Re: [Fis] Physics of computing

[Robin Faichney]

Hi Bruno,

This is very interesting for me, my approach to information is via the
mind-body and hard problems, and I'm sympathetic to
computationalism. On the other hand, I have difficulties understanding
much of what you say here. Let me focus on one point for now though.

Tuesday, April 17, 2012, 8:48:48 AM, Bruno wrote:

 Let me sketch the reasoning shortly. If I can survive with a
 digitalizable brain, then I am duplicable. For example I could, in
 principle, be read and cut in Helsinki (say) and pasted in two
 different places, like Moscow and Washington (to fix the thing).

 The subject to such a duplication experiment, knowing the protocol
 in advance, is unable to predict in advance where he will *feel to
 be* after the duplication. We can iterate such process and prove
 that at such iteration the candidate, seeing if he feels to be in W
 or in M, receive a bit of information, and that his best way to
 predict his experience, will be, in this case, to predict a random
 experience (even algorithmic random experience): like WWMWWWMMMWM
 , for example. That is the first person indeterminacy.

It seems to me that, if I believe I am duplicable, and understand the
protocol, I must predict that I will experience being in both Moscow
and Washington. The process bifurcates one person, who becomes two
people with absolutely identical physique and memories immediately
afterwards, which will then begin to diverge. Both, looking back to
pre-bifurcation times, will say that was me, and both will be
correct. There is no essence to be randomly (or non-randomly)
assigned to one location and not the other. The individual is now two
people and therefore can be and is in both cities.

-- 
Robin Faichney
http://www.robinfaichney.org/

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

Re: [Fis] Physics of computing

[Bruno Marchal]

On 17 Apr 2012, at 11:44, Loet Leydesdorff wrote:

 It seems to me that, if I believe I am duplicable, and understand the
 protocol, I must predict that I will experience being in both Moscow  
 and
 Washington. The process bifurcates one person, who becomes two  
 people with
 absolutely identical physique and memories immediately afterwards,  
 which
 will then begin to diverge.

OK. Then the uncertainty is bearing on the outcome of that divergence

You can predict this, in Helsinki:

(I will feel to be in W) and (I will feel to be in M)

But here you adopt a 3-view on your future 1-views.

But we assume comp, so we know that both copies will *feel* to be  
entire and complete in only one city. So from the first person point  
of view, it is

(I will feel to be in W) or (I will feel to be in M).

Assuming comp and the correct substitution level, you will never feel  
to be simultaneously in W and in M. This would entail a telepathic  
element which, given that we have chosen the right substitution level,  
would have a non computable element, and contradict comp.

We can verify this by asking the copy in W, and he will assesses to  
feel to be in W, and not in M, and having only an intellectual (3- 
view) belief of the existence of its copy in M. He cannot even know  
for sure that the copy has already been reconstituted there or not.


 Both, looking back to pre-bifurcation times,
 will say that was me, and both will be correct.

Absolutely so. That is why we have to listen to both of them, and both  
of them agree to feel to be in only one city. One sees english  
speakers around him, the other sees russian speakers, and none of them  
can realy *know* if their doppelganger has been reconstituted. Nor  
could they know in advance that they would hear russians or americans.

The advantage of proceeding with such thought experience is that it  
avoids the need to agree on personal identity. The indeterminacy bears  
only on experience which can be noted in a diary.

Of course, the experience suggest that personal identity is an  
illusion. If you keep your identity on both copies, then we can argue  
that we are all the same amoeba, who duplicates itself a lot since a  
long time. But this remark needs not to be agreed upon to understand  
that computationalism reverses physics and the information/computer/ 
number science.

If you really believe that the you-in W and the you-in M are really  
still exactly the same person, having different experience, then I can  
argue that you and me are already exactly the same person. Why not?  
Perhaps God, playing hide-and-seek with itself :)
But here we try to predict direct accessible results of self- 
localization after a self-duplication, and without a non computable  
telepathic link, the answer of the copies are different.


 There is no essence to
 be randomly (or non-randomly) assigned to one location and not the  
 other.

But there are human beings, knowing in which city they feel to be.  
None will write I feel to be in both M and W at once. Each will  
write I feel to be in just the city X, with X being M or W  
respectively. They can only bet, intellectually, about the existence  
of the other. Indeed, the guy in W would not been able to see I have  
cheated on him, and that I did not reconstitute him in M. OK?


 The individual is now two people and therefore can be and is in both  
 cities.

Only from a third person point of view. From the point of view of each  
copies, despite both being the same person as the one in Helsinki,  
they both feel right now to be in only one city. And the first person  
indeterminacy bears on such feeling, not on the bodies to which we can  
attriibute consciousness, but on the content of the consciousness,  
which in this case corresponds to the result of the self-localization  
(W, M?) which they will write in their diaries. None will write in the  
diary I feel to be in W and M.

Just replace humans by robots having some amount of inference  
inductive power. And imagine the iteration of the experience. So after  
finding themselves in some city, they buy a ticket to come back by  
plane to Helsinki, and they do the experience again and again. After  
iterating that experience 64 times, there will be 2^64 copies, and  
each of them will have, written in their respective personal diaries a  
specific sequence of W and M. Such robots can have already well  
defined elementary inference inductive power to guess that their  
sequences are non algorithmically compressible. Each of them cannot  
predict the next outcome of the self-duplication. Of course, some of  
them will develop theories. For example the one having the story  
W...W, will be tempted to predict W, but we know she will  
have many descendants contradicting that theory, and in this  
setting, they are deluded.

Of course real life will not be a sequence of self-duplication, but  
it will be a sequence of self-multiplication or differentiation 

Re: [Fis] Physics of computing

[Robin Faichney]

Hi again Bruno,

Heeding Pedro's kind reminder, this is my second and therefore last
message to the list this week. However, I'll be happy to continue the
discussion off-list (and to copy in any others who signal their
interest).

Tuesday, April 17, 2012, 10:57:41 AM, Bruno wrote:

 The guy know all this in advance. He knows that if comp is true, he
 will survive the duplication, and that, in all possible future
 personal situation, he will feel to be in only one city, with an
 inferred doppelganger in the other city.

No, in my view he will experience being in each city (both cities)
with an inferred doppelganger in the other city, because he is
one before the procedure and two after. This is very counter-intuitive
regarding personal identity but it is the logical consequence of your
assumptions.

 So, if he is asked in Helsinki where he will feel to be, he can
 only answer that he will feel to be in W or in M, but without being
 able to be sure if he will feel to be in W or that he will feel to be in M.

Looking forward, pre-bifurcation, the rational expectation is that his
identity will split, so that both post-bifurcation versions are
genuinely him, and there is no reason for the pre-bifurcation version
to choose either city as his destination, he genuinely has two
simultaneous destinations, in this scenario one person
(pre-bifurcation) can be in two places at once (post-bifurcation).

-- 
Robin Faichney
http://www.robinfaichney.org/

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

Re: [Fis] Physics of computing

[Pedro C. Marijuan]

Dear Joseph and FIS collegues,

The only item I can remember formally addressing the topic is La 
logique du vivant, by Francois Jacob in very early 70's. But it was 
perhaps more a philosophy of life than a rigorous approach or overall 
theoretical description of life processes. In any case it was original 
(bricolage) and inspiring. Nowadays my main criticism to visions 
inspired in physics would run as follows: imagine we are dealing with 
computers; any general approach to their performances, should it be 
based on solid state physics? Nope. You would need a theoretical, 
brand new vision, eg Turing machine on universal computation, or 
something similar attending to structures of computing processes and 
computing machinery. It would extend completely beyond physics, as the 
informatics realm is situated... pure technological creativity due to 
software and hardware engineers (of course, always mastering and slaving 
natural processes at the bottom, but in artful ways and multilevel 
purposes).


Regarding bio, the new theoretical integrated or unified approach 
(logic or whatever) would be similar to the above creativity. Grounded 
on some central bio characteristic, in my opinion self construction, as 
von Neumann started with his unfinished theory of self-constructing 
machines. Cells (and organisms) are the only entities rigorously 
selfconstructing themselves. Actually biology would be the science of 
selfconstruction... where a new notion of info related to the impact of 
communication on selfconstructing processes (meaning) would be 
central. It may look challenging, but without protein synthesis there is 
no meaning!


My criticism to current bio-doctrines extends to systems biology and 
other fashions (synthetic biology, bioinspired computing, artificial 
life...). Some ideas thrown in Inbiosa meetings could enter into the 
discussion too, I think.


best wishes

---Pedro

joe.bren...@bluewin.ch escribió:

Dear Pedro,

Thank you, Pedro, for bringing up the question of logics. My 
suggestion of a Logic in Reality is to open the debate, rather than to 
claim it is the only over-arching logic possible. Nevertheless, it 
would be useful for me and perhaps others if you could make your 
critique more specific by pointing to at least one logic that is used 
biologically that addresses the dynamics of complex processes. So far, 
I have not identified any such logical system that is more than a 
metaphorical use of the term logic or refers to some more or less 
reproducible characteristics of such processes. Otherwise, logics seem 
to me to refer only to abstracted linguistic aspects of processes that 
of course follow classical propositional logic but equate to tautologies.


Because Logic in Reality is grounded in physics, it is able to express 
somewhat more about change, evolution, etc. than any logic of which I 
am aware. I would be glad to learn of other candidates for this role.


Thank you and best wishes,

Joseph


Ursprüngliche Nachricht
Von: pcmarijuan.i...@aragon.es
Datum: 11.04.2012 10:44
An: fis@listas.unizar.es
Betreff: Re: [Fis] Physics of computing

Dear John and colleagues,

Nice to hear that you are OK after that dangerous intoxication
--our best wishes for your complete recovery!
About physical information I think that Landauer clarified the
panorama, at least concerning the relationship between information
theory and thermodynamics. According to his principle, any
logically irreversible transformation of classical information is
necessarily accompanied by the dissipation of at least k T ln(2)
of heat per lost bit (about 3 x 10 exp -21 Joules at 300 K
temperature), where obviously k is the Boltzmann constant and T
the temperature. Recently this principle has been verified
experimentally (Nature, 8 March 2012, p. 187). By the way, in his
past message Loet enters Watts in a similar expression (?). To
insist, Entropy and Information are dimensionless and do not
explicitly incorporate any units... About the quantum management
of info theory, it is another matter, quite more tricky.

Beyond that immediate physicality, things get quite obscure as our
contradictory meaning messages witness. The point made by Joseph
on an overarching logic, is rather difficult to be maintained --at
least in my small province of the biological signaling pathways.
Too many logics are used biologically in too many different
contexts or niches, either molecularly or neuronally... I bet that
they are not susceptible of integration in any logical system. 
Maybe Inbiosa parties would also disagree with me in this regard.


best wishes to all,

---Pedro

John Collier escribió:

Folks,
I have been in the hospital for almost three weeks due to
bleeding from warfarin. I had to have three blood transfusions
and an operation. I am only now getting my strength back

Re: [Fis] Physics of computing

[Gordana Dodig-Crnkovic]

Dear Pedro and FIS colleagues,

When connecting information to physics, I believe you may like the following 
view, from the abstract of an invited article
for a special issue of the journal Information on Information and Energy/Matter 
(currently in review):

INFORMATION PHYSICS—TOWARDS A NEW CONCEPTION OF PHYSICAL REALITY
Philip Goyal
Department of Physics, University at Albany (SUNY), 1400 Washington Av., 
Albany, NY 1, USA
Version April 10, 2012 submitted to Information.

Abstract: The concept of information plays a fundamental role in our everyday 
experience, but is conspicuously absent in framework of classical physics. Over 
the last century, quantum theory and a series of other developments in physics 
and related subjects have brought the concept of information and the interface 
between an agent and the physical world into increasing prominence. As a 
result, over the last few decades, there has arisen a growing belief amongst 
many physicists that the concept of information may have a critical role to 
play in our understanding of the workings of the physical world, both in more 
deeply understanding existing physical theories and in the formulation of new 
theories. In this paper, I explicate the origin of the informational view of 
physics, illustrate some of the work inspired by this view, and give some 
indication of its implications for the development of a new conception of 
physical reality.

Goyal talks about all of physics, reformulated in terms of information, not 
only one part of it like quantum mechanics.
If you combine this approach with Mark Burgin’s view that computation in 
general is information processing,
then Philip Goyal’s article can be understood in terms of computation.

I am looking forward to see the complete special issue which is taking shape 
these days, several articles are in review,
and there are several already published interesting contributions on to the 
relationship between information and physics:
http://www.mdpi.com/journal/information/special_issues/matter/

With best regards,
Gordana


http://www.mrtc.mdh.se/~gdc/
https://sites.google.com/site/naturalcomputingaisbiacap2012




From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On 
Behalf Of Pedro C. Marijuan
Sent: den 16 april 2012 17:54
To: fis@listas.unizar.es
Subject: Re: [Fis] Physics of computing

Dear Joseph and FIS collegues,

The only item I can remember formally addressing the topic is La logique du 
vivant, by Francois Jacob in very early 70's. But it was perhaps more a 
philosophy of life than a rigorous approach or overall theoretical description 
of life processes. In any case it was original (bricolage) and inspiring. 
Nowadays my main criticism to visions inspired in physics would run as follows: 
imagine we are dealing with computers; any general approach to their 
performances, should it be based on solid state physics? Nope. You would need 
a theoretical, brand new vision, eg Turing machine on universal computation, or 
something similar attending to structures of computing processes and computing 
machinery. It would extend completely beyond physics, as the informatics realm 
is situated... pure technological creativity due to software and hardware 
engineers (of course, always mastering and slaving natural processes at the 
bottom, but in artful ways and multilevel purposes).

Regarding bio, the new theoretical integrated or unified approach (logic or 
whatever) would be similar to the above creativity. Grounded on some central 
bio characteristic, in my opinion self construction, as von Neumann started 
with his unfinished theory of self-constructing machines. Cells (and organisms) 
are the only entities rigorously selfconstructing themselves. Actually biology 
would be the science of selfconstruction... where a new notion of info related 
to the impact of communication on selfconstructing processes (meaning) would 
be central. It may look challenging, but without protein synthesis there is no 
meaning!

My criticism to current bio-doctrines extends to systems biology and other 
fashions (synthetic biology, bioinspired computing, artificial life...). Some 
ideas thrown in Inbiosa meetings could enter into the discussion too, I think.

best wishes

---Pedro

joe.bren...@bluewin.chmailto:joe.bren...@bluewin.ch escribió:
Dear Pedro,

Thank you, Pedro, for bringing up the question of logics. My suggestion of a 
Logic in Reality is to open the debate, rather than to claim it is the only 
over-arching logic possible. Nevertheless, it would be useful for me and 
perhaps others if you could make your critique more specific by pointing to at 
least one logic that is used biologically that addresses the dynamics of 
complex processes. So far, I have not identified any such logical system that 
is more than a metaphorical use of the term logic or refers to some more or 
less reproducible characteristics of such processes. Otherwise, logics seem to 
me to refer only

Re: [Fis] Physics of computing

[Dr. Plamen L. Simeonov]

Dear Gordana,

thank you for the interesting reference and comments which actually
confirms what Bruno Marchal has been talking here all the time. Bruno, it
is your turn now.

Best wishes,

Plamen



On Mon, Apr 16, 2012 at 7:00 PM, Gordana Dodig-Crnkovic 
gordana.dodig-crnko...@mdh.se wrote:

  Dear Pedro and FIS colleagues,

 ** **

 When connecting information to physics, I believe you may like the
 following view, from the abstract of an invited article
 for a special issue of the journal Information on Information and
 Energy/Matter (currently in review):

 ** **

 INFORMATION PHYSICS—TOWARDS A NEW CONCEPTION OF PHYSICAL REALITY

 Philip Goyal

 Department of Physics, University at Albany (SUNY), 1400 Washington Av.,
 Albany, NY 1, USA

 Version April 10, 2012 submitted to Information. 

 ** **

 Abstract: The concept of information plays a fundamental role in our
 everyday experience, but is conspicuously absent in framework of classical
 physics. Over the last century, quantum theory and a series of other
 developments in physics and related subjects have brought the concept of
 information and the interface between an agent and the physical world into
 increasing prominence. As a result, over the last few decades, there has
 arisen a growing belief amongst many physicists that the concept of
 information may have a critical role to play in our understanding of the
 workings of the physical world, both in more deeply understanding existing
 physical theories and in the formulation of new theories. In this paper, I
 explicate the origin of the informational view of physics, illustrate some
 of the work inspired by this view, and give some indication of its
 implications for the development of a new conception of physical reality.*
 ***

 ** **

 Goyal talks about all of physics, reformulated in terms of information,
 not only one part of it like quantum mechanics.

 If you combine this approach with Mark Burgin’s view that computation in
 general is information processing,
 then Philip Goyal’s article can be understood in terms of computation.

 ** **

 I am looking forward to see the complete special issue which is taking
 shape these days, several articles are in review,
 and there are several already published interesting contributions on to
 the relationship between information and physics:

 http://www.mdpi.com/journal/information/special_issues/matter/

 ** **

 With best regards,

 Gordana

 ** **

 ** **

 http://www.mrtc.mdh.se/~gdc/

 https://sites.google.com/site/naturalcomputingaisbiacap2012  

 ** **

 ** **

 ** **

 ** **

 *From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
 *On Behalf Of *Pedro C. Marijuan
 *Sent:* den 16 april 2012 17:54
 *To:* fis@listas.unizar.es
 *Subject:* Re: [Fis] Physics of computing

 ** **

 Dear Joseph and FIS collegues,

 The only item I can remember formally addressing the topic is La logique
 du vivant, by Francois Jacob in very early 70's. But it was perhaps more a
 philosophy of life than a rigorous approach or overall theoretical
 description of life processes. In any case it was original (bricolage)
 and inspiring. Nowadays my main criticism to visions inspired in physics
 would run as follows: imagine we are dealing with computers; any general
 approach to their performances, should it be based on solid state
 physics? Nope. You would need a theoretical, brand new vision, eg Turing
 machine on universal computation, or something similar attending to
 structures of computing processes and computing machinery. It would extend
 completely beyond physics, as the informatics realm is situated... pure
 technological creativity due to software and hardware engineers (of course,
 always mastering and slaving natural processes at the bottom, but in
 artful ways and multilevel purposes).

 Regarding bio, the new theoretical integrated or unified approach (logic
 or whatever) would be similar to the above creativity. Grounded on some
 central bio characteristic, in my opinion self construction, as von Neumann
 started with his unfinished theory of self-constructing machines. Cells
 (and organisms) are the only entities rigorously selfconstructing
 themselves. Actually biology would be the science of selfconstruction...
 where a new notion of info related to the impact of communication on
 selfconstructing processes (meaning) would be central. It may look
 challenging, but without protein synthesis there is no meaning!

 My criticism to current bio-doctrines extends to systems biology and other
 fashions (synthetic biology, bioinspired computing, artificial life...).
 Some ideas thrown in Inbiosa meetings could enter into the discussion too,
 I think.

 best wishes

 ---Pedro

 joe.bren...@bluewin.ch escribió: 

 Dear Pedro,

 Thank you, Pedro, for bringing up the question of logics. My suggestion of
 a Logic in Reality is to open the debate, rather than to claim

Re: [Fis] Physics of computing

[Bill Seaman]

I recently came across the work of Gotthard Gunther while at the archives of 
the Biological Computer Lab. at University of Illionois, formerly run by von 
Foerster.

Two papers of interest in english...
http://www.vordenker.de/ggphilosophy/gg_new_approach.pdf
http://www.thinkartlab.com/pkl/archive/Cyberphilosophy.pdf

Most of his texts are in German but I am still researching:

Precursors – Biological Computing Lab

“M-valued Logic” – Gotthard Gunther

Proposal For a Basic Study of the Semantic and Syntactic Properties of 
Many-Valued and Morphogrammatic Systems of Logic. 1962

Morphogrammatic Logic 
 
“Logic which uses morphograms instead of values as basic operational units 
might be able to cope with the specific properties of self coding systems of 
mind-like or mental character.”

“The ultimate aim of the cybernetical systems-approach is to design computers 
as fully self-reflective systems. The theory of resolvable functions suggests 
that logical relations between individual values do not properly represent the 
complex characteristics of reflection…This indicates that in order to represent 
reflection we have to look for a different (and more complex) logical unit. 
This seems to be the morphogram.”

See also
http://vordenker.de/contribs.htm - under Gotthard Gunther

rudolf kaehr - special non two value logic:

http://works.bepress.com/cgi/viewcontent.cgi?article=1015context=thinkartlabsei-redir=1referer=http%3A%2F%2Fwww.google.com%2Furl%3Fsa%3Dt%26rct%3Dj%26q%3Drudolf%2520kaehr%2520-%2520special%2520non%2520two%2520value%2520logic%26source%3Dweb%26cd%3D1%26ved%3D0CCIQFjAA%26url%3Dhttp%253A%252F%252Fworks.bepress.com%252Fcgi%252Fviewcontent.cgi%253Farticle%253D1015%2526context%253Dthinkartlab%26ei%3D-TqHT4feOK2I8gH51NW-CA%26usg%3DAFQjCNGu_-JW00NR_5TIw8X8Qa9GlG3ZRA#search=%22rudolf%20kaehr%20-%20special%20non%20two%20value%20logic%22

Best
Bill







Bill Seaman
Professor, Department of Art, Art History  Visual Studies
DUKE UNIVERSITY 
114 b East Duke Building
Box 90764   
Durham, NC 27708, USA   
+1-919-684-2499 
http://billseaman.com/
http://fds.duke.edu/db/aas/AAH/faculty/william.seaman
http://www.dibs.duke.edu/research/profiles/98-william-seaman

RadioSeaman
Paste into itunes (Advanced/open audio streams) for internet radio:
http://smw-aux.trinity.duke.edu:8000/radioseaman



On Apr 12, 2012, at 8:25 PM, joe.bren...@bluewin.ch wrote:

 Dear Pedro,
 
 Thank you, Pedro, for bringing up the question of logics. My suggestion of a 
 Logic in Reality is to open the debate, rather than to claim it is the only 
 over-arching logic possible. Nevertheless, it would be useful for me and 
 perhaps others if you could make your critique more specific by pointing to 
 at least one logic that is used biologically that addresses the dynamics of 
 complex processes. So far, I have not identified any such logical system that 
 is more than a metaphorical use of the term logic or refers to some more or 
 less reproducible characteristics of such processes. Otherwise, logics seem 
 to me to refer only to abstracted linguistic aspects of processes that of 
 course follow classical propositional logic but equate to tautologies.
 
 Because Logic in Reality is grounded in physics, it is able to express 
 somewhat more about change, evolution, etc. than any logic of which I am 
 aware. I would be glad to learn of other candidates for this role.
 
 Thank you and best wishes,
 
 Joseph
 
 
 Ursprüngliche Nachricht
 Von: pcmarijuan.i...@aragon.es
 Datum: 11.04.2012 10:44
 An: fis@listas.unizar.es
 Betreff: Re: [Fis] Physics of computing
 
 Dear John and colleagues,
 
 Nice to hear that you are OK after that dangerous intoxication --our best 
 wishes for your complete recovery! 
 About physical information I think that Landauer clarified the panorama, at 
 least concerning the relationship between information theory and 
 thermodynamics. According to his principle, any logically irreversible 
 transformation of classical information is necessarily accompanied by the 
 dissipation of at least k T ln(2) of heat per lost bit (about 3 x 10 exp -21 
 Joules at 300 K temperature), where obviously k is the Boltzmann constant and 
 T the temperature. Recently this principle has been verified experimentally 
 (Nature, 8 March 2012, p. 187). By the way, in his past message Loet enters 
 Watts in a similar expression (?). To insist, Entropy and Information are 
 dimensionless and do not explicitly incorporate any units... About the 
 quantum management of info theory, it is another matter, quite more tricky. 
 
 Beyond that immediate physicality, things get quite obscure as our 
 contradictory meaning messages witness. The point made by Joseph on an 
 overarching logic, is rather difficult to be maintained --at least in my 
 small province

Re: [Fis] Physics of computing

[Pedro C. Marijuan]

Dear John and colleagues,

Nice to hear that you are OK after that dangerous intoxication --our 
best wishes for your complete recovery!
About physical information I think that Landauer clarified the panorama, 
at least concerning the relationship between information theory and 
thermodynamics. According to his principle, any logically irreversible 
transformation of classical information is necessarily accompanied by 
the dissipation of at least k T ln(2) of heat per lost bit (about 3 x 10 
exp -21 Joules at 300 K temperature), where obviously k is the Boltzmann 
constant and T the temperature. Recently this principle has been 
verified experimentally (Nature, 8 March 2012, p. 187). By the way, in 
his past message Loet enters Watts in a similar expression (?). To 
insist, Entropy and Information are dimensionless and do not explicitly 
incorporate any units... About the quantum management of info theory, it 
is another matter, quite more tricky.


Beyond that immediate physicality, things get quite obscure as our 
contradictory meaning messages witness. The point made by Joseph on an 
overarching logic, is rather difficult to be maintained --at least in my 
small province of the biological signaling pathways. Too many logics are 
used biologically in too many different contexts or niches, either 
molecularly or neuronally... I bet that they are not susceptible of 
integration in any logical system.  Maybe Inbiosa parties would also 
disagree with me in this regard.


best wishes to all,

---Pedro

John Collier escribió:

Folks,
 
I have been in the hospital for almost three weeks due to bleeding 
from warfarin. I had to have three blood transfusions and an 
operation. I am only now getting my strength back. Some of my 
comments, therefore, may be dated.
 
Physical has a variety of overlapping meanings (a Wittgensteinian 
family resemblence). For example Quine takes the physical to be 
anything accessible to the senses or inferences therefrom. Ladyman, 
Ross, Collier an Spurrett take the physical to be the most fundamental 
laws of our (part of) the universe. I did not agree with this, among 
some other crucial points, so I was not a primary author. Information 
is at least physical in both of these senses. Quine's approach might 
make it entirely physical. I prefer to relate it to the causal, which 
always has physical parametres, as far as we know. But there are many 
ways of approaching this issue, and disentangling them will be a major 
advance in foundations of information theory.
 
My Best,

John

 
Professor John Collier 
Philosophy, University of KwaZulu-Natal

Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292
F: +27 (31) 260 3031
email: colli...@ukzn.ac.za mailto:colli...@ukzn.ac.za On 
2012/03/16 at 01:19 PM, in message 4f6321c3.5000...@aragon.es, 
Pedro C. Marijuan pcmarijuan.i...@aragon.es wrote:

Dear discussants,

I tend to disagree with the motto information is physical if taken 
too strictly. Obviously if we look downwards it is OK, but in the 
upward direction it is different. Info is not only physical then, 
and the dimension of self-construction along the realization of life 
cycle has to be entered. Then the signal, the info, has content and 
meaning. Otherwise if we insist only in the physical downward 
dimension we have just conventional computing/ info processing. My 
opinion is that the notion of absence is crucial for advancing in the 
upward, but useless in the downward.
By the way, I already wrote about info and the absence theme in a 1994 
or 1995 paper in BioSystems...


best

---Pedro



walter.riof...@terra.com.pe escribió:


Thanks John and Kevin to update issues in information, computation, 
energy and reality.


 I would like point out to other articles more focused in how 
coherence and entanglement are used by living systems (far from 
thermal equilibrium):


 

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


 

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


 

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


 

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


 

 


Sincerely,

 

 


Walter

 

 





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


--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 

Re: [Fis] Physics of computing

[Loet Leydesdorff]

Dear Pedro, 

 

You are right: the dimensionality of thermodynamic entropy is Joule/Kelvin.

Probabilistic entropy/uncertainty/information is dimensionless and measured
in bits.

 

Configurational information (a point of access to measuring meaning) is also
measured in bits, but it is not a Shannon entropy (Krippendorff, 2009). It
can be considered as a redundancy = reduction of uncertainty = a difference
which makes a difference.

 

Best, 

Loet

 

  _  

Loet Leydesdorff 

Professor, University of Amsterdam
Amsterdam School of Communications Research (ASCoR), 
Kloveniersburgwal 48, 1012 CX Amsterdam. 
Tel.: +31-20- 525 6598; fax: +31-842239111
l...@leydesdorff.net  mailto:l...@leydesdorff.net ;
http://www.leydesdorff.net/ ;
http://scholar.google.com/citations?user=ych9gNYJ
http://scholar.google.com/citations?user=ych9gNYJhl=en hl=en 

 

From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On
Behalf Of Pedro C. Marijuan
Sent: Wednesday, April 11, 2012 10:44 AM
To: fis@listas.unizar.es
Subject: Re: [Fis] Physics of computing

 

Dear John and colleagues,

Nice to hear that you are OK after that dangerous intoxication --our best
wishes for your complete recovery! 
About physical information I think that Landauer clarified the panorama, at
least concerning the relationship between information theory and
thermodynamics. According to his principle, any logically irreversible
transformation of classical information is necessarily accompanied by the
dissipation of at least k T ln(2) of heat per lost bit (about 3 x 10 exp -21
Joules at 300 K temperature), where obviously k is the Boltzmann constant
and T the temperature. Recently this principle has been verified
experimentally (Nature, 8 March 2012, p. 187). By the way, in his past
message Loet enters Watts in a similar expression (?). To insist, Entropy
and Information are dimensionless and do not explicitly incorporate any
units... About the quantum management of info theory, it is another matter,
quite more tricky. 

Beyond that immediate physicality, things get quite obscure as our
contradictory meaning messages witness. The point made by Joseph on an
overarching logic, is rather difficult to be maintained --at least in my
small province of the biological signaling pathways. Too many logics are
used biologically in too many different contexts or niches, either
molecularly or neuronally... I bet that they are not susceptible of
integration in any logical system.  Maybe Inbiosa parties would also
disagree with me in this regard.

best wishes to all,

---Pedro

John Collier escribió: 

Folks,

 

I have been in the hospital for almost three weeks due to bleeding from
warfarin. I had to have three blood transfusions and an operation. I am only
now getting my strength back. Some of my comments, therefore, may be dated.

 

Physical has a variety of overlapping meanings (a Wittgensteinian family
resemblence). For example Quine takes the physical to be anything accessible
to the senses or inferences therefrom. Ladyman, Ross, Collier an Spurrett
take the physical to be the most fundamental laws of our (part of) the
universe. I did not agree with this, among some other crucial points, so I
was not a primary author. Information is at least physical in both of these
senses. Quine's approach might make it entirely physical. I prefer to relate
it to the causal, which always has physical parametres, as far as we know.
But there are many ways of approaching this issue, and disentangling them
will be a major advance in foundations of information theory.

 

My Best,

John

 

Professor John Collier  
Philosophy, University of KwaZulu-Natal
Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292
F: +27 (31) 260 3031
email: colli...@ukzn.ac.za On 2012/03/16 at 01:19 PM, in message
mailto:4f6321c3.5000...@aragon.es 4f6321c3.5000...@aragon.es, Pedro C.
Marijuan  mailto:pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es
wrote:


Dear discussants,

I tend to disagree with the motto information is physical if taken too
strictly. Obviously if we look downwards it is OK, but in the upward
direction it is different. Info is not only physical then, and the dimension
of self-construction along the realization of life cycle has to be entered.
Then the signal, the info, has content and meaning. Otherwise if we
insist only in the physical downward dimension we have just conventional
computing/ info processing. My opinion is that the notion of absence is
crucial for advancing in the upward, but useless in the downward. 
By the way, I already wrote about info and the absence theme in a 1994 or
1995 paper in BioSystems...

best

---Pedro



walter.riof...@terra.com.pe escribió: 

Thanks John and Kevin to update issues in information, computation, energy
and reality.

 I would like point out to other articles more focused in how coherence and
entanglement are used by living systems (far from thermal equilibrium): 

 

Engel G.S., Calhoun T.R., Read E.L

Re: [Fis] Physics of Computing

[John Collier]

Hi Gavin and others. 
 
Try Information in biological systems ( 
http://web.ncf.ca/collier/papers/Information%20in%20Biological%20Systems.pdf ) 
(Handbook of Philosophy of Science, vol 8, Philosophy of Information ( 
http://www.elsevier.com/wps/find/bookdescription.cws_home/716648/description#description
 ), 2008, Chapter 5f). It isn't complete (you need some of my other papers to 
get the quantity of information innate, transmitted (causally) and received, as 
well as its effects. 
http://web.ncf.ca/collier/papers/Information%20in%20Biological%20Systems.pdf
Information, causation and computation ( 
http://web.ncf.ca/collier/papers/CollierJohn%20formatted.pdf ) (Information and 
Computation: ( http://astore.amazon.co.uk/books-books-21/detail/9814295477 ) 
Essays on Scientific and Philosophical Understanding of Foundations of 
Information and Computation, Ed by Gordana Dodig Crnkovic and Mark Burgin, 
World Scientific) http://web.ncf.ca/collier/papers/CollierJohn%20formatted.pdf
 
Causation is the Transfer of Information ( 
http://web.ncf.ca/collier/papers/causinf.pdf ) (1999) 
http://web.ncf.ca/collier/papers/causinf.pdf
 
Complexly Organised Dynamical Systems ( 
http://web.ncf.ca/collier/papers/Cods.pdf ) with C.A. Hooker (1999) 
http://web.ncf.ca/collier/papers/Cods.pdf
 
Hierarchical dynamical information systems with a focus on biology ( 
http://www.mdpi.org/entropy/papers/e5020100.pdf ) (Entropy 2003) 
http://www.mdpi.org/entropy/papers/e5020100.pdf
 
There are others that might be relevant on my web page 
http://web.ncf.ca/collier/papers.html
 
John
 
 
 

 
 
Professor John Collier  
Philosophy, University of KwaZulu-Natal
Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292
F: +27 (31) 260 3031
email: colli...@ukzn.ac.za On 2012/03/16 at 11:14 PM, in message 
1331932479.81758.yahoomail...@web96106.mail.aue.yahoo.com, Gavin Ritz 
garr...@xtra.co.nz wrote:

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

And if so show me the relationship with conceptual mathematics?

Regards
Gavin




Dear FISers:
 
Pedro and Plamen raise good and welcomed points regarding the nature of 
physics, information, and biology. Although I believe in a strong relationship 
between information and physics in biology, there are striking examples where 
direct correspondences between information, physics, and biology seem to 
depart. Scientists are only beginning to tease out these discrepancies which 
will undoubtedly give us a better understand of information.
 
For example, in the study of cognition by A. Khrennikov and colleagues and J. 
Busemyer and colleagues, decisional processes may conform to quantum statistics 
and computation without necessarily being mediated by quantum mechanical 
phenomena at a biological level of description. I found this to be true in 
ciliates as well, where social strategy search speeds and decision rates may 
produce quantum computational phases that obey quantum statistics. In such 
cases, a changing classical diffusion term of response regulator 
reaction-diffusion parsimoniously accounts for the transition from classical to 
quantum information processing. Thus, there is no direct correspondence between 
quantum physicochemistry and quantum computation. Because the particular 
reaction-diffusion biochemistry is not unique to ciliates (i.e., the same 
phenomena is observed in plants, animals, and possibly bacteria), this 
incongruity may be widespread across life.
 
Best regards,
 
Kevin Clark

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



Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Physics of computing

[Bruno Marchal]

 did not 'perceive' the  
information.  If the information merely causes a transient  
fluctuation of the internal dynamics, then the perceived  
information was not meaningful to the system.  At least this is a  
sketch of my view that I hope illustrates why the notions of  
'content' and 'meaning' does not depart the physical realm for me.


I can prove that if we are machine at some description level, then  
the physical is both ontologically and epistemologically emerging  
from numbers relation. The hypothesis of mechanism can be shown  
logically incompatible with very weak form of materialism. Physics  
can not be fundamental, it emerges from mathematics, indeed from  
what has been called the sharable part of mathematics (sharable  
between classical logicians and intuitionist logicians, it is  
basically arithmetic or something recursively equivalent). We can  
already derive propositional quantum logic from classical number  
self-reference. Arithmetic is full of life at the start, and matter  
appears to be arithmetical truth as seen from inside.


Poetically, to be short, numbers dreams, and physical realities are  
dream sharing. The quantum emerges, if mechanism is correct, from a  
statistics on all computations. This makes both matter and  
consciousness NON Turing emulable. In particular digital physics can  
be shown self-contradictory. Those (actually old) results are not  
well known but have been verified by many people. I don't think  
there is a flaw, but we never can be sure, of course.


Bruno Marchal

PS see below for a concise version of the proof:
http://iridia.ulb.ac.be/~marchal/publications/SANE2004MARCHALAbstract.html





Regards,

Guy

From: Pedro Clemente Marijuan Fernandez pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.es 


Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science fis@listas.unizar.es 
mailto:fis@listas.unizar.es

Subject: Re: [Fis] Physics of computing

Dear discussants,

I tend to disagree with the motto information is physical if  
taken too strictly. Obviously if we look downwards it is OK, but  
in the upward direction it is different. Info is not only  
physical then, and the dimension of self-construction along the  
realization of life cycle has to be entered. Then the signal, the  
info, has content and meaning. Otherwise if we insist only in  
the physical downward dimension we have just conventional  
computing/ info processing. My opinion is that the notion of  
absence is crucial for advancing in the upward, but useless in the  
downward.
By the way, I already wrote about info and the absence theme in a  
1994 or 1995 paper in BioSystems...


best

---Pedro



walter.riof...@terra.com.pemailto:walter.riof...@terra.com.pe  
escribió:


Thanks John and Kevin to update issues in information, computation,  
energy and reality.


I would like point out to other articles morefocused in how  
coherence and entanglement are used by living systems (far from  
thermal equilibrium):




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




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




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




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






Sincerely,





Walter








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



--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11ª
50009 Zaragoza, Spain
Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554
pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.eshttp://sites.google.com/site/pedrocmarijuan/
-


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


http://iridia.ulb.ac.be/~marchal/



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


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


http://iridia.ulb.ac.be/~marchal/


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

Re: [Fis] Physics of Computing

[Dr. Plamen L. Simeonov]

Dear Gavin et.FIS,

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

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

1. Vrancisco Varela's self-reference calculus:

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

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

and its implications:

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

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

You could find more about it on Google

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

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

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

I will stop here for now.

Best,

Plamen






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

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

 And if so show me the relationship with conceptual mathematics?

 Regards
 Gavin



 Dear FISers:

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

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

 Best regards,

 Kevin Clark

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



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




-- 
___ ___ ___

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

Re: [Fis] Physics of computing

[Bruno Marchal]

On 16 Mar 2012, at 18:43, Guy A Hoelzer wrote:


Greetings All,

While I like to think that I am not limited to reductionistic  
thinking, I find it difficult to understand any perspective on  
information that is not limited to physical manifestation. I would  
appreciate further justification for a non-physicalist perspective  
on information.  How can something exist in the absence of physical  
manifestation?


If you are realist about elementary arithmetic, that is if you agree  
that elementary arithmetical proposition like 17 is prime are true  
independently of you, then, by arithmetic's Turing universality, you  
can show that the numbers exchange information relatively to universal  
numbers, which are playing the role of relative interpreters.





 I am not interested in a metaphysical perspective here, which might  
have heuristic value even if it is not 'real'.  The issue of  
'content' and 'meaning' strikes me as entirely physical, so  
mentioning those issues doesn't help me understand what non-physical  
information might be.  I would say that if information is physically  
manifested by contrasts (gradients, negentropy, …), then content or  
meaning refers to the internal dynamics of complex systems induced  
by interaction between the system and the physically manifested  
information.  If there is no affect on internal dynamics, then the  
system did not 'perceive' the information.  If the information  
merely causes a transient fluctuation of the internal dynamics, then  
the perceived information was not meaningful to the system.  At  
least this is a sketch of my view that I hope illustrates why the  
notions of 'content' and 'meaning' does not depart the physical  
realm for me.


I can prove that if we are machine at some description level, then the  
physical is both ontologically and epistemologically emerging from  
numbers relation. The hypothesis of mechanism can be shown logically  
incompatible with very weak form of materialism. Physics can not be  
fundamental, it emerges from mathematics, indeed from what has been  
called the sharable part of mathematics (sharable between classical  
logicians and intuitionist logicians, it is basically arithmetic or  
something recursively equivalent). We can already derive propositional  
quantum logic from classical number self-reference. Arithmetic is full  
of life at the start, and matter appears to be arithmetical truth as  
seen from inside.


Poetically, to be short, numbers dreams, and physical realities are  
dream sharing. The quantum emerges, if mechanism is correct, from a  
statistics on all computations. This makes both matter and  
consciousness NON Turing emulable. In particular digital physics can  
be shown self-contradictory. Those (actually old) results are not well  
known but have been verified by many people. I don't think there is a  
flaw, but we never can be sure, of course.


Bruno Marchal

PS see below for a concise version of the proof:
http://iridia.ulb.ac.be/~marchal/publications/SANE2004MARCHALAbstract.html





Regards,

Guy

From: Pedro Clemente Marijuan Fernandez pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.es 


Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science fis@listas.unizar.es 
mailto:fis@listas.unizar.es

Subject: Re: [Fis] Physics of computing

Dear discussants,

I tend to disagree with the motto information is physical if taken  
too strictly. Obviously if we look downwards it is OK, but in the  
upward direction it is different. Info is not only physical then,  
and the dimension of self-construction along the realization of life  
cycle has to be entered. Then the signal, the info, has content  
and meaning. Otherwise if we insist only in the physical downward  
dimension we have just conventional computing/ info processing. My  
opinion is that the notion of absence is crucial for advancing in  
the upward, but useless in the downward.
By the way, I already wrote about info and the absence theme in a  
1994 or 1995 paper in BioSystems...


best

---Pedro



walter.riof...@terra.com.pemailto:walter.riof...@terra.com.pe  
escribió:


Thanks John and Kevin to update issues in information, computation,  
energy and reality.


I would like point out to other articles morefocused in how  
coherence and entanglement are used by living systems (far from  
thermal equilibrium):




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




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




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

Re: [Fis] Physics of computing

[Pedro C. Marijuan]

Dear discussants,

I tend to disagree with the motto information is physical if taken too 
strictly. Obviously if we look downwards it is OK, but in the upward 
direction it is different. Info is not only physical then, and the 
dimension of self-construction along the realization of life cycle has 
to be entered. Then the signal, the info, has content and meaning. 
Otherwise if we insist only in the physical downward dimension we have 
just conventional computing/ info processing. My opinion is that the 
notion of absence is crucial for advancing in the upward, but useless in 
the downward.
By the way, I already wrote about info and the absence theme in a 1994 
or 1995 paper in BioSystems...


best

---Pedro



walter.riof...@terra.com.pe escribió:


Thanks John and Kevin to update issues in information, computation, 
energy and reality.


 I would like point out to other articles more focused in how 
coherence and entanglement are used by living systems (far from 
thermal equilibrium):


 

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


 

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


 

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


 

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


 

 


Sincerely,

 

 


Walter

 

 





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


--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11ª
50009 Zaragoza, Spain
Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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

Re: [Fis] Physics of computing

[Guy A Hoelzer]

Greetings All,

While I like to think that I am not limited to reductionistic thinking, I find 
it difficult to understand any perspective on information that is not limited 
to physical manifestation. I would appreciate further justification for a 
non-physicalist perspective on information.  How can something exist in the 
absence of physical manifestation?  I am not interested in a metaphysical 
perspective here, which might have heuristic value even if it is not 'real'.  
The issue of 'content' and 'meaning' strikes me as entirely physical, so 
mentioning those issues doesn't help me understand what non-physical 
information might be.  I would say that if information is physically manifested 
by contrasts (gradients, negentropy, …), then content or meaning refers to the 
internal dynamics of complex systems induced by interaction between the system 
and the physically manifested information.  If there is no affect on internal 
dynamics, then the system did not 'perceive' the information.  If the 
information merely causes a transient fluctuation of the internal dynamics, 
then the perceived information was not meaningful to the system.  At least this 
is a sketch of my view that I hope illustrates why the notions of 'content' and 
'meaning' does not depart the physical realm for me.

Regards,

Guy

From: Pedro Clemente Marijuan Fernandez 
pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.es
Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science 
fis@listas.unizar.esmailto:fis@listas.unizar.es
Subject: Re: [Fis] Physics of computing

Dear discussants,

I tend to disagree with the motto information is physical if taken too 
strictly. Obviously if we look downwards it is OK, but in the upward 
direction it is different. Info is not only physical then, and the dimension of 
self-construction along the realization of life cycle has to be entered. Then 
the signal, the info, has content and meaning. Otherwise if we insist only 
in the physical downward dimension we have just conventional computing/ info 
processing. My opinion is that the notion of absence is crucial for advancing 
in the upward, but useless in the downward.
By the way, I already wrote about info and the absence theme in a 1994 or 1995 
paper in BioSystems...

best

---Pedro



walter.riof...@terra.com.pemailto:walter.riof...@terra.com.pe escribió:

Thanks John and Kevin to update issues in information, computation, energy and 
reality.

 I would like point out to other articles morefocused in how coherence and 
entanglement are used by living systems (far from thermal equilibrium):



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



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



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



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





Sincerely,





Walter








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



--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11ª
50009 Zaragoza, Spain
Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554
pcmarijuan.i...@aragon.esmailto:pcmarijuan.i...@aragon.eshttp://sites.google.com/site/pedrocmarijuan/
-


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

[Fis] Physics of Computing

[Kevin Clark]

Dear FISers:
 
Pedro and Plamen raise good and welcomed points regarding the nature of 
physics, information, and biology. Although I believe in a strong relationship 
between information and physics in biology, there are striking examples where 
direct correspondences between information, physics, and biology seem to 
depart. Scientists are only beginning to tease out these discrepancies which 
will undoubtedly give us a better understand of information.
 
For example, in the study of cognition by A. Khrennikov and colleagues and J. 
Busemyer and colleagues, decisional processes may conform to quantum statistics 
and computation without necessarily being mediated by quantum mechanical 
phenomena at a biological level of description. I found this to be true in 
ciliates as well, where social strategy search speeds and decision rates may 
produce quantum computational phases that obey quantum statistics. In such 
cases, a changing classical diffusion term of response regulator 
reaction-diffusion parsimoniously accounts for the transition from classical to 
quantum information processing. Thus, there is no direct correspondence between 
quantum physicochemistry and quantum computation. Because the particular 
reaction-diffusion biochemistry is not unique to ciliates (i.e., the same 
phenomena is observed in plants, animals, and possibly bacteria), this 
incongruity may be widespread across life.
 
Best regards,
 
Kevin Clark___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Physics of Computing

[Gavin Ritz]

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

And if so show me the relationship with conceptual mathematics?

Regards
Gavin





Dear FISers:
 
Pedro and Plamen raise good and welcomed points regarding the nature of 
physics, information, and biology. Although I believe in a strong relationship 
between information and physics in biology, there are striking examples where 
direct correspondences between information, physics, and biology seem to 
depart. Scientists are only beginning to tease out these discrepancies which 
will undoubtedly give us a better understand of information.
 
For example, in the study of cognition by A. Khrennikov and colleagues and J. 
Busemyer and colleagues, decisional processes may conform to quantum statistics 
and computation without necessarily being mediated by quantum mechanical 
phenomena at a biological level of description. I found this to be true in 
ciliates as well, where social strategy search speeds and decision rates may 
produce quantum computational phases that obey quantum statistics. In such 
cases, a changing classical diffusion term of response regulator 
reaction-diffusion parsimoniously accounts for the transition from classical to 
quantum information processing. Thus, there is no direct correspondence between 
quantum physicochemistry and quantum computation. Because the particular 
reaction-diffusion biochemistry is not unique to ciliates (i.e., the same 
phenomena is observed in plants, animals, and possibly bacteria), this 
incongruity may be widespread across life.
 
Best regards,
 
Kevin Clark
___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis___
fis mailing list
fis@listas.unizar.es
https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] Physics of Computing

[Gordana Dodig-Crnkovic]

Dear Kevin and FIS,
Searching for Andrei's articles, I found 
http://arxiv.org/ftp/arxiv/papers/0906/0906.4952.pdf
and in the abstract there is a claim:
 Therefore, mental states, during perception cognition of ambiguous figures, 
follow quantum mechanics.

I am not an expert by any means but I find this claim very plausible from my 
personal experience as a cognitive agent in case of ambiguous figures.
When I cannot decide what an ambiguous figure actually is I keep number of 
plausible hypotheses actual in mind waiting for contextual clues to help me 
make disambiguation.
The state of mind about an ambiguous figure can be written as a superposition 
of possible states with corresponding weights and that superposition
can be likened with a quantum mechanical superposition of states.
It seems to me that there could be very natural mechanisms for this phenomenon, 
and really nothing non-physical.
Maybe Andrei can help elucidate the exact meaning of similar statistical forms 
found in several different fields, as the title of his book says:
Ubiquitous quantum structure: from psychology to finance.


Best,
Gordana

PS
Back to Pedro's original reference to physical levels of information, Deacon 
made a useful distinction between three different levels of information.

Deacon's three types of information parallel his three levels of emergent 
dynamics which in Salthe's notation looks like:
[1. thermo- [2. morpho- [3. teleo-dynamics]]] with corresponding mechanisms

 [1. mass-energetic [2. self-organization [3. self-preservation (semiotic)]]] 
and corresponding Aristotle's causes

 [1. efficient cause [ 2. formal cause [ 3. final cause]]]

In the above, thermodynamics and semiotic layers of organization are linked via 
intermediary layer of morphodynamics (spontaneous form-generating processes), 
and thus do not communicate directly (so it looks like mind communicating with 
matter via form).
Of course there is physics at the bottom.


http://www.mrtc.mdh.se/~gdc/

https://sites.google.com/site/naturalcomputingaisbiacap2012




From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On 
Behalf Of Kevin Clark
Sent: den 16 mars 2012 21:56
To: fis@listas.unizar.es
Subject: [Fis] Physics of Computing

Dear FISers:

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

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

Best regards,

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

[Fis] Physics of Computing

[Kevin Clark]

Thank you Gordana for your reply. But I'm not sure whether not you 
misunderstood my comments about a direct correspondence between information and 
physics in biology. So, I thought I should stress my point from a slightly 
different approach.

Khrennikov and colleagues, for instance, often refer to their observations as 
quantum-like. The reasons for doing so are because the quantum computational 
observations are inherently supported by biological phenomena and concepts in 
quantum statistical mechanics, but not necessarily a quantum mechanical 
physical manifestation. I have used the term quantum-like with with several of 
my own findings. Clearly ciliate decision making is a biological process and, 
therefore, a natural one. But quantum computation by ciliates, or any 
other life form, might not always be caused by a quantum physical 
manifestation. Indeed, quantum-level social strategy searches by ciliates are 
likely mediated by classical and not quantum diffusion in the 
reaction-diffusion of Ca2+ ions. Most people would present an a priori argument 
that for quantum computation to be realized by a biological system, such as 
ciliates, a physical manifestation of quantum mechanics, such as
 quantum diffusion, must also occur. This necessity just doesn't seem always to 
be the case.

These sorts of incongruities have started some debate in the quantum biology 
community. Some people simply believe that conceptual and statistically 
supported quantum computations by biological systems should not be 
considered quantum mechanical unless they are mediated by physical 
manifestations of quantum mechanics.

I will not respond for a few days to allow further debate from other FISers.

Best regards,

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

Re: [Fis] Physics of Computing

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

Dear Gordana,

There are for me many question marks in ascriptions of quantum properties to 
complex cognitive phenomena. The inversion of perspective I propose. using 
Deacon's term, is to see processes of superposition as common both to quantum 
phenomena as simplified projections of mental processes and to the mental 
processes themselves. This does not require, as many people seem rather 
desperately to want, that any given figure -ground event involve quanta at that 
higher level. In this case, your useful term likened with a quantum mechanical 
superposition can be replaced, usefully I suggest, by a weighting of the 
degrees of actuality and potentiality of the components of a evolving complex 
process. This is both where information is and what it is.

In this connection, I call all FIS'ers attention to the very pertinent concept 
of another Andrei, Andrei Igamberdiev, described in his book, of Internal 
Quantum States. The difference is, if I understand both sets of ideas 
correctly, is that Igamberdiev is talking about the foundations of theoretical 
biology. He does not require that Nature at higher levels actually instantiate 
quantum structures in any sense other than that, as Gordana says, there is 
nothing non-physical and quanta are involved a priori.

Cheers,

Joseph 



Ursprüngliche Nachricht

Von: gordana.dodig-crnko...@mdh.se

Datum: 16.03.2012 23:11

An: Kevin Clarkkbclark...@yahoo.com, 
fis@listas.unizar.esfis@listas.unizar.es

Kopie: andrei.khrenni...@msi.vxu.seandrei.khrenni...@msi.vxu.se

Betreff: Re: [Fis] Physics of Computing



@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:Times New Roman,serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.mark
{mso-style-name:mark;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:Calibri,sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
-
[if gte mso 9]

[if gte mso 9]




Dear Kevin and FIS,
Searching for Andrei’s articles, I found 
http://arxiv.org/ftp/arxiv/papers/0906/0906.4952.pdf

and in the abstract there is a claim:
 “Therefore,
mental states, during perception cognition of ambiguous figures, follow quantum
mechanics.”
 
I am
not an expert by any means but I find this claim very plausible from my
personal experience as a cognitive agent in case of ambiguous figures.
When I
cannot decide what an ambiguous figure actually is I keep number of plausible
hypotheses actual in mind waiting for contextual clues to help me make
disambiguation.
The
state of mind about an ambiguous figure can be written as a superposition of 
possible
states with corresponding weights and that superposition 

can be likened with a quantum mechanical superposition of states.
It
seems to me that there could be very natural mechanisms for this phenomenon, and
really nothing non-physical.
Maybe
Andrei can help elucidate the exact meaning of similar statistical forms found
in several different fields, as the title of his book says:
“Ubiquitous
quantum structure: from psychology to finance”.
 
 
Best,
Gordana
 
PS
Back to Pedro’s original reference to physical levels of
information, Deacon made a useful distinction between three different levels of
information.
 
Deacon’s three types of information parallel his three
levels of emergent dynamics which in Salthe’s notation looks like: 
[1. thermo- [2. morpho- [3. teleo-dynamics]]] with corresponding
mechanisms
 
 [1. mass-energetic [2. self-organization [3.
self-preservation (semiotic)]]] and corresponding Aristotle’s causes
 
 [1. efficient cause [ 2. formal cause [ 3. final cause]]]
 
In the above, thermodynamics and semiotic layers of organization
are linked via intermediary layer of morphodynamics (spontaneous
form-generating processes), and thus do not communicate directly (so it looks
like mind communicating with matter via form).
Of course there is physics at the bottom.
 

http://www.mrtc.mdh.se/~gdc/
 
https://sites.google.com/site/naturalcomputingaisbiacap2012 

 
 
 
 


From: fis-boun...@listas.unizar.es
[mailto:fis-boun...@listas.unizar.es] On Behalf Of Kevin Clark

Sent: den 16 mars 2012 21:56

To: fis@listas.unizar.es

Subject: [Fis] Physics of Computing


 


Dear FISers:


 


Pedro and Plamen raise good and
welcomed points regarding the nature of physics, information, and biology.
Although I believe in a strong relationship between information and physics in
biology

[Fis] Physics of computing

[walter . riofrio]

Thanks John and Kevin to update issues in information,
computation, energy and reality.
I would like point out to other articles more focused
in how coherence and entanglement are used by living systems (far from thermal
equilibrium): 

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

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

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

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


Sincerely,


Walter

  

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

[Fis] Physics of computing

[John Collier]

Dear folks,
This is a further article demonstrating that information is physical. It
is nice to be getting some empirical results.

http://www.nature.com/news/the-unavoidable-cost-of-computation-revealed-1.10186?WT.ec_id=NEWS-20120313

The previous article, which I mentioned on this list, is Toyabe, S.,
Sagawa, T., Ueda, M., Muneyuki, E.  Sano, M. Nature Phys. 6, 988–992
(2010). It demonstrated that information could be converted to energy,
which I consider a no brainer on first principles, but many people have
been sceptical.
The new article is Bérut, A. et al. Nature 483, 187–189 (2012).

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



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

[Fis] Physics of Computing

[Kevin Clark]

Thank you John for your update (FIS Digest 559, Issue 4) on the cost of 
computation. It's good to see experimental verification of Landauer's 
Principle. For those FISers interested in related topics on Landauer's 
Principle, you might also read:

1) Clark, K.B. (2010). Bose-Einstein condensates form in heuristics learned by 
ciliates deciding to signal 'social' commitments. BioSystems, 99(3), 167-178. 
http://www.ncbi.nlm.nih.gov/pubmed/19883726

2) Clark, K.B. (2010). Arrhenius-kinetics evidence for quantum tunneling in 
microbial social decision rates. Communicative  Integtrative Biology, 3(6), 
540-544. http://www.landesbioscience.com/journals/cib/article/12842

Best regards,

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