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,



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 <> 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 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 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:
> 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:
> 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 <
>> 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 <>:
>>> 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.iacs@aragon.es
>>> -------------------------------------------------
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