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

2016-06-10 Thread Dr. Plamen L. Simeonov
Dear All,

one last thing before closing this session on phenomemnology in medicine
today. All FIS fellows intending to contribute to the 2017 special issue on
integral biomathics and East-West scientific exchange should send me a note
with the paper title until the end of June 2016. I will need this
information to begin my talks with Elsevier. The abstract deadline remains
the same as earlier announced: 31. August 2016.

Have a nice weekend.

With best wishes,

Plamen



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

(note: free access to all articles until July 19th, 2016)

2013 JPBMB Special Issue on Integral Biomathics: Can Biology Create a
Profoundly New Mathematics and Computation?


2012 Integral Biomathics: Tracing the Road to Reality


2011 INtegral BIOmathics Support Action (INBIOSA) 




On Thu, Jun 9, 2016 at 11:07 PM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

> Dear All,
>
> we are indeed approaching the end of this series of sessions on life
> science, phenomenology and mathematics. Your note sent 2 weeks ago with the
> reference to your new book did not remain unnoticed, Francesco. Therefore I
> will try to respond to it and make some final comments on what we have done
> so far and what remains for the future. We can hardly become exhaustive on
> all these issues raised with relation the central problems in science. It
> is clear to most of us that some of them, in particular the antagonistic
> ones, are due to the increased specialisation in the disciplines which
> makes the establishment of a multi-rogue (to cite Bateson) difficult. The
> last example  was the one of George Mutter with the results of the medical
> expert consultation on cancer heterogeneity with the result of an
> additional split of cancers into precancels and cancers. Such domain
> differentiations happen all the time. Without clear definitions and focused
> problems science cannot advance. And at the same time we are criticising
> reductionism as dominating modern science. In a follow-up posting I told
> George that we are actually interested in both types of heterogeneity, the
> (histological) one of precancels in groups of patients and in the
> microbiological-genetical one of cancers of individual patients both on
> temporal and spacial scale. But can we embrace all the different aspects of
> studying and understanding cancer within a single methodologically sound
> theoretical and experimental framework? Based on the discussions I had with
> many of you in the past 7 years, I believe that we have such a
> predisposition.
>
> My summary from Francesco’s note is that we cannot ignore the stimulating
> role of other, at first sight remote disciplines, when trying to understand
> life. In particular the metaphors about its “currency” and good/bad
> “economy” are very powerful means to address matter, energy and information
> transfer and transformation at all their levels of organisation. The
> self-organised criticality (SOC) theme we continued this last session on
> 3-phi integrative medicine after the one on physics looks like an enhanced
> model of Varela's and Maturana’s autopoiesis. We can improve and recombine
> (as Pedroo suggested) in the same manner Robert Rosen’s reaction-diffusion
> systems, Allan Turing’s biochemical morphogenesis and oracle machines, von
> Neuman’s cellular automata and even Penrose-Hameroff’s Orchestrated OR
> theory. All of them and many others represent some valid aspect of life.
>
> Our effort here in the past 4 months was to try investigating the role
> which philosophical phenomenology could play in enriching these models of
> life and how mathematics and computation can formalise them in an adequate
> manner, although we know that not everything in life is formalisable. We
> touched upon some exciting questions and puzzles, even on not so well
> defined concepts such as the one about wether the understanding that
> quantum properties of matter do emerge from geometry can be mistakenly
> interpreted as a relation between potentiality and actuality, an issue by
> Joe Brenner in a personal correspondence. I hope that most of you remain
> satisfied with the scope and deepness of this online discussion intended as
> continuation and feedback to the authors of the selected field
> contributions of our
>
> 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences,
> Mathematics and Phenomenological Philosophy
> 
> (note: free access to all articles until July 19th, 2016)
>
> and 

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

2016-06-09 Thread Dr. Plamen L. Simeonov
Dear All,

we are indeed approaching the end of this series of sessions on life
science, phenomenology and mathematics. Your note sent 2 weeks ago with the
reference to your new book did not remain unnoticed, Francesco. Therefore I
will try to respond to it and make some final comments on what we have done
so far and what remains for the future. We can hardly become exhaustive on
all these issues raised with relation the central problems in science. It
is clear to most of us that some of them, in particular the antagonistic
ones, are due to the increased specialisation in the disciplines which
makes the establishment of a multi-rogue (to cite Bateson) difficult. The
last example  was the one of George Mutter with the results of the medical
expert consultation on cancer heterogeneity with the result of an
additional split of cancers into precancels and cancers. Such domain
differentiations happen all the time. Without clear definitions and focused
problems science cannot advance. And at the same time we are criticising
reductionism as dominating modern science. In a follow-up posting I told
George that we are actually interested in both types of heterogeneity, the
(histological) one of precancels in groups of patients and in the
microbiological-genetical one of cancers of individual patients both on
temporal and spacial scale. But can we embrace all the different aspects of
studying and understanding cancer within a single methodologically sound
theoretical and experimental framework? Based on the discussions I had with
many of you in the past 7 years, I believe that we have such a
predisposition.

My summary from Francesco’s note is that we cannot ignore the stimulating
role of other, at first sight remote disciplines, when trying to understand
life. In particular the metaphors about its “currency” and good/bad
“economy” are very powerful means to address matter, energy and information
transfer and transformation at all their levels of organisation. The
self-organised criticality (SOC) theme we continued this last session on
3-phi integrative medicine after the one on physics looks like an enhanced
model of Varela's and Maturana’s autopoiesis. We can improve and recombine
(as Pedroo suggested) in the same manner Robert Rosen’s reaction-diffusion
systems, Allan Turing’s biochemical morphogenesis and oracle machines, von
Neuman’s cellular automata and even Penrose-Hameroff’s Orchestrated OR
theory. All of them and many others represent some valid aspect of life.

Our effort here in the past 4 months was to try investigating the role
which philosophical phenomenology could play in enriching these models of
life and how mathematics and computation can formalise them in an adequate
manner, although we know that not everything in life is formalisable. We
touched upon some exciting questions and puzzles, even on not so well
defined concepts such as the one about wether the understanding that
quantum properties of matter do emerge from geometry can be mistakenly
interpreted as a relation between potentiality and actuality, an issue by
Joe Brenner in a personal correspondence. I hope that most of you remain
satisfied with the scope and deepness of this online discussion intended as
continuation and feedback to the authors of the selected field
contributions of our

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

(note: free access to all articles until July 19th, 2016)

and successor of

2013 JPBMB Special Issue on Integral Biomathics: Can Biology Create a
Profoundly New Mathematics and Computation?


It is time to announce our *third special issue on Integral Biomathics
planned for 2017 *and *dedicated to the scientific and philosophical
exchange between East and Wes*t. I’ll be pleased if some of you decide to
contribute to it with an original article or a sequel of a previous one
from the earlier publications of this row. *Abstracts are due by August
31st 2016. *
Official announcements with detailed CFP will be disseminated by the end of
June.

Finally, please allow me to place an announcement by Don Favareau, who
would be pleased to obtain your feedback on one of the topics in this
online discussion: *biosemiotics*.

With my best wishes for a spectacular UEFA soccer championship in France
(starting tomorrow), summer Olympics in Brazil, and of course a
(re-)creative and inspiring research summer.

Yours,

Plamen

___

Hi Plamen!



Thanks for giving me the opportunity to draw upon the collective insight
and expertise of this group!



By way of explanation: One concern that joins the FIS with the Biosemiotics
group is the need to come up with a biological but not anthropomorphic
understanding of the notion of *intentionality* – or, as Terrence Deacon
suggests replacing this perhaps already 

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

2016-06-06 Thread Dr. Plamen L. Simeonov
Dear Pedro, Francesco, Bob, Joe and All,

we are approaching the end of this session (10.6) and I am going to make
some concluding remarks on it. This does not excludes the chance for
 submitting contributions until the end, but we have to follow our plan.
Your thoughts expanded significantly the scope of the  topic I began this
final chapter on medicine and phenomenology which was supposed to have more
applied character. As Pedro and I mentioned earlier, the focused base SOC
from the previous section ion physics is only one of the possible
underpinning theories that can be “adducted” (to use a medical term) in
solving modelling problems in medicine. Indeed, all themes in the previous
chapters on biology, mathematics, biosemiotics and physics were
representative samples of a study we made together reflecting on the
relation between natural sciences, mathematics and phenomenology. In a
private communication Joe Brenner suggested that the prefix “self” in SOC
should be opened up to allow for external processes to participate. This is
an interesting moment I wish to draw your attention to. I agreed with him
and noted that what we actually need is a kind of “membrane-like open close
*d*ness” of the processes to consider. I was really happy with this
expansion of the base which Alex may have implied in his chapter, but did
not came explicitly. Joe accepted this argument and noted that this kind of
models can be addressed by his constructive Logic in Reality (LIR) as a
novel perspective going beyond formal logical reasoning, ontology and
metaphysics that can be “basically seen in terms of change and stability,
being and becoming” (introduction to his 2008 Springer book). I have not
read this book yet, but I am certain it is a gem deserving our attention.
However, what is possibly missed there, and also in our agreed
“membrane-like open closedness” is the first-person phenomenological
perspective of Maxine Sheets-Johnstone, Shaun Gallagher, Steven M. Rosen
and others made explicit in our 2015 special issue. We are still too inert
in respect, judging by the reflections this forum. In de-fining such terms
we actually limit their application; Francesco, please correct me if I am
wrong in my Latin/Italian interpretation. This is what science is used to.
But in phenomenology we have this “mixture” between internal and external
perspectives, object and subject that perplex entirely our ontological
categories in science. So, how about such a "logic in a phenomenological
reality”? I think there is still a long way to go until we truly
internalise the phenomenological perspective in our scientific models. The
kind of reasoning we need should be flexible, adaptive, integrative and
recombinant, metaphorically following a scientific methodology close to the
molecular recognition principle of Emil Fischer and his successors that
Pedro addressed in one of his previous postings. This is indeed the other
kind of thinking that led Richard Feynman to the idea quantum computing.
Correct, the physics is embedded deeply into the architectural and
functional constraints of the living system. But living systems have
“personalities”, insight-out identities as such at all scales which enforce
the perpetuation of life. Perhaps we can try to better understanding this
by investigating the “first phenomenon”, the cell, which Howard Pattee
addressed in his paper in the 2015 JPBMB special issue. Pedro and his team
also reflected this in their contribution there. Interestingly that these
ideas are conform with those of Brian J. Ford on the intelligence of
the individual cell. This is a remarkable field which can be only enriched
by such metaphorical and poetic stimuli (necessary in science according to
Stu Kauffman) as those of Francesco from economy who regards stem cells as
a kind biological currency. There is pretty much to be discovered and
creatively recombined in our postings.

One last remark regarding the cancer modelling problem, which came from a
colleague, I recently met at a congress in Berlin. I am publishing his
comment in full length, assuming his permission, because I think it is
important to know about this phenomenon and about how far we can go when
trying to address such challenging issues in interdisciplinary circles like
the FIS forum.

+++

  Plamen,



   Tumor heterogeneity usually refers to divergent genotypes within cells
of one tumor.  But I think you are interested in tumors of different
patients, and what the shared characteristics are, that offset this from
normal tissues.  This is not a cancer discussion, but rather a precancer
definition.  We had a workshop about this several years ago, which I have
attached.  It took two days of interactive discussions between a dozen
experts to get this far.

One of the barriers we are facing here is cultural - the unfiltered and
voluminous discussion format of e-communication favored by physical
scientists is uncommon amongst biologists.  There is just too 

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

2016-06-02 Thread 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

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

2016-06-02 Thread 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.)

2016-06-02 Thread 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