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


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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 sel

Re: [Fis] Physics of computing

[Bruno Marchal]

On 17 Apr 2012, at 11:23, Robin Faichney wrote:


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.


You are right. That is why in more lengthy explanations I introduce  
the key distinction between the first person points of view, and the  
third person points of view.
For the simple case of self-duplication the first person account can  
be defined by the content of a personal diary brought by the  
candidate: which means that it will be read and cut itself and  
reconstituted in both cities. Here the third person account is  
provided by the memory, or the content of a diary of an external  
observers, and is not going to be annihilated and reconstituted.


The indeterminacy bears on the first person experience(s). You are  
read and cut in Helsinki, and reconstituted in W and M.
You are asked to predict where you will *feel* to be after the  
duplication.


We suppose that you assume comp, and so you believe that you will  
survive such duplication. We assume also that the correct level of  
substitution has been chosen, and all the default assumptions (no  
bugs, no asteroids demolishing a reconstitution machine, etc).


So you can predict, with this relative to comp certainty, that you  
will survive, and that indeed, you will survive in both city. But comp  
prevents the existence of some telepathy between the two copies. So  
you know in advance that both of "you" (the M-you and the W-you) will  
both *feel* to be in only one city.


One will write in his diary: "Oh, I see that I am in Washington and I  
can only intellectually believe that I have a doppelganger in Moscow",  
and the other will write "Oh, I see that I am in Moscow, and I can  
only intellectually believe that I have a doppelganger in Washington".


So from both their first personal point of view, they get one bit of  
information.


The indeterminacy comes from the fact that they cannot have predicted  
in advance which one they will become, before the duplication.


If, in Helsinki the candidate predicts that he will feel to be in W,  
the guy in M will  rightly consider that he was wrong in his  
prediction made before in Helsinki, and vice versa.
As you say yourself, bot copies shares their memory-life up to the  
experience in Helsinki, and to evaluate their uncertainty, they have  
to take into account all the future copies discourses.


If this is not clear, let me copy you a slightly more elaborate  
account. It is called "step 3", because it is the step 3 of the  
Universal Dovetailer Argument, which is the main argument showing the  
reversal between physics and information/computer science following  
the comp assumption. It takes into account preview critics similar to  
what you said.
 In fact you attribute your consciousness and identity to both copies  
(it is a 3-person-view on the 1-person-view, but the indeterminacy is  
on the 1-view themselves). You can say "tomorrow, you can join me in W  
and in M". But from your personal perspective you get after the  
duplication, you will feel to be one and entire in a well defined city  
(W *or* M).


If you get this, don't read what follows. If it is still unclear, read  
what follows, and if some questions remain, I will answer them here.




== UDA step 3 == (from the FOAR mailing list) == ( 
http://groups.google.com/group/foar?hl=en.)

I assume

Re: [Fis] Physics of computing

[Loet Leydesdorff]

> 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.

But this ignores the second law: one can expect unavoidable error in the
replication. :-)  !  L.

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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


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Re: [Fis] Physics of computing

[Loet Leydesdorff]

Dear Bruno, 

 

(*) You might look at my short article:

http://www.scitopics.com/The_first_person_computationalist_indeterminacy.htm
l

 

I read your paper and think that I understood it, but I don’t understand
immediately how it relates to this discussion. I understand that there is a
remaining uncertainty of 1 bit (0 or 1) that cannot be foreseen or dissolved
by an omniscient being. The latter seems to me something from the times of
Leibniz and Descartes when the omniscient being had to guarantee that
empirical and mathematical knowledge were in accordance. Can an omniscient
being know the uncertainty of empirical distributions without measuring
them? 

 

Huygens (1690): “It is not well to identify certitude with clear and
distinct perception, for it is evident that there are, so to speak, various
degrees of that clearness and distinctness. We are often deluded in things
which we think we certainly understand. Descartes is an example of this, it
is so with his laws of communication of motion by collision of bodies.”

 

Anyhow: while one can define a system and therewith its maximum information
content (log(N)), the expected information content and redundancy have to be
measured. A system which generates more redundancy than information
(uncertainty) can be considered as a meaning-processing system because the
number of options proliferates faster than the historical filling of the
options. Obviously, new possibilities (meanings) are generated.

 

For reasons of consistency with the second law (which is valid since S= k(B)
H), such a system would operate against the arrow of time: meaning is
provided from the perspective of hindsight; incursively. Such a system would
therefore be an anticipatory system. For example, meaning incurs on us as
such systems. Furthermore, meaning is provided with reference to other
possible meanings, that is, “horizons of meaning”.

 

Does this accord with your approach?

 

Best wishes,

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=ych9gNYJ&hl=en> &hl=en 

 

From: Bruno Marchal [mailto:marc...@ulb.ac.be] 
Sent: Wednesday, April 11, 2012 6:48 PM
To: Loet Leydesdorff
Cc: 'Pedro C. Marijuan'; fis@listas.unizar.es
Subject: Re: [Fis] Physics of computing

 

Dear Loet, dear Pedro,

On 11 Apr 2012, at 11:28, Loet Leydesdorff wrote:





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.

 

I agree. Redundancy is the key, in my opinion (and work). Note that if you
enumerate the partial computable functions (from N to N to fix the thing),
there is an important redundancy which cannot be removed in any computable
way.

 

Information is then generated from the first person point of view of the
(universal, Löbian) machine trying to bet on its most probable universal
neighbors. (cf the first person indeterminacy(*)). Hard calculus because the
redundancy is infinite.

 

I distinguish the finite information, available locally by machine, and
which can be treated as numbers, but with extensional and intensional roles
(cf 17 is prime versus 17 is the number address of the café) from what a
universal number (machine) do with that number. This provides a clean base
for the distinction between information capable of quantitative evaluation
and meaning, although it is only just a tiny part of the meaning which is
addressed here, of course. The meaning admits many quantitative aspect, but
cannot be characterized by one measurement.

 

A Löbian machine or number is a universal machine or number which knows, in
some technical sense, that he.she/it is universal. It is aware of its
ignorance, notably about the universal neighbors.

 

Bruno

 

(*) You might look at my short article:

http://www.scitopics.com/The_first_person_computationalist_indeterminacy.htm
l

 

 

 

 


  _  


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 ; http://www.leydesdorff.net/ ;
http://scholar.google.com/citations?user=ych9gNYJ
<http://scholar.google.com/citations?user=ych9gNYJ&hl=en> &hl=en

 

From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.un

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
>

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.ch<mailto: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 s

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: 
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 warf

Re: [Fis] Physics of computing

[Bill Seaman]

Morphogrammatics and Computational Reflection
Applying insights from the retro-grade recursivity concept of morphogrammatics 
to questions of reflectionality and interactionality of programming


Possibly of interest:
http://memristors.memristics.com/MorphoReflection/Morphogrammatics%20of%20Reflection.html

Rudolf Kaehr Dr. phil@
ThinkArt Lab Glasgow ISSN 2041-4358



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 10:39 PM, Bill Seaman wrote:

> 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=1015&context=thinkartlab&sei-redir=1&referer=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, evol

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=1015&context=thinkartlab&sei-redir=1&referer=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: 
> 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 physicali

Re: [Fis] Physics of computing

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

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: 

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. 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
<4f6321c3.5000...@aragon.es>, "Pedro C. Marijuan"
 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 

Re: [Fis] Physics of computing

[Bruno Marchal]

Dear Loet, dear Pedro,
On 11 Apr 2012, at 11:28, Loet Leydesdorff wrote:


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.


I agree. Redundancy is the key, in my opinion (and work). Note that if  
you enumerate the partial computable functions (from N to N to fix the  
thing), there is an important redundancy which cannot be removed in  
any computable way.


Information is then generated from the first person point of view of  
the (universal, Löbian) machine trying to bet on its most probable  
universal neighbors. (cf the first person indeterminacy(*)). Hard  
calculus because the redundancy is infinite.


I distinguish the finite information, available locally by machine,  
and which can be treated as numbers, but with extensional and  
intensional roles (cf 17 is prime versus 17 is the number address of  
the café) from what a universal number (machine) do with that number.  
This provides a clean base for the distinction between information  
capable of quantitative evaluation and meaning, although it is only  
just a tiny part of the meaning which is addressed here, of course.  
The meaning admits many quantitative aspect, but cannot be  
characterized by one measurement.


A Löbian machine or number is a universal machine or number which  
knows, in some technical sense, that he.she/it is universal. It is  
aware of its ignorance, notably about the universal neighbors.


Bruno

(*) You might look at my short article:
http://www.scitopics.com/The_first_person_computationalist_indeterminacy.html





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 ; http://www.leydesdorff.net/ ; 
http://scholar.google.com/citations?user=ych9gNYJ&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 wi

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=ych9gNYJ&hl=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> 
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 a

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 , 
"Pedro C. Marijuan"  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

 

 





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Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 2

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 
 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

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Re: [Fis] Physics of computing

[John Collier]

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
<4f6321c3.5000...@aragon.es>, "Pedro C. Marijuan"
 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
 
 
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Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11*
50009 Zaragoza, Spain
Telf: 34 976 71 3526 (& 6818) Fax: 34 976 71
5554pcmarijuan.iacs@aragon.eshttp://sites.google.com/site/pedrocmarijuan/-

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Re: [Fis] Physics of computing

[Bruno Marchal]

cally 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 mailto:pcmarijuan.i...@aragon.es 
>>

Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science <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.pe<mailto: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








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-
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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<mailto:pcmarijuan.i...@aragon.es>http://sites.google.com/site/pedrocmarijuan/
-


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



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Re: [Fis] Physics of computing

[Stanley N Salthe]

Bruno -- As an idealist, I think you have it all backward!  I would argue
that cardinal numbers are the most 'crisp' entities that we know, and this
disqualifies them or being primeval.  That is, I think it makes sense to
see all developments as beginning relatively vaguely and then becoming more
definite over time.  So, then, it will have taken these numbers a very long
period of evolution (passing through the 'real' stage) to have become as
definite as they are now. Or, even if cardinal numbers became quite crisp
at the time, say, of the origin of chemistry, that too will have been a
long way from primeval.

STAN

On Sat, Mar 17, 2012 at 4:38 AM, Bruno Marchal  wrote:

> 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  mailto: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/

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 mailto:pcmarijuan.i...@aragon.es 
>>

Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science <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.pe<mailto: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., 

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  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
>
>
>
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>


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fax/ums:   +49.30.48.49.88.26.4
mobile: +44.12.23.96.85.69
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Re: [Fis] Physics of Computing

[Gordana Dodig-Crnkovic]

Dear Kevin, Joe, FIS

What worried me in the recent exchanges was (possibly based on my 
misunderstanding) an implicit suggestion that information somehow can be 
unphysical when it becomes semantic.
Exactly as Joe says (and Deacon as well in his book), absentials are defined in 
relation to (regularities of) that which is present. Indeed there is the 
figure-background connection;
there are no absentials without “presentials” which are physical.

I will also now wait for FIS debate.
Best wishes,
Gordana


http://www.mrtc.mdh.se/~gdc/<http://www.mrtc.mdh.se/%7Egdc/>

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

From: joe.bren...@bluewin.ch [mailto:joe.bren...@bluewin.ch]
Sent: den 17 mars 2012 05:54
To: Gordana Dodig-Crnkovic; fis@listas.unizar.es
Subject: AW: Re: [Fis] Physics of Computing

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 Clark", 
"fis@listas.unizar.es"
Kopie: "andrei.khrenni...@msi.vxu.se"
Betreff: Re: [Fis] Physics of Computing

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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 [ 

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 Clark", 
"fis@listas.unizar.es"

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

Betreff: Re: [Fis] Physics of Computing



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[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 b

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
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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
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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 
mailto:pcmarijuan.i...@aragon.es>>
Date: Fri, 16 Mar 2012 04:19:31 -0700
To: Foundations of Information Science Information Science 
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.pe<mailto: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








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--
-
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<mailto:pcmarijuan.i...@aragon.es>http://sites.google.com/site/pedrocmarijuan/
-


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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

 

 





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--
-
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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/
-

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