[Fis] _ Re: Fis Digest, Vol 24, Issue 46

2016-03-31 Thread Louis H Kauffman
Dear Rukhsan,
You raise the most important issue. Quantum theory is embedded in all the 
matthematics that we have developed since the Greeks.
All this mathematics contributes to our understanding of physics. It is 
possible that certain aspects of that mathematics will develop naturally into 
new insights into
the nature of the physical world. The Grassmann and Clifford algebras are good 
examples of this sort of development.
Best,
Lou K.

> On Mar 31, 2016, at 2:04 PM, Rukhsanulhaq  wrote:
> 
> Dear All
> As Prof Kauffman has pointed out that there are many mysteries in quantum 
> theory which need to be decoded. The measurement problem being the central 
> one. And I agree with Prof Kauffman that taking the eigenvalue aspect of 
> quantum theory seriously and relating to Lambda calculus can help us to 
> understand its deeper aspects.
> However I would like to point to yet another related aspect. Spin is called 
> essentially quantum mechanical property which has no classical analogue. Yet 
> when one does construct the formalism to treat spin we just use SU(2) group 
> which provides the double cover for SO((3) group and all of it was known 
> before quantum theory as well. Similarly fermions are also very quantum 
> objects but their algebra was once again developed by Grassmann in an 
> entirely different context. It begs the question how does the Grassmann 
> algebra which was developed to understand geometry is exactly the same for 
> building blocks of matter. Is somehow quantum
> properties of matter coming from geometry. You will be surprised that in 
> recent developments in quantum theory(Berry phases) it has been found that 
> important physical properties of matter are related to geometry and topology 
> of space of quantum states.
> So all of it suggests that we have a long way to go before we resolve the 
> paradoxes of quantum theory. Geometry and topology are going to be beacon 
> lights in this endeavor. I am not forgetting algebra and logic which are 
> already there in the quantum theory itself,Heisenberg commutation relations 
> are algebraic and logical expressions of underlying quantum world.
> 
> Rukhsan
> 
> On Thu, Mar 31, 2016 at 6:28 PM,  > wrote:
> Send Fis mailing list submissions to
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>1. _ Re: Fis Digest, Vol 24, Issue 45 (Rukhsanulhaq)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 31 Mar 2016 18:28:28 +0530
> From: Rukhsanulhaq >
> To: fis@listas.unizar.es 
> Subject: [Fis] _ Re: Fis Digest, Vol 24, Issue 45
> Message-ID:
> 

[Fis] TOWARDS A NEW SESSION: SOEREN BRIER

2016-03-31 Thread PEDRO CLEMENTE MARIJUAN FERNANDEZ
Dear FISers,

Tomorrow we will start the new session on Infobiosemiotics, by Soeren Brier. 
Before so, let me pen some comments.

First, to join Plamen and others in thanking Louis. Particularly interesting 
for me was his last text on recursive distinctioning. Quite curiously, an old 
work of mine I mentioned weeks ago was about a sort of algebra for distinctions 
(to be applied to a putative "language of cells" via signaling systems) that 
contains remarkable similarities. Our elimination of items in the letter 
strings was based on three principles: symmetry, economy, and parsimony... we 
used "0" and inverse elements, and after the arrival of some new letters-signs 
the whole set/node was collapsing and "emitting", etc. etc. Anyhow, I will 
re-read with high interest, looking for further connections & ideas.

About some of the biological points raised in the discussion a few days ago 
(unfortunately I was caught in administrative compromises), I would reiterate 
that the present day biomolecular panorama of the simplest cells suggests a 
more cogent relationship between self-production and communication. I already 
gave some arguments: direct communication with the world is a prerequisite for 
organizing a metabolically efficient cellular system. Such direct communication 
via "one component systems" outnumbers any other signaling tools; this is well 
known in signaling science more than 10 years ago but has had no general impact 
yet.  The prokaryote is not really so autopoietic, it could be something else 
(maybe "infopoietic", but is the label needed??)... What the theme strongly 
suggests is a reconceptualization on how the cell "is in the world," only 
viable through unending communication tricks with the environment. 
Communication for "eking out" a life runs densely across the whole evolutionary 
process. Even more, it runs very deeply in the innards of our social life, in a 
curious trans-kingdom evolutionary twist. As I remarked in the previous session 
with Maxine, the origins of our own human communication via language are 
closely related to our wild "microbiome experiment". Given that we count with 
50% less microbiota in our gut and we have to produce an extra 20% of metabolic 
output, the social knitting via language for group feeding (cooking, 
fermentation, etc.) made the miracle. The big, communicative "social brain" 
(Allman, Dunbar) was essentially born for achieving group nutritional survival. 
Group communion... as is symbolically reminded in some religious rites. (Well, 
as an aside, my own mini-group is cooperating in some microbiome research on a 
very essential nutrient, with very curious results that we will publicize quite 
soon. I cannot help but having the theme in mind!). Anyhow, the final point 
from this ignored vital dependence and from similar ones is that we live 
crisscrossed by multitude of information flows that we are unaware of. That 
some disciplines could have deciphered faster some of them has had a tremendous 
influence on how we have approached during last two generations the whole 
information phenomena. Witness the terrible conceptual problems we have in 
whatever aggregate scales (often, already navigated elegantly by nervous 
systems).

The gist of the above tangents, is that some sort of premature closure in the 
the relationship between life and formal/philosophical arenas has introduced an 
unnecessary, cumbersome complexity. New forms of thought and of expression may 
be at hand to clarify the biological/social roots of information/communication 
phenomena, also for better capturing the personal meanings of life in these 
strange times of information and complexity overload. McLuhan revisited... And 
finally, a hint addressed to the quantum oriented colleagues: "When we look at 
a biological system we are looking at the face of the underlying physics of the 
universe." (Michael Conrad, First FIS Conference, Madrid 1994).

It will be quite interesting continuing the present discussion under the new 
themes proposed by Soeren.

Best regards
--Pedro


El 31/03/2016 a las 9:49, Louis H Kauffman escribió:
Dear Folks,
I will close with some comments about the relationship between recursive 
distinctioning and replication in biology.
This will be another example of the sort of modeling excursion that one can 
make by looking at patterns and analogies.
See
homepages.math.uic.edu/~kauffman/RD.html


RECURSIVE DISTINCTIONING

This folder contains links to papers related to Recursive Distinctioning. 
Recursive Distinctioning means just what it says. A pattern of distinctions is 
given in a space based on a graphical structure (such as a line of print or a 
planar lattice or given graph). Each node of the graph is occupied by a letter 
from some arbitrary alphabet. A specialized alphabet is given that can indicate 
distinctions about neighbors of a given node. The neighbors of a node are all 
nodes that are 

Re: [Fis] Fis Digest, Vol 24, Issue 46

2016-03-31 Thread Rukhsanulhaq
Dear All
As Prof Kauffman has pointed out that there are many mysteries in quantum
theory which need to be decoded. The measurement problem being the central
one. And I agree with Prof Kauffman that taking the eigenvalue aspect of
quantum theory seriously and relating to Lambda calculus can help us to
understand its deeper aspects.
However I would like to point to yet another related aspect. Spin is called
essentially quantum mechanical property which has no classical analogue.
Yet when one does construct the formalism to treat spin we just use SU(2)
group which provides the double cover for SO((3) group and all of it was
known before quantum theory as well. Similarly fermions are also very
quantum objects but their algebra was once again developed by Grassmann in
an entirely different context. It begs the question how does the Grassmann
algebra which was developed to understand geometry is exactly the same for
building blocks of matter. Is somehow quantum
properties of matter coming from geometry. You will be surprised that in
recent developments in quantum theory(Berry phases) it has been found that
important physical properties of matter are related to geometry and
topology of space of quantum states.
So all of it suggests that we have a long way to go before we resolve the
paradoxes of quantum theory. Geometry and topology are going to be beacon
lights in this endeavor. I am not forgetting algebra and logic which are
already there in the quantum theory itself,Heisenberg commutation relations
are algebraic and logical expressions of underlying quantum world.

Rukhsan

On Thu, Mar 31, 2016 at 6:28 PM,  wrote:

> Send Fis mailing list submissions to
> fis@listas.unizar.es
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> or, via email, send a message with subject or body 'help' to
> fis-requ...@listas.unizar.es
>
> You can reach the person managing the list at
> fis-ow...@listas.unizar.es
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Fis digest..."
>
>
> Today's Topics:
>
>1. _ Re: Fis Digest, Vol 24, Issue 45 (Rukhsanulhaq)
>
>
> --
>
> Message: 1
> Date: Thu, 31 Mar 2016 18:28:28 +0530
> From: Rukhsanulhaq 
> To: fis@listas.unizar.es
> Subject: [Fis] _ Re: Fis Digest, Vol 24, Issue 45
> Message-ID:
> 

[Fis] _ Interlude: emotional shock

2016-03-31 Thread Karl Javorszky
In the present Interlude after the session chaired by Lou on Symmetry and
before the coming one, allow me to enlarge on something Bruno raised.



Bruno wrote:





*Then this confirms the "computationalist theory of everything", which is
given by any formalism, like Robinson Arithmetic (the rest is given by the
internal machine's phenomenology, like the one deducible from
incompleteness). Indeed, in that theory, the stable (predictible)
observable have to be given by a statistics on all computation going
through our actual state. This (retro-)predicts that the physical obeys to
some quantum logic, and it can be derived from some intensional nuance on
the Gödel self-referential provability predicate (like beweisbar('p') &
consistent('t')).*



*In quantum mechanics without collapse of the wave during observation, the
axiom 3 is phenomenological, and with computationalism in the cognitive
science (the assumption that there is a level of description of the brain
such that my consciousness would proceed through any such emulation of my
brain or body at that level or below) the whole "physical" is
phenomenological. *

*Physics becomes a statistics on our consistent sharable first person
(plural) experiences. With "our" referring to us = the universal numbers
knowing that they are universal (Peano Arithmetic, Zermelo Fraenkel Set
Theory, viewed as machine, are such numbers).*



*An actuality is a possibility seen from inside, somehow, in this context
or theory (QM without collapse, or Computationalism). *



*Personally, it seems that quantum mechanics, when we agree on the internal
phenomenological of actuality in the possibilities, confirms the most
startling, perhaps shocking, consequence of computationalism (digital
mechanism). Note that it does not make the physical itself computable a
priori.*



Of these thoughts, let us focus on the following:

“…. when we agree on the internal phenomenological of actuality in the
possibilities, confirms the *most startling, perhaps shocking*, consequence
of computationalism (digital mechanism). …”



Now how does “shocking” enter a discourse on quantum concepts and the idea
that there is knowledge and wisdom in them there natural numbers?


Obviously, and let us thank Bruno for having pointed it out, there is an
element of reticence, unwillingness, resistance and protracted, unpleasant
surprise in the thought that Life, and the world in general may be much
more mechanistic and trivial than thought before.


The person pre-shock believes in something, the person post-shock knows
that he has been robbed a dream. It is like a child has to realise that
Santa Claus is not a real person, and that little babies do come about the
way they come about.

Many ideas have to be laid to rest during the process of familiarising
oneself to the idea that the glue that holds the world together – and
within it, our ideas about the world – is best described by the well-known
form of *a+b=c* as known from good old elementary school.


Discussing what forms and appearances the order can produce which rules
Nature, and within Nature, us and our thoughts, is unfortunately equivalent
to discussing, what kinds of order we can look into and discover within
*a+b=c*,  as this old, well-chewed bone is the backbone of rational
concepts.


The disillusionment will be individually instrumented for each of us, as
Tolstoy had said about the unhappiness of families, each in their own way.
The resulting – remaining – denotation, after having lost its connotations,
will be made up of the simple grey, standard, industrial units of
abstraction, order as a running fight among, and a compromise between *b-a,
a-2b, a+b, 2b-3a, *and the like.


Please accept my apologies for the shock the insight may cause that we are
indeed just an experiment in combinatorics, and probably the elves,
fairies, trolls and unicorns do not exist neither.
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Re: [Fis] concluding by beginning

2016-03-31 Thread Dr. Plamen L. Simeonov
Dear FIS Fellows,

I was also about writing some concluding remarks, since our time for math
in bio is about to end this week, but realized that Lou was fast with an
excellent final comment and list of references for postprocessing. I am
happy that after some initial hesitation on the forum the key messages came
accross and we were able to cover within short time the broad span of views
within short time. You are very welcome to continue the discussion also
privately and of course, within the scope of the next themes to come:
bio/cybersemiotics with Soeren Brier and physics with Alex Hankey, which
were nicely introduced by some earlier comments and associations like Bob's
triad from his inspiring book "The Third Window" which I see related to
C.S. Pierce's initiations in math, philosophy and semiotics. It became
clear that such important issues as circularity and recursion/repetition in
biology are closely related to distiction, (autocatalytic re)action,
memory, (negative) feedback, automation, self-organization, autocells on
the one side and (prime) numbers, fractional calculus,
triangular/quadrangular/polihedral structures, (Riemann) wave function
(analysis), QM and fractal geometry on the other, with opening room for
covering even more phenomenology and creating ideas along the multiple
lines of causation up to the limits of thought and imagination, nicely
reflected by the participants in the discussion. So I have no other chance
but to say: that's real life in a nutshell of exchanged messages! The most
astonishing characteristic of this communication which comes to end, but
just began in my eyes, is that we succeed to build together something that
is capabloe to not only link remote and sometimes obscure and absurd ideas
and question, but also attribute, enfold and evolve them with what we call
a trace of information, an ontology of a creative development process we
are participating, as if life becomes that what we really discover, revolve
and impress just in time: in Alex's words "a living from that e can
interact with, and (which) we are". And this is recursively wraped again
within Francesco's phrase: "la conoscenca ha fondamenti biologici ... e
viceversa, la biologia ha fondamenti quantistici". How could I say this in
Latin? Thank you all for this precious present! And welcome to the
next/this discussion topic again.


Plamen




On Thu, Mar 31, 2016 at 9:49 AM, Louis H Kauffman  wrote:

> Dear Folks,
> I will close with some comments about the relationship between recursive
> distinctioning and replication in biology.
> This will be another example of the sort of modeling excursion that one
> can make by looking at patterns and analogies.
> See
> homepages.math.uic.edu/~kauffman/RD.html
>
> *RECURSIVE DISTINCTIONING This folder contains links to papers related to
> Recursive Distinctioning. Recursive Distinctioning means just what it says.
> A pattern of distinctions is given in a space based on a graphical
> structure (such as a line of print or a planar lattice or given graph).
> Each node of the graph is occupied by a letter from some arbitrary
> alphabet. A specialized alphabet is given that can indicate distinctions
> about neighbors of a given node. The neighbors of a node are all nodes that
> are connected to the given node by edges in the graph. The letters in the
> specialized alphabet (call it SA) are used to describe the states of the
> letters in the given graph and at each stage in the recursion, letters in
> SA are written at all nodes in the graph, describing its previous state.
> The recursive structure that results from the iteration of descriptions is
> called Recursive Distinctioning. Here is an example. We use a line graph
> and represent it just as a finite row of letters. The Special Alphabet is
> SA = { =, [, ], O} where "=" means that the letters to the left and to the
> right are equal to the letter in the middle. Thus if we had AAA in the line
> then the middle A would be replaced by =. The symbol "[" means that the
> letter to the LEFT is different. Thus in ABB the middle letter would be
> replaced by [. The symbol "]" means that the letter to the right is
> different. And finally the symbol "O" means that the letters both to the
> left and to the right are different. SA is a tiny language of elementary
> letter-distinctions. Here is an example of this RD in operation where we
> use the proverbial three dots to indicate a long string of letters in the
> same pattern. For example,... AABAA ... is replaced by ...
> =]O[= ... is replaced by ... ]OOO[ ... is
> replaced by ... ===]O[=]O[=== ... . Note that the element ]O[
> appears and it has replicated itself in a kind of mitosis. To see this in
> more detail, here is a link to a page from a mathematica program written by
> LK that uses a 'blank' or 'unmarked state' instead of the '=" sign. 

[Fis] Possible sudentships to study theories of information

2016-03-31 Thread David.Chapman
Dear all,

I hope you will excuse this, especially since I have not been active in the 
discussions of this group. (I wish I had more time to engage - I keep seeing 
interesting things in the messages but know that if I get involved my list of 
other things I should have done but haven't will grow even larger!  Thank you 
to Pedro for running the group.)

The Department of Computing and Communications at The Open University in Milton 
Keynes, UK, is recruiting for two full-time PhD studentships.  See 
http://www.jobs.ac.uk/job/ANH409/two-studentships-in-computing-and-communications/.
 Among the topics of interest is the study of the nature of information. See 
the list of topics here: 
http://www9.open.ac.uk/mct-cc/study/research-degrees/student-projects and note 
especially the topics which identity Magnus Ramage or me as the contact.

Note also the short timescale - applications close 22nd April.

Thank you and best wishes to all on the list - hope I'll meet many of you in 
Gothenburg next year.

David

--
Dr. David A. Chapman CEng, FIET, FHEA
Senior Lecturer
Department of Computing and Communications
The Open University http://www9.open.ac.uk/mct-cc/people/david.chapman
Intropy blog: http://www.intropy.co.uk/
T. +44 1908 652919  Twitter @dachapman

The Open University is incorporated by Royal Charter (RC 000391), an exempt 
charity in England & Wales and a charity registered in Scotland (SC 038302).


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