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

[Dr. Plamen L. Simeonov]

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 <http://www.sciencedirect.com/science/journal/00796107/131>  *

* 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 <
ajime...@iisaragon.es> 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. The six big branches in perfect periferic colussion and
> confusion. Could a blockchain, along its full develpment in time, represent
> a fundamental cartography of the originating fusion nucleous?
>
> About dataism enchantment, well, too many times we have been said "look,
> finally this is the great, definitive scientific approach"--behaviorism,
> artificial intelleigence, artifficial catastrophe & complexity theory, and
> so on. Let us wait and see. Welcome in the extent to which it really
> responds to unanswered questions. And let us be aware of the technocratic
> lore it seems to drag.
>
> This was my second cent for the week.
>
> best--Pedro
>
>
>
> On Fri, 9 Mar 2018 10:30:01 +0100 "Dr. Plamen L. Simeonov" wrote:
>
> These are wise words, Pedro.
> What I was meaning with 

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

[Dr. Plamen L. Simeonov]

Dear Alberto, Pedro, and FIS Colleagues,

I think you got the message. All in all, an effort to
organize scientific/intellectual potential in this forum and others of that
kind into a kind of currency of a much higher value than money and other
material and virtual resources on Earth deserves to be made. For me, the
term "blockchain" is a bad word match for what this vision may really
become in future.  [Maybe this is because of my past history from Eastern
Europe, which made me feel "blocked" and "chained" for a long time of my
life.] I would rather prefer a term that means unblocking and unchaining
instead. But it should be certainly one thing: trusted information of a
high value like patents, articles, discoveries, and discussions like those
we have here can be ranked on, especially in the era of "fake news" and
spam surrounding us. What we are talking about is not new. It only has a
new "fashion" name. We can regard it as an extension of the internet,
beyond the semantic one, an intelligent and active, but also trusted and
self-organized network of humans, animals, plants, and technical devices, a
welcome tool extending our senses to feel an entire ecosystem of evolving
things.

I have not read an article discussing "blockchain" in the above sense,
maybe because like most phenomena in "dataism"  the term is currently only
unilaterally exploited by the majority, held under the umbrella of
finances, trade, insurances, contracts, encryption, etc. trivial
"high-impact" fields, similarly to the unilateral understanding of AI,
machine learning, and even quantum computing. They all are still understood
(by the majority of our contemporaries) as means to maintain the status quo
of science, economy, and society. But they can be also used to change the
paradigm. If we stay in the loop accepting data-driven hypothesis and
machine-generated theory only because we have sunk in the self-created
ocean of data, this would mean to betray human mind at the end. On the
other hand, we could use all these tools to empower and perpetuate human
mind activities like those in this forum. Therefore, I wish to ask you if
you would eventually support a future experiment for creating a "human mind
capital" currency based on the trustfulness of the idea transactions in
this forum. I think we can get even funding for this experiment.

All the best.

Plamen

___ ___ ___

Dr. Plamen L. Simeonov
simeio.org |  ibiomath.org | inbiosa.eu
___

2017 Towards a First Implementation of the WLIMES Approach in Living System
Studies Advancing the Diagnostics and Therapy in Personalized Medicine
<https://www.sciencedirect.com/science/article/pii/S0303264717302204>

2017 JPBMB Focused Issue on Integral Biomathics: The Necessary Conjunction
of Western and Eastern Thought Traditions for Exploring the Nature of Mind
and Life <http://www.sciencedirect.com/science/journal/00796107/131>  *

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




On Sat, Mar 10, 2018 at 11:46 PM, Alberto J. Schuhmacher <
ajime...@iisaragon.es> 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 crissc

Re: [Fis] Simple amswer: NOT!

[Dr. Plamen L. Simeonov]

Dea FISes,

with respect to this big data and machine learning cults today, which I
consider as somewhat useful fragments of a much bigger paradigm but not the
non-plus-ultra tendency in science, let me ask you a bit different question:

What do you think about the other more interesting phenomenon recently: the
blockchain technology and the chances for a forum like FIS to use it for
perpetuating knowledge to change the paradigm of conventional thinking
towards a global intellectual standard currency? Perhaps this is what
deserves your attention.

All the best.

Plamen




On Wed, Mar 7, 2018 at 9:09 PM, Krassimir Markov  wrote:

> Dear Alberto,
>
> Let imagine that we are at the naturist beach, i.e. naked.
> OK!
> You will see all what I am and I will se the same for you.
>
> Well, will you know what I think or shall I know the same for you?
>
> Simple answer: NOT!
>
> No Data base may contain any data about my current thoughts and feelings.
> Yes, the stupid part of humanity may be controlled by big data centers.
> But all times it had been controlled. Nothing new.
>
> The pseudo scientists may analyze data and may create tons of papers.
> For such “production” there was and will exist corresponded more and more
> big cemeteries.
> I had edited more than one thousand papers.
> Only several was really very important and with great scientific value !!!
>
> Collection of data is important problem and it will be such for ever.
> But the greater problem for humanity is collection of money [image: Smile]
>
> And the last cause the former!
> And the last is many times more dangerous than former!
>
> Do not worry of Data-ism!
> Be worried of the Money-ism!
>
> I will continue next week because this is my second post  ( Thanks to
> wisdom of Pedro who had limited Writing-letter-ism in our list! ).
>
> Friendly greetings
> Krassimir
>
>
>
>
>
>
> *From:* Alberto J. Schuhmacher 
> *Sent:* Tuesday, March 06, 2018 10:23 PM
> *To:* fis 
> *Subject:* [Fis] Is Dataism the end of classical hypothesis-driven
> research and the beginning of data-correlation-driven research?
>
>
> Dear FIS Colleagues,
>
> I very much appreciate this opportunity to discuss with all of you.
>
> My mentors and science teachers taught me that Science had a method, rules
> and procedures that should be followed and pursued rigorously and with
> perseverance. The scientific research needed to be preceded by one or
> several hypotheses that should be subjected to validation or refutation
> through experiments designed and carried out in a laboratory. The Oxford
> Dictionaries Online defines the scientific method as "a method or procedure
> that has characterized natural science since the 17th century, consisting
> in systematic observation, measurement, and experiment, and the
> formulation, testing, and modification of hypotheses". Experiments are a
> procedure designed to test hypotheses. Experiments are an important tool of
> the scientific method.
>
> In our case, molecular, personalized and precision medicine aims to
> anticipate the future development of diseases in a specific individual
> through molecular markers registered in the genome, variome, metagenome,
> metabolome or in any of the multiple "omes" that make up the present
> "omics" language of current Biology.
>
> The possibilities of applying these methodologies to the prevention and
> treatment of diseases have increased exponentially with the rise of a new
> religion, *Dataism*, whose foundations are inspired by scientific
> agnosticism, a way of thinking that seems classical but applied to
> research, it hides a profound revolution.
>
> Dataism arises from the recent human desire to collect and analyze data,
> data and more data, data of everything and data for everything-from the
> most banal social issues to those that decide the rhythms of life and
> death. “Information flow” is one the “supreme values” of this religion. The
> next floods will be of data as we can see just looking at any electronic
> window.
>
> The recent development of gigantic clinical and biological databases, and
> the concomitant progress of the computational capacity to handle and
> analyze these growing tides of information represent the best substrate for
> the progress of Dataism, which in turn has managed to provide a solid
> content material to an always-evanescent scientific agnosticism.
>
> On many occasions the establishment of correlative observations seems to
> be sufficient to infer about the relevance of a certain factor in the
> development of some human pathologies. It seems that we are heading towards
> a path in which research, instead of being driven by hypotheses confirmed
> experimentally, in the near future experimental hypotheses themselves will
> arise from the observation of data of previously performed experiments. Are
> we facing the end of the wet lab? Is 

Re: [Fis] in a literal translation

[Dr. Plamen L. Simeonov]

Dear Emanuel,

nice to hear such a response.
I am curious to know your opinion and those of the FIS colleagues about the
difference between "with" and "within".
The strict lines of separation typical for reductionist science should be
better avoided. In many cases, I have the feeling that it is "God's will"
that we make this distinction, but what it actually means is a distinct
state of collective consciousness, which can be activated on demand like in
the "mother tree" scene of the movie "Avatar".

Best,

Plamen





On Sat, Mar 3, 2018 at 1:30 PM, Emanuel Diamant <emanl@gmail.com> wrote:

> Dear all,
>
>
>
> My name – Emanuel – in a literal translation means “God with us”.
>
> Despite of that, for the purpose of our current discussion, I would like
> to mention:
>
> The external observer, which provide us with the needed semantic
> information used (as a reference) for physical information interpretation,
> at the very beginning was: or the Nature itself, or (more specific) the
> natural evolution, or (even more specific) the natural selection.
>
> Best regards,
>
> Emanuel.
>
>
>
> --------
>
> *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Dr.
> Plamen L. Simeonov
> *Sent:* Friday, March 02, 2018 11:36 AM
> *To:* Loet Leydesdorff
> *Cc:* fis
> *Subject:* Re: [Fis] Meta-observer?
>
>
>
> I know him: his name is God, the meta-observer + meta-actor at the same
> time.
>
> Correct, Bruno?
>
> ;-)
>
>
>
> best, Plamen
>
> …..
>
> *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Loet
> Leydesdorff
> *Sent:* Friday, March 02, 2018 9:53 AM
> *To:* Koichiro Matsuno; fis@listas.unizar.es
> *Subject:* Re: [Fis] Meta-observer?
>
>
>
> Dear Pedro, Koichiro, and colleagues,
>
>
>
> At the level of observers, indeed, a hierarchy may be involved for the
> change of focus (although this is empirical  and not necessarily the case).
> The communication, however, as a system different from the communicators
> may contain mechanisms such as "translation" which make it possible to
> redirect.
>
>
>
> Best, Loet
>
>
>
> --
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Meta-observer?

[Dr. Plamen L. Simeonov]

I know him: his name is God, the meta-observer + meta-actor at the same
time.
Correct, Bruno?
;-)

best,

Plamen






On Fri, Mar 2, 2018 at 8:53 AM, Loet Leydesdorff 
wrote:

> Dear Pedro, Koichiro, and colleagues,
>
> At the level of observers, indeed, a hierarchy may be involved for the
> change of focus (although this is empirical  and not necessarily the case).
> The communication, however, as a system different from the communicators
> may contain mechanisms such as "translation" which make it possible to
> redirect.
>
> Best,
> Loet
>
> --
>
> Loet Leydesdorff
>
> Professor emeritus, 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 Fellow, Birkbeck , University of London;
> http://scholar.google.com/citations?user=ych9gNYJ=en
>
>
> -- Original Message --
> From: "Koichiro Matsuno" 
> To: fis@listas.unizar.es
> Sent: 3/2/2018 6:41:12 AM
> Subject: Re: [Fis] Meta-observer?
>
> On 28 Feb 2018 at 10:34 PM, PedroClemente Marijuan Fernadez wrote:
>
> A sort of "attention" capable of fast and furious displacements of the
> focus...  helas, this means a meta-observer or an observer-in-command.
>
>Pedro, it is of course one thing to conceive of a hierarchy of
> observers for our own sake, but quite another to figure out what the
> concrete participants such as molecules are doing out there. They are doing
> what would seem appropriate for them to do without minding what we are
> observing. At issue must be how something looking like a chain of command
> could happen to emerge without presuming such a chain in the beginning.
> Prerequisite to its emergence would be the well-being of each participant
> taken care of locally, as a replenishable inevitable. That is an issue of
> the origins of life. The impending agenda is on something general universal
> as an object, and yet concrete particular enough in process. The richness
> resides within the concreteness down to the bottom.
>
>
>
>Apropos, the communications among the local participants differ from
> computation despite the seemingly concrete outlook of the latter.
> Computation upon the notion of time as the linear sequence of the now
> points is not available to the local participants because of the lack of
> the physical means for guaranteeing the sharing of the same now-point among
> themselves.
>
>
>
>Koichiro Matsuno
>
>
>
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Game over! A Curious Story

[Dr. Plamen L. Simeonov]

Dear Terry and FISers,

I know that there is probably theoretical “no proof” or guarantee in the
mathematical sense, but this should not mean that irresponsible experiments
can be carried out on a large scale like Tesla did them a century ago. What
you suggest about “experiments of nature” sounds reasonable. Hawking's
argument is also good. But he was also wrong a couple of times.  What you
say about maths is also true, but the issue is more about the moral and
methodology of science. We cannot afford doing Frankenstein experiments on
this small Earth. Do we know the consequences of all these experiments for
our ecology? Polynesia is still suffering the French H-bomb tests in the
1950s:
https://www.theguardian.com/world/2013/jul/03/french-nuclear-tests-polynesia-declassified
. As I told Lou, if the experiments were made in another remote galaxy, I
would not have a problem as an observer. But they are made here, under our
feet, and there is no guarantee that they cannot go wrong. We cannot escape
anywhere. Again, this has nothing to do with the statistics of airplane or
lift crashes. The entire human civilisation of 100.000 years can disappear
within a minute. Maybe not with this experiment, but with the next one. Of
course, this could happen also with an asteroid or  a comet hit, or a
series of volcano eruptions and earthquakes, but don’t we have other,  more
important problems to solve here on Earth?

All the best.

Plamen






On Tue, Jan 10, 2017 at 8:12 PM, Terrence W. DEACON <dea...@berkeley.edu>
wrote:

> Mathematic analysis seldom provides "proof" of any physical theory or
> prediction. This is of course why we do empirical experiments. So being
> unpersuaded by either side's theoretical analysis and prior to running the
> actual experiment on the LHC, what is the best approach? I think that there
> is another option than simply avoiding performing any such experiment until
> reaching mathematical certainty. I am much more persuaded by the results of
> "experiments of nature" than by anyone's calculations. And there is ample
> evidence from the results of such "experiments" that the predicted
> catastrophic consequences will not occur (because they have not, despite
> millions of replications). I quote again from
>
> http://press.cern/backgrounders/safety-lhc
>
> "Collisions releasing greater energy occur millions of times a day in the
> earth's atmosphere and nothing terrible happens."  Prof. Steven Hawking,
> Lucasian Professor of Mathematics, Cambridge University
>
> "Nature has already done this experiment. ... Cosmic rays have hit the
> moon with more energy and have not produced a black hole that has swallowed
> up the moon. The universe doesn't go around popping off huge black holes."
>  Prof. Edward Kolb, Astrophysicist, University of Chicago
>
> Math is not the ultimate arbiter. But if we didn't have this empirical
> background it would have been a good reason to seek out empirical
> counter-examples before running our own test. Of course this sort of
> caution was not heeded when we tested nuclear weapons.
>
> — Terry
>
> On Tue, Jan 10, 2017 at 9:47 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>>
>> Well, these are only citations. What if all of them are wrong?
>> What if the data that were measured are incorrect?
>> We have had this many times in human history. Titanik was considered
>> unsinkable.
>> Bismark too. But both went down to the seaground.
>> Where is the mathematical proof or the computer simulation?
>>
>> Best,
>>
>> Plamen
>>
>>
>> 
>>
>>
>> On Tue, Jan 10, 2017 at 6:32 PM, <tozziart...@libero.it> wrote:
>>
>>> "The operation of the LHC is safe, not only in the old sense of that
>>> word, but in the more general sense that our most qualified scientists have
>>> thoroughly considered and analyzed the risks involved in the operation of
>>> the LHC. [Any concerns] are merely hypothetical and speculative, and
>>> contradicted by much evidence and scientific analysis."
>>>
>>> Prof. Sheldon Glashow, Nobel Laureate in Physics, Boston University,
>>>
>>> Prof. Frank Wilczek, Nobel Laureate in Physics, Massachusetts Institute
>>> of Technology,
>>>
>>> Prof. Richard Wilson, Mallinckrodt Professor of Physics, Harvard
>>> University
>>>
>>> "The world will not come to an end when the LHC turns on. The LHC is
>>> absolutely safe. ... Collisions releasing greater energy occur millions of
>>> times a da

Re: [Fis] A Curious Story

[Dr. Plamen L. Simeonov]

Dear Louis, Pedro and FISers,

I have been knowing Otto for about a litle less than 10 years now.
What I have learned from him is that he has a very subtle sense of humor
and wisdom.
What I conclude about this issue with CERN's LHC is that he wishes nothing
more/less than an a priori theoretical proof that the black hole
experiments will not lead to a collaps of the Earth.
He would be more than happy if somebody provides this proof and his
concerns about our future appear ungrounded, so that the experiments can
continue without any fear about the possible end of humanity. But as he
said, nobody has done this until now. Nobody has taken these concerns
seriously. The key question for us is why do we allow such experiments
without having such a proof? Why do we play with fire in our own kitchen
without being sure that we can deal with its breakout? If the accident
occurs, then it will be too late to prevent the danger, unless we have a
time machine, which is not the case at the moment, I am afraid.

So, I think that Otto's appeal can be considered as a challenge not less
important than the one with the proof of Fermat's last theorem.
While there was no danger from keeping this problem unsolved for 300+
years, we may have a real problem now.
So, why not trying to administer science for being performed in a
reasonable way: to not place the horses (experimental science) before the
cabin (theoretical science) - which is the case with LHC?
Otto only wishes to say: "We should not do such experients, until we have a
theoretical proof or at least to have a computer simulation demonstrating
that the chance of having such a disaster is diminishing." And even if this
is the case, we should carry a referendum over 4+ billion people on Earth
on wether to allow such experiments or not. They are not only an issue ofr
a government or of an over-excited community of physicists. Please correct
me if I am wrong, Otto.

I hope this helps.

All the best.

Plamen





On Tue, Jan 10, 2017 at 6:09 PM, Louis H Kauffman  wrote:

> 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 
> wrote:
>
> 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 <
> pcmarijuan.i...@aragon.es> 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 

[Fis] Biological Organisation as the True Foundation of Reality

[Dr. Plamen L. Simeonov]

Dear All,

I would like to disseminate this lecture given by Brian Josephson at the
2016  Lindau Nobel Laureates Meeting on June 29t:

http://sms.cam.ac.uk/media/2277379

Best wishes,

Plamen


___ ___ ___

Dr. Plamen L. Simeonov
mobile:   +49.17.37.81.63.37
landline: +49.30.83.21.20.70
email:pla...@simeio.org
URL:  www.simeio.org / LinkedIn <http://lnkd.in/aqn39k>


2016 Foundations of Information Science Forum: Five Discussion Sessions on
Phenomenology and Life (February-May, 2016)
<http://fis.sciforum.net/fis-discussion-sessions/>

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)

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>

2012 Integral Biomathics: Tracing the Road to Reality
<http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-642-28110-5>

2011 INtegral BIOmathics Support Action (INBIOSA) <http://www.inbiosa.eu>


___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

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

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

2012 Integral Biomathics: Tracing the Road to Reality
<http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-642-28110-5>

2011 INtegral BIOmathics Support Action (INBIOSA) <http://www.inbiosa.eu>




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 Biomat

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

[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.)

[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 

[Fis] _ Re: Cancer Cure?

[Dr. Plamen L. Simeonov]

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.
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.

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.

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.

All the best,

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





On Tue, May 31, 2016 at 12:43 AM, Robert E. Ulanowicz 
wrote:

>
> > And yet, SOC is only one of the theoretical options that can resonate
> > together. What I am interested to know is: do yo think that SOC is a good
> > point to start from when moving from physics to biology?
>
> Dear Plamen:
>
> Most renditions of SOC with which I am familiar involve single homogeneous
> variables. I am of the opinion that physics is preoccupied with
> homogeneity, whereas biology is all about heterogeneity. Therefore, I am
> skeptical whether descriptions in terms of homogeneous variables (e.g.,
> matter, energy, charge, mass) can ever be sufficient descriptors of
> biological systems. Mind you, they may still be true (e.g., Bejan's
> constructual law), but because they do not explicitly embody
> heterogeneity, they will always be inadequate long-term descriptors of
> living systems.
>
> The common assumption has been that one can advance from homogeneous
> variables to heterogeneous systems via the formulation of intricate
> boundary-value statements connecting the many dimensions, but this is
> usually impossible for both epistemic and ontological reasons. (One is
> unable because of combinatorics to predicate the full link-up conditions
> [epistemic], and the underlying many equations possess insufficient
> stability to track complex systems [ontic].)
>
> Somehow, explicit account needs be taken of system heterogeneity, such as
> is done with some network metrics. The world of complexity is one of
> *massive* heterogeneity. Physics, the study of the homogeneous, can't cut
> it alone. (As Stu Kauffman puts it, we have reached the end of the "Era of
> Physics". Not that physics won't still advance, but that not every event
> and behavior in the complex world needs to be referred back to it.)
>
> My personal opinion, of course.
>
> Best wishes,
> Bob
>
>
>
___
Fis mailing list

[Fis] _ Re: _ Re: Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

Dear Pedro and All,

coming back to my earlier suggestion from this weekend to explore the
particular case of using self-organised criticality and cancer, I suggest
to read and comment on this arXiv paper by J.C. Phillips:
*Self-Organized Criticality: A Prophetic Path to Curing Cancer*
https://arxiv.org/ftp/arxiv/papers/1210/1210.0048.pdf.

I look forward to your opinion, in particular those of Alex, Lou and Maxine
(with respect to making the turn towards phenomenology).

With best wishes for a fruitful week,

Plamen


On Sun, May 22, 2016 at 3:31 PM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

> Dear Pedro and All,
>
> I was not quite correct im my earlier email of today when I said that that
> there is not much novelty to be reported in the studying the phenomenology
> of dying and death in the West. What should be noticed is definitely the
> research of such pioneers as Elisabeth Kübler-Ross  (
> http://www.wikiwand.com/en/Kübler-Ross_model) and Lawrence LeShan (
> http://www.wikiwand.com/en/Lawrence_LeShan) and many others whose line
> can be traced back to Newton’s alchemic experiments, incl. those of the
> circle of prominent scientists and humanists who founded the British
> Society for Psychical Research in 1882, in an era when the Eiffel Tower and
> the Manhattan Building were ascending on both sides of the Atlantic Ocean
> and the first direct current lightning began its path around the globe from
> the New York”s Pearl Street power station, in the dawn of the birth of two
> great physical theories that would reshape the world as no knowledge ever
> before. We appear to be a little bit lost and helpless with playing “Bits &
> Bolts" (https://www.youtube.com/watch?v=AuUxLplR_TI) in our era.
>
> Best,
>
> Plamen
>
>
>
> On Sun, May 22, 2016 at 12:34 PM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>> Dear Pedro and Colleagues,
>>
>> thank you for your comments and insightful suggestions where see there is
>> a need to focus research in the field.  We know well that a good physician
>> is usually less successful than a good car mechanic, but also that cars
>> cannot self-repair (yet). It is true that the matter is complex and tough,
>> but also well-studied: healing methods that worked has been applied before
>> science as such has emerged. Yet in the past, stress has been given to the
>> importance of the bond healer - patient, whereas in the last century with
>> the “industrialisation" of medicine and more applied research, the patient
>> became impersonalised with attention slowly shifting from a bilateral
>> relation to a trilateral (physician  - drug - patient), or even
>> a quadrilateral  (physician - computer - drug - patient) one. Great
>> discoveries of how we are structured and how we operate were made, before
>> realising (again) that all these formations and processes in the human body
>> are very individual and have their own history and future, despite knowing
>> and classifying every single detail. And yet, we still hope with the
>> collection of more and more data and putting more resolution, skill and
>> intelligence in our exploration devices to find patters of emergence that
>> will allow us to detect and understand regress/illness to repair and
>> re-engineer the ill parts of our virtual bodies, and from there the
>> physical ones. Is modern medicine a science or an engineering discipline,
>> or both perhaps, because it is so important to us? Things are complex and
>> tough in medicine not because of much detail and chaos/messiness, but
>> because we keep an eye-in-eye contact at the phenomenology of death, which
>> have been largely ignored for a long time in our modern Western
>> society: without understanding it much from our objective, even if shared,
>> viewpoint in science. Dying is a very personal experience, but quite well
>> documented, even if not that extensively like love and hate in human
>> literature. I am not aware of much (phenomenological) detail provided by
>> contemporary science in the process of dying beyond what is known about the
>> six transitional states described by Tibetian Buddhism (
>> http://www.wikiwand.com/en/Bardo), perhaps because shared evidence and
>> reproducibility of scientific results is the common guideline for science.
>> Yet, is therefore everything else simply "non-science"? Is not our entire
>> research in life science and medicine targeting life and youth perpetuation
>> (and commercialisation) for ever?
>>
>>
>> On Thu, May 19, 2016 at 8:02 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ <
>> pcmarijuan.i...@aragon.es> wrote:
>>
>

[Fis] _ Re: Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

Dear Pedro and All,

I was not quite correct im my earlier email of today when I said that that
there is not much novelty to be reported in the studying the phenomenology
of dying and death in the West. What should be noticed is definitely the
research of such pioneers as Elisabeth Kübler-Ross  (
http://www.wikiwand.com/en/Kübler-Ross_model) and Lawrence LeShan (
http://www.wikiwand.com/en/Lawrence_LeShan) and many others whose line can
be traced back to Newton’s alchemic experiments, incl. those of the circle
of prominent scientists and humanists who founded the British Society for
Psychical Research in 1882, in an era when the Eiffel Tower and the
Manhattan Building were ascending on both sides of the Atlantic Ocean and
the first direct current lightning began its path around the globe from the
New York”s Pearl Street power station, in the dawn of the birth of two
great physical theories that would reshape the world as no knowledge ever
before. We appear to be a little bit lost and helpless with playing “Bits &
Bolts" (https://www.youtube.com/watch?v=AuUxLplR_TI) in our era.

Best,

Plamen



On Sun, May 22, 2016 at 12:34 PM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

> Dear Pedro and Colleagues,
>
> thank you for your comments and insightful suggestions where see there is
> a need to focus research in the field.  We know well that a good physician
> is usually less successful than a good car mechanic, but also that cars
> cannot self-repair (yet). It is true that the matter is complex and tough,
> but also well-studied: healing methods that worked has been applied before
> science as such has emerged. Yet in the past, stress has been given to the
> importance of the bond healer - patient, whereas in the last century with
> the “industrialisation" of medicine and more applied research, the patient
> became impersonalised with attention slowly shifting from a bilateral
> relation to a trilateral (physician  - drug - patient), or even
> a quadrilateral  (physician - computer - drug - patient) one. Great
> discoveries of how we are structured and how we operate were made, before
> realising (again) that all these formations and processes in the human body
> are very individual and have their own history and future, despite knowing
> and classifying every single detail. And yet, we still hope with the
> collection of more and more data and putting more resolution, skill and
> intelligence in our exploration devices to find patters of emergence that
> will allow us to detect and understand regress/illness to repair and
> re-engineer the ill parts of our virtual bodies, and from there the
> physical ones. Is modern medicine a science or an engineering discipline,
> or both perhaps, because it is so important to us? Things are complex and
> tough in medicine not because of much detail and chaos/messiness, but
> because we keep an eye-in-eye contact at the phenomenology of death, which
> have been largely ignored for a long time in our modern Western
> society: without understanding it much from our objective, even if shared,
> viewpoint in science. Dying is a very personal experience, but quite well
> documented, even if not that extensively like love and hate in human
> literature. I am not aware of much (phenomenological) detail provided by
> contemporary science in the process of dying beyond what is known about the
> six transitional states described by Tibetian Buddhism (
> http://www.wikiwand.com/en/Bardo), perhaps because shared evidence and
> reproducibility of scientific results is the common guideline for science.
> Yet, is therefore everything else simply "non-science"? Is not our entire
> research in life science and medicine targeting life and youth perpetuation
> (and commercialisation) for ever?
>
>
> On Thu, May 19, 2016 at 8:02 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ <
> pcmarijuan.i...@aragon.es> wrote:
>
>> Dear Plamen and FIS Colleagues,
>>
>> Discussing on integrative attempts in medicine is really challenging.
>>
>
> In the course of these medicine studies, I realised that integration has
> many different interpretations here. It is not easy to place a term for
> making clear what one has in mind and avoid misunderstanding. Therefore I
> made this first note in my opening session. I began with it, because this
> was our starting point: what does integral biomathics mean in the context
> of medicine? We are moving in a domain very close to the humanities, and
> obtaining a label “exotic” or “esoteric” by the mainstream researchers is
> not promoting. Hence this effort to differentiate.
>
>
>> I do not think that the marriage proposed by Stan, yoking medicine with
>> semiotics in films grounds, will have much progeny.
>>
>
> I think

Re: [Fis] Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

. We tried to
> do something in that style for a European Project, but we did not pass the
> 2nd cut.
>
> 2. In physiological matters, there is much to say from criticality,
> balancing, symmetry, symmetry breaking and restoration, network science,
> etc. Some time ago there was a "Physiome" European Project, "From Molecules
> to HumanKind" trying to capture the whole map of physiological regulation.
> But in my impression it is a bioengineering repository of models and
> resources. It could be done differently. The emphasis by Alex, Plamen on
> criticality and of mine on signaling would not be too bad complementary
> directions.
>
> 3. Finally, on integration, I would propose "knowledge recombination"
> instead. The usual way to understand integration is unbounded, without
> space-time limits, like the processing of a Turing Machine. Rather the
> human practice of knowledge, and paradigmatically medicine,
> is characterized by a growing difficulty in integration matters within
> dozens and dozens of disciplines. Heterogeneous fields of knowledge can
> hardly be integrated at all. What living beings have had to rely upon is
> "recombination"--either genetically, neuronal, or socially. It is the
> unending combination of fragments of heterogeneous pieces of knowledge
> brought into action not randomly but in space-temporal frameworks that
> allow the mutual cross-fertilization. The idea, developed specifically for
> the biomedical arena can be discussed at length in [Information 2011, 2,
> 651-671; doi:10.3390/info2040651] and in [*Scientomics*: An Emergent
> Perspective in Knowledge. Organization. Knowledge Organization. 39(3),
> 153-164. 2012]. In philosophical terms it is sort of a realization of
> Ortega y Gasset's perspectivism... the peculiar phenomenology of the
> great Spanish philosopher.
>
> Better if I stop here. Greetings to all--Pedro
>


These are very good points which I thankfully adopt in the "IB 4 medicine"
scheme.  In particular, the last one of “recombination", extended by
"creative inclusion and adaptation”, just in the way as mitochondria were
adopted by the cell in the process of its evolution, is a very powerful
principle of life which we experience in our macro societal structures now.
And this is a point that Ortega y Gasset was well aware many years ago

How about trying to come back again to criticality and try to trace jointly
at least one complete possible investigative path to the puzzle of illness
and recovery for one of the 3 examples I mentioned earlier in kind of a  3φ
or 4φ (or even "powers of φ”) "recombinant solution” from the standpoint
of contemporary science and phenomenology? I vote for cancer, but we can
take any of the other two if there are sufficient votes.

Have a great last week of May!

Plamen




>
> --
> *De:* Fis [fis-boun...@listas.unizar.es] en nombre de Dr. Plamen L.
> Simeonov [plamen.l.simeo...@gmail.com]
> *Enviado el:* miércoles, 18 de mayo de 2016 11:39
> *Para:* Karl Javorszky
> *Cc:* fis
> *Asunto:* Re: [Fis] Towards a 3φ integrative medicine
>
> One more thing on the example with the heart failure. If you go to a
> cardiologist with the same problem, s/he will prescribe a series of
> exampinations related to your heart only (checking your blood pressure, EEG
> & EMG tests incl. 24h recording and physical performance tests,  etc.).
> Rarely you can expect a blood sample analysis related to some kidney or
> liver failure, or a cervical examination because of a possible supply
> shortage of the vertebral artery (in case you have reported accompanying
> headaches) because of a grown bone spur with the first examination.
> Finally, depending on all these tests you will usually obtain a pill
> prescription to keep yopur blood pressure low for the rest of your life and
> some advise to avoid salty and spicy food. Period. If you at some point in
> time give up to find out and fix the real cause(s) for this "simple" heart
> failure, it is your problem, and not the one of the physician or the
> insurance company.
>
> Now let's turn to the giraffe and the okapi and see how they have managed
> to develop a strong heart with the evolution:
> http://science.psu.edu/news-and-events/2016-news/Cavener5-2016
> http://www.cbsnews.com/news/genes-reveal-clues-to-giraffes-long-neck/.
> http://www.nature.com/ncomms/2016/160517/ncomms11519/full/ncomms11519.html
>
> Thus, science can still give important clues to solving problems, incl.
> what is a bonus or threat, but it is not the only source. The central issue
> is the integration of knowledge and sign(al)s about the operation and
> interaction of whole body systems, I think.
>
> Best,
>
> Plame

[Fis] _ Re: _ Re: _ Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

Dear Colleagues,

the link to the PDF version of my thesis has changed:
https://dl.dropboxusercontent.com/u/39020576/Towards%20a%203%CF%86%20integrative%20medicine.pdf

For most browsers also the link to the text version at FIS should be
readable with small exceptions:
http://listas.unizar.es/pipermail/fis/2016-May/000955.html.

It is called "*[Fis] _ Towards a 3φ integrative medicine*" and began on
Saturday, May 14th.

Best wuishes,

Plamen





On Sun, May 15, 2016 at 7:03 AM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

>
> Dear Colleagues,
>
> for those whose email systems do not support special characters like Greek
> letters (s. first concept explained in note 1), I have placed a PDF version
> of my opening on the cloud:
> https://dl.dropboxusercontent.com/u/39020576/Plamen-Intro.pdf.
> Please let me know if you register other problems in the communication.
>
> Best,
>
> Plamen
>
>
> ________________
>
>
> On Sat, May 14, 2016 at 9:49 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>> 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 a system at
>> its critical point generated by self-organization during a long transient
>> period at the complexity edge between order/stability/predictability and
>> disorder/chaos/unpredictability.
>>
>>
>>
>> *Regulation of growth, form and function as a balance between health and
>> illness.* The role of regulation and homeostasis in maintaining the
>> structure and function of living systems is critical. Every deviation from
>> a regulated state of being leads to imbalances, failures and subsystem
>> dysfunction that is usually transitory, but could also become
>> life-threatening, if the organism cannot find a way to restore quickly to a
>> balanced, healthy state. Living beings are robust and fault-tolerant with
>> respect to hazards; they possess multiple alternative pathways for
>> supplying and maintaining their existential functions. However, some state
>> transitions in response to severe harms can become practically
>> irreversible, because of the deep evolutionary interlocking between the
>> participating entities and processes. Sometimes the normal functioning of
>> the organism cannot be easily restored by its natural repair processes,
>> especially when adversities reoccur frequently, and the organism fails ill.
>>
>>
>>
>> *Synchron

Re: [Fis] Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

One more thing on the example with the heart failure. If you go to a
cardiologist with the same problem, s/he will prescribe a series of
exampinations related to your heart only (checking your blood pressure, EEG
& EMG tests incl. 24h recording and physical performance tests,  etc.).
Rarely you can expect a blood sample analysis related to some kidney or
liver failure, or a cervical examination because of a possible supply
shortage of the vertebral artery (in case you have reported accompanying
headaches) because of a grown bone spur with the first examination.
Finally, depending on all these tests you will usually obtain a pill
prescription to keep yopur blood pressure low for the rest of your life and
some advise to avoid salty and spicy food. Period. If you at some point in
time give up to find out and fix the real cause(s) for this "simple" heart
failure, it is your problem, and not the one of the physician or the
insurance company.

Now let's turn to the giraffe and the okapi and see how they have managed
to develop a strong heart with the evolution:
http://science.psu.edu/news-and-events/2016-news/Cavener5-2016
http://www.cbsnews.com/news/genes-reveal-clues-to-giraffes-long-neck/.
http://www.nature.com/ncomms/2016/160517/ncomms11519/full/ncomms11519.html

Thus, science can still give important clues to solving problems, incl.
what is a bonus or threat, but it is not the only source. The central issue
is the integration of knowledge and sign(al)s about the operation and
interaction of whole body systems, I think.

Best,

Plamen


On Wed, May 18, 2016 at 8:56 AM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

>
> This is an interesting question, Karl. Without giving a full account, I
> think there can be said the following.
> It is usually not the (chemical) nature of a substrate or the availability
> of an external source that makes it a poison, but its ratio.
> Small amounts are harmless, larger amounts are dangerous. But there is no
> general recipe to detect harms.
> If you stay for 15 minutes on the sun (UV light) this will stimulate the
> production of vitamin D in your body which in turn will stimulate the
> strengthening of your bones. But if you stay longer, there is a danger of a
> sunstroke or melanoma. Our brains simply do not obtain all these alarming
> signals from damaging the (skin) cells to the production and cumulation of
> toxic substances. We have specific organs to sense color, smell and taste,
> but not radiation.
>
> The problem with contemporary (allopathic) medicine is that it is
> basically symptomatic and the diagnosis is usually reductionistic,
> detecting one source of damage related to the failed organ (heart, kidney,
> liver, etc.) associated with the ailment; so is the therapy, until a second
> or a third failure are detected and medicated sequentially and
> independently from each other. Yet, in most cases, the failures are
> occurring at the same time in multiple organs and systems, but we do not
> have the information about that to act, or the information comes too late
> and on an isolated place, covering the other alarm signals under the
> threshold of detection by the organism.
>
> However, if you go to a TCM practitioner with the complaint of e.g. heart
> palpitations as a symptom of restlessness after examining your pulse and
> tongue, you will obtain three medications (herbs): one for lowering the
> blood pressure, one for detoxifying the kidneys and one for detoxifying the
> liver. In addition to that you may become an acupuncture session for
> regulating the “qi/chi flow" inside the body - a substance which is a
> complete mystery for science - and a prescription of what to eat and how to
> sleep.
>
> So, decrypting the body sign(al)s in their multiplicity as result of the
> interaction of systems and organs is the clue. Regarding human bodies as
> licked buckets that need to be repaired from multiple punches is probably a
> good metaphor.
>
> Best,
>
> Plamen
>
>
> 
>
>
> On Wed, May 18, 2016 at 12:44 AM, Karl Javorszky <karl.javors...@gmail.com
> > wrote:
>
>> Just a small detail on the information density of food (air, water,
>> sensory input, etc.) in medicine:
>>
>> The DNA has a high informational value for the organism. Can it be said
>> that poison has also an informational value?
>>
>> Can the de-constructive effect of a substance quantified based on the
>> same semiotic system of references as the constructive effect of a
>> substance can be referred to in that same system of references?
>>
>> ___
>> Fis mailing list
>> Fis@listas.unizar.es
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>
>>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] _ Re: _ Re: _ Re: _ Re: _ Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

Dear Colleagues,

I’d like to share a possible sensation as of today if true:

http://phys.org/news/2016-05-complex-life-billion-years-earlier.html

What would this mean in terms of our discussion about life and medicine?

Best.

Plamen





On Tue, May 17, 2016 at 6:27 PM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

> This is a very interesting note for me, John!
> So, the modern symptomatic medicine, the collection of data about illness
> characteristics has its roots in philosophy?
>
> Best,
>
> Plamen
>
>
> 
>
>
> On Tue, May 17, 2016 at 6:16 PM, John Collier <colli...@ukzn.ac.za> wrote:
>
>> Ironically, “semiotic” originally was a medical term referring to signs
>> (symptoms) of disease. John Locke (my favourite modern philosopher)
>> introduced the term as we use it today, and may have derived it from the
>> Greek *seme*.  But he also knew a lot about medicine (and just about
>> everything else at the time, but he apparently lacked a sense of humour).
>>
>>
>>
>> From an online dictionary (the other I found had the first known use in
>> 1880. Which is clearly wrong. So beware!):
>>
>> 1615-20; (def 3) < Greek *sēmeiōtikós* significant, equivalent to
>> *sēmeiō-,*verbid stem of *sēmeioûn* to interpret as a sign (derivative of
>>  Greek *sēmeîon*sign) + *-tikos* -tic
>> <http://www.dictionary.com/browse/-tic>; (def 4) < Greek *sēmeiōtik**ḗ*
>> *,* noun use of feminine of*sēmeiōtikós,* adapted by John Locke (on the
>> model of Greek *logik**ḗ* logic <http://www.dictionary.com/browse/logic>,
>> etc.; see -ic <http://www.dictionary.com/browse/-ic> ) to mean “the
>> doctrine of signs”; (defs 1, 2) based on Locke'scoinage or a reanalysis
>> of the Gk word
>>
>>
>>
>> Also, from a medical dictionary:
>>
>> semiotic
>>
>>  /se·mi·ot·ic/ (se″me-ot´ik)
>>
>> *1. **pertaining* to signs or symptoms.
>>
>> *2. **pathognomonic*
>> <http://medical-dictionary.thefreedictionary.com/pathognomonic>.
>>
>> Dorland's Medical Dictionary for Health Consumers. © 2007 by Saunders, an
>> imprint of Elsevier, Inc. All rights reserved.
>>
>>
>>
>> For which, if like me, you may further need:
>>
>> pathognomonic
>>
>>  [path″og-no-mon´ik]
>>
>> specifically *distinctive*
>>  or characteristic of a disease or pathologic condition; denoting a sign or 
>> symptom on which adiagnosis can be made.
>>
>>
>>
>>
>>
>> John Collier
>>
>> Professor Emeritus and Senior Research Associate
>>
>> University of KwaZulu-Natal
>>
>> http://web.ncf.ca/collier
>>
>>
>>
>> *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Stanley
>> N Salthe
>> *Sent:* Tuesday, 17 May 2016 4:21 PM
>> *To:* Dr. Plamen L. Simeonov <plamen.l.simeo...@gmail.com>; fis <
>> fis@listas.unizar.es>
>> *Subject:* [Fis] _ Re: _ Re: _ Re: _ Towards a 3φ integrative medicine
>>
>>
>>
>> Plamen, Pedro --
>>
>>
>>
>> It seems to me that perhaps Medicine should not look to mathematics for
>> support or underpinning so much as to SEMIOTICS (that is, Peircean
>> semiotics, being worked today as biosemiotics).  Biosemiotics is, in the
>> verbal conceptual realm, almost as complex and messy as medicine, and so
>> the two might be matched up fruitfully!
>>
>>
>>
>> STAN
>>
>>
>>
>> On Tue, May 17, 2016 at 9:03 AM, Dr. Plamen L. Simeonov <
>> plamen.l.simeo...@gmail.com> wrote:
>>
>> Daer Pedro,
>>
>> thank you for your entertaining way of presenting my Sisyphus theme about
>> medicine in a nutshell, which was mostly enjoyable to read. Actually, you
>> are right, medicine is "messy", which qualifies it more like a liberal art
>> discipline rather than science, full of workshop type of hustle and bustle,
>> ad hoc insights of mystic adepts followed by faithful scholars and mixed
>> with cutting edge technology wherever possible (in the Western world). It
>> appears that every effort to organize it in the manner we know in
>> mathematics and physics is doomed to failure.  I realise that the subject's
>> depth reflected in my presentation is indeed overwhelming. Yet, it was not
>> my intention to put a Sisyphus rock upon this forum. Thank you for your and
>> Koichiro's simplified pedestrian analysis of the theme. We can go with thes
>> rephrased set of questions fur

[Fis] _ Re: _ Re: _ Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

ving and non-living
matter. This is something that "matters". Of course, one could take
"autopoiesis" instead, which is also a good choice. I am not sure how far
we can go with this this "criticality" bus. I had to start somewhere my
talk, and I made this choice to facilitate the transition to medicine. If
anyone has a better suggestion, I do not mind.


> It is a long story of looking for responses "where the physical/math light
> is" and not where the biol. problems are.
>
>
I agree. This is the real issue. How can ""3φ",  "4φ",  or "3φ+ 1ψ + µ "
help us is the question.

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.
>

Unfortunately, you appear to be right. I am also not convinced that Big
Data is blessing rather than a curse.


> 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.
>

The question we could try to answer here is: can we do something to
disentangle the spaghetti dish of medicine?

>
> Sorry if seemingly I have joined the  "Cassandra" club!
>

I don't think so. Yours are fair concerns.

Best,

Plamen



> 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 a system at its
> critical point generated by self-organization during a long transient
> period at the complexity edge between order/stability/predictability and
> disorder/chaos/unpredictability.
>
>
>
> *Regulation of growth, form and function as a balance between health and
> illness.* The role of regulation and homeostasis in maintaining the
> structure and function of living systems is critical. Every deviation from
> a regulated state of being leads to imbalances, failures and subsystem
> dysfunction that is usually transitory, but could also become
> life-threatening, if the organism cannot find a way to restore quickly to a
> balanced, healthy state. Living beings are robust and fault-tolerant with
> respect to hazards; they possess multiple alternative pathways for
> supplying and maintaining their existential functions. However, some state
> transitions in respons

[Fis] _ Towards a 3φ integrative medicine

[Dr. Plamen L. Simeonov]

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 a system at its
critical point generated by self-organization during a long transient
period at the complexity edge between order/stability/predictability and
disorder/chaos/unpredictability.



*Regulation of growth, form and function as a balance between health and
illness.* The role of regulation and homeostasis in maintaining the
structure and function of living systems is critical. Every deviation from
a regulated state of being leads to imbalances, failures and subsystem
dysfunction that is usually transitory, but could also become
life-threatening, if the organism cannot find a way to restore quickly to a
balanced, healthy state. Living beings are robust and fault-tolerant with
respect to hazards; they possess multiple alternative pathways for
supplying and maintaining their existential functions. However, some state
transitions in response to severe harms can become practically
irreversible, because of the deep evolutionary interlocking between the
participating entities and processes. Sometimes the normal functioning of
the organism cannot be easily restored by its natural repair processes,
especially when adversities reoccur frequently, and the organism fails ill.



*Synchronicity of action and information between the building blocks of a
living system.* There is a need for every physiological function to be
correctly coordinated with all other “peer” functions. Information flows
within a living system interconnect all physiological functions and organs
at multiple levels into a single mesh of regulatory interconnections.
Multiple feedback-control loops enable the cross-functional interlocking of
both healthy and ill state changes of the organism.
Adjacent/peripheral/secondary homeostasis processes act as fine-tuning
catalyzers of substrate ratios and process rates exchanged within the
living system. Imbalances of these quantities lead to excess/blockage or
scarcity/draining of essential nourishment and information exchange
pathways.



*Regulation at criticality* not only fine-tunes a process, it *optimizes*
it for survival: with respect to a given generation’s available
possibilities in the light of the past generations’ possibilities. To
survive an organism or a species needs to develop optimal *response-ability*
to environmental distress.


*New ecological definition of life according to Hankey: self-regulating,
self-reproducing systems that maximize efficiency of function to maximize
competitiveness in their chosen environment. *



*Summary: Elements of self-organized criticality*



   1. Criticality
   2. Edge of the chaos
   3. Self-organized criticality
   4. 1/f fractal patterns of response



*… and beyond*



I wish to add a 5th aspect to this definition from the perspective of
integral biomathics:



   1. *Phenomenology*



The latter is a largely studied matter in contemporary medicine (s. ref.
list D), at least at the macro, interpersonal *level*.



*Note 2*: A level refers to the compositional hierarchy defining levels by
scale.



*The key question in such a 

Re: [Fis] _ Re: _ Discussion

[Dr. Plamen L. Simeonov]

Dear All,

I think that in the context of what Maxine, Lou, Soeren and others
exchanged a little while ago it makes sense to refer to Kalevi Kull’s paper
in the Biosemiotics section V of this collection below which initiated our
discussion:

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)

Of course, you are welcome to read all papers there.

Best wishes,

Plamen


On Mon, Apr 18, 2016 at 7:43 AM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

> Dear Maxine, Lou, Pedro, Loet, John, Soeren and Colleagues,
>
> first of all I wish to thank Maxine for providing a bit different
> perspective upon the overall subject of the discussion theme, namely
> phenomenology or better said “phenomenological philosophy” (since
> “phenomenology” has acquired different meanings in the sciences in the
> years). Despite that “action", as Pedro said, has been a widely discussed
> topic, I think that Maxine’s note was meaning something else which deserves
> attention and more thought.
>
> On Tue, Apr 12, 2016 at 6:41 AM, Maxine Sheets-Johnstone <m...@uoregon.edu>
> wrote:
>
>> To all colleagues,
>>
>> I hope I may voice a number of concerns that have arisen in the course
>> of the ongoing discussions that are ostensibly about phenomenology and
>> the life sciences.
>>
>> The concerns begin with a non-recognition of what is surely the ground
>> floor of real-life, real-time realities, namely, animation, not in the
>> sense of being alive or in opposition to the inanimate, but in the sense
>> of motion, movement, kinetics. As Aristotle cogently remarked,
>> “Nature is a principle of motion and change. . . . We must therefore see
>> that we understand what motion is; for if it were unknown, nature too
>> would be unknown” (Physics 200b12-14).
>>
>> Through and through--from animate organisms to an ever-changing world--
>> movement is foundational to understandings of subject and world, and of
>> subject/world relationships, and this whether subject and world are
>> examined phenomenologically or scientifically. In short, movement is at
>> the core of information and meaning, at the core of mind and
>> consciousness,
>> at the core of both gestural and verbal language, at the core of nervous
>> system and organic functionings, at the core of molecular transformations,
>> at the core of ellipses, electrons, gravity, waves, particles, and so on,
>> and further, at the core of time, the concept, measurement, and meaning of
>> time.
>>
>>
> That the origins of meaning and purpose can be found in movement and life
> is an interesting thought.
> I think that this is what one could say about the ultimate goal of
> Aristotle’s physics. It began being explained with the equations of Newton
> about inanimate matter and finally landed at its origin ---  a curious loop
> of recursion, reflection and self-reference --- with Schrödinger”s question
> about what is life in the search of the lost purpose on the way to
> explaining all kinds of movements.
>
> All this is to remind us, that there are two kinds of knowledge (and
> meaning): the incremental one with which most of us are accustomed, and
> the“forked” one, similar to Everett’s split universes, providing a new
> options for scrutinising, interpretation and understanding of the world we
> live in. I think that this is the message which Maxine disseminates in this
> forum. Maxine, please correct me if I am wrong. Understanding Husserl,
> Heidegger and Marleau-Ponty is almost that difficult as understanding
> quantum mechanics by non-specialists (as Alex Hankey told me in one of our
> conversations), or Gödel by non-logicians and non-mathematicians. It is
> difficult to follow the reasoning in each one of these domains, without
> investing years of dedicated study, that only a few can afford in a single
> life span. But that’s the reason why we have come together in this forum to
> state opinions, ask questions and clarify remote subjects that are tough to
> grasp alone.
>
>
>
>> I enumerate below specifics with respect to what is essentially the
>> foundational dynamic reality. The summary concerns are followed by
>> references that document each concern.
>
>
> These are indeed the concerns that motivated and moved human inquiry in
> the era of the Greek philosophers, when theatre and mathematics were not
> that far from each other. We need to come back to this kind of thinking and
> understanding far-fetched stuff also by utilising our intuition, because
> the

[Fis] _ Re: _ Discussion

[Dr. Plamen L. Simeonov]

Dear Maxine, Lou, Pedro, Loet, John, Soeren and Colleagues,

first of all I wish to thank Maxine for providing a bit different
perspective upon the overall subject of the discussion theme, namely
phenomenology or better said “phenomenological philosophy” (since
“phenomenology” has acquired different meanings in the sciences in the
years). Despite that “action", as Pedro said, has been a widely discussed
topic, I think that Maxine’s note was meaning something else which deserves
attention and more thought.

On Tue, Apr 12, 2016 at 6:41 AM, Maxine Sheets-Johnstone 
wrote:

> To all colleagues,
>
> I hope I may voice a number of concerns that have arisen in the course
> of the ongoing discussions that are ostensibly about phenomenology and
> the life sciences.
>
> The concerns begin with a non-recognition of what is surely the ground
> floor of real-life, real-time realities, namely, animation, not in the
> sense of being alive or in opposition to the inanimate, but in the sense
> of motion, movement, kinetics. As Aristotle cogently remarked,
> “Nature is a principle of motion and change. . . . We must therefore see
> that we understand what motion is; for if it were unknown, nature too
> would be unknown” (Physics 200b12-14).
>
> Through and through--from animate organisms to an ever-changing world--
> movement is foundational to understandings of subject and world, and of
> subject/world relationships, and this whether subject and world are
> examined phenomenologically or scientifically. In short, movement is at
> the core of information and meaning, at the core of mind and consciousness,
> at the core of both gestural and verbal language, at the core of nervous
> system and organic functionings, at the core of molecular transformations,
> at the core of ellipses, electrons, gravity, waves, particles, and so on,
> and further, at the core of time, the concept, measurement, and meaning of
> time.
>
>
That the origins of meaning and purpose can be found in movement and life
is an interesting thought.
I think that this is what one could say about the ultimate goal of
Aristotle’s physics. It began being explained with the equations of Newton
about inanimate matter and finally landed at its origin ---  a curious loop
of recursion, reflection and self-reference --- with Schrödinger”s question
about what is life in the search of the lost purpose on the way to
explaining all kinds of movements.

All this is to remind us, that there are two kinds of knowledge (and
meaning): the incremental one with which most of us are accustomed, and
the“forked” one, similar to Everett’s split universes, providing a new
options for scrutinising, interpretation and understanding of the world we
live in. I think that this is the message which Maxine disseminates in this
forum. Maxine, please correct me if I am wrong. Understanding Husserl,
Heidegger and Marleau-Ponty is almost that difficult as understanding
quantum mechanics by non-specialists (as Alex Hankey told me in one of our
conversations), or Gödel by non-logicians and non-mathematicians. It is
difficult to follow the reasoning in each one of these domains, without
investing years of dedicated study, that only a few can afford in a single
life span. But that’s the reason why we have come together in this forum to
state opinions, ask questions and clarify remote subjects that are tough to
grasp alone.



> I enumerate below specifics with respect to what is essentially the
> foundational dynamic reality. The summary concerns are followed by
> references that document each concern.


These are indeed the concerns that motivated and moved human inquiry in the
era of the Greek philosophers, when theatre and mathematics were not that
far from each other. We need to come back to this kind of thinking and
understanding far-fetched stuff also by utilising our intuition, because
the roots of both science and the humanities are the same: our human
nature. Some folks from these remote fields, like Pauli and Jung, were able
to speak to each other. Others, despite being geniuses in their fields
remained stuck in them and could not follow a different viewpoint, and yet
they felt there is something beyond their own perspective and were longing
for it.

Anyway, I will stop here thanking Lou for his note on Gödel that reminded
us that this man has spent many years pondering on his theorems before
revealing them to the world. How many people are doing this today in our
publish-or-perish modern world of science?
It is not easy to acquire groundbreaking knowledge. Thanks to the
philosophers for reminding us of Kuhn’s work.

Have a nice week!

Plamen



> If further specifics are wanted or
> if specific articles are wanted, kindly contact m...@uoregon.edu
>
> (1). Instincts and/or feelings motivate animate organisms to move.
> Without such instincts or feelings there would be no disposition
> to move. An ‘animate organism’ would in truth be akin to a statue,
> a statue 

[Fis] _ Re: Fis Digest, Vol 25, Issue 3

[Dr. Plamen L. Simeonov]

Dear Rukhsan,

thank you for your kind message. Please leave the polite qualification
“Dr.’ We are all Drs here ;-)
Our minds are entangled. I just sent you and Lou a message privately,
because I think that the open FIS discussion on math was closed and we
should let the forum discuss the next topic on biosemiotics. Therefore here
only some final remarks to you and everyone who wishes to discuss these
issues: please feel free to contact me.


On Sat, Apr 2, 2016 at 10:23 AM, Rukhsanulhaq <rukhsanul...@gmail.com>
wrote:

> Dear Dr Plamen
> I find many common themes in your work and my approach
> to the foundational questions of physics mathematics and biology.
> I find integral biomaths approach very appealing and it fits very well
> with my understanding from quantum field theory approach to
> quantum matter.
>

That”s right. it is a good starting point and I am glad that there are some
voices defending QFT.
But they should know that physics and science are still in crisis today
(cf. Lee Smolin, for instance).


> I would like to know about the biologists who use Grassmann algebra.
> As regards your criticism about the quantum approach to biology my reply
> is that quantum theory shares the categorical structure with biology.
>

That’s right. But since we speak of mathematics, category theory is the
foundation for both and not the QT.


> In other
> words to see how quantum theory is related to biology we must realize
> that both quantum theory and biology have category theoretical formulations
> and hence both share the similar algebraic structures and hence the
> underlying
> philosophy is Whiteheadean process philosophy which has been discussed
> by authors like Henry Stapp.
>

I absolutely agree with this! That’s the right approach to the issue.


> I emphasize that one fundamental difference between classical mechanics
> and quantum
> mechanics is that the latter has scope of accommodating life and mind
> which is because
> of the reason that logical foundations of quantum theory are entirely
> different.
>

Yes, and it is not an accident that we are also trying to involve quantum
logic in addressing biological phenomena.
We can use the toolbox of QM, but we should not leave it there where it was
50 years ago.
I think we all agree that we need to develop our mathematical apparatus,
but this time from the viewpoint of the biological phenomena. Otherwise we
will stay puzzling at paradoxes like APR and don’t dare stepping beyond
them.


> I resonate
> here with Robert Rosen who has worked out the logic of biology and I find
> striking similarities
> between his work and quantum theory.
>

Yes. This is a good beginning, but he was also not perfect. Nobody is.
We need to develop such formalisms, but I also agree with Lou and others
that there is always some delta of the real world that is unformalisable.
Dealing with impredicativity is not the only issue we have to do in
biology. We learn this from the very moment we face real problems like
those in cancer research which I will try to address in my session.


> So it opens up a field of research where we
> need to use category theory to bring biology under the umbrella of quantum
> theory.
>

 I am not sure that QT is the ultimate theory of all things, but I think
the effort is worth doing it, since we hardly have anything else to step on
now.

I invite all those interested in this endeavor to join the hands!
>
> PLease refer me to the works about Grassmann algebra in biology.
>

It was a suggestion by a colleague and supporter, Edwin Brezina, who is no
more under us now, but I will do my best to find out what he was meaning.

Good luck to us all.

All the best.

Plamen



>
> Rukhsan
>
> On Fri, Apr 1, 2016 at 7:41 PM, <fis-requ...@listas.unizar.es> wrote:
>
>> Send Fis mailing list submissions to
>> fis@listas.unizar.es
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>> or, via email, send a message with subject or body 'help' to
>> fis-requ...@listas.unizar.es
>>
>> You can reach the person managing the list at
>> fis-ow...@listas.unizar.es
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Fis digest..."
>>
>>
>> Today's Topics:
>>
>>1. _ Re: Postface on math:  Fis Digest, Vol 24, Issue 46
>>   (Dr. Plamen L. Simeonov)
>>
>>
>> --
>>
>> Message: 1
>> Date: Fri, 1 Apr 2016 16:11:03 +0200
>> From: "Dr. Plamen L. Simeonov" <plamen.l.simeo...@gmail.com>
>> To: Rukhsanulhaq <rukhsanul...@gmail.co

Re: [Fis] concluding by beginning

[Dr. Plamen L. Simeonov]

 a kind of mitosis. To see this in
> more detail, here is a link to a page from a mathematica program written by
> LK that uses a 'blank' or 'unmarked state' instead of the '=" sign. Program
> and Output <https://dl.dropbox.com/u/11067256/RDL.pdf>. Elementary RD
> patterns are fundamental and will be found in many structures at all
> levels. To see an cellular automaton example of this phenomenon, look at
> the next link. Here we see a replicator in 'HighLife' a modification of
> John Horton Conway's automaton 'Life'. The Highlife Replicator follows the
> same pattern as our RD Replicator! We can begin to understand how the RD
> Replicator works. This gives a foundation for understanding how the more
> complex HighLife Replicator behaves in its context. HighLife Replicator.
> <https://en.m.wikipedia.org/wiki/Highlife_(cellular_automaton)> Finally,
> here is an excerpt from a paper by LK about replication in biology and the
> role of RD. Excerpt.
> <https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf>*
>
> *See RDLetter. <http://homepages.math.uic.edu/~kauffman/RDLetter.pdf> This
> is the Isaacson-Kauffman report on RD, summarized in a letter-to-the-editor
> of JSP, Vol. 4, No. 1, Spring 2015, directly accessed on this server.*
>
> *See Patent.
> <https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf>This is
> Joel Isaacson's patent document for RD.*
>
>
> *See Biological Replication.
> <https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf> This is a related
> paper by Kauffman.You see above a very simple distinction making/using
> automaton that produces a ‘cell’  ]O[ from an elementary distinction (of
> B from the background of equal A’s),and that this cell then undergoes
> mitosis. Then as an observer you must look again and note that the nothing
> that happens in this automaton is local. The cell happensbecause of the
> global structure of the one-dimensional automata space. The apparent
> splitting from the inside of the cell is actually a consequence of the
> global condition of the cell in the whole space. The entire evolution of
> the process is a repeated articulation of the distinctions that are present
> in the process. This isa new holistic modeling paradigm and we are
> exploring with simple examples the extent to which it will apply to more
> complex phenomena.A more extended paper by myself and Joel Isaacson will be
> available soon.Best,Lou Kauffman*
>
> On Mar 30, 2016, at 7:18 AM, Pedro C. Marijuan <pcmarijuan.i...@aragon.es>
> wrote:
>
> Sorry but the dancing time is over... maybe tomorrow or on Friday Lou
> could send some concluding comment, and next Monday Soeren would start the
> new part. The present Q. discussion can surface again during the coming
> session...
> best--Pedro
>
>
> El 30/03/2016 a las 1:06, Dr. Plamen L. Simeonov escribió:
>
> I think you are right, Lou, with respect to Deutsch who actually met
> Everett III with the multiple universe hypothesis. The sole name
> “constructor theory” invoked associations beyond the quantum frame in me,
> but he did not went that far. As for Josephson, I am not quite sure about
> his notion. Brian remains firmly on the quantum level in the papers I
> referred earlier, but he often returns to Ilexa Yarley”s “circular theory”
> which offers a much broader interpretation in my opinion. I expected your
> mentioning of (the vibrations of) “thought forms”, which are supposed to
> invoke the emergence of word and action. I welcome your understanding for
> the necessity of a deeper QM to make the links between actuality and the
> bounded potentiality more comprehensive.
>
> Best,
>
> Plamen
>
>
>
>
> On Wed, Mar 30, 2016 at 12:33 AM, Louis H Kauffman < <kauff...@uic.edu>
> kauff...@uic.edu> wrote:
>
>> Josephson and Deutsh are not ‘deeper than QM’. Deutsch for example is a
>> very literal interpretation of QM that says that all the trajectories in
>> the Feynman path sum are real, and they occur in parallel universes. This
>> is a nice mathematical way to think, but it is not deeper than present QM!
>> Energy is conserved, but ‘particles’ and indeed universes can be created
>> from vacuum. If we want to go to discussion of ‘holy spirit’ then one
>> should look at the structure of thought itself. For it is at the level of
>> thought that every concept has a life behind it. Every idea is real and
>> alive. Platonism asserts this directly in the belief in the existence of
>> form and this form is a living form that we interact with and we are. How
>> these notions are related to QM probably does await the emergence of a
>> deeper QM.
>>
>> On Mar 29, 2016, at 4:43 PM,

[Fis] _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Dr. Plamen L. Simeonov]

Thank you for your responses, Lou and Stan. I am aware about the details of
the autopoietic model. What I was actually addressing by the transition
from abiotic to biotic structures and the later emergence of RNA and DNA
was  this elusive aspect of “mass action” which Stan mentioned, that in my
opinion must have emerged out of the field of “triggered  (by resonance)
potentialities  which deeper theories than QM are trying to develop (cf.
Josephson and Deutsch mentioned earlier). This enigmatic emergence of
action out of nothing (vacuum or pure potentiality) naturally allows  the
(co-)existence of such  heretic ideas as the immaterial “Holy Spirit” or
Hans Driesch”s vitalism, Jean Sharon’s eternal electron, or “The Matrix of
Matter and Life”at the sub-Planckian scale. How about this possible link to
Platonism, theology, logic and algebra?

All the best,

Plamen

PS. I do not know why my notes appear twice on this list.



On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman <kauff...@uic.edu> wrote:

> This is a reply to Plamen’s comment about autopoeisis. In their paper
> Maturana,Uribe and Varela give a working model (computer model) for
> autopoeisis.
> It is very simple, consisting of a subtrate of nodal elements that tend to
> bond when in proximity, and a collection of catalytic nodal elements that
> promote bonding in their vicinity. The result of this dynamics is that
> carapaces of linked nodal elements form around the catalytic elements and
> these photo-cells tend to keep surviving the perturbations built into the
> system. This model shows that cells can arise from a very simple dynmamic
> geometric/topological substrate long before anything as sophisticated as
> DNA has happened.
>
> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe <ssal...@binghamton.edu>
> wrote:
>
> Plamen wrote:
>
>  I begin to believe that the transition from abiotic to biotic structures,
> incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
> matrix/”skeleton”/”programme” which has nothing in common with the nature
> of DNA, and that DNA and RNA as we know them today may have emerged as
> secondary or even tertiary “memory” of something underlying deeper below
> the microbiological surface. It is at least worth thinking in this
> direction. I do not mean necessarily the role of the number concept and
> Platonic origin of the universe, but something probably much more “physical”
>
>
>
> S: An interesting recently published effort along these lines is:
>
> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and
> Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences
> 12) Springer
>
> They seek a materialist understanding of biology as a system, attempting
> to refer to the genetic system as little as possible.
>
> I have until very recently attempted to evade/avoid mechanistic thinking
> in regard to biology, but, on considering the origin of life generally
> while keeping Howard Pattee's thinking in mind, I have been struck by the
> notion that the origin of life (that is: WITH the genetic system) was the
> origin of mechanism in the universe.  Before that coding system, everything
> was mass action.  I think we still do not understand how this mechanism
> evolved.
>
> STAN
>
> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>>
>> Dear Lou, Pedro and All,
>>
>>
>>
>> I am going to present a few opportunistic ideas related to what was said
>> before in this session. Coming back to Pivar’s speculative
>> mechano-topological model of life excluding genetics I wish to turn your
>> attention to another author with a similar idea but on a sound mathematical
>> base, Davide Ambrosi with his resume at
>> https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
>> :
>>
>> “Davide Ambrosi:
>>
>> A role for mechanics in the growth, remodelling and morphogenesis of
>> living systems  In the XX Century the interactions between mechanics in
>> biology were much  biased by a bioengineering attitude: people were
>> mainly interested in  evaluating the state of stress that bones and
>> tissues undergo in order to  properly design prosthesis and devices.
>> However in the last decades a new vision is emerging. "Mechano-biology" is
>> changing the point of view, with respect to "Bio-mechanics", emphasizing
>> the biological feedback. Cells, tissues and organs do not only deform when
>> loaded: they reorganize, they duplicate, they actively produce dynamic
>> patterns that apparently have multiple biological aims.
>>
>> In this talk I will concentrat

[Fis] On mathematical theories and models in biology

[Dr. Plamen L. Simeonov]

Dear Lou, Pedro and All,



I am going to present a few opportunistic ideas related to what was said
before in this session. Coming back to Pivar’s speculative
mechano-topological model of life excluding genetics I wish to turn your
attention to another author with a similar idea but on a sound mathematical
base, Davide Ambrosi with his resume at
https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
:

“Davide Ambrosi:

A role for mechanics in the growth, remodelling and morphogenesis of living
systems  In the XX Century the interactions between mechanics in biology
were much  biased by a bioengineering attitude: people were mainly
interested in  evaluating the state of stress that bones and tissues
undergo in order to  properly design prosthesis and devices. However in the
last decades a new vision is emerging. "Mechano-biology" is changing the
point of view, with respect to "Bio-mechanics", emphasizing the biological
feedback. Cells, tissues and organs do not only deform when loaded: they
reorganize, they duplicate, they actively produce dynamic patterns that
apparently have multiple biological aims.

In this talk I will concentrate on two paradigmatic systems where the
interplay between mechanics and biology is, in my opinion, particularly
challenging: the homeostatic stress as a driver for remodeling of soft
tissue and the tension as a mechanism to transmit information about the
size of organs during morphogenesis. In both cases it seems that mechanics
plays a role which at least accompanies and enforces the biochemical
signaling.”





Some more details about this approach can be found here:

http://rsta.royalsocietypublishing.org/content/367/1902/3335

http://biomechanics.stanford.edu/paper/MFOreport.pdf

In other words, for the core information theorists in FIS, the question is:
is there really only (epi)genetic evolution communication in living
organisms. Stan Salthe and Lou Kauffman already provided some answers. I
begin to believe that the transition from abiotic to biotic structures,
incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
matrix/”skeleton”/”programme” which has nothing in common with the nature
of DNA, and that DNA and RNA as we know them today

http://www.sciencedirect.com/science/article/pii/S0022519314006778

http://www.sciencedirect.com/science/article/pii/S0022519316001260

https://www.sciencedaily.com/releases/2015/01/150107101405.htm

may have emerged as secondary or even tertiary “memory” of something
underlying deeper below the microbiological surface. It is at least worth
thinking in this direction. I do not mean necessarily the role of the
number concept and Platonic origin of the universe, but something probably
much more “physical” or at least staying at the edge between
physical/material and immaterial such as David Deutsch’s constructor theory
(http://constructortheory.org/) and Brian Josephson’s “structural/circular
theory” (http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf;
http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf;
http://arxiv.org/pdf/1108.4860.pdf) searching for the theories underpinning
the foundations of the physical laws (and following Wheeler’s definition
for a “Law without Law”.

Some of you may say that QT and Gravitation Theory are responsible for such
kind of strange effects, but I would rather leave the brackets open,
because the recent discussion about potentialities and actualities in QM
brings up the idea that there are still different ways of looking at those
concepts (although they are strictly defined in their core domains). This
was actually also the lesson from the last special issue on integral
biomathics (2015) dedicated to phenomenology, with the different opinions
of scientists and philosophers on obviously clear matters in their domains.
This is why also the question of what we define as science needs to be
probably revised in future to include also such issues that are “felt”
rather than “reasoned”, even if we do not have the “proofs” yet, because
the proofs also emerge as subjective (or perhaps “suggested”! – ask the
psychologists for that aspect) thoughts in the minds of the mathematicians.
I am really glad that we began such a phenomenological discussion on this
aspect such as Hipolito’s paper (
http://www.sciencedirect.com/science/article/pii/S0079610715000899) that
was widely commented in the reviewer’s circle. In many cases when we have a
“fuzzy” intuition about a certain relationship or analogy we miss the
correct definitions and concepts, and so in a creative act to hold down the
flying thought we move to using examples, metaphors, pictures. Pedro
correctly addressed the explanatory problem of science which presupposes a
certain causative and predicative “workflow” to derive a conclusion from
the facts, and this is the way in which also proofs are (selectively) made.
As a young scholar I often wondered how artificially people like Gauss,
Cauchy and 

Re: [Fis] SYMMETRY & _ On BioLogic

[Dr. Plamen L. Simeonov]

Dear Lou and Colleagues,

yes, I agree: an artistic approach can be very fruitful. This is like what
Stuart Kauffman says about speaking with metaphors. At some point our
mathematical descriptive tools do not have sufficient expressional power to
grasp more global general insights and we reach out to the domains of
narration, music and visualisation for help. And this is the point where
this effort of reflection upon a subject begins to generate and develop new
expressional forms of mathematics (logics, algebras, geometries). I think
that you and Ralph Abraham noted this in your contributions about the
mystic of mathematics in the 2015 JPBMB special issue. Therefore I ask
here, if we all feel that there is some grain of imaginative truth in the
works of Pivar and team, what piece of mathematics does it needs to become
a serious theory. Spencer-Brown did also have similar flashy insights in
the beginning, but he needed 20+ years to abstract them into a substantial
book and theory. This is what also other mathematicians do. They are
providing complete works. Modern artists and futurists are shooting fast
and then moving to the next “inspiration”, often without “marketing” the
earlier idea. And then they are often disappointed that they were not
understood by their contemporaries. The lack of They are often arrogant and
do not care about the opinion of others like we do in our FIS forum. But
they often have some “oracle” messages. So, my question to you and the
others here is: Is there a way that we, scientists, can build a solid
theory on the base of others' artistic insights? Do you think you can help
here as an expert in topology and logic to fill the formalisation gaps in
Pivar’s approach and develop something foundational. All this would take
time and I am not sure if such artists like Pivar would be ready to
participate a scientific-humanitarian discourse, because we know that most
of these talents as extremely egocentric and ignorant and we cannot change
this. What do you think?

Best,

Plamen




On Thu, Mar 17, 2016 at 8:09 AM, Louis H Kauffman <lou...@gmail.com> wrote:

> Dear Plamen,
> I do not know why Gel-Mann supported this. It is interesting to me anyway.
> It is primarily an artistic endeavor but is based on some ideas of visual
> development of complex forms from simpler forms.
> Some of these stories may have a grain of truth. The sort of thing I do
> and others do is much more conservative (even what D’Arcy Thompson did is
> much more conservative). We look for simple patterns that definitely seem
> to occur in complex situations and we abstract them and work with them on
> their own grounds, and with regard to how these patterns work in a complex
> system. An artistic approach can be very fruitful.
> Best,
> Lou
>
> On Mar 16, 2016, at 9:43 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
> Dear Lou, Pedro and Colleagues,
>
> I have another somewhat provoking question about the "constructive" role
> of topology in morphogenesis. What do you think about the somewhat
> artistic, but scientifically VERY controversial theory about the origin and
> development of life forms based on physical forces from classical mechanics
> and topology only, thus ignoring all of genetics, Darwinism and Creationism:
>
> http://www.ilasol.org.il/ILASOL/uploads/files/Pivar_ILASOL-2010.pdf
>
> What part of this can be regarded as science at all, and If there is
> something missing what is it? Why did a person like Murray Gel-Mann support
> this?
>
>
> Best
>
> Plamen
>
> 
>
>
> On Tue, Mar 15, 2016 at 12:00 PM, Pedro C. Marijuan <
> pcmarijuan.i...@aragon.es> wrote:
>
>> 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 

Re: [Fis] _ On BioLogic

[Dr. Plamen L. Simeonov]

Thank you, Lou.

On Wed, Mar 9, 2016 at 8:24 PM, Louis H Kauffman <lou...@gmail.com> wrote:

> Dear Plamen,
> I will make comments in the text.
> Best,
> Lou
>
> On Mar 9, 2016, at 7:21 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
> Dear Lou,
>
> thank you for your response.
>
> On Wed, Mar 9, 2016 at 9:53 AM, Louis H Kauffman <lou...@gmail.com> wrote:
>
>> Dear Plamen,
>> I suspect that what you would like to know about ‘distinction logic’ is
>> how distinctions arise in natural systems.
>> I would like to know more about this also!
>>
>
> I suspect Spencer-Brown has beeen working on this too.
>
>
> LK. We all work on this. But recall that Laws of Form begins “We take a
> given the idea of distinction and the idea of indication and that one
> cannot have and indication without drawing a distinction. We talk therefore
> the form of distinction for the form.”. This sentence, as Heinz von
> Foerster noted in his review of Laws of Form, cuts through 2000 years of
> semantic weeds.
> There is no conversation, no thought without distinction, without form.
> And yet we containually try to create a theory of the emergence of form.
> Each such theory is structured by the basic distinctions with which it
> begins.
>

"Let there be light."


>
>
>
>> One can imagine that complex interactions can under appropriate
>> circumstances lead to dynamic closed loops of interaction and even
>> concomitant spatial distinctions (in the eye of an observer of the system).
>> Such patterns would be the subject of a distinction logic or a logic of
>> distinctions for that observer. There is the related question of how
>> observers can arise but this is looped around with the first question. The
>> two questions are linked with one another and one can imagine that systems
>> that produce partly stable looping processes can begin to create naming and
>> reference.
>>
>
> This sounds intriguing. Does not this go into biosemiotics?
>
> LK. I suppose it does go into biosemiotics, and also it is related to the
> work of Stuart Kauffman. I am thinking about it in an elemental way. That
> large scale patternings that lead to partially stable recursive structures
> will lead internally to the development of the apparently infinitely clever
> devices we see in evolution. We see this in the exploration of spaces of
> rules and actions of simple structures like cellular automata.
>

Stu was also invited to this session. I hope he will be also able to tell
something. He recently mentions the role of metaphors in our informal
narrative description of the world. By using them we can flash “light”,
i.e. sweeping distinctions, nut the problem is that they are
language-dependent / anthropocentric and cannot always capture the
associations in one’s mind. Do you think there could be a formal way, a
categorisation of basic metaphoric notions?

>
>
>> If they can do that, they will not be far from self-reference. Exactly
>> how this could be done is a mystery. But that it happens is evident in the
>> biological world.
>>
>
> So we come back to the old Searle thesis about self-reference?
>
> https://halshs.archives-ouvertes.fr/ijn_00089222/document
>
>  LK. Hmm… I will have to look at Searle’s assertions about self ref. What
> I mean is that if a system can name processes then it can find a name for
> its own process of naming.
>
> LK. When it does this, it has found the linguistic I. “I am the one who
> says I.”  I am the one who makes names and reference.” “I name myself I.”
> “I am that I am."
>
>
>> On the other hand you may be interested in the simplicities of the
>> calculus of indications or variations of that. I would be happy to talk
>> about that. When I do it is at the level of human observer and our mutual
>> abilities to distinguish, agree and disagree.
>>
>
> I see. This is the level of the scientist.
> This should be doable. Self-referential microbes are out of question for
> the moment.
>
> LK. Maybe maybe now. The Spencer-Brown Mark refers to itself since it
> refers to any distinction and it is itself seen to be a distinction by the
> observer who is him or her self a Mark.
> So is the microbe, but just how doth the microbe make observations. Answer
> through its interactions. And so … We must reflect on this.
>

This is interesting. So, it should be possible to develop a formal "virus
theory" that interacts with the external world (icl. human beings) from the
viewpoint of the virus, right?

Best,

Plamen.

>
>> On Mar 9, 2016, at 1:10 AM, Dr. Plamen L. Simeonov <
>> plamen.l.simeo...@gmail.com> wrote:

[Fis] _ Re: _ On BioLogic

[Dr. Plamen L. Simeonov]

Dear Lou,

thank you for your response.

On Wed, Mar 9, 2016 at 9:53 AM, Louis H Kauffman <lou...@gmail.com> wrote:

> Dear Plamen,
> I suspect that what you would like to know about ‘distinction logic’ is
> how distinctions arise in natural systems.
> I would like to know more about this also!
>

I suspect Spencer-Brown has beeen working on this too.


> One can imagine that complex interactions can under appropriate
> circumstances lead to dynamic closed loops of interaction and even
> concomitant spatial distinctions (in the eye of an observer of the system).
> Such patterns would be the subject of a distinction logic or a logic of
> distinctions for that observer. There is the related question of how
> observers can arise but this is looped around with the first question. The
> two questions are linked with one another and one can imagine that systems
> that produce partly stable looping processes can begin to create naming and
> reference.
>

This sounds intriguing. Does not this go into biosemiotics?


> If they can do that, they will not be far from self-reference. Exactly how
> this could be done is a mystery. But that it happens is evident in the
> biological world.
>

So we come back to the old Searle thesis about self-reference?

https://halshs.archives-ouvertes.fr/ijn_00089222/document



>
> On the other hand you may be interested in the simplicities of the
> calculus of indications or variations of that. I would be happy to talk
> about that. When I do it is at the level of human observer and our mutual
> abilities to distinguish, agree and disagree.
>

I see. This is the level of the scientist.
This should be doable. Self-referential microbes are out of question for
the moment.

Thanks!

Plamen




> Best,
> Lou
>
> On Mar 9, 2016, at 1:10 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>
> Dear Lou, Pedro and Colleagues,
>
>
> I think that Pedro made an interesting comment suggesting an extension of
> Lou’s original model that another sort of recursion can be injected from
> the outside world in terms of multiple nested loops of action. That the
> species (r)evolution was accelerated and “harmonized” via “cross-cultural”
> exchange of DNA segments invoked by viruses is a known fact now. It also
> changes to some extent the meaning of infection diseases from something
> “bad” to fight into a sort of necessary symbiosis for the co-evolution of
> the system Earth/Cosmos. So, it makes sense to think and ask whether by
> creating more and more artificial drugs and vaccines against infections we
> do not intervene in the mutation of viruses in a way that cannot be
> regarded as response-able, because of also being too reductionistic with
> respect to what are the consequences for both ourselves and the BIG unknown
> ecosystem outside our bodies. I am curious to know what do you think about
> the option to try integrating Turing Oracle Machines in such extended
> recursive models of living systems, which integrate viruses in the
> evolutionary loop. This idea was suggested in the course of our integral
> biomathics discussions in the past. In other words, what do you think about
> linking a formal biomathematical representation and a biocomputation
> responsive mechanism in maintaining an autonomous biologic? Perhaps we need
> multiple layers of abstraction, i.e. multiple  biologics, and not only the
> bimolecular and cellular ones. And also, do you think there are other
> mechanisms for information transfer, e.g. in prokaryotic cells and archaea,
> also addressing the principles of circularity and recursion?
>
>
> Another question I have is ignited from Pedro’s reflections upon your
> circularity model for reproduction and directed to both of you. If
> biological “clocks” such as the circadian rhythm are the result of an
> evolutionary impressed repetition of action, are they the carrier or the
> carried, or perhaps both, and if so how does this come into being? I recall
> a paper by Koichiro Matsuno in the former 2013 IB special issue “Making
> Biological Theory More Down to Earth” which said something interesting
> about the role of cycles in maintaining identity and life, also from the
> phenomenological perspective concerning the distinction between self and
> outer world. Here is where I’d like to learn more about the distinction
> logic like Pedro.
>
>
> Thank you.
>
>
> All the best.
>
>
> Plamen
>
>
> 
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] _ On BioLogic

[Dr. Plamen L. Simeonov]

Dear Lou, Pedro and Colleagues,



I think that Pedro made an interesting comment suggesting an extension of
Lou’s original model that another sort of recursion can be injected from
the outside world in terms of multiple nested loops of action. That the
species (r)evolution was accelerated and “harmonized” via “cross-cultural”
exchange of DNA segments invoked by viruses is a known fact now. It also
changes to some extent the meaning of infection diseases from something
“bad” to fight into a sort of necessary symbiosis for the co-evolution of
the system Earth/Cosmos. So, it makes sense to think and ask whether by
creating more and more artificial drugs and vaccines against infections we
do not intervene in the mutation of viruses in a way that cannot be
regarded as response-able, because of also being too reductionistic with
respect to what are the consequences for both ourselves and the BIG unknown
ecosystem outside our bodies. I am curious to know what do you think about
the option to try integrating Turing Oracle Machines in such extended
recursive models of living systems, which integrate viruses in the
evolutionary loop. This idea was suggested in the course of our integral
biomathics discussions in the past. In other words, what do you think about
linking a formal biomathematical representation and a biocomputation
responsive mechanism in maintaining an autonomous biologic? Perhaps we need
multiple layers of abstraction, i.e. multiple  biologics, and not only the
bimolecular and cellular ones. And also, do you think there are other
mechanisms for information transfer, e.g. in prokaryotic cells and archaea,
also addressing the principles of circularity and recursion?



Another question I have is ignited from Pedro’s reflections upon your
circularity model for reproduction and directed to both of you. If
biological “clocks” such as the circadian rhythm are the result of an
evolutionary impressed repetition of action, are they the carrier or the
carried, or perhaps both, and if so how does this come into being? I recall
a paper by Koichiro Matsuno in the former 2013 IB special issue “Making
Biological Theory More Down to Earth” which said something interesting
about the role of cycles in maintaining identity and life, also from the
phenomenological perspective concerning the distinction between self and
outer world. Here is where I’d like to learn more about the distinction
logic like Pedro.



Thank you.



All the best.



Plamen



___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] _ Closing the Session with Maxine Sheets-Johnstone

[Dr. Plamen L. Simeonov]

Dear Maxine and Colleagues,

thank you for your responses and agile responses in the second week of the
schedule.
I wish to announce that we are about closing the session on Maxine's theme
soon and move to the next presenter, Louis H. Kauffman with the following
annotations as follows.



On Tue, Mar 1, 2016 at 12:01 AM, Maxine Sheets-Johnstone 
wrote:

> To FIS Colleagues,
>
> There are common threads running through communications from Mark, Loet,
> Jerry, and Marcus that I would like to address. I thank them for their
> concerns and the issues they raise. I thank Plamen too for his response,
> specifically for upholding the value of phenomenology, though disagreeing
> with him in his giving prominence to Merleau-Ponty as a phenomenologist. I
> would like to comment on that point of disagreement first.
>

I am glad abou this disagreement, Maxine, since it demonstrates again what
is phenomenology all about. (Fortunately I was not the author of the
extended special issue CFP. It was one of my-coeditors.) Diverging opinions
are something normal in the humanity disciplines. They are not trimmed into
searching the absolute truth or measuring and mapping the real world
outside, but instead into explaining the diverse nuances of the inner self,
which is of course very subjective and therefore ignored by science.
However without this differences and subjectivity we would not be human
beings at all. As a matter of fact scientists are also a subclass of this
group and when doing research they cannot completely escape subjectivity.
This is so to say, the other side of the Moon and the "whole truth" we are
trying to see with one eye, but alas Therefore, I can understand both
sides, the defenders of the novelty role of Merleau-Ponty for philosophy
and the opponents. Each side can certainly deliver its pro and contra
arguments. I think that even if Merleau-Ponty may not be seen as
phenomenologists by some members of this group, his works on the ontology
of the flesh, on the phenomenology and primacy of perception, the visible
and invisible, etc. can be classified as such according to Stanford's
Encyclopedia of Philosophy
http://plato.stanford.edu/entries/self-consciousness-phenomenological/. Of
course, he might be categorized to be just an interesting author like J.
Anker Larson or Leo Tolstoi or even a journalist for the lack of a
phenomenological methodology. But he certainly was a reformer, an unusual
one. So, just as in many other fields of humanities we are allowed to
maintain different opinions about him.

Closing all this I wish to cordially thank Maxine and you all for your
participation, questions, responses and opinions in this first session. I
do hope that Maxine was able to obtain some iteresting feedback from the
FIS community that can become a gain for her research, and vice versa, that
the FIS members were able to learn somenthing new and different from Maxine
that will extend the horizon of their research. All this is about beginning
and maintaining a dialogue between the different camps of scientists and
philosophers targeting mutual understanding (at least to a certain degree)
with the purpose to  advance research on both sides. I hope you have
enjoyed the discourse. Please send me your questions directly, if any. I am
going to hand-over to Pedro who will introduce the next presenter.

With best wishes,

Plamen
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] _ Just my two cents worth.

[Dr. Plamen L. Simeonov]

Dear Jerry, Maxine, Marcus and All,

I will come back later on discussing this interesting issue because, I have
a major project deadline by tomorrow.
But let me just give you this link to educate you on what Phenomenological
Philosophy is really about:
http://ibiomath.org/on-phenomenological-philosophy/
It was provided to explain the domain of the special issue  to natural
scientists as an extended CFP (s. link below), which Maxine contributed to.

One more thing about Husserl: Have you ever tried to read and understand
his over 100 years notes?
Believe me, no matter how old they are, there is still something to
discover there.
The same holds for C.S. Pierce, William James and others of that size.
What is novelty of archaeology and palaeontology then?
Just digging in the dust??? All these people are discovering new facts
about the past.
The result is restructuring of our present and correcting the view about
the future.
Even if microbiology was not known at the time of Husserl, it can be seen
with other eyes from the perspective of phenomenological philosophy now.

Have a nice day.

Best,

Plamen



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

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




On Mon, Feb 29, 2016 at 12:10 AM, Jerry LR Chandler <
jerry_lr_chand...@me.com> wrote:

> Maxine, List:
>
> Just my two cents worth.
> After puzzling about the potential connections between your
> interpretations of Husserl and evolutionary biology, I remain uncertain
> about where this line of reasoning starts and where it leads.
>
> I should say at the beginning that I am a hardcore realist and a
> pragmatist. The value of vague philosophies for doing science is
> problematic, in my opinion.  The value of the philosophy of mathematics can
> be quite useful for scientific practice, if the appropriate correspondence
> relations can be symbolized and exploited. The necessity for rigorous
> symbolic relations between the meta-languages of science and logic of the
> sciences is well known.  (See Malatesta, The Primary Logic, 1999?).
>
> Husserl’s (1859-1938)  writings are about a Century old.  What does he
> bring to the table today?
>
> Molecular biology barely existed in his day.
>
> In this context, the concept of oscillators is proposed as the linkage
> between movement and mathematical modeling.  Yet, the physical basis of the
> mathematical oscillators is Hook’s Law for springs.  The mental image for a
> two dimensional network of oscillators is a the old-fashioned
> “bed-spring”.  Admittedly, a hypothetical oscillator model was used for a
> few decades to model the source of epileptic seizures, but it is so crude
> that it is hardly more than a metaphor.  (For a review, NeuroQuantology |
> June 2006 | Vol. 4 | Issue 2 | 155-165 155 Velazquez JLP. Coupled
> oscillators field
>
>
> Molecular biology requires the use of the atomic numbers in arithmetic
> operations.
> It further requires the use of three - dimensional asymmetric structures
> to describe handedness (even for dance!).
>
> These two facts suggest to me that Husserlian vagueness can be improved
> upon in the modern inquiry into the conceptualization of motion and its
> relationships to evolutionary biology.
>
> A different line of reasoning concerns the questions raised by Pedro.
> That is, the cultural roots of the tremendous array of dance movements and
> the encoding of ballad movements into a symbol system.
> This issue raises the far wider issue of the roles of diagrammatic logic
> in relation to dance “logic”.  Has anyone explored how the diagrammatic
> logic of CS Peirce may relate to dance?  Or even Venn diagrams?  Or how are
> the diagrams of chemical logic related to dance symbols, if at all?  Or,
> should we follow Hilbert and simply ignore the role of diagrams in the
> mathematics of evolutionary biology.  (see: Greaves, The Philosophical
> Status of Diagrams (2001))
>
> Another topic worth exploring is the communication among ballad dancers
> during a performance.  The range of emotions exhibited during a ballad
> performance can be truly spectacular.  How is this accomplished from an
> informational theory perspective?
>
> Thus, I would close with a question:
> Does the modern state of human communication and information exchange go
> far beyond early 20th Century German Philosophy?  An essay on either
> Kantian or Shelling’s philosophy, as contrasted with Husserl, could be of
> substantial interest to me.
>
> Cheers
>
> Jerry
>
> Research Professor
> Krasnow Institute for Advanced Studies
> GMU
>
> Headwater House
> On the Banks of the Mississippi
>
>
>
>
>
>
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> 

[Fis] Introduction of the First Contribution to the discussion session “Phenomenology, Life, and Information Science"

[Dr. Plamen L. Simeonov]

Dear FIS Colleagues,

The new discussion session "Phenomenology, Life, and Information Science"
is the interactive continuation of the recently published

2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics
and Phenomenological Philosophy
<http://www.sciencedirect.com/science/journal/00796107/119/3>



(with free access to all articles, incl. those of the following 5
presenters until July 19th, 2016).



The announcement is here: http://fis.sciforum.net/fis-discussion-sessions/



As Pedro already mentioned, it is planned to continue for about three
months (ending around May 30th), with 2-3 weeks devoted to each theses.
Most of the authors of this volume and from a few related projects are
joining the FIS list for this series of discussions in the following weeks.


All participants are encouraged to provide their feedback to the
presenters. Please take care to make thorough and concise statements when
commenting and inquiring about details of the authors’ theses, while
limiting to the FIS customary *two messages per week*. Depending on the
intensity of the exchange traffic a limit of one message per week per user
may be established. The responses of the presenters and the moderators are
the only exceptions according to the FIS rules. For those who are new in
the FIS community I strongly recommend to explore the web site
http://fis.sciforum.net before the discussion.

Here is again the list of contributors for the particular fields:

- Maxine Sheets-Johnstone: from Biology

- Louis H. Kauffman: from Mathematics

- Soeren Brier: from Bio/Cybersemiotics

- Alex Hankey: from Physics

- Plamen L. Simeonov: with a challenging subject in integrative medicine

I am going to moderate the discussions along with Pedro.



We will start now with *Maxine Sheets-Johnstone*’s theme “*Phenomenology
and Evolutionary Biology*”. She is an interdisciplinary scholar affiliated
with the Department of Philosophy at the University of Oregon where she
taught periodically in the 1990s and where she now holds an ongoing
Courtesy Professor appointment. She has a B.A. in French and Comparative
Literature, an M.A. in Dance, a Ph.D. in Dance and Philosophy, and an
incomplete second doctorate in Evolutionary Biology. Maxine began her
career as a choreographer/dancer, professor of dance/dance scholar. She has
published near 80 articles in humanities, science, and art journals. Her
book publications include The Phenomenology of Dance; Illuminating
Dance: Philosophical
Explorations; the “roots” trilogy: The Roots of Thinking, The Roots of
Power: Animate Form and Gendered Bodies, and The Roots of Morality; Giving
the Body Its Due; The Primacy of Movement; The Corporeal Turn: An
Interdisciplinary Reader; Putting Movement Into Your Life; A Beyond Fitness
Primer, and (forthcoming 2016) Insides and Outsides: Interdisciplinary
Perspectives on Animate Nature. She was awarded a Distinguished Fellowship
at the Institute of Advanced Study at Durham University, UK, in 2007 for
her continuing research on xenophobia, an Alumni Achievement Award by the
School of Education, University of Wisconsin in 2011, and was honored with
a Scholar’s Session by the Society of Phenomenology and Existential
Philosophy in 2012.



Maxine, you have the word.



@All: Enjoy your discussion.




Best regards


Plamen

__ ___ ___

Dr. Plamen L. Simeonov
mobile:   +49.17.37.81.63.37
URLs:   www.simeio.org / LinkedIn <http://lnkd.in/aqn39k>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Focused EC Funding Calls on Future and Emerging Technologies

[Dr. Plamen L. Simeonov]

Dear Colleagues,

a former colleague and EC research officer asked me to disseminate the
following information for upcoming EC funding calls that might be of
particular interest for you. Please feel free to forward this information
further in your social networks.

Have a nice weekend.

All the best.

Plamen


__ ___ ___

Dr. Plamen L. Simeonov
<http://lnkd.in/aqn39k>


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)




There is an open call on EC FET Proactive with a couple of themes that seem
very relevant for "adventurous communities":


*Being human in a technological world* see
https://ec.europa.eu/futurium/en/content/being-human-technological-world

*Intra- and inter-cell bio-technologies* see
https://ec.europa.eu/futurium/en/content/intra-and-inter-cell-bio-technologies

*Bio-electronic medicines and therapies* see*
https://ec.europa.eu/futurium/en/content/bio-electronic-medicines-and-therapies
<https://ec.europa.eu/futurium/en/content/bio-electronic-medicines-and-therapies>*

*Cognitive neuro-technologies* see
https://ec.europa.eu/futurium/en/content/bio-electronic-medicines-and-therapies



The full topic description is here: *FET Proactive call
<http://ec.europa.eu/research/participants/portal/desktop/en/opportunities/h2020/topics/2217-fetproact-01-2016.html>.
*


These can be great and thoroughly interdisciplinary projects that will
serve as a future reference to the field ('lighthouse projects', 4 to 10
Million and up to 5 years, not meaning that they require large consortia).
There are just two months to go the deadline (April 12).
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Free Promotional Access to all articles in the 2015 JPBMB Special Issue on Integral Biomathics

[Dr. Plamen L. Simeonov]

Dear All,

I have some good news for you. Elsevier allowed us to disseminate *the link
to all articles* of the 2015 JPBMB special issue for *free promotional
access* in our social community networks that will be available for 6
months *until July 19th 2016*. Please feel free to distribute this link

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


and enjoy your reading!


With my best wishes for 2016!

Yours,

Plamen
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] JPBMB 2015 SI on Integral Biomathics: 3 free articles and reference link at ScienceDirect

[Dr. Plamen L. Simeonov]

Dear Colleagues,

I would like to share with you three out of 41 contributions to the 2015
Special Issue on Integral Biomathics focused on Life Sciences, Mathematics
and Phenomenological Philosophy
<http://www.sciencedirect.com/science/journal/00796107/119/3>. They are
published in the Elsevier Journal Progress in Biophysics and Molecular
Biology (JPBMB), Volume 119, Issue 3:

   1. *“Editorial”: *http://authors.elsevier.com/a/1SHN~I6VGOrAK,


   1. *“Yet another time about time… Part I: An Essay on the Phenomenology
   of Physical Time”*: http://authors.elsevier.com/a/1SAT6I6VGOr75,


   1. *“Integral Biomathics Reloaded: 2015”*:
   http://authors.elsevier.com/a/1SHN~I6VGOrAb.

The articles are available for* free access until February 16th, 2016*.
Please feel free to distribute the links to your community circles.

The entire list of contributions to this special issue can be downloaded
here
<http://www.simeio.org/pages/details/papers/presentations/JPBM_SI_IB_119_3_TOC.pdf>
.

I wish you a peaceful and successful New Year 2016!

Plamen L. Simeonov


__ ___ ___

Dr. Plamen L. Simeonov
mobile:   +49.17.37.81.63.37
landline: +49.30.83.21.20.70
fax/ums: +49.30.48.49.88.26.4

___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Answer to Mark. Phenomenology and Speculative Realism

[Dr. Plamen L. Simeonov]

Dear colleagues,

I think that this discussion about phenomenology, or better said
phenomenological philosophy, is essential, but may go in the wrong
direction. As for the common grounds that Loet addressed in his note, I
assume that some of us are continuing the path of Varela’s naturalisation
of phenomenology. If you are a bit patient, you can see the results of our
effort in this direction by the end of the year:

http://www.journals.elsevier.com/progress-in-biophysics-and-molecular-biology/call-for-papers/special-theme-issue-on-integral-biomathics-life-sciences-mat/

This special volume is a collection of 41 papers discussing the aspects of
phenomenological philosophy in mathematics, physics, biology and
biosemiotics, incl. FIS contributors (Marijuan, Matsuno, Marchal, Goranson)
and other prominent scientists representing their fields.

I suggest to continue this discussion next year on the grounds of this
volume.

Best wishes,

Plamen



On Sun, Aug 2, 2015 at 9:09 AM, Loet Leydesdorff l...@leydesdorff.net
wrote:

 Dear colleagues,



 Without wishing to defend Husserl, let me try to formulate what is
 according to my knowledge core to his contribution. The message is that the
 transcendental intersubjectivity is phenomenologically present in our
 reality. He therefore returns to Descartes' (much rejected) distinction
 between *res extensa* and *res cogitans*. Intersubjectivity is *res
 cogitans*. It is not being like in the Latin *esse*, but it remains
 reflexively available. Thus, we cannot test it. The philosophy of science
 which follows (in *The Crisis*) is anti-positivistic. The
 intersubjectivity is constructed and we live in these constructions.



 Descartes focused on the subjective *Cogito*. According to him, we meet
 in the doubting, the Other as not limited and biologically constrained,
 that is, God or the Transcendency. Husserl shifts the attention to the
 *cogitatum*: that about what we are in doubt. We no longer find a hold in
 Transcendency, but we find the other as other persons. Persons relate to
 one another not only in being, but also in terms of expectations. This
 was elaborated as dual contingency (among others, by Parsons). The
 dynamics of inter-personal expectations, for example, drive scholarly
 discourses, but also stock exchanges.



 Alfred Schutz was a student and admirer of Husserl, but he did not accept
 the Cartesian duality implied. He writes: As long as we are born from
 mothers ... He then developed sociological phenomenology (Luckmann and
 others), which begins with the meta-individual phenomena. This is close to
 Mannheim's position: one cannot analyze the content of the sciences
 sociologically, but only the manifestations. The strong program in the
 sociology of science (SSK: sociology of scientific knowledge) positioned
 that socio-cognitive interests can explain the substantive development of
 the sciences (Bloor, Barnes, and others) in the 1970s. It returns to a kind
 of materialism.



 Luhmann criticized Husserl for not taking the next step and to consider
 meaning (*Sinn*) as constructed in and by communication. In my opinion,
 this is an important step because it opens the realm of a communication
 theory based on interhuman interactions as different from basing theories
 (micro-foundationally) on human agency (e.g., the *homo economicus* or
 agent-based modelling). The communications can be considered as first-order
 attributes to agents; the analysis of communications is in terms of
 second-order attributes; for example, codes of communication. This is very
 much the domain of the information sciences (although Luhmann did not see
 this connection).



 In sum, “phenomenological” is sometimes used as an appeal to return to the
 phenomena without invoking explaining principles *a priori*. The
 question, however, remains whether our intuitions, imaginations, etc. are
 also part of this “reality”. Are they limited (constrained; enabled?) by
 material conditions or epi-phenomenological consequences of them? Husserl’s
 critique of the modern sciences was the reduction of the very concept of
 “reality” to *res extensa* (that what “is”). Derivatives of *esse* such
 as ontology dominate the scene. Shannon-type information, however, is the
 *expected* uncertainty in a distribution. Thus, we stand on common ground
 that does not exist. J



 Note that this discussion is different from the one about “being” versus
 “becoming” (Prigogine), but also shares some aspects with it. Is
 “life”/biology considered as a monad different from physics that studies
 “nature” as a given? How can one perhaps distinguish scientific domains in
 these terms?



 Best,

 Loet





 -Original Message-
 From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Robert E.
 Ulanowicz
 Sent: Sunday, August 02, 2015 1:04 AM
 To: Joseph Brenner
 Cc: fis
 Subject: Re: [Fis] Answer to Mark. Phenomenology and Speculative Realism



 Dear Joseph et al.,



 I'm afraid I can't 

Re: [Fis] Reminder: CFP for Special Issue on Integral Biomathics

[Dr. Plamen L. Simeonov]

Dear Colleagues,

I wish to remind you that the abstract submission deadline for our latest
call for papers dedicated to Life Sciences, Mathematics and Philosophical
Phenomenology is 15. January 2015:
http://www.journals.elsevier.com/progress-in-biophysics-and-molecular-biology/call-for-papers/special-theme-issue-on-integral-biomathics-life-sciences-mat/

Please pay attention to the new Note for Authors.
We look forward to your interesting contributions.
With best wishes,
__ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile:  +49.17.43.56.41.75
email:pla...@simeio.org
URL:  www.simeio.org / LinkedIn http://lnkd.in/aqn39k


2015 CFP JPBMB Special Issue on Integral Biomathics:
Life Sciences, Mathematics and Phenomenological Philosophy
http://www.journals.elsevier.com/progress-in-biophysics-and-molecular-biology/call-for-papers/special-theme-issue-on-integral-biomathics-life-sciences-mat/
http://ibiomath.org/2015-cfp/; http://www.inbiosa.eu
.

2013 JPBMB SI IB
http://www.sciencedirect.com/science/journal/00796107/113/1

2012 Integral Biomathics: Tracing the Road to Reality
http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-642-28110-5


___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Fwd: CFP Special issue of JPBMB on Integral Biomathics: Life Sciences, Mathematics, and Phenomenological Philosophy

[Dr. Plamen L. Simeonov]

. Series on Knots and Everything. Volume 18. ISBN-10: 9812835814;
ISBN-13: 978-9812835819.

[6] Heidegger, M. 1927. *Sein und Zeit* (Tübingen): Niemeyer. 19. Aufl.
(2006), ISBN-10: 3484701536; ISBN-13: 978-3484701533. *Being and Time*.
Translated by John Macquarrie and Edward Robinson. New York: Harper and
Row, 1962. Harper Perennial Modern Thought edition (2008). ISBN-10:
0061575593; ISBN-13*:*978-0061575594.

[7] Merleau-Ponty, M. 1945. *Phénoménologie de la perception.* (Paris):
Gallimard. *Phenomenology of Perception*. Translated by Colin Smith New
York: Humanities Press, and London: Routledge  Kegan Paul, 1962. Routledge
(2013). ISBN-10: 0415834333; ISBN-13: 978-0415834339.

[8] ———. 1964. “Eye and Mind.” In *The Primacy of Perception*, edited by
James M. Edie, 159–90. Evanston, IL: Northwestern University Press.
ISBN-10: 0810101645; ISBN-13: 978-0810101647.
++

Kind regards,

___ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile: +49.17.43.56.41.75
email: pla...@simeio.org
URL:  www.simeio.org
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] [Fwd: Fw: [bisc-group] The Curse of Efficiency]

[Dr. Plamen L. Simeonov]

 in the case of
 children. Once the consequences were understood, the use of lead additives,
 at least in the United States, was phased out.

 Another example is the use of antibiotics in animal feed. In this case,
 improvement in efficiency has led to the development of drug-resistant
 bacteria and a growing number of allergic reactions in the general
 population. A more recent example is the unfreezing of land rents in
 Egypt―aimed at improving the efficiency of land utilization―which may
 pauperize hundreds of thousands of tenant farmers and lead to serious
 social unrest.

 Second, a move to improve efficiency generally leads to a small gain for
 many and a large loss for few. A classic example is a reduction in tariffs
 on importa. In this case, many gain a little and a few experience the
 trauma of losing their jobs. Another example is our health care systems. In
 this instance, an improvement in efficiency leads to lower health care
 costs for many and a substantially reduced income for a relatively small
 number of specialized medical personnel.

 At what point does a small gain for many outweigh a large loss for a few?
 There is no theory of justice or rationality that provides an answer to
 this fundamental question and it is not likely that there will be one in
 the foreseeable future.

 A basic issue that relates to efficiency plays a pivotal role in the
 current turmoil in financial markets.

 In the United States, it is an article of faith that deregulation,
 privatization, free trade and globalization lead to higher efficiency and
 bring about economic growth. However, in a paper which I wrote in 1974, I
 suggested that the growing degree of interdependence brought about by
 technological progress and its concomitant globalization necessitate a
 higher degree of coordination and regulation to maintain stability and
 prevent catastrophic failures. This necessity is in conflict with
 acceptance of deregulation as a prime component of economic policy.

 The problem is that in democracies the electorate is resistant to higher
 levels of coordination, regulation and taxation, and future generations
 have no vote. The result is a growing imbalance which I described as the
 crisis of undercoordination. In my view, it is primarily this imbalance
 that underlies the financial, economic and social crises that are spreading
 in extent and growing in intensity.

 --
 Lotfi A. Zadeh Professor Emeritus
 Director, Berkeley Initiative in Soft Computing (BISC) BISC Homepage URLs
 URL: http://zadeh.cs.berkeley.edu/


 --
 --**---
 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/http://sites.google.com/site/pedrocmarijuan/
 --**---


 *

 Berkeley Initiative in Soft Computing (BISC)
 *


 If you ever want to remove yourself from this mailing list,
 you can send mail to sy...@lists.eecs.berkeley.edu with the following
 command in the body of your email message:
 unsubscribe bisc-group
 or from another account,
 unsubscribe bisc-group your_email_adress


 ___
 fis mailing list
 fis@listas.unizar.es
 https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis



 ___
 fis mailing list
 fis@listas.unizar.es
 https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis




-- 
___ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile: +49.17.43.56.41.75
email: pla...@simeio.org
URL:  www.simeio.org



recent project: http://www.inbiosa.eu/en/

recent book:
http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-642-28110-5

current activity:
http://www.inbiosa.eu/en/Calls-For-Papers-View.html?article=can-biology-create-a-profoundly-new-mathematics-and-computation
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Physics of computing

[Dr. Plamen L. Simeonov]

 equilibrium):
 

 Engel G.S., Calhoun T.R., Read E.L., Ahn T.K., Mancal T., Cheng Y.C.,
 Blankenship R.E., Fleming G.R. (2007) Evidence for wavelike energy transfer
 through quantum coherence in photosynthetic systems. Nature, 446(7137):
 782-786.

 Collini E., Scholes G. (2009) Coherent intrachain energy in migration in a
 conjugated polymer at room temperature.  Science, vol. 323 No. 5912 pp.
 369-373.

 Gauger E.M., Rieper E., Morton J.J.L., Benjamin S.C., Vedral V. (2011)
 Sustained Quantum Coherence and Entanglement in the Avian Compass. Phys.
 Rev. Lett., 106: 040503.

 Cia, J. et al, (2009)  Dynamic entanglement in oscillating molecules.
 arXiv:0809.4906v1 [quant-ph]

 Sincerely,

 Walter



 

   --

   ** **

 ___

 fis mailing list

 fis@listas.unizar.es

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

   



 

 --

 -

 Pedro C. Marijuán

 Grupo de Bioinformación / Bioinformation Group


 Instituto Aragonés de Ciencias de la Salud

 Avda. Gómez Laguna, 25, Pl. 11ª

 50009 Zaragoza, Spain

 Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554

 pcmarijuan.i...@aragon.es

 http://sites.google.com/site/pedrocmarijuan/

 -

 

   ** **

 Please find our Email Disclaimer here--: *
 http://www.ukzn.ac.za/disclaimer* 

 --

 ** **

 ___

 fis mailing list

 fis@listas.unizar.es

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

   



 

 --

 -

 Pedro C. Marijuán


 Grupo de Bioinformación / Bioinformation Group

 Instituto Aragonés de Ciencias de la Salud

 Avda. Gómez Laguna, 25, Pl. 11ª

 50009 Zaragoza, Spain

 Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554

 pcmarijuan.i...@aragon.es

 http://sites.google.com/site/pedrocmarijuan/

 -

 

 ** **

 ** **



 

 -- 

 -

 Pedro C. Marijuán

 Grupo de Bioinformación / Bioinformation Group


 Instituto Aragonés de Ciencias de la Salud

 Avda. Gómez Laguna, 25, Pl. 11ª

 50009 Zaragoza, Spain

 Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554

 pcmarijuan.i...@aragon.es

 http://sites.google.com/site/pedrocmarijuan/

 -


 ___
 fis mailing list
 fis@listas.unizar.es
 https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis




-- 
___ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile: +44.12.23.96.85.69
email: pla...@simeio.org
URL:  www.simeio.org
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Physics of Computing

[Dr. Plamen L. Simeonov]

Dear Gavin et.FIS,

Information processing is omnipresent in biology.
Alan Turing's reaction-diffusion model of morphogenesis is certainly
well-known.

Here are a few more examples implying information processing within
biological systems:

1. Vrancisco Varela's self-reference calculus:

http://www.slideshare.net/PriMate_PaTagOn/francisco-varela-a-calculus-for-selfreference-1707403

http://homepages.math.uic.edu/~kauffman/VarelaCSR.pdf

and its implications:

http://homepages.math.uic.edu/~kauffman/NetworkSynthesis.pdf

http://onlinelibrary.wiley.com/doi/10.1002/sres.1105/abstract;jsessionid=8CC55298874EE9F1A9A0D886491099EA.d04t04?systemMessage

You could find more about it on Google

2. Robert Rosen's Anticipatory Systems and category theoretical studies on
Life Itself (cf.. Amazon) and Aloisius Louie's continuation of that path
with More than Life Itself.

3. Andree Ehresmann's dynamic CT based Memory Evolutive Systems (MES) (cf.
Amazon)

There are still many aspects of living systems that were not captured at
the roots of the phenomena by mathematics and computation to this moment,
despite several attempts for over 60 years. This is a huge field to be
explored yet. But the complexity of the biological phenomena does not imply
the automatic application of standard physicalistic approaches.I am not the
first who claims that an H2O molecule in an the cat Tom is different form
the one in the mouse Jerry, and then from the one in the pool in the
garden. This is e.g. one of the issues where physics as it is cannot help
further (individuality). Using and refining the tools we have in one field,
does not imply a dogmatic denial of the necessity to invent new tools for
another field that could be more effective there. Mathematics and physics
as such cannot explain biology to the extent we need to know. They need to
be developed to include the peculiarities of the phenomena at hand.

I will stop here for now.

Best,

Plamen






On Fri, Mar 16, 2012 at 10:14 PM, Gavin Ritz garr...@xtra.co.nz wrote:

 Hi FISers
 Can anyone show me a calculus for Information relating to biological
 systems?

 And if so show me the relationship with conceptual mathematics?

 Regards
 Gavin



 Dear FISers:

 Pedro and Plamen raise good and welcomed points regarding the nature of
 physics, information, and biology. Although I believe in a strong
 relationship between information and physics in biology, there are striking
 examples where direct correspondences between information, physics, and
 biology seem to depart. Scientists are only beginning to tease out these
 discrepancies which will undoubtedly give us a better understand of
 information.

 For example, in the study of cognition by A. Khrennikov and colleagues and
 J. Busemyer and colleagues, decisional processes may conform to quantum
 statistics and computation without necessarily being mediated by quantum
 mechanical phenomena at a biological level of description. I found this to
 be true in ciliates as well, where social strategy search speeds and
 decision rates may produce quantum computational phases that obey quantum
 statistics. In such cases, a changing classical diffusion term of response
 regulator reaction-diffusion parsimoniously accounts for the transition
 from classical to quantum information processing. Thus, there is no direct
 correspondence between quantum physicochemistry and quantum computation.
 Because the particular reaction-diffusion biochemistry is not unique to
 ciliates (i.e., the same phenomena is observed in plants, animals, and
 possibly bacteria), this incongruity may be widespread across life.

 Best regards,

 Kevin Clark

 ___
 fis mailing list
 fis@listas.unizar.es
 https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis



 ___
 fis mailing list
 fis@listas.unizar.es
 https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis




-- 
___ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile: +44.12.23.96.85.69
email: pla...@simeio.org
URL:  www.simeio.org
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Updated submission deadlines for events on Integral Biomathics

[Dr. Plamen L. Simeonov]

Dear colleagues,

we are looking for your contributions to our 3 events in August 2011:
http://www.inbiosa.eu/en/Workshops-And-Conferences.html
The submission deadlines were extended. I look forward to meeting you in San
Jose, Paris and/or Stirling!

Kind regards,

___ ___ ___

Dr. Plamen L. Simeonov
landline:   +49.30.38.10.11.25
fax/ums:   +49.30.48.49.88.26.4
mobile: +49.15.22.89.02.26.4
email: pla...@simeio.org
URL:  www.simeio.org
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis