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

Dr. Plamen L. Simeonov plamen.l.simeonov at gmail.com
Thu Jun 9 23:07:21 CEST 2016


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
<http://www.sciencedirect.com/science/journal/00796107/119/3>
(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?
<http://www.sciencedirect.com/science/journal/00796107/113/1>

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 overly-mentalistic term with,
*“ententionality”,
*which he defines as:



“a generic adjective to describe all phenomena that are intrinsically
incomplete in the sense of being in relationship to, constituted by,
or *organized
to achieve* something non-intrinsic…[such] *ententional *phenomena include:
*functions* that have satisfaction conditions, *adaptations* that have
environmental correlates, *thoughts* that have contents, *purposes* that
have goals, *subjective experiences* that have a self/other perspective,
and v*alues* that have a ‘self’ that is benefited or harmed (Deacon
2012:27; italics added).



Such an understanding, again, is one that is needed both in Biology and in
Information Science, and so it seems to me that the current questionnaire
that is now circulating around in Biosemiotics circles concerning how to
best go about conceiving and researching this phenomenon for those purposes
would be very much of interest to those on the FIS list-serve also.



So with your kind permission, I would like to ask you to make the following
two online survey links available to this group for their input and
consideration:



PART 1 of this survey consists of 5 simple short answer QUESTIONS regarding
the notion of *intentionality*, as you think it might be conceptualized for
the purposes of 21st century science, and may be accessed by clicking here:
https://www.surveymonkey.com/r/MKHPT97



PART 2 of the survey asks its respondants to consider how the term
“intentionality” has been conceptualized in a small number of previously
published QUOTES and to click on the response that best reflects their
opinion of their suitability for use 21st century science. This part of the
survey can be accessed by clicking here:
https://www.surveymonkey.com/r/T66XDMH



Respondents van pick and choose those questions that they wish to respond
to (the system will not require that they respond to them all), and can
also choose to remain anonymous, if they wish, when the results of this
questionnaire are published later in the year in the journal* Biosemiotics.*



I do hope that the members of the listserve that were involved in the
Special Issue on Integral Biomathematics of the *PBMB* will take the
opportunity to join us in this project, as we work to expand our
understanding of this neglected organizing principle in both Biology and
Information Science.



All best wishes and thanks again!



Don Favareau

National University of Singapore

++++++++++++++++++++++++++++++++++




On Thu, Jun 2, 2016 at 8:04 PM, Francesco Rizzo <13francesco.rizzo en gmail.com
> wrote:

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