Re: [Fis] Fwd: Re: Cancer Cure? (Plamen S.)

[Francesco Rizzo]

Caro Plamen e cari Tutti,
circa dieci giorni fa ho composto e inviato un messaggio in-centrato sul
rapporto antagonista tra riduzionismo (specialismo) e armonia (olismo), ma
non ha riscosso tanto successo, e non solo perché scrivo in lingua
italiana. Non ripeto quel che ho già comunicato, ma mi limito a confessare
che andando avanti negli anni la specializzazione professionale o
settorializzazione del sapere mi attrae e convince sempre di meno. Da
economista, invece, divento sempre più consapevole dell'armonia
(dell'equilibrio e del dis-equilibrio) che domina il mondo.Tutto ciò è
provato anche dall'ultimo mio libro che è uscito il 1 aprile scorso: "Una
scienza non può non essere umana, civile, sociale, ECONOMI(C)A,enigmatica,
nobile, profetica"(Aracne editrice, Roma, 2016).
Allora in questa circostanza desidero spendere qualche parola sulla terna:
asimmetria/simmetria, auto-similarità o geometria frattale, legge di
potenza o sviluppo esponenziale che vale sia per le cellule sane sia per le
cellule malate. Tuttavia, questa terna vale di più per le cellule malate di
cancro, il cui sviluppo è molto più intenso ed esponenziale di quello che
caratterizza le cellule sane. Interessante sarebbe in questa prospettiva
indagare in modo specifico le cellule staminali, più o meno potenti o
pluri-potenti, ma non sono un esperto di queste cose. Dico solo che le
cellule staminali sono una forma di moneta biologica.
Ragionando per schemi  simmetria e asimmetria si alternano e/o convivono
contemporaneamente e continuamente. La simmetria si ad-dice ai momenti di
conservazione e stabilità, l'asimmetria invece caratterizza i momenti di
rottura o discontinuità che si verificano tra uno stato di simmetria e/o di
equilibrio e l'altro. Tutta l'attività economica, essendo dinamica,non è
altro che il passare irreversibile da uno stato di dis-equilibrio
all'altro. La natura della fisica di tutto ciò che è stato creato o si è
formato ci fa capire o sapere che se immediatamente dopo il Big Bang non si
fosse rotta la simmetria tra materia e antimateria, creandosi un'asimmetria
vitale (solo materia perché l'anti-materia pareche sia sparita), noi e il
resto non saremmo a questo mondo. Anzi, non ci sarebbe nemmeno il mondo
stesso. La stessa particella di Dio o il Bosone di Higgs senza la rottura
della simmetria di gauge non avrebbe interagito con se stessa formandosi la
massa nè con le altre particelle altrettanto bisognose di massa. Il
discorso potrebbe continuare con i buchi neri, ma mi fermo qui per questo
punto.
L'auto-similarità contrassegna la geometria frattale e la rende irregolare,
discontinua, disordinata e imprevedibile.
La legge di potenza o esponenziale vale per i sistemi complessi, non
lineari e lontani dall'equilibrio.
Ho il sospetto che oggi le parole di un economista non valgano molto. Ma
bisogna stare attenti a non confondere la teoria economica, con l'attività
o la pratica economica e, comunque, non è nè teoria o pratica economica la
professione dei ladri, dei briganti e dei pirati , ad es. della finanza.La
chiamano economia, ma è solo ruberia o ladrocinio. Beninteso, la finanza
speculativa.
In ogni caso, ormai, posso ben dire di avere scoperto una nuova scienza o
conoscenza economica, come i miei testi dimostrano, proprio aprendomi alla
conoscenza delle scienze dell'uomo e della natura.
Non sono un presuntuoso e so quel che affermo.
Vi saluto con un grazie e un abbraccio affettuoso a Tutti.
Francesco.

2016-06-02 18:00 GMT+02:00 Pedro C. Marijuan :

> Dear Plamen, Bob, and FIS Colleagues,
>
> I respond to ideas previously expressed on the connection of living cells
> with physics. SOC may be one of the ways, but there are other instances, eg
> "constructal law", catastrophe theory, tensegrity (at least, all of these
> are well related to development), and many others... My own bet regarding
> the centrality and potential extension of the construct is "molecular
> recognition". Elevating beyond heterogeneity, its conflation with symmetry
> makes sense on the polymerization and supramolecular strategies of life.
>
> Molecular recognition appears as the key element from which the whole
> biochemical and evolutionary universe is constructed. Like any other
> chemical reaction, recognition between molecules is based on the “making
> and breaking of bonds”. This ––and only this–– is what makes possible the
> mutual recognition and the formation of complexes between biomolecular
> partners. The big problem with biomolecular recognition instances is that
> they involve an amazing variety and combinatorics of almost any type of
> chemical interaction: hydrogen bonds, hydrophobic / hydrophilic forces,
> dipole forces, van der Waals forces, ionic Coulombian forces, etc. Dozens
> or even hundreds of weak bonds participate, for instance, in the formation
> of a protein-protein specific complex. Quite probably, measuring molecular
> recognition and establishing its crucial parameters and variables can only
> be realized biologically 

Re: [Fis] Fwd: Re: Cancer Cure? (Plamen S.)

[Pedro C. Marijuan]

Dear Plamen, Bob, and FIS Colleagues,

I respond to ideas previously expressed on the connection of living 
cells with physics. SOC may be one of the ways, but there are other 
instances, eg "constructal law", catastrophe theory, tensegrity (at 
least, all of these are well related to development), and many others... 
My own bet regarding the centrality and potential extension of the 
construct is "molecular recognition". Elevating beyond heterogeneity, 
its conflation with symmetry makes sense on the polymerization and 
supramolecular strategies of life.


Molecular recognition appears as the key element from which the whole 
biochemical and evolutionary universe is constructed. Like any other 
chemical reaction, recognition between molecules is based on the “making 
and breaking of bonds”. This ––and only this–– is what makes possible 
the mutual recognition and the formation of complexes between 
biomolecular partners. The big problem with biomolecular recognition 
instances is that they involve an amazing variety and combinatorics of 
almost any type of chemical interaction: hydrogen bonds, hydrophobic / 
hydrophilic forces, dipole forces, van der Waals forces, ionic 
Coulombian forces, etc. Dozens or even hundreds of weak bonds 
participate, for instance, in the formation of a protein-protein 
specific complex. Quite probably, measuring molecular recognition and 
establishing its crucial parameters and variables can only be realized 
biologically on a case-by-case basis. At least this is the current trend 
in most molecular biological and molecular dynamic approaches. But a few 
"classic" references have provided some interesting insights about 
molecular-recognition generalities. First, *W. Meggs* about “biological 
homing”, mainly from a Coulombian “lock and key” combinatory point of 
view; then *Shu-Kun Lin* about the changes in thermodynamic entropy of 
mixing derived from molecular similarity changes; and finally *M. 
Carlton*, with original proposals for measuring the information content 
of any complex molecular system.


Anyhow, the result of the whole organization of molecular recognition 
instances would remind our artificial computers--is it interesting to 
connect them "meaningfully" with physics? Yes, the physics is all 
around, but it is submerged very deep into the architectural and 
functional constraints of the living system. No royal road, no "camino 
real" to explain the entirety, a pleiad of disciplines has to be 
involved. For cancer, or for biomaterial engineering, recombination of 
multiple disciplines becomes the basic research enterprise of our times. 
We have to combine the surfing of many disciplines with the occasional 
fundamental insights (from physics, maths, symmetry, information 
science, etc.). But neither reductionism, nor wholism, nor 
phenomenology, nor perspectivism, nor... are going very far making sense 
of the whole social intelligence caught into action (blind spots 
included). We made the "artistic" drawing below.


Enough for today. Greetings to all, and congratulations to Xueshan for 
his Magnus Opus! --Pedro





*Disciplines involved in modern biomaterial research. The representation 
is based on the description made by bioengineer **James Kirkpatrick 
(2009) and also del Moral et al., (2011).*




El 02/06/2016 a las 13:20, Pedro C. Marijuan escribió:





On Tue, May 31, 2016 at 6:54 PM, Robert E. Ulanowicz  
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.



--
-
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] Fwd: Re: Cancer Cure? (Plamen S.)

[Robert E. Ulanowicz]

>  Mensaje reenviado 
> Asunto:   Re: [Fis] Cancer Cure?
> Fecha:Tue, 31 May 2016 19:54:05 +0200
> De:   Dr. Plamen L. Simeonov 
> Para: Robert Ulanowicz 
> CC:   Pedro C. Marijuan 
> 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.

Dear Plamen and Pedro,

Thank you for your kind words. I hope I am not going over my weekly quota
by answering, but I will remain quiet for a while after this.

> 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.

I am no expert in any kind of logic, but am acutely aware that our world
requires more than the standard Aristotelian sort. (Just ask Joe Brenner.)
As for quantum behavior at macroscopic scales, I remain quite skeptical
that it is the same phenomenon that operates at atomic and subatomic
scales. On the other hand, I am quite open to quantum-like behaviors at
macroscales. I think a few investigators are aware of this ontological
difference and are treating the subject in the right manner --
dimensionally speaking.

For example, Dr. Diederik Aerts  of the
Vrije Universiteit Brussel  was able to show that quantum-like behavior
can transpire in macrosystems in total abstraction of the Planck distance
and the quantum vacuum

. His associate, Dr. Sandro Sozzo
, has applied Aerts' ideas to
ecology.

> 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.

I acknowledge self-similarity in physical systems and imagine some of that
behavior bleeds over into biology (as for example, with Aert's work that I
just mentioned). I don't see self-similarity as a major player in biology,
however. My familiarity with dimensional analysis tells me that one should
always look for qualitatively different behavior at different scales and
that asymmetry plays a greater role in biology than it does in physics.

> How about the
> biosemiotics aspect which I mentioned earlier?

I think biosemiotics provides a viable pathway to understanding living
systems.  I wasn't
always a fan of it, thinking that its narrative  was too anthropomorphic.
Jesper Hofmeyer, however, showed me some convincing examples that were
decidedly not anthropomorphic.

> Tell me what do you think could be a promising approach to tackle a
tough health problem.

As you possibly may know, my hobby horse has been quantified flow
networks, because they force one to think in holisitc terms. (Not that
holism is all there is, but it is usually a player in any living system.)
In my first book, Growth and Development (p160) and later in my second
book, Ecology, the Ascendent Perspective (pp149-151), I mentioned how
medicine needed to consider more than just oncogenes in their approach to
cancer therapy. I suggested that more attention needed to be paid to whole
system behaviors, especially that of the immune system. Well, of course
immunotherapy has now become the most promising therapy against cancer
(but unfortunately not because of my remarks :).

> Is there anybody out there? :-)
> All the best,
> Plamen

Some of us are listening! :)

The best,
Bob



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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 
Para:   Robert Ulanowicz 
CC: Pedro C. Marijuan 



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 > 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 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
 

[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 
Responder a:u...@umces.edu
Para:   Dr. Plamen L. Simeonov 
CC: 	Robert Ulanowicz , Pedro C. Marijuan 






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
.) 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


.

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[Fis] A Book: Information Science：Concept，System and Perspective

[Xueshan Yan]

Dear Rafael and Moisés,

 

I write here some compressed words due to the limit of two posts one week.

 

Beat regards,

Xueshan

==

From: Rafael Capurro [mailto:raf...@capurro.de] 
Sent: Wednesday, June 01, 2016 11:16 PM
To: y...@pku.edu.cn
Subject: Re: [Fis] Information Science: Concept, System and Perspective 
(Contents Only) - Invitation to view


Dear Xeushan,

   Thank you, this helps me to understand what your book is about.

I think that this is a very comprehensive view of the subject.

I would very much like to read what you say about Information Science in China 
before and after 1948.

Is there any root of information science in Ancient Chinese?

【According to present understanding about “Information Science”, we can’t find 
any root of it in Ancient Chinese.】

Is there a connection between information and DAO?

【If we can divide Information Science as Materialist Information Science and 
Informatist Information Science, then it is inevitable that INFORMATION has a 
relationship with DAO in the Informatist Information Science.】

Is the word information in Ancient Chinese the same you use after 1948?

【Basically, same.】

 

Best

Rafael

==

From: Moisés André Nisenbaum [mailto:moises.nisenb...@ifrj.edu.br] 
Sent: Thursday, June 02, 2016 1:51 AM
To: y...@pku.edu.cn
Subject: I will accept your help :-)


Dear Xueshan.

I understand what you said about the book. But there must be many people like 
me waiting for the opportunity of reading it. 

【Thank you Moisés, I hope so.】

Thank you very much for kindly offer me help. And I, obviously, will accept :-)

【You are wellcome!】

I really would like very much if you have 30 minutes to an interview via Skype 
or WebEx. I would like to ask you some specific questions about your book and 
also about the "crucial" relationship between Physics and IS that you 
commented. 

【Good suggestion, I hope you can postpone this step. Um abraço.】

If you don't have time, I will understand, no problem. Anyway, I will soon send 
a survey to FIS list.

Thank very much for your kind attention.

In Portuguese we use to say "um abraço" at the end of messages that 
approximately means "a hug". Something cultural that I cannot translate.

 

So, um abraço!

Moisés.

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