/01/2018 a las 15:33, JOHN TORDAY escribió:
Dear FIS colleagues, Pedro has pointed out some rookie errors in my 
post. You can find my paper "From cholesterol to consciousness" at 
https://www.ncbi.nlm.nih.gov/pubmed/28830682. Hopefully you have 
access to the paper without having to buy it. If you don't please 
email me at jtor...@ucla.edu <mailto:jtor...@ucla.edu> and i will send 
you a copy. As for addressing consciousness at the cellular/molecular 
level, I understand that the mental health professionals have a 
problem with consciousness beyond the brain/mind. But I consider that 
anthropocentric. Just like every other aspect of our physiology, 
consciousness is the endogenization of environmental factors. In the 
case of consciousness it is the vertical integration of calcium fluxes 
for all of the cells of the organism. All organisms are conscious of 
their surroundings to one degree or another. And self-reference is, in 
my opinion, a result of the Singularity/Big Bang, so it would apply to 
all organisms, unicellular and multicellular alike. I refer to the 
experiments of Helmut Plattner, exposing paramecia to glucose. When 
the paramecium homes in on the sugar its 'nervous system' of calcium 
flux lights up just like the neurons in our brains. And as to the 
extrapolation from individual consciousness to cosmology based on the 
homologies between Quantum Mechanics and Evolutionary Biology, I see 
that as a means of fully understanding the significance of 
consciousness as the connection between the animate and inanimate as 
one continuous Singularity. It is only in that way that the true 
nature of Nature can be fully understood. As for smaller increments, 
the work of Daniel Fels on electromagnetic communication between cells 
may hold the answer 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793142/).


Best, John

On Wed, Jan 24, 2018 at 5:41 AM, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:


Dear John and FIS colleagues,

It was nice hearing your response. For technical reasons of the
server, _attachments are unwelcome_ (and often directly rejected).
Send please a web address where interested people can download
your document. Also, it is better if you send directly your
response to FIS list (_*fis@listas.unizar.es
<mailto:fis@listas.unizar.es>*_). About your content, I see a
couple of problems introducing "consciousness" at the
cellular/molecular level. For this term has a very definite
meaning in the /ad hoc/ research that is taken place during last
decades. Conflating it with basic cellular processes may not be
necessary, given that other terms (more realistic ones?) are
available. For instance, I referred to self-referential cognition.
In any case, I agree that classical autopoiesis  falls too short
of what is needed... Besides, about the cosmological relationship
with fundamental physics, is it a convenient step? Does it
introduce a premature closure in the bio-informational thinking
process?

Best--Pedro


El 22/01/2018 a las 16:02, JOHN TORDAY escribió:

Dear FISers, I greatly appreciate Pedro's comments regarding my
New Year Lecture. I fully agree with his comment " That

Re: [Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear John and FIS colleagues,

It was nice hearing your response. For technical reasons of the server, 
_attachments are unwelcome_ (and often directly rejected). Send please a 
web address where interested people can download your document. Also, it 
is better if you send directly your response to FIS list 
(_*fis@listas.unizar.es*_). About your content, I see a couple of 
problems introducing "consciousness" at the cellular/molecular level. 
For this term has a very definite meaning in the /ad hoc/ research that 
is taken place during last decades. Conflating it with basic cellular 
processes may not be necessary, given that other terms (more realistic 
ones?) are available. For instance, I referred to self-referential 
cognition. In any case, I agree that classical autopoiesis  falls too 
short of what is needed... Besides, about the cosmological relationship 
with fundamental physics, is it a convenient step? Does it introduce a 
premature closure in the bio-informational thinking process?


Best--Pedro

El 22/01/2018 a las 16:02, JOHN TORDAY escribió:
Dear FISers, I greatly appreciate Pedro's comments regarding my New 
Year Lecture. I fully agree with his comment " That life's physiology 
is based on the conjunction of a few principles: neguentropy, 
chemiosmosis, and homeostasis-homeorhesis" applies to non-living 
states too. I did not intend to make that statement exclusive, and if 
it sounded like that Pedro's clarification is important. In fact have 
just published a paper entitled "Quantum Mechanics Predicts 
Evolutionary Biology" which is predicated on the hypothesis that 
self-referential self-organization is the result of 
the Singularity/Big Bang, Newton's Third Law of Thermodynamics that 
every action has an equal and opposite reaction. That idea would apply 
to both evolutionary biology and to balanced chemical reactions alike. 
As for the question of the emergence of self-referential consciousness 
'right at the beginning', I am in favor of that concept, as I have 
expressed it in a recent paper, entitled "From Cholesterol to 
Consciousness" (see attached) so I look forward to reading your 
comments about that idea as well, since it has the potential to fully 
integrate physics and biology in my humble opinion.


On Mon, Jan 22, 2018 at 4:01 AM, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:


Dear FISers,

Going to the extreme, I think this year opening lecture can be
summarized in three contentious points.

1. That life's physiology is based on the conjunction of a few
principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.

2. That communication (cell signaling) is an essential factor in
the multicellular evolution towards complexity.

3. That epigenetic inheritance and the obligate recursion to the
unicellular state become the basis of a new evolutionary theory.

I disagree with point 1, as I think some nonliving states could
also be characterized by those principles (eg, chemical
cycles/hypercycles in marine vents, and other outcomes derived
from "energy flows"); besides, some previous "info stuff" has to
be in place. Then I completely agree with point 2, for signaling
is not just another characteristic of the cell, it is "the"
eukaryotic trait par excellence.  And I am curious on how point 3
could be further substantiated... In this respect I recommend the
two papers that Bill sent to the list a few weeks ago. Do we need
to postulate the emergence of a form of "self-referential
cognition" right at the beginning?
Perhaps!

All the best--Pedro



El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest,
all of  which have all been occasioned by John Torday's profound
insights about the nature of evolutionary development in light of
the importance of cell-cell signaling and molecular biology. 
From the comments, it is clear that there is a strong impulse to

seek a means of integrating the role of symbiogenesis, viruses
and mobile elements, multilevel selection, niche construction,
genomic plasticity into a common narrative with an informational
perspective at its foundation.
In the spirit of that line of discussion, I am offering two
links that discuss evolution as an biologic information
management system. Some of this work shares direct commonality
with John's, since he and I are frequent collaborators.

http://www.mdpi.com/2079-7737/5/2/21/htm
<http://www.mdpi.com/2079-7737/5/2/21/htm>

https://www.sciencedirect.com/science/article/pii/S007961071730233X
<https://www.sciencedirect.com/science/article/pii/S007961071730233X>

Both of these articles can be considered as complem

Re: [Fis] Summing up: New Year Lecture--J.Torday

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: [Fis] Summing up: New Year Lecture
Fecha:  Mon, 22 Jan 2018 07:02:42 -0800
De: JOHN TORDAY <jtor...@ucla.edu>
Para:   Pedro C. Marijuan <pcmarijuan.i...@aragon.es>



Dear FISers, I greatly appreciate Pedro's comments regarding my New Year 
Lecture. I fully agree with his comment " That life's physiology is 
based on the conjunction of a few principles: neguentropy, chemiosmosis, 
and homeostasis-homeorhesis" applies to non-living states too. I did not 
intend to make that statement exclusive, and if it sounded like that 
Pedro's clarification is important. In fact have just published a paper 
entitled "Quantum Mechanics Predicts Evolutionary Biology" which is 
predicated on the hypothesis that self-referential self-organization is 
the result of the Singularity/Big Bang, Newton's Third Law of 
Thermodynamics that every action has an equal and opposite reaction. 
That idea would apply to both evolutionary biology and to balanced 
chemical reactions alike. As for the question of the emergence of 
self-referential consciousness 'right at the beginning', I am in favor 
of that concept, as I have expressed it in a recent paper, entitled 
"From Cholesterol to Consciousness" (see attached) so I look forward to 
reading your comments about that idea as well, since it has the 
potential to fully integrate physics and biology in my humble opinion.



On Mon, Jan 22, 2018 at 4:01 AM, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:


   Dear FISers,

   Going to the extreme, I think this year opening lecture can be
   summarized in three contentious points.

   1. That life's physiology is based on the conjunction of a few
   principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.

   2. That communication (cell signaling) is an essential factor in the
   multicellular evolution towards complexity.

   3. That epigenetic inheritance and the obligate recursion to the
   unicellular state become the basis of a new evolutionary theory.

   I disagree with point 1, as I think some nonliving states could also
   be characterized by those principles (eg, chemical
   cycles/hypercycles in marine vents, and other outcomes derived from
   "energy flows"); besides, some previous "info stuff" has to be in
   place. Then I completely agree with point 2, for signaling is not
   just another characteristic of the cell, it is "the" eukaryotic
   trait par excellence.  And I am curious on how point 3 could be
   further substantiated... In this respect I recommend the two papers
   that Bill sent to the list a few weeks ago. Do we need to postulate
   the emergence of a form of "self-referential cognition" right at the
   beginning?
   Perhaps!

   All the best--Pedro



   El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest,
all of  which have all been occasioned by John Torday's profound
insights about the nature of evolutionary development in light of
the importance of cell-cell signaling and molecular biology.  From
the comments, it is clear that there is a strong impulse to seek a
means of integrating the role of symbiogenesis, viruses and mobile
elements, multilevel selection, niche construction, genomic
plasticity into a common narrative with an informational
perspective at its foundation.
In the spirit of that line of discussion, I am offering two
links that discuss evolution as an biologic information management
system. Some of this work shares direct commonality with John's,
since he and I are frequent collaborators.

http://www.mdpi.com/2079-7737/5/2/21/htm
<http://www.mdpi.com/2079-7737/5/2/21/htm>

https://www.sciencedirect.com/science/article/pii/S007961071730233X
<https://www.sciencedirect.com/science/article/pii/S007961071730233X>

Both of these articles can be considered as complementary to
Pedro's very fine article, 'How prokaryotes ‘encode’ their
environment: Systemic tools for organizing the information flow',
which is in BioSystems.

I am grateful to John for inviting me to participate in the forum
and to Pedro for encouraging me to share these manuscripts.

Best regards,
Bill

William B. Miller, Jr., M.D.
602-463-5236 <tel:%28602%29%20463-5236>
wbmill...@cox.net <mailto:wbmill...@cox.net>


   -- 
   -

   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 0
   50009 Zaragoza, Spain
   Tfno.+34 976 71 3526 <tel:+34%20976%2071%2035%2026>  (& 6818)
   pcmarijuan.i.

[Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear FISers,

Going to the extreme, I think this year opening lecture can be 
summarized in three contentious points.


1. That life's physiology is based on the conjunction of a few 
principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.


2. That communication (cell signaling) is an essential factor in the 
multicellular evolution towards complexity.


3. That epigenetic inheritance and the obligate recursion to the 
unicellular state become the basis of a new evolutionary theory.


I disagree with point 1, as I think some nonliving states could also be 
characterized by those principles (eg, chemical cycles/hypercycles in 
marine vents, and other outcomes derived from "energy flows"); besides, 
some previous "info stuff" has to be in place. Then I completely agree 
with point 2, for signaling is not just another characteristic of the 
cell, it is "the" eukaryotic trait par excellence.  And I am curious on 
how point 3 could be further substantiated... In this respect I 
recommend the two papers that Bill sent to the list a few weeks ago. Do 
we need to postulate the emergence of a form of "self-referential 
cognition" right at the beginning?

Perhaps!

All the best--Pedro



El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest, all 
of  which have all been occasioned by John Torday's profound insights 
about the nature of evolutionary development in light of the 
importance of cell-cell signaling and molecular biology.  From the 
comments, it is clear that there is a strong impulse to seek a means 
of integrating the role of symbiogenesis, viruses and mobile elements, 
multilevel selection, niche construction, genomic plasticity into a 
common narrative with an informational perspective at its foundation.
In the spirit of that line of discussion, I am offering two links 
that discuss evolution as an biologic information management system. 
Some of this work shares direct commonality with John's, since he and 
I are frequent collaborators.


http://www.mdpi.com/2079-7737/5/2/21/htm

https://www.sciencedirect.com/science/article/pii/S007961071730233X

Both of these articles can be considered as complementary to Pedro's 
very fine article, 'How prokaryotes ‘encode’ their environment: 
Systemic tools for organizing the information flow', which is in 
BioSystems.


I am grateful to John for inviting me to participate in the forum and 
to Pedro for encouraging me to share these manuscripts.


Best regards,
Bill

William B. Miller, Jr., M.D.
602-463-5236
wbmill...@cox.net


--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Code Biology

[Pedro C. Marijuan]

 Dear FISers, this Conference in Code Biology may be of interest to 
some parties. It will be in beautiful Granada (Spain), next June. 
Although the deadline for abstract submission is too close, there would 
be a longer term if requested to the organizers.


I hpe to see you there. Best--Pedro

--



*Fifth International Conference in Code Biology*





/Call for Papers /

The /International Conferences in Code Biology/ aim at bringing together 
scholars and researchers who are interested in the study of all codes of 
life, from the genetic code to the codes of culture.


The /Fifth International Conference in Code Biology/ will take place in 
Granada (Spain)from 5 to 9 June 2018. The Conference will host 
individual talks, poster sessions, a roundtable discussion and the 
Annual General Assembly of the Code Biology Society.


People who wish to deliver individual talks are invited to email an 
Abstract of between 200-500 words to granada-abstra...@codebiology.org 



Abstracts should be sent as one-page files written in a format such as 
.doc or .rtf (no PDF please).


The deadline for Abstract submission is *15 January 2018*.

Earlier submission is highly recommended.

More details are available in the Conference homepage

http://www.codebiology.org/conferences/Granada2018/

Looking forward to receiving your Abstract and to seeing you in Granada

/Julyan Cartwright, Marcello Barbieri and Jannie Hofmeyr/

Julyan Cartwright

/Local Conference organizer /
Instituto Andaluz de Ciencias de la Tierra (IACT) CSIC- Universidad de 
Granada

Av. de las Palmeras, 4.
18100 Armilla, Granada, Spain
julyan.cartwri...@csic.es //

Marcello Barbieri and Jannie Hofmeyr

/On behalf of the Code Biology Society/


--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] New Year Lecture

[Pedro C. Marijuan]

Dear  Soeren and Colleagues,

The symbiogenesis theme (Margulis' endosymbiotic theory) is one of the 
aspects to reconsider/reenter into the basically evo-info (if I may say) 
novissima synthesis. Margulis views were received in the 70's and 80's 
with tremendous hostility from the Neo-Darwinian orthodoxy. After a long 
series of turmoils it was accepted in many realms, particularly in 
popular science and textbooks industry, and even by the always reluctant 
Neo-Darwinians. Paradoxically in recent times the bioinformatic and omic 
research on the origins of eukaryotes has put into question basic tenets 
of that theory. The "deep sequencing" research on protein families has 
also be problematic for symbiogenesis. It does not mean that it is 
wrong, but that it is more complicated than previously thought... That 
is my opinion at least. In the present discussion, however, there are 
very knowledgeable parties that can give more specific arguments about that.


Talking about Neo-Darwinians, the paragraph from John Torday that I 
highlighted (see at the bottom) reminds me strongly from that other from 
Richard Dawkins' (in The Selfish Gene):



 /“We are survival machines – robot vehicles blindly programmed to
 preserve the selfish molecules known as genes. This is a truth which
 still fills me with astonishment.”/

If we compare both paragraphs, the essential difference relies on 
information. Torday's unicells develop not really multicell robots, but 
info agents that collect information  about the environment, including 
the whole elements of the niche (i.e., including in the human case from 
the "microbiome" to the "sociotype"). And fortunately the emphasis on 
"selfishness" has disappeared. Perhaps one of the consequences of 
Margulis work has been ideological, implying some general opening of 
views. Besides that, we should pay close attention to some "invisible 
threads" inside/outside those robots, like puppet strings: let me 
emphasize the enormous evolutionary importance of viruses in eukaryotic 
origins and evolution, and in epigenetic phenomena. Really masterminding 
the whole topological/architectural molecular processes.


In any event, for the purpose of the discussion, I bet that the new 
synthesis, the "novissimima", has to be evo-info... or it won't be!

(spoonful of salt, please)
All the best--Pedro


El 06/01/2018 a las 18:05, Søren Brier escribió:


Dear Pedro

I am wondering why no one seems to think that Lynn Margulis’ theory 
that cell organelles such as mitochondria and chloroplasts were once 
independent bacteria  is a crucial contribution to cell biology in 
evolution theory ?


Best wishes

Søren Brier

2017 JPBMB Focused Issue on Integral Biomathics: The Necessary 
Conjunction of Western and Eastern Thought Traditions for Exploring 
the Nature of Mind and Life 
  *


* free promotional access to all focused issue articles until June 
20th 2018


*From:*Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *PEDRO 
CLEMENTE MARIJUAN FERNANDEZ

*Sent:* 5. januar 2018 14:40
*To:* JOHN TORDAY ; fis@listas.unizar.es
*Subject:* Re: [Fis] New Year Lecture

head>

Dear John and FIS Colleagues,

Many thanks for this opening text of the NY Lecture. Indeed 
you have presented us an intricate panorama on one of the most obscure 
scientific problems of our time: the central theory of biology. As you 
say, we find with astonishment that there is literally no cell biology 
in evolution theory. And I would ad that there is no "information 
biology" either. A central theory becomes sort of a big Hall, where 
plenty of disciplinary corridors converge and later criss-cross among 
themselves. Darwinian theory is not that common hall for the really 
big, big science domain of biology. What are or where are the elements 
to rebuild the common Hall of the biological domain? I quote from your 
opening text:


*/"It is as if the unicellular state delegates its progeny to interact 
with the environment as agents, collecting data to inform the 
recapitulating unicell of ecological changes that are occurring. 
Through the acquisition and filtering of epigenetic marks via meiosis, 
fertilization, and embryogenesis, even on into adulthood, where the 
endocrine system dictates the length and depth of the stages of the 
life cycle, now known to be under epigenetic control, the unicell 
remains in effective synchrony with environmental changes."/*


It is really brilliant: a heads up reversal perspective. I think out 
of these ideas there are plenty of disciplinary excursions to make. 
One is "informational", another "topological". Putting together two 
different algorithmic descriptions and making them to build a torus 
(i.e., gastrula") as a universal departure for multicellularity also 
reminds the ideas of Stuart Pivart ("Omnia Ex Torus") about the 
primordials of multicellularity and the role of mechanical forces in 
the 

[Fis] Reflections on Evolution Theory, by J. S. Torday

[Pedro C. Marijuan]

­Given that the archive system does not preserve the attached files, 
I include herewith the whole text of the NY Lecture


Best--Pedro

---


New Year Essay for FIS

*Reflections on Evolution Theory. J. S. Torday*

1. *BRIEF CRITICISM of Current Evolution Theory***


When I think of evolutionary biology I think of Paul Gauguin’s 
painting“Where Do We Come From? What Are We? Where Are We Going 
”. 
These questions arise from time to time. In a sense, Darwin’s reply was 
to free us from The Great Chain of Being, only to leave us in limbo with 
metaphors like random mutation and Natural Selection, which are 
scientifically untestable and unrefutable. I seriously began addressing 
this problem about 20 years ago, having come across a new addition to 
the Modern Synthesis, the application of developmental biology to 
evolution theory, or EvoDevo. Thinking that the evolutionists had 
discovered the kind of science being done by me and my peers on the 
cell-cell communication mechanisms that mediate embryogenesis. Only to 
find that _there is literally no cell biology in evolution theory*^1 *_. 
This gap in the Evolutionary Biology literature is apparently the result 
of a historic glitch, the evolutionists relinquishing the work being 
done by Haeckel (‘Ontogeny Recapitulates Phylogeny’) and Spemann 
(‘Organizer’ hypothesis) at the end of the 19^th Century for want of 
mechanisms for these concepts that would advance the field of 
Evolutionary Biology. Instead, the evolutionists embraced genetics as 
their means of promoting evolution science. **


In retrospect, that was an unfortunate decision since embryogenesis is 
the only mechanism we know of that generates form and function, which is 
the essence of evolutionary change. But the mechanism of embryogenesis 
through growth factor signaling between cells would have to wait until 
the mid-20^th Century. Having made one of the original observations in 
support of cell-cell signaling and lung development, after 50 years of 
investigation we had assembled a working model of lung alveolar 
structure and function in 2007 *^2 *, employing dynamic space-time 
mechanisms of cell-cell signaling necessary for alveolar formation and 
function. Such a deep, transcendent perspective on the origins of 
biologic gas-exchange, referring all the way back to the cellular 
adaptation to gravity, begged the question as to how and why this 
mechanism evolved. So I decided to apply what I knew about lung 
development, phylogeny and pathophysiology at the cellular-molecular 
level as a means of deconvoluting lung evolution *^3 *.


**

*2.**EPIGENESIS: new findings***

Such musings about the cellular origins of the organ of gas-exchange 
were further advanced by the discovery in our laboratory that the cause 
of childhood asthma was epigenetic *^4 *. Exposure of pregnant rats to 
nicotine, the biologically active ingredient in cigarette smoke that 
causes asthma, could induce this disease molecularly, cellularly and 
phenotypically for at least three generations, opening up to new ideas 
about how organisms directly inherit genetic traits from their 
environment, as first suggested by Jean-Baptiste Lamarck in the 18^th 
Century. The prospect of epigenetic inheritance being a major effector 
of evolution gave rise to a novel way of thinking about evolution, not 
as the Darwinian merging of gene pools for reproduction, but as a 
heritable change in DNA readout, particularly with reference to The 
First Principles of Physiology- negentropy, chemiosmosis and 
homeostasis-homeorhesis- that emerged from the cellular approach to the 
mechanism of evolutionary adaptation. Again, because there is such a 
breadth and depth of knowledge of lung biology across species in 
combination with lung pathobiology, it became apparent that there was a 
causal relationship between geochemical changes during the Earth’s 
history and their affects on the evolution of gas-exchange, reinforcing 
the idea that evolution was non-random and that the forces of evolution 
were those of Nature- gravity, gases, ions, heavy metals. By reducing 
the phenotypes of development and phylogeny to their cellular-molecular 
elements in relationship to what was occurring in the environment, a 
narrative for evolution could be formed *^5 *.


*3. EPIGENESIS: its evolutionary significance *

For example, recent data on the history of oxygen levels in the 
atmosphere have made it apparent that they have not gone up gradually, 
but have gone up and down fairly dramatically, varying between 15 and 
35% over the last 

[Fis] Season Greetings / Merry Christmas

[Pedro C. Marijuan]

Dear FIS Colleagues,

Herewith the customary Christmas scene at El Pilar Basilica of Zaragoza.
It is a really beautiful place that you should visit... I promise not to 
be a bad amphitryon ;)


As for the next sessions, we will have the traditional New Year Lecture, 
and then another two sessions on data-driven science and on 
combinatorial logicsin biological information.


Have a Merry Christmas and a Happy New Year!

All the best--Pedro


--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] Fwd: Re: Informatics of DNA (From Sungchul)

[Pedro C. Marijuan]

quot; completely at last?


I don't think so, because all genes carry information but not all 
information carriers are genes.



All the best.


Sung





*From:* Fis <fis-boun...@listas.unizar.es> on behalf of Xueshan Yan 
<y...@pku.edu.cn>

*Sent:* Thursday, November 30, 2017 8:35 AM
*To:* FIS Group
*Subject:* Re: [Fis] Informatics of DNA

Dear Sungchul,

1. I highly appreciate your informational parsing on cell language and 
the comparative study of cell language and human language. By the end of 
last century, the main topics of (Human) Linguistics have been basically 
completed. It is not known whether human language study can get any 
inspiration from cell language study.


2. What kind of information definition and principle(s) have you got 
from the cell language study? To what extent are they applicable to 
other information fields? Exactly, your conclusions are mainly from the 
analysis of genetic cell. Among the biological information, the second 
major field of information application is neural cell. Are they 
effective in Neuroscience?


3. At the macro level, in your seven (six) steps of information flow 
scheme, we can consider all the content as "cell information / genetic 
information". But on the step 6, what you call it: Cell Functions→Human 
Behaviors, they transform cell information / genetic information into 
human information. If some information can be understood by a cell, it 
must not be understood by a (human) brain, and vice versa. How do you 
think of it?


4. In your information flow scheme of 
DNA→pre-mRNA→mRNA→proteins→IDS→Cell Functions→Human Behaviors, should 
the leftmost DNA be molecule? So far, we have seen that many researches 
thought that there are communication between molecules. From your 
research experience, are there any real examples of information 
communication took place between molecules?


5. Before 1952, the concept of "information" was rarely used in the 
works of Genetics. After Molecular Genetics, or after Crick's "central 
dogma", in Genetics research, many places used to use "gene" were 
replaced by "information". Do you think is it feasible to replace all 
"gene" with "information" completely at last?


Best wishes,

Xueshan

*From:*fis-boun...@listas.unizar.es 
[mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Pedro C. Marijuan

*Sent:* Wednesday, November 29, 2017 9:41 PM
*To:* 'fis' <fis@listas.unizar.es>
*Subject:* [Fis] Informatics of DNA (Sungchul Ji)

Hi FISers,

We may have in DNA a golden opportunity to define what *information* is.

*(1)*We now know that we are different from mice because our 
DNA sequences are different from those of mice [1].  That is, we are 
different from mice because our DNA carries different kinds (both 
with respect to /quality/ and /quantity/) of INFORMATIONfrom the mouse DNA:


”When it comes to protein-encoding genes, mice are 85% similar to 
humans.  For non-coding genes, it's only about 50%. The National Human 
Genome  Research Institute attributes this similarity to a shared 
ancestor about 80 million years ago.” 
http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5 
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thisisinsider.com%2Fcomparing-genetic-similarity-between-humans-and-other-things-2016-5=02%7C01%7Csji%40pharmacy.rutgers.edu%7C65e6d35da38f42a35c0608d537f75fe4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636476457988945872=jpAs7QGzTxeIP6qyqUV1jcjOk1OWwKERTNK8V%2FHrg0E%3D=0>


 (*2*) We also know that our properties or behaviors are at least 
in part determined by both DNA sequences (i.e., /genetics/) and the way 
they are turned on or off  by environment-sensitive cells constituting 
our body (i.e., /epigenetics/): We are the products of both our 
/genes/ and our /environment/.  The causal link between DNA and our 
behaviors can be briefly summarized as follows:


*1  2 3   
 456*


*DNA** > pre-mRNA -> mRNA -> proteins ->  IDS -> 
Cell Functions  -> Human Behaviors

^ |
| |
| 
  |
| 
|

   
|_|*

*7*

***Figure A. *The flow of genetic and epigenetic informations between 
DNA and the human behavior.  IDS stands for the /In//tracellular 
Dissipative Structures /(also called the /Dissipative Structures of 
Prigogine/) such as ion gradients across cell membranes and within the 
cytoplasm without any membrane barriers.  According to the Bhopalator, a 
molecular model of the living cell proposed in

[Fis] Info Meta-Science?

[Pedro C. Marijuan]

Dear FISers,

The recent message by Sung (& Karl), and a previous one by John T. make 
me the impression that what they are considering becomes closer to a 
meta-science of information rather than to the nucleus of a possible 
information science discipline. Sung's and John's views are widely 
different but both share a translation of fundamental principles of 
life's organization slanted towards the physical. A detailed critique of 
their contents is beyond the scope of the present message (previously, 
it is a must applauding the very brilliant contents both have developed 
in their respective research).


To the point: imagine we have a computer, a lap top, then--what should 
be the fundamental explanation of its functioning? It depends on the 
audience, of course. In principle, it does not make much sense to relate 
it to solid state physics and electronics unless we are talking to 
engineers working in VLSI design; rather, depending on the subjects' 
user level we will need some basics of programming and computer science 
(von Neumann scheme, Turing machine,  commercial informatics, etc.). 
Imagining now the parallel with the living cell, a sort of 
"reverse-engineering" approach to the informational scheme of the cell 
is needed, but a new one, as present views are still terribly biased by 
classical molecular biology (Crick's "Central Dogma"), shallow systems 
biology, and uninteresting Darwinian tenets. Without systematically 
entering the external "information flow", the inner informational 
architectures, the different codes related to the variety of functions, 
the structure of a life cycle, the molecular "meaning"of exchanged 
signals, etc., and tying good portions of all that stuff in formal 
terms, our explanation will  not be relevant in information terms.


Bioenergetics parties have already done their fundamental work. See for 
instance the arch in between the "energy flow" by Morowitz in the 60's 
and the "scaling" work by Geoffrey West in our times. Bio-information 
parties are far away from constituting a similar explanatory arch. And 
this is in my view the very nucleus of info sci as a consistent 
discipline. Beyond that we can enter many other theoretical tools 
already developed, and ascend in scales of complexity to the emerging 
communicational realms stemming out from Life. That some of the new 
communicational/semiotic/economic/cultural realms become more or less 
independent, at least in the way they are currently conceptualized, 
seems OK. We should not forget, however, that the human life cycle, with 
all its materiality and aspirations, stands at the very heart of 
everything we may exchange, from conversation to goods, to money, to 
artworks.


Otherwise, prematurely going towards a grand narrative connected with 
physics, or with maths, becomes close to a strategic error as we 
overextend a confuse info idea into a meta-science (taking this with a 
pinch of salt, as one never knows how our Gordian knot will be cut). 
Maybe it is better leaving the possible extensions/overextensions into 
the critical hands of information philosophy practitioners.


Best wishes

--Pedro

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Informatics of DNA (Sungchul Ji)

[Pedro C. Marijuan]

Message from Sungchul Ji

It was too heavy for the list server. You can see the complete version at:
http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf 



-

Hi FISers,


We may have in DNA a golden opportunity to define what *information* is.

*(1)*We now know that we are different from mice because our 
DNA sequences are different from those of mice [1].  That is, we are 
different from mice because our DNA carries different kinds (both 
with respect to /quality/ and /quantity/) of INFORMATION from the mouse DNA:


  ”When it comes to protein-encoding genes, mice are 85% 
similar to humans.  For non-coding genes, it's only about 50%. The 
National Human Genome  Research Institute attributes


  this similarity to a shared ancestor about 80 million years ago.” 
http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5


(*2*)  We also know that our properties or behaviors are at least 
in part determined by both DNA sequences (i.e., /genetics/) and the way 
they are turned on or off by environment-sensitive cells constituting 
our body (i.e., /epigenetics/): We are the products of both our 
/genes/ and our /environment/.  The causal link between DNA and our 
behaviors can be briefly summarized as follows:


*12 3  45
   6***


*DNA > pre-mRNA -> mRNA -> proteins ->  IDS -> Cell 
Functions  -> Human Behaviors

^ |
| |
| 
  |
| 
|

   
|_|*

*7*

**

*Figure A. *The flow of genetic and epigenetic informations between 
DNA and the human behavior. IDS stands for the /Intracellular 
Dissipative Structures /(also called the /Dissipative Structures of 
Prigogine/) such as ion gradients across cell membranes and within the 
cytoplasm without any membrane barriers.  According to the Bhopalator, a 
molecular model of the living cell proposed in 1985 in a meeting held 
in Bhopal, India, IDS's are postulated to be the immediate or the 
proximal causes for all cell functions [2].  The seven steps in the 
scheme are


*1* = transcription

*2* = splicing

*3* = translation (explained in (3) in more detail.)

*4* = enzyme catalysis

*5* = cell motions

*6* = body motions
*7* = the effect of human behavior or emotion on gene expression, e.g., 
see the phenomenon of the /c//onserved//t//ranscriptional //r//esponse 
to //a//dversity/ (CTRA) [3].


I hope that the /information flow scheme/ shown in* Figure A* can 
serve as a concrete example of information inaction as 
information scientists strive to come up with a generally acceptable 
definition of what INFORMATIONis.



(*3*)  Unlike in Steps 1 and 2 where the same kinds of molecules, i.e., 
the nucleic acids, DNA and RNA, directly interact (or contact or touch 
each other) via the Watson-Crick base-paring mechanism (see the second 
row in *Figure 1* below), in Step 3, there is no such direct interaction 
between mRNA and amino acids, but rather their interactions are mediated 
by tRNA which recognizes mRNA  at  its /a//nti-codon arm/ and amino 
acids at its 3/'-acceptor stem/, about 60 angstroms away (see the blue 
region in the mechanism of translation shown at 
https://www.quora.com/Why-are-ribosomes-so-important-in-plant-cells). 
The universality of the wave-particle duality demonstrated in [4] 
suggest that the tripartite coupling  among codon, anticodon, and amino 
acidin the ribosome-mRNA-tRNA complex may be mediated by /resonant 
vibrations/ or /standing waves/ (also called /resonance/ or /resonant 
waves/) generated within the complex, just as the vibratioal patterns 
located at distant regions on the Chladni (1756-1827)  plate [5, 6] are 
coordinated via resonance.


The Chladni plate [5, 6] is an ideal model for illustrating the role of 
resonance in molecular biology.  At a given resonance frequency, the 
particles on remote regions of the Chaldni plate are coordinated without 
any direct interactions between them and yet form ordered patterns.  To 
me this is similar to what happens in the ribosome system when a peptide 
molecule is synthesized; i.e, different components of the 
ribosome-mRNA-tRNA complex execute their motions that are so coordinated 
as to achieve the peptide synthesis.   The ribosome and the Chladni 
plate are compared at several levels in*T**able 1.*


.

Sungchul Ji 

The message continues at:
http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf 



--
-
Pedro C. Marijuán

[Fis] some notes

[Pedro C. Marijuan]

Dear All,

Herewith some notes on the exchanges of past weeks (sorry, I was away in 
bureaucratic tasks).


1. Agents & Information. There were very good insights exchanged; 
probably both terms make a fertile marriage. Actually I have been 
writing about "informational entities" or "subjects" as 
receivers/builders of information but taking into account the other 
disciplines around, "agents" look as the most natural companion of 
information. The only thing I don't quite like is that they usually 
appear as abstract, disembodied communicative entities that do not need 
self-producing. Their communication is free from whatever life 
maintenance...


2. Eigenvectors of communication. Taking the motif from Loet, and 
continuing with the above, could we say that the life cycle itself 
establishes the eigenvectors of communication? It is intriguing that 
maintenance, persistence, self-propagation are the essential motives of 
communication for whatever life entities (from bacteria to ourselves). 
With the complexity increase there appear new, more sophisticated 
directions, but the basic ones probably remain intact. What could be 
these essential directions of communication?


3. About logics in the pre-science, Joseph is quite right demanding that 
discussion to accompany principles or basic problems. Actually 
principles, rules, theories, etc. are interconnected or should be by a 
logic (or several logics?) in order to give validity and coherence to 
the different combinations of elements. For instance, in the 
biomolecular realm there is a fascinating interplay of activation and 
inhibition among the participating molecular partners (enzymes and 
proteins) as active elements.  I am not aware that classical ideas from 
Jacob (La Logique du vivant) have been sufficiently continued; it is not 
about Crick's Central Dogma but about the logic of pathways, circuits, 
modules, etc. Probably both Torday and Ji have their own ideas about 
that-- I would be curious to hear from them.


4. I loved Michel's response to Arturo's challenge. I think that the two 
"zeros" I mentioned days ago (the unsolved themes around the cycle and 
around the observer) imply both multidisciplinary thinking and 
philosophical speculation...


Best wishes--Pedro

-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] The two very important operations of Infos

[Pedro C. Marijuan]

Dear Loet and colleagues,

One of the advantages of a new discipline is the simplification of 
discourse, the creation of a new space where you can easily build new 
knowledge without copious management of other unnecessary, 
circumstantial ideas. I have already quoted in this list the famous 
quotation by Whitehead about the "mental liberation" in arithmetic that 
implied the use of zero. Something similar may happen nowadays 
concerning the wide reaching domains of information. But I see two 
problems about delineating the "information zero".
One, that life is not incorporated yet as the starting point of 
communication (I do not mean "biology"--rather it is each one's 
biography, historically and evolutionarily augmented/contemplated). At 
the end, every living agent "communicates" with other living agents, and 
the available tools to do that are signals that mean "portions" of its 
own life-cycle. We humans have shared sensorimotor tools that provide 
the common ground for our communication, for exporting those missing 
portions or needs in our lives. Formalizing the life cycle is quite 
problematic, however.
And the second "zero" concerns the need to constitute a new 
informational observer, endowed with the general mental characteristics 
required for information science. The observer of physics, chemistry, 
etc., is well equipped and we assume that his/her mind is properly 
"charged" with the corresponding principles, theories, experiences, etc. 
But in the case of info science, the topic matter is open-ended. What is 
the "charge" of this new observer? Depending on our specializations, we 
equip this observer with our preferred approach; so our unending back 
and forth. But many other knowledge bodies (or at least the 4-5 basic 
disciplines that Xueshan was commenting) may be needed to make sense of 
that particular informational/communicational phenomenon in cells, 
organisms, people, disciplines, enterprises, countries... If we accept 
this "ecumenical" contemplation of information science, how can that 
multi-observer be viable at all? Our cognitive limitations are so 
obvious... An elementary provisional solution (a pre-zero, a pre-science 
tool) for making it possible was suggested in those ten principles weeks 
ago.
In any case, I think these two absences or "zeroes" might be 
successfully filled in, without having to wait for too long.


Best wishes--Pedro

El 26/10/2017 a las 20:08, Loet Leydesdorff escribió:

Dear Terry and colleagues,

(...) , there cannot be interminable regress of this displacement to 
establish these norms. At some point normativity requires ontological 
grounding where the grounded normative relation is the preservation 
of the systemic physical properties that produce the norm-preserving 
dynamic.
I have problems with the words "ontological" and "physical" here, 
whereas I agree with the need of grounding the normative. Among human 
beings, this grounding of subjective normativity can be found in 
intersubjectivity. Whereas the subjective remains/cogitans/ (in 
doubt), the intersubjective can be considered as/cogitatum/ (the thing 
about which one remains in doubt).


For Descartes this/cogitatum/ is the Other of the/Cogito./ 
The/Cogito/ knows itself to be incomplete, and to be distinguished 
from what transcends it, the Transcendental or, in Descartes' 
terminology, God. (This is the ontological proof of God's presence. 
Kant showed that this proof does not hold: God cannot be proven to 
exist.) Husserl (1929) steps in on this point in the/Cartesian 
Meditations/: the/cogitatum/ which transcends us is intersubjectivity. 
It is not physical. The physical is/res extensa/, whereas this 
remains/res cogitans./ It cannot be retrieved, but one has reflexive 
access to it.


Interestingly, this philosophy provides Luhmann's point of departure. 
The intersubjective can be operationalized as (interhuman) 
communication. The codes in the communication can relatively be 
stabilized. One can use the metaphor of eigenvectors of a 
communication matrix. They remain our constructs, but they guide the 
communication. (Luhmann uses "eigenvalues", but that is a 
misunderstanding.) Using Parsons' idea of symbolic generalization of 
the codes of communication, one can continue this metaphor and 
consider other than the first eigenvector as "functional 
differentiations" which enable the communication to process more 
complexity. The model is derived from the /Trias Politica/: problems 
can be solved in one of the branches or the other. The normativity of 
the judiciary is different from the normativity of the legislative 
branch, but they both ground the normativity that guides us.


The sciences are then a way of communication; namely, scholarly 
communication about rationalized expectations. Scholarly communication 
is different from, for example, political communication. An agent 
("consciousness" in Luhmann's terminology) recombines reflexively and 
has to integrate because of 

[Fis] Fwd: Re: Verification of the Principle of Information Science--John Torday

[Pedro C. Marijuan]

(Message from John Torday --Note: neither the list nor the server do 
accept attachments)



 Mensaje reenviado 
Asunto: Re: [Fis] Verification of the Principle of Information Science
Fecha:  Thu, 19 Oct 2017 06:45:07 -0700
De: JOHN TORDAY <jtor...@ucla.edu>
Para:   Pedro C. Marijuan <pcmarijuan.i...@aragon.es>



Dear All, I feel like the beggar at the banquet, having arrived at the 
FIS of late in response to Pedro's invitation to participate, having 
reviewed our paper on 'ambiguity' in Progress in Biolphyics and 
Molecular Biology (see attached). In my deconvolution of evolution as 
all of biology (Dobzhansky), I have reduced the problem to the 
unicellular state as the arbiter of information and communication, 
dictated by The First Principles of Physiology- negative entropy, 
chemiosmosis and homeostasis. I arrived at that idea by following the 
process of evolution as ontogeny and phylogeny backwards from its most 
complex to its simplest state as a continuum, aided by the concept that 
evolution is a series of pre-adaptations, or exaptations or co-options. 
With that mind-set, the formation of the first cell from lipids immersed 
in water generated 'ambiguity' by maintaining a negative entropic free 
energy within itself in defiance of the external positive energy of the 
physical environment, and the Second Law of Thermodynamics. The 
iterative resolution of that ambiguous state of being is what we refer 
to as evolution. For me, information and communication are the keys, but 
they are not co-equals. I say that because in reducing the question of 
evolution to the single cell, I have been able to 'connect the dots' 
between biology and physics, such elements of Quantum Mechanics as 
non-localization and the Pauli Exclusion Principle being the basis for 
pleiotropy, the distribution of genetics throughout the organism, and 
The First Principles of Physiology, respectively. So now, thinking about 
the continuum from physics to biology, literally, the Big Bang generated 
the magnitude and direction of both the Cosmos and subsequently biology, 
i.e. life is a verb not a noun, a process, not a thing. For these 
reasons I place communication hierarchically 'above' information. 
Moreover, this perspective offers answers to the perennial questions as 
to how and why life is 'emergent and contingent'. The emergence is due 
to the pleiotropic property, the organism having the ability to retrieve 
'historic' genetic traits for novel purposes. And the contingence is on 
The First Principles of Physiology. So we exist between the boundaries 
of both deterministic Principles of Physiology and the Free Will 
conferred by homoestatic control, offering a range of set-points that 
may/not evolve when necessary, depending on the prevailing environmental 
conditions.


And by the way, this way of thinking plays into Pedro's comments about 
the impact of such thinking on society because in conceiving of the cell 
as the first Niche Construction (see attached), all that I have said 
above plays out as the way in which organisms interact with one another 
and with their environment based on self-referential self-organization, 
which is the basis for consciousness, all emanating from the Big Bang as 
their point source. So with all due respect, Information is the medium, 
but communication is in my opinion the message, not the other way 
around. I see this as a potential way of organize information in a 
contextually relevant way that is not anthropocentric, but objective, 
approximating David Bohm's 'implicate order'. Ciao for now, I 
hopeJohn Torday



On Thu, Oct 19, 2017 at 4:35 AM, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:


   Dear All,

   After Xueshan clarion call, I partially change what I was writing.
   Of course I have to thank him for his support of the 10 principles.
   Actually, in connection with the recent exchanges, particularly with
   Gordana's and John (Torday) posts, I was working in some ideas
   further related to the principles. On the one side the general view
   on the "new kind of natural science/philosophy" around information,
   and on the other side the transcendentalism of life... I think they
   also connect with Xueshan call of synthesis between info disciplines
   in his last paragraph. Trying to be concise I present herewith three
   points:

   First. "There is Life--and Information."
   Second. "We contemplate the World."
   Third. "The society around us."

   1. Life and Information: In biology, information is the new mantra.
   All kinds of scientific-technological-entrepreneurial gurus have
   proclaimed it, based on the revolutionary discoveries and gigantic
   bio-data accumulations. But scientifically, few people are trying to
   accommodate a new central theory of biology that could incorporate
   that new empirical reality of amaz

Re: [Fis] Verification of the Principle of Information Science

[Pedro C. Marijuan]

Dear All,

After Xueshan clarion call, I partially change what I was writing. Of 
course I have to thank him for his support of the 10 principles. 
Actually, in connection with the recent exchanges, particularly with 
Gordana's and John (Torday) posts, I was working in some ideas further 
related to the principles. On the one side the general view on the "new 
kind of natural science/philosophy" around information, and on the other 
side the transcendentalism of life... I think they also connect with 
Xueshan call of synthesis between info disciplines in his last 
paragraph. Trying to be concise I present herewith three points:


First. "There is Life--and Information."
Second. "We contemplate the World."
Third. "The society around us."

1. Life and Information: In biology, information is the new mantra. All 
kinds of scientific-technological-entrepreneurial gurus have proclaimed 
it, based on the revolutionary discoveries and gigantic bio-data 
accumulations. But scientifically, few people are trying to accommodate 
a new central theory of biology that could incorporate that new 
empirical reality of amazing complexity. In my own preliminary approach 
I describe how the simplest cells confront "the information flows" of 
their environment and couple them with the inner information flows 
related to their self-production, always doing it adaptively. Regarding 
the excellent work that John Torday has done on the evolutionary 
organizational achievements of multicellulars, as he mentioned, there 
are ample possibilities of mutual connection... Everything is rather  
preliminary but at least we can open the door so that other people 
behind could do it better.
In any case, around life and information, we see an amazing world of 
molecular complexity in action that contains some of the fundamentals of 
the new info perspective. The living cell can really "perceive" selected 
portions of the world around (information flow) and regularly intercepts 
them by means of its sensory apparatus (signaling system). Then it 
reacts adaptively, modifying its processes and structures according to 
inner stocks of permanent information (knowledge), sculpting a life 
cycle, also communicating with other living cells, and really building 
"molecular meaning" upon the received signals. Besides, the pervasive 
horizontal gene transfer in microbial ecosystems (phages, viruses, 
plasmids, sex...) has generated a collective multi-species assemblage or 
genuine "planetary library" of global molecular knowledge. It is not 
bombastic, as all planetary cycles of fundamental elements that sustain 
all present life are based on trillions of molecular machines of 
prokaryotes that have been churning around for eons. This Molecular 
Internet of sorts (Sorin Sonea dixit) was the beginning, and made 
possible so many things that now we may call in so many ways: 
evolvability, autopoiesis, agency, informational existence, ecological 
webs, ecosphere, GAIA, etc.
We may discuss quite legitimately about information physics, but 
clarifying first the scientific discourse about biological information 
by means of a new consistent viewpoint looks a priority (at the same 
level, at least).


2. Looking at the World: After the incredible complexification of life, 
nervous systems, etc. we, the improbable, the unexpected, are here. And 
like our humble bacterial ancestors, we have to confront the world for 
our individual living, and so we regularly contemplate and are immersed  
into the quasi-infinite information flows of the environment. But this 
time, by means of language, acting both as our new social communication 
tool and as an open-ended symbolic system, our collective capabilities 
of relating with the world have boomed. And historically we have 
developed those social repositories or stocks of knowledge we call 
science and all kinds of accompanying technological tools that allow us 
a new contemplation and action onto the world around. Now we can sense 
the most remote perceptions, we can colligate them with the different 
disciplines, and produce adaptive (or non adaptive) responses, with 
supposedly the final goal of advancing our lives both individually and 
collectively.
The new kind of science/philosophy to establish around this 
informational "looking at the world"  would demand a new "observer", in 
this case starting from a differentiated set of disciplinary principles 
of observation. But that creates a lot of logic and scientific 
difficulties. Recognizing the limitation of the agent/observer is one of 
them; leaving open-ended the observable is another. I am aware of the 
invincible circularity that easily surrounds all of this. So the need of 
a set of new principles sidestepping the worst problems and allowing 
fresh new thought. Probably, the easiest part would be the parallel 
realization of a new synthesis incorporating a new stock of scientific 
concepts (admittedly, most of them in the making yet); at least it could 

Re: [Fis] Fw: PRINCIPLES OF IS. The Pre-Science of Information

[Pedro C. Marijuan]

 development of
this thread.

Best wishes,

    Joseph

- Original Message -
*From:* Pedro C. Marijuan <mailto:pcmarijuan.i...@aragon.es>
*To:* 'fis' <mailto:fis@listas.unizar.es>
*Sent:* Friday, September 15, 2017 2:13 PM
*Subject:* [Fis] PRINCIPLES OF IS

Dear FIS Colleagues,

As promised herewith the "10 principles of information
science". A couple of previous comments may be in order.
First, what is in general the role of principles in science? I
was motivated by the unfinished work of philosopher Ortega y
Gasset, "The idea of principle in Leibniz and the evolution of
deductive theory" (posthumously published in 1958). Our
tentative information science seems to be very different from
other sciences, rather multifarious in appearance and
concepts, and cavalierly moving from scale to scale. What
could be the specific role of principles herein? Rather than
opening homogeneous realms for conceptual development, these
information principles would appear as a sort of "portals"
that connect with essential topics of other disciplines in the
different organization layers, but at the same time they
should try to be consistent with each other and provide a
coherent vision of the information world.
And second, about organizing the present discussion, I bet I
was too optimistic with the commentators scheme. In any case,
for having a first glance on the whole scheme, the opinions of
philosophers would be very interesting. In order to warm up
the discussion, may I ask John Collier, Joseph Brenner and
Rafael Capurro to send some initial comments / criticisms?
Later on, if the commentators idea flies, Koichiro Matsuno and
Wolfgang Hofkirchner would be very valuable voices to put a
perspectival end to this info principles discussion (both
attended the Madrid bygone FIS 1994 conference)...
But this is FIS list, unpredictable in between the frozen
states and the chaotic states! So, everybody is invited to get
ahead at his own, with the only customary limitation of two
messages per week.

Best wishes, have a good weekend --Pedro

*10 **PRINCIPLES OF INFORMATION SCIENCE*

1. Information is information, neither matter nor energy.

2. Information is comprehended into structures, patterns,
messages, or flows.

3. Information can be recognized, can be measured, and can be 
processed (either computationally or non-computationally).


4. Information flows are essential organizers of life's
self-production processes--anticipating, shaping, and mixing
up with the accompanying energy flows.

5. Communication/information exchanges among adaptive
life-cycles underlie the complexity of biological
organizations at all scales.

6. It is symbolic language what conveys the essential
communication exchanges of the human species--and constitutes
the core of its "social nature."

7. Human information may be systematically converted into
efficient knowledge, by following the "knowledge instinct" and
further up by applying rigorous methodologies.

8. Human cognitive limitations on knowledge accumulation are
partially overcome via the social organization of "knowledge
ecologies."

9. Knowledge circulates and recombines socially, in a
continuous actualization that involves "creative destruction"
of fields and disciplines: the intellectual /Ars Magna./

10. Information science proposes a new, radical vision on the
information and knowledge flows that support individual lives,
with profound consequences for scientific-philosophical
practice and for social governance.

-- 
-

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 0
50009 Zaragoza, Spain
Tfno.+34 976 71 3526 <tel:+34%20976%2071%2035%2026>  (& 6818)
pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>
http://sites.google.com/site/pedrocmarijuan/
<http://sites.google.com/site/pedrocmarijuan/>
-


___ Fis mailing
list Fis@listas.unizar.es <mailto:Fis@listas.unizar.es>
http://listas.u

Re: [Fis] Fwd: Re[2]: Heretic

[Pedro C. Marijuan]

Dear FIS Colleagues,

There is no problem with heretics in this list. They are very welcome as 
they make us think on our favorite ideas in a different way or even from 
an opposed angle. We must always maintain the scholarly tone, that's the 
only condition! (well, apart from the "two messages per week" sacred 
rule)... From the many --exciting-- recent exchanges, let me pick from 
Lars: /"assuming that Information is a property, an entity is not 
necessary. We can proceed with scientific research, using any 
information concept we think useful, without assuming it refers to 
anything."/ Something similar but perhaps less clearly formulated was in 
my proposal of the indefinability of information and the reference to 
notions such as "propagating influence" and "distinction on the adjacent."


Therefore I friendly disagree with Yixin below: /"//the definition of 
information is the real foundation of information science//"/, although 
I acknowledge the value and interest of his whole approach from the 
background of formal/computational approaches to our problem/field. 
Somehow, defining information universally is like looking for the "red 
herring", but it doesn't mean that we must condemn the term to 
obscurity. We can develop the foundations of information science without 
that definition, and indeed the advancement during last ten years has 
been promising.


My personal strategy, beyond the 10 public points I formulated, consists 
on theoretical/empirical work about "informational entities". Those 
entities, the existence of which depends on a special relationship with 
the environment, are able to continuously distinguish - say - energy 
flows from information flows, intertwining both kinds of flows with 
their own survival and maintenance processes. An excellent parallel can 
be made with Harold Morowitz on the energy flow and Geoffrey West on 
scaling entities. The former for the micro-perspective (& ecological 
perspective) and the latter for the macro-perspective on the 
organizational dynamics of cells, organisms, enterprises, cities...


The closest realm we can consider, and acknowledge almost completely at 
the molecular scale, is the living cell. That's the most strategic 
theater where we can define a series of essential concepts: first the 
information flow, then the signaling system, the life cycle, the 
cell-cell communication, the complexity growth, etc. etc. This was the 
origins of the genuine existential openness to tiny informational 
signals from the environment. I bet that there is something fundamental 
to learn about this bio-informational way of existence that can be 
usefully carried on to physical quarters and also to the social. There 
is a common informational philosophy of organization, e.g. reminding 
Joseph Brenner's LIR, that at the time being we don't recognize 
basically for two reasons: first the dogmas around the reductionist 
physical approach (the imperialism of physics), and second the relative 
poverty  of theoretical biology (the Darwinian organizational 
blindness)... Anyhow , in a few weeks I will publish a rather complete 
description of the prokaryotic information flow. I hope it will 
stimulate reflections from other FIS parties. As I have often cited 
Michael Conrad in this list: /"when we look at a biological system, we 
are looking at the face of the underlying physics of the universe"./


Best--Pedro


El 05/10/2017 a las 12:03, 钟义信 escribió:

Dear friends,

The debate on the definition of information is of significance because 
the definition of information is the real foundation of information 
science. It is noticed that many contravercies in information science 
either in the past or at present time are more or less related to the 
different understandings of the concept of information.


It is not difficult to accept that there are two concepts of 
information, related and also different to each other. The first one 
is the information presented by the objects existed in 
environment_before the subject's perceiving_ and the second one is the 
information _perceived and understood by the subject._ The first one 
can be termed the object information and the second one the perceived 
information. The latter is perceived by the subject from the former.


The object information is just the object's "state of the object and 
the pattern with which the state varyies". _No meaning and no utility 
at the stage_.


The perceived information is the information, perceive by the subject 
from the object information. So, it should have the form component of 
the object (syntactic information), the meaning component of the 
object (semantic information), and the utility component of the object 
with respect to the subject's goal (pragmatic information). _Only at 
this stage, the "meaning" comes out_.


What is new, we discovered that the meaning (semantic information) is 
the 'function' of the union of the syntactic information and the 
pragmatic information. 

Re: [Fis] Principles of IS

[Pedro C. Marijuan]

Dear FISers,

I also agree with Ji and John Torday about the tight relationship 
between information and communication. Actually Principle 5 was stating 
: "Communication/information exchanges among adaptive life-cycles 
underlie the complexity of biological organizations at all scales." 
However, let me suggest that we do not enter immediately in the 
discussion of cell-cell communication, because it is very important and 
perhaps demands some more exchanges on the preliminary info matters.


May I return to principles and Aristotle? I think that Rafael and Michel 
are talking more about principles as general concepts than about 
principles as those peculiar foundational items that allow the beginning 
of a new scientific discourse. Communication between principles of the 
different disciplines is factually impossible (or utterly irrelevant): 
think on the connection between Euclidean geometry and politics, 
biology, etc. I think Ortega makes right an interpretation about that. 
When Aristotle makes the first classification of the sciences, he is 
continuing with that very idea. Theoretical sciences, experimental or 
productive sciences, and applied or practical sciences--with an emphasis 
on the explanatory theoretical power of both physics and mathematics 
(ehm, Arturo will agree fully with him). I have revisited my old reading 
notes and I think that the Aristotelian confrontation with the Platonic 
approach to the unity of knowledge that Ortega comments is extremely 
interesting for our current debate on information principles.


There is another important aspect related to the first three principles 
in my original message (see at the bottom). It would be rather strategic 
to achieve a consensus on the futility of struggling for a universal 
information definition. Then, the tautology of the first principle 
("info is info") is a way to sidestep that definitional aspect. 
Nevertheless, it is clear that interesting notions of information may be 
provided relative to some particular domains or endeavors. For instance, 
"propagating influence" by our colleague Bob Logan, Stuart Kauffman and 
others, and many other notions or partial definitions as well--I include 
my own "distinction on the adjacent" as valuable for the informational 
approach in biology. Is this "indefinability" an undesirable aspect? To 
put an example from physics, time appears as the most undefinable of the 
terms, but it shows up in almost all equations and theories of 
physics... Principle three means that one can do a lot of things with 
info without the need of defining it.


As for the subject that is usually coupled to the info term, as our 
discussion advances further, entering the "information flows" will tend 
to clarify things. The open-ended relationship with the environment that 
the "informational entities" maintain via the channeling of those info 
flows--it is a very special coupling indeed--allows these entities the 
further channeling of the "energy flows" for self-maintenance. Think on 
the living cells and their signaling systems, or think on our "info" 
societies. Harold Morowitz's "energy flow in biology" has not been 
paralleled yet by a similar "information flow in biology". One is 
optimistic that the recent incorporation of John Torday, plus Shungchul 
Ji and others, may lead to a thought-collective capable of illuminating 
the panorama of biological information.


(shouldn't we make an effort to incorporate other relevant parties, also 
interested in biological information, to this discussion?)


Best wishes--Pedro

El 23/09/2017 a las 21:27, Sungchul Ji escribió:


Hi Fisers,


I agree.

Communication may be the key concept in developing a theory of informaton.


Just as it is impossible to define what energy is without defining the 
thermodynamic system under consideration (e.g., energy is conserved 
only in an isolated system and not in closed or open systems; 
the Gibbs free energy content decreases only when a spontaneous 
process  occurs in non-isolsted systems with a constant temperature 
and pressure, etc), so it may be that 'information' cannot be defined 
rigorously without  first defining the "communication system" under 
consideration.   If this analogy is true, we can anticipate that, just 
as there are many different kinds of energies depending on the 
characteristics of the thermodynamic systems involved, so there may be 
many different kinds of 'informations' depending on the nature of the 
communication systems under consideration.



The properties or behaviors of all thermodynamic systems depend on 
their environment, and there are three  system-environment relations 
-- (i) isolated (e.g., the Universe, or the thermos bottle), (ii) 
closed (e.g., refriegerator), and (iii) open (e.g., the biosphere, 
living cells).



It is interesting to note that, all communication systems (e.g., cell, 
organs, animals, humans) may embody ITR (Irreducible Triadic Relation) 
which I  found it 

Re: [Fis] Fwd: PRINCIPLES OF IS

[Pedro C. Marijuan]

Dear FISers,

Taking seriously the idea of information principles, quite probably 
demands a specific discussion on principles. Why do we need "principles" 
at all? Because of our cognitive limitations. An infinite intellect 
would traverse all spans of knowledge without any 
discontinuity--presumably. In our collective scientific enterprise, 
however, we create special disciplines in order to share understandable 
discourses between the limited individuals of each thought-collective. 
As knowledge accumulates and gets more and more complex, particularly in 
the encounter with other discourses, the growing epistemic distances 
fragment the original discipline, and a new subdiscipline becomes 
necessary. It starts then a fresh new discourse, with its own 
principles. In my brief mention of Ortega, what he accuses Leibnitz is 
that being the champion of principles in science, he becomes fragmentary 
and asystematic in his meta-scientific/philosophical "mode of thinking": 
the hypersystematic expresses himself fragmentarily (Ortega dixit). It 
is curious that along the survey of principles in Ortega's book, the 
most frequent interlocutor is not Leibnitz, but Aristotle! Although 
Husserl, Heidegger, Descartes, Pappus, Plato, Suarez, Spinoza... and 
some others big names also appear, his main concern (to my taste) is 
discussing Aristotle's view of specialized disciplines starting from 
their respective principles, empirically-sensuously obtained and 
"uncommunicated" in between the different fields. It is very intriguing.


If the principles of different disciplines are factually 
uncommunicated,  the info science view of a new body of knowledge 
running across all scales is caught into a difficult "principled" 
position. Nevertheless,  the three blocks I distinguished (info per se, 
bioinfo, ecology of knowledge) seem to allow some fertile conjugation 
inside/outside... but the problem remains. I think it is solvable, as in 
our times there is a central element that allows a whole new scientific 
discourse on information. The dense relationship between life and 
information has nowadays acquired a formidable empirical background, 
leveraged by the most basic disciplines--physics, chemistry, computer 
science, and biology itself.


More concretely, the notion of the "information flow" can almost be 
sketched properly, both in its signaling textures and in the fundamental 
relationship with the life cycle--and not very differently along the 
evolutionary process. Thereafter, recombination appears as one of the 
fundamental emergences in the growing complexity of the evolving 
information dynamics around life cycles and information/energy flows. 
The recombination phenomenon happens for the knowledge-stocks of cells, 
nervous systems, enterprises, sciences-technologies-cultures... It 
accumulates amazing combinatoric, topological, dynamic, and closure 
properties in the different realms, flowing up and down among scales, 
multidimensionally, and maintaining afloa the whole game of adaptive 
existences.


Our disciplines may apparently work by themselves, autonomously, but 
actually they do not. Rather than "on top", they work "on tap". They 
endlessly recombine in the ecology of knowledge, differently for each 
problem and for each occasion, creating new theoretical and applied 
subdisciplines in the thousands. Information science has to shed light 
on that fundamental factor of contemporary societies. And more 
"psychologically" this discipline has to put LIFE, both individual life 
and social life, at the very center of the sharing of meaning. A new way 
of thinking starting from specific information principles will liberate 
our limited intellects to more creative endeavors. It is time to quote 
Whitehead: "Civilization advances by extending the number of important 
operations which we can perform without thinking about them. Operations 
of thought are like cavalry charges in a battle —they are strictly 
limited in number, they require fresh horses, and must only be made at 
decisive moments."


Best wishes--Pedro


El 20/09/2017 a las 17:46, Michel Godron escribió:


My remarks are written in red

Bien reçu votre message. MERCI. Cordialement. M. Godron
Le 20/09/2017 à 13:54, Pedro C. Marijuan a écrit :

Dear FISers,

Many thanks for all the comments and criticisms. Beyond concrete 
agreements/disagreements the discussion is lively, and that is the 
main point. It is complicate pointing at some fundamental, ultimate 
reality based on disciplinary claims. Putting it differently, the 
hierarchies between scientific disciplines were fashionable 
particularly in the reductionism times; but now fortunately those 
decades (70s, 80s) are far away. Actually, the new views taking shape 
are not far from the term "knowledge recombination" that appears in 
some of the principles discussed. Modern research 

[Fis] Fwd: Re: PRINCIPLES OF IS

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: [Fis] PRINCIPLES OF IS
Fecha:  Tue, 19 Sep 2017 09:21:51 +0200
De: Rafael Capurro <raf...@capurro.de>
Responder a:raf...@capurro.de
Para:   Pedro C. Marijuan <pcmarijuan.i...@aragon.es>



Dear Pedro,

a short comment to your intro to the 10 principles: I very much agree 
with your views (following Ortega) that information science can be 
conceived as a multifaceted or "multifarious" network of concepts and 
theories dealing phenomena partly related partly not (yet) related with 
each other for which we need different languages/concepts and 
'translations' and kinds of calculations also with regard to their goals 
and 'utility'.


If this makes sense, then we should try to develop some kind of 
'principles' or 'archai' in the Greek sense, i.e., of 'initial forces' 
that give rise to possibilities of 'un-concealing' different kinds of 
phenomena that we could not see when disregarding other paths or by not 
entering through other 'portals' each portal announcing different kinds 
of what makes sense or not when entering the path.


Sometimes it makes sense to go up and see the landscapes from the top, 
knowing that this view(s) from the top also conceal a lot of things on 
the bottom. It is easiear to understand these 'principles' if we have 
experience with walking in the mountains (but also in other natural and 
artificial environments like a forest, a desert, cities etc.). Maybe we 
could learn from such experiences which kind of 'principles' are to be 
conssidered in the 'methods' (hodos = path)  of scientific research.


So, my suggestion is to invite our FIS colleagues to describe 
phenomenologically their walking experiences and 'principles' in 
different enviroments (mountains etc.) and try to 'translate' 
(trans-late) them into the field of information science.


Best

Rafael


Dear FIS Colleagues,

As promised herewith the "10 principles of information science". A 
couple of previous comments may be in order.
First, what is in general the role of principles in science? I was 
motivated by the unfinished work of philosopher Ortega y Gasset, "The 
idea of principle in Leibniz and the evolution of deductive theory" 
(posthumously published in 1958). Our tentative information science 
seems to be very different from other sciences, rather multifarious in 
appearance and concepts, and cavalierly moving from scale to scale. 
What could be the specific role of principles herein? Rather than 
opening homogeneous realms for conceptual development, these 
information principles would appear as a sort of "portals" that 
connect with essential topics of other disciplines in the different 
organization layers, but at the same time they should try to be 
consistent with each other and provide a coherent vision of the 
information world.
And second, about organizing the present discussion, I bet I was too 
optimistic with the commentators scheme. In any case, for having a 
first glance on the whole scheme, the opinions of philosophers would 
be very interesting. In order to warm up the discussion, may I ask 
John Collier, Joseph Brenner and Rafael Capurro to send some initial 
comments / criticisms? Later on, if the commentators idea flies, 
Koichiro Matsuno and Wolfgang Hofkirchner would be very valuable 
voices to put a perspectival end to this info principles discussion 
(both attended the Madrid bygone FIS 1994 conference)...
But this is FIS list, unpredictable in between the frozen states and 
the chaotic states! So, everybody is invited to get ahead at his own, 
with the only customary limitation of two messages per week.


Best wishes, have a good weekend --Pedro

*10 **PRINCIPLES OF INFORMATION SCIENCE*

1. Information is information, neither matter nor energy.

2. Information is comprehended into structures, patterns, messages, or 
flows.


3. Information can be recognized, can be measured, and can be  
processed (either computationally or non-computationally).


4. Information flows are essential organizers of life's 
self-production processes--anticipating, shaping, and mixing up with 
the accompanying energy flows.


5. Communication/information exchanges among adaptive life-cycles 
underlie the complexity of biological organizations at all scales.


6. It is symbolic language what conveys the essential communication 
exchanges of the human species--and constitutes the core of its 
"social nature."


7. Human information may be systematically converted into efficient 
knowledge, by following the "knowledge instinct" and further up by 
applying rigorous methodologies.


8. Human cognitive limitations on knowledge accumulation are partially 
overcome via the social organization of "knowledge ecologies."


9. Knowledge circulates and recombines socially, in a continuous 
actualization that involves "creative destruction" of fields and 
discipl

[Fis] PRINCIPLES OF IS

[Pedro C. Marijuan]

Dear FIS Colleagues,

As promised herewith the "10 principles of information science". A 
couple of previous comments may be in order.
First, what is in general the role of principles in science? I was 
motivated by the unfinished work of philosopher Ortega y Gasset, "The 
idea of principle in Leibniz and the evolution of deductive theory" 
(posthumously published in 1958). Our tentative information science 
seems to be very different from other sciences, rather multifarious in 
appearance and concepts, and cavalierly moving from scale to scale. What 
could be the specific role of principles herein? Rather than opening 
homogeneous realms for conceptual development, these information 
principles would appear as a sort of "portals" that connect with 
essential topics of other disciplines in the different organization 
layers, but at the same time they should try to be consistent with each 
other and provide a coherent vision of the information world.
And second, about organizing the present discussion, I bet I was too 
optimistic with the commentators scheme. In any case, for having a first 
glance on the whole scheme, the opinions of philosophers would be very 
interesting. In order to warm up the discussion, may I ask John Collier, 
Joseph Brenner and Rafael Capurro to send some initial comments / 
criticisms? Later on, if the commentators idea flies, Koichiro Matsuno 
and Wolfgang Hofkirchner would be very valuable voices to put a 
perspectival end to this info principles discussion (both attended the 
Madrid bygone FIS 1994 conference)...
But this is FIS list, unpredictable in between the frozen states and the 
chaotic states! So, everybody is invited to get ahead at his own, with 
the only customary limitation of two messages per week.


Best wishes, have a good weekend --Pedro

*10 **PRINCIPLES OF INFORMATION SCIENCE*

1. Information is information, neither matter nor energy.

2. Information is comprehended into structures, patterns, messages, or 
flows.


3. Information can be recognized, can be measured, and can be processed 
(either computationally or non-computationally).


4. Information flows are essential organizers of life's self-production 
processes--anticipating, shaping, and mixing up with the accompanying 
energy flows.


5. Communication/information exchanges among adaptive life-cycles 
underlie the complexity of biological organizations at all scales.


6. It is symbolic language what conveys the essential communication 
exchanges of the human species--and constitutes the core of its "social 
nature."


7. Human information may be systematically converted into efficient 
knowledge, by following the "knowledge instinct" and further up by 
applying rigorous methodologies.


8. Human cognitive limitations on knowledge accumulation are partially 
overcome via the social organization of "knowledge ecologies."


9. Knowledge circulates and recombines socially, in a continuous 
actualization that involves "creative destruction" of fields and 
disciplines: the intellectual /Ars Magna./


10. Information science proposes a new, radical vision on the 
information and knowledge flows that support individual lives, with 
profound consequences for scientific-philosophical practice and for 
social governance.


--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] FIS New Course discussions

[Pedro C. Marijuan]

Dear FIS Colleagues,

The leisure time of vacations is over and it would be time to reassume 
the list exchanges. There were several interesting sessions which had 
been planned for this new course, but unfortunately none of them seems 
possible in a short term. In order that these "dry" months --even 
previous to the IS4SI conference-- come to an end, let me request the 
involvement of FIS parties, either volunteering for session chairs or 
suggesting interesting new themes & parties for future sessions. At the 
time being my personal capability to produce new sessions seems rather 
low...


Anyhow, as a means to break the ice of this new course I have revisited 
some notes I took during a very fertile round table coordinated by Yixin 
Zhong on "ecologies of knowledge" in the Gotheborg IS4SI meeting. I have 
realized that with some tweaking a short list of, say "10 principles for 
information science", was emerging. Could this rather idiosyncratic 
stuff be tolerable for the high diversity of points of view in FIS? 
Maybe not. But at least I hope it will support some lively discussion.


In order to have some operativity, I will post the principles this 
Friday, and then the comments will fly or not... Well, I had initially 
thought that each principle could have an initial commentator (just 
based on my terribly subjective views). To list them: Marcin (for princ. 
1), Jerry (2), Gordana (3), Terry (4), Stan (5), Soeren (6), Tozzi (7), 
Yixin (8), Loet (9), Howard (10). Probably this is rather complex, so 
after some rounds of general comments on the whole scheme we will see 
whether this detailed analysis can be performed or not.


Best wishes to all,

--Pedro

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] CFP - 6th WORLD CONGRESS ON UNIVERSAL LOGIC - Vichy, June 2018 (From Jean-Yves)

[Pedro C. Marijuan]

Dear FIS colleagues,
herewith an interesting announcement from Jean-Yves Beziau.
Next week I will send some comments to start our discussions...
Best postvacational greetings!
--Pedro

 Mensaje reenviado 

Asunto: CFP - 6th WORLD CONGRESS ON UNIVERSAL LOGIC - Vichy, June 2018
Fecha:  Tue, 05 Sep 2017 11:48:52 +0200
De: Jean-Yves Beziau 
Responder a:j...@jyb-logic.org
Para:   pcmarijuan.i...@aragon.es



The 6th WORLD CONGRESS  ON UNIVERSAL LOGIC
will take place in Vichy, France, June 21-26, 2018
after previous editions in Montreux 2005, Xi'an 2007, Lisbon 2010, Rio
2013 and  Istanbul 2015:
http://www.uni-log.org/vichy2018

Deadline to submit a one page  abstract is September 15, 2017
You can either submit an abstract to the general organization at
unilog2...@yandex.com
or to a specific workshop, see details in the website.

There will be aboput 15 workshops within UNILOG'2018:
- Proof Theory
- The Logic of Social Practices
- Around Peirce
- Logical Geometry
- Logic and Music
- The Logic of Social Practices
- Reflections on Paraconsistency
- Naming Logic(s) II
- The Lvov-Warsaw School: Past, Present and Future
- The Relevance of Non-classical Logic for Semantic Technologies
- Logics and Metalogics
- Logic and Categories
- Around Hintikka
- Practices of Writing and Reading in Logic
- Logic, Probability and Credence
- Logic for Children

UNILOG is a logic event in a broad sense. It gathers people from many
horizons
(philosophy,  mathematics, linguistics, computer science, semiotics,
cognitive science ...)
and the idea is to promote interaction between all these people.
For this edition there will be the award of of Logic Prizes from about
10 countries:
http://www.uni-log.org/logic-prize-world
Before the congress, June 16-20, 2018, there will be a school with 30
tutorials.

Vichy is a charming relaxing thermal city at the middle of France,
developed by Napoleon III in the second half of the 19th century, who in
particular created beautiful parks with species of trees from all over
the world.  Vichy, in the Duchy of Bourbon, a region full of castles,
is a  small city,  where  it is possible to go everywhere just by
walking.
The event will take place at the university campus nearby the Celestins
spring,
the banks of the Allier river (where it is possible to swim) and the
city center.
June is a very nice time to be in Vichy with lots of animations,
including  on June 21 a very lively musical day celebrating summertime.

Looking forward to seeing you in Vichy in June 2018
Jean-Yves Beziau (University of Brazil, Rio de Janeiro and Ecole Normale
Supérieure, Paris)
Christophe Rey (University Clermont Auvergne, CNRS, LIMOS)
Organizers of UNILOG'2018
---
U N I L O G  -  World Congress and School on Universal Logic -  U N I LO
G
Montreux 2005, Xi'an 2007, Lisbon 2010, Rio 2013, Istanbul 2015, Vichy
2018
http://www.uni-log.org/vichy2018

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[Fis] Fwd: THANK YOU FOR IS4SI GÖTEBORG & POST-SUMMIT MATTERS

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: THANK YOU FOR IS4SI GÖTEBORG & POST-SUMMIT MATTERS
Fecha:  Mon, 19 Jun 2017 09:11:51 +0200
De: i...@sciforum.net
Responder a:do...@chalmers.se
Para:   gordana.dodig-crnko...@chalmers.se



DIGITALISATION FOR A SUSTAINABLE SOCIETY

Dear Colleagues!

One week of IS4SI Gothenburg is over and soon all of you will be back 
home. What remains from our summit are memories of great moments, and 
experiences, meetings with people, sharing knowledge, friendly, 
open-minded and inclusive atmosphere, five intense days in beautiful 
Gothenburg in truly transdisciplinary setting. We enjoyed very much the 
presentations and discussions, excellent plenaries with panels and 
keynotes, lunch breaks with lively debates when all the congress center 
was vibrating of engaged and friendly voices. Excursion to the beautiful 
Elfsborg fortress with enchanting nature and joyful boat tour, the 
banquet with the inspirational talk of Bo Dahlbom, and artistic moments 
- concrete poetry of Hans-Jörg Kreowski, AI choreography of Louise 
Crnkovic-Friis and incredibly beautiful algorithmic music performance by 
Palle Dahlstedt – made an impression that will surely last.


The whole complex organisation (with the program of 70 pages) worked 
flawless and technical support was always there, efficient and helpful 
when we needed it. Student volunteers’ help was invaluable. MeeteX took 
care of registration that wen quickly and smoothly.


Thank you all for your excellent contributions, for self-organizing into 
such a great event!


What remains now is practical questions connected to the financial 
issues like reimbursements, certificates etc.


Please contact MeetX for that, who will help you,

e-mail: is4si-2017is4si-2...@meetx.se 

In the coming weeks I will collect photographs from the conference.

At the moment I already have several hundreds but if you have something 
special that you want to share, send it to me.


Already on the web page you will find two group photos.

http://is4si-2017.org/news/

The next step regards publication activities, that are important for the 
impact of our work. There are a lot of possibilities to publish in front 
of us – we will come back to you in that regard.

http://is4si-2017.org/publications/

The first one is Proceedings journal, for which we will come back to you.

The last day of the conference, on Friday we have elected Terrence 
Deacon for our new President and Marcin Schroeder for President Elect. 
By that my function becomes Immediate Past President. My role will be to 
support Terry in matters of web information about the Society and the 
Board and its activities.


The next summit will be organized by Terry Deacon in the US, on 
Berkeley, Stanford of Santa Clara – soon we will know more.


Thank you again and bye for now,

Gordana

Sciforum.net is a platform published and maintained by MDPI AG.
For technical support, e-mail i...@sciforum.net

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[Fis] Gothenburg 2017

[Pedro C. Marijuan]

Dear FIS Colleagues,

The Third IS4SI Conference, and at the same time the Seventh of FIS, in 
Gothenburg 2017 is over. Many thanks to our colleague Gordana and the 
organization team around her for making possible the event. It was a 
very fine experience indeed. Like in Vienna 2015, there were many 
parallel tracks and many presentations and many colleagues around. 
Amidst the inevitable heterogeneity there was somehow a new sense of 
having passed some threshold, that more links had been established 
between the themes, and that a growing community of information 
scientists is emerging...


For our online discussions, we will have several themes that hopefully 
will be organized in a consistent agenda for the next course: from 
critical stances on digitalization, to narrative in science and 
elsewhere, medieval mechanical intelligence, Church-Turing Thesis, new 
social ICT engineering, biomolecular combinatorics, principles of 
information science, ecologies of knowledge, etc.


We are entering into vacation time. The list remains open for any 
comment (with the usual constraint of only two messages per week). Right 
now I am also entering Gordana's farewell message to the conference 
participants.


All the best--Pedro

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] Causation is transfer... and something else

[Pedro C. Marijuan]

Dear Hector and colleagues,

I have found very interesting your message. It has reminded me in 
another level the problems we have in this list to keep focused 
discussions particularly regarding disciplinary (non philosophical, non 
general) matters. Most people in the list pay lip tribute to 
multidisciplinarity concerning the problem of establishing the 
foundations of information science. But in actuality only the 
"generalist" community including philosophers and people close to 
information theory have sufficient critical mass to voluntarily or 
involuntarily bias the debate towards their views, specially the 
preoccupation for these big questions that (fortunately) at the time 
being can not be answered.


In my particular stance, already commented upon in my last message, and 
in quite a few previous ones, the most strategic problem relates to the 
biological origins of meaning, that hiatus that notoriously separates 
the inanimate/objective from the animate/subjective forms of 
information. The recent revolution in signaling science has a few things 
to say about that, how life cycles are advanced among constellations of 
colligated info flows and how the meaning of signals is 
molecularly fabricated, not so far away from our social "narratives". 
But helas I have failed to capture the attention and interest of my FIS 
colleagues --a complain, to myself, which is widely shared among most, 
if not all of us!! In any case I omit self-propaganda of my papers on 
the matter.


Please, do not take that as a manifestation of bitterness. The fact is 
that we have a serious imbalance in the composition of our discussion 
community. In part, enlisting practicing research scientists in a 
generalist list like this one is very difficult. And maintaining topical 
discussions on their specialized matters of interest is almost 
impossible given the lack of critical mass, and the disinterest of broad 
segments of the list. See for instance the poor performance of most 
specialized sessions organized so far. Spontaneous "tangents" come to 
the rescue, as they have always been accepted in this list, and can be 
genuinely creative, but most of the derivations go again and again to 
those ghostly questions.


Now, going to the positive part, I have recently proposed to the board 
of IS4SI, the common info society into which FIS integrated, the 
arrangement of Working Groups, or Interest Groups, so that maintaining a 
general discussion list be compatible with parallel exchanges among more 
homogeneous participants. For instance, here at FIS it wouldn't be too 
difficult arranging a working group on info philosophy and another on 
info theory and the definition of information (the quest for 
establishing standards); and perhaps we could try one in biophysics and 
neurodynamics, and another group in bioinformation, plus social info 
matters... Who knows? I think it is an interesting step to try in order 
to achieve some "ratchet effect", and we could count with fis' own web 
pages to support the new works, and perhaps it would be easier to get 
some financing for small meetings face to face... Well, I offer myself 
to start working with the bioinfo club, and if anyone is interested in 
the initial coordination of one of these possible teams, just speak up 
(either in the list or offline). If any of these could work a little 
among us, we would have made advancements to arrange the idea in wider 
scale.


Best wishes--Pedro

El 30/03/2017 a las 22:01, Terrence W. DEACON escribió:

Dear Hector,

Whenever I read an email or hear a response that begins with the 
phrase "With all due respect" I fear that what follows will indeed be 
disrespectful and self-promoting. Scholarly respect is particularly 
important when the diversity of backgrounds of the contributors is so 
broad and their level of erudition in these different fields is 
likewise broad. Best to begin with the assumption that all are 
well-read expert scholars rather than complaining about others' 
ignorance of what you refer to—an assumption that is often mistaken.


In our short email notes one cannot expect each author to provide a 
list of all current mathematical and non-mathematical formal 
definitions of information, or to provide an evidentiary list of their 
own papers on the topic as a proof of competence, in order to make a 
point. Since we are inevitably forced to use short-hand terms to 
qualify our particular usages, my only suggestion is that we need to 
find mutially understandable qualifiers for these different uses, to 
avoid pointless bickering about what 'information' is or how it should 
be used.


The term "information" is not "fixed" to a particular technical 
definition currently standard to only one or two fields like 
mathematics, physics, or computation theory. Nor can we assume that 
technical approaches in one field will be relevant to problems outside 
that field. I would hope that we are collectively attempting to expand 
our 

[Fis] MODERATION NOTE Re: Causation is transfer of information

[Pedro C. Marijuan]

To ALL discussants:

Please, take into account that posting in this list is restricted to two 
messages per week. It is the Second Rule of our info club...


Best--Pedro
Fis List moderator

El 30/03/2017 a las 11:12, John Collier escribió:


Dear Hector,

Personally I agree that algorithmic information theory and the related 
concepts of randomness and Bennett’s logical depth are the best way to 
go. I have used them in many of my own works. When I met Chaitin a few 
years back we talked mostly about how unrewarding and controversial 
our work on information theory has been. When I did an article on 
information for the Stanford Encyclopaedia of Philosophy it was 
rejected in part becausewe of fierce divisions between supporters of 
Chaitin and supporters of Kolmogorov!  The stuff I put in on Spencer 
Brown was criticized because “he was some sort of Buddhist, wasn’t 
he?” It sounds like you have run into similar problems.


That is why I suggested a realignment of what this group should be 
aiming for. I think the end result would justify our thinking, and 
your work certainly furthers it. But it does need to be worked out. 
Personally, I don’t have the patience for it.


John Collier

Emeritus Professor and Senior Research Associate

Philosophy, University of KwaZulu-Natal

http://web.ncf.ca/collier

*From:*Hector Zenil [mailto:hzen...@gmail.com]
*Sent:* Thursday, 30 March 2017 10:48 AM
*To:* John Collier ; fis 
*Subject:* Re: [Fis] Causation is transfer of information

Dear John et al. Some comments below:

On Thu, Mar 30, 2017 at 9:47 AM, John Collier > wrote:


I think we should try to categorize and relate information
concepts rather than trying to decide which is the “right one”. I
have tried to do this by looking at various uses of information in
science, and argue that the main uses show progressive
containment: Kinds of Information in Scientific Use
.
2011. cognition, communication, co-operation. Vol 9, No 2


There are various mathematical formulations of information as
well, and I think the same strategy is required here. Sometimes
they are equivalent, sometimes close to equivalent, and sometimes
quite different in form and motivation. Work on the foundations of
information science needs to make these relations clear. A few
years back (more than a decade) a mathematician on a list
(newsgroup) argued that there were dozens of different
mathematical definitions of information. I thought this was a bit
excessive, and argued with him about convergences, but he was
right that they were mathematically different. We need to look at
information theory structures and their models to see where they
are equivalent and where (and if) they overlap. Different
mathematical forms can have models in common, sometimes all of them.

The agreement among professional mathematicians is that the correct 
definition of randomness as opposed to information is the Martin Loef 
definition for the infinite asymptotic case, and Kolmogorov-Chaitin 
for the finite case. Algorithmic probability (Solomonoff, Levin) is 
the theory of optimal induction and thus provides a formal universal 
meaning to the value of information. Then the general agreement is 
also that Bennett's logical depth separates the concept of randomness 
from information structure. No much controversy in in there on the 
nature of classical information as algorithmic information. Notice 
that 'algorithmic information' is not just one more definiton of 
information, IS the definition of mathematical information (again, by 
way of defining algorithmic randomness). So adding 'algorithmic' to 
information is not to talk about a special case that can then be 
ignored by philosophy of information.


All the above builds on (and well beyond) Shannon Entropy, which is 
not even very properly discussed in philosophy of information beyond 
its most basic definition (we rarely, if ever, see discussions around 
mutual information, conditional information, Judea Pearl's 
interventionist approach and counterfactuals, etc), let alone anything 
of the more advanced areas mentioned above, or a discussion on the now 
well established area of quantum information that is also comletely 
ignored.


This is like trying to do philosophy of cosmology discussing Gamow and 
Hubble but ignoring relativity, or trying to do philosophy of language 
today discussing Locke and Hume but not Chomsky, or doing philosophy 
of mind discussing the findings of Ramon y Cajal and claiming that his 
theories are not enough to explain the brain. It is some sort of 
strawman fallacy contructing an opponent living in the 40s to claim in 
2017 that it fails at explaining everything about information. Shannon 

[Fis] PLANCKIAN INFORMATION: A NEW MEASURE OF ORDER (From S. Ji)

[Pedro C. Marijuan]

Note: what follows is an abbreviated text taken from the presentation.
The whole file, too big for our list, can be found at fis web pages:
http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Planckian_information.pdf
A very recent article developing similar ideas: 
http://www.mdpi.com/2078-2489/8/1/24

Greetings to all--Pedro
--- 




*What is the Planckian information ?*

*S**UNGCHUL JI*

/Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University/
/s...@pharmacy.rutgers.edu/

*
*
The Planckian information (I_P) is defined as the information produced 
(or used) by the so-called Planckian processes which are in turn defined 
as any physicochemical or formal processes that generate long-tailed 
histograms fitting the Planckian Distribution Equation (PDE),


y = (A/(x + B^5)/(Exp(C/(x + B)) – 1)(1)

where A, B and C are free parameters, x is the class or the bin to 
whichobjects or entities belong, and y is the frequency [1, 1a].The PDE 
was derived in 2008 [2] from the blackbody radiation equation discovered 
by M. Planck (1858-1947) in 1900, by replacing the universal constants 
and temperature with free parameters, A, B and C.PDE has been found to 
fit not only the blackbody radiation spectra (as it should) but also 
numerous other long-tailed histograms [3, 4] (see Figure 1).


One possible explanation for the universality of PDE is that many 
long-tailed histograms are generated by some selection mechanisms acting 
on randomly/thermally accessible processes [3]. Since random processes 
obey the Gaussian distribution, the ratio of the area under the curve 
(AUC) of PDE to that of Gaussian-like symmetric curves can be used as a 
measure of non-randomness or the order generated by the Planckian processes.


As can be seen in *Figs. 1 (g), (i), (k), (o), (r) *and*(t), *the curves 
labeled ‘Gaussian’ or ‘Gaussian-like’ overlap with the rising phase of 
the PDE curves.The ‘Gaussian-like’ curves were generated by Eq. (2), 
which was derived from the Gaussian equation by replacing its 
pre-exponential factor with free parameter A:


y = Ae^– (x – ^μ ^)^2/(2 ^σ ^^2) (2)

The degree of mis-match between the area under the curve (AUC) of PDE, 
Eq. (1), and that of GLE, Eq. (2), is postulated to be a measure of 
/non-randomness/ (and hence /order/).GLE is associated with random 
processes, since it is symmetric with respect to the sign reversal of in 
its exponential term, (x - µ).This /measure of order/ is referred to as 
the Planckian Information (I_P ) defined quantitatively as shown in Eq. 
(3) or Eq. (4):


I_P = log_2 (AUC(PDE)/AUC(GLE))bits(3)

or


I_P= log_2 [∫P(x)dx/∫G(x)dx]bits(4)

where P(x) and G(x) are the Plackian Distribution Equation and the 
Gaussian-Like Equation, respectively.


It is generally accepted that there are at least three basic aspects to 
information – /amount/, /meaning, /and /value. //Planckian information/ 
is primarily concerned with the /amount/ (and hence the /quantitative/ 
aspect) of information.There are numerous ways that have been suggested 
in the literature for /quantifying information/ bedside the well-known 
Hartley information, Shannon entropy, algorithmic information, etc 
[5].The Planckian information, given by Equation (3), is a new measure 
of information that applies to the /Planckian process/ generally defined 
as in (5):


“Planckian processes are the physicochemical, neurophysiological, (5)
biomedical, mental, linguistic, socioeconomic, cosmological, or any

other processes that generate long-tailed histograms obeying the
Planckian distribution equation (PDE).”

The Planckian information represents the degree of organization of 
physical (or nonphysical) systems in contrast to the Boltzmann or the 
Boltzmann-Gibbs entropy which represents the disorder/disorganization of 
a physical system, whether the system involved is atoms, enzymes, cells, 
brains, human societies, or the Universe.I_P is related to the 
“organized complexity” and S is realted to “disorganized complexity” of 
Weaver [6].The organization represented by I_P results from 
/symmetry-breaking selection/ /processes /applied to some randomly 
accessible (and hence symmetrically distributed) processes, whether the 
system involved is atoms, enzymes, cells, brains, languages, human 
societies, or the Universe [3, 4], as schematically depicted in *Figure 2*.


There is a great confusion in science and philosophy concerning the 
relation between the concepts of /information/ and /entropy/ as pointed 
out by Wicken [7].A large part of this confusion may be traced back to 
the suggestions made by Schrödinger in 1944 [8] and others subsequently 
(e.g., von Neumann, Brillouin, etc.) that /order/ can be measured as the 
/inverse of/ /disorder/ (D) and hence that information can be measured 
as negative entropy (see the second column in *Table 1*).

[Fis] New Discussion Session: PLANCKIAN INFORMATION

[Pedro C. Marijuan]

Dear FIS Colleagues,

Almost on the eve of the Göteborg summit IS4SI 2017, with a FIS 
conference there (http://is4si-2017.org/program/conferences/fis-2017/), 
it may be a good idea to re-ignite our discussions with a very enticing 
topic: the proposal of a specific type of  information with widespread 
reach.


*PLANCKIAN INFORMATION: A NEW MEASURE OF ORDER*

It will be imparted by:

*S**UNGCHUL JI*

Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University

We will start it in the next days.

Best wishes to all,
--Pedro

-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Fwd: Unpleasant answer ? From Bruno Marchal

[Pedro C. Marijuan]

Dear Pedro, dear Jerry, dear List,



On 07 Mar 2017, at 04:36, Jerry LR Chandler wrote:

de Chardin has also cast a long and durable shadow over my mind for 
decades for decades. His writings both provides some guidance on the 
form of time and opens rich questions that bring fruit.



  While I appreciate the flow of concepts emerging from Bruno’s 
“poetry”, its guidance appears to exclude chemistry and biology.



The approach that I have sketched here is top down.


I show that if we assume a (rather weak compared to most version in the 
literature) Digital Mechanist hypothesis, biology and chemistry/physics 
have to be derived from arithmetic. To be exact, physics has to be 
derived from the introspective "theology" of the universal machine 
(which has the cognitive ability to know that she is universal), and 
that is reducible to elementary arithmetic (although the complete logic 
of the proper theological part escape its computable part: after Gödel 
we know that elementary arithmetic is in-exhaustively complicated. The 
amazing thing is that the propositional part of that theology is 
decidable, and that is enough to get the propositional part of the 
physics and compare it with the logic of the observable (quantum logic).



I can explain more or give references. It is not obvious and ask for 
some amount of work, even more for those not familiar with the work of 
Church, Post, Kleene, Turing, Gödel and many others.



We have something like:


Number(with + and *) => Number's dreams statistics => Physics => human 
biology




Thus, Bruno’s  associations are not so clear to me.


This provides evidence you have a sane mind :)


 No problem. I am summarizing many years of work based on results which 
are not well known as I have eventually understood.


The basic idea is simple, but hard to swallow for the physicalists, and 
they are somehow mocked and insulted, as pagan theology, since 1500 years.




So, I will be a “spoil sport” and look toward a more “life-friendly” 
flow of both symbols and numbers with only a tad of poetry.


On Mar 3, 2017, at 11:51 AM, Bruno Marchal > wrote:




My favorite de Chardin's proposition is, from memory:


   "We are not human beings having spiritual experiences, we are 
spiritual beings having human experiences.




That is close to the theology of the neopytagorean Moderatus of Gades, 
and close to the neoplatonist Plotinus, Porphyry, ... And they are 
formally close to the "theology" of the universal numbers. (and even 
intuitively so assuming the computationalist hypothesis in cognitive 
science, through sequence of thought experiences).



The tensions between the computational natures of discrete and the 
“continuous” numbers haunts  any attempt to make mathematical sense out 
of scientific hypotheses. I am uncertain as to the logical implication 
of the “computationalist’s hypothesis" in this context.




If you are aware of the notion of first person indeterminacy, it is not 
so difficult to understand how the appearance of the continuum can be 
explained to be unavoidable in the digital-mechanist frame. The physical 
reality will emerge from a statistics on infinities of computations 
(including many with Oracles). Amazingly, in the digitalist frame, it is 
the digital which remains hard to understand a priori, but the 
mathematics of self-reference gives important clue.



The key here is that mechanism makes us duplicable, and we can't be 
aware if some delay is made for the reconstitution of one of the copy. 
It is that invariance for the delays of reconstitution which makes 
indetermined on an infinity of computational relations, themselves 
embedded in non computational relations with many numbers. But we cannot 
invoke oracles, except the halting oracle and the random oracle. 
Mechanism predicts the necessity of an apparent continuum at least.





Is the reference grounded in Curry’s combinatorial logic or otherwise?


It does not. The reasoning is independent of any basic universal theory 
chosen. We get the same laws of physics, if we assume only combinators, 
or only number, or a quantum computer, etc. I use the numbers because 
people are familiar with them, and they are not "physicalist", so we 
can't be accused of "treachery" in the derivation of physics.



Of course, it is more difficult to prove that elementary arithmetic is 
Church-Turing Universal than the same for the combinators, but it is a 
well known standard result in logic.






It reminds me also of Shrî Aurobindo, when he said:


"What, you ask, was the beginning of it all?


And it is this ...

Existence that multiplied itself

For sheer delight of being

And plunged into numberless trillions of forms

So that it might

Find

Itself

Innumerably"


I have some minor problems with the present essay, but substituting some 
of the excessively teleological "purposive" terms about life (perhaps 
all of them?), and using instead a 

[Fis] Fwd: Re: WHY WE ARE HERE? ...AN UNPLEASANT ANSWER?! From Jerry Chandler

[Pedro C. Marijuan]

 Mensaje reenviado 
Asunto: Re: [Fis] WHY WE ARE HERE? ...AN UNPLEASANT ANSWER?!
Fecha:  Mon, 6 Mar 2017 21:36:55 -0600
De: Jerry LR Chandler 
Para:   fis Webinar 
CC: 	Pedro Marijuan , Bruno Marchal 





Bruno, List:

de Chardin has also cast a long and durable shadow over my mind for 
decades for decades. His writings both provides some guidance on the 
form of time and opens rich questions that bring fruit.


  While I appreciate the flow of concepts emerging from Bruno’s 
“poetry”, its guidance appears to exclude chemistry and biology.


Thus, Bruno’s  associations are not so clear to me.  So, I will be a 
“spoil sport” and look toward a more “life-friendly” flow of both 
symbols and numbers with only a tad of poetry.


On Mar 3, 2017, at 11:51 AM, Bruno Marchal > wrote:




My favorite de Chardin's proposition is, from memory:

 "We are not human beings having spiritual experiences, we are 
spiritual beings having human experiences.



That is close to the theology of the neopytagorean Moderatus of Gades, 
and close to the neoplatonist Plotinus, Porphyry, ... And they are 
formally close to the "theology" of the universal numbers. (and even 
intuitively so assuming the computationalist hypothesis in cognitive 
science, through sequence of thought experiences).


The tensions between the computational natures of discrete and the 
“continuous” numbers haunts  any attempt to make mathematical sense out 
of scientific hypotheses. I am uncertain as to the logical implication 
of the “computationalist’s hypothesis" in this context.


Is the reference grounded in Curry’s combinatorial logic or otherwise?



It reminds me also of Shrî Aurobindo, when he said:


"What, you ask, was the beginning of it all?

And it is this ...
Existence that multiplied itself
For sheer delight of being
And plunged into numberless trillions of forms
So that it might
Find
Itself
Innumerably"


I have some minor problems with the present essay, but substituting 
some of the excessively teleological "purposive" terms about life 
(perhaps all of them?), and using instead a more austere description 
of organizational facts who knows! If life contains a unitary 
principle, I think it is more subtle, and cannot be expressed in 
unilateral physical terms



Provably so if we assume mechanism. Contrarily to a widely spread 
opinion: mechanism is not compatible with even quite weak form of 
materialism, or physicalism.


The connotations of the term “mechanism” varies widely from discipline 
to discipline.
The sense of “mechanism” in chemistry infers an electrical path among 
the discrete paths of  illations that “glue” the parts into a whole.  By 
sublation, this same sense is used in molecular biology and the 
biomedical sciences.


Bruno, could you expand on your usage in this context?  How do the 
senses of “computationism" and “mechanism” refer to the material world, 
if at all?





such as maximum entropy production, symmetry restoration, free energy 
maximization, etc. Well, symmetry and information have more clout and 
hidden complexity, so I express not a rejection but some uneasiness 
regarding too direct "orthogenetic" views on biological and social 
evolution.


My further suggestion --could it be a good idea that you change 
Monod's style "unpleasantness" (Oh, we the accidental discover that 
we are alone in the cosmos!) and point towards some of Teilhard's and 
Vernadsky's noosphere and the Omega Point? You would have several 
curious items to choose...


More opinions??



God created the natural numbers, and saw that it was good.


Would it be more accurate to that “"God" created the internal creativity 
of the atomic numbers."


Then she said: add yourself, and saw that is was good.

Then she said: multiply yourself. And then ... she said: oops, ... and 
lose control.


The addition of the atomic numbers has bounds because it is not linked 
to the concept of variables.  How does one see the internal controls 
without the geometry associated with variables?   (In the absence of a 
Cartesian co-ordinate system?)


Like the complexity of the prime numbers distribution already 
illustrates, the logicians know that classical logic + addition of 
integers + multiplication of integers leads to the Church-Turing 
Universality of the reality under concern, "generating *all* universal 
numbers, and they know that the universal machines, or universal 
numbers put a lot of mess in Plato Heaven. The price of universality 
is loss of controllability, and the appearances of realms defying all 
complete theories.


The perplexity of the atomic numbers creates its internal co-ordination 
without an apparent source of “universality” or “universal numbers”. 
 The ampliative logic of electrical bindings appears to create 
irregular self-regulation without a 

Re: [Fis] Further Discussion . . .

[Pedro C. Marijuan]

Dear Howard,

In any extent, your beautiful questions are beyond my reach. I think 
that the physical characterization of life cannot even provide a whim on 
your demands; but something of the informational might provide some 
limited inroads: prokaryots could not achieve any significant progress 
in morphological or differentiation capabilities within their 
"colonies". Conversely, eukaryotes developed multicellularity due to 
their far higher information content (genome), their far improved 
signaling resources, their endless energy supply in support of the 
general combinatoric problem-solving tools (mitochondria), and the 
incorporation of a new locus (cytoskeleton) capable of feeling the force 
field and reacting to it. A chain of amazing inventions is behind any of 
the existing branches of complex life... can do they admit a general 
explanation, not just based on natural selection, but on the improved 
evolvability that has been obtained by being able to explore any 
molecular-recognition contraption (within partially collapsed solution 
state-spaces, a la Wagner?). Otherwise we are lead to admit a deep 
enigma, still uncharted, or to look for external "intelligence" 
solutions outside the limits of current scientific paradigms.


What is your own opinion??

Best wishes--Pedro

   El 09/02/2017 a las 22:44, howlbl...@aol.com escribió:

fascinating thinking, pedro.
it triggers this:

The stages of development are far more than real-world problem 
solvers.They set artificial challenges, then achieve them.Making a 
caterpillar that works is anenormously complex challenge.Making a 
working butterfly is also immensely more complex than any simple 
challenge mounted by the environment.Changing from caterpillar to 
butterfly in one lifetime is unachievable beyond all belief.And these 
grotesquely artificial goals can’t be accounted for by a simple goal 
of survival.The goal, if anything, seems to be to accomplish the 
ornate, the unnecessary, the flamboyant, and the impossible.How does a 
drive toward impossible flamboyance get built intolife?How doesit get 
built into the cosmos?


with warmth and oomph--howard
--
Howard Bloom
Howardbloom.net
author of : The Lucifer Principle: A Scientific Expedition Into the 
Forces of History ("mesmerizing"-The Washington Post), Global Brain: 
The Evolution of Mass Mind from the Big Bang to the 21st Century  
("reassuring and sobering"-The New Yorker), The Genius of the Beast: A 
Radical Re-Vision of Capitalism ("Impressive, stimulating, and 
tremendously enjoyable."James Fallows, National Correspondent, The 
Atlantic), The God Problem: How A Godless Cosmos Creates ("Bloom's 
argument will rock your world." Barbara Ehrenreich), How I 
Accidentally Started the Sixties (“a monumental,epic, glorious 
literary achievement.” Timothy Leary), and The Muhammad Code:  How a 
Desert Prophet Gave You ISIS, al Qaeda, and Boko Haram--or How 
Muhammad Invented Jihad (“a terrifying book…the best book I’ve read on 
Islam,” David Swindle, PJ Media).
Former Core Faculty Member, The Graduate Institute; Former Visiting 
Scholar—Graduate Psychology Department, NewYork University
Founder: International PaleopsychologyProject; founder and chair, 
Space Development Steering Committee; Founding Board Member: Epic of 
Evolution Society; Founding Board Member, The Darwin Project; Board Of 
Governors, National Space Society; Founder: The Big Bang Tango Media 
Lab; member: New York Academy of Sciences, American Association for 
the Advancement of Science, American Psychological Society, Academy of 
Political Science, Human Behavior and Evolution Society, International 
Society for Human Ethology, Scientific Advisory Board Member, Lifeboat 
Foundation.
In a message dated 2/9/2017 3:22:55 P.M. Eastern Standard Time, 
pcmarijuan.i...@aragon.es writes:


Dear Marcus and Colleagues,

Thanks for your interest. The Chengdu's Conference represented for
me an occasion to return to my beginnings, in the 80's, when I
prepared a PhD Thesis: "Natural Intelligence: On the evolution of
biological information processing". It was mostly following a top
down approach. But in some of the discussions outdoors of the
conference (a suggestion for the next one in Shanghai: plenary
discussion sessions should also be organized) I realized that
biomolecular things have changed quite a lot. One could go
nowadays the other way around: from the molecular-informational
organization of cellular life, to intelligence of the cell's
behavior withing the environment. The life cycle es essential. It
provides the source of "meaning" (as I have often argued in
discussions in the list) but it is also the reference for
"intelligence". Communicating with the environment and
self-producing by means of the environmental affordances have to
be smoothly organized so that the stages of the life cycle may be
advanced, and that the "problems" arising from the 

[Fis] Further Perspectives

[Pedro C. Marijuan]

Dear FISers,

After the Lecture, Many Thanks to Otto, for bringing us that Curious 
Story... let us hope that an outcome will be found, as Jerry stated: "I 
see this “curious” behavior as a political problem that can be addressed 
by seeking a political solution that respects scientific traditions and 
hence, to motivate senior CERN officials to act honorably in the best 
interests of all."


In next weeks some further discussion might be started, but at the time 
being, the slot is empty (any ideas?). In the meantime I include 
information about _two conferences_ organized by FIS parties, one by 
Krassimir Markov and the other by Marcin Schroeder, and also about_two 
books_ from FIS colleagues as well, Maxine Sheets-Johnstone and Hans von 
Baeyer.


*_From Krassimir:_*

I kindly invite everybody to take part in the ITHEA ITA conferences in 
Varna, Bulgaria, where there exists the General Information Theory (GTI) 
International Conference.
Please see the Call For Papers at the ITHEA web site: 
http://www.ithea.org/conferences/conferences.html
In addition, during ITA 2017 International Summer School on Informatics 
(ISSI), also in Varna, a Workshop on the General Information Theory is 
planned as well. Two specific FIS meetings already took place in this 
Summer School.

Friendly greetings to all.

*_From Marcin:_*

This Symposium has as its main goal an exchange of views and opinions, 
sharing knowledge and discussion of the methods to integrate curriculum 
helping to educate new generations in the manner propagating a holistic 
world view. Mathematics and increased level of abstraction are natural 
sources of the methods of unification of knowledge and of curriculum. 
The concept of symmetry provides an example of the program of 
unification of the methods of inquiry across virtually all disciplines 
of human intellectual activity. Whether successful or not, it can serve 
as a starting point for the discussion of the curricular reforms. We 
invite contributions to the discussion in the form of oral presentations 
of relevant papers.
Integrative Methods of Inquiry in Education. Symposium at Akita 
International University
Akita Japan, March 29-30, 2017 https://amsig.github.io/IMIE2017/ __ 
 

(Deadline for abstract submission March 1, 2017)

*Book from Maxine: *Insides and Outsides: Interdisciplinary Perspectives 
on Animate Nature. Imprinting Academic, 2016.
*Book from Hans: *QBism: The Future of Quantum Physics Hardcover. 
Harvard University Press, 2017.


Best wishes to all--Pedro

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] End of the NY Lecture (From Otto Rossler)

[Pedro C. Marijuan]

Dear Pedro and dear Plamen, dear FIS list:


Thank you very much for your kindness.

Can I simply say the following? I call it

"A Confession"

It is beautiful to find oneself in a still existing 
theoretical-biological community, as I learned to swim in under the 
guidance of my friend Bob Rosen. I also enjoyed the friendship of 
Gregory Bateson. And of Michael Conrad, pupil of Dirac's. And of Jack 
Hudson. And Okan Gurel and Benoit Mandelbrot and Edward Lorenz. To date, 
we all celebrate the ongoing strength of Ralph Abraham who was always 
singularly fearless. And there are the Japanese schools of Kunihiko 
Kaneko and Ichiro Tsuda and Yukio-Pegio Gunji. And there is the 
optimal-foraging genius Eric L. Charnov in the Midwest.


The brain equation was made possible by my early discussions with Konrad 
Lorenz in 1966 which led to the distinction between "metabolic 
adaptation" (Darwin) and "positional adaptation" which has the asset of 
being independent of historical accidents and therefore being 
mathematically predictable. I could hereby integrate my experience made 
with bonding in a young doomed child which I was not allowed to adopt as 
a youth. Later, my young son had to leave at 7 3/4. Most recently, 
Szilamandee arose from those combined emotional and 
theoretical-biological experiences, if I may call them so: from the 
"smile theory." The fact that the therapeutic professions refused to 
employ it for 40 years as a causal therapy of early childhood autism, is 
a burden on me. In recent times, my courses on philosophy held at 
Ottersberg University enabled me to go farther than ever in the 
interaction with young minds. But also my Tübingen students are a 
fountain of mutual affirmation.


All of this is classical thinking in the footsteps of Teilhard, if you 
so wish. But there is this other reality of the quanta and of the 
strange observer-centered speed of light. Here I was blessed with the 
friendship of John Wheeler and John Bell, and through the latter along a 
long line with the Dalai Lama who never learned of this connection I am 
sure. Here most recently, the quantum satellite of Anton Zeilinger and 
Jianwei Pan's makes it possible to empirically decide between the 
rational quantum mechanics of Everett ("the world is made for me") and 
the bland irrational version of Niels Bohr's that Einstein abhorred so 
profoundly.


If you wish, these theories are also nothing but theoretical biology -- 
the endophysical approach.


But: none of this has anything to do with the CERN-based dialog which 
developed in the present community recently, for which fact I am so much 
endebted to you. The insight that only people who have learned to think 
in the biological way can shoulder the task of criticizing naive 
physicists, is a new one to me.


I mean, to in a maximally naive pride generate the hottest resident spot 
anywhere in the universe down on earth (underneath a Swiss town) and to 
boast to thereby have "pulled the Big Bang down onto earth" (a deeply 
erroneous concept in itself) is odd enough to watch. Even more so is it 
to then see them stick for 9 years to the order "zero risk" so that even 
their learned old safety report LSAG could no longer be renewed since 9 
years was an "interesting" experience to make for a theoretical 
biologist. Only people who have learned to think in terms of systems -- 
not to say in the way of the "Rashevsky-Rosen school" -- are able to 
independently judge the naive pseudo-military thoughts and doings of 
physicists who never saw any of the complexity of life in their more 
narrow-minded education.


I mentioned Szilamandee and the Thailand Royal house? It was my 
philosophy students in Ottersberg who triggered the proposed superperson 
experiment: That it is possible to find a higher earthly intelligence 
who can explain in a tactful manner (as I can't) why humankind was 
unable to abandon warfare over 15 millennia. I have to bow before 
Mandela here who worked a miracle in history within one country, and 
already a second one has followed. He also lost a 7 years old child.


C. Andy Hilgartner, the belated pupil of the Polish theoretical 
biologistAlfred Korzybski's, must be mentioned here too, a uniquely 
modest and independent active thinker almost a decade my senior. And 
without ever having had any contact, I must also acknowledge the 
strength and spirit of Freeman Dyson.


Presently, we have the chance to pull a fledgling president over onto 
our side. I still hope that one of his advisors can make it plausible to 
him that, when the whole physics discipline cannot renew the safety 
report of its "Big Bang drawn down onto earth" experiment for nine years 
in a row, it is not a bad idea to demand from them to first renew their 
for so long outdated safety report LSAG before being allowed to continue 
if they can. But at this point the needle in my vinyl has hit a periodic 
orbit: Shall I start anew?


Take care, my dear friends -- your brother Otto

Re: [Fis] Fw: A Curious Story

[Pedro C. Marijuan]

Dear Joseph, Bob, and Otto --and All,

Thanks for the responses. First to Joseph and Bob: my interpretation of 
Conrad's is not literal, at least at the time being, as I think that the 
information themes are changing very fast in the quantum --recent 
interpretations of entanglement and black holes by the group IT FROM 
QUBIT say extremely interesting "generative" things about 
space-time-info and cosmology. See Juan Maldacena (Sci. Am. Nov. 2016) 
and Clara Moskowitz (Sci.Am. Jan. 2017). The way I take Conrad's is as a 
call to a new way of thinking on physical information, biologically 
inspired, rather than the common opposite direction. And also I extend 
it to reconsider the nature of physical reality and of "laws of nature" 
themselves--the distributed "genomes" of this cosmos. Our recurrent 
discussions on what's info cannot consolidate until we adumbrate a good 
portion of such new way of thinking--I am not criticizing them, but 
asking for augmented doses of tolerance and patience. Let me be a little 
provocative: none of us has walked yet the extra mile(s) needed. We have 
to recognize that we are far from the new info paradigm and must keep 
circling around Jericho walls...


Unless until the little thing that Otto is warning knocks in our doors. 
I cannot respond to the symmetry difference and to the probability 
arguments--the main question to debate indeed. Sure that the previous 
scientific generation would have entered nonchalantly to this debate. 
But not the business-politics oriented figures of today (social networks 
panic). Well, at least I can comment on the last paragraphs on the 
framework surrounding the frustrated discussion. The global health and 
adaptability of the scientific enterprise seem to be in jeopardy. 
Coincidentally, we are lead to remind Conrad's tradeoff between 
computation and adaptability/evolvability? As computing has enormously 
increased its efficiency and social reach, the social adaptability via 
new thought and new research is decreasing and surrounding itself in a 
tunnel vision. See for instance what are the coming flagship programs in 
the EUnion after the Human Brain Project: "Future of [digital] 
Healthcare" and "Robot Companions for Citizens." Yeah, a lot of people 
--elderly-- will be alone: let's make nice robots for them. Even they 
will learn to smile and laugh, and we will create bonds with them as the 
Szilamandee paper from Otto says--and also my own research on laughter 
(see link below). Techno-pseudo-happiness for everybody... Yes, fresh 
new views from social science and humanities would have plenty to say.


Best wishes--Pedro
http://www.emeraldinsight.com/doi/abs/10.1108/K-02-2016-0026


El 21/01/2017 a las 9:32, Joseph Brenner escribió:

Dear Pedro and All,
Thanks to Pedro again for this thought-provoking theme. We are all in 
states of greater or lesser ignorance regarding it!
Here is just, again, a thought about your quote of Conrad: "/when we 
look at a biological system we/ are looking at the face of the 
underlying /physics of the universe/."
I.M.H.O., this statement is true but only partially so. There are 
non-thermodynamic parts of the underlying physics of the universe that 
are not visible at the biological level of reality, and a coupling 
between them remains to be demonstrated. Quantum superposition and 
self-duality have analogies in macroscopic physics, but quantum 
non-locality and sub-quantum fluctuations do not.
Of course, if you allow slightly altered laws of nature, many things 
may be possible as Smolin suggests. However, I suggest that the domain 
of interaction between actual and potential states in our everyday 
'grown-up' world also has things to tell us, /e.g./, about 
information, that can be looked at more easily.

Best wishes,
Joseph
- Original Message -
*From:* Pedro C. Marijuan <mailto:pcmarijuan.i...@aragon.es>
*To:* 'fis' <mailto:fis@listas.unizar.es>
*Sent:* Friday, January 20, 2017 1:58 PM
*Subject:* Re: [Fis] A Curious Story

Dear Otto and colleagues,

Thanks for the curious story and sorry that my absorption in low level 
administrative themes has knocked me down-down during these weeks. But 
not being a physicist, and even not a third rate aficionado, I can 
contribute very little to the exchanges. At least I will try to remark 
a couple of lateral aspects:


First, when I heard about this story, I was amazed how hysterical the 
web records were. On the one side, the tabloid style comments and the 
malicious personal attacks, and on the other side the offended, 
irritated scientists. That your opinion deserved a "Charge of the 
Nobel Brigade" with all those big names hurried together to smitten 
any possible doubt, was sort of humorous. Wasn't from Horace that 
saying of "vociferant montes et parturient ridiculus mus"? My 
impression is that all those hyperactive new media have deteriorated 
the e

Re: [Fis] A Curious Story

[Pedro C. Marijuan]

Dear Otto and colleagues,

Thanks for the curious story and sorry that my absorption in low level 
administrative themes has knocked me down-down during these weeks. But 
not being a physicist, and even not a third rate aficionado, I can 
contribute very little to the exchanges. At least I will try to remark a 
couple of lateral aspects:


First, when I heard about this story, I was amazed how hysterical the 
web records were. On the one side, the tabloid style comments and the 
malicious personal attacks, and on the other side the offended, 
irritated scientists. That your opinion deserved a "Charge of the Nobel 
Brigade" with all those big names hurried together to smitten any 
possible doubt, was sort of humorous. Wasn't from Horace that saying of 
"vociferant montes et parturient ridiculus mus"? My impression is that 
all those hyperactive new media have deteriorated the exchange and 
maturation of scientific opinion. The fate of your position on those 
hypothetic risks was irrationally discounted.


And about the theme itself, I join one of the initial comments on the 
energy of singular cosmic rays, probabilistically having to cause such 
microscopic destructive  black holes in The Moon and somewhere else. The 
wide swaths of the cosmos we watch today do not show sudden instances of 
planet or star disappearance.  As many thousands and millions of those 
are well followed nowadays without reports of sudden destruction: can 
this "stable" cosmos be an extra argument in the discussion? Let me 
improvise some further views: Black holes relate "quite a bit" to 
information matters. The controversy between Hawking, Penrose, etc. 
about the fate of the quantum information engulfed seemingly emitted is 
not the end of the story I think. If everything should make functional 
sense in an integrated "organismic" cosmos, the functionality of black 
holes is really enigmatic. They just become a reservoir of dark matter 
for gravity? In this point our common friend Michael Conrad (1996) 
put"/when we look at a biological system we/ are looking at the face of 
the underlying /physics of the universe/." Thereupon, I have always 
thought about the similarity between cellular proteasomes (protein 
destructing machines) and the cosmic (destructive) black holes. But the 
former RECYCLE and emit single amino acid components for reuse, and then 
would the latter provide only residual gravity? Lee Smolin said 
something bold: they recycle too, and produce "baby universes" with 
slightly altered laws of nature. Our planet final blimps would have some 
more fun incorporated (with the big IF, of course)...


Best wishes

--Pedro



  lEl 11/01/2017 a las 11:33, Otto E. Rossler escribió:

I like this response from Lou,
Otto


--------
*From:* Louis H Kauffman <lou...@gmail.com>
*To:* Pedro C. Marijuan <pcmarijuan.i...@aragon.es>
*Cc:* fis <fis@listas.unizar.es>
*Sent:* Tuesday, January 10, 2017 6:09 PM
*Subject:* Re: [Fis] A Curious Story

Dear Folks,
It is very important to not be hasty and assume that the warning 
Professor Rossler made is to be taken seriously.
It is relatively easy to check if a mathematical reasoning is true or 
false.
It is much more difficult to see if a piece of mathematics is 
correctly alligned to physical prediction.

Note also that a reaction such as
"THIS STORY IS A GOOD REASON FOR SHUTTING DOWN CERN PERMANENTLY AND 
SAVING A LOT OF LARGELY WASTED MONEY.”.
Is not in the form of scientific rational discussion, but rather in 
the form of taking a given conclusion for granted

 and using it to support another opinion that is just that - an opinion.

By concatenating such behaviors we arrive at the present political 
state of the world.


This is why, in my letter, I have asked for an honest discussion of 
the possible validity of Professor Rossler’s arguments.


At this point I run out of commentary room for this week and I shall 
read and look forward to making further comments next week.

Best,
Lou Kauffman


On Jan 9, 2017, at 7:17 AM, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:



From Alex Hankey
 Mensaje reenviado 
Asunto: Re: [Fis] A Curious Story
Fecha:  Sun, 8 Jan 2017 19:55:55 +0530
De: Alex Hankey <alexhan...@gmail.com> <mailto:alexhan...@gmail.com>
Para: 	PEDRO CLEMENTE MARIJUAN FERNANDEZ <pcmarijuan.i...@aragon.es> 
<mailto:pcmarijuan.i...@aragon.es>




THIS STORY IS A GOOD REASON FOR SHUTTING DOWN CERN PERMANENTLY AND 
SAVING A LOT OF LARGELY WASTED MONEY.


On 5 January 2017 at 16:36, PEDRO CLEMENTE MARIJUAN FERNANDEZ 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote:


Dear FISers,

Herewith the Lecture inaugurating our 2017 sessions.
I really hope that this Curious Story is j

[Fis] Fwd: Re: A Curious Story (L. Kauffman)

[Pedro C. Marijuan]

 Mensaje reenviado 
Asunto: Re: [Fis] A Curious Story
Fecha:  Sun, 8 Jan 2017 10:36:07 -0600
De: Louis H Kauffman 
Para:   PEDRO CLEMENTE MARIJUAN FERNANDEZ 
CC: fis@listas.unizar.es 



Dear Pedro,
Ok. Can we have the text of Professor Rossler’s proof that these 
mini-black holes


  * cannot Hawking evaporate
  * grow exponentially inside matter?


It would be very interesting to debate the details.

I find on the web:
http://www.wissensnavigator.com/documents/ottoroesslerminiblackhole.pdf

http://www.science20.com/big_science_gambles/blog/interview_professor_otto_rössler_takes_lhc-31449 



http://www.telegraph.co.uk/news/worldnews/europe/2650665/Legal-bid-to-stop-CERN-atom-smasher-from-destroying-the-world.html

http://environmental-impact.web.cern.ch/environmental-impact/Objects/LHCSafety/NicolaiComment-en.pdf

Best,
Lou Kauffman


On Jan 5, 2017, at 5:06 AM, PEDRO CLEMENTE MARIJUAN FERNANDEZ 
> wrote:


Dear FISers,

Herewith the Lecture inaugurating our 2017 sessions.
I really hope that this Curious Story is just that, a curiosity.
But in science we should not look for hopes but for arguments and 
counter-arguments...


Best wishes to All and exciting times for the New Year!
--Pedro




*De:*Otto E. Rossler [oeros...@yahoo.com ]
*Enviado el:*miércoles, 04 de enero de 2017 17:51
*Para:*PEDRO CLEMENTE MARIJUAN FERNANDEZ
*Asunto:* NY session
--

*A Curious Story*
Otto E. Rossler, University of Tübingen, Germany

Maybe I am the only one who finds it curious. Which fact would then 
make it even more curious for me. It goes like this: Someone says “I 
can save your house from a time bomb planted into the basement” and 
you respond by saying “I don’t care.” This curious story is taken from 
the Buddhist bible.
It of course depends on who is offering to help. It could be a lunatic 
person claiming that he alone can save the planet from a time-bomb 
about to be planted into it. In that case, there would be no reason to 
worry. On the other hand, it could also be that you, the manager, are 
a bit high at the moment so that you don't fully appreciate the offer 
made to you. How serious is my offer herewith made to you today?
I only say that for eight years' time already, there exists no 
counter-proof in the literature to my at first highly publicized proof 
of danger. I was able to demonstrate that the miniature black holes 
officially attempted to be produced at CERN do possess two radically 
new properties:


  * they cannot Hawking evaporate
  * they grow exponentially inside matter

If these two findings hold water, the current attempt at producing 
ultra-slow miniature black holes on earth near the town of Geneva 
means that the slower-most specimen will get stuck inside earth and 
grow there exponentially to turn the planet into a 2-cm black hole 
after several of undetectable growth. Therefore the current attempt of 
CERN's to produce them near Geneva is a bit curious.
What is so curious about CERN's attempt? It is the fact that no one 
finds it curious. I am reminded of an old joke: The professor informs 
the candidate about the outcome of the oral exam with the following 
words “You are bound to laugh but you have flunked the test.” I never 
understood the punchline. I likewise cannot understand why a never 
refuted proof of the biggest danger of history leaves everyone 
unconcerned. Why NOT check an unattended piece of luggage on the 
airport called Earth?
To my mind, this is the most curious story ever -- for the very reason 
that everyone finds it boring. A successful counter-proof would thus 
alleviate but a single person’s fears – mine. You, my dear reader, are 
thus my last hope that you might be able to explain the punch line to 
me: “Why is it that it does not matter downstairs that the first floor 
is ablaze?” I am genuinely curious to learn why attempting planetocide 
is fun.  Are you not?


For J.O.R.
---



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[Fis] Fwd: Re: A Curious Story (J. Brenner)

[Pedro C. Marijuan]

 Mensaje reenviado 
Asunto: Re: [Fis] A Curious Story
Fecha:  Sun, 8 Jan 2017 10:32:50 +0100
De: Joseph Brenner 
Responder a:Joseph Brenner 
Para: 	PEDRO CLEMENTE MARIJUAN FERNANDEZ , 
fis@listas.unizar.es




Dear All,
Happy New Year indeed! Let us all 'hope' (here OK) that 2017 does not 
turn into 1984. . .

Regarding the proposed discussion topic, I have two suggestions:
1) everyone should read, at least, the excellent and recent (Dec., 2016) 
Wikipedia article on Small Black Holes, so that we can share a minimum 
background (sic);
2) Otto should please tell us his theory of why miniature black holes 
from any source should not Hawking evaporate after exhausting the matter 
within a Fermi distance, thus eliminating the possibility of further growth.

'Cheers',
Joseph

   - Original Message -
   *From:* PEDRO CLEMENTE MARIJUAN FERNANDEZ
   
   *To:* fis@listas.unizar.es 
   *Sent:* Thursday, January 05, 2017 12:06 PM
   *Subject:* [Fis] A Curious Story

   Dear FISers,

   Herewith the Lecture inaugurating our 2017 sessions.
   I really hope that this Curious Story is just that, a curiosity.
   But in science we should not look for hopes but for arguments and
   counter-arguments...

   Best wishes to All and exciting times for the New Year!
   --Pedro



   
   *De:* Otto E. Rossler [oeros...@yahoo.com]
   *Enviado el:* miércoles, 04 de enero de 2017 17:51
   *Para:* PEDRO CLEMENTE MARIJUAN FERNANDEZ
   *Asunto:* NY session
   --

   *A Curious Story*
   Otto E. Rossler, University of Tübingen, Germany

   Maybe I am the only one who finds it curious. Which fact would then
   make it even more curious for me. It goes like this: Someone says “I
   can save your house from a time bomb planted into the basement” and
   you respond by saying “I don’t care.” This curious story is taken
   from the Buddhist bible.
   It of course depends on who is offering to help. It could be a
   lunatic person claiming that he alone can save the planet from a
   time-bomb about to be planted into it. In that case, there would be
   no reason to worry. On the other hand, it could also be that you,
   the manager, are a bit high at the moment so that you don't fully
   appreciate the offer made to you. How serious is my offer herewith
   made to you today?
   I only say that for eight years' time already, there exists no
   counter-proof in the literature to my at first highly publicized
   proof of danger. I was able to demonstrate that the miniature black
   holes officially attempted to be produced at CERN do possess two
   radically new properties:

 * they cannot Hawking evaporate
 * they grow exponentially inside matter

   If these two findings hold water, the current attempt at producing
   ultra-slow miniature black holes on earth near the town of Geneva
   means that the slower-most specimen will get stuck inside earth and
   grow there exponentially to turn the planet into a 2-cm black hole
   after several of undetectable growth. Therefore the current attempt
   of CERN's to produce them near Geneva is a bit curious.
   What is so curious about CERN's attempt? It is the fact that no one
   finds it curious. I am reminded of an old joke: The professor
   informs the candidate about the outcome of the oral exam with the
   following words “You are bound to laugh but you have flunked the
   test.” I never understood the punchline. I likewise cannot
   understand why a never refuted proof of the biggest danger of
   history leaves everyone unconcerned. Why NOT check an unattended
   piece of luggage on the airport called Earth?
   To my mind, this is the most curious story ever -- for the very
   reason that everyone finds it boring. A successful counter-proof
   would thus alleviate but a single person’s fears – mine. You, my
   dear reader, are thus my last hope that you might be able to explain
   the punch line to me: “Why is it that it does not matter downstairs
   that the first floor is ablaze?” I am genuinely curious to learn why
   attempting planetocide is fun.  Are you not?

   For J.O.R.
   ---



   
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[Fis] Fwd: Re: A Curious Story

[Pedro C. Marijuan]

From Alex Hankey

 Mensaje reenviado 

Asunto: Re: [Fis] A Curious Story
Fecha:  Sun, 8 Jan 2017 19:55:55 +0530
De: Alex Hankey 
Para:   PEDRO CLEMENTE MARIJUAN FERNANDEZ 



THIS STORY IS A GOOD REASON FOR SHUTTING DOWN CERN PERMANENTLY AND 
SAVING A LOT OF LARGELY WASTED MONEY.


On 5 January 2017 at 16:36, PEDRO CLEMENTE MARIJUAN FERNANDEZ 
> wrote:


   Dear FISers,

   Herewith the Lecture inaugurating our 2017 sessions.
   I really hope that this Curious Story is just that, a curiosity.
   But in science we should not look for hopes but for arguments and
   counter-arguments...

   Best wishes to All and exciting times for the New Year!
   --Pedro



   
   *De:* Otto E. Rossler [oeros...@yahoo.com ]
   *Enviado el:* miércoles, 04 de enero de 2017 17:51
   *Para:* PEDRO CLEMENTE MARIJUAN FERNANDEZ
   *Asunto:* NY session
   --

   *A Curious Story*
   Otto E. Rossler, University of Tübingen, Germany

   Maybe I am the only one who finds it curious. Which fact would then
   make it even more curious for me. It goes like this: Someone says “I
   can save your house from a time bomb planted into the basement” and
   you respond by saying “I don’t care.” This curious story is taken
   from the Buddhist bible.
   It of course depends on who is offering to help. It could be a
   lunatic person claiming that he alone can save the planet from a
   time-bomb about to be planted into it. In that case, there would be
   no reason to worry. On the other hand, it could also be that you,
   the manager, are a bit high at the moment so that you don't fully
   appreciate the offer made to you. How serious is my offer herewith
   made to you today?
   I only say that for eight years' time already, there exists no
   counter-proof in the literature to my at first highly publicized
   proof of danger. I was able to demonstrate that the miniature black
   holes officially attempted to be produced at CERN do possess two
   radically new properties:

 * they cannot Hawking evaporate
 * they grow exponentially inside matter

   If these two findings hold water, the current attempt at producing
   ultra-slow miniature black holes on earth near the town of Geneva
   means that the slower-most specimen will get stuck inside earth and
   grow there exponentially to turn the planet into a 2-cm black hole
   after several of undetectable growth. Therefore the current attempt
   of CERN's to produce them near Geneva is a bit curious.
   What is so curious about CERN's attempt? It is the fact that no one
   finds it curious. I am reminded of an old joke: The professor
   informs the candidate about the outcome of the oral exam with the
   following words “You are bound to laugh but you have flunked the
   test.” I never understood the punchline. I likewise cannot
   understand why a never refuted proof of the biggest danger of
   history leaves everyone unconcerned. Why NOT check an unattended
   piece of luggage on the airport called Earth?
   To my mind, this is the most curious story ever -- for the very
   reason that everyone finds it boring. A successful counter-proof
   would thus alleviate but a single person’s fears – mine. You, my
   dear reader, are thus my last hope that you might be able to explain
   the punch line to me: “Why is it that it does not matter downstairs
   that the first floor is ablaze?” I am genuinely curious to learn why
   attempting planetocide is fun.  Are you not?

   For J.O.R.
   ---




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--
Alex Hankey M.A. (Cantab.) PhD(M.I.T.)
Distinguished Professor of Yoga and Physical Science,
SVYASA, Eknath Bhavan, 19 Gavipuram Circle
Bangalore 560019, Karnataka, India
Mobile (Intn'l): +44 7710 534195
Mobile (India) +91 900 800 8789


2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, 
Mathematics and Phenomenological Philosophy 

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[Fis] List problems

[Pedro C. Marijuan]

Dear FISers,

The problems with the spam filters continue. My own message with the 
Lecture was delayed 3 days.

Further responses by Joseph, Lou, Terry and others have not appeared yet.
I am talking with the University of Zaragoza officers in charge of the 
server...

It is appalling that we have to suffer all these incidents

Sorry about that.
--Pedro

PS. Please, send all your messages with copy to me.

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Season Greetings

[Pedro C. Marijuan]

Dear FIS Colleagues,

As is customary in this list, let me wish all of you Merry Xmas and a 
Happy New Year.


Herewith a Nativity Scene taken from "El Pilar" Cathedral in Zaragozal.

As is customary too, the NEW YEAR LECTURE will be announced in a few days.

All the best--Pedro



NATIVITY SCENE

*
*

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] dimensions and symmetries... About KP Collins

[Pedro C. Marijuan]

Dear Arturo and FISers,

The last paragraphs of your chess game, pretty exciting, remind me 
strongly on the role that I have been attributing to cellular signaling 
systems, and the radical difference they have with metabolic cellular 
networks, although finally both are interrelated into the advancement of 
a life cycle at the cellular scale. As I have often commented, it is 
like reading the newspaper versus eating a sandwich, or better reading 
the menu carte versus devouring it.


Going back to nervous systems, the approach presented reminds me, more 
and more, the work of Kenneth Paul Collins in late 1980s and early 90s. 
His work was condensed in : /"On the Automation of Knowledge Within 
Central Nervous Systems."/ Unpublished Manuscript, presented as a poster 
at the AAAS Meeting in 1991, Boston. (Sorry Malcolm for giving the 
"reference" so late). I talked with him there, and was impressed by his 
work and kept in touch with him for several years. With his permission, 
I translated it into Spanish, changing some not well-solved aspects and 
adding a few more stuff: /"El Cerebro Dual: Un Acercamiento 
Interdisciplinar a la Naturaleza del Conocimiento Humano y Biológico" 
/Authors: KP Collins and PC Marijuan, published by /Editorial Hacer, 
Barcelona (1997)/. "The central principle of Duality Theory [am quoting 
from Kenneth, p.3] is that the neural arrays of the vertebrate Central 
Nervous System are physically organized so that their functioning will 
blindly minimize the sum of the topologically-distributed ratios of 
excitation to inhibition that occur within them."


Many more interesting quotations could be cited. But his manuscript of 
more than 100 dense pages did not attract any attention except a very 
few parties (essentially, me). He went down and down and my final 
indirect news were from some discussion lists where he was trolling in a 
sick way. At that time, I had received some alarming news from himself 
about his own deteriorating mental health... (late 90s/early 2000s).


Anyhow, in 1997 I published /"The Topological Inventions of Life: From 
the Specialization of Multicellular Colonies to the Functioning of the 
Vertebrate Brain."/ World Futures, 1997. 50. 617-631., where I was 
summarizing the basic tenets of his theory, and I have kept mentioning 
him in some of my publications. The point is that his work anticipated 
basic ideas nowadays developed by Arturo and James, Friston, Sengupta, 
etc. about CNS overall optimization principles, entropy/information, 
symmetries & antisymmetries, dynamic connectome, learning & trophic 
mechanisms, behavioral propensities, etc. He was particularly great 
connecting the abstract processing of neural information with human 
behavior, learning biases, emotional reactions ("the prejudice towards 
the familiar", violence, depression). With today's' new knowledge, some 
gaps in those views may be filled in, and viceversa, we could work and 
throw a new light upon his great behavioral insights. That's my personal 
opinion, of course, that was not very well received when I tried to talk 
about with relevant neuroscientists.


Well, it was a good occasion to tell this story in the list, that has 
always troubled me, and that now finally has found avantgarde germane 
developments.


Best wishes--Pedro

//

El 12/12/2016 a las 16:44, tozziart...@libero.it escribió:



Coming back to our chessboard, this means that information can be 
studied in terms of systems’ symmetries and changes in dimensions, 
rather than in terms of entropies and energetic gradient descents. 
  An object (on an event) embedded in an environment encompasses a 
certain amount of information, but such information increases when you 
add a further dimension to the environment (NOTE: non necessarily a 
spatial dimension, but also other possible ones, such as an increase 
of complexity).  Indeed, a dimension more gives you a coordinate more, 
and therefore more information.  To make the usual example, the 2D 
shadow of a cat encompasses less information than a 3D cat.  Some 
authors start from a very low number of dimensions (e.g., the 
holographic Universe of t’Hooft and Susskind), others from an high 
number (claims dating back to Spinoza and Kant and going through our 
Universe made of eleven-dimensional Kaluza-Klein manifolds and 
subsequent decrease of dimensions, until our 3D plus time perceivable 
environment).  It does not matter: when projecting among levels, 
information is always a function of the number of dimensions.
In such a framework, the role of energy is different from the role of 
information: the energy is something "injected" from the external 
"environment" into the system, in order to produce the change of 
coordinates into the system; on the other side, the changes of 
information can be detected into the system, and depend on the energy 
just indirectly (second-hand).  In other words:
a)  the system's change of dimensions  dictates the change in 

Re: [Fis] A provocative issue

[Pedro C. Marijuan]

Dear Arturo and FISers

We will forgive your life!  Some other people in this list also have 
strong reservations to a single, canonical approach to information, 
either from Shannon, Boltzmann, or Fisher backgrounds. In my case, 
mostly biologically and socially grounded ("sociotype"), I see a complex 
panorama of biological information, mostly "relative" concerning 
communication with the environment (via cellular signaling systems), but 
sort of "objective" concerning the inner self-production processes 
(shared DNA and genetic/translation and many other codes). But both are 
elegantly intertwined in the advancement of a life cycle. My hunch is 
that this type of relative/objective duality culminating in existential 
maintenance has some generality and could be "exported" to physics too. 
It is curious that some oriental thinkers (Chu-Hsi or Zhu Xi, 9 
Centuries ago) had already advanced sort of similar ideas... Well, above 
all, info is "paradoxical" and has kept all of us amused in this list, 
at least for the past twenty years!


Best--Pedro
PS. Let me remind that you have not answered yet my topo-evo comments in 
the earliest messages. That point is, I think, very important in the 
present discussion.


El 11/12/2016 a las 16:57, tozziart...@libero.it escribió:



Dear FISers,

I know that some of you are going to kill me, but there’s something 
that I must confess.


I notice, from the nice issued raised by Francesco Rizzo, Joseph 
Brenner, John Collier, that the main concerns are always 
energetic/informational arguments and accounts.


Indeed, the current tenets state that all is information, information 
being a real quantity that can be measured through informational 
entropies.


But… I ask to myself, is such a tenet true?

When I cook the pasta, I realize that, by my point of view, the cooked 
pasta encompasses more information than the not-cooked one, because it 
acquires the role of something that I can eat in order to increase my 
possibility to preserve myself in the hostile environment that wants 
to destroy me.  However, by the point of view of the bug who eats the 
non-cooked pasta, my cooked pasta displays less information for sure.  
Therefore, information is a very subjective measure that, apart from 
its relationship with the observer, does not mean very much…  Who can 
state that an event or a fact displays more information than another one?


And, please, do not counteract that information is a quantifiable, 
objective reality, because it can be measured through informational 
entropy… Informational entropy, in its original Shannon’s formulation, 
stands for an ergodic process (page 8 of the original 1948 Shannon’s 
seminal paper), i.e.: every sequence produced by the processes is the 
same in statistical properties, or, in other words, a traveling 
particle always crosses all the points of its phase space.  However, 
in physics and biology, the facts and events are never ergodic. 
 Statistical homogeneity is just a fiction, if we evaluate the world 
around us and our brain/mind.


Therefore, the role of information could not be as fundamental as 
currently believed.


P.S.: topology analyzes information by another point of view, but it’s 
an issue for the next time, I think…



*Arturo Tozzi*

AA Professor Physics, University North Texas

Pediatrician ASL Na2Nord, Italy

Comput Intell Lab, University Manitoba

http://arturotozzi.webnode.it/




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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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Fwd: Response to Jerry LR Chandler (From Arturo Tozzi)

[Pedro C. Marijuan]

(sorry, the problems continue, seemingly, and I have to re-enter the 
messages--Pedro)

---

Dear Jerry,

Thanks for the intriguing questions!

I thank our guest, Pedro Marijuan, for giving us the opportunity to talk 
with such high-ranked scientists.


 Let’s start!

/The questions raised in this post are highly provocative.  From the 
perspective of physical phenomenology, it is necessary to identify 
corresponding illations between the electric fields of brain dynamics 
(such as EEG patterns) and the mathematics of electric fields / 
electro-magnetism.  It goes without saying that such correspondences 
must associate the measured quantities with the theoretical quantities. 
 In other words, the units of measurements of “brain activity" should 
be associated with Maxwell’s equations./


Are we really sure that this proposition is true? How does central 
nervous system process information? Current theories are based on two 
tenets: (a) information is transmitted by action potentials, the 
language by which neurons communicate with each other—and (b) 
homogeneous neuronal assemblies of cortical circuits operate on these 
neuronal messages where the operations are characterized by the 
intrinsic connectivity among neuronal populations. In this view, the 
size and time course of any spike is stereotypic and the information is 
restricted to the temporal sequence of the spikes; namely, the “neural 
code”. However, an increasing amount of novel data point towards an 
alternative hypothesis: (a) the role of neural code in information 
processing is overemphasized. Instead of simply passing messages, action 
potentials play a role in dynamic coordination at multiple spatial and 
temporal scales, establishing network interactions across several levels 
of a hierarchical modular architecture, modulating and regulating the 
propagation of neuronal messages. (b) Information is processed at all 
levels of neuronal infrastructure from macromolecules to population 
dynamics. For example, intra-neuronal (changes in protein conformation, 
concentration and synthesis) and extra-neuronal factors (extracellular 
proteolysis, substrate patterning, myelin plasticity, microbes, 
metabolic status) can have a profound effect on neuronal computations. 
This means molecular message passing may have cognitive connotations. 
This essay introduces the concept of “supramolecular chemistry”, 
involving the storage of information at the molecular level and its 
retrieval, transfer and processing at the supramolecular level, through 
transitory non-covalent molecular processes that are self-organized, 
self-assembled and dynamic. Finally, we note that the cortex comprises 
extremely heterogeneous cells, with distinct regional variations, 
macromolecular assembly, receptor repertoire and intrinsic 
microcircuitry. This suggests that every neuron (or group of neurons) 
embodies different molecular information that hands an operational 
effect on neuronal computation.


For further details, see:

http://link.springer.com/article/10.1007/s11571-015-9337-1

/ In the philosophy of science, this is the basic distinction between 
traditional mathematical narratives as pure abstractions and APPLIED 
mathematical theories of explanations of scientific facts. /


Pursuing Quine’s naturalized epistemology, we are aware that we need to 
make testable previsions, in order to “link” mathematical theories with 
explanations of scientific facts.  This is exactly what we (try to) do.


The best example is the following, that shows how a novel approach might 
lead to unpredictable testable results:


Current advances in neurosciences deal with the functional architecture 
of the central nervous system, paving the way for general theories that 
improve our understanding of brain activity. From topology, a strong 
concept comes into play in understanding brain functions, namely, the 4D 
space of a “hypersphere’s torus”, undetectable by observers living in a 
3D world. The torus may be compared with a video game with biplanes in 
aerial combat: when a biplane flies off one edge of gaming display, it 
does not crash but rather it comes back from the opposite edge of the 
screen. Our thoughts exhibit similar behaviour, i.e. the unique ability 
to connect past, present and future events in a single, coherent picture 
as if we were allowed to watch the three screens of past-present-future 
“glued” together in a mental kaleidoscope. Here we hypothesize that 
brain functions are embedded in a imperceptible fourth spatial dimension 
and propose a method to empirically assess its presence. Neuroimaging 
fMRI series can be evaluated, looking for the topological hallmark of 
the presence of a fourth dimension. Indeed, there is a typical feature 
which reveal the existence of a functional hypersphere: the simultaneous 
activation of areas opposite 

[Fis] Fwd: NEW DISCUSSION SESSION--TOPOLOGICAL BRAIN (From Karl Javorszky)

[Pedro C. Marijuan]

Asunto: [Fis] NEW DISCUSSION SESSION--TOPOLOGICAL BRAIN
Fecha:  Wed, 30 Nov 2016 08:46:32 +0100
De: Karl Javorszky <karl.javors...@gmail.com>
Responder a:karl.javors...@gmail.com
Para:   fis <fis@listas.unizar.es>
CC:     Pedro C. Marijuan <pcmarijuan.i...@aragon.es>, tozziart...@libero.it



Topology

The session so far has raised the points: meta-communication, 
subject-matter, order, spaces.


a.) Meta-communication

Gordana’s summary explicates the need to have a system of references 
that FIS can use to discuss whatever it wishes to discuss, be it the 
equivalence between energy and information or the concept of space in 
the human brain. Whatever the personal background, interests or 
intellectual creations of the members of FIS, we each have been taught 
addition, multiplication, division and the like. We also know how to 
read a map and remember well where we had put a thing as we are going to 
retrieve it. When discussing the intricate, philosophical points which 
are common to all formulations of this session, it may be helpful to use 
such words and procedures that are well-known to each one of us, while 
describing what we do while we use topology.


b.)Subject-matter

Topology is managed by much older structures of the central nervous 
system than those that manage speech, counting, abstract ideas. Animals 
and small children remember their way to food and other attractions. 
Children discover and use topology far before they can count. Topology 
is a primitive ancestor to mathematics; its ideas and methods are 
archaic and may appear as lacking in refinement and intelligence.


c.) Order

There is no need to discuss whether Nature is well-ordered or not. Our 
brain is surely extremely well ordered, otherwise we had seizures, tics, 
disintegrative features. In discussing topology we can make use of the 
condition that everything we investigate is extremely well ordered. We 
may not be able to understand Nature, but we may get an idea about how 
our brain functions, in its capacity as an extremely well ordered 
system. We can make a half-step towards modelling artificial 
intelligence by understanding at first, how artificial instincts, and 
their conflicts, can be modelled. Animals apparently utilise a different 
layer of reality of the world while building up their orientation in it 
to that which humans perceive as important. The path of understanding 
how primitive instincts work begins with a half-step of dumbing down. It 
is no more interesting, how many they are, now we only look at where it 
is relative to how it appears, compared with the others.


d.)Spaces

Out of sequences, planes naturally evolve. Whether out of the planes 
spaces can be constructed, depends on the kinds of planes and of common 
axes. Now the natural numbers come in handy, as we can demonstrate to 
each other on natural numbers, how in a well-ordered collection the 
actual mechanism of place changes creates by itself two rectangular, 
Euclidean, spaces. These can be merged into one common space, but in 
that, there are four variants of every certainty coming from the 
position within the sequence. Furthermore, all these spaces are 
transcended by two planes. The discussion about an oriented entity in a 
space of n dimensions can be given a frame, placed into a context that 
is neutral and shared as a common knowledge by all members of FIS.



2016. nov. 29. 15:15 ezt írta ("Karl Javorszky" 
<karl.javors...@gmail.com <mailto:karl.javors...@gmail.com>>):


   Topology

   The session so far has raised the points: meta-communication,
   subject-matter, order, spaces.

   a.) Meta-communication

   Gordana’s summary explicates the need to have a system of references
   that FIS can use to discuss whatever it wishes to discuss, be it the
   equivalence between energy and information or the concept of space
   in the human brain. Whatever the personal background, interests or
   intellectual creations of the members of FIS, we each have been
   taught addition, multiplication, division and the like. We also know
   how to read a map and remember well where we had put a thing as we
   are going to retrieve it. When discussing the intricate,
   philosophical points which are common to all formulations of this
   session, it may be helpful to use such words and procedures that are
   well-known to each one of us, while describing what we do while we
   use topology.

   b.)Subject-matter

   Topology is managed by much older structures of the central nervous
   system than those that manage speech, counting, abstract ideas.
   Animals and small children remember their way to food and other
   attractions. Children discover and use topology far before they can
   count. Topology is a primitive ancestor to mathematics; its ideas
   and methods are archaic and may appear as lacking in refinement and
   intelligence.

   c.) Order

   Th

[Fis] MODERATION NOTE

[Pedro C. Marijuan]

Dear FIS Colleagues,

The list server has been out of work during last 48 h. Sorry about the 
incident. Now it seems to be working again.
Please, all those with pending messages are asked to re-send them... 
moderately. As one of our colleagues has written me offline:


"Now regarding the current FIS discussion – it is very exciting, 
rewarding and thought provoking.
Topological approaches seem to be very important and fundamental in a 
variety of fields, so great to learn about them.
However I think that Arturo goes faster than the majority of others can 
follow. That is visible from the discussion so far.
Perhaps he should slow down and explain to the colleagues with different 
backgrounds, on a more basic level what he is doing.
As they really express wish to collaborate interdisciplinary, it is 
important to find common ground so that the list can share this exciting 
idea

to use topology to understand the brain-mind processes..."

So, let us continue, with the reminder that it is better not to respond 
immediately--wait to the next day and produce a more seasoned response...

Best--Pedro

--
-
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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] Fis Digest, Vol 32, Issue 28 [ Request for complete citations ]

[Pedro C. Marijuan]

Dear FIS Colleagues,

Briefly responding to Malcolm, scientific communication involves 
different styles and contexts, from the highly informal to the rigors of 
standard publication. This list embraces such plurality, but above all 
emphasizes the deep values of scholarship: openness, tolerance, 
kindness... just the opposite of the acid styles frequent in social 
networks and the like. I appreciate his interest about those requested 
references, and they will spontaneously appear along the ongoing 
discussion (it was a way to present the new invitees in this session). 
But the case of KPC is too complex (really a "story"). I will be glad to 
tell it in some pause of the discussion. Better if we keep the focus on 
the exciting ideas presented...


Best--Pedro

El 24/11/2016 a las 19:18, Malcolm Dean escribió:
As this is an academic/scientific list, may I request that when an 
author is mentioned, such as Kenneth Paul Collins or the Fingelkurts, 
at least some rudimentary citationdata is provided?


An ISBN, a link to Google Books or Amazon, a catalog ID... 
something... anything...


Surely, that should be a minimum requirement for scholarly discourse?

-- Malcolm Dean


Message: 1
Date: Thu, 24 Nov 2016 17:45:05 +0100
    From: "Pedro C. Marijuan" <pcmarijuan.i...@aragon.es
<mailto:pcmarijuan.i...@aragon.es>>
To: "'fis'" <fis@listas.unizar.es <mailto:fis@listas.unizar.es>>
Subject: Re: [Fis] NEW DISCUSSION SESSION--TOPOLOGICAL BRAIN
Message-ID: <92dc9904-38f3-a720-dae1-23c0b70ec...@aragon.es
<mailto:92dc9904-38f3-a720-dae1-23c0b70ec...@aragon.es>>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

** At the time being I am not aware of similar directions, except
a few
isolated papers and a remarkable maverick working in late 1980s
(Kenneth
Paul Collins), with whom I could cooperate a little (with his help, I
prepared a booklet in Spanish) .

** I think Collins was a (doomed, ill-fated) precursor of both the
topological ideas and the quest for dynamic optimization principles,
somehow reminding contemporary ideas, eg, the great work of Alexander
and Andrew Fingelkurts, who are also inscribed in the list for this
discussion.



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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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] NEW DISCUSSION SESSION--TOPOLOGICAL BRAIN

[Pedro C. Marijuan]

Dear Arturo, James, and FIS Colleagues,

Thanks for the intriguing presentation. Maybe it is difficult to make 
sense in depth of these curious topological views applied to nervous 
systems function. In an offline exchange with the authors I was arguing 
that the countless mappings among cerebral areas, both cortical and 
subcortical, are almost universally described as "topographical" and 
that the information related to deformations, twisting, gradients, 
inversions, bifurcating "duplications", etc. is not considered much 
valuable for the explanatory schemes. However, just watching any of 
those traditional "homunculus" described for both motor and 
somatosensory mappings, the extent of deformations and irregularities 
becomes an eloquent warning that something else is at play beyond the 
strictly topographic arrangement.


Now, what we are being proposed --in my understanding-- is sort of an 
extra-ordinary cognitive role for crucial parts of the whole topological 
scheme. Somehow, the projection of brain "metastable dynamics" 
(Fingelkurts) to higher dimensionalities could provide new integrative 
possibilities for information processing. And that marriage between 
topology and dynamics would also pave the way to new evolutionary 
discussions on the emergence of the "imagined present" of our minds. Our 
bi-hemispheric cortex so densely interconnected could also be an 
exceedingly fine topological playground with respect to the previous 
organizational rudiments in the midbrain (in non-mammalian brains). 
Therefore, couldn't we somehow relate emergent topological-dynamic 
properties and consciousness characteristics?...


In what follows am trying to respond the initial questions posed:

1)Could we use projections and mappings, in order to describe brain 
activity?


**Yes, quite a bit; in my opinion, they are an essential ingredient of 
complex brains.


2)Is such a topological approach linked with previous claims of old 
“epistemologists” of recent “neuro-philosophers”?


** At the time being I am not aware of similar directions, except a few 
isolated papers and a remarkable maverick working in late 1980s (Kenneth 
Paul Collins), with whom I could cooperate a little (with his help, I 
prepared a booklet in Spanish) .


3)Is such a topological approach linked with current neuroscientific models?

** I think Collins was a (doomed, ill-fated) precursor of both the 
topological ideas and the quest for dynamic optimization principles, 
somehow reminding contemporary ideas, eg, the great work of Alexander 
and Andrew Fingelkurts, who are also inscribed in the list for this 
discussion.


4)The BUT and its variants display four ingredients, e.g., a continuous 
function, antipodal points, changes of dimensions and the possibility of 
types of dimensions other than the spatial ones. Is it feasible to 
assess brain function in terms of BUT and its variants?


**  I think it should be explored. Future directions to investigate this 
aspect could also contemplate the evolutionary changes in central 
nervous system structures and behavioral/cognitive performances.


5)How to operationalize the procedures?

** Today's research in connectomics can help. Some very new 
neurotechnologies about cell-to-cell visualization of neuronal activity 
and gene expression could also help for future operationalization 
advancements.


6)Is it possible to build a general topological theory of the brain?

** Topology, Dynamics, Neuroinformation and also elements of Systems 
Biology and Signaling Science should go hand-with-hand for that crazy 
purpose.


7)Our “from afar”  approach takes into account the dictates of far-flung 
branches, from mathematics to physics, from algebraic topology, to 
neuroscience.  Do you think that such broad multidisciplinary tactics 
could be the key able to unlock the mysteries of the brain, or do you 
think that more specific and “on focus” approaches could give us more 
chances?


** In my view, both the disciplinary specific and the multidisciplinary 
synthetic have to contribute. Great syntheses performed upon great 
analyses--and which should be updated after every new epoch or new 
significant advancements. One of the founding fathers of neuroscience, 
Ramón y Cajal, made a great neuro-anatomical (and functional) synthesis 
with the elements of his time at the beginning of the past century. It 
was called the "doctrine of the neuron" and marked the birth of modern 
neuroscience...


Finally, before saying goodbye, half dozen new Chinese parties from the 
recent conference in Chengdu have joined the list; they have ample 
expertise in neuroscientific fields and in theoretical science domains. 
At their convenience, it would be quite nice hearing from them in this 
discussion.


Greetings to all, and thanks again to Arturo and James for their valiant 
work,


--Pedro

-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto 

[Fis] NEW DISCUSSION SESSION--TOPOLOGICAL BRAIN

[Pedro C. Marijuan]

Dear FIS Colleagues,

We continue with our customary discussion sessions. This time the topic is:

*"A TOPOLOGICAL APPROACH TO BRAIN FUNCTION"*

And our invitees chairing the session are:
*
**Arturo Tozzi*
AA Professor Physics, University North Texas
Pediatrician ASL Na2Nord, Italy
Comput Intell Lab, University Manitoba
http://arturotozzi.webnode.it/

*James F. Peters **
*Professor Computational Intelligence Laboratory
ECE Department
University of Manitoba, Canada
https://www.researchgate.net/profile/James_Peters/?ev=hdr_xprf

The kickoff text will be posted tomorrow.

Best wishes to all

--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] Intelligence & Meaning & The Brain

[Pedro C. Marijuan]

Dear Christophe and FIS Colleagues,

In my second cent of the week, let me thank for the positive comments on 
the presentation. You raise a very interesting point that can be 
analyzed from quite different angles. Strategically, my opinion is that 
information science (or information studies) should not abandon its 
tight interrelationship with humanities, because we are too weak to 
loose an important allied at the time being, and because most of the 
humanities' contents are excellent manifestations of 
combinatory-informational-symmetrical games. The series of meetings 
regularly organized by our Symmetry Institute colleagues are showing 
that interweaving very elegantly. How to tell a story, the nucleus of 
drama, poetry, novels, movie making, and all sort of "narratives", is 
one of the bulwarks to be won "informationally". Intelligence as the 
efficient organization of information flows around adaptive purposes in 
the advancement of a life cycle should not be so far from attempting 
some explanation of what a story is: a condensate of human communication 
(quite interesting the recent book by Randy Olson: Houston we have a 
narrative. Why science needs story. 2015). Maybe in the next session on 
brain dynamics and topology we could find some further connection with 
this topic.
Another different reason to strengthen the link with humanities would be 
to consider that they are in themselves closer to the "social" domain, 
and that Great Domains should not be multiplied, so that they not loose 
their integrative appeal. And also, if we let things speak by 
themselves, what would be the most cogent interpretation of the contents 
the disciplinary-citation maps are showing? Initially Rosenbloom 
proposed the three leaves "clover" (demanding extra room for the 
computational), I have advocated the four leaves (substituting for the 
informational), and you were arguing the five leaves... That's fine. In 
part, the interpretation depends on the further goals, and we both are 
sharing the societal concern. I think discussion on this vision of the 
Great Domains may be important for the future cohesion of information 
studies in front of the enormous power of the technological world and 
the tunnel vision their new means of communication are imprinting on our 
societies (Brexit, USxit, and so on)...


All the best
--Pedro

El 17/11/2016 a las 16:31, Christophe escribió:


Dear Pedro,
Thanks for the copy of your ICIS 2016 presentation which covers a lot 
of evolutionary aspects regarding intelligence and the information flow.
Perhaps one aspect of that subject may deserve a bit more. It is 
“human mind”.
For instance, your chart (N°39) on the four domains of science 
(physical, biological, social, informational) could contain a 5^th 
component: “humanities” in order to explicitly take into account human 
mind. This because it is a key step in the evolution of our universe 
(energy, matter, life, human mind) that cannot be today deduced from 
the other domains. And also because an understanding of human mind 
could introduce possible evolutions of human motivations for the 
better of mindkind (you remember the evolutionary scenario where the 
proposed interactions of anxiety management with self-consciousness 
introduce possibilities for new understandings on human nature in 
terms of motivations and actions. I think (and hope) that human 
evolution is not over and this is in the direction of sheding some 
light on a possible maturing of human self-consciousness for the 
better of mankind). (http://philpapers.org/rec/MENPFA-3).


<http://philpapers.org/rec/MENPFA-3>

Christophe Menant, Proposal for an evolutionary approach ... 
<http://philpapers.org/rec/MENPFA-3>

philpapers.org
Christophe Menant (2010). Evolutionary Advantages of 
Inter-Subjectivity and Self-Consciousness Through Improvements of 
Action Programs (2010). Dissertation, Tucson ...




Best
Christophe

*De :* Fis <fis-boun...@listas.unizar.es> de la part de Pedro C. 
Marijuan <pcmarijuan.i...@aragon.es>

*Envoyé :* jeudi 17 novembre 2016 14:09
*À :* 'fis'
*Objet :* [Fis] Intelligence & Meaning & The Brain
Dear FIS Colleagues,

Herewith the dropbox link to the Chengdu's presentation on Intelligence
and the Information Flow (as kindly requested by Christophe and Gordana).

https://www.dropbox.com/sh/wslnk41c3lquc55/AADpm_U6xuhm6jHK0esyN-29a?dl=0

About the ongoing exchanges on language and meaning, there could be some
additional arguments to consider:

1. Evolutionary origins of language (Terry can say quite a bit about
that). It is difficult to establish a clear stage into which well formed
oral language would have emerged. That the basis was both gestural
(Susan Goldin Meadow) and emotional utterances seems to be more and more
accepted. Alarm calls for instance in some monkeys conta

[Fis] Intelligence & Meaning & The Brain

[Pedro C. Marijuan]

Dear FIS Colleagues,

Herewith the dropbox link to the Chengdu's presentation on Intelligence 
and the Information Flow (as kindly requested by Christophe and Gordana).


https://www.dropbox.com/sh/wslnk41c3lquc55/AADpm_U6xuhm6jHK0esyN-29a?dl=0

About the ongoing exchanges on language and meaning, there could be some 
additional arguments to consider:


1. Evolutionary origins of language (Terry can say quite a bit about 
that). It is difficult to establish a clear stage into which well formed 
oral language would have emerged. That the basis was both gestural 
(Susan Goldin Meadow) and emotional utterances seems to be more and more 
accepted. Alarm calls for instance in some monkeys contain distinct 
sound codes that clearly imply an associated meaning on what is the 
specific predator to take care of (aerial, felines, snakes) with 
differentiated behavioral escape responses in each case. Pretty more 
complex in human protolanguages.
2. Nervous Systems functioning. The action-perception cycle in advanced 
mammals would be the engine of information processing and meaning 
generation. The advancement of the life cycle would be the source and 
sink of the communicative exchanges and the ultimate reference for 
meaning. (This connects with the info flows and intelligence of my 
presentation).
3. Human "sociotype" maintenance. As the natural social groups of humans 
grew out of proportion regarding other Anthropoidea (see Dunbar's 
number), a new form of "grooming" and group consensus was established 
around language and other emotional utterances (importance of laughter). 
Paradoxically, language's meaning becomes downsized to the level of 
small talk, just chattering to keep social bonds afloat.  The "social 
brain hypothesis" on the origins of language developed by Robin Dunbar 
and other scholars points in this direction.


In my opinion, points 1 and 3 have already appeared in this list. But 
point 2 has been very rarely discussed among us (how the brain 
fabricates meaning). So, tentatively, the next discussion session will 
deal with some of this neurodynamic stuff (in preparation yet: "The 
Topological Brain"). In the meantime, Maybe Mark would like to make some 
concluding comments in order to close the present session... Thanks are 
due to him both for his preparation-work and for his patience regarding 
all the tangents in this session!


Best wishes
--Pedro


El 16/11/2016 a las 15:51, Dai Griffiths escribió:
Many (most?) linguistic interactions are not propositional in the 
sense that you imply.


There is no verifiable equivalent to opening the fridge door for 
utterances like "Cool", "Give us a hand won't you", "You're welcome", 
"Justin Bieber is wonderful", "You go and sneak in round the back 
while I distract them at the front door", and so on.


So I doubt your 'usually', and the application to natural language.

Dai


On 15/11/16 15:05, Bruno Marchal wrote:
A model is a mathematical structure making a sentence (proposition) 
true or false, and this, in my opinion applies to meaning in the 
natural language, where usually some notion of reality is involved: 
 the proposition "there is two beers in the fridge" is judged 
meaningful because we believe in a reality with fridge containing, or 
not, beers.




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Re: [Fis] Scientific communication

[Pedro C. Marijuan]

Dear Mark and FIS colleagues,

It was a pity that our previous replies just crossed in time, otherwise 
I would have continued along your thinking lines. However, your 
alternative focus on who has access to the "Brownian chamber motion" is 
pretty exciting too.


Following our FIS colleague Howard Bloom ("The Global Brain", 2000), 
universities and the like are a social haven for a new type of 
personality that does not match very well within the social order of 
things. It is the "Faustian type" of mental explorers, dreamers, 
creators of thought, etc. Historically they have been extremely 
important but the way they are treated (even in those "havens" 
themselves!), well, usually is rather frustrating except for a few 
fortunate parties. A long list of arch-famous scientific figures ended 
very badly indeed.


So, in this view, people "called to the box" are the Faustians of the 
locality... But of course, other essential factors impinge on the box 
composition and inner directions, often very rudely. SCIENTIA POTESTAS 
EST: it means that as the box's outcomes are so much influential in the 
technology, religion, culture, richness, prosperity, and military power, 
etc., a mixing of socio-political interests will impress a tough 
handling in the external guidance and inner contents of the poor box.


And finally, the education --as you have implied-- that very often is 
deeply imbued with classist structures and class selection. The vitality 
of the Brownian box would most frequently hang from these educational 
structures --purses-- for both financing and arrival of new people. And 
that implies further administrative strings and been involved in 
frequent bureaucratic internecine conflicts. The book of Gregory Clark 
(2014, The Son also Raises) is an excellent reading on class "iron 
statistics" everywhere, particularly in education.


E puor si muove! All those burdens have a balance of positive supporting 
and negative discouraging influences, different in each era. Perhaps far 
better in our times, but who knows... The good thing relating our 
discussion is that, from immemorial times, all those Brownian boxes 
around are wonderfully agitated and refreshed by the external 
communication flows of scientific publications via the multiple channels 
(explosive ones today, almost toxic for the Faustian).


Maintaining a healthy, open-minded scientific system... easy said than done.

Best regards
--Pedro





El 16/10/2016 a las 16:07, Mark Johnson escribió:

Dear Pedro,

Thank you for bringing this back down to earth again. I would like to
challenge something in your first comment - partly because contained
within it are issues which connect the science of information with the
politics of publishing and elite education.

Your 'bet' that "that oral exchange continues to be the central
vehicle. It is the "Brownian Motion" that keeps running and infuses
vitality to the entire edifice of science." is of course right.
However, there is a political/critical issue as to who has ACCESS to
the chamber with the Brownian motion.

It is common for elite private schools in the UK (and I'm sure
elsewhere) to say "exams aren't important to us. What matters are the
things around the edges of formal education... character-building
activities, contact with the elite, etc". What they mean is that they
don't worry about exams because their processes of pre-selection and
'hot-housing' mean that all their students will do well in exams
anyway. But nobody would argue that exams are not important for
personal advancement in today's society, would they?

Similarly, elite universities may say "published papers are not that
important - what happens face-to-face is what matters!". Those
universities do not have to worry so much about publishing in
high-quality journals because (often) the editors of those journals
are employed by those universities. But when, at least in the last 10
years or so, did anybody get an academic job in a university with no
publications?

I draw attention to this not because it seems like a stitch-up
(although it is). It is because it skews what you call the "Brownian
motion". At worst we end up with the kind of prejudice that was
expressed by Professor Tim Hunt last year
(https://www.theguardian.com/uk-news/2015/jun/10/nobel-scientist-tim-hunt-female-scientists-cause-trouble-for-men-in-labs).
More fundamentally, the doubts and uncertainties of the many are very
important, and in this system, they are not only not heard, but in the
increasingly rarefied and and specialised exchanges in the "Brownian
motion chamber", as the elite scholars endlessly discuss ontological
arguments for the existence of information (!), everyone else is
effectively locked-out.

The economic crisis and the economists is a good example of this kind
of pathology. It was pretty obvious that the economic system was
heading for trouble quite some time before 2008; it was also obvious
to a few economists on the fringes (who became 

[Fis] Fwd: Scientific communication (MARK)

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: Scientific communication
Fecha:  Sun, 16 Oct 2016 15:07:25 +0100
De: Mark Johnson <johnsonm...@gmail.com>
Para: 	Pedro C. Marijuan <pcmarijuan.i...@aragon.es>, fis 
<fis@listas.unizar.es>


---

Dear Pedro,

Thank you for bringing this pback down to earth again. I would like to
challenge something in your first comment - partly because contained
within it are issues which connect the science of information with the
politics of publishing and elite education.

Your 'bet' that "that oral exchange continues to be the central
vehicle. It is the "Brownian Motion" that keeps running and infuses
vitality to the entire edifice of science." is of course right.
However, there is a political/critical issue as to who has ACCESS to
the chamber with the Brownian motion.

It is common for elite private schools in the UK (and I'm sure
elsewhere) to say "exams aren't important to us. What matters are the
things around the edges of formal education... character-building
activities, contact with the elite, etc". What they mean is that they
don't worry about exams because their processes of pre-selection and
'hot-housing' mean that all their students will do well in exams
anyway. But nobody would argue that exams are not important for
personal advancement in today's society, would they?

Similarly, elite universities may say "published papers are not that
important - what happens face-to-face is what matters!". Those
universities do not have to worry so much about publishing in
high-quality journals because (often) the editors of those journals
are employed by those universities. But when, at least in the last 10
years or so, did anybody get an academic job in a university with no
publications?

I draw attention to this not because it seems like a stitch-up
(although it is). It is because it skews what you call the "Brownian
motion". At worst we end up with the kind of prejudice that was
expressed by Professor Tim Hunt last year
(https://www.theguardian.com/uk-news/2015/jun/10/nobel-scientist-tim-hunt-female-scientists-cause-trouble-for-men-in-labs).
More fundamentally, the doubts and uncertainties of the many are very
important, and in this system, they are not only not heard, but in the
increasingly rarefied and and specialised exchanges in the "Brownian
motion chamber", as the elite scholars endlessly discuss ontological
arguments for the existence of information (!), everyone else is
effectively locked-out.

The economic crisis and the economists is a good example of this kind
of pathology. It was pretty obvious that the economic system was
heading for trouble quite some time before 2008; it was also obvious
to a few economists on the fringes (who became very unpopular) that
economics was in a mess many years before, concocted out of spurious
mathematical models and a published discourse which would admit little
else. As Tony Lawson says here (this is worth watching:
https://www.youtube.com/watch?v=b_vMLHis5cE), after the crisis it's
easier to claim that economics is in a mess. But doing something about
it is a different matter.

As a side note about Brownian motion: Tony Lawson is based in
Cambridge as has, over the last 20 years, held a bi-weekly seminar
series open to all called the Cambridge Realist Workshop. Some of the
brightest minds in the University attend these. They all have deep
discussions about economics, ontology, society... basically, about
"everyone else". But "everyone else" isn't in the room.

This is the problem. Were "everyone else" to be there, for it to be
truly open, honest and democratic I think we would have a better
science of society, information, education, etc... A small step to
achieving this is to communicate our doubts in different, more open
and more creative ways.

Best wishes,

Mark

On 14 October 2016 at 13:25, Pedro C. Marijuan
<pcmarijuan.i...@aragon.es> wrote:

Dear Mark and FIS Colleagues,

Apart from the very interesting "elevated" comments, let me refer to more
mundane aspects of scientific communication.

First, is really publishing the essential form of scientific communication?
Or is it complementary to other more basic form? My bet is that oral
exchange continues to be the central vehicle. It is the "Brownian Motion"
that keeps running and infuses vitality to the entire edifice of science.
The success of some new techs (eg, emails, discussion lists) is that they
share some curious characteristics with oral discussion groups.
"Publishing", is very old too (Plato, Aristotle, Alexandrian Library...),
and saves time and space constraints, and provides "textual" shared memories
as well, but without the face-to-face contact it does not mark efficiently
changes of thought. Learning Institutions carefully preserve the
infrastr

[Fis] Fwd: Scientific communication (---from Mark)

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: [Fis] Scientific communication (from Mark)
Fecha:  Fri, 14 Oct 2016 13:04:06 +0100
De: Mark Johnson <johnsonm...@gmail.com>
Para: 	fis <fis@listas.unizar.es>, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es>


Dear Karl, Loet and Bruno,

On reflection, I had been thinking this discussion about scientific
communication had been a bit 'quiet'... now it is less quiet: there's
nothing like throwing 'god' into the equation to liven up discussions!
Why?

More seriously (and sorry, this is a long post) there are three
fundamental distinctions and an example which I want to draw in the
light of your comments. They are:
1. The distinction between IS and OUGHT in arguments about scientific
communication
2. The distinction between an EXPLANATION and a DESCRIPTION
3. Issues about ONTOLOGY and INFORMATION
4. A musical example

1. IS - OUGHT
There are critical worries in Bruno's comments about making "theology,
the science, vulnerable, as reason is no more allowed in, and that
leaves the place for emotion and wishful thinking, which are quickly
exploited by manipulators, usually to steal our money, or control us
in some ways". Clearly, we ought not allow this to happen. In my
second video, I used the example of the swindler whose speech acts are
chosen in full knowledge of the constraints of the victim. Of course
there are unscrupulous religious people who do this; but there are
equally (and possibly more so) unscrupulous scientists (particularly,
I'm afraid, psychologists and economists (if they are to be considered
scientists - as they would like)). I like Bruno's theology of the
machine - it looks very similar to Ashby's concept of variety (the set
of propositions true about the machine = the set of possible states
the machine can exist in)... which brings us back to information,
Shannon, etc.

I agree with Karl in his suggestion "to focus on the dichotomy
creating the foreground, lifting it off from the background. Patterns
connect the two: it is reasonable, in my view, to work on the subject
of patterns.". But it is easy to say that we "ought" to do this. I'd
prefer to see the pathologies that we see in education and publishing
are a direct consequence of our not doing this, and to describe the
ontological mechanisms. It is the business of arguing how our
scientific communication should be conducted in the light of what we
know about our science.

Hume's famous passage in dealing with the dichotomy of "is" and
"ought" is worth reflecting on:

"In every system of morality, which I have hitherto met with, I have
always remarked, that the author proceeds for some time in the
ordinary ways of reasoning, and establishes the being of a God, or
makes observations concerning human affairs; when all of a sudden I am
surprised to find, that instead of the usual copulations of
propositions, is, and is not, I meet with no proposition that is not
connected with an ought, or an ought not. This change is
imperceptible; but is however, of the last consequence. For as this
ought, or ought not, expresses some new relation or affirmation, 'tis
necessary that it should be observed and explained; and at the same
time that a reason should be given; for what seems altogether
inconceivable, how this new relation can be a deduction from others,
which are entirely different from it."

His complaint is about slippage from "is" to "ought" (he does not deny
the possibility of deriving an ought from an is - the logical
positivists misrepresented him).

In my argument about scientific publishing I have tried to be careful
in avoiding 'oughts' and ground an argument for a richer embrace of
technological expression on the basis of describing how today's
science is. I'm arguing (not much differently from David Bohm whose
work on communication is new to me) that the nature of the science
entails the need for new practices of communication.

There is a critical dimension (which I don't think is an Ought - it's
just a warning): if we continue to communicate in the way that we did
in the 17th century, then our communication won't work because it
works against the scientific ontology. I'm speculating that this
pathology feeds into financialisation processes which produce social
crisis. In Hume's argument, communication between scientists and an
ontology of regularity were tied together; now we have have to admit
multiple contingencies in our scientific practices, the communication
cannot be unchanged - can it?

2. EXPLANATION and DESCRIPTION
In the posts of Bruno and Karl, there is reference to science's search
for universal explanation. This is clearly a very deep issue, but it
fundamentally concerns our conception of causation. What is causation?
What is causal explanation? For Hume, causal explanations are
constructs produced in discourse (i.e. communication) between
scientists in the lig

Re: [Fis] Scientific Communication and Publishing

[Pedro C. Marijuan]

Dear Mark and Colleagues,

Thanks for the well crafted work. Actually you have presented us a 
tightly linked work along perspectives of philosophical, historical, and 
present day criticisms stances. For my taste, Sections 1 and 2 are a 
matter of opinion, of philosophical orientation, closer in this case to 
critical stances. Speech social-construction, status function, scarcity 
declaration, communication definition, information-uncertainty sciences, 
etc. Some of these topics are or have been subject to hot debate in this 
list, so I decline entering--anyhow, my personal impression is that such 
kind of oriented approach although formally consistent, leave aside 
important aspects of the phenomenon. But it is good that you have made 
the consistent scheme.


Historically, the parallel between publication in that transitional 
period of the "scientific revolution" and our times of "information 
revolution" is well developed. Just to enlarge the panorama, I recommend 
/Information Ages/. Literacy, Numeracy, and the Computer Revolution. 
Michael E. Hobart and Zachary S. Schiffman. (2000). The publication 
practices around the "papiri era", culminating in the Alexandrian 
Library, and the "codices era", around the monastic system first and 
later around the university system are the two big precedents. The 
underlying phenomenon in all eras revolves around the "sharing of 
knowledge", a genuine cognitive instinct that is channeled in different 
ways by existing social orders and available technical resources. Not 
much different from the artistic pulsion--and often closely interlinked 
(paradigmatic Leonardo da Vinci).


In our times, there is a famous sentence by premier Zhou Enlai "It is 
too early to say"... However personally I share most of the concerns 
raised by Mark, adding a pessimistic note on the impact that the new 
techs are having in the "creative engine" of science. Although multiple 
new fields have been open thanks to the computer upheaval (precision 
medicine, omic revolution, nanosciences, social physics, social 
neurosceince, social networks, big data everywhere, etc etc), the 
amazing bounty has been accompanied by new problems. On the one side a 
new aristocracy related to big sceince projects and techno-utopian 
goals, more and more distanced of the common researcher, plus an 
enormous increase of computer-mediated bureaucratization. Besides, the 
really easy communication tools and the multiplicity of channels have 
derived in an unselected overflow that impacts negatively on the slow 
reflection needed in science: rushing from screen to screen, no time to 
think. Something similar is happening in technically mediated social 
relationships--terrible for instance in adolescents. If we are going 
toward a symbiosis man-machine, the prospects are not fascinating.


Well, these are comments from a late baby boomer, hardly adapted to the 
new order...

Best greetings to all
--Pedro




I El 26/09/2016 a las 9:55, Mark Johnson escribió:
Dear FIS Colleagues, To kick-start the discussion on scientific 
publishing, I have prepared a short (hopefully provocative) video. It 
can be found at: https://www.youtube.com/watch?v=3Bh3vqM98-U (if 
anyone's interested, the software I used for producing it is

called 'Videoscribe')

I have also produced a paper which is attached.

I hope you find these interesting and stimulating!

Best wishes,

Mark


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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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] CORRECTION: NEW COURSE: NEW DISCUSSION SESSION

[Pedro C. Marijuan]

Dear FISers,

Google search trumped me: our presenter *Mark Johnson* is lecturer in 
educational technology at the University of Liverpool. Sorry for the 
confusion.


It is a good occasion to remind the old dictum /aliquando bonus dormitat 
Homerus/!


Best--Pedro



 Mensaje reenviado 
Asunto: [Fis] NEW COURSE: NEW DISCUSSION SESSION
Fecha:  Thu, 22 Sep 2016 13:13:39 +0200
De: Pedro C. Marijuan <pcmarijuan.i...@aragon.es>
Para:   'fis' <fis@listas.unizar.es>



Dear FIS Colleagues,

We start the 2016-2017 course, and as usual during quite a few years we 
continue with the discussion sessions. The next one will deal with the 
theme of SCIENTIFIC COMMUNICATION (& PUBLISHING), and will be chaired by 
our colleague *Mark Johnson*, who is is Knight Professor of Liberal Arts 
and Sciences in the Department of Philosophy at the University of 
Oregon. At his convenience, around this weekend, Mark will post the 
opening text.


Suggestions for future discussion sessions will be much appreciated 
(send please offline to my address).


Best regards to all!

--Pedro




--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] NEW COURSE: NEW DISCUSSION SESSION

[Pedro C. Marijuan]

Dear FIS Colleagues,

We start the 2016-2017 course, and as usual during quite a few years we 
continue with the discussion sessions. The next one will deal with the 
theme of SCIENTIFIC COMMUNICATION (& PUBLISHING), and will be chaired by 
our colleague *Mark Johnson*, who is is Knight Professor of Liberal Arts 
and Sciences in the Department of Philosophy at the University of 
Oregon. At his convenience, around this weekend, Mark will post the 
opening text.


Suggestions for future discussion sessions will be much appreciated 
(send please offline to my address).


Best regards to all!

--Pedro




--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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[Fis] Fwd: Information Cultures in the Digital Age

[Pedro C. Marijuan]

Dear FIS Colleagues,

I think this new book to appear celebrating our colleague Rafael Capurro 
can be of interest.


Best--Pedro

-- 



New book to be published by Springer in July 2016.

/Information Cultures in the Digital Age: A Festschrift in Honor of 
Rafael Capurro /(Edited by Matthew Kelly & Jared Bielby)


For several decades Rafael Capurro has been at the forefront of defining 
the relationship between information and modernity through both 
phenomenological and ethical formulations. In exploring both of these 
themes Capurro has re-vivified the transcultural and intercultural 
expressions of how we bring an understanding of information to bear on 
scientific knowledge production and intermediation. Capurro has long 
stressed the need to look deeply into how we contextualize the 
information problems that scientific society creates for us and to 
re-incorporate a pragmatic dimension into our response that provides a 
balance to the cognitive turn in information science.


With contributions from 35 scholars from 15 countries,/Information 
Cultures in the Digital Age/ focuses on the culture and philosophy of 
information, information ethics, the relationship of information to 
message, the historic and semiotic understanding of information, the 
relationship of information to power and the future of information 
education. This Festschrift seeks to celebrate Rafael Capurro’s 
important contribution to a global dialogue on how information 
conceptualisation, use and technology impact human culture and the 
ethical questions that arise from this dynamic relationship.


The Editors: Matthew Kelly is a scholar at Curtin University’s 
Department of Information Studies and at the International Institute for 
Hermeneutics. Jared Bielby currently serves as Co-Chair for the 
International Center for Information Ethics and Editor for the 
International Review of Information Ethics.
More information at www.infoculturesbook.com 



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[Fis] Concluding The Session

[Pedro C. Marijuan]

Dear FIS Colleagues,

We are entering in the vacation season, after a tough series of 
discussion sessions in a row. Perhaps it is time to put an end to the 
ongoing session and take a rest. Thanks to Marcus for the work done and 
the ideas discussed, and to all the presenters during this long period. 
As usual the list remains open to whatever comments may look 
interesting... always abiding by the golden rule of only two messages 
per week.


Greetings to all, and enjoy the vacations!

--Pedro



--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] Essential Core?

[Pedro C. Marijuan]

Dear FIS Colleagues,

Some brief responses to the different parties:

Marcus: there were several sessions dealing with info physics, where I 
remember some historical connotations with mechanics emerged. Mostly 
1998 and 2002 chaired by Koichiro Matsuno and 2004 by Michel Petitjean. 
Afterwards the theme has surfaced relatively often. About the present 
possibilities for a UTI, my opinion is that strictly remaining within 
Shannon's and anthropocentric discourse boundaries there is no way out. 
I do not think that machine communication is going to advance the 
generalization either (but who knows? In conjunction with computational 
neuroscience and the "Bayesian" brain we may have surprises). Actually, 
my personal bet is for reconsidering the evolutionary origins, attending 
to the infrastructure of our cellular communication and to the bacterial 
origins of everything. I think we share some parts along this 
exploratory way, at least the curiosity.


To Loet, bacteria never apologize (not much different from some humans, 
eg politicians) but chimps often do ("grooming" after conflicts, with 
the winner offering peace to the defeated). The restrictive use of the 
term communication as proposed is contrary to the existing body of 
research, not only in biology. That "biology as a science itself is 
communication" is a strange argument. For the same token it is also 
observation, reflection, action, learning, experiment, tradition... and 
biology, and whatever science, is also a form of knowledge necessarily 
performed by a living subject--so all science is "biology" following 
with that strange argument. Finally, talking about "priorities" or 
hierarchies in mutual relationships between bodies of knowledge is out 
of our times; priorities have to be won by cooperation/competence within 
the global knowledge-recombination markets of science. Rather than 
closing doors, establishing multidisciplinary teams and directions is 
the new mantra.


To Jerry, given that explicitly my approach to biological information 
/communication is based on molecular recognition, your generative 
approach to the nature of molecular information under the banner of 
electrical fields and atomic numbers looks congruent. It is a pity that 
so few biophysical approaches have been devoted to the general 
problematic of molecular recognition and molecular complexity. The way 
living cells rely on different informational architectures is a showcase 
of amazing multiplicity achieved from a few model-patterns. But it is 
very difficult establishing appropriate ontologies on the enormous 
functional complexity that emerges.  It relates to the last question of 
your message, I think.


To Francesco, thanks, I also believe that the relationship between 
economic and biomolecular "currencies" share a similar inner logic. 
Information has "value", indeed... And finally I should clarify that the 
universals scheme proposed around bacterial communication is a mere 
initial draft --it will get worst! Actually it crystallized during the 
first days of these discussions, thinking about the limits of the 
present mechanical-Shannonian communication paradigm.


Again, thanking the patience
--Pedro


El 07/07/2016 a las 18:44, Francesco Rizzo escribió:

Caro Pedro,
ho apprezzato moltissimo quella magnifica sintesi tra vita, 
auto-riproduzione e comunicazione con l'ambiente nella prospettiva o 
logica della moneta biologica. Problematica che ho affrontato più 
volte anch'io dal punto di vista della "Nuova economia". Le pagine 
120-130 di "Valore e valutazioni" (FrancoAngeli, Milano, 1999) ne sono 
una testimonianza.

Grazie e buone vacanze a Te e a Tutti.
Francesco

2016-07-07 13:53 GMT+02:00 Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>>:


Dear FISers,

[NOTE: I have just seen the new post from Marcus right now: I
should modify parts of the discussion below, but it is too much
work! Better left for a future exchange...]

About the a priori modeling of information --and meaning-- which
was the focus of Marcus' presentation, putting together Shannon,
Bateson, and Darwin, I am not sure how that scheme would translate
into the "real" living stuff. Mostly thinking on the work my team
has done on bacterial communication for years, I mentioned days
ago three basic points about that: universals,
species-specificity, and essential cores.

How a plurality of those information universals could be wrapped
or articulated around an essential core? That's the toughest point
in my opinion. It becomes a matter for freewheeling speculation,
badly needed of Schrodinger's disclaimer. Well, let us consider
that communication and self-production are but the two inseparable
sides of the bio "coin" --in order to self-produce the living has
to

[Fis] Fwd: Re: Shannonian Mechanics? From M. Godron

[Pedro C. Marijuan]

Asunto: Re: [Fis] [SPAM] Shannonian Mechanics?
Fecha:  Sat, 2 Jul 2016 11:17:02 +0200
De: Michel Godron <migod...@wanadoo.fr>
Para:   Pedro C. Marijuan <pcmarijuan.i...@aragon.es>



in red

 Cordialement. M. Godron
Le 01/07/2016 à 13:59, Pedro C. Marijuan a écrit :

Dear Marcus and FIS Colleagues,

You are right in your complaint. We have been saying very similar 
things concerning information generation--and also in your symbolic 
introduction of Darwin in your scheme concerning that series of 
complementary questions. Sorry for being so brief but I need some 
extra time to re-read your initial doc in this light and the very 
cogent responses you have been producing, particularly to Loet's 
points. In my first penny of next week I will comment on those 
matters. Now I respond to other comments (which partially dovetail 
with your themes).


To Loet, fine, we think very differently. Rather than Althusser's 
derogatory remark, I look at Schrodinger's disclaimer in his famous 
"What is Life": /"...[necessaryly] some of us should venture to embark 
on a synthesis of facts and theories, albeit with second hand and 
incomplete knowledge of some of them—and at the risk of making fools 
of ourselves.” /Whether such kind of synthetic approaches (performed 
by each new scientific generation) can be successful or not today, is 
something that neither you nor me can foretell. At the very least, the 
enormous expansion of bio-info-comp disciplines in our times makes 
this demand more necessary than ever. No "hidden program" in my 
previous post but the open constatation that we have an excellent 
opportunity today in order to delineate those potential "universals" 
and "essential core" in an almost completely describable living 
system--bacteria.
The  informatinal structure ( = "essential core" ?) of living beings _at 
five scales_ has been decribed in /Ecologie et évolution du monde vivant 
/Ed. L'Harmattan Paris/. /At the molecular scale, the link betsween 
information and tehrmodynamic negentropy is established. I could send 
some paragraphs of this book to the colleagues interested by any scale.//
At least the rudiments of such approach appear in my team's work on 
Proyariotic Signaling Systems and in "How the Living...".

Could you send it to me ?
Anyhow, when I referred to "principles" I was not meaning your 
interpretation as "origins" but to the usual way practicing scientists 
work on them. For instance, after more than 30 years of painful 
experimental, microscopy work on nervous systems, Ramon y Cajal wrote 
his formidable "Textura del Sistema Nervioso del Hombre y los 
Vertebrados", considered as the foundational opus of modern 
neurosceince. There he exposed the new "Doctrine of the Neuron", based 
on a few revolutionary principles... Mutatis mutandis, it might be an 
interesting case-model regarding the info science renewal commented in 
the previous post.


To Alex, I see the opposite. Making the "universals" species specific 
means that you can communicate and share gestalts far more easily 
within your own phylum or class, or order, than with the far distant 
ones. So, other mammals can approximately "read" your facial 
expressions and postural stance, and get your meaning, while starfish 
or insects will not. Don't you think so?


To Bob (offline comment), many thanks for the comprehension. I am 
happy that from different angles we see in common some stumbling 
blocks to win. Actually, one needs both kinds of criticisms, positive 
and negative, in order to advance a little more in this viscous 
terrain... but making constructive criticisms becomes a more difficult 
task.


Apologies if I have missed some other more brief comments. And sorry 
Marcus if this was sort of a disruption, but I think that your 
discussion topic invites quite a lot to transgress the boundaries.


Best--Pedro
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Re: [Fis] [SPAM] Shannonian Mechanics?

[Pedro C. Marijuan]

Dear Marcus and FIS Colleagues,

You are right in your complaint. We have been saying very similar things 
concerning information generation--and also in your symbolic 
introduction of Darwin in your scheme concerning that series of 
complementary questions. Sorry for being so brief but I need some extra 
time to re-read your initial doc in this light and the very cogent 
responses you have been producing, particularly to Loet's points. In my 
first penny of next week I will comment on those matters. Now I respond 
to other comments (which partially dovetail with your themes).


To Loet, fine, we think very differently. Rather than Althusser's 
derogatory remark, I look at Schrodinger's disclaimer in his famous 
"What is Life": /"...[necessaryly] some of us should venture to embark 
on a synthesis of facts and theories, albeit with second hand and 
incomplete knowledge of some of them—and at the risk of making fools of 
ourselves.” /Whether such kind of synthetic approaches (performed by 
each new scientific generation) can be successful or not today, is 
something that neither you nor me can foretell. At the very least, the 
enormous expansion of bio-info-comp disciplines in our times makes this 
demand more necessary than ever. No "hidden program" in my previous post 
but the open constatation that we have an excellent opportunity today in 
order to delineate those potential "universals" and "essential core" in 
an almost completely describable living system--bacteria. At least the 
rudiments of such approach appear in my team's work on Proyariotic 
Signaling Systems and in "How the Living...". Anyhow, when I referred to 
"principles" I was not meaning your interpretation as "origins" but to 
the usual way practicing scientists work on them. For instance, after 
more than 30 years of painful experimental, microscopy work on nervous 
systems, Ramon y Cajal wrote his formidable "Textura del Sistema 
Nervioso del Hombre y los Vertebrados", considered as the foundational 
opus of modern neurosceince. There he exposed the new "Doctrine of the 
Neuron", based on a few revolutionary principles... Mutatis mutandis, it 
might be an interesting case-model regarding the info science renewal 
commented in the previous post.


To Alex, I see the opposite. Making the "universals" species specific 
means that you can communicate and share gestalts far more easily within 
your own phylum or class, or order, than with the far distant ones. So, 
other mammals can approximately "read" your facial expressions and 
postural stance, and get your meaning, while starfish or insects will 
not. Don't you think so?


To Bob (offline comment), many thanks for the comprehension. I am happy 
that from different angles we see in common some stumbling blocks to 
win. Actually, one needs both kinds of criticisms, positive and 
negative, in order to advance a little more in this viscous terrain... 
but making constructive criticisms becomes a more difficult task.


Apologies if I have missed some other more brief comments. And sorry 
Marcus if this was sort of a disruption, but I think that your 
discussion topic invites quite a lot to transgress the boundaries.


Best--Pedro


El 29/06/2016 a las 17:31, Marcus Abundis escribió:

Dear Pedro, thank you for your excellent post.

Oddly, I have the feeling you think that you and I differ, but I saw 
little to disagree with in your note. As with Loet(?), I believe that 
*for now* I simply focus on a different level.


> the limits of the received Shannonian approach and <
> the (narrow?) corridors left for advancement . . highly <
> reminiscent of what happened with Mechanics long ago . .<
• If I did not see those limits I could not pursue this project. 
Still, it seems many do fail to see the limits here; especially in 
computer science (or *fill in the blank*). I suggested an origin for 
this “iceberg“ in my post on Cultural Legacy. Terry Deacon has also 
noted this odd “scientific failure“ – I say, so glaring that it would 
be comic if it were not so tragic.


• Re Mechanics, can you please point me to a time frame for that 
session so I can see what the archives hold?



>far from useful --nefarious?-- for humanities and for the<
> future of psychological and social science studies. <
• This is a bit painful to read, when I started the project I saw it 
as attempting a new structural psychology (social and individual). My 
thinking became more reductive (a priori) as I sought a firm base for 
modeling. Videos are available on this other "elevated" aspect 
(vimeo.com/evolv ), but they stray for the 
focus of *this* session.



>The why, the what, the how long, the with whom, and other<
> aspects of the information phenomenon do not enter. <
• You name Loet’s post here, and I saw the same issue – “processing 
meaning” versus “generating meaning.” But then my model synthesizes 
Shannon, Bateson, and Darwin; at the least Darwin targets why, what, 
how long, whom, 

[Fis] Shannonian Mechanics?

[Pedro C. Marijuan]

Dear Marcus, Loet, Bob... and All,

Again very briefly, your exchanges make clear the limits of the received 
Shannonian approach and the (narrow?) corridors left for advancement. I 
find this situation highly reminiscent of what happened with Mechanics 
long ago: an excellent theory (but of limited scope) was overstretched 
and used as a paradigm of what All science should be... it contributed 
well to technology and to some other natural science disciplines, but 
was far from useful --nefarious?-- for humanities and for the future of 
psychological and social science studies.


The figure from Weaver in Loet's excellent posting leaves a few aspects 
outside. The why, the what, the how long, the with whom, and other 
aspects of the information phenomenon do not enter. By doing that we 
have streamlined the phenomenon... and have left it ready for applying a 
highly successful theory, in the technological and in many other realms 
(linguistics, artif. intelligence, neurodynamics, molec. networks, ecol. 
networks, applied soc. metrics, etc). Pretty big and impressive, but is 
it enough? Shouldn't we try to go beyond?


I wonder whether a far wider "phenomenology of information" is needed 
(reminding what Maxine argued months ago about the whole contemplation 
of our own movement, or Plamen about the "war on cancer"?). If that 
inquiry is successful we could find for instance that:


1. There are UNIVERSALS of information. Not only in the transmission or 
in the encoding used, well captured by the present theory, but also in 
the generation, in the "purpose", the "meaning", the targeted subject/s, 
in the duration, the cost, the value, the fitness or adaptive 
"intelligence", etc.


2. Those UNIVERSALS are SPECIES' SPECIFIC.

3. Those UNIVERSALS would be organized, wrapped, around an ESSENTIAL 
CORE. It would consist in the tight ingraining of self-production and 
communication (almost inseparable, and both information based!). In the 
human special case, it is the whole advancement of our own lives what 
propels us to engage in endless communication --about the universals of 
our own species-- but with the terrific advantage of an open-ended 
communication system, language.


4. Those UNIVERSALS would have been streamlined in very different ways 
and taken as "principles" or starting points for a number of 
disciplines--remembering the discussion about the four Great Domains of 
Science. A renewed Information Science should nucleate one of those 
domains.


Best regards to all,
(and particular greetings to the new parties joined for this discussion)
--Pedro


El 27/06/2016 a las 12:43, Marcus Abundis escribió:


Dear Loet,

I hoped to reply to your posts sooner as of all the voices on FIS 
I often sense a general kinship with your views. But I also confess I 
have difficulty in precisely grasping your views – the reason for my 
delay.


>[while Shannon’s] concept of information (uncertainty) <
> is counter-intuitive. It enables us among other things <
> to distinguish between "information" and "meaningful <
> information". <
• Easily agreed; *how* to distinguish a presumed meaning (or 
meaningless-ness) then becomes the remaining issue.


> Providing . . . meaning presumes the specification <
> of a system of reference; for example, an observer.<
• It is telling for me (in viewing our differences and likenesses) 
that you suggest an observer. My “system of relating“ accommodates but 
does not require an observer (okay – observer, defined how?), as shown 
immediately below.


>Different[ly] . . . expected information is dimensionless<
> ("a priori"). <
• I suggest the act of “expectation“ already infers minimal dimensions 
– for example, who/what/how is doing the expecting? Thus, in my view, 
this is not truly a priori. A “readiness“ or a compelling functional 
need innate to any “system of relating“ has bearing. For example, a 
single Oxygen atom has a compelling/innate need to react with other 
elements, just as any agent is compelled to react to “nutrients.“ Both 
imply dimensional expectations, no? (obviously – of different 
orders/types).


> In my opinion, a "real theory of meaning" should enable <
> us to specify/measure meaning as redundancy / reduction <
> of uncertainty given . . . I took this further in . . . <
> The Self-Organization of Meaning and the Reflexive . . .<
• My weak grasp of the concepts in this paper leads me to think you 
are actually modeling the “processing of meaning,“ 
related-to-but-distinct-from “generating meaning“ that I target. I 
also vaguely recall(?) in an offline exchange I asked you if you saw 
this paper as presenting a “theory of meaning“ and you answered “No.“


• In your later response to Pedro, I found your citation matrix a 
interesting example of your thinking, but still too “high-order“ for 
my reductive-but-meaningful aim. Your matrix (for me) presents an 
essential complexity of high-order views, but in itself it is too 
simple to detail *how* a 

Re: [Fis] _ Reply to Annette (A Priori Modeling)

[Pedro C. Marijuan]

Dear Marcus and All,

As usual I find a crucial element missing in both your initial text and 
in the responses up to now. How can I express that abscence in two or 
three lines?
"Agency" is missing. It is factually minimized under the form of 
constraints and uncertainty. Communication occurs because some kind of 
"emitter" agent operates as a "source" and sends "messages" via an 
appropriate "channel" to some "receiver". I have put quotations to the 
standard Shannonian terms. My central question: could there be any form 
of non-living agency? And then, What different forms of life could 
receive the "agent" label? How being alive biases the non-at-all-free 
communication game?


These questions will be refined next days...
Best--Pedro

respect El 23/06/2016 a las 8:37, Loet Leydesdorff escribió:


Dear Bob, Stan and colleagues,

The Shannon formula measures "capacity" for information, *not* 
information itself. Consider the "snow" pattern on a TV without a 
signal. Its Shannon measure is much higher than when a picture appears 
onscreen, yet we know that the snow pattern carries no information.


The expected information of a message that an event has taken place 
can be measured precisely in terms of bits of information using the 
Shannon formulas. As Weaver noted (and Shannon was aware), this 
concept of information (uncertainty) is counter-intuitive. It enables 
us among other things to distinguish between “information” and 
“meaningful information”. A screen with noise carries maximal 
information, but this information is not meaningful.


Providing Shannon-type information with meaning presumes the 
specification of a system of reference; for example, an observer. 
Different from observed information, expected information is yet 
dimensionless (“a priori”). The analytical distinction between 
information processing and meaning processing enables us also to 
specify (perhaps measure as redundancy) the different meanings that 
can be provided to the same uncertainty by different systems of 
reference. For example, the white noise on the screen may be 
unexpected or not (since the antenna was not correctly plugged in).


“The concept of information developed in this theory at first seems 
disappointing and bizarre—disappointing because it has nothing to do 
with meaning … I think, however, …  that this analysis has so 
penetratingly cleared the air that one is now, perhaps for the first 
time, ready for a real theory of meaning.” (Weaver, 1949, p. 27)


In my opinion, a “real theory of meaning” should enable us to 
specify/measure meaning as redundancy / reduction of uncertainty given 
information as uncertainty. I took this further in: Loet Leydesdorff, 
Alexander Petersen, and Inga A. Ivanova, The Self-Organization of 
Meaning and the Reflexive Communication of Information. 
/Social Science Information /(in press).


Best,

Loet



Loet Leydesdorff

Professor, University of Amsterdam
Amsterdam School of Communication Research (ASCoR)

l...@leydesdorff.net ; 
http://www.leydesdorff.net/
Associate Faculty, SPRU, University of 
Sussex;


Guest Professor Zhejiang Univ. , 
Hangzhou; Visiting Professor, ISTIC, 
Beijing;


Visiting Professor, Birkbeck , University of 
London;


http://scholar.google.com/citations?user=ych9gNYJ=en




--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] MARCUS' PRESENTATION

[Pedro C. Marijuan]

Dear FIS Colleagues,

After the phenomenological turn, we reassume our customary discussion 
sessions. The present one corresponds to Marcus Abundis, on "A PRIORI 
MODELING OF INFORMATION". It is based on, and continues with, the 
presentation he made in the past FIS & ISIS Conference in Vienna last 
year.  He will post the kickoff text at his earliest convenience.


Greetings to all,

--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] Towards the end of the Med Session and Phenomenology

[Pedro C. Marijuan]

Dear FIS Colleagues,

It is time to conclude a long session on phenomenology, information and 
the life sciences. First of all, we should thank Maxine, Lou, Soeren, 
Alex, and Plamen for their time and dedication in conducting the 
discussion sessions. The contact with phenomenology from the point of 
view of information, with all of its ups and downs, has been a curious 
experience. Even the most reluctant hard-nosed scientists will have to 
accept that in this period of upmost intense transformations of science 
--particularly in biology and medicine-- we are missing something 
important in our collective practice. The endless complexity of life in 
all of its domains seems to defy all our bodies of knowledge, from the 
most philosophical and basic to the most applied, and force them to 
participate in the collective game of Knowledge Recombination. My 
personal question to Plamen (sure he has some further comments to make), 
apart from thanking him all the organization job during these months, is 
whether we should envision a new "phenomenology of information" so as to 
guide us in the KR survival game...


Best wishes to all
--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] Fwd: Re: Cancer Cure? (Plamen S.)

[Pedro C. Marijuan]

 Mensaje reenviado 
Asunto: Re: [Fis] Cancer Cure?
Fecha:  Tue, 31 May 2016 19:54:05 +0200
De: Dr. Plamen L. Simeonov <plamen.l.simeo...@gmail.com>
Para:   Robert Ulanowicz <u...@umces.edu>
CC:     Pedro C. Marijuan <pcmarijuan.i...@aragon.es>



Dear Bob and All,

it is a compliment for me to read your notes on the subject. You don't 
need to excuse. It is indeed a complex world of relations. And tt is 
good that you rmentioned all this again from your perspective. We do not 
know how many have entered the discussion later. Reiterations and 
questions are always good and welcome. Well, I was expecting a vigorous 
discussion on this subject which approaches its end now. But it is still 
better to have one feedback rather than writing all this on paper of my 
own without knowing what the reviewer or the reader would say at the 
end. I still hope to hear a few more voices on that. We could take on 
some of the other two major groups of diseases mentioned in the opening 
session. Bob, I am glad that you mentioned quantum logic. Do you think 
we can try using it to express the emergent state of a disease (in 
combination or not with heterogeneity afine SOC) We are not limited to 
cancer only. In fact I am also interested to know your opinion on such 
aspects as self-similarity or symmetry/asymetry during the development 
of a disease throughout all transition phases. These issues have been 
often discussed in a different context at FIS. How about the 
biosemiotics aspect which I mentioned earlier? Tell me what do you think 
could be a promising approach to tackle a tough health problem.


Is there anybody out there? :-)

All the best,

Plamen




On Tue, May 31, 2016 at 6:54 PM, Robert E. Ulanowicz <u...@umces.edu 
<mailto:u...@umces.edu>> wrote:


   > Dear Bob,
>
> thank you for your response. What you said in the core -
   heterogeneity -
> resonated with the first suggested example I began this session
   with: the
> puzzle of registering the heterogeneity of cancer, both in the
> molecular-biological and histological level, both in space and
   time. It
> appears that exactly this elusive property of matter, liveness,
   from the
> single cell to entire eco-systems, which implies intelligence
   throughout
> all scales (as Brian Ford states) is what we still cannot in
   system(s)
> biology put on the feet of statistical mechanics and classical
> physics.Aren't tumors such intelligent clusters of heterogeneous cell
> computers interacting within internaly secured invasive networks that
> escape our medical enigma code breakers placed in our synthetic
   drugs and
> radiation devices? Also such undesired life is not easy to kill. 
   And yet

> cancer cannot win the battle unless our own internal systems
   surrender and
> become allies of the invador.

   Dear Plamen,

   To begin, please allow me to apologize for joining the conversation
   midway
   without having read your earlier postings.

   It's obvious that you also expressed the sense of what I was saying.
   There
   are about 6 fundamental laws of physics, which allows for several
   hundred
   combinations among the laws. Meanwhile, most living systems consist
   of at
   least 40 identifiable constituents, which can interact on some 10^47
   possible ways. It should be no surprise that (many?) more than one
   combination can satisfy any specification of the laws. So the laws
   are not
   broken; they simply lose their power to *determine* a unique outcome.

   As you say, sufficiently heterogeneous living system can usually find a
   way around most obstacles in their way.

> And yet, healthy systems have some sort of regularity, layered
   structure
> and hierarchies as those we observe in a skin biopsy sample.Genetic
> mutations do not remain local at the damaged spot; they are
   signaled to
> other "mentally weak" cells which are turned into traitors,also
   perhaps
> even via non-local induction. Are wandering "bad" cells and
   accelerated
> replication the only sources of growing agressive cancers? Here
   is perhaps
> where biosemiotics and phenomenology could help along with
   creating new*
> heterogeneous* SOC models, as you mentioned. You are right, the
   call for
   > devising a mathematics that can  handle heterogeneous sets,
> vectors,matrices, categories and other sorts of organisation in
   biology
> simultateously was already spread by Bob Root-Bernstein in his
   opening
> article to our 2012 edition of integral biomathics (see last link
   in my
> signature). We do not have such an underpinning mathematics and its
> related
> computation yet. Therefore we remain still stuck in the old system
> biological models ro

[Fis] Fwd: Re: Cancer Cure? (Bob Ulanowicz)

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: [Fis] Cancer Cure?
Fecha:  Tue, 31 May 2016 12:54:20 -0400
De: Robert E. Ulanowicz <u...@umces.edu>
Responder a:u...@umces.edu
Para:   Dr. Plamen L. Simeonov <plamen.l.simeo...@gmail.com>
CC: 	Robert Ulanowicz <u...@umces.edu>, Pedro C. Marijuan 
<pcmarijuan.i...@aragon.es>





Dear Bob,

thank you for your response. What you said in the core - heterogeneity -
resonated with the first suggested example I began this session with: the
puzzle of registering the heterogeneity of cancer, both in the
molecular-biological and histological level, both in space and time. It
appears that exactly this elusive property of matter, liveness, from the
single cell to entire eco-systems, which implies intelligence throughout
all scales (as Brian Ford states) is what we still cannot in system(s)
biology put on the feet of statistical mechanics and classical
physics.Aren't tumors such intelligent clusters of heterogeneous cell
computers interacting within internaly secured invasive networks that
escape our medical enigma code breakers placed in our synthetic drugs and
radiation devices? Also such undesired life is not easy to kill.  And yet
cancer cannot win the battle unless our own internal systems surrender and
become allies of the invador.


Dear Plamen,

To begin, please allow me to apologize for joining the conversation midway
without having read your earlier postings.

It's obvious that you also expressed the sense of what I was saying. There
are about 6 fundamental laws of physics, which allows for several hundred
combinations among the laws. Meanwhile, most living systems consist of at
least 40 identifiable constituents, which can interact on some 10^47
possible ways. It should be no surprise that (many?) more than one
combination can satisfy any specification of the laws. So the laws are not
broken; they simply lose their power to *determine* a unique outcome.

As you say, sufficiently heterogeneous living system can usually find a
way around most obstacles in their way.


And yet, healthy systems have some sort of regularity, layered structure
and hierarchies as those we observe in a skin biopsy sample.Genetic
mutations do not remain local at the damaged spot; they are signaled to
other "mentally weak" cells which are turned into traitors,also perhaps
even via non-local induction. Are wandering "bad" cells and accelerated
replication the only sources of growing agressive cancers? Here is perhaps
where biosemiotics and phenomenology could help along with creating new*
heterogeneous* SOC models, as you mentioned. You are right, the call for
devising a mathematics that can handle heterogeneous sets,
vectors,matrices, categories and other sorts of organisation in biology
simultateously was already spread by Bob Root-Bernstein in his opening
article to our 2012 edition of integral biomathics (see last link in my
signature). We do not have such an underpinning mathematics and its
related
computation yet. Therefore we remain still stuck in the old system
biological models rooted in physics at best.


I should have mentioned that SOC can also possibly apply to heterogeneous
systems. For example, we have plotted the countervailing properties of
networks -- their efficient performance vs. their reliability, and we have
found that ecosystems from various habitats all achieve about the same
balance between these two traits. (See Fig. 7 on p1890 in
<http://people.clas.ufl.edu/ulan/files/Dual.pdf>.) These metrics do have
heterogeneity built into them. (They are calculated on n-dimensional
networks -- each node representing a distinct constituent.) Some have
suggested that the balance point is very near a critical point. Ergo, SOC
can apply to heterogeneous systems.


Many of us hope that the right answers to all this will be given once we
understand quantum gravitation and master quantum computation. But I have
my doubts in such hopes too.


I have severe doubts about quantum gravity -- at least quantum in the
sense of Planck. (Quantum logic is another matter, and may apply to
gravity.) The Planck constant and the gravitational constant are separated
by some 43 orders of magntude. The engineering rule of thumb is that
phenomena characterized by dimensionless parameters greater than 10^5 or
less than 10^(-5) are dynamically independent.

Quantum computing, on the other hand, might prove quite helpful in
addressing the combinatorics of heterogeneous systems. Let us hope.


The questions I ask are those of an ex product planner colecting customer
feedback to devise a new product. Perhaps we can succeed in doing that
together. Thank you for this.


So then you are quite aware of the combinatorics and surprises connected
with dialogs! It's a complicated world!

Thank you for your contributions to FIS, and I apologize again for not
having read your earlier postings.


All the best,

Plamen


Peace!
Bob


.

_

[Fis] Cancer Cure?

[Pedro C. Marijuan]

Dear Plamen and FIS Colleagues,

Finally I could find some spare time for the paper you mentioned. It is 
very interesting. The analysis of hydrophobic profiles for proteins 
shows rather unexpectedly a power law (self similar) scaling--self 
organized criticality (SOC). How much hydrophobic the protein becomes 
seems to be subject to Darwinian evolution in the relationship with its 
target in the host. For instance, in the virulence of Influenza and 
other types. Yes, it looks as if a new analytical tool can be 
incorporated to the existing plethora of 
biomolecular/biophysical/bioinformatic medical resources.


I have serious doubts, however, that the formidable claim in the title 
"SOC: A Prophetic Path to Curing Cancer" has any chance to be realized. 
Although not being a biomedical expert in cancer at all, I think that 
the NDV oncolytic virus --the proposed magic tool-- has not proved its 
general efficacy for all tumors and metastasis. I mean just in vitro. 
The complexity of cancer types, of cancer ecologies, and of the 
interactions with the immune system, suggest that "massive doses by 
arterial injection" as the author proposes might never be dreamed of for 
any clinical trial. Given the complete lack of evidence, no ethical 
committee would devote more than 5 seconds to consider the issue.


Let me reiterate that the the analysis of hydrophobic profiles looks 
very interesting, but directly jumping to prophetic cures of cancer... 
Some years ago, a mathematician also claimed that incorporating 
non-linearity analysis in the timing of anti-cancer combined therapies, 
tremendous advancements could be achieved. After the media immediate 
uproar, the final conclusion was that only in a few cases there could be 
an improvement of the treatment.


So, as you Plamen were pointing some days ago, medicine is very 
important for us, a matter of life or death, of deep knowledge and high 
anxiety. That means that withing the messiness of the whole disciplines 
and informal practices involved, there always be quacks and prophets 
playing with wild cards, trumping the credulity of people for 
self-promotion or for marketing reasons. It is chilling that entire 
practices in industrialized medicine may be regularly caught into those 
blind games. But it is not only medicine, our scientific technological 
civilizations are blind in so many regards!


All the best-- Pedro

--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] _ Re: _ Towards a 3φ integrative medicine

[Pedro C. Marijuan]

Dear Plamen,

Thanks for the synthetic attempt. You have put together pretty complex 
strands of thought that become too demanding for a general response. I 
will concentrate in a few points.


What is Medicine? In what extent is it amenable to "integration"? Is 
reductionism an anathema in medicine? Can we regularly ascend from 
cellular info flows to organs/systems, and to healthy 
individuals/environments?


The history of Medicine shows messiness in the highest degree. To note 
that it was not included in the Trivium/Quadrivium medieval scheme of 
knowledge, and was only accepted within the "mechanical arts" after Hugh 
of St. Victor compilation (XIII Century), many decades after the first 
Faculties of Medicine were created in Italy. Why medicine is so messy? 
Just go the wiki pages on the topic: hundreds of subspecialties are 
listed, and under all those terms we imply all the internal and external 
("natural") phenomena that can derail and put out of track the 
advancement of a life cycle. Each one of those specialties has to 
arrange its own world of knowledge, with lots of analytical and 
synthetic avenues not amenable to neat overall schemes and to formal 
approaches except in some reduced pockets. Successful reductionist 
strategies and analytical techniques are piled up with holistic views, 
and reams of tacit knowledge (indeed medicine is a very stratified small 
world of "lords", "masters", "disciples", "servants", and "beginners").


So, like in engineering, one has to be suspicious of far reaching 
implications for the term "integrative". Not necessarily in this case 
with the "3φ" connotation. But the strong reliance on criticality could 
be subject to scrutiny. Quite many cellular / biomolecular phenomena do 
not especially rely on criticality --perhaps the most essential ones, 
related to "codes", genomic maintenance, protein synthesis, protein 
degradation, signaling, apoptosis, etc. Why the integrative strategy 
should rely on a term that notwithstanding strong physical grounds,has 
relatively thin explanatory capability in the biological? It is a long 
story of looking for responses "where the physical/math light is" and 
not where the biol. problems are.


My view, I can be wrong but I have worked considerably on the matter, is 
that cellular signaling, the crisscrossing of info flows that provide 
the singular intelligence and adaptability of organisms, is not well 
articulated yet. Neither in evo-devo, nor in physiology, medicine and 
health. In this regard all the present parlance on information 
processing that accompanies the tremendous technological info-tech 
revolution does not represent a help, maybe the opposite. The deep info 
problems are taken as already solved and articulated synthesis are 
undertaken as mere agglutinations. Maybe the problem is too deeply 
complex, and medicine is as always too messy.


Sorry if seemingly I have joined the  "Cassandra" club!
Best--Pedro



El 14/05/2016 a las 9:49, Dr. Plamen L. Simeonov escribió:

Dear Colleagues,

My contribution will finalize the discussion on phenomenology in the 
domains of biology, mathematics, cyber/biosemiotics and physics by the 
previous speakers (Maxine, Lou, Sœren and Alex) with a “challenging 
topic” in _3φ integrative medicine_. *You may wish to skip the small 
font text notes following each underscored phrase like the one below.*


_Note 1:_Although this term is often used as synonym for holistic 
healing (s. ref. list A), its meaning in this context with the prefix 
3φ goes much “deeper” into the disciplines’ integration leaving no 
room for speculations by mainstream scientists. The concept is a 
linguistic choice of mine for the intended merge of the complexity 
sciences _ph_ysics and _ph_ysiology with _ph_enomenology for 
application in modern medicine along the line of integral biomathics 
(s. ref. list B).


It is rooted in the last presentation of Alex Hankey, since it 
naturally provides the link from physics to physiology and medicine, 
and thus to an anthropocentric domain implying a leading part of 
phenomenological studies. To begin, I compiled a précis of Alex’ 
thesis about self-organized criticality (s. ref. list C) from his 
paper “A New Approach to Biology and Medicine” -- the download link to 
it was distributed in a previous email of him -- and extended it with 
my reflections including some questions I hope you will resonate on.



I am curious of your opinion about how to apply the scientific method, 
and in particular mathematics and information science, to study 
illness and recovery as complex phenomena.


*Alex Hankey: self-organized criticality and regulation in living systems*

*There is a continuous growth and change at the end of a phase 
transition in an organism, i.e. at its critical point, which is the 
end point of phase equilibrium.*


**

*Both endo and exo, genetics and epigenetics are important for life.*

**

*Self-organized criticality*is a characteristic state of 

Re: [Fis] The phenomenology of life

[Pedro C. Marijuan]

Dear Alex and colleagues,

Thanks for the opportunity to ad a few lines on signaling matters. I 
would not discard any organizational aspect of signaling pathways. I 
have put below a diagram that approaches the dynamics of some major 
ones.Your analogy with mobile phones would be right, provided that 
conversations were mixed, that a number of receivers were just random, 
and that a component of "experience information" would be entered too 
--I think it can apply to the dynamics of second messengers, where 
multitudes of microevents and pathways may be integrated via lots of 
feedbacks (See the box in the figure below). Symmetry is a big word 
concerning the organization of pathways in the construction of 
multicellular development... opposed paths, tipping points, collective 
(populational) symmetry breakings, massive feedbacks, etc.


By the way, when we commented days ago on Tononi's phi, both from John 
Collier and myself, the idea was to consider it as applied to the 
closure of meaning episodes in language. How "getting" the meaning of 
some linguistic episode (eg, a joke) provokes a sudden change of 
transient connectivity between areas...


Apart from meaning, it may also be interesting that there seems to be a 
strong asymmetry in between the incoming / outgoing information 
flows--the "social info loops" around. In most human organizations, the 
ratio is in between 3 and 4. It means that you and me are ordered by 
upper levels in around 80 % of our exchanges, while what we send upwards 
becomes a meager 20 %. It is from a statistics on business communication 
metrics. The generalization is far from direct, but maybe it would occur 
in the cells too--amazingly there is very little literature on cellular 
"signal emission".


Anyhow, how the whole ascending and descending info flows give raise to 
all the varieties of organizational complexity is a fascinating problem,


All the  best--Pedro



*Figure 6: Prototypical signaling pathways of multicellularity.*From 
left to right, a stimulus in the intercellular space binds to a 
transmembrane receptor (sensor) on its extracellular domain. Upon 
binding, the receptor undergoes a transient modification of its 
cytoplasmic domain; this effect triggers a transient modification of a 
series of proteins in the cell, each one acting as an intermediate in 
the signal transduction pathway (signal processing), with characteristic 
hierarchies of protein kinases and second messengers. The last 
components are actuators or effectors that activate or inhibit proteins 
and channels that control several cellular functions, notably gene 
expression by means of transcriptional switches that may interact with 
several coactivator partners. The whole biochemical changes produced in 
the cell represent the response to the received signal —its /molecular 
meaning/.





 El 26/04/2016 a las 10:10, Alex Hankey escribió:

Dear Pedro,

Thank you for the comments on my presentation, and particularly for 
reminding us all that life transmits information of many different 
kinds by very specific and selective processes in chemical signally 
molecules.


I must confess that I had assumed that such kinds of signals could be 
considered special cases of digital information analogous to the codes 
transmitted by a digital signalling tower in a mobile telephone 
network, where the initial code has to name the device that the rest 
of that message section is meant to receive.


In mobile phone systems, individual devices are sent information by 
identifiers. If we have a nervous system working with several 
neurotransmitters, or a cell signalling system working with a number 
of cytokines, each with a specific regulatory influence / purpose, are 
these individual items not performing in ways that are covered by the 
usual combination of Wiener and Shannon, and therefore in principle 
understood, and AS YOU SPECIFICALLY POINT OUT, with no particular 
"experience" component.


I wonder whether the material I transmitted made the following point 
succinctly / precisely enough:
David Chalmers specifically hypothesized that 'experience information' 
(my terminology) mst have a double aspect, and that the 'loop' arising 
from criticality specifically fulfils his hypothesis in a new and 
potent way.
(The material contains so many points that this, to my mind, really 
significant one may have got buried.)


Thank you also for appreciating the amplification of Tononi's 
contribution
(Tononi, I personally regard as of real significance). The internal 
loop creates
the internal coherence that is required to form the 'integrated 
information'.


I have a suspicion that the following propositions are probably correct:
a. any information structure that is truly 'non-reductive'
(Chalmers requirement 3) must possess long range coherence.
b. any information structure with long-range coherence will be a form 
of integrated information.

c. Hence Chalmers requirement 3 in fact specifies 

[Fis] Meaning in neurosceinces

[Pedro C. Marijuan]

Dear FIS colleagues,

This is the month of deadlines in my Institute, so I can only draft a 
few comments on the past messages.


To Maxine: the action theme is very rich, and very well acquainted and 
discussed in last decades neuroscience. Gallistel C.R: with his 
magisterial "The Organization of Action: A New Synthesis" (1980) 
heralded the new views. More recently Alain Berthoz "The Brain's Sense 
of Movement" was boldly claiming "In the beginning was the deed", "In 
principio erat actum" so replacing "verbum" (the concept) for actum the 
act. Joaquin Fuster (Cortex and Mind, 2002) also was debunking the 
traditional views on concepts, claiming instead for "cognits", with both 
perceptual sides and motor sides... One can argue a lot about that, but 
most of these visions are well grounded and fertile. Berthoz's book is 
very elegant and makes for a rewarding reading.


As for Soeren, another explicit vision of meaning comes from Gerald 
Edelman (his neural darwinism, later on "evolved" to more integrative 
views). I copy from Oliver Sacks notes (sorry if it is a little bit long):


/"With his Theory of Neuronal Group Selection (also called Neural 
Darwinism in analogy of the Darwinism in the immune system) Gerald 
Edelman presents a neurobiological theory of the mind. He and his 
colleagues at the Neurosciences Institute have been developing it over 
the past 15 years. He imagines a comprehensive theory of a dozen 
disciplines of neuroscience. The outline of the theory is as follows: /


/After birth a set of inborn values (feelings) //allows us to begin 
building the structure of the brain. The smallest entity of this 
structure is a group of neurons (map) //in which internal links 
represent our experience. Maps are then used as new building blocks and 
interconnected with links into scenes //representing what we experience 
as the present. Ever richer maps are constructed//, ultimately //maps of 
meaning//. In our search for meaning our mind develops up the 
evolutionary //ladder to consciousness//until we form the new categories 
of "past" and "future". /


/On this way, the building blocks acquire step by step more internal 
structure that can be accessed. A continuous stream of //establishing 
and testing of hypotheses//on the basis of the existing interconnections 
weakens or strengthens existing connections or builds new ones//. The 
fittest maps and connections survive (thus the name neural Darwinism). 
These maps are //dynamic //in that they are continually redrawn 
//according to our perceptions//..."//

/

To Loet: building upon the above, a disciple of Edelman, Giulio Tononi, 
has coined the term "integrated information" phi as a sort of 
informational metrics, which is based in an information theory approach 
to the structure of mapping exchanges between neural areas. Seemingly 
the values of phi beyond some threshold indicate the emergence of 
consciousness as a brain epiphenomenon ("PHI: A Voyage from the Brain to 
the Soul", 2012). The view, well built upon info theory (almost Loet's 
style), has attracted a lot of discussion, but ultimately the approach 
continues to be more structurally focused than dynamic... critics have 
argued that the phi value of a smart cell phone is nowadays quite close 
to self-consciousness.


The suggestion (to all) is to explore whether phi, rather than relating 
it to the emergence of consciousness, would relate to the emergence of 
meaning. All the fast circulating activations and inhibitions between 
neural mappings, usually involving opposing flows of neuronal "energy" 
and informational "entropy", when they finally "click" and achieve 
convergence on an optimized state, it represents the collective 
achievement of meaning. Thus, phi would be a highly dynamic, fluctuating 
indicator showing the evolution of the cascades of meaning. Let us 
imagine the thresholds pointed by Bob in ecological networks, but 
circulating at a fiendish speed (could values of phi and resilience 
indexes have similar nature?): The ecosystem of the mind...


To emphasize finally that multiple disciplines may approach meaning, but 
explaining it I think does correspond in our times to explorations like 
the above, neurodynamic. Like the biological phenomenon of heredity... 
after centuries speculating in all realms of inquiry, finally it was 
explained molecularly by Watson and Crick in 1953.


Anyhow, all of the above is very hurried, and it just points to the 
necessity of discussing in depth these exciting matters.


Best regards


--Pedro

 
-

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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

Re: [Fis] DISCUSSION SESSION: INFOBIOSEMIOTICS

[Pedro C. Marijuan]

Dear FIS Colleagues,

A brief note on the variety of exchanges. It is quite intriguing that 
fundamental questions on mathematics (geometry/algebra), computation, 
quantum mechanics, and biology converge on a pretty similar "information 
stuff". Considering the social sciences domain too, where information 
becomes obvious (helas, too obvious to inquire on it!), the timeliness 
of our discussions is exciting.


I disagree about putting "meaning" outside the scope of natural 
sciences. The current bio-info revolution concerning omic disciplines, 
evo-devo, ecology, etc. has stumbled upon meaning although most often in 
empirical, applied domains. What does mean this or that signal? Gene 
knockouts, microarrays, computational inference, etc. provide a massive 
response that has to be interpreted functionally via the new ontologies. 
Perhaps most theoretical interpretations have gone towards the "in 
silico" worlds and bio-computational perspectives, but there is plenty 
of stirring in most fields.


In neuroscience, a similar revolution has been occurring, although 
perhaps at a slower pace, via all the advancements in imaging, 
connectomics, massive modeling procedures, etc. Meaning is explicitly 
considered by authors such as Edelman, Fuster, Berthoz, Dehaene, Tononi, 
Sporns, Frinston, etc. Well, one would like to see how the different 
notions of info, meaning, memory, knowledge, etc. are elegantly cohered, 
articulated, and well connected --in my view, always around the 
advancement of a life cycle. And that should also include the origins 
and evolutionary path of nervous systems (curiously, they did not appear 
for info concerns but for osmotic/trophic functions).


In both biological and neuronal sciences, this enterprise of linking the 
advancement of a life cycle with the communication with the environment 
needs philosophical commitment too, as the itinerary is full of 
"provincial" ways of thinking that have created artificial borders to 
the intercommunication of ideas. Some parties have argued that a new 
info philosophy should be framed, and that should include contribution 
of the closest schools of thinking (perspectivism/phenomenology for my 
personal taste).


The convergence with physics does not look so far away (as has been 
properly claimed by some discussants). Self-production via communication 
with the environment by assemblages of excitable elements, counting with 
algorithmic devices that mirror how the inner and outer worlds coalesce, 
in one case genomes and in the other mystical or Platonic "laws of 
nature" (what strange existentiality do they have!), may finally 
represent a common panorama.


About the ways and means to overcome the complexity crisis that 
surrounds even the more modest steps in the information adventure... I 
have no idea (but to establish a shield with basic consensus in 
"principled" matters).


Best regards--Pedro

El 07/04/2016 a las 13:05, Christophe escribió:


Dear Soren,
To avoid a possible misunderstanding let me say that the MGS has no 
ambition to reach a ’full Peircean semiotic framework’.
The Meaning Generator System has been designed to introduce what 
looked to me as missing in the young ‘science of cognition’ in the mid 
90’s. ‘Meaning’ was a key concept without any model for meaning 
generation in an evolutionary perspective. The MGS was designed to 
fill the gap. At that time I did not know about Peirce (was at IBM on 
very different subjects). Information on Peirce work came in later.
The MGS has some compatibility with the Peircean approach as both rely 
on interpretation. But two key points of the MGS are not really 
present in the Peircean framework: the evolutionary story from animals 
to humans and the development of a meaning generation process (Peirce 
tells about the generated meaning (the Interpretant) but does not tell 
much about a meaning generation process (the Interpreter)).
So my question about the MGS as a possible introduction to the 
concepts of meaning and experience is not to be understood as strictly 
part of the Perceian semiotic framework. And the question is still 
being asked.

Best
Christophe



*De :* Søren Brier 
*Envoyé :* mercredi 6 avril 2016 02:04
*À :* 'Christophe'
*Cc :* fis@listas.unizar.es
*Objet :* SV: [Fis] _ DISCUSSION SESSION: INFOBIOSEMIOTICS

Dear Christophe

Never the less we consider that cats and dogs or dolphins –I have 
played with them all – to have an inner experimental life in order 
also to support their perceptual skills for instance and they have 
memory and recognition capabilities.


I do appreciate that you work with these things and try to move your 
modelling more towards a Peircean biosemiotic paradigm. But in what I 
have seen from you so far I do not think you have moved to a full 
Peircean semiotic framework.


But even if, then biosemiotics is certainly not (yet?) accepted as a 
natural 

[Fis] _ DISCUSSION SESSION: INFOBIOSEMIOTICS

[Pedro C. Marijuan]

Dear FIS Colleagues,

I am attaching herein Soeren's presentation. If you have any trouble 
with the attachment, the file is in fis web pages too:


http://fis.sciforum.net/fis-discussion-sessions/

By clicking on Soeren Brier's session (highlighted in red) you can 
immediately obtain it.


Nevertheless, below there is a selection of more general ideas from the 
paper. For those interested in FIS "archeology", Soeren presented in 
January 2004 a discussion session on Information, Autopoiesis, Life and 
Semiosis. It  can be found by scrolling in the same above link.


Best greetings--Pedro

-


 Infobiosemiotics


Søren Brier, CBS

This discussion aims at contributing to the definition of a universal 
concept of information covering objective as well as subjective 
experiential and intersubjective meaningful cognition and communication 
argued in more length in Brier (2015a). My take on the problem is that 
information is not primarily a technological term but a phenomenon that 
emerges from intersubjective meaningful sign based cognition and 
communication in living systems. The purpose of this discussion is to 
discuss a possible philosophical framework for an integral and more 
adequate concept of information uniting all isolated disciplines (Brier, 
2010, 2011, 2013a+b+c).


The attempts to create /objective concepts/ of information were good for 
technology (Brilliouin 1962) and the development of AI, but not able to 
develop theories that could include the /experiential (*subjective*) 
aspect/ of informing that leads to meaning in the social setting (Brier 
2015b). The statistical concept of Shannon (Shannon and Weaver 
1963/1948) is the most famous objective concept but it was only a 
technical invention based on a mathematical concept of entropy, but 
never intended to encompass meaning.Norbert Wiener (/1963) /combined the 
mathematics statistical with Boltzmann’s thermodynamically entropy 
concept and defined information as neg-entropy. Wiener then saw the 
statistical information’s entropy as a representation for mind and the 
thermodynamically entropy as representing matter. So he thought he had 
solved the mind matter problem through his and Schrödinger’s (1944/2012) 
definition of information as neg-entropy. The idea was developed further 
into an evolutionary and ecological framework by Gregory Bateson (1972, 
1979, 19827) resulting in an ecological cybernetic concept of mind as 
self-organized differences that made a difference for a cybernetically 
conceptualized mind (Brier 2008b). But this concepts that could not 
encompass meaning and experience of embodied living and social systems 
(Brier 2008a, 2010, 2011).


My main point is that from the present material, energetic or 
informational ontologies worldview we do not have any idea of how life, 
feeling, awareness and qualia could emerge from that foundation.


Ever since Russell and Whitehead’s attempt in Principia Mathematica to 
make a unified mathematical language for all sciences and logical 
positivism failed (Carnap, 1967 & Cartwright et.al. 1996),the strongest 
paradigm attempting in a new unification is now the info-computational 
formalism based on the mathematic calculus developed by Gregory Chaitin 
(2006 and 2007) ). The paradigm is only in its early beginning and is 
looking for a concept of natural computing (Dodig-Crnkovic, 2012) going 
beyond the Turing concept of computing. But even that still does not 
encompass the experiential feeling mind and the meaning orienting aspect 
of intersubjective communication wither be only sign or also language based.


So far there is no conclusive evidence to make us believe that the core 
of reality across nature, culture, life and mind is purely absolute 
mathematical law as Penrose (2004) seems to suggest or purely 
computational.Meaning is a way of making ‘sense’ of things for the 
individual in the world perceived. It is a non-mathematical existential 
feeling aspect of life related to reflection past, present and future of 
existence in the surrounding environment, in humans enhanced by 
language, writings, pictures, music through culture. In animals 
cognition and communication are connected to survival, procreation and 
pleasure. In humans beings cognition develops into consciousness through 
subjective experiential and meaning based (self-) reflection of the 
individual’s role in the external world and becomes an existential aspect.


My conclusion is therefore that a broader foundation is needed in order 
to understand the basis for information and communication in living 
systems. Therefore we need to include a phenomenological and 
hermeneutical ground in order to integrate a theory of 
interpretative//subjective/ and intersubjective meaning and 
signification with a theory of /objective/ information, which has a 
physical grounding (see for instance Plamen, Rosen & Gare 2015). Thus 
the question is how can we 

[Fis] IMPORTANT TECHNICAL INFO

[Pedro C. Marijuan]

Dear Colleagues,

Some parties have asked about the original text from Louis opening the 
session. It can be found at the link:


http://fis.sciforum.net/fis-discussion-sessions/

By clicking on Louis H. Kaufman session (highlighted in red) you can 
immediately obtain it.


Besides, we have just realized that Louis' messages were systematically 
blocked by the server, for he was posting to fis as "cc". It is the 
wrong procedure: one should always post  fis@listas.unizar.es as "to". 
Otherwise it may pass or not.
When you have doubts on whether your own message has passed or not, go 
to the distribution archive and check:

http://listas.unizar.es/pipermail/fis/

Best greetings--Pedro/
/--- 

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[Fis] Fwd: Discussion

[Pedro C. Marijuan]

From Louis H Kauffman 
DNA Topology Kauffman and Lambropoulou] 

It is in this domain, that I became interested in looking at the 
self-reproduction of DNA as an instance of an abstract self-replication 
schema. There is much more to be done here in linking this abstraction back
to the topology and to the actualities of the biology. The investigation 
led to a number of analogies with structure of quantum mechanics and 
this will in turn related to quantum topology. This is in development.


2. Further topological/geometric work is very possible. The sort of 
thing seen in Pivar could be examined for mathematical problems to be 
articulated. We are aware that biological forms must arise via 
self-assembly  and this is in itself a possibly new field of geometry! 
The simplest example of self-assembly as a model is the model of 
autopoesis of Maturana, Uribe and Varela from long ago. Their model 
shows how a two dimensional cell boundary can arise naturally from an 
abstract ‘chemical soup’.


3. While I do not agree with Max Tegmark that Mathematics is identical 
to Reality, I do believe that the key to actuality is in the essence of 
relationships. The essence of relationships is often accompanied by a 
mathematical essence or simple fundamental pattern. This is so striking 
in the case of DNA reproduction (e.g.) that I cannot help but feel that 
some real progress can occur in looking at that whole story from the 
abstract and recursive self-replication to how it is instantiated in the 
biology. The question in general is: What can we see about the way 
mathematical models are instantiated in actuality?!


I will stop here in the interest of brevity.

Best,

Lou
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Re: [Fis] SYMMETRY & _ On BioLogic

[Pedro C. Marijuan]

Dear FIS Colleagues,

For my taste the ongoing conversation is running too fast. We have 
passed, via Louis, Plamen, and other colleagues, along essential themes 
on the relationship between life and formal approaches, perhaps too 
cavalierly.


I am still stuck with the problem of explanation in biology and the role 
of Darwinism as a supposed central theory of the biologic, motivated by 
the initial exchanges. The apparent centrality of natural selection when 
confronted with biomolecular, physiological, developmental, 
populational, and ecological arenas becomes often the overstretching of 
a paradigm (of not so brilliant performance in my opinion), and also the 
lack of alternative general frameworks to reflect more consistently on 
the knowns and unknowns of the whole biological complexity. The parallel 
with mechanics in physics could be illustrative--classical, statistical, 
fluid, quantum... what is finally "mechanics"? For Wilczek, a successful 
"culture".


More explanatory dimensions are needed in biology, and herein we have 
been commenting on topology, morphology, and other lateral points. 
Living systems have discovered and introjected so many laws of nature 
and emergent morpho-geometric constraints, that a whole signaling pack 
devoted to deal with mechanical force (mostly via cytoskeleton and 
adhesion molecules) has become essential for organismic development. 
Stress and adhesion dictate gene expression, powerfully. That some 
coding counterparts have to exist is OK, but the explanatory burden 
belongs to the very morpho-topological phenomena and to the functional 
tricks that realize it cellularly on the biomolecular and physiological 
scales. The same regarding the amazing emergences derived from the 
handling of electrical and electromagnetic fields.  A doctrinarism close 
to the sectarian takes the existence of the encoding --by natural 
selection, and what else?-- as the only significant point to reiterate, 
endlessly. In an equivalence with modern technology, would we talk about 
market competition as the only creative engine of inventions?


The sort of explanatory art needed (quite OK with Plamen's call and Dr. 
Pivar's exploration), would mean following the appropriate disciplinary 
tributaries, irrespective of their origins, and not only the officially 
established main course. In my view, we maintain explanatory styles of 
other epochs, with far less complicated systems of knowledge.


An interesting point, perhaps more concrete, would rely on the 
capability of the cellular "engine" to attain a quasi universal 
problem-solving capability. Whatever the problem at hand, the adequate 
mixing of positional, differentiating, and mecano-morphological 
capabilities of cells will produce adequate inventions. The ways and 
means to achieve those inventions is our explanatory problem. A little 
detail is why prokaryotes were unable to conquer morphology, while 
eukaryotes excelled. Was it because of the lack of cytoskeleton and the 
associated lack of mechano-topological mastery (or mainly for lacking 
DNA handling virtuosity)? More other expl. branches to the "river"?


Anyhow, excuse these torpid attempt to rekindle a discussion that for me 
is very important, yes, in informational matters.


best regards--Pedro

--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] SYMMETRY & _ On BioLogic

[Pedro C. Marijuan]

Louis, a very simple question: in your model of self-replication, when 
you enter the environment, could it mean something else than just 
providing the raw stuff for reproduction? It would be great if related 
to successive cycles one could include emergent topological (say 
geometrical-mechanical) properties. For instance, once you have divided 
three times the initial egg-cell, you would encounter three symmetry 
axes that would co-define the future axes of animal 
development--dorsal/ventral, anterior/posterior, lateral/medial. Another 
matter would be about the timing of complexity, whether mere repetition 
of cycles could generate or not sufficient functional diversity such as 
Plamen was inquiring in the case of molecular clocks (nope in my 
opinion).  best--Pedro


--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] SYMMETRY & _ On BioLogic

[Pedro C. Marijuan]

Dear FIS Colleagues,

Let me start by announcing the *special session on *_*INFORMATION & 
SYMMETRY*_, in the Symmetry gathering this Summer in Vienna (18-22 July) 
http://festival.symmetry.hu/ The deadline for abstract reception in this 
session has been enlarged until beginnings of next month. Tentatively, 
it will be chaired by our colleagues Jerry Chandler and Abir 
Igamberdiev. A special issue has been planned in cooperation with the 
journal "Information" too. We will celebrate the near 20th anniversary 
of the first joint session with FIS on information and symmetry 
(Washington 1995) and the subsequent special issues (Symmetry & Culture, 
1996 and 97). It will be a good occasion to meet again and pass over the 
views developed in this period. Old FISers and members of this list are 
invited to attend.


And then about the ongoing discussion--responding to the exciting 
exchanges by Louis and Plamen. This type of abstract discussion is 
rarely fertile for biological fundamentals, where structure and function 
become so intertwined that the concrete mechanisms obliterate the quest 
for too far-reaching generalizations, but it may be interesting for 
approaching problems such as "distinctions". Some time ago I tried an 
approach not so different from Spencer Brown's. It was based on 
"multidimensional partitions", a development of Karl Javorszky (of this 
list) for set theory out from classical Euler's partitions (the 
different ways to decompose additively a natural number). It was very 
interesting finding a natural limit for the total distinctional between 
members of given set, finding a curious info dynamics of distinctional 
gains and losses after addition of just one sign or a few signs in the 
set, a sort of power law in the total decomposition, etc. (most of this 
was coming from previous works by Karl--we somehow improved the 
algorithmic, with a few colleagues here in Zaragoza). Then we tried to 
apply it to prokaryotic complex receptors (2CS, 3CS) and to the 
"language of cells"... but we reached our math limits very soon (anyhow, 
some elementary drafts and publc. were left). I keep thinking that it 
was a serious approach to cellular "distinctions" that could be 
escalated upwards. Later on, in a couple of papers in BioSystems (2010, 
99, 94-103; and  2013, 114, 8-24) we roughly described prokaryotic and 
eukaryotic signaling machinery in relation with the intelligent 
advancement of the life cycle of each cell.


About viruses in evolution, we could listen in Vienna (IS4IS & FIS 2015 
Conference) to one of the most advanced thinkers, Guenther Witzany. What 
Plamen suggests about a virus theory from the viewpoint of viruses is 
not science fiction. It is astonishing what a few crucial proteins of 
HIV "know" about hundred molecular components of our lymphocytes. It is 
as if they had conspired with structurally enslaved pieces of former 
viruses temporarily joining them to create havoc in the machinery of the 
cellular host. If just 30% of what Guenther says is right, we have to 
revise the Symbiotic Theory, the Central Dogma, the RNA (inner) cloud, 
gene expression, biosemiosis, etc.


Echoing the final debates of the previous session, description should go 
first. And in bio-informational matters there is still plenty to describe.


Best regards--Pedro




--
-
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.i...@aragon.es
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[Fis] MODERATION NOTE

[Pedro C. Marijuan]

Dear FIS Colleagues,

Let me remind you all that this new session is a little bit special. 
Around 70 new parties have joined our list to maintain a common dialog 
based on the different presentations. I know we are accustomed to many 
years of "tangents" and parallel discussions, but this time you are 
kindly requested to narrow the focus and to directly involve the 
presenters' themes (Maxine's) in the discussions. Quite probably, any 
newcomer does not understand what all this give and take is about. The 
discussion should not drift into other themes and we need to involve the 
newcomers and not leave them alone pulling and giving the word to a few 
more active old members. This is not the idea of the common dialog that 
Plamen and me thought could be a fertile and interesting experience to 
both parties, I guess.


Maxine, please, you have the word.

Thanking in advance--Pedro

--
-
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.i...@aragon.es
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[Fis] _ Re: Maxine’s presentation

[Pedro C. Marijuan]

Dear Maxine and Colleagues,

Concerning your presentation I have a couple of questions. About dance, 
first, let me inquire about another important aspect it may have, 
perhaps a "vital" one . In a number of species, dance is related to the 
mutual pre-exploration between potential reproductive partners. The 
individual fitness of the candidate(s) are evaluated quite strategically 
along the movements of dance, at least in the essential adaptive traits. 
Cultural layers of human societies may have created further "meanings" 
to dance (artistic, gimnastic, educative, therapeutic, etc.) but at the 
very roots of this human phenomenon the exploration between genders 
continues to be of the essence, I think. Those qualities you mention of 
tensional, linear, aerial, and projectional are in themselves excellent 
ways to observe the whole person: not only in the motoric dimension, but 
also concerning some related intellectual-emotional capabilities. The 
"gestalts" Alex mentions are colored very differently depending on the 
social/cultural contexts in which the same dance may take place. It is 
quite interesting that the folk inter-gender dance is performed in 
"safe" public spaces, and that it often conveys a feminine advantage 
(better synchronization of movements, more interest for fashionable 
pieces), etc. etc. Although perhaps it does not apply to most of present 
day "disco dance". Along your points, I was reminded that many years 
ago, someone in fis list wrote about the informational implications of 
"Tango" (originally a dance between castaway males in Argentina's 
immigrant squalors) ... it is a pity I can remember very little about that.


And the second comment concerns the paleoanthropological tools. The 
analogy between the two major forms of tools and the two major tooth 
forms is very well developed.I quite agree, and also would like to ad a 
relationship with human gut-microbiome. We needed "artificial" teeth 
because with our terrific brain growth, the overall metabolic needs 
escalated almost 20%. However, at the same time the gut size (& 
contained microbiome) was reduced 50% in comparison with any 
Anthropoidea of our size. This is an impossible budget to maintain, 
unless the development of collective intelligence applied to our feeding 
and created completely original ways. These new ways were made possible 
by language, group identities, tools and artifact creation... but it was 
the new feeding style what pushed along this adaptive loop. We have 
called the new ways as "cooking", but actually it was a pre- or external 
digestion, achieved with those artifactual "molars and incisives", plus 
boiling, roasting, etc. And also by incorporating "external 
microbiomes"--fermentation-- for our service: bread, wine, beer, cheese, 
etc. The essential new foods of civilization. Cooking made us humans... 
how a "social brain" was created, and how our phenomenology became 
captive of group collective thinking might be a topic deserving further 
analysis.


Thanking in advance for the tolerance!

Best--Pedro

-


*Phenomenology and Evolutionary Biology*


***(1): Phenomenology
*As written in the Preface to the 2^nd edition (1979) of The 
Phenomenology of Dance, “Certainly words carry no patented meanings, 
but the term ‘phenomenology’ does seem stretched beyond its limits 
when it is used to denote either mere reportorial renderings of 
perceptive behaviors or actions, or /any/ descriptive rendering at all 
of perceptible behaviors or actions. At the least, ‘phenomenology’ 
should be recognized as a very specific mode of epistemological 
inquiry, a method of eidetic analysis invariably associated with the 
name Edmund Husserl, the founder of phenomenology; and at the most 
‘phenomenology’ should be recognized as a philosophically-spawned 
terms, that is, a term having a rich philosophical history and 
significance.”


A phenomenological analysis of movement given in The Phenomenology of 
Dance follows the rigorous methodology set forth by Husserl. The 
methodology is integral to understandings of phenomenology as well as 
to its practice. Husserl distinguished two modes of the methodology. 
One mode is termed “static,” the other is termed “genetic.” The aim in 
static phenomenology is to uncover the essential character of the 
phenomenon in question or under investigation. The aim in genetic 
phenomenology is to uncover the source and development of meanings and 
values we hold.


The abbreviated phenomenological analysis of movement set forth below 
follows a static phenomenology. The abbreviated phenomenological 
analysis of the origin of tool-making follows a genetic phenomenology. 
The first analysis elucidates the inherently dynamic character of 
movement, and in ways quite contrary to the idea that movement is a 
force in time and in space 

[Fis] _ Re: Otto--re closing lecture

[Pedro C. Marijuan]

Dear FISers,

Just a couple of brief comments to Howard and Jerry.

To Howards: thanks for the exciting New Year Lecture closure! However, 
your text below to Otto makes irresistible for me indulging in a final 
criticism. It is clear in the text that the boundaries of force are the 
very determinants of information/communication. Forces everywhere. From 
quark forces to the forces of history. It is exactly the 20th century 
dominant physicalism with an info/comm. aggiornamento. I cannot blame it 
all, of course, as your historical analysis is very original, but all 
the other physicalist conglomerate is not so useful/interesting. When 
life romps in this tiny corner of the universe, a new set of 
info-dynamics are set into motion, completely different, and capable of 
overcoming the boundary conditions of force. The life cycle dominates 
and commands the environment: selfproducing, communicating, engaging 
with other life cycles, transforming everything, etc. This constructive 
power goes beyond anything seen in the cosmos. It is an informational 
constructivismthat does not follow smoothly from the atomistic 
narrative--there is a big divide... Historically it is a similar trend 
of informational constructivism what leads to overcome the Luciferine 
solvent power. See France and Germany: after 300 years of wars, 
treaties, armistices, hostilities, etc. finally are efficiently united 
in a common European purpose (or look at the endless wars between Spain 
and the United Kingdom). Thanks to collective intelligence in action 
(wisdom, justice, kindness) a group of enlightened politicians after 
WWII achieved a great design, like Founding Fathers in US 18th Century. 
These grand designs are the key to overcome so many contemporary 
Luciferine catastrophes around... But we would continue arguing for too 
long, so I stop  and thank you again for the Lecture!


To Jerry: you are quite right in the demand for some "scientific meat" 
around the notion of communicating, interconnected life cycles. I will 
try to provide a few portions:


1. "Active Matter", it is a new scientific field that is getting more 
and more fashionable. Basically it consists on computer simulations and 
real experimental molecular settings where active molecules (usually 
enzyme/proteins) interact with some motive power (ATP, 
electrical/magnetic fields, metal beads) and get interconnected in their 
"work cycles", with the emergence of amazing collective patterns 
apparently only restricted to the biological. This interconnection of 
"working cycles" is the genuine precursor to what I was meaning above.


2. Coupled oscillators. A lot of theoretical and experimental work done 
around very elementary oscillators (eg, famous Kuramoto model) applied 
to chemical, neuronal and theoretical physics fields. It is also known 
as "synchronization networks", very well worked by Winfree, Strogatz, 
Duncan Watts, etc., about biological clocks, fireflies, crickets, heart 
cells, and neurons. Very complex theoretical oscillators built (not far 
from the cell-cycle style, though realms of complexity below).


3. Pharmacology: it has been claimed that 80% of the current drugs 
produce their effects through the signaling system, by binding to the 
receptors, channels, etc. So, they interfere in the communication system 
of the cell to modify the life cycle events at a vast scale of whole 
tissues and organs. Now we have direct external action on interconnected 
cell-cycles, with myriads of models, drug designs, silicon and wet 
experimental works, etc.


4. Physiology. There is little doubt that the whole physiology relates 
finally to interconnected cellular life cycles. Unfortunately (or 
fortunately, who knows) most of physiology was conceived before there 
was even a dream or a hunch about cell-to-cell communication via  
especial signaling systems... We should ad neuroscience too, but it 
would be to much scientific meat for the lunch.


To recap, once life is "on", there is a certain discourse about 
informational constructivity (to emphasize: which is based on the 
intertwining of self-production and communication via interconnected 
life cycles) that can reach quite high in order to better understand the 
info dynamics of those rare entities based in the informational way of 
existence... I think Howard's lecture has put us in front of very 
intriguing possibilities of social information science explanation.


Best regards
--Pedro


the force cosmovision El 03/02/2016 a las 7:10, howlbl...@aol.com escribió:


Otto, an interesting call, for a theory that brings together the brute 
force of an abiotic universe and information.


Here's a short timeline that pulls the brute force elements together 
as informational exchange:


The evolution of information, sociality, social structure, and 
the emergent properties of societies


(all dates ABB, After the Big Bang)

10(-31) ABBprimitive communication between quarks via the strong 
force.The 

[Fis] Interconnected life cycles

[Pedro C. Marijuan]

Dear Howard and colleagues,

Once settled most of the dust, the balance seems to favor the need to 
disentangle the two phenomena, biotic communication vs. particulate 
"excommunication". As some FISers have suggested, maybe a revised 
conceptualization of the generative phenomena in the quantum could turn 
out to approach and even to equate the two phenomena.


Is it of any importance clearly tying communication to life, to the 
advancement of the life cycle? I think so. On the one side, we 
naturalize freewheeling approaches to meaning and to some other 
informational concepts (signals, adaptation, value, intelligence). On 
the other side, quite many events of human life (social info flows) 
either of the technological realm, or economic, legal or political, 
would receive a more rational grounding or a higher level framework to 
conceptually adjust. It is the primacy of life, at all levels.


Even the Lucifer Principle, the leit motif of this New Year Lecture, may 
be formulated with improved cogency in that way. Both super-organisms 
and pecking order are direct products of communication phenomena among 
life cycles, within increasing layers of complexity but surviving the 
self-maintenance ethos of life and its communication retinue. Memes are 
different--I think the term is catchy but unproductive (too long to 
discuss now). By the way, Howard, to insist: the LP needs a balance, 
lets call it Archangel or Angelic Principle. It is when their balance, 
the symmetry between them gets broken and none of the restoration 
mechanisms may get hold, that the human beast gets free... Our political 
and social systems, at least in most democratic countries, are wisely 
full of "checks and balances"--not a bad term.


All the best
--Pedro

--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] _ RE: _ Re: Cho 2016 The social life of quarks

[Pedro C. Marijuan]

 
understandable in any one meta-language or any pair of meta-languages. 
 In order for symbolic chemical communication to occur, the language 
must go far beyond such simplistic notions of a primary interaction 
among forces, such as centripetal orbits or even the four basic forces.


The early metalanguage of chemistry was merely terms within ordinary 
language, such as the names of elements. Or, the common names for oils 
from various sources. Around the turn of the 19 th Century, the 
metalanguage of chemistry started it century-long journey to become a 
meta-language of mathematics with the development of the concepts of 
atomic weights for each singular elements and molecular weight, and 
molecular formula for each different molecule.


The critical distinction that separates the meta-language of chemistry 
from other metalanguages is the absolute requirement for specification 
of the name of any object on the basis of it’s distinction from other 
signs or collections of signs.


Thus, chemical information theory, in terms of metalanguages, requires 
the exact usage of the meta-languages of both physics and mathematics 
in order to define the origin of its symbolic logic, as well as the 
natural metalanguage of ordinary human communication.


Biological information theory is grounded on chemical information 
theory, using a particular encoding of meaning within dynamical 
systems, to communicate among the 5 essential metalanguages necessary 
for the practice of the medical arts.  And, I might add, for human 
history.


The failure of luke-warm physics to serve as a foundation for a 
generalized information theory is the lack of terminology that can be 
used to communicate among the symbolic logics used in more advanced 
modes of human communication.


In summary, in the 21 st Century, the foundation of human symbolic 
communication  requires multiple metalanguages and symbol systems, 
that is, a generalized information theory.  Such a generalized theory 
 of information must necessarily include the symbolic logic of 
chemistry, which is essential to span the  symbolic gaps between the 
disciplines.


(For those of you who are familiar with my background, this email 
illuminates some of the reasoning behind the development of the 
perplex number system and perplex systems theory within the 
associative symbolic logic of graph theory.)


Cheers

Jerry



Begin forwarded message:

    *From: *"Pedro C. Marijuan" <pcmarijuan.i...@aragon.es
<mailto:pcmarijuan.i...@aragon.es>>

*Subject: Re: [Fis] Cho 2016 The social life of quarks*

*Date: *January 18, 2016 at 5:50:40 AM CST

*To: *'fis' <fis@listas.unizar.es <mailto:fis@listas.unizar.es>>

Dear Howard and colleagues,

OK, you can say that quarks communicate, but immediately we need
to create another term for "real" communication. I mean, there are
quarks (fermions) and bosons (particle forces) everywhere:
planets, stars, galaxies, etc. Their multiple interactions
constitute most of the contents of physics. If you want to term
"communication" to some basic categories of physical interactions
based on force exchange --of some of the 4 fundamental forces,
whatever-- we run into difficulties to characterize the
communication that entails signals, agents and meanings, and
responses. That's the "real" communication we find after the
origins of that singular organization we call life --essential
then for the later emergence of superorganisms, peaking order,
memes, etc. You have oceans of interacting fermions and bosons
around, but the new communicating phenomenology is only found in
our minuscule planet.

As an explanatory metaphor, it is not a good idea, almost wrong I
dare say. But as a free-wheeling, literary metaphor it belongs to
the author's choice. The problem is that both realms of
information, so to speak, have relatively overlapping components,
depending on the explanatory framework used (see the ongoing
exchanges by Stan, John, Terry,  etc.) And that kind of apparent
homogenization blurs the effort to establish the distinctions and
advance in a unifying perspective (I think!!). In any case, it
deserves more discussion. In your Jan. 14th message you ad more
elements--I will think twice!.

All the best--Pedro

PS. Clarifying the two messages per week rule (responding to
offline quests): the two messages should be counted along the
"international business week": starting on Monday until the end of
Sunday, Greenwich Time. Thanks to all for respecting this
"boundary condition"!




--
-
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
50

[Fis] Season Greetings / Merry Christmas

[Pedro C. Marijuan]

Dear FIS Colleagues,

Herewith the customary Nativity scene at El Pilar Basilica of Zaragoza.
Have a Merry Christmas and a Happy New Year!

--Pedro


navidad sauce

--
-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] Symmetry Conference in Vienna

[Pedro C. Marijuan]

Dear FIS Colleagues,

This is an invitation to arrange a FIS session on Information and 
Symmetry in the Conference next year in Vienna (18-22 July 2016).
I am trying to attach a descriptive file, but probably the server will 
reject it. So herewith a brief description:


SYMMETRY FESTIVAL 2016
The World Largest Multidisciplinary Conference & Art Festival in 
Symmetry Studies
Organized by SYMMETRION, under the auspices of the International 
Symmetry Association,
in cooperation with the Bertalanffy Center for Systems Science and the 
Technical University of Wien.


INFORMATION
www.festival.symmetry.hu
i...@symmetry.hu

PROGRAMS
-International Scientific Conference, including Talks and Workshops
-Art Exhibits, including Contemporary Art and Origami Exhibition
-Teacher Programs and Book Shows Concerts, Performances and Movies
-Family Day and Public Programs

REGISTRATION DEADLINES:
15 February 2016 -- Abstract Submission
1 June 2016 -- Early Bird Registration.

Other worldwide symmetry events in the past:
Symmetry Festival 2013 Delft; SF 2009, SF 2006, SF 2003 Budapest;
Symmetry Congress 1998 Haifa; SC 1995, Washington D.C.;
SC 1992, Hiroshima; Symmetry of Structure Symposium 1989 Budapest.

FIS interested parties may send me their participation intent offline, 
so that we can finally arrange a fis section

(as we did in some other Symmetry events in the past).

Best greetings to all,
--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] [Fwd: RE: Sustainability through multilevel research:] From Loet

[Pedro C. Marijuan]

 Original Message 
Subject:RE: [Fis] Sustainability through multilevel research:
Date:   Sat, 12 Dec 2015 08:13:36 +0100
From:   Loet Leydesdorff <l...@leydesdorff.net>
Reply-To:   <l...@leydesdorff.net>
Organization:   University of Amsterdam
To: 	'Pedro C. Marijuan' <pcmarijuan.i...@aragon.es>, 'fis' 
<fis@listas.unizar.es>






Dear Pedro,



Although I agree with some of your remarks, the following note:



/Revolution was preceded by what has been called the silent “corporate 
revolution” (Huff, 2011), which opened the way for collective 
organizations legally autonomous in European cities during XIII and XIV 
centuries: universities, parliaments, counsels, municipalities, 
professional colleges, guilds, mercantile associations, charities, 
schools, etc. It was this Medieval awakening in the cities of Western 
Europe what made possible the later hyperinflation of autonomous 
collective organizations, –“information based”– growing exponentially 
and propelling all the further complexity of modern societies./




Various authors have attributed the transformation (“modernity”) to 
different factors. Marx, for example, pointed to double bookkeeping, 
Weber to the protestant ethics, the printing press, etc. It seems to me 
that the source of the protestant/individual revolution has to be found 
in the individual mandate provided by the Gospel itself: one is 
responsible for one’s own soul. (This was a collective fate of the 
Jewish people in Judaism.) First, Christianity took the Roman form of 
Catholicism. When this eroded, a return to the original Gospel became 
possible: /imitatio Christi/ (Thoma a Kempis), Luther’s /sola 
scriptura./ Indeed, Luther had the major advantage of the printing press 
(when compared with Jan Hus a century before him.) Both Jan Hus and 
Luther translated the bible into the vernacular. (Henry VIII followed in 
1535.)




The issue is that the order of meaning processing changed from top-down 
(/Roma dixit/) to bottom up. This was institutionalized in the Dutch 
revolution (1581) which led to war with Spain. (You may wish to put me 
in your virtual prison. J)




Best,

Loet




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Re: [Fis] Sustainability through multilevel research:

[Pedro C. Marijuan]

Dear FISers,

I agree with Loet's views (for once! :-) ).  The energy flow supporting 
the biosphere and society as a whole have not much explanatory power 
regarding the bonding complexity of contemporary societies. Of course, 
it is an interesting exercise, particularly concerning the limits of 
sustainability, but we have had so much thermodynamic inflation that it 
is very difficult adding anything relevant. Irrespective of its 
sophistication, the energetic realm can hardly substitute for the 
informational realm.
About the intriguing interrelationship between kinship and nonkinsip 
modalities of human bonding, a very interesting view was drafted by 
Francis Fukuyama (1995), centered on "trust". He was distinguishing 
between "familial" centered societies and "high trust" societies. In 
European terms (exaggerating), it is the dichotomy between the 
Mediterranean societal culture and the Anglosaxon culture. It is not a 
black and white narrative, as each polarity has advantages and 
disadvantages (think on wine & Mediterranean food!), and actually today 
each country and each culture has some terrible mix of everything, but 
it is interesting just to see how the two kinds of bonding may interact 
within a complex society.  I also penned a few ideas about the matter in 
my recent "How the Living is in the world"  (DOI information: 
10.1016/j.pbiomolbio.2015.07.002.) I am copying below a paragraph (maybe 
a little bit long--excuses). /


This coarse reflection on the dynamics of successive “informational 
entities” helps us make sense of fundamentals of social evolution. The 
transition to a new social order, more or less ‘revolutionary’, tends to 
be produced by new information channels and communication practices that 
support the emergence of new ways to organize the structures of social 
self-production. Thus, the development of social complexity appears as 
irreversibly linked to a chain of historical inventions for 
communication and knowledge generation: numbers, writing, alphabet, 
codices, universities, printing press, books, steam engines, means of 
communication, computers, Internet, etc. (Stonier, 1990; Hobart and 
Schiffman, 1998). This succession of fundamental inventions has 
dramatically altered the “infostructure” of modern societies, and 
subsequently the informational formula for being in the world has been 
applied with multiple variants along that complexity runaway: with 
plenty of room generated by the new information tools, not at the bottom 
but at the supra-individual top. We should not forget that the momentous 
Scientific Revolution was preceded by what has been called the silent 
“corporate revolution” (Huff, 2011), which opened the way for collective 
organizations legally autonomous in European cities during XIII and XIV 
centuries: universities, parliaments, counsels, municipalities, 
professional colleges, guilds, mercantile associations, charities, 
schools, etc. It was this Medieval awakening in the cities of Western 
Europe what made possible the later hyperinflation of autonomous 
collective organizations, –“information based”– growing exponentially 
and propelling all the further complexity of modern societies./


All the best--Pedro

Loet Leydesdorff wrote:


Dear colleagues,

 

I don’t consider it as fruitful to recycle the argument that society 
were to be modeled as a meta-biology. The biological explanation can 
perhaps explain behavior of individuals and institutions; but social 
coordination more generally involves also the dynamics of 
expectations. These are much more abstract although conditioned by the 
historical layer. For example, one cannot expect to explain the /trias 
politica/ or the rule of law biologically. These cultural constructs 
regulate our behavior from above, whereas the biological supports 
existence and living from below. The historical follows the axis of 
time, whereas the codification (albeit historical in the 
instantiations) also restructures and potentially intervenes and 
reorganizes social relations from the perspective of hindsight.


 

In analogy to codifications such as the juridical ones, scientific 
knowledge provides the code for technological intervention. This type 
of knowledge is human-specific; perhaps, we are also able to build 
machines that mimick it. This technological evolution is going on for 
centuries. If I look up from my screen, I look into the gardens which 
have a typical Dutch polder vegetation. The polder was made in the 
17^th century and replaced the natural ecology of marsh land and 
lakes. The order of the explanation was thus inverted: the constructed 
structures (instead of the constructing agencies) increasingly carry 
the system. The constructs don’t have to be material; see my example 
of the rule of law. It is not a religion, but a dynamics of 
expectations. Replacing it with a biology misses the point.


 


Best,

Loet

 

Re: [Fis] Hierarchy of Information

[Pedro C. Marijuan]

Dear Xueshan and colleagues,

Your points about hierarchies are quite interesting. Let me remind
however, in my second message of this week, the discussion in last month
about "momenta" and "itineraries". It is another way to approach the
hierarchy discussion that comes closer, I think, to the enormous variety
of contents that one can find in those different realms. Aligning the
different momenta, as I understand that Nikhil has been proposing for
those self-organizing instances, discards the rhetorical excesses and
allows a better concentration on the essential topics. One can arrange
an autonomous "informational entity" in many ways, provided that the
necessary communication and self-production activities are properly
intertwined so that they allow sufficient adaptation to the changing
environment. Life has been playing that game endlessly, so we find
plenty of parallels ("momenta to align") with most of our
social-informational problems. For instance, in the organization of
metabolism, the use of inner "depots" as a backup of the whole metabolic
network (ATP, GTP, and a few others) strongly reminds the currency
problem --from a different angle, not just from the ecosystemic one or
from the gut microbiome. It is clear that advancing on the
sustainability problems has to be socially distributed, and put both
into the accounting of States, and of the companies and Institutions,
and even more into the citizenship at large. A new scientific
description on how info circulates among all those realms, via
individuals and e-machines, is not an easy matter at all. It belongs
more to the parlance of "phase transitions", and even more to the
"organismic" dimension mentioned below. And so... in this juncture we are!

Best--Pedro
PS. to Nikhil, in Jared Diamond book (Guns, Germs...) there is an
excellent table summarizing the "info inventions" necessary for
societies to transcend the basic complexity of natural groups. It is
another way to approach the theme you deal with in last message.


Xueshan Yan wrote:
> Dear Stan，
> Generally speaking, we have two kinds of Information Science, one is
> materialist, another is imformationist. Of course, what FIS colleagues
> are discussing here is materialist one. As to the imformationist
> information science, it sprang from John Wheeler and is becoming
> confirmative in some frontiers of physics recently, for example, the
> string-net theory advocated by some theoretical physicists of MIT.
> In materialistic information science, self-organization and
> autopoiesis are two wonderful criteria, they can exclude those
> information sciences based on information technology from real
> information science for their hetero-organization and heteropoiesis.
> As to the information science based on library science spread through
> the United States, whether it is a real information science,
> undoubtedly, it is questionable.
> Let’s come back to our topic. Facing so many kinds of information and
> disciplines of information theory/informatics/information science, we
> urgently need a classification to handle them, and the hierarchy
> consideration maybe is more fundamental. Which was activated by Pedro
> (He said it is Fisher’s idea, really Pedro?) with Cell, Brain, Firm
> many years ago, and advanced by Joshi these days.
> In fact, Joseph and I had some private communication about this issue
> several weeks ago, the topic is something I named “From Mechanism to
> Organicism” which was arisen when I predict the paradigm shift of
> information studies in the next 10 years or more. In those mails, we
> have touched this problem.
> According to your expression, we have several different hierarchies:
> 1. [firm [brain [cell]]]: Pedro
> 2. [society [cell [molecule]]]: Joshi
> 3. [social [organism [cell [molecular [microphysical ]: Stan
> 4. [organism [cell [molecule [fundamental particle: Xueshan
> 5. [organism [cell [molecule]]]: Xueshan
> From its narrow sense, social character only belongs to organism, so
> we can absorb “society” into “organism”. In the organism group, we
> have animal and plant. In animal, we have man, chicken, dog, tiger,
> lion, etc. Of course, our main object is man, just like medicine and
> physiology that claim their object over all animals, but man is their
> main object. Man’s information problem is our main aim here.
> From communication standpoint, that man (of course also all organism),
> cell, molecule (at lest organic molecule) can communicate each other
> are undoubtedly, so the information disciplines can emerge from this
> level undoubtedly naturally. But question is: can communication take
> places between two fundamental particles, such as two atoms? So, I am
> not sure if we can have a physical informatics at last.
> It is very humorous, this will bring us to the FIS discussion 13 year
> ago again: Is informational existences still only start with the
> biological? Is it still a huge black hole? (Gyorgy Darvas).
> Best wishes,
> Xueshan
> 

Re: [Fis] Sustainability through multilevel research: The Lifel, Deep Society Build-A-Thon - 1

[Pedro C. Marijuan]

Dear Nikhil and colleagues (Bob, Stan...),

Let me concur with Stan's arguments.  I think you are working with 
original ideas about two different instances of self-organization in  
Nature where  metabolic-energetic flows  are modulated  by third parties 
in order to maintain some maximum of stability in a very complex 
co-assemblage so that it may result compatible with the existing 
limitations of the global environment. It is sort of a fiscal agency or 
an energy police-body that keeps an overall adaptive order in the 
multifarious exchange of flows.


The two instances you describe are widely independent, in spite of the 
relative links existing (in the ecosphere, it is very difficult the 
complete independence). Forcing them into a hierarchy is not the best 
idea, in my opinion, as the two description are quite interesting, 
original, and advanced by themselves--particularly in order to land on 
the global problems of the economic order of our times. Connecting 
meaningfully with the path discussed by Bob and his colleagues requires 
quite a bit of further thinking. Economic organization is based finally 
on symmetry and symmetry breaking at different "levels" (just from the 
double-entry accounting of the agent to the collective market prices and 
valuation of stocks, to the financial coupling with the "real" economy). 
Like in the biological organization of information flows, there is a 
generalized dialectics of balances and modulations, of symmetry and 
symmetry breakings, yes, in some hierarchical framework. Unfortunately 
the information/symmetry topic is far from being properly developed as a 
"complexity engine", except maybe in physics, and we prefer indulging in 
independent disciplinary conceptualizations, preferably inspired in 
mechanics, that obfuscate understanding.


It is a rather difficult discussion... Further efforts from yours and 
your colleagues, and other parties in the list would be needed.  From my 
part, this weekend I will re-read your papers and Bob's links. We cannot 
renounce to advance in this discussion.


All the best--Pedro


Nikhil Joshi wrote:

Dear Stan,
You raise a very interesting and important question.


Recent findings suggest that mycorrhiza could modulate the rate of 
assimilation of molecules (driven by changing rates of photosynthesis) 
across groups of plants by modulating the flow of phosphorous (from 
the subsoil sources) across competing autotrophic species. Such 
modulation alters the overall conversion of geochemical (molecular) 
resources into biomass. Hence the modulatory effects of mycorrhizal 
modulation are at the level of molecular flows between geo-cycles and 
autotrophs (level 1).


What is suggested here is that gut bacteria are involved in the 
modulation of rate of reproduction of cellular and multicellular 
species. Hence their effect is at a cellular level (level 2)
Hence the activities of the two modulator systems are at two different 
scales- molecular and cellular. 

A multilevel view reveals a growing complexity in the species involved 
in exchange networks across ascending levels (compositional hierarchy) 
from molecules, to cells, multicellular species, and social 
Organization. A compositional hierarchy is also seen at each level in 
the emergence of community structure at each level. However, I agree 
that these observations do not constitute a complete description of 
the hierarchal relationships in these systems. The developing a formal 
hierarchical view would provide much clearer view of these systems and 
their interconnections. Given my limited knowledge of formal 
hierarchies, I would appreciate your assurance and views on this. 
Thanking you, 
Warm regards,
Nikhil 


Sent from my iPhone
Nikhil Joshi



--
-
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)
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[Fis] Sustainability Opening Text (Nikhil Joshi)

[Pedro C. Marijuan]

Some parties have reported me that the message was truncated (no figure 
and half the text missing.). So herewith the whole text, and the figure 
too. People willing to read the original message with correct formatting 
should go to the link indicated just below.

Greetings to all--Pedro

*-

(This email post has also been archived in the drop box. In case you are 
unable to read this entire post, please download from this link 
)

**
Sustainability through multilevel research: The Lifel, Deep Society 
Build-A-Thon*


Dear FIS Colleagues,

Over the last fifty years or so, we have made significant progress in 
enhancing our theoretical understanding of self-organizing complex 
systems. When it comes to self-organization in complex living systems, 
along with advances in theoretical research, advances in disciplines 
like prebiotic evolution, molecular biology, complexity, linguistics, 
information systems, ecology, bacteriology, soil microbiology, 
sociology, and economics have all contributed to provide deeper insights 
into the processes and organization in living systems at multiple 
different levels.


Having reached here we can ask the questions- can this new science help 
us develop a unified view of our socio-economic and natural systems? Can 
such a view reveal new systemic ways to align economics and ecosystems?


This series of articles [1-3] are a part of the "Lifel Deep Society 
Build-A-Thon" initiative. A research Build-A-Thon that aims to bring 
together domain level researchers, philosophers and theoretical 
researchers, and other problem solvers to build a multilevel model that 
can prove to be useful in enhancing our understanding of the combined 
ecosystem-economics system. This initiative provides exciting new 
opportunities for researchers to both further their own research, while 
also contributing towards addressing the larger problem of 
ecosystem-economics alignment.


The first article [1] reveals an important common multilevel 
organizational pattern in self-organization of living systems that 
proposes that socio-economic organizations could be an extension of a 
larger multilevel organizational pattern in natural self-organization. 
In this paper, two new classes of systems have been defined to capture 
important characteristics of internal organization in living systems 
across multiple levels. An examination of multilevel living systems 
through the lens of these definitions reveals a common multilevel level 
organizational pattern (CMOP) that extends across levels from molecular, 
to ecological and to social self-organization. The outcomes of the 
common multilevel organizational pattern are discussed, with important 
implications and areas for further research.


The second article [2] examines the possibility of organizational and 
role similarities between banks and financial investment networks in 
social self-organization, and networks of subsoil Mycorrhiza and 
gut-bacterial networks in ecosystems. The multilevel model of 
self-organizing living systems developed previously, has been used to 
pose questions and make multilevel organizational comparisons to glean 
new insights into the roots of our banking and financial investment 
networks in self-organizing living systems. Research findings point to 
the possibility that banks and financial investment networks play a role 
in social self-organization that could be in some ways similar to that 
played by Mycorrhiza and gut bacterial networks in the self-organization 
of ecosystems. A multilevel understanding of these systems could help us 
not only understand the roots of financial investment systems in 
self-organizing systems but also help better align financial systems and 
economics with natural ecosystems, and further the agenda of ecological 
sustainability. Some implications, questions and avenues for further 
research have been discussed.


The third article is an extended abstract and presents an overview of 
this initiative [3].


Taken together the two articles [1,2] present a cascading organization 
where autotrophic species arise through the transformation of 
geochemical molecules into biomass. This biomass becomes food for 
heterotrophic species, and leads to the emergence of ecological exchange 
networks between autotrophs and heterotrophs. Further, the emergence of 
sociality in heterotrophic species initially gives rise to kinship based 
social groups like families and extended communities based on shared 
adaptation among multiple family units, followed by non-kinship based 
social groups, and exchange networks of human resources between kinship 
based social groups like families and non-kinship based social groups 
like businesses in our economic system.


Three levels of modulator systems modulate resource flows between 

[Fis] Tragedy in France

[Pedro C. Marijuan]

Dear FIS Collegues,

On behalf of the group, let me express our collective condolences to the 
French Colleagues of our list. Civilized words are of little use in 
front of such repulsive, barbaric actions. But in the long term it is 
the most efficient tool. The terrible problem is that it takes 
generations to deflate a terrorist wave, and once it is over, a new one 
comes in...


Our solidarity with French citizens,
--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] TOWARDS A NEW SESSION ON ECOLOGICAL ECONOMICS

[Pedro C. Marijuan]

Dear FIS colleagues,

In a few days we will start a new discussion session on a 
multidisciplinary theme that is getting more and more attention in our 
times: ECOLOGICAL ECONOMICS.


The session will be chaired by:
Nikhil Joshi

Lifel.Org, Mumbai, India

A new perspective will be offered on how we evaluate our social 
interactions with Nature, and how we could find new solutions in 
aligning economics and ecosystems.


Best greetings
--Pedro

-
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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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[Fis] [Fwd:Re: Short article by Chaitin on information incompleteness]--J. Brenner

[Pedro C. Marijuan]

- Original Message -
*From:* Joseph Brenner 
*To:* John Collier  ; fis 


*Sent:* Tuesday, October 27, 2015 4:52 PM
*Subject:* Re: [Fis] Short article by Chaitin on information incompleteness

Dear John,

I hope the metamorphosis went smoothly.

Thanks for posting the Chaitin link. It is indeed a clear statement, or 
group of statements, and many of them confirm the respect due to to 
Chaitin as a mathematician.


However, my respect does not extend to the following, at the end of the 
article:


"To me as a pure mathematician, metabiology is justified if it enables 
us to prove beautiful theorems. More generally, software models and 
current work on quantum information and randomness show the importance 
of an idealistic as opposed to a materialist conception of nature. 
Information and computation are better than matter and energy. I expect 
that this is just the beginning and that, if we are fortunate, we will 
continue to see idealism supersede materialism, particularly in the 
much-to-be-desired basic theoretical understanding of consciousness and 
mind."


This kind of dichotomous dogma may sit well with the 'sponsors', but it 
does not bode well for progress in information science or philosophy. Is 
there anyone who feels it does? 


Best wishes,

Joseph

   - Original Message -
   *From:* John Collier 
   *To:* fis 
   *Sent:* Tuesday, October 27, 2015 12:21 PM
   *Subject:* [Fis] Short article by Chaitin on ionformation incompleteness

   A particularly clear statement of basic results of incompleteness,
   randomness, creativity, and a proposal for application to metabiology.




   http://inference-review.com/article/an-algorithmic-god




   John Collier

   Professor Emeritus, UKZN

   http://web.ncf.ca/collier




   
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--
-
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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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
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Re: [Fis] Five Momenta. Five Itineraries

[Pedro C. Marijuan]

Dear FIS colleagues,

Thanks to all for the valuable insights. Responding briefly:

To Joseph: perhaps your points, although interesting, are not truly an 
itinerary. For instance, WuKun and Lupasco belong to the First Momentum 
(philos.). I agree that they can be adequate first steps (but there 
might be some others, such as Merleau Ponty, Ortega y Gasset, etc.). 
Once some temporary philo basis is attained, one has to visit --I 
think--the neurodynamic counterpart of those tenets (Momentum 3, neuro). 
From there, a complex evo-devo panorama opens (visiting Momentum 2). 
Then it would be high time to return to M1, to consolidate the basis 
within an adequate heuristic 
"neuro-biologic-ethologic.cognitive-philosophic" approach to human 
prosocial capabilities, language included. Time for visiting M5 
(infoeconomics of social complexity, development of human history). From 
there, to M6 (contemporary info revolution, problems of our time). Back 
to M1, proposing an overall new way of thinking, plus quite many further 
movements of refinement and deeper analysis...


To Stan: if hierarchy helps to move into the previous multidisciplinary 
entanglement fine, otherwise it is a useless item to be kept into the 
lean mental "backpack" needed for this itinerary...


To Loet and Marcus: let us agree that disciplines are based on 
"communities of inquiry" that follow strict laws of "intellectual 
economy". Our limited capabilities force us to establish disciplinary 
specialization, and that's good, but a healthy knowledge system would 
also establish quite many "vertical" multidisciplines integrating the 
"horizontal" disciplines that apply simultaneously into concrete 
subjects (as happens in eg, medicine, engineering, anthrolpology, etc.).


To Steven and Soeren, Francesco, and all: Should'nt we distinguish the 
above itinerary elements (actually smallish parts from a number of 
disciples and subdisciplines) from the "instrumental" fields of 
knowledge that can be used "on tap" but quite often are used "on top"? I 
mean, classical and new Info theories, von Neumann theories (automata, 
machines, games), Turing and computational approaches, symmetry studies, 
entropy studies, quantum information, physical information, mathematical 
optimization procedures, etc. should not occupy the leading seat in this 
trip. To insist, they are instrumental just to help, strictly kept under 
command, along the different elaboration stages of the itinerary.


In the extent to which a similar scheme would be valid intelectually, 
would it be feasible too?  "If we were rich" a system of scientific 
committees could be created, seriously working during several years, at 
the style of the serious international cooperative work that have lead 
to the International System of Measurement Standards. So important was 
and has been the standardization of measurements, and we take it for 
granted. Curiously, it has an essential informational content regarding 
the "social brain"... Anyhow, only an important university could take 
charge of this genuine FIS itinerary. Alternatively, "if we were Linus", 
a Infopedia could organize the whole voluntary work... but how could we 
find our Linus?


Best wishes to all,

--Pedro


Marcus Abundis wrote:
Perdo  – awesome post, great synthesis, thanks! Still, I do not share 
your (apparent?) skepticism on an eventual happy result – although 
said result is certainly not guaranteed.


Hi Loet,

First, thank you for your excellent post (Thu Oct 15 14:38:54) as it 
offered the insight I craved.


> . . . "unity of science" principles are outdated. At issue is to 
specify how the sciences

and specialties are different; in which respects and why? <

If I take your meaning correctly (not sure) . . . While I agree 
notions of some "facile unity" should NOT be allowed to (solely) 
capture our collective imaginations, is it not possible to seek unity 
and difference at that same time? One view being "objective 
perspective" and another being a "meta perspective?" It seems to me 
Bateson was on this track with "A Necessary Unity" and "a difference 
that makes . . . "  Or perhaps there is some even-more-basic issue I 
miss here . . . 

In my view, shifts in perspective (sometimes subtle) can afford shifts 
in insight, while also threatening apparent ambiguity. Or in the words 
of F. Scott Fitzgerald "The test of a first-rate intelligence is the 
ability to hold two opposed ideas in mind at the same time and still 
retain the ability to function." My apologies if I simply misinterpret 
your post . . . 

If I may say without meaning offense, some recent posts seem to head 
into a more "wooly" direction . . . that I confess to feeling some 
kinship with. Particularly with comments on creativity, ambiguity, and 
the tao. I have been watching closely, but also feel unsure of how or 
if I should engage – in the context of this group. I am not sure how 
productive that direction might (or might not) prove to be.


My