Re: [Fis] New Year Lecture

[Francesco Rizzo]

ement as the "Josephson conjecture" in [3].  When I
> visited him in Cambridge last summer to discuss this statement, he did not
> object to his name being used in this manner.
>
>
> (*6*)  If the concepts of the "Linguistic Return" in biology and
> the Josephson conjecture  in physics prove to be correct in the coming
> decades and centuries, it may be possible to conclude that *philosophy*,
> *biology, *and *physics* are finally united/integrated in the framework
> of semiotics viewed as a generalized linguistics.
>
>
> All the best.
>
>
> Sung
>
>
>
>
>
>
>
>
>   [1] Ji, S. (2012).  The Zeldovich-Shakhnovich and MTLC Models of
> Evolution <http://www.conformon.net/?attachment_id=1112>: From Sequences
> to Species.  In: Molecular Theory of the Living Cell: concepts, Molecular
> Mechanisms, and Biomedical Applications.  Sprinter, New York.  Pp. 509-519.
> PDF at http://www.conformon.net/model-of-evolution/
>[2] Ji, S. (2012).  The Isomorphism between Cell and Human Languages: The
> Cell Language Theory <http://www.conformon.net/?attachment_id=1098>. In: 
> *Molecular
> Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomedical
> Applications.*  Springer, New York.  Section  6.1.2, pp. 164-168. PDF at
> http://www.conformon.net/cell_language_theory_pp_164_168/|
>[3] Ji, S. (2017).  The Cell Language Theory: Connecting Mind and
> Matter.  World Scientific Publishers, New Jersey.
>
>
>
>
> --
> *From:* Fis <fis-boun...@listas.unizar.es> on behalf of PEDRO CLEMENTE
> MARIJUAN FERNANDEZ <pcmarijuan.i...@aragon.es>
> *Sent:* Friday, January 5, 2018 8:39 AM
> *To:* JOHN TORDAY; fis@listas.unizar.es
> *Subject:* Re: [Fis] New Year Lecture
>
> head>
>
> Dear John and FIS Colleagues,
>
> Many thanks for this opening text of the NY Lecture. Indeed
> you have presented us an intricate panorama on one of the most obscure
> scientific problems of our time: the central theory of biology. As you say,
> we find with astonishment that there is literally no cell biology in
> evolution theory. And I would ad that there is no "information biology"
> either. A central theory becomes sort of a big Hall, where plenty of
> disciplinary corridors converge and later criss-cross among themselves.
> Darwinian theory is not that common hall for the really big, big science
> domain of biology. What are or where are the elements to rebuild the common
> Hall of the biological domain? I quote from your opening text:
>
> *"It is as if the unicellular state delegates its progeny to interact with
> the environment as agents, collecting data to inform the recapitulating
> unicell of ecological changes that are occurring. Through the acquisition
> and filtering of epigenetic marks via meiosis, fertilization, and
> embryogenesis, even on into adulthood, where the endocrine system dictates
> the length and depth of the stages of the life cycle, now known to be under
> epigenetic control, the unicell remains in effective synchrony with
> environmental changes."*
>
> It is really brilliant: a heads up reversal perspective. I think out of
> these ideas there are plenty of disciplinary excursions to make. One is
> "informational", another "topological". Putting together two different
> algorithmic descriptions and making them to build a torus (i.e., gastrula")
> as a universal departure for multicellularity also reminds the ideas of
> Stuart Pivart ("Omnia Ex Torus") about the primordials of multicellularity
> and the role of mechanical forces in the patterning of developmental
> processes.
>
> Echoing the ideas discussed in the Royal Society meeting (November 2016),
> there is a pretty long list of elements to take into account together with
> epigenetic inheritance (symbiogenesis, viruses and mobile elements,
> multilevel selection, niche construction, genomic evolution...). As I have
> suggested above, essential informational ideas are missing too, and this
> absence of the informational perspective in the ongoing evo discussions is
> not a good thing.
>
> i any case, it is such a great theme to ponder...
>
> Best wishes to all
>
> --Pedro
>
>
>
>   On Wed, 3 Jan 2018 07:15:43 -0800 JOHN TORDAY wrote:
> blockquote>
>
> Dear FIS Colleagues, I have attached my New Year Lecture at the invitation
> of Professor Pedro Clemente Marijuan Fernandez. The content relates a novel
> perspective on the mechanism of evolution from a cellular-molecular
> vantage-point. I welcome any and all comments and criticisms in the spirit
> of sharing ideas openly and constructively. Best Wishes,
>
>
>
> John S. Torday PhD
>
> Professor
>
> Evolutionary Medicine
>
> UCLA
> /div>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
___
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Fis@listas.unizar.es
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Re: [Fis] New Year Lecture

[Sungchul Ji]

Theory<http://www.conformon.net/?attachment_id=1098>. In: 
Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and 
Biomedical Applications.  Springer, New York.  Section  6.1.2, pp. 164-168. PDF 
at http://www.conformon.net/cell_language_theory_pp_164_168/|
   [3] Ji, S. (2017).  The Cell Language Theory: Connecting Mind and Matter.  
World Scientific Publishers, New Jersey.




From: Fis <fis-boun...@listas.unizar.es> on behalf of PEDRO CLEMENTE MARIJUAN 
FERNANDEZ <pcmarijuan.i...@aragon.es>
Sent: Friday, January 5, 2018 8:39 AM
To: JOHN TORDAY; fis@listas.unizar.es
Subject: Re: [Fis] New Year Lecture

head>

Dear John and FIS Colleagues,

Many thanks for this opening text of the NY Lecture. Indeed you have presented 
us an intricate panorama on one of the most obscure scientific problems of our 
time: the central theory of biology. As you say, we find with astonishment that 
there is literally no cell biology in evolution theory. And I would ad that 
there is no "information biology" either. A central theory becomes sort of a 
big Hall, where plenty of disciplinary corridors converge and later criss-cross 
among themselves. Darwinian theory is not that common hall for the really big, 
big science domain of biology. What are or where are the elements to rebuild 
the common Hall of the biological domain? I quote from your opening text:

"It is as if the unicellular state delegates its progeny to interact with the 
environment as agents, collecting data to inform the recapitulating unicell of 
ecological changes that are occurring. Through the acquisition and filtering of 
epigenetic marks via meiosis, fertilization, and embryogenesis, even on into 
adulthood, where the endocrine system dictates the length and depth of the 
stages of the life cycle, now known to be under epigenetic control, the unicell 
remains in effective synchrony with environmental changes."

It is really brilliant: a heads up reversal perspective. I think out of these 
ideas there are plenty of disciplinary excursions to make. One is 
"informational", another "topological". Putting together two different 
algorithmic descriptions and making them to build a torus (i.e., gastrula") as 
a universal departure for multicellularity also reminds the ideas of Stuart 
Pivart ("Omnia Ex Torus") about the primordials of multicellularity and the 
role of mechanical forces in the patterning of developmental processes.

Echoing the ideas discussed in the Royal Society meeting (November 2016), there 
is a pretty long list of elements to take into account together with epigenetic 
inheritance (symbiogenesis, viruses and mobile elements, multilevel selection, 
niche construction, genomic evolution...). As I have suggested above, essential 
informational ideas are missing too, and this absence of the informational 
perspective in the ongoing evo discussions is not a good thing.

i any case, it is such a great theme to ponder...

Best wishes to all

--Pedro



  On Wed, 3 Jan 2018 07:15:43 -0800 JOHN TORDAY wrote:

blockquote>

Dear FIS Colleagues, I have attached my New Year Lecture at the invitation of 
Professor Pedro Clemente Marijuan Fernandez. The content relates a novel 
perspective on the mechanism of evolution from a cellular-molecular 
vantage-point. I welcome any and all comments and criticisms in the spirit of 
sharing ideas openly and constructively. Best Wishes,




John S. Torday PhD

Professor

Evolutionary Medicine

UCLA

/div>


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Re: [Fis] New Year Lecture

[Ulanowicz, Robert]

Just a few short comments in response to Mark & John:

We definitely must reconsider the logic of biology! To start with, we must
abandon the Aristotelian prohibition of circular causality, as Alicia
Juarrero suggests. Life is all about recursion! Then there's the inherent
dialectical nature of living systems, as espoused by Lupasco and championed
by Joseph.

Although more a matter of perspective than logic, we need to focus on life
as configurations of processes, rather than objects moving according to
universal laws. I have even suggested that this shift entails an entire
revision of scientific metaphysics <
https://people.clas.ufl.edu/ulan/publications/philosophy/3rdwindow/>.

And there's the position of communication in regard to information theory.
Historically, of course, IT emerged out of communication theory. It has
grown, however, to envelop constraint in general, as Stan points out. One
can speak of the information inhering in a structure in abstraction from
any consideration of communication. John Collier calls this "enformation"
and it is quite amenable to treatment by IT. One can quantify the
information in a stable structure, or more importantly as regards life, in
a configuration of processes <
https://people.clas.ufl.edu/ulan/publications/ecosystems/ecolasc/>.

With regard to what is driving the adaptation that John cites among cells
and their environment, there is the centripetality that is a consequence of
autocatalytic configurations, an attribute that was not yet included in
Varela's autopoietic narrative (ibid.) Way back in 1960 Bertrand Russell
pointed to it as the "drive behind all of evolution", but few have taken up
his lead. For over 20 years I have been advocating the inclusion of this
phenomenon among the fundamental characteristics of life -- one that
provides directionality to living entities and the origin of selfhood and
striving. Terry is now working on a book describing an independent
treatment of the phenomenon.

Finally, there's the need to move beyond the confines of the positivist
thinking that constitutes most of physics and seriously to consider
heterogeneity and absence. As Elsasser indicated, heterogeneity pushes us
beyond the control of the universal laws  and the circumscribed logic of
physics . The universal
laws are not broken, but the combinatorics of heterogeneity implies that
they can only constrain, but not determine outcomes in a universe rife with
contingency . As to
reckoning absence, IT is the perfect vehicle to quantify entropic absence
that is so critical to sustainable life <
https://people.clas.ufl.edu/ulan/files/Reckon.pdf>.

In all, I would posit that, if we want to accomplish a true understanding
of living phenomena, we need to start thinking outside the current box --
WAY OUTSIDE!!

My best to all,
Bob

On Wed, Jan 10, 2018 at 5:08 AM, Mark Johnson  wrote:

> Dear John,
>
> Thank you very much for this - a great way to start the new year!
>
> I'd like to ask about "communication" - it's a word which is
> understood in many different ways, and in the context of cells, is
> hard to imagine.
>
> When you suggest that “the unicellular state delegates its progeny to
> interact with the environment as agents, collecting data to inform the
> recapitulating unicell of ecological changes that are occurring.
> Through the acquisition and filtering of epigenetic marks via meiosis,
> fertilization, and embryogenesis, even on into adulthood, where the
> endocrine system dictates the length and depth of the stages of the
> life cycle, now known to be under epigenetic control, the unicell
> remains in effective synchrony with environmental changes.” It seems
> that this is not communication of ‘signs’ in the Peircean sense
> supported by the biosemioticians (Hoffmeyer). But is it instead a
> recursive set of transductions, much in the spirit of Bateson’s
> insight that:
>
> “Formerly we thought of a hierarchy of taxa—individual, family line,
> subspecies, species, etc.—as units of survival. We now see a different
> hierarchy of units—gene-in-organism, organism-in environment,
> ecosystem, etc. Ecology, in the widest sense, turns out to be the
> study of the interaction and survival of ideas and programs (i.e.,
> differences, complexes of differences, etc.) in circuits.” (from his
> paper "Pathologies of Epistemology" in Steps to an Ecology of Mind)
>
> Recursive transduction like this is a common theme in cybernetics –
> it's in Ashby's "Design for a Brain", Pask's conversation theory, and
> in Beer’s Viable System Model, where “horizon scanning” (an
> anticipatory sub-system gathering data from the environment) is an
> important part of the metasystem which maintains viability of the
> organism (It’s worth noting that Maturana and Varela's autopoietic
> theory overlooks this).
>
> "Communication" would then be much more like 

Re: [Fis] New Year Lecture

[Bill]

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest, all 
of  which have all been occasioned by John Torday's profound insights 
about the nature of evolutionary development in light of the importance 
of cell-cell signaling and molecular biology.  From the comments, it is 
clear that there is a strong impulse to seek a means of integrating the 
role of symbiogenesis, viruses and mobile elements, multilevel 
selection, niche construction, genomic plasticity into a common 
narrative with an informational perspective at its foundation.
    In the spirit of that line of discussion, I am offering two links 
that discuss evolution as an biologic information management system. 
Some of this work shares direct commonality with John's, since he and I 
are frequent collaborators.


http://www.mdpi.com/2079-7737/5/2/21/htm

https://www.sciencedirect.com/science/article/pii/S007961071730233X

Both of these articles can be considered as complementary to Pedro's 
very fine article, 'How prokaryotes ‘encode’ their environment: Systemic 
tools for organizing the information flow', which is in BioSystems.


I am grateful to John for inviting me to participate in the forum and to 
Pedro for encouraging me to share these manuscripts.


Best regards,
Bill

William B. Miller, Jr., M.D.
602-463-5236
wbmill...@cox.net



On 1/9/2018 5:19 AM, Pedro C. Marijuan wrote:

Dear  Soeren and Colleagues,

The symbiogenesis theme (Margulis' endosymbiotic theory) is one of the 
aspects to reconsider/reenter into the basically evo-info (if I may 
say) novissima synthesis. Margulis views were received in the 70's and 
80's with tremendous hostility from the Neo-Darwinian orthodoxy. After 
a long series of turmoils it was accepted in many realms, particularly 
in popular science and textbooks industry, and even by the always 
reluctant Neo-Darwinians. Paradoxically in recent times the 
bioinformatic and omic research on the origins of eukaryotes has put 
into question basic tenets of that theory. The "deep sequencing" 
research on protein families has also be problematic for 
symbiogenesis. It does not mean that it is wrong, but that it is more 
complicated than previously thought... That is my opinion at least. In 
the present discussion, however, there are very knowledgeable parties 
that can give more specific arguments about that.


Talking about Neo-Darwinians, the paragraph from John Torday that I 
highlighted (see at the bottom) reminds me strongly from that other 
from Richard Dawkins' (in The Selfish Gene):



  /“We are survival machines – robot vehicles blindly programmed to
  preserve the selfish molecules known as genes. This is a truth which
  still fills me with astonishment.”/

If we compare both paragraphs, the essential difference relies on 
information. Torday's unicells develop not really multicell robots, 
but info agents that collect information  about the environment, 
including the whole elements of the niche (i.e., including in the 
human case from the "microbiome" to the "sociotype"). And fortunately 
the emphasis on "selfishness" has disappeared. Perhaps one of the 
consequences of Margulis work has been ideological, implying some 
general opening of views. Besides that, we should pay close attention 
to some "invisible threads" inside/outside those robots, like puppet 
strings: let me emphasize the enormous evolutionary importance of 
viruses in eukaryotic origins and evolution, and in epigenetic 
phenomena. Really masterminding the whole topological/architectural 
molecular processes.


In any event, for the purpose of the discussion, I bet that the new 
synthesis, the "novissimima", has to be evo-info... or it won't be!

(spoonful of salt, please)
All the best--Pedro


El 06/01/2018 a las 18:05, Søren Brier escribió:


Dear Pedro

I am wondering why no one seems to think that Lynn Margulis’ theory 
that cell organelles such as mitochondria and chloroplasts were once 
independent bacteria  is a crucial contribution to cell biology in 
evolution theory ?


Best wishes

Søren Brier

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


*From:*Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *PEDRO 
CLEMENTE MARIJUAN FERNANDEZ

*Sent:* 5. januar 2018 14:40
*To:* JOHN TORDAY <jtor...@ucla.edu>; fis@listas.unizar.es
*Subject:* Re: [Fis] New Year Lecture

head>

Dear John and FIS Colleagues,

Many thanks for this opening text of the NY Lecture. Indeed 
you have presented us an intricate panorama on one of the most 
obscure scientific problems of our time: the central theory of 
biology. As you say, we find with astonishment t

Re: [Fis] New Year Lecture

[Mark Johnson]

Dear John,

Thank you very much for this - a great way to start the new year!

I'd like to ask about "communication" - it's a word which is
understood in many different ways, and in the context of cells, is
hard to imagine.

When you suggest that “the unicellular state delegates its progeny to
interact with the environment as agents, collecting data to inform the
recapitulating unicell of ecological changes that are occurring.
Through the acquisition and filtering of epigenetic marks via meiosis,
fertilization, and embryogenesis, even on into adulthood, where the
endocrine system dictates the length and depth of the stages of the
life cycle, now known to be under epigenetic control, the unicell
remains in effective synchrony with environmental changes.” It seems
that this is not communication of ‘signs’ in the Peircean sense
supported by the biosemioticians (Hoffmeyer). But is it instead a
recursive set of transductions, much in the spirit of Bateson’s
insight that:

“Formerly we thought of a hierarchy of taxa—individual, family line,
subspecies, species, etc.—as units of survival. We now see a different
hierarchy of units—gene-in-organism, organism-in environment,
ecosystem, etc. Ecology, in the widest sense, turns out to be the
study of the interaction and survival of ideas and programs (i.e.,
differences, complexes of differences, etc.) in circuits.” (from his
paper "Pathologies of Epistemology" in Steps to an Ecology of Mind)

Recursive transduction like this is a common theme in cybernetics –
it's in Ashby's "Design for a Brain", Pask's conversation theory, and
in Beer’s Viable System Model, where “horizon scanning” (an
anticipatory sub-system gathering data from the environment) is an
important part of the metasystem which maintains viability of the
organism (It’s worth noting that Maturana and Varela's autopoietic
theory overlooks this).

"Communication" would then be much more like “conversation”…
etymologically, "con-versare"… "to turn together”… dancing! Does this
fit?

A further point is to then ask whether a logic of evolutionary biology
is a logic of recursive transductions over history. The critical point
is what Joseph Brenner argued before Christmas in objecting to Peirce:
we struggle to express the specificity and basis for change in our
logic. Do we need a different kind of logic?

Best wishes and Happy new year,

Mark

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Re: [Fis] New Year Lecture

[Karl Javorszky]

Dear Professor Torday,



thank you for your insightful analysis of the complex system which is
genetics. Your viewpoints cover from the molecular, cellular, physiological
level up to that of cosmic changes affecting the whole of the Earth. Your
work is truly a tour d’horizon of the subject.

Random mutation or natural selection: this is a relatively minor aspect of
the overall interdependence. On this subject it may be helpful to take a
look at what the numbers say. The Darwin concept of survival of the fittest
creates a linear order among the animals: fittest thru the medium down to
the least fit, which get eaten and therefore by their absence in the
genetic pool influence the future composition of the multitude. External
influences exist and they exert their influence by creating a sorted
collection. The pressure exerted by natural selection can well be modelled
by simple arithmetic of sorting.

Having at least two external influences at work at any time, one may assume
that in the multitude the laws of transition between two orders are valid.
(For the organism it may be of advantage to have more fat, to be well
prepared for the winter; having more fat may be irrelevant for the ability
to make mimicry.) Competing external influences may well bring forth
situations, where the organism has to decide whether to be prepared for
future danger type A or for future danger type B.

This is the moment where random mutation can appear. Being sorted and
ordered in aspects A and B means that there exist groups among elements
that make the change together. The element does not change its position on
its own: it is embedded in a community with other elements, forming a kind
of convoy, a string, a filament. Permutations consist of cycles.

The concept of cycles brings a temporal dimension to the proceedings. The
cycle elements *e* are in, progresses through slices of logical truth: each
such a moment which is true is true for one element *e_i*, had been true
just before for one element *e_(i-1)*, and will be true just next for one
element *e_(i+1)*. Cycles of interest being composed of more than a very
few members, such elements of the corpus, which will be true later, are a
potential subject of seduction. Assuming that there is concurrently a
reordering procedure between aspects C and D, there are great chances that
any element that is not being certified true, may change its properties
before being nailed down by truth having arrived for him, too. Lots of room
for random results.

Random mutation can well be connected to the mechanisms that govern natural
selection. The two ideas are not unreconciliable.

There are many more ideas in your expose which can be supported by the
numbers. The numbers are here, ready to serve you.



2018-01-03 16:15 GMT+01:00 JOHN TORDAY :

> Dear FIS Colleagues, I have attached my New Year Lecture at the invitation
> of Professor Pedro Clemente Marijuan Fernandez. The content relates a novel
> perspective on the mechanism of evolution from a cellular-molecular
> vantage-point. I welcome any and all comments and criticisms in the spirit
> of sharing ideas openly and constructively. Best Wishes,
>
> John S. Torday PhD
> Professor
> Evolutionary Medicine
> UCLA
>
> ___
> 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] New Year Lecture

[Pedro C. Marijuan]

Dear  Soeren and Colleagues,

The symbiogenesis theme (Margulis' endosymbiotic theory) is one of the 
aspects to reconsider/reenter into the basically evo-info (if I may say) 
novissima synthesis. Margulis views were received in the 70's and 80's 
with tremendous hostility from the Neo-Darwinian orthodoxy. After a long 
series of turmoils it was accepted in many realms, particularly in 
popular science and textbooks industry, and even by the always reluctant 
Neo-Darwinians. Paradoxically in recent times the bioinformatic and omic 
research on the origins of eukaryotes has put into question basic tenets 
of that theory. The "deep sequencing" research on protein families has 
also be problematic for symbiogenesis. It does not mean that it is 
wrong, but that it is more complicated than previously thought... That 
is my opinion at least. In the present discussion, however, there are 
very knowledgeable parties that can give more specific arguments about that.


Talking about Neo-Darwinians, the paragraph from John Torday that I 
highlighted (see at the bottom) reminds me strongly from that other from 
Richard Dawkins' (in The Selfish Gene):



 /“We are survival machines – robot vehicles blindly programmed to
 preserve the selfish molecules known as genes. This is a truth which
 still fills me with astonishment.”/

If we compare both paragraphs, the essential difference relies on 
information. Torday's unicells develop not really multicell robots, but 
info agents that collect information  about the environment, including 
the whole elements of the niche (i.e., including in the human case from 
the "microbiome" to the "sociotype"). And fortunately the emphasis on 
"selfishness" has disappeared. Perhaps one of the consequences of 
Margulis work has been ideological, implying some general opening of 
views. Besides that, we should pay close attention to some "invisible 
threads" inside/outside those robots, like puppet strings: let me 
emphasize the enormous evolutionary importance of viruses in eukaryotic 
origins and evolution, and in epigenetic phenomena. Really masterminding 
the whole topological/architectural molecular processes.


In any event, for the purpose of the discussion, I bet that the new 
synthesis, the "novissimima", has to be evo-info... or it won't be!

(spoonful of salt, please)
All the best--Pedro


El 06/01/2018 a las 18:05, Søren Brier escribió:


Dear Pedro

I am wondering why no one seems to think that Lynn Margulis’ theory 
that cell organelles such as mitochondria and chloroplasts were once 
independent bacteria  is a crucial contribution to cell biology in 
evolution theory ?


Best wishes

Søren Brier

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


*From:*Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *PEDRO 
CLEMENTE MARIJUAN FERNANDEZ

*Sent:* 5. januar 2018 14:40
*To:* JOHN TORDAY <jtor...@ucla.edu>; fis@listas.unizar.es
*Subject:* Re: [Fis] New Year Lecture

head>

Dear John and FIS Colleagues,

Many thanks for this opening text of the NY Lecture. Indeed 
you have presented us an intricate panorama on one of the most obscure 
scientific problems of our time: the central theory of biology. As you 
say, we find with astonishment that there is literally no cell biology 
in evolution theory. And I would ad that there is no "information 
biology" either. A central theory becomes sort of a big Hall, where 
plenty of disciplinary corridors converge and later criss-cross among 
themselves. Darwinian theory is not that common hall for the really 
big, big science domain of biology. What are or where are the elements 
to rebuild the common Hall of the biological domain? I quote from your 
opening text:


*/"It is as if the unicellular state delegates its progeny to interact 
with the environment as agents, collecting data to inform the 
recapitulating unicell of ecological changes that are occurring. 
Through the acquisition and filtering of epigenetic marks via meiosis, 
fertilization, and embryogenesis, even on into adulthood, where the 
endocrine system dictates the length and depth of the stages of the 
life cycle, now known to be under epigenetic control, the unicell 
remains in effective synchrony with environmental changes."/*


It is really brilliant: a heads up reversal perspective. I think out 
of these ideas there are plenty of disciplinary excursions to make. 
One is "informational", another "topological". Putting together two 
different algorithmic descriptions and making them to build a torus 
(i.e., gastrula") as a universal departure for multicellularity also 
reminds th

Re: [Fis] New Year Lecture

[Stanley N Salthe]

Torday's work generally boils down to a concern for PREADAPTATION in
organic evolution.  This is a material necessity.  Preadaptation has been
ignored by the neoDarwinian evolutionary biologists, who have viewed their
task to concern the dynamics of natural selection (even in simple models).
So evolutionary biology has become quite abstract (mathematical), while
Torday's work is very materialistic. The information perspective can likely
better be applied to the materialist perspective than to the abstract
neoDarwinian perspective.  I think Charley D would have preferred Torday!

STAN

On Fri, Jan 5, 2018 at 8:39 AM, PEDRO CLEMENTE MARIJUAN FERNANDEZ <
pcmarijuan.i...@aragon.es> wrote:

> head>
>
> Dear John and FIS Colleagues,
>
> Many thanks for this opening text of the NY Lecture. Indeed
> you have presented us an intricate panorama on one of the most obscure
> scientific problems of our time: the central theory of biology. As you say,
> we find with astonishment that there is literally no cell biology in
> evolution theory. And I would ad that there is no "information biology"
> either. A central theory becomes sort of a big Hall, where plenty of
> disciplinary corridors converge and later criss-cross among themselves.
> Darwinian theory is not that common hall for the really big, big science
> domain of biology. What are or where are the elements to rebuild the common
> Hall of the biological domain? I quote from your opening text:
>
> *"It is as if the unicellular state delegates its progeny to interact with
> the environment as agents, collecting data to inform the recapitulating
> unicell of ecological changes that are occurring. Through the acquisition
> and filtering of epigenetic marks via meiosis, fertilization, and
> embryogenesis, even on into adulthood, where the endocrine system dictates
> the length and depth of the stages of the life cycle, now known to be under
> epigenetic control, the unicell remains in effective synchrony with
> environmental changes."*
>
> It is really brilliant: a heads up reversal perspective. I think out of
> these ideas there are plenty of disciplinary excursions to make. One is
> "informational", another "topological". Putting together two different
> algorithmic descriptions and making them to build a torus (i.e., gastrula")
> as a universal departure for multicellularity also reminds the ideas of
> Stuart Pivart ("Omnia Ex Torus") about the primordials of multicellularity
> and the role of mechanical forces in the patterning of developmental
> processes.
>
> Echoing the ideas discussed in the Royal Society meeting (November 2016),
> there is a pretty long list of elements to take into account together with
> epigenetic inheritance (symbiogenesis, viruses and mobile elements,
> multilevel selection, niche construction, genomic evolution...). As I have
> suggested above, essential informational ideas are missing too, and this
> absence of the informational perspective in the ongoing evo discussions is
> not a good thing.
>
> i any case, it is such a great theme to ponder...
>
> Best wishes to all
>
> --Pedro
>
>
>
>   On Wed, 3 Jan 2018 07:15:43 -0800 JOHN TORDAY wrote:
> blockquote>
>
> Dear FIS Colleagues, I have attached my New Year Lecture at the invitation
> of Professor Pedro Clemente Marijuan Fernandez. The content relates a novel
> perspective on the mechanism of evolution from a cellular-molecular
> vantage-point. I welcome any and all comments and criticisms in the spirit
> of sharing ideas openly and constructively. Best Wishes,
>
>
>
> John S. Torday PhD
>
> Professor
>
> Evolutionary Medicine
>
> UCLA
> /div>
>
>
>
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>
>
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Re: [Fis] New Year Lecture

[PEDRO CLEMENTE MARIJUAN FERNANDEZ]

Dear John and FIS Colleagues,
Many thanks for this opening text of the NY Lecture. Indeed 
you have presented us an intricate panorama on one of the most obscure 
scientific problems of our time: the central theory of biology. As you say, 
we find with astonishment that there is literally no cell biology in 
evolution theory. And I would ad that there is no "information biology" 
either. A central theory becomes sort of a big Hall, where plenty of 
disciplinary corridors converge and later criss-cross among themselves. 
Darwinian theory is not that common hall for the really big, big science 
domain of biology. What are or where are the elements to rebuild the common 
Hall of the biological domain? I quote from your opening text:  
"It is as if the unicellular state delegates its progeny to interact with 
the environment as agents, collecting data to inform the recapitulating 
unicell of ecological
changes that are occurring. Through the acquisition and filtering of 
epigenetic marks via meiosis, fertilization, and embryogenesis, even on into 
adulthood, where the endocrine system dictates the length and depth of the 
stages of the life cycle, now known to be under epigenetic control, the 
unicell remains in effective synchrony with environmental changes."
It is really brilliant: a heads up reversal perspective. I think out of 
these ideas there are plenty of disciplinary excursions to make. One is 
"informational", another "topological". Putting together two different 
algorithmic descriptions and making them to build a torus (i.e., gastrula") 
as a universal departure for multicellularity also reminds the ideas of 
Stuart Pivart ("Omnia Ex Torus") about the primordials of multicellularity 
and the role of mechanical forces in the patterning of developmental 
processes. 

Echoing the ideas

discussed in the Royal Society meeting (November 2016), there is a pretty 
long list of elements to take into account together with epigenetic 
inheritance (symbiogenesis, viruses and mobile elements, multilevel 
selection, niche construction, genomic evolution...). As I have suggested 
above, essential informational ideas are missing too, and this absence of 
the informational perspective in the ongoing evo discussions is not a good 
thing. 

i any case, it is such a great theme to ponder...
Best wishes to all
--Pedro


  On Wed, 3 Jan 2018 07:15:43 -0800 JOHN TORDAY  wrote:

Dear FIS Colleagues, I have attached my New Year Lecture at the invitation of 
Professor Pedro Clemente Marijuan Fernandez. The content relates a novel 
perspective on the mechanism of evolution from a cellular-molecular 
vantage-point. I welcome any and all comments and criticisms in the spirit of 
sharing ideas openly and

constructively. Best Wishes,



John S. Torday PhD
Professor
Evolutionary Medicine
UCLA


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[Fis] New Year Lecture

[PEDRO CLEMENTE MARIJUAN FERNANDEZ]

Dear FIS Colleagues,
 
Happy New Year to everybody!

Following ourtradition we are going to hold the New Year Lecture:
 
"REFLECTIONS ON EVOLUTION THEORY"
 
It will be imparted by:
 
JOHN S. TORDAY

Professor of Evolutionary Medicine
Harbor-UCLAMedical Center
Los Angeles
 
It will be posted, at hisconvenience, during the coming days.

Best wishes---Pedro


Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. San Juan Bosco, 13, planta 0, 50009 Zaragoza, Spain
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/

 
 
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[Fis] New Year Lecture

[PEDRO CLEMENTE MARIJUAN FERNANDEZ]

Dear FIS Colleagues,

The 2017 New Year Lecture will be entitled:

"A Curious Story"

It will be imparted by:

Otto E. Rossler
University of Tuebingen

It will be posted in a few days, at the author's convenience. In the interim, 
discussants are kindly requested to take a rest, stop the exchanges, and enjoy 
the festivities (note: given the proximity of the IS4SI event in Gothenburg, we 
might organize a specific session on the what-is-info topic discussed these 
days--suggestions are welcome offline).
Best wishes to all for the New Year!
--Pedro
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[Fis] NEW YEAR LECTURE

[PEDRO CLEMENTE MARIJUAN FERNANDEZ]

Dear FIS Colleagues,

During these early days of 2016, we will have the customary New Year Lecture, 
entitled:

THE NEW FORCES OF HISTORY

Imparted by:

Howard Bloom

Author of: The Lucifer Principle: A Scientific Expedition Into the Forces of 
History
Member: New York Academy of Sciences, American Association for the Advancement 
of Science, American Psychological Society, Academy of Political Science, Human 
Behavior and Evolution Society, International Society for Human Ethology, 
Scientific Advisory Board Member, Lifeboat Foundation; Editorial Board Member, 
Journal of Space Philosophy; Board member and member of Board of Governors, 
National Space Society. Etc.

Best wishes to all, and a Happy New Year!
--Pedro

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[Fis] New Year Lecture – The Correct Level of Analysis?

[Marcus Abundis]

Hi Terry – and “first-time greetings“ to FIS colleagues,


First, Terry, thank you for your continued effort with this contentious
topic. It is truly necessary and worthwhile “heavy lifting.“


Second, in reading all prior postings I am drawn to your 30 Jan. note:

 . . . I haven't felt that the specific components of this proposal have
been addressed in this thread. 

I find myself wondering if this is still the case, in the current thread.
This also prompts me to wonder WHY is this “informational topic“ so
doggedly contentious? Your January essay and your April preamble both
emphasize a need for “reductive“ study of the topic, but which does not
seem to truly arise here. This drives me to ask, indeed: “What is the
correct level of analysis?“, and what is the level of analysis exhibited.
To be clear, I support the reductive vista you seem to endorse.


My impression is that there is little focus on the MOST reductive issues,
and there is a bit of reasonable “jumping around“ as people reach for
exemplars to explain/explore/connect their own view of things. But I also
think a problem is buried in “jumping explanatory levels“ due to the nature
of “emergent things.“ The unavoidable (co-incident?) inclusion of emergent
elements (homunculi?), due to jumping explanatory levels seems likely to
introduce logical gaps, that can leave people confused and argumentative.
In some ways, your teleodynamic model may even encourage jumping around,
simply due to its ambitious nature. Thus, I wonder if that ambitiousness
hinders the model’s accessibility. Thoughts? (Yes, some ambitiousness is,
generally speaking, required).


Third, I am a bit confused (or just unclear) on your assertion of a
“non-dual model.“(?) I suspect you must recognize some “dual material
aspect,“ at least, as part of Shannon’s model (noise  signal), and your
January essay seems to aim to explore a “dual aspect“ vis-a-vis Boltzmann
and Shannon – yes, they are connected, but there are also clear
distinctions to be made too, no?


Marcus
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Re: [Fis] New Year Lecture – The Correct Level of Analysis?

[Francesco Rizzo]

Caro Marcus Abundis,
il non-duale o l'uni-duale modello non è costituito da rumore (entropia) 
segnale, ma da interpretazione  informazione (neg-entropia). E se vogliamo
approssimarci di più alla realtà liberamente creata dobbiamo analizzare
l'uni-trialità: entropia (rumore), interpretazione, neg-entropia
(segnalazione) o significazione (informazione). Come se l'interpretazione
fosse l'interfaccia tra entropia e neg-entropia o tra Boltzmann e Shannon
in un quadro più ampio comprendente l'informazione naturale o
termodinamica, genetica, matematica o cibernetica e semantica. Cfr. anche
l'e-mai inviata a Tutti il 25 aprile scorso.
Saluti cordiali.
Francesco Rizzo

2015-04-27 13:32 GMT+02:00 Marcus Abundis 55m...@gmail.com:

 Hi Terry – and “first-time greetings“ to FIS colleagues,


 First, Terry, thank you for your continued effort with this contentious
 topic. It is truly necessary and worthwhile “heavy lifting.“


 Second, in reading all prior postings I am drawn to your 30 Jan. note:

  . . . I haven't felt that the specific components of this proposal have
 been addressed in this thread. 

 I find myself wondering if this is still the case, in the current thread.
 This also prompts me to wonder WHY is this “informational topic“ so
 doggedly contentious? Your January essay and your April preamble both
 emphasize a need for “reductive“ study of the topic, but which does not
 seem to truly arise here. This drives me to ask, indeed: “What is the
 correct level of analysis?“, and what is the level of analysis exhibited.
 To be clear, I support the reductive vista you seem to endorse.


 My impression is that there is little focus on the MOST reductive issues,
 and there is a bit of reasonable “jumping around“ as people reach for
 exemplars to explain/explore/connect their own view of things. But I also
 think a problem is buried in “jumping explanatory levels“ due to the nature
 of “emergent things.“ The unavoidable (co-incident?) inclusion of emergent
 elements (homunculi?), due to jumping explanatory levels seems likely to
 introduce logical gaps, that can leave people confused and argumentative.
 In some ways, your teleodynamic model may even encourage jumping around,
 simply due to its ambitious nature. Thus, I wonder if that ambitiousness
 hinders the model’s accessibility. Thoughts? (Yes, some ambitiousness is,
 generally speaking, required).


 Third, I am a bit confused (or just unclear) on your assertion of a
 “non-dual model.“(?) I suspect you must recognize some “dual material
 aspect,“ at least, as part of Shannon’s model (noise  signal), and your
 January essay seems to aim to explore a “dual aspect“ vis-a-vis Boltzmann
 and Shannon – yes, they are connected, but there are also clear
 distinctions to be made too, no?


 Marcus





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Re: [Fis] New Year Lecture: Aftermath

[Francesco Rizzo]

Cari Tutti,
a proposito della uni-dualità tra informazione e interpretazione, non
bisogna essere per forza pragmatici tifosi di R. Rorty per affermare che i
fatti-segni o segni-fatti restano chiusi nella loro arbitrarietà o
irrazionalità semiotica senza un'interpretazione o  ermeneutica adeguata.
Purtroppo, questo non l'hanno capito gran parte dei sor-passati economisti
e di tanti filosofi ancora alla ricerca dell'Araba Fenice del pensiero
assoluto, mentre contrassegna il poderoso avanzamento delle scienze fisiche
e matematiche. Ecco perché la sessione precedente, appena conclusa, a mio
giudizio ha avuto una grandissima importanza. La nostra esistenza e la
nostra conoscenza sono un grande mistero che sola la poesia e la musica,
impregnate di tenerezza o amore divino e umano, possono educarci a
com-prendere.
Un abbraccio affettuoso da un poverino esponenziale, quale sono io, che
per il disegno o progetto di Dio può diventare un Io sono. E ciò vale per
tutti, credenti e non credenti. Oggi, più che mai, affascina la ricerca di
Un incontro d'amore tra il cuore della fede e l'intelligenza della
scienza (F. Rizzo,Aracne editrice, Roma, 2014). Il valore dell'uomo non
dipende da ciò che è, ha, sa, ma dalla capacità di uscire da se stesso,
aprendosi e amando gli altri.La co-scienza dell'amore, vale più dell'amore
della scienza. Grazie.
Francesco Rizzo.


2015-04-25 8:00 GMT+02:00 Loet Leydesdorff l...@leydesdorff.net:

 Dear Pedro, Terrence, and colleagues,





 *“… to explain how this interpretive capacity couldpossibly originate in a
 universe where direct contiguity of causalinfluence is the rule.*



 The contiguity is relational. However, meaning is generated not
 relationally, but positionally. As the network system is shaped in terms of
 relations, it can be expected to develop an architecture. The structure is
 based on correlations, that is, patterns of relations

 including zeros. For example, two synonyms may have similar meaning
 without co-occurring ever in a single text.



 In other words, the vectors of relations span a vector space in which both
 nodes and links are positioned. A link may then mean something different
 for node A and node B; the link becomes directed because of its function in
 the network. The correlational analysis of the vector space adds to the
 graph analysis of the networks of relations.



 Reflexivity adds to the mutual contingency in the relations by bringing
 the patterns of relations to bear. Human reflexivity enables us to change
 (self-organize) additionally the diaphragm of the reflection. Thus, degrees
 of freedom can be added recursively using the same principle that the
 network of relations develops a next-order architecture.



 Best,

 Loet


 --

 Loet Leydesdorff

 *Emeritus* University of Amsterdam
 Amsterdam School of Communication Research (ASCoR)

 l...@leydesdorff.net ; http://www.leydesdorff.net/
 Honorary Professor, SPRU, http://www.sussex.ac.uk/spru/University of
 Sussex;

 Guest Professor Zhejiang Univ. http://www.zju.edu.cn/english/,
 Hangzhou; Visiting Professor, ISTIC,
 http://www.istic.ac.cn/Eng/brief_en.htmlBeijing;

 Visiting Professor, Birkbeck http://www.bbk.ac.uk/, University of
 London;

 http://scholar.google.com/citations?user=ych9gNYJhl=en



 *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Pedro C.
 Marijuan
 *Sent:* Friday, April 24, 2015 2:34 PM
 *To:* Terrence W. DEACON; 'fis'
 *Subject:* Re: [Fis] New Year Lecture: Aftermath



 Dear Terry and colleagues,

 I hope you don't mind if I send some suggestions publicly. First, thank
 you for the aftermath, it provides appropriate closure to a very intense
 discussion session. Second, I think you have encapsulated very clearly an
 essential point (at least in my opinion):












 *Among these givens is the question of what is minimally necessary for a
 system or process to be interpretive, in the sense of being able to utilize
 presentintrinsic physical properties of things to refer to absent
 ordisplaced properties or phenomena. This research question is
 ignorablewhen it is possible to assume human or even animal interpreters
 aspart of the system one is analyzing. At some point, however, itbecomes
 relevant to not only be more explicit about what is beingassumed, but also
 to explain how this interpretive capacity couldpossibly originate in a
 universe where direct contiguity of causalinfluence is the rule.*My
 suggestion concerns the absence phenomenon (it also has appeared in some
 previous discussion in this list --notably from Bob's). You imply that
 there is an entity capable  of dynamically building upon  an external
 absences, OK quite clear,  but what about internal absences? I mean at
 the origins of communication there could be the sensing of the internal--
 lets call it functional voids, needs, gaps, deficiencies, etc. Cellularly
 there are some good arguments about that, even in the 70's there was a
 metabolic code

Re: [Fis] New Year Lecture: Aftermath

[Guy A Hoelzer]

Hi Terry,

I have used the term ‘perception’ in referring to in-formation that affects 
internal structure or dynamics.  This would contrast with forms of potential 
information that might pass through the system without being ‘perceived’.  For 
example, we have a finite number of mechanisms we call senses, each of which is 
sensitive to particular modes of information we encounter in our environment, 
but we are not able to perceive every form of information that we encounter 
(e.g., UV light).  I think you are using the term ‘interpretation’ to describe 
the same thing.  Do you agree?  Do you think the notions of perception and 
interpretation are effectively the same thing?

Cheers,

Guy

Guy Hoelzer, Associate Professor
Department of Biology
University of Nevada Reno

Phone:  775-784-4860
Fax:  775-784-1302
hoel...@unr.edumailto:hoel...@unr.edu

On Apr 24, 2015, at 10:22 AM, Terrence W. DEACON 
dea...@berkeley.edumailto:dea...@berkeley.edu wrote:

Hi Pedro,

Indeed, you capture a fundamental point of my work. I entirely agree with your 
comment about living processes and their internal informative organization. 
The three exceedingly simple molecular model systems (forms of autogenesis) 
that I discuss toward the end of the paper were intended to exemplify a minimal 
life-like unit that—because of its self-reconstituting and self-repairing 
features—could both exemplify an origin of life transition and a first simplest 
system exhibiting interpretive competence. It is only because these autogenic 
systems respond to disruption of their internal organizational coherence that 
they can be said to also interpret aspects of their environment with respect to 
this. My goal in this work is to ultimately provide a physico-chemical 
foundation for a scientific biosemiotics, which is currently mostly exemplified 
by analogies to human-level semiotic categories.

Thank you for your thoughtful comments and your mediation of these discussions.

Sincerely, Terry

On Fri, Apr 24, 2015 at 5:34 AM, Pedro C. Marijuan 
pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.es wrote:
Dear Terry and colleagues,

I hope you don't mind if I send some suggestions publicly. First, thank you for 
the aftermath, it provides appropriate closure to a very intense discussion 
session. Second, I think you have encapsulated very clearly an essential point 
(at least in my opinion):

Among these givens is the question of what is minimally necessary for
 a system or process to be interpretive, in the sense of being able to utilize 
present
intrinsic physical properties of things to refer to absent or
displaced properties or phenomena. This research question is ignorable
when it is possible to assume human or even animal interpreters as
part of the system one is analyzing. At some point, however, it
becomes relevant to not only be more explicit about what is being
assumed, but also to explain how this interpretive capacity could
possibly originate in a universe where direct contiguity of causal
influence is the rule.

My suggestion concerns the absence phenomenon (it also has appeared in some 
previous discussion in this list --notably from Bob's). You imply that there is 
an entity capable  of dynamically building upon  an external absences, OK quite 
clear,  but what about internal absences? I mean at the origins of 
communication there could be the sensing of the internal-- lets call it 
functional voids, needs, gaps, deficiencies, etc. Cellularly there are some 
good arguments about that, even in the 70's there was a metabolic code 
hypothesis crafted on the origins of cellular signaling. For instance, one of 
the most important environmental  internal detections concerns cAMP, which 
means you/me are in an energy trouble... some more evolutionary arguments can 
be thrown.  Above all, this idea puts the life cycle and its self-production 
needs in the center of communication, and in the very origins of the 
interpretive capabilities. Until now I have not seen much reflections around 
the life cycle as the true provider of both communications and meanings, maybe 
it conduces to new avenues of thought interesting to explore...

All the best!
--Pedro


Pedro C. Marijuan wrote:

Dear FIS colleagues,
Herewith the comments received from Terry several weeks ago. As I said
yesterday, the idea is to properly conclude that session, not to restart
the discussion. Of course, scholarly comments are always welcome, but
conclusively and not looking for argumentative rounds. Remember that in
less than ten days we will have a new session on info science and library
science. best --Pedro

--

Retrospective comments on the January 2015 FIS discussion

Terrence Deacon (dea...@berkeley.edumailto:dea...@berkeley.edu)

During the bulk of my career since the early 1980s I studied brain
organization with a particular focus on its role in the production and
interpretation of communication 

Re: [Fis] New Year Lecture: Aftermath

[joe.bren...@bluewin.ch]

Dear Pedro, Dear Terry,
Always an optimist, I was convinced that there could be a convergence of your 
approaches and my Logic in Reality starting from the domain of absence. What 
Pedro refers to as functional voids, needs, gaps,
deficiencies (absences) are all predominantly negative aspects of systems that 
operate especially in living systems 'together' with their positive 
counterparts (presences). The evolution of these elements in the 
physico-chemical domain follows this logic, in which negative elements always 
are given the necessary ontological 'status'. They are the basis for the 
emergence of higher level entities, following Terry's hierarchies of dynamics.
Thus we may have, to further support a scientific biosemiotics, a dynamic logic 
to replace the analogies to human-level semiotic categories many of which 
(read: Peirce) do not instantiate the necessary ontological complexity and 
commitment. 
Cheers,
Joseph
Message d'origine
De : dea...@berkeley.edu
Date : 24/04/2015 - 10:22 (PST)
À : pcmarijuan.i...@aragon.es
Cc : fis@listas.unizar.es
Objet : Re: [Fis] New Year Lecture: Aftermath
Hi Pedro,
Indeed, you capture a fundamental point of my work. I entirely agree with your 
comment about living processes and their internal informative organization. 
The three exceedingly simple molecular model systems (forms of autogenesis) 
that I discuss toward the end of the paper were intended to exemplify a minimal 
life-like unit that—because of its self-reconstituting and self-repairing 
features—could both exemplify an origin of life transition and a first simplest 
system exhibiting interpretive competence. It is only because these autogenic 
systems respond to disruption of their internal organizational coherence that 
they can be said to also interpret aspects of their environment with respect to 
this. My goal in this work is to ultimately provide a physico-chemical 
foundation for a scientific biosemiotics, which is currently mostly exemplified 
by analogies to human-level semiotic categories.
Thank you for your thoughtful comments and your mediation of these discussions.
Sincerely, Terry
On Fri, Apr 24, 2015 at 5:34 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es 
wrote:
  
Dear Terry and colleagues, 
I hope you don't mind if I send some suggestions publicly. First, thank
you for the aftermath, it provides appropriate closure to a very
intense discussion session. Second, I think you have encapsulated very
clearly an essential point (at least in my opinion): 
Among these givens is the question of what is minimally necessary
for
 a system or process to be interpretive, in the sense of being able to
utilize present
intrinsic physical properties of things to refer to absent or
displaced properties or phenomena. This research question is ignorable
when it is possible to assume human or even animal interpreters as
part of the system one is analyzing. At some point, however, it
becomes relevant to not only be more explicit about what is being
assumed, but also to explain how this interpretive capacity could
possibly originate in a universe where direct contiguity of causal
influence is the rule.
My suggestion concerns the absence phenomenon (it also has appeared
in some previous discussion in this list --notably from Bob's). You
imply that there is an entity capable  of dynamically building upon  an
external absences, OK quite clear,  but what about internal absences?
I mean at the origins of communication there could be the sensing of
the internal-- lets call it functional voids, needs, gaps,
deficiencies, etc. Cellularly there are some good arguments about that,
even in the 70's there was a metabolic code hypothesis crafted on the
origins of cellular signaling. For instance, one of the most important
environmental  internal detections concerns cAMP, which means
you/me are in an energy trouble... some more evolutionary arguments
can be thrown.  Above all, this idea puts the life cycle and its
self-production needs in the center of communication, and in the very
origins of the interpretive capabilities. Until now I have not seen
much reflections around the life cycle as the true provider of both
communications and meanings, maybe it conduces to new avenues of
thought interesting to explore...
All the best!
--Pedro
Pedro C. Marijuan wrote:
  
  
Dear FIS colleagues,
Herewith the comments received from Terry several weeks ago. As I said
yesterday, the idea is to properly conclude that session, not to restart
the discussion. Of course, scholarly comments are always welcome, but
conclusively and not looking for argumentative rounds. Remember that in
less than ten days we will have a new session on info science and library
science. best --Pedro
--
Retrospective comments on the January 2015 FIS discussion
  
Terrence Deacon (dea...@berkeley.edu)
During the bulk of my career since the early 1980s I studied brain
organization

Re: [Fis] New Year Lecture: Aftermath

[Terrence W. DEACON]

Hi Pedro,

Indeed, you capture a fundamental point of my work. I entirely agree with
your comment about living processes and their internal informative
organization. The three exceedingly simple molecular model systems (forms
of autogenesis) that I discuss toward the end of the paper were intended to
exemplify a minimal life-like unit that—because of its self-reconstituting
and self-repairing features—could both exemplify an origin of life
transition and a first simplest system exhibiting interpretive competence.
It is only because these autogenic systems respond to disruption of their
internal organizational coherence that they can be said to also interpret
aspects of their environment with respect to this. My goal in this work is
to ultimately provide a physico-chemical foundation for a scientific
biosemiotics, which is currently mostly exemplified by analogies to
human-level semiotic categories.

Thank you for your thoughtful comments and your mediation of these
discussions.

Sincerely, Terry

On Fri, Apr 24, 2015 at 5:34 AM, Pedro C. Marijuan 
pcmarijuan.i...@aragon.es wrote:

  Dear Terry and colleagues,

 I hope you don't mind if I send some suggestions publicly. First, thank
 you for the aftermath, it provides appropriate closure to a very intense
 discussion session. Second, I think you have encapsulated very clearly an
 essential point (at least in my opinion):












 *Among these givens is the question of what is minimally necessary for  a
 system or process to be interpretive, in the sense of being able to utilize
 present intrinsic physical properties of things to refer to absent or
 displaced properties or phenomena. This research question is ignorable when
 it is possible to assume human or even animal interpreters as part of the
 system one is analyzing. At some point, however, it becomes relevant to not
 only be more explicit about what is being assumed, but also to explain how
 this interpretive capacity could possibly originate in a universe where
 direct contiguity of causal influence is the rule. *My suggestion
 concerns the absence phenomenon (it also has appeared in some previous
 discussion in this list --notably from Bob's). You imply that there is an
 entity capable  of dynamically building upon  an external absences, OK
 quite clear,  but what about internal absences? I mean at the origins of
 communication there could be the sensing of the internal-- lets call it
 functional voids, needs, gaps, deficiencies, etc. Cellularly there are some
 good arguments about that, even in the 70's there was a metabolic code
 hypothesis crafted on the origins of cellular signaling. For instance, one
 of the most important environmental  internal detections concerns cAMP,
 which means you/me are in an energy trouble... some more evolutionary
 arguments can be thrown.  Above all, this idea puts the life cycle and its
 self-production needs in the center of communication, and in the very
 origins of the interpretive capabilities. Until now I have not seen much
 reflections around the life cycle as the true provider of both
 communications and meanings, maybe it conduces to new avenues of thought
 interesting to explore...

 All the best!
 --Pedro


 Pedro C. Marijuan wrote:

 Dear FIS colleagues,
 Herewith the comments received from Terry several weeks ago. As I said
 yesterday, the idea is to properly conclude that session, not to restart
 the discussion. Of course, scholarly comments are always welcome, but
 conclusively and not looking for argumentative rounds. Remember that in
 less than ten days we will have a new session on info science and library
 science. best --Pedro*
 --

 Retrospective comments on the January 2015 FIS discussion*

 Terrence Deacon (dea...@berkeley.edu)
 During the bulk of my career since the early 1980s I studied 
 brainorganization with a particular focus on its role in the production 
 andinterpretation of communication in vertebrate animals and humans. Onecore 
 target of these studies was to understand the neurologicalchanges that led to 
 the evolution of the human language capacity andwhy it is so anomalous in the 
 context of the other diversecommunication systems that have evolved. This 
 work was largelyconducted using standard lab-based neuroscience tools—from 
 axonaltracer techniques, to fetal neural transplantation, to MRI imaging,and 
 more—and studying a diverse array of animal brains. Besidesevolutionary and 
 developmental neuroscience, this path led me toexplore ethology, linguistics, 
 semiotic theories, information theoriesand the philosophical issues that 
 these research areas touched upon.Indeed, my first co-authored book was not 
 on neuroscience but on thedesign of the early Apple desktop computers. So I 
 came at the issuesexplored in my FIS essay from this diverse background. This 
 has led meto pose what may be more basic questions than are usually 
 considered,and to 

Re: [Fis] New Year Lecture: Aftermath

[Terrence W. DEACON]

Hi Guy,

Yes. At the very basic level that I explore with these ultra simple model
systems it would not be easy to distinguish perception and reaction. Both
involve interpretive steps, in that only some material
features—specifically those with potentially disruptive or constructive
potential for system organization—are assigned informative value in
consequence of the self-rectifying dynamics they correlate with.

— Terry

On Fri, Apr 24, 2015 at 11:09 AM, Guy A Hoelzer hoel...@unr.edu wrote:

  Hi Terry,

  I have used the term ‘perception’ in referring to in-formation that
 affects internal structure or dynamics.  This would contrast with forms of
 potential information that might pass through the system without being
 ‘perceived’.  For example, we have a finite number of mechanisms we call
 senses, each of which is sensitive to particular modes of information we
 encounter in our environment, but we are not able to perceive every form of
 information that we encounter (e.g., UV light).  I think you are using the
 term ‘interpretation’ to describe the same thing.  Do you agree?  Do you
 think the notions of perception and interpretation are effectively the same
 thing?

  Cheers,

  Guy

 Guy Hoelzer, Associate Professor
 Department of Biology
 University of Nevada Reno

 Phone:  775-784-4860
 Fax:  775-784-1302
 hoel...@unr.edu

  On Apr 24, 2015, at 10:22 AM, Terrence W. DEACON dea...@berkeley.edu
 wrote:

  Hi Pedro,

  Indeed, you capture a fundamental point of my work. I entirely agree
 with your comment about living processes and their internal informative
 organization. The three exceedingly simple molecular model systems (forms
 of autogenesis) that I discuss toward the end of the paper were intended to
 exemplify a minimal life-like unit that—because of its self-reconstituting
 and self-repairing features—could both exemplify an origin of life
 transition and a first simplest system exhibiting interpretive competence.
 It is only because these autogenic systems respond to disruption of their
 internal organizational coherence that they can be said to also interpret
 aspects of their environment with respect to this. My goal in this work is
 to ultimately provide a physico-chemical foundation for a scientific
 biosemiotics, which is currently mostly exemplified by analogies to
 human-level semiotic categories.

  Thank you for your thoughtful comments and your mediation of these
 discussions.

  Sincerely, Terry

 On Fri, Apr 24, 2015 at 5:34 AM, Pedro C. Marijuan 
 pcmarijuan.i...@aragon.es wrote:

  Dear Terry and colleagues,

 I hope you don't mind if I send some suggestions publicly. First, thank
 you for the aftermath, it provides appropriate closure to a very intense
 discussion session. Second, I think you have encapsulated very clearly an
 essential point (at least in my opinion):












 *Among these givens is the question of what is minimally necessary for
  a system or process to be interpretive, in the sense of being able to
 utilize present intrinsic physical properties of things to refer to absent
 or displaced properties or phenomena. This research question is ignorable
 when it is possible to assume human or even animal interpreters as part of
 the system one is analyzing. At some point, however, it becomes relevant to
 not only be more explicit about what is being assumed, but also to explain
 how this interpretive capacity could possibly originate in a universe where
 direct contiguity of causal influence is the rule. *My suggestion
 concerns the absence phenomenon (it also has appeared in some previous
 discussion in this list --notably from Bob's). You imply that there is an
 entity capable  of dynamically building upon  an external absences, OK
 quite clear,  but what about internal absences? I mean at the origins of
 communication there could be the sensing of the internal-- lets call it
 functional voids, needs, gaps, deficiencies, etc. Cellularly there are some
 good arguments about that, even in the 70's there was a metabolic code
 hypothesis crafted on the origins of cellular signaling. For instance, one
 of the most important environmental  internal detections concerns cAMP,
 which means you/me are in an energy trouble... some more evolutionary
 arguments can be thrown.  Above all, this idea puts the life cycle and its
 self-production needs in the center of communication, and in the very
 origins of the interpretive capabilities. Until now I have not seen much
 reflections around the life cycle as the true provider of both
 communications and meanings, maybe it conduces to new avenues of thought
 interesting to explore...

 All the best!
 --Pedro


 Pedro C. Marijuan wrote:

 Dear FIS colleagues,
 Herewith the comments received from Terry several weeks ago. As I said
 yesterday, the idea is to properly conclude that session, not to restart
 the discussion. Of course, scholarly comments are always welcome, but
 conclusively and not looking for argumentative 

[Fis] New Year Lecture: Aftermath

[Pedro C. Marijuan]

Dear FIS colleagues,
Herewith the comments received from Terry several weeks ago. As I said
yesterday, the idea is to properly conclude that session, not to restart
the discussion. Of course, scholarly comments are always welcome, but
conclusively and not looking for argumentative rounds. Remember that in
less than ten days we will have a new session on info science and library
science. best --Pedro
*
--

Retrospective comments on the January 2015 FIS discussion*

Terrence Deacon (dea...@berkeley.edu)

During the bulk of my career since the early 1980s I studied brain
organization with a particular focus on its role in the production and
interpretation of communication in vertebrate animals and humans. One
core target of these studies was to understand the neurological
changes that led to the evolution of the human language capacity and
why it is so anomalous in the context of the other diverse
communication systems that have evolved. This work was largely
conducted using standard lab-based neuroscience tools—from axonal
tracer techniques, to fetal neural transplantation, to MRI imaging,
and more—and studying a diverse array of animal brains. Besides
evolutionary and developmental neuroscience, this path led me to
explore ethology, linguistics, semiotic theories, information theories
and the philosophical issues that these research areas touched upon.
Indeed, my first co-authored book was not on neuroscience but on the
design of the early Apple desktop computers. So I came at the issues
explored in my FIS essay from this diverse background. This has led me
to pose what may be more basic questions than are usually considered,
and to reconsider even the most unquestioned assumptions about the
nature of information and the origins of its semiotic properties.

I am aware that many who are following this discussion have a
career-long interest in some aspect of human communication or
computation. In these realms many researchers —including many of
you— have provided sophisticated analytical tools and quite extensive
theories for describing these processes. Though it may at first seem
as though I am questioning the validity of some of this (now accepted)
body of theory, for the most part I too find this adequate for the
specific pragmatic issues usually considered. The essay I posted did
not critique any existing theory. It rather explored some assumptions
that most theories take for granted and need not address.

I believe, however, that there remain a handful of issues that have
been set aside and taken as givens that need to be reconsidered. For
the most part, these assumptions don't demand to be unpacked in order
to produce useful descriptions of communicative and information
processes at the machine or interpersonal level. Among these givens is
the question of what is minimally necessary for a system or process to
be interpretive, in the sense of being able to utilize present
intrinsic physical properties of things to refer to absent or
displaced properties or phenomena. This research question is ignorable
when it is possible to assume human or even animal interpreters as
part of the system one is analyzing. At some point, however, it
becomes relevant to not only be more explicit about what is being
assumed, but also to explain how this interpretive capacity could
possibly originate in a universe where direct contiguity of causal
influence is the rule. Although, this may appear to some readers as a
question that is merely of philosophical concern, I believe that
failure to consider it will impede progress in exploring some of the
most pressing scientific issues of our time, including both the nature
an origins of living and mental processes, and possibly even quantum
processes.

In this respect, my exposition was not in any respect critical of other
approaches but was rather an effort to solicit collaboration in digging
into issues that have —for legitimate pragmatic reasons— not been a
significant focus of most current theoretical analysis. I understand why
some readers felt that the whole approach was peripheral to their current
interests. Or who thought that I was re-opening debates that had long-ago
been set aside. Or who just thought that I was working at the wrong level,
on the conviction that the answer to such questions lies in other realms, 
e.g. quantum theories or panpsychic philosophies. To those of you who fell

into these categories, I beg your indulgence.

The issues involved are not merely of philosophical interest. They are of
critical relevance to understanding biological and neurological information.
So if there are any readers of this forum who are interested in the issue 
of the whether reference and significance are physically explainable irrespective

of human subjective observation, and who have been quietly reflecting on my
proposals, I would be happy to carry on an email dialogue outside of
this forum.

For the 

Re: [Fis] New Year Lecture - redux

[Pedro C. Marijuan]

Thanks Marcus, it is nice to greet to new, interesting parties joining 
the list. The aftermath message was received some weeks ago --Terry's 
agenda made him very difficult to continue the discussions of the New 
Year Lecture, which on the other side was planned for no longer than 4 
weeks or so. It is not intended to start the discussion anew... but to 
conclude it (will it be possible?). Tomorrow I will post it.


best--Pedro

Marcus Abundis wrote:

Hi Pedro,

In this reprise of Deacon's(?) talk, I assume the discussion will 
orient around the same paper Terry made available to the group 
earlier. If a new version of that paper is to be considered, please 
let me know. I am new to the FIS group and presently busy going over 
last January's notes in order to get unto speed. Thanks!


Marcus Abundis



--
-
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/
-

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[Fis] New Year Lecture - redux

[Marcus Abundis]

Hi Pedro,

In this reprise of Deacon's(?) talk, I assume the discussion will
orient around the same paper Terry made available to the group earlier. If
a new version of that paper is to be considered, please let me know. I am
new to the FIS group and presently busy going over last January's notes in
order to get unto speed. Thanks!

Marcus Abundis
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[Fis] FIS NEW YEAR LECTURE

[Pedro C. Marijuan]

Dear FIS Colleagues,

Following our recently established tradition, for the 2015 FIS New Year 
Lecture we will count with:

*
_Terrence W. Deacon_*
Professor of Anthropology
Cognitive Science Faculty
University of California at Berkeley

He will impart the Lecture:

_*Steps to a Theory of Reference  Significance in Information*_

Members of the thought collective The Pirates are also invited to the 
discussion.
The theme will be developed in an Essay attached to my next message. In 
order to facilitate discussion I will copy within the message's body the 
Introduction and some of the concluding comments of the Essay. Let us 
anticipate a really exciting discussion!


Best wishes to all, FISers and Pirates, and Happy New Year!

--Pedro

-
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/
-

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[Fis] New Year Lecture wrap-up

[Dino Buzzetti]

Dear Hans,

Thank you very much again for your lecture and your
subsequent comments and replies.  I dare posting a new
comment as an aftermath to your wrap-up and to Pedro's
official closure.  But I am sure you agree with me, that the
matter cannot be settled yet and that a continuation of the
discussion is a sign of the fruitfulness of your lecture.  As
a matter of fact, when I received Pedro's official closure
announcement I was a little disappointed because I had
been gathering some evidence in support of a previous
comment of mine, which probably was not clear enough.
I would not like to bother you any more, but since you
mention the usefulness of a philosophical outlook, here
is a philosophical observation I was able to find.

According to Jules Vuillemin (*Necessity or Contingency*,
Stanford CA, CSLI Publications, 1996), “probability in the
classical sense,” as is well known, is “relative to our ignorance
only” (p. 261), but “probability amplitude is something
altogether different” (264). For “when physicists today make
reference to [...] probability amplitudes [...] they indeed
allude to second order probabilities” (167). Therefore, the
distinction “between a probability and a probability amplitude”
entails a “new distinction in the history of modal notions,”
a distinction that Vuillemin describes in the following way:

“Classical physics was content with the opposition 'This particle
passes through A' versus 'This particle has the probability π
of passing through A'. This opposition has nothing to do with
ontology: it incorporates what is due to our ignorance into the
determination of natural phenomena. Instead of attributing
a property or magnitude to a physical system, we attribute it
a disposition or propensity to have that property or magnitude.
Probability measures that disposition or propensity that belongs
to the system in act. A probability amplitude is something
altogether different. We can compare it to an embryonic
probability as the inventors of the infinitesimal calculus
compared the moment of motion to an embryonic motion
that an integration would bring to a state of whole motion.
But the comparison limps. For the probability amplitude,
which is generally a complex quantity, does not figure among
the elements of reality. To obtain a probability we must multiply
two conjugated probability amplitudes. This means that, when
we attribute that amplitude to a system, it is attributed neither
as an actual property or magnitude nor as an actual disposition
or propensity to having such property or magnitude, but as a
purely virtual disposition or propensity to having it. The second-
order potentiality, as it were, thus put into play is no longer the
measure of an ignorance that might have some chance of being
only provisional. It is physical. It describes nature.” (264-65)

This is just the conclusion of a long-winded argument, but if
Vuillemin is right, then, the interpretation of a superposition
of probability amplitudes cannot be Bayesian, or “relative to
our ignorance only.” (261)

As S. Barry Cooper observes (
*Definability in the Real Universe*, http://arxiv.org/abs/1109.1416 ), “the
Laplacian
model has a deeply ingrained hold on the rational mind.
For a bromeliad-like late flowering of the paradigm we tend
to think of Hilbert and his assertion of very general expectations
for axiomatic mathematics. Or of  the state of physics before
quantum mechanics.”  From this point of view, QBism might
be described, to use Barry Cooper's own words, as “a defensive
response to an uncompleted paradigm change” (p. 4).

Kind regards,  -dino buzzetti




On 18 January 2014 18:47, Hans von Baeyer henrikrit...@gmail.com wrote:

 Dear Friends: In keeping with the message of my lecture, that knowledge of
 the world is based on the ensemble of individual experiences, more than on
 assumed objective, actual properties of an external reality, I will tell
 you about my experiences of writing and discussing the New Year Lecture. I
 enjoyed the entire process enormously, and wish once more to applaud Pedro
 for inventing this new tradition!

 Even as I started this email I learned something that piqued my interest.
  Gregory Bateson was quoted: Kant argued long ago that this piece of chalk
 contains a million potential facts (Tatsachen) but that only a very few of
  these become truly facts by affecting the behavior of entities capable of
  responding to facts.  Google.de informed me that Tatsache is probably an
 18th century translation of the English matter of fact. Tat is a deed,
 a factum, something done or performed, while Sache means a thing or a
 matter.  This tenuous etymology connects factuality with action rather than
 with some intrinsic essence. Kant's words affecting, behavior and
 responding are QBist to the core. More and more I realize that philosophy
 matters. Chris Fuchs, the chief spokesman for QBism, is among the rare
 physicists who give credit to philosophers for the contributions 

Re: [Fis] New Year Lecture Closure

[Pedro C. Marijuan]

Dear Hans,
Dear colleagues,

Thanks a lot for the good, generous job done. It has been a pleasure 
attending to your Lecture and to the discussion it has originated. There 
are quite many reflections to make and to develop in the future. QBism 
has general overtones, as was cogently explained, that overlap with the 
informational view of science itself; it is quite intriguing what the 
scientific method(s) of communication achieves regarding co-ordination 
of action when contemplated from the information-communication 
perspective. In these decades physics itself is getting into turmoil, 
once again, but nowadays the reinvention it is experimenting (the 
physics 3.0) relates in essential aspects with information. From the 
Newtonian conceptual cluster of particles and forces (physics 1.0), to 
the Maxwellian fields and Einstein-Schrödinger-Bohr waves and 
probabilities (physics 2.0), to where? Famously John Wheeler was 
asked, not much ago (in the new millennium hype) what was the essential 
topic of physics for the new decades: information was his succinct 
response.

Well, and that was it. The idea of this New Year Lecture, and of 
successive ones, is to put in communication our own information science 
community with the new stuff that different scientific vanguards are 
crafting and which may be of interest for our discussions. Hopefully the 
coming Lectures will be as exciting as this one!
 
Thanks to all the participants,

---Pedro

PS. Francesco's very positive comments are warmly acknowledged.


-
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/
-


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Re: [Fis] New Year Lecture wrap-up

[Francesco Rizzo]

Caro Pedro e cari tutti,
questa e-mail dell'egregio Hans von Baeyer mi ha stimolato a segnalare,
ancora una volta, quanto sia stato anticipatore il mio pensiero
scientifico-economico sull'importanza della legge dell'informazione a
partire, ad es.,dagli inizi degli anni Ottanta. Sia chiaro, non rivendico
nè presumo niente, bensì da poverino esponenziale come mi auto-definisco
sento tutto il piacere bambino di portare alla Vostra conoscenza che sul
processo di tras-in-form-azione ho scritto e pubblicato più di una dozzina
di libri. Qualcuno di essi l'ho inviato al carissimo Pedro che mi auguro
continui a tenermi non solo nella mente, ma anche nel cuore.
Grazie e saluti augurali nel nome del Signore mio e di tutti,  credenti e
 non credenti.
Francesco Rizzo, già professore di Economia e organizzazione aziendale
nella Facoltà di Ingegneria di Catania.


2014/1/18 Hans von Baeyer henrikrit...@gmail.com

 Dear Friends: In keeping with the message of my lecture, that knowledge of
 the world is based on the ensemble of individual experiences, more than on
 assumed objective, actual properties of an external reality, I will tell
 you about my experiences of writing and discussing the New Year Lecture. I
 enjoyed the entire process enormously, and wish once more to applaud Pedro
 for inventing this new tradition!

 Even as I started this email I learned something that piqued my interest.
  Gregory Bateson was quoted: Kant argued long ago that this piece of chalk
 contains a million potential facts (Tatsachen) but that only a very few of
  these become truly facts by affecting the behavior of entities capable of
  responding to facts.  Google.de informed me that Tatsache is probably an
 18th century translation of the English matter of fact. Tat is a deed,
 a factum, something done or performed, while Sache means a thing or a
 matter.  This tenuous etymology connects factuality with action rather than
 with some intrinsic essence. Kant's words affecting, behavior and
 responding are QBist to the core. More and more I realize that philosophy
 matters. Chris Fuchs, the chief spokesman for QBism, is among the rare
 physicists who give credit to philosophers for the contributions they make
 to natural science.  In return he hopes that they will listen to physicists
 who bring news from the furthest reaches of nature.

 My most intense experience in connection with the New Year Lecture was the
 writing of it.  The first challenge was brevity: The letter I have
 written today is longer than usual because I lacked the time to make it
 shorter quipped Blaise Pascal. In order to introduce QBism to you, I had
 to explain the Q and the B.  How to do that within the allotted length?
  The distinction between Bayesian and frequentist probability is an old
 subject among mathematicians, so I was able to steal from them. (Schreiben
 ist Borgen, writing is borrowing, according to the aphorist G.C.
 Lichtenberg.) But in order to talk about the Q, I had to show succinctly
 what's so special about quantum mechanics. At this point I was considerably
 aided by the GHZ prediction and its fairly recent corroboration, because,
 unlike all previous experiments, GHZ is a one-shot deal, rather than a
 subtle statistical effect. Like finding a single white raven to falsify the
 claim that all ravens are black.  But even so, although I could easily
 demonstrate the WRONG classical prediction, I was not able to show those of
 you who are not trained in theoretical physics how the correct quantum
 mechanical prediction for GHZ comes about.  Unfortunately I would need a
 semester for that!  In any case, by keeping to the prescribed format of the
 lecture, I was able to clarify my own thinking and to streamline my
 presentation of the unfamiliar topic.

 My timing  was very fortunate in that two unusually accessible articles
 about QBism appeared in November and December 2013 -- both available for
 free at arxiv.org. (ID numbers  1311.5253v1 and 1312.7825.) What a
 welcome coincidence!  It reassured me that the topic I had chosen for my
 lecture is emerging from its niche in quantum foundations research and
 slowly seeping out into the broader community.

 From the subsequent discussion I discovered several important things that
 are new to me.  I learned that there is the possibility, by means on
 non-Kolmogorovian probabilities, to avoid the troublesome certainty of
 probability 0 and 1 -- in particular via Logic in Reality.  I learned about
 the interesting concept of feed-forward, in contrast to feedback, which
 corrects for disruptions of a system BEFORE the disrupting influence kicks
 in. (In order to do that, the mechanism has to make use of an accurate
 model of the system's performance, so that it can PREDICT how the system
 will react.  I think it's an exaggeration to call this maneuver inverting
 the cause-and-effect sequence, but it comes close.)  I learned about
 instrumentalism, and will try to understand how it relates to pragmatism.

[Fis] New Year Lecture wrap-up

[Hans von Baeyer]

Dear Friends: In keeping with the message of my lecture, that knowledge of
the world is based on the ensemble of individual experiences, more than on
assumed objective, actual properties of an external reality, I will tell
you about my experiences of writing and discussing the New Year Lecture. I
enjoyed the entire process enormously, and wish once more to applaud Pedro
for inventing this new tradition!

Even as I started this email I learned something that piqued my interest.
 Gregory Bateson was quoted: Kant argued long ago that this piece of chalk
contains a million potential facts (Tatsachen) but that only a very few of
 these become truly facts by affecting the behavior of entities capable of
 responding to facts.  Google.de informed me that Tatsache is probably an
18th century translation of the English matter of fact. Tat is a deed,
a factum, something done or performed, while Sache means a thing or a
matter.  This tenuous etymology connects factuality with action rather than
with some intrinsic essence. Kant's words affecting, behavior and
responding are QBist to the core. More and more I realize that philosophy
matters. Chris Fuchs, the chief spokesman for QBism, is among the rare
physicists who give credit to philosophers for the contributions they make
to natural science.  In return he hopes that they will listen to physicists
who bring news from the furthest reaches of nature.

My most intense experience in connection with the New Year Lecture was the
writing of it.  The first challenge was brevity: The letter I have written
today is longer than usual because I lacked the time to make it shorter
quipped Blaise Pascal. In order to introduce QBism to you, I had to explain
the Q and the B.  How to do that within the allotted length?  The
distinction between Bayesian and frequentist probability is an old subject
among mathematicians, so I was able to steal from them. (Schreiben ist
Borgen, writing is borrowing, according to the aphorist G.C. Lichtenberg.)
But in order to talk about the Q, I had to show succinctly what's so
special about quantum mechanics. At this point I was considerably aided by
the GHZ prediction and its fairly recent corroboration, because, unlike all
previous experiments, GHZ is a one-shot deal, rather than a subtle
statistical effect. Like finding a single white raven to falsify the claim
that all ravens are black.  But even so, although I could easily
demonstrate the WRONG classical prediction, I was not able to show those of
you who are not trained in theoretical physics how the correct quantum
mechanical prediction for GHZ comes about.  Unfortunately I would need a
semester for that!  In any case, by keeping to the prescribed format of the
lecture, I was able to clarify my own thinking and to streamline my
presentation of the unfamiliar topic.

My timing  was very fortunate in that two unusually accessible articles
about QBism appeared in November and December 2013 -- both available for
free at arxiv.org. (ID numbers  1311.5253v1 and 1312.7825.) What a
welcome coincidence!  It reassured me that the topic I had chosen for my
lecture is emerging from its niche in quantum foundations research and
slowly seeping out into the broader community.

From the subsequent discussion I discovered several important things that
are new to me.  I learned that there is the possibility, by means on
non-Kolmogorovian probabilities, to avoid the troublesome certainty of
probability 0 and 1 -- in particular via Logic in Reality.  I learned about
the interesting concept of feed-forward, in contrast to feedback, which
corrects for disruptions of a system BEFORE the disrupting influence kicks
in. (In order to do that, the mechanism has to make use of an accurate
model of the system's performance, so that it can PREDICT how the system
will react.  I think it's an exaggeration to call this maneuver inverting
the cause-and-effect sequence, but it comes close.)  I learned about
instrumentalism, and will try to understand how it relates to pragmatism.

I was surprised when the conversation on the list veered from probability
and epistemology to communication and information.  But I shouldn't have
been.  The QBist point of view divides science into two realms.  On the one
hand each individual agent assembles the totality of her experiences
(experimenting, reading, talking, calculating...) into a web of probability
assignments that is as coherent and comprehensive as possible. That's the
easy part, and, as usual, physicists have picked it as their domain. But
the hard part is the effort of agents to correlate their private
experiences -- i.e. to communicate with each other in order to develop a
common scientific worldview. Agent A's description of an experience serves
as input for updating B's personal probability assignments via Bayes' law.
And this is done through language as well as math.  Niels Bohr more clearly
than any of the other pioneers of quantum mechanics realized the importance
of language 

Re: [Fis] New Year Lecture

[John Collier]

At 02:55 AM 2014/01/03, Joseph Brenner wrote:
Happy New Year and
Goodwill to all FIS'ers and distinguished guests!

I found the concept of Quantum Bayesianism as presented by
Professor von Baeyer most interesting. From the point of view of bringing
the subject-object balance back into physics it is very congenial to
Logic in Reality (LIR). I have several criticisms of this approach,
however, which I will try to make clear in the absence of any real skills
in quantum mechanics:

1. QBism seems not to consider the option of using
non-standard, non-Kolmogorivian probabilities to describe quantum and
non-quantum nature, that is, with values 0 but 1.

2. It excludes the case, impossible by classical logic, but
basic to physics and LIR, of a dynamic interaction between the subject
and the object which allows both views (belief and
facts) to be partly true or better operative at the same time
or at different times.

3. Since the QBism interpretation does not deal with points
1. and 2. above (also in the Fuchs, Mermin, Shack paper), it leaves the
door open to an anti-realist interpretation not only of quantum
mechanical reality, but of reality /tout court/ which must be based on
and reflect the quantum 'situation'. 
Sorry Joseph, but I don't understand your point 1. Could you
expand?
On 3, I think all forms of Bayesianism not only leave the door open to
antirealist interpretations, but are antirealist by their nature that
subjective probabilities are what probabilities are (Hume was the first
to declare this point, to the best of my knowledge). Bayes Theorem itself
is not antirealist, and can be applied to systems both internally and
externally. It is also a theorem of information theory that applies
whether you take information to be a subjective interpretation or an
objective intrinsic property of systems. But Bayesianism is subjective by
tradition and largely (there are exceptions in applications of
algorithmic information theory along Wallace's lines) by usage. I find
that people get a visceral reaction to Bayesianism much like they do to
generalized antirealism (as opposed to antirealism about a class of
things, which everyone accepts). Before an examination of a (realist)
thesis, another (antirealist) member of the examining committee joked to
me that being a realist or antirealist must be genetic. It is certainly
deep seated.
John





Professor John
Collier
colli...@ukzn.ac.za
Philosophy and Ethics, University of KwaZulu-Natal, Durban 4041 South
Africa
T: +27 (31) 260 3248 / 260 2292 F:
+27 (31) 260 3031

Http://web.ncf.ca/collier



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Re: [Fis] New Year Lecture

[PEDRO CLEMENTE MARIJUAN FERNANDEZ]

Dear Hans and FIS colleagues,

Thanks for the elegant text! It marks a great beginning for the FIS tradition 
of celebrating a Lecture with the New Year!

Not being very conversant with QM interpretations let me restrict myself to 
general aspects of QBism that grab my attention. First, about the 
reinterpretation of the relationship between subject and object. In my own 
views, as discussed in the recent Xian meeting, self-production and 
communication (signaling) should go hand with hand in the definition of the 
basic informational entities. The way these two aspects interlock and how 
inferences are made by the informational entity strongly reminds me the 
reappraisal of human experience proposed by QBism. How should we contemplate 
the necessarily social dimension of human knowledge? The quotations in the text 
and those from Schrodinger and Freud in Ref. 2 are excellent. About that, in 
middle 90's I worked (following maverick K.P. Collins) on the automatization 
of knowledge within central nervous systems. I think some of those ideas are 
still valid and in strong sync with these Bayesian inspired views. The 
intrinsic duality of knowledge was one of the outcomes.

Information in QM, whatever the interpretation, becomes itself a big word. 
Technically, Quantum Information Science has become a pan-inclusive term also 
encompassing Q Computing. Let me put a minor question then: would QBism 
become the most natural framework for Qbitsm? Or perhaps the subjective 
understanding of qubits might not be totally compatible with their applied use 
in quite definite computations? But it is really a minor thing. What I most 
like of this new quantum approach is the radicalism regarding meaning, 
experience, knowledge, science... This is good news for the people who sees 
information science as an occasion to contemplate anew the relationship of the 
individual with the increasing stock of knowledge accumulated by our 
civilization, where the ratio of our individual experience to the total is 
acceleratedly approaching zero!, and where the blind spots of collective 
intelligence are shining in too many areas of global life... It is healthy that 
the explicit limitation of the individual is also a message contained in QBism, 
at least in my understanding --seemingly, one of the proponents of QBism, 
Robert Spekkens, has developed some of the fundamental characteristics of 
QTheory by imposing a knowledge balance principle on the bits that a limited 
observer can exchange with its environment.

In comparison with other interpretations, there is QBism's good sense (Occam's 
razor) in not multiplying the universes just to save a theory, like the 
many-worlds interpretation does. Probably, as John says, there is something 
visceral in how realist and antirealist positions are taken, or in how the 
Bayesian or the frequentist approach to probability are taken. In any case, we 
have a lot to gain in information science by staying closer and cooperating 
with our Q Information colleagues, particularly with this new QBism 
interpretation.  Altough these topics are really difficult, we should try to 
connect... at least I promise to re-read the references and get more to the 
point during next weeks.

Thanks again for your brilliant opening lecture Hans, in the best style. 
Hopefully there will be great continuators too in the coming years.

---Pedro
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[Fis] New Year Lecture

[Hans von Baeyer]

*Quantum Bayesianism (QBism): An interpretation of quantum mechanics based
on quantum information theory*

Hans Christian von Baeyer, Professor of Physics, emeritus

College of William and Mary, Williamsburg, Virginia

January 2014



I am honored and proud to be asked by Pedro to inaugurate the
tradition of “New Year Lecture” to the FIS community, in the spirit of the
Royal Institution’s “Christmas Lectures”, which have been presented in
London almost every year since 1825.  Those shows were originally intended
for a “juvenile audience”, but have always captivated young and old alike.
My electronic lecture is not for children, but like many of its famous
predecessors it features a mind-boggling experiment.  In spite of the
scholarly nature my topic – the interpretation of quantum mechanics – my
principal message is simple, and I hope relevant to our quest for the
meaning of information.  I look forward to a lively discussion after my
virtual lecture!

QBism (with a capital B) is a radical new interpretation of
quantum mechanics that resolves many of the paradoxes that have bedeviled
the theory since its invention. The technical successes of quantum theory
are unchanged and undisputed -- only the meaning of the formalism is
re-appraised.   The revision has far-reaching implications for the
scientific worldview in general.

The crucial move for QBism, inspired by quantum information
theory, is very simple.  It consists of revising the predominant
interpretation of probability.  Most physicists accept the frequentist
interpretation of probability as “favorable outcomes/all possible
outcomes”.   Even though this definition becomes rigorous only in the
unrealistic limit of an infinite number of trials, it is claimed to be
objective.  QBism is based instead on the older Bayesian interpretation,
which defines probability as “degree of belief.”  Specifically, the
probability that an event will occur is an agent’s personal assignment of
betting odds for the occurrence of the event.  It is based on all the
information available to the agent, and is explicitly subjective.  Bayesian
probability, unlike frequentist probability, is meaningful for a single,
unrepeatable event.

Bayesianism is more general than frequentism.  In many cases,
such as normal laboratory practice, Bayesian probability can be *measured *by
conventional frequentist procedures, but the *meaning *of the result
remains Bayesian. (Similarly, temperature is measured by a thermometer, but
its meaning runs much deeper.) Bayesianism thus absorbs the successes of
frequentism.

By combining Bayesian probability with conventional quantum
mechanics, QBism locates the result of a calculation in the mind of the
agent who makes it. The Schrödinger wavefunction, which is a compendium of
information about a quantum system, and in turn yields probabilities for
the outcomes of future experiments, becomes subjective as well.  Input for
assigning betting odds comes from the experiments the agent performs
herself, added to information she gathers from the written and oral records
of science, i.e. from the totality of her personal experiences.  Since
wavefunctions are not real in this scheme, the problems associated with
such phenomena as the “collapse of the wavefunction” (when probability
snaps into certainty as a result of a measurement), Schrödinger’s cat,
nonlocality, and Bell inequalities, issues that were interminably debated
during the twentieth century, all dissolve.

The notorious problem of wavefunction collapse, for example,
which defies both mathematical description and the relativistic speed
limit, is interpreted as the modification of a probability assignment by a
measurement.  It is a straightforward application of Bayes’ Law (also known
as Bayes’ Theorem or Rule) for updating a probability upon the acquisition
of new information.  In this way QBism provides a natural and convincing
explanation of the mysterious collapse.

Apparent nonlocality is displayed most dramatically in an
experiment suggested in 1989 by Daniel Greenberger, Michael Horne, and
Anton Zeilinger (GHZ).  The spin of a “spin 1/2 particle” (such as an
electron) can be measured along one axis at a time -- say pointing up or
down (U/D) along the z axis, or, alternatively, right or left (R/L) along
the x axis.  Three identical particles are brought into close contact, and
prepared in the special GHZ configuration, in which they are said to be
“entangled.”  They are then separated by large distances and it is found
that whenever two of them point in the same horizontal direction, the third
one points UP. (DOWN, if the first two point in opposite directions.) Thus
LLU, RRU, RLD and LRD are found among the measurement results, but LLD,
RRD, RLU and LRU never occur.  A mnemonic: If your two index fingers point
in the same horizontal direction, one thumb (representing the third
particle,) points up. If they